-InMrc 18feb27f_CTD_00011gr_00002sq_v01_00002hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00002hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.342e-01 9.985e-02 CC threshold: 0.733 Mean Std: 39.36 6.68 Num Hot pixels: 159 Hot pixel threshold: 79.44 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 3.105316 Iteration 2 Error: 0.684255 Iteration 3 Error: 0.226111 Iteration 4 Error: 0.092508 Iteration 5 Error: 0.035412 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.04 -0.35 ...... Frame ( 3) shift: -0.08 -0.70 ...... Frame ( 4) shift: -0.12 -1.04 ...... Frame ( 5) shift: -0.16 -1.39 ...... Frame ( 6) shift: -0.10 -1.54 ...... Frame ( 7) shift: 0.04 -1.48 ...... Frame ( 8) shift: 0.19 -1.43 ...... Frame ( 9) shift: 0.33 -1.34 ...... Frame ( 10) shift: 0.46 -1.22 ...... Frame ( 11) shift: 0.60 -1.10 ...... Frame ( 12) shift: 0.81 -0.99 ...... Frame ( 13) shift: 1.09 -0.87 ...... Frame ( 14) shift: 1.38 -0.75 ...... Frame ( 15) shift: 1.59 -0.66 ...... Frame ( 16) shift: 1.72 -0.58 ...... Frame ( 17) shift: 1.85 -0.50 ...... Frame ( 18) shift: 2.02 -0.41 ...... Frame ( 19) shift: 2.21 -0.31 ...... Frame ( 20) shift: 2.41 -0.20 ...... Frame ( 21) shift: 2.58 -0.13 ...... Frame ( 22) shift: 2.72 -0.10 ...... Frame ( 23) shift: 2.86 -0.06 ...... Frame ( 24) shift: 3.01 -0.02 ...... Frame ( 25) shift: 3.17 0.03 ...... Frame ( 26) shift: 3.33 0.09 ...... Frame ( 27) shift: 3.51 0.14 ...... Frame ( 28) shift: 3.71 0.21 ...... Frame ( 29) shift: 3.92 0.27 ...... Frame ( 30) shift: 4.09 0.34 ...... Frame ( 31) shift: 4.23 0.43 ...... Frame ( 32) shift: 4.38 0.51 ...... Frame ( 33) shift: 4.57 0.58 ...... Frame ( 34) shift: 4.80 0.63 ...... Frame ( 35) shift: 5.04 0.67 ...... Frame ( 36) shift: 5.25 0.73 ...... Frame ( 37) shift: 5.43 0.80 ...... Frame ( 38) shift: 5.62 0.87 ...... Frame ( 39) shift: 5.80 0.94 ...... Frame ( 40) shift: 5.98 1.01 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.817248 Iteration 2 Error: 0.124330 Iteration 3 Error: 0.051507 Iteration 4 Error: 0.016484 Align patch 2 23 left Iteration 1 Error: 1.057325 Iteration 2 Error: 0.282439 Iteration 3 Error: 0.089557 Iteration 4 Error: 0.042468 Align patch 3 22 left Iteration 1 Error: 1.345778 Iteration 2 Error: 0.240046 Iteration 3 Error: 0.107689 Iteration 4 Error: 0.032923 Align patch 4 21 left Iteration 1 Error: 1.043406 Iteration 2 Error: 0.303178 Iteration 3 Error: 0.084303 Iteration 4 Error: 0.033949 Align patch 5 20 left Iteration 1 Error: 1.248202 Iteration 2 Error: 0.541134 Iteration 3 Error: 0.183098 Iteration 4 Error: 0.063082 Iteration 5 Error: 0.018459 Align patch 6 19 left Iteration 1 Error: 1.058418 Iteration 2 Error: 0.205299 Iteration 3 Error: 0.039739 Align patch 7 18 left Iteration 1 Error: 0.644865 Iteration 2 Error: 0.107427 Iteration 3 Error: 0.022751 Align patch 8 17 left Iteration 1 Error: 1.183723 Iteration 2 Error: 0.217453 Iteration 3 Error: 0.060977 Iteration 4 Error: 0.021277 Align patch 9 16 left Iteration 1 Error: 1.127410 Iteration 2 Error: 0.239272 Iteration 3 Error: 0.054527 Iteration 4 Error: 0.023687 Align patch 10 15 left Iteration 1 Error: 0.804643 Iteration 2 Error: 0.184903 Iteration 3 Error: 0.041474 Align patch 11 14 left Iteration 1 Error: 0.557133 Iteration 2 Error: 0.112447 Iteration 3 Error: 0.041525 Align patch 12 13 left Iteration 1 Error: 0.639170 Iteration 2 Error: 0.168742 Iteration 3 Error: 0.052071 Iteration 4 Error: 0.016999 Align patch 13 12 left Iteration 1 Error: 0.767455 Iteration 2 Error: 0.117050 Iteration 3 Error: 0.047491 Align patch 14 11 left Iteration 1 Error: 0.979022 Iteration 2 Error: 0.168639 Iteration 3 Error: 0.082034 Iteration 4 Error: 0.036130 Align patch 15 10 left Iteration 1 Error: 1.100399 Iteration 2 Error: 0.274536 Iteration 3 Error: 0.058179 Iteration 4 Error: 0.020313 Align patch 16 9 left Iteration 1 Error: 1.214379 Iteration 2 Error: 0.553569 Iteration 3 Error: 0.281920 Iteration 4 Error: 0.167535 Iteration 5 Error: 0.073310 Align patch 16 9 left Iteration 1 Error: 0.933043 Iteration 2 Error: 0.171117 Iteration 3 Error: 0.032983 Align patch 17 8 left Iteration 1 Error: 0.950344 Iteration 2 Error: 0.300404 Iteration 3 Error: 0.202995 Iteration 4 Error: 0.126207 Iteration 5 Error: 0.069417 Align patch 17 8 left Iteration 1 Error: 1.774547 Iteration 2 Error: 0.342066 Iteration 3 Error: 0.079080 Iteration 4 Error: 0.030226 Align patch 18 7 left Iteration 1 Error: 0.915145 Iteration 2 Error: 0.225351 Iteration 3 Error: 0.071829 Iteration 4 Error: 0.027139 Align patch 19 6 left Iteration 1 Error: 0.900657 Iteration 2 Error: 0.477145 Iteration 3 Error: 0.228605 Iteration 4 Error: 0.166366 Iteration 5 Error: 0.092025 Align patch 19 6 left Iteration 1 Error: 0.702647 Iteration 2 Error: 0.101698 Iteration 3 Error: 0.024607 Align patch 20 5 left Iteration 1 Error: 0.797174 Iteration 2 Error: 0.606129 Iteration 3 Error: 0.273270 Iteration 4 Error: 0.284338 Iteration 5 Error: 0.125749 Align patch 20 5 left Iteration 1 Error: 1.072684 Iteration 2 Error: 0.118105 Iteration 3 Error: 0.024667 Align patch 21 4 left Iteration 1 Error: 1.335029 Iteration 2 Error: 0.373364 Iteration 3 Error: 0.097638 Iteration 4 Error: 0.045961 Align patch 22 3 left Iteration 1 Error: 1.166127 Iteration 2 Error: 0.401950 Iteration 3 Error: 0.154507 Iteration 4 Error: 0.086559 Iteration 5 Error: 0.033237 Align patch 23 2 left Iteration 1 Error: 1.826505 Iteration 2 Error: 0.554792 Iteration 3 Error: 0.282640 Iteration 4 Error: 0.150876 Iteration 5 Error: 0.080042 Align patch 23 2 left Iteration 1 Error: 1.585395 Iteration 2 Error: 0.290019 Iteration 3 Error: 0.081395 Iteration 4 Error: 0.021103 Align patch 24 1 left Iteration 1 Error: 0.773582 Iteration 2 Error: 0.190901 Iteration 3 Error: 0.097516 Iteration 4 Error: 0.026074 Align patch 25 0 left Iteration 1 Error: 1.038879 Iteration 2 Error: 0.152290 Iteration 3 Error: 0.048890 3D Fitting completed. Patch alignment time: 26.53(sec) Local motion has been corrected. Process thread exits. Computational time: 43.110992 sec Total time: 51.165951 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00002hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00002hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.581828s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00002hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.821264s ........................................ >>>>>>TIME<<<<<< FFT: 1.471958s Defocus_U Defocus_V Angle CCC 25486.38 26365.29 0.21 0.041743 Final Values Defocus_U Defocus_V Angle CCC 25445.75 26343.42 0.53 0.066191 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00002hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00002hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.991e-02 CC threshold: 0.734 Mean Std: 38.97 6.60 Num Hot pixels: 155 Hot pixel threshold: 78.58 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.467600 Iteration 2 Error: 0.608912 Iteration 3 Error: 0.261482 Iteration 4 Error: 0.091966 Iteration 5 Error: 0.045607 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.03 -0.35 ...... Frame ( 3) shift: 0.06 -0.69 ...... Frame ( 4) shift: 0.08 -1.04 ...... Frame ( 5) shift: 0.11 -1.39 ...... Frame ( 6) shift: 0.22 -1.54 ...... Frame ( 7) shift: 0.41 -1.51 ...... Frame ( 8) shift: 0.59 -1.48 ...... Frame ( 9) shift: 0.74 -1.40 ...... Frame ( 10) shift: 0.85 -1.26 ...... Frame ( 11) shift: 0.96 -1.12 ...... Frame ( 12) shift: 1.13 -1.00 ...... Frame ( 13) shift: 1.36 -0.88 ...... Frame ( 14) shift: 1.59 -0.77 ...... Frame ( 15) shift: 1.77 -0.66 ...... Frame ( 16) shift: 1.89 -0.58 ...... Frame ( 17) shift: 2.02 -0.49 ...... Frame ( 18) shift: 2.11 -0.42 ...... Frame ( 19) shift: 2.18 -0.38 ...... Frame ( 20) shift: 2.25 -0.34 ...... Frame ( 21) shift: 2.40 -0.26 ...... Frame ( 22) shift: 2.63 -0.16 ...... Frame ( 23) shift: 2.87 -0.05 ...... Frame ( 24) shift: 3.15 0.05 ...... Frame ( 25) shift: 3.48 0.14 ...... Frame ( 26) shift: 3.81 0.23 ...... Frame ( 27) shift: 4.02 0.30 ...... Frame ( 28) shift: 4.12 0.36 ...... Frame ( 29) shift: 4.21 0.41 ...... Frame ( 30) shift: 4.33 0.48 ...... Frame ( 31) shift: 4.48 0.56 ...... Frame ( 32) shift: 4.63 0.65 ...... Frame ( 33) shift: 4.81 0.72 ...... Frame ( 34) shift: 5.04 0.77 ...... Frame ( 35) shift: 5.26 0.82 ...... Frame ( 36) shift: 5.43 0.87 ...... Frame ( 37) shift: 5.54 0.91 ...... Frame ( 38) shift: 5.65 0.95 ...... Frame ( 39) shift: 5.76 0.98 ...... Frame ( 40) shift: 5.87 1.02 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.051502 Iteration 2 Error: 0.362601 Iteration 3 Error: 0.091308 Iteration 4 Error: 0.053060 Iteration 5 Error: 0.013951 Align patch 2 23 left Iteration 1 Error: 1.833916 Iteration 2 Error: 0.274719 Iteration 3 Error: 0.108166 Iteration 4 Error: 0.045398 Align patch 3 22 left Iteration 1 Error: 2.025507 Iteration 2 Error: 0.311613 Iteration 3 Error: 0.065295 Iteration 4 Error: 0.032642 Align patch 4 21 left Iteration 1 Error: 1.217935 Iteration 2 Error: 0.204541 Iteration 3 Error: 0.070753 Iteration 4 Error: 0.030951 Align patch 5 20 left Iteration 1 Error: 1.142314 Iteration 2 Error: 0.297705 Iteration 3 Error: 0.083126 Iteration 4 Error: 0.043609 Align patch 6 19 left Iteration 1 Error: 0.733662 Iteration 2 Error: 0.132852 Iteration 3 Error: 0.049291 Align patch 7 18 left Iteration 1 Error: 0.822049 Iteration 2 Error: 0.214407 Iteration 3 Error: 0.075843 Iteration 4 Error: 0.018329 Align patch 8 17 left Iteration 1 Error: 1.140229 Iteration 2 Error: 0.453116 Iteration 3 Error: 0.204159 Iteration 4 Error: 0.111383 Iteration 5 Error: 0.052123 Align patch 8 17 left Iteration 1 Error: 0.811898 Iteration 2 Error: 0.088277 Iteration 3 Error: 0.025196 Align patch 9 16 left Iteration 1 Error: 1.027978 Iteration 2 Error: 0.163772 Iteration 3 Error: 0.053587 Iteration 4 Error: 0.019783 Align patch 10 15 left Iteration 1 Error: 1.150363 Iteration 2 Error: 0.258612 Iteration 3 Error: 0.135146 Iteration 4 Error: 0.071992 Iteration 5 Error: 0.026679 Align patch 11 14 left Iteration 1 Error: 0.864311 Iteration 2 Error: 0.223919 Iteration 3 Error: 0.059930 Iteration 4 Error: 0.013067 Align patch 12 13 left Iteration 1 Error: 1.114153 Iteration 2 Error: 0.268236 Iteration 3 Error: 0.088296 Iteration 4 Error: 0.031339 Align patch 13 12 left Iteration 1 Error: 0.790314 Iteration 2 Error: 0.175811 Iteration 3 Error: 0.064596 Iteration 4 Error: 0.020079 Align patch 14 11 left Iteration 1 Error: 0.869278 Iteration 2 Error: 0.219267 Iteration 3 Error: 0.106495 Iteration 4 Error: 0.030261 Align patch 15 10 left Iteration 1 Error: 1.055056 Iteration 2 Error: 0.264904 Iteration 3 Error: 0.096361 Iteration 4 Error: 0.028451 Align patch 16 9 left Iteration 1 Error: 0.976410 Iteration 2 Error: 0.172061 Iteration 3 Error: 0.055014 Iteration 4 Error: 0.027149 Align patch 17 8 left Iteration 1 Error: 0.835291 Iteration 2 Error: 0.150197 Iteration 3 Error: 0.049811 Align patch 18 7 left Iteration 1 Error: 0.843628 Iteration 2 Error: 0.149500 Iteration 3 Error: 0.044712 Align patch 19 6 left Iteration 1 Error: 0.917248 Iteration 2 Error: 0.139897 Iteration 3 Error: 0.032319 Align patch 20 5 left Iteration 1 Error: 0.785271 Iteration 2 Error: 0.138769 Iteration 3 Error: 0.049330 Align patch 21 4 left Iteration 1 Error: 0.512439 Iteration 2 Error: 0.150406 Iteration 3 Error: 0.056361 Iteration 4 Error: 0.022131 Align patch 22 3 left Iteration 1 Error: 1.146337 Iteration 2 Error: 0.364276 Iteration 3 Error: 0.071062 Iteration 4 Error: 0.025249 Align patch 23 2 left Iteration 1 Error: 0.800071 Iteration 2 Error: 0.119666 Iteration 3 Error: 0.032079 Align patch 24 1 left Iteration 1 Error: 0.950022 Iteration 2 Error: 0.194881 Iteration 3 Error: 0.052664 Iteration 4 Error: 0.021270 Align patch 25 0 left Iteration 1 Error: 0.948947 Iteration 2 Error: 0.091613 Iteration 3 Error: 0.043021 3D Fitting completed. Patch alignment time: 19.17(sec) Local motion has been corrected. Process thread exits. Computational time: 38.428493 sec Total time: 46.393570 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00002hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00002hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.603708s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00002hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 5.107596s ........................................ >>>>>>TIME<<<<<< FFT: 1.499540s Defocus_U Defocus_V Angle CCC 24992.19 25859.38 2.54 0.040681 Final Values Defocus_U Defocus_V Angle CCC 25020.31 25787.50 2.23 0.060809 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00002hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00002hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.989e-02 CC threshold: 0.734 Mean Std: 39.98 6.70 Num Hot pixels: 155 Hot pixel threshold: 80.16 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.463932 Iteration 2 Error: 0.605165 Iteration 3 Error: 0.229118 Iteration 4 Error: 0.087472 Iteration 5 Error: 0.039908 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.06 -0.11 ...... Frame ( 3) shift: 0.12 -0.23 ...... Frame ( 4) shift: 0.18 -0.34 ...... Frame ( 5) shift: 0.24 -0.46 ...... Frame ( 6) shift: 0.36 -0.46 ...... Frame ( 7) shift: 0.53 -0.36 ...... Frame ( 8) shift: 0.69 -0.26 ...... Frame ( 9) shift: 0.92 -0.16 ...... Frame ( 10) shift: 1.20 -0.06 ...... Frame ( 11) shift: 1.47 0.04 ...... Frame ( 12) shift: 1.68 0.14 ...... Frame ( 13) shift: 1.82 0.23 ...... Frame ( 14) shift: 1.96 0.32 ...... Frame ( 15) shift: 2.16 0.43 ...... Frame ( 16) shift: 2.42 0.54 ...... Frame ( 17) shift: 2.67 0.66 ...... Frame ( 18) shift: 2.89 0.77 ...... Frame ( 19) shift: 3.06 0.88 ...... Frame ( 20) shift: 3.23 0.99 ...... Frame ( 21) shift: 3.36 1.07 ...... Frame ( 22) shift: 3.44 1.13 ...... Frame ( 23) shift: 3.53 1.19 ...... Frame ( 24) shift: 3.70 1.25 ...... Frame ( 25) shift: 3.95 1.32 ...... Frame ( 26) shift: 4.20 1.39 ...... Frame ( 27) shift: 4.41 1.46 ...... Frame ( 28) shift: 4.57 1.53 ...... Frame ( 29) shift: 4.72 1.60 ...... Frame ( 30) shift: 4.89 1.65 ...... Frame ( 31) shift: 5.07 1.66 ...... Frame ( 32) shift: 5.25 1.68 ...... Frame ( 33) shift: 5.38 1.73 ...... Frame ( 34) shift: 5.46 1.83 ...... Frame ( 35) shift: 5.54 1.92 ...... Frame ( 36) shift: 5.67 1.99 ...... Frame ( 37) shift: 5.84 2.02 ...... Frame ( 38) shift: 6.02 2.06 ...... Frame ( 39) shift: 6.19 2.09 ...... Frame ( 40) shift: 6.37 2.13 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.189011 Iteration 2 Error: 0.143997 Iteration 3 Error: 0.038484 Align patch 2 23 left Iteration 1 Error: 1.529070 Iteration 2 Error: 0.283175 Iteration 3 Error: 0.106125 Iteration 4 Error: 0.042935 Align patch 3 22 left Iteration 1 Error: 0.945319 Iteration 2 Error: 0.201475 Iteration 3 Error: 0.052968 Iteration 4 Error: 0.032222 Align patch 4 21 left Iteration 1 Error: 1.367152 Iteration 2 Error: 0.217989 Iteration 3 Error: 0.046086 Align patch 5 20 left Iteration 1 Error: 1.475579 Iteration 2 Error: 0.180341 Iteration 3 Error: 0.059871 Iteration 4 Error: 0.015438 Align patch 6 19 left Iteration 1 Error: 0.934107 Iteration 2 Error: 0.311596 Iteration 3 Error: 0.076377 Iteration 4 Error: 0.031195 Align patch 7 18 left Iteration 1 Error: 1.018323 Iteration 2 Error: 0.268520 Iteration 3 Error: 0.079766 Iteration 4 Error: 0.034931 Align patch 8 17 left Iteration 1 Error: 0.818911 Iteration 2 Error: 0.152285 Iteration 3 Error: 0.067500 Iteration 4 Error: 0.019922 Align patch 9 16 left Iteration 1 Error: 1.149631 Iteration 2 Error: 0.244077 Iteration 3 Error: 0.070725 Iteration 4 Error: 0.026205 Align patch 10 15 left Iteration 1 Error: 1.034412 Iteration 2 Error: 0.140678 Iteration 3 Error: 0.050061 Iteration 4 Error: 0.016040 Align patch 11 14 left Iteration 1 Error: 0.727891 Iteration 2 Error: 0.114895 Iteration 3 Error: 0.023444 Align patch 12 13 left Iteration 1 Error: 0.735347 Iteration 2 Error: 0.166557 Iteration 3 Error: 0.036581 Align patch 13 12 left Iteration 1 Error: 0.613676 Iteration 2 Error: 0.179236 Iteration 3 Error: 0.079281 Iteration 4 Error: 0.035061 Align patch 14 11 left Iteration 1 Error: 0.888707 Iteration 2 Error: 0.132986 Iteration 3 Error: 0.035591 Align patch 15 10 left Iteration 1 Error: 0.613765 Iteration 2 Error: 0.201866 Iteration 3 Error: 0.059367 Iteration 4 Error: 0.016900 Align patch 16 9 left Iteration 1 Error: 0.633677 Iteration 2 Error: 0.129600 Iteration 3 Error: 0.043182 Align patch 17 8 left Iteration 1 Error: 1.127461 Iteration 2 Error: 0.194071 Iteration 3 Error: 0.051951 Iteration 4 Error: 0.014562 Align patch 18 7 left Iteration 1 Error: 0.495468 Iteration 2 Error: 0.122987 Iteration 3 Error: 0.043890 Align patch 19 6 left Iteration 1 Error: 1.047790 Iteration 2 Error: 0.268922 Iteration 3 Error: 0.069664 Iteration 4 Error: 0.026537 Align patch 20 5 left Iteration 1 Error: 0.857516 Iteration 2 Error: 0.259213 Iteration 3 Error: 0.089882 Iteration 4 Error: 0.028169 Align patch 21 4 left Iteration 1 Error: 1.245756 Iteration 2 Error: 0.233286 Iteration 3 Error: 0.056733 Iteration 4 Error: 0.014451 Align patch 22 3 left Iteration 1 Error: 1.344897 Iteration 2 Error: 0.211499 Iteration 3 Error: 0.058121 Iteration 4 Error: 0.022547 Align patch 23 2 left Iteration 1 Error: 1.063689 Iteration 2 Error: 0.246097 Iteration 3 Error: 0.116110 Iteration 4 Error: 0.054775 Iteration 5 Error: 0.019650 Align patch 24 1 left Iteration 1 Error: 0.867573 Iteration 2 Error: 0.168509 Iteration 3 Error: 0.067076 Iteration 4 Error: 0.033013 Align patch 25 0 left Iteration 1 Error: 1.318000 Iteration 2 Error: 0.279627 Iteration 3 Error: 0.142415 Iteration 4 Error: 0.061478 Iteration 5 Error: 0.033090 3D Fitting completed. Patch alignment time: 20.09(sec) Local motion has been corrected. Process thread exits. Computational time: 36.128510 sec Total time: 44.372314 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00002hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00002hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.431304s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00002hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.944670s ........................................ >>>>>>TIME<<<<<< FFT: 1.343976s Defocus_U Defocus_V Angle CCC 23968.78 23402.35 85.36 0.041841 Final Values Defocus_U Defocus_V Angle CCC 23964.01 23435.27 85.36 0.067043 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00002hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00002hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.989e-02 CC threshold: 0.734 Mean Std: 39.22 6.64 Num Hot pixels: 151 Hot pixel threshold: 79.06 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.593298 Iteration 2 Error: 0.623021 Iteration 3 Error: 0.211912 Iteration 4 Error: 0.085283 Iteration 5 Error: 0.046317 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.03 -0.26 ...... Frame ( 3) shift: -0.05 -0.52 ...... Frame ( 4) shift: -0.08 -0.78 ...... Frame ( 5) shift: -0.10 -1.04 ...... Frame ( 6) shift: -0.04 -1.14 ...... Frame ( 7) shift: 0.12 -1.09 ...... Frame ( 8) shift: 0.28 -1.03 ...... Frame ( 9) shift: 0.51 -0.92 ...... Frame ( 10) shift: 0.79 -0.76 ...... Frame ( 11) shift: 1.07 -0.60 ...... Frame ( 12) shift: 1.31 -0.45 ...... Frame ( 13) shift: 1.50 -0.31 ...... Frame ( 14) shift: 1.69 -0.18 ...... Frame ( 15) shift: 1.86 -0.06 ...... Frame ( 16) shift: 2.01 0.05 ...... Frame ( 17) shift: 2.16 0.16 ...... Frame ( 18) shift: 2.28 0.28 ...... Frame ( 19) shift: 2.39 0.41 ...... Frame ( 20) shift: 2.49 0.55 ...... Frame ( 21) shift: 2.63 0.69 ...... Frame ( 22) shift: 2.79 0.82 ...... Frame ( 23) shift: 2.94 0.95 ...... Frame ( 24) shift: 3.12 1.07 ...... Frame ( 25) shift: 3.32 1.18 ...... Frame ( 26) shift: 3.52 1.29 ...... Frame ( 27) shift: 3.67 1.39 ...... Frame ( 28) shift: 3.77 1.46 ...... Frame ( 29) shift: 3.87 1.54 ...... Frame ( 30) shift: 3.98 1.61 ...... Frame ( 31) shift: 4.09 1.69 ...... Frame ( 32) shift: 4.20 1.77 ...... Frame ( 33) shift: 4.33 1.81 ...... Frame ( 34) shift: 4.49 1.81 ...... Frame ( 35) shift: 4.64 1.82 ...... Frame ( 36) shift: 4.79 1.83 ...... Frame ( 37) shift: 4.92 1.86 ...... Frame ( 38) shift: 5.06 1.89 ...... Frame ( 39) shift: 5.19 1.91 ...... Frame ( 40) shift: 5.32 1.94 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.688900 Iteration 2 Error: 0.207345 Iteration 3 Error: 0.105405 Iteration 4 Error: 0.040740 Align patch 2 23 left Iteration 1 Error: 1.302840 Iteration 2 Error: 0.171373 Iteration 3 Error: 0.067943 Iteration 4 Error: 0.024399 Align patch 3 22 left Iteration 1 Error: 1.476546 Iteration 2 Error: 0.298914 Iteration 3 Error: 0.090980 Iteration 4 Error: 0.026664 Align patch 4 21 left Iteration 1 Error: 0.826921 Iteration 2 Error: 0.205650 Iteration 3 Error: 0.062777 Iteration 4 Error: 0.025090 Align patch 5 20 left Iteration 1 Error: 1.622000 Iteration 2 Error: 0.302542 Iteration 3 Error: 0.090221 Iteration 4 Error: 0.034983 Align patch 6 19 left Iteration 1 Error: 1.038876 Iteration 2 Error: 0.339834 Iteration 3 Error: 0.144577 Iteration 4 Error: 0.066851 Iteration 5 Error: 0.038754 Align patch 7 18 left Iteration 1 Error: 1.270770 Iteration 2 Error: 0.284082 Iteration 3 Error: 0.101204 Iteration 4 Error: 0.057947 Iteration 5 Error: 0.026981 Align patch 8 17 left Iteration 1 Error: 0.736879 Iteration 2 Error: 0.126243 Iteration 3 Error: 0.039056 Align patch 9 16 left Iteration 1 Error: 0.852540 Iteration 2 Error: 0.126137 Iteration 3 Error: 0.051812 Iteration 4 Error: 0.017045 Align patch 10 15 left Iteration 1 Error: 1.057116 Iteration 2 Error: 0.228228 Iteration 3 Error: 0.087162 Iteration 4 Error: 0.024276 Align patch 11 14 left Iteration 1 Error: 0.820020 Iteration 2 Error: 0.189642 Iteration 3 Error: 0.065887 Iteration 4 Error: 0.028537 Align patch 12 13 left Iteration 1 Error: 0.755520 Iteration 2 Error: 0.128788 Iteration 3 Error: 0.032797 Align patch 13 12 left Iteration 1 Error: 1.017429 Iteration 2 Error: 0.313328 Iteration 3 Error: 0.072492 Iteration 4 Error: 0.034373 Align patch 14 11 left Iteration 1 Error: 0.853731 Iteration 2 Error: 0.174729 Iteration 3 Error: 0.058250 Iteration 4 Error: 0.019556 Align patch 15 10 left Iteration 1 Error: 0.895123 Iteration 2 Error: 0.222525 Iteration 3 Error: 0.107741 Iteration 4 Error: 0.045254 Align patch 16 9 left Iteration 1 Error: 0.615755 Iteration 2 Error: 0.186323 Iteration 3 Error: 0.046265 Align patch 17 8 left Iteration 1 Error: 1.233104 Iteration 2 Error: 0.148452 Iteration 3 Error: 0.046560 Align patch 18 7 left Iteration 1 Error: 0.537611 Iteration 2 Error: 0.118688 Iteration 3 Error: 0.041479 Align patch 19 6 left Iteration 1 Error: 0.854527 Iteration 2 Error: 0.204208 Iteration 3 Error: 0.052662 Iteration 4 Error: 0.026849 Align patch 20 5 left Iteration 1 Error: 0.591529 Iteration 2 Error: 0.137869 Iteration 3 Error: 0.032784 Align patch 21 4 left Iteration 1 Error: 1.208494 Iteration 2 Error: 0.309868 Iteration 3 Error: 0.089026 Iteration 4 Error: 0.045465 Align patch 22 3 left Iteration 1 Error: 0.646455 Iteration 2 Error: 0.115307 Iteration 3 Error: 0.028723 Align patch 23 2 left Iteration 1 Error: 0.551198 Iteration 2 Error: 0.081976 Iteration 3 Error: 0.020127 Align patch 24 1 left Iteration 1 Error: 1.041770 Iteration 2 Error: 0.242342 Iteration 3 Error: 0.058596 Iteration 4 Error: 0.027867 Align patch 25 0 left Iteration 1 Error: 0.914035 Iteration 2 Error: 0.171784 Iteration 3 Error: 0.052259 Iteration 4 Error: 0.022251 3D Fitting completed. Patch alignment time: 16.48(sec) Local motion has been corrected. Process thread exits. Computational time: 28.776529 sec Total time: 36.992134 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00002hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00002hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.270579s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00002hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.847722s ........................................ >>>>>>TIME<<<<<< FFT: 1.318571s Defocus_U Defocus_V Angle CCC 27773.46 26984.39 84.47 0.038726 Final Values Defocus_U Defocus_V Angle CCC 27698.44 26984.41 86.36 0.059916 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00003hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00003hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.342e-01 9.986e-02 CC threshold: 0.733 Mean Std: 39.17 6.66 Num Hot pixels: 166 Hot pixel threshold: 79.14 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 6.279723 Iteration 2 Error: 0.816659 Iteration 3 Error: 0.095171 Iteration 4 Error: 0.015450 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.04 -0.15 ...... Frame ( 3) shift: 0.07 -0.30 ...... Frame ( 4) shift: 0.11 -0.46 ...... Frame ( 5) shift: 0.14 -0.61 ...... Frame ( 6) shift: 0.24 -0.63 ...... Frame ( 7) shift: 0.39 -0.52 ...... Frame ( 8) shift: 0.55 -0.42 ...... Frame ( 9) shift: 0.79 -0.24 ...... Frame ( 10) shift: 1.11 0.02 ...... Frame ( 11) shift: 1.43 0.27 ...... Frame ( 12) shift: 1.68 0.52 ...... Frame ( 13) shift: 1.84 0.76 ...... Frame ( 14) shift: 2.00 1.00 ...... Frame ( 15) shift: 2.20 1.20 ...... Frame ( 16) shift: 2.43 1.37 ...... Frame ( 17) shift: 2.66 1.54 ...... Frame ( 18) shift: 2.92 1.70 ...... Frame ( 19) shift: 3.22 1.84 ...... Frame ( 20) shift: 3.52 1.98 ...... Frame ( 21) shift: 3.80 2.14 ...... Frame ( 22) shift: 4.05 2.33 ...... Frame ( 23) shift: 4.30 2.51 ...... Frame ( 24) shift: 4.55 2.71 ...... Frame ( 25) shift: 4.82 2.91 ...... Frame ( 26) shift: 5.09 3.11 ...... Frame ( 27) shift: 5.34 3.27 ...... Frame ( 28) shift: 5.56 3.38 ...... Frame ( 29) shift: 5.79 3.49 ...... Frame ( 30) shift: 6.05 3.64 ...... Frame ( 31) shift: 6.33 3.82 ...... Frame ( 32) shift: 6.62 4.00 ...... Frame ( 33) shift: 6.89 4.20 ...... Frame ( 34) shift: 7.16 4.42 ...... Frame ( 35) shift: 7.43 4.64 ...... Frame ( 36) shift: 7.69 4.90 ...... Frame ( 37) shift: 7.95 5.18 ...... Frame ( 38) shift: 8.20 5.47 ...... Frame ( 39) shift: 8.46 5.75 ...... Frame ( 40) shift: 8.71 6.04 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.984103 Iteration 2 Error: 0.325383 Iteration 3 Error: 0.113746 Iteration 4 Error: 0.046423 Align patch 2 23 left Iteration 1 Error: 1.051110 Iteration 2 Error: 0.315391 Iteration 3 Error: 0.140444 Iteration 4 Error: 0.071458 Iteration 5 Error: 0.032743 Align patch 3 22 left Iteration 1 Error: 1.012159 Iteration 2 Error: 0.371589 Iteration 3 Error: 0.119439 Iteration 4 Error: 0.057526 Iteration 5 Error: 0.014002 Align patch 4 21 left Iteration 1 Error: 0.914127 Iteration 2 Error: 0.209731 Iteration 3 Error: 0.044839 Align patch 5 20 left Iteration 1 Error: 0.771030 Iteration 2 Error: 0.088139 Iteration 3 Error: 0.009436 Align patch 6 19 left Iteration 1 Error: 0.727788 Iteration 2 Error: 0.303208 Iteration 3 Error: 0.082551 Iteration 4 Error: 0.038006 Align patch 7 18 left Iteration 1 Error: 1.096424 Iteration 2 Error: 0.258919 Iteration 3 Error: 0.064259 Iteration 4 Error: 0.020904 Align patch 8 17 left Iteration 1 Error: 0.619066 Iteration 2 Error: 0.239298 Iteration 3 Error: 0.112554 Iteration 4 Error: 0.054681 Iteration 5 Error: 0.031258 Align patch 9 16 left Iteration 1 Error: 0.496308 Iteration 2 Error: 0.039563 Align patch 10 15 left Iteration 1 Error: 0.714023 Iteration 2 Error: 0.053485 Iteration 3 Error: 0.007003 Align patch 11 14 left Iteration 1 Error: 0.929146 Iteration 2 Error: 0.152853 Iteration 3 Error: 0.046803 Align patch 12 13 left Iteration 1 Error: 0.648679 Iteration 2 Error: 0.222503 Iteration 3 Error: 0.112363 Iteration 4 Error: 0.037079 Align patch 13 12 left Iteration 1 Error: 1.608213 Iteration 2 Error: 0.397908 Iteration 3 Error: 0.127449 Iteration 4 Error: 0.033545 Align patch 14 11 left Iteration 1 Error: 0.330418 Iteration 2 Error: 0.018620 Align patch 15 10 left Iteration 1 Error: 0.875771 Iteration 2 Error: 0.145591 Iteration 3 Error: 0.026572 Align patch 16 9 left Iteration 1 Error: 1.386979 Iteration 2 Error: 0.401894 Iteration 3 Error: 0.148204 Iteration 4 Error: 0.069615 Iteration 5 Error: 0.027618 Align patch 17 8 left Iteration 1 Error: 1.329012 Iteration 2 Error: 0.460389 Iteration 3 Error: 0.113368 Iteration 4 Error: 0.050810 Iteration 5 Error: 0.016647 Align patch 18 7 left Iteration 1 Error: 0.291069 Iteration 2 Error: 0.034716 Align patch 19 6 left Iteration 1 Error: 0.382448 Iteration 2 Error: 0.054444 Iteration 3 Error: 0.009751 Align patch 20 5 left Iteration 1 Error: 0.847745 Iteration 2 Error: 0.378910 Iteration 3 Error: 0.123194 Iteration 4 Error: 0.062637 Iteration 5 Error: 0.028516 Align patch 21 4 left Iteration 1 Error: 1.171860 Iteration 2 Error: 0.214493 Iteration 3 Error: 0.041845 Align patch 22 3 left Iteration 1 Error: 1.109173 Iteration 2 Error: 0.133577 Iteration 3 Error: 0.018418 Align patch 23 2 left Iteration 1 Error: 1.054766 Iteration 2 Error: 0.070365 Iteration 3 Error: 0.004669 Align patch 24 1 left Iteration 1 Error: 1.206763 Iteration 2 Error: 0.272371 Iteration 3 Error: 0.051426 Iteration 4 Error: 0.025302 Align patch 25 0 left Iteration 1 Error: 1.236273 Iteration 2 Error: 0.339030 Iteration 3 Error: 0.100235 Iteration 4 Error: 0.058342 Iteration 5 Error: 0.032387 3D Fitting completed. Patch alignment time: 20.54(sec) Local motion has been corrected. Process thread exits. Computational time: 35.222034 sec Total time: 43.684048 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00003hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00003hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.574520s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00003hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.942629s ........................................ >>>>>>TIME<<<<<< FFT: 1.784882s Defocus_U Defocus_V Angle CCC 26501.95 27244.15 6.28 0.057723 Final Values Defocus_U Defocus_V Angle CCC 26500.38 27245.71 6.90 0.091069 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00003hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00003hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.986e-02 CC threshold: 0.733 Mean Std: 38.90 6.60 Num Hot pixels: 165 Hot pixel threshold: 78.47 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.802545 Iteration 2 Error: 0.639787 Iteration 3 Error: 0.269576 Iteration 4 Error: 0.105349 Iteration 5 Error: 0.047072 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.01 -0.34 ...... Frame ( 3) shift: -0.03 -0.68 ...... Frame ( 4) shift: -0.04 -1.02 ...... Frame ( 5) shift: -0.06 -1.36 ...... Frame ( 6) shift: 0.07 -1.44 ...... Frame ( 7) shift: 0.34 -1.27 ...... Frame ( 8) shift: 0.61 -1.09 ...... Frame ( 9) shift: 0.87 -0.94 ...... Frame ( 10) shift: 1.11 -0.82 ...... Frame ( 11) shift: 1.35 -0.70 ...... Frame ( 12) shift: 1.52 -0.55 ...... Frame ( 13) shift: 1.63 -0.35 ...... Frame ( 14) shift: 1.74 -0.16 ...... Frame ( 15) shift: 1.91 0.01 ...... Frame ( 16) shift: 2.14 0.14 ...... Frame ( 17) shift: 2.36 0.28 ...... Frame ( 18) shift: 2.50 0.41 ...... Frame ( 19) shift: 2.55 0.53 ...... Frame ( 20) shift: 2.61 0.66 ...... Frame ( 21) shift: 2.71 0.82 ...... Frame ( 22) shift: 2.85 1.02 ...... Frame ( 23) shift: 2.99 1.22 ...... Frame ( 24) shift: 3.13 1.38 ...... Frame ( 25) shift: 3.28 1.50 ...... Frame ( 26) shift: 3.43 1.61 ...... Frame ( 27) shift: 3.61 1.71 ...... Frame ( 28) shift: 3.84 1.79 ...... Frame ( 29) shift: 4.07 1.86 ...... Frame ( 30) shift: 4.27 1.94 ...... Frame ( 31) shift: 4.43 2.01 ...... Frame ( 32) shift: 4.59 2.09 ...... Frame ( 33) shift: 4.75 2.20 ...... Frame ( 34) shift: 4.91 2.34 ...... Frame ( 35) shift: 5.07 2.49 ...... Frame ( 36) shift: 5.19 2.62 ...... Frame ( 37) shift: 5.27 2.74 ...... Frame ( 38) shift: 5.35 2.87 ...... Frame ( 39) shift: 5.44 2.99 ...... Frame ( 40) shift: 5.52 3.11 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.712316 Iteration 2 Error: 0.360007 Iteration 3 Error: 0.090762 Iteration 4 Error: 0.052784 Iteration 5 Error: 0.020564 Align patch 2 23 left Iteration 1 Error: 1.536918 Iteration 2 Error: 0.485662 Iteration 3 Error: 0.174162 Iteration 4 Error: 0.071044 Iteration 5 Error: 0.032091 Align patch 3 22 left Iteration 1 Error: 1.222063 Iteration 2 Error: 0.138951 Iteration 3 Error: 0.050949 Iteration 4 Error: 0.014857 Align patch 4 21 left Iteration 1 Error: 1.529038 Iteration 2 Error: 0.296190 Iteration 3 Error: 0.097366 Iteration 4 Error: 0.030118 Align patch 5 20 left Iteration 1 Error: 0.986717 Iteration 2 Error: 0.310872 Iteration 3 Error: 0.077120 Iteration 4 Error: 0.035543 Align patch 6 19 left Iteration 1 Error: 0.920148 Iteration 2 Error: 0.203607 Iteration 3 Error: 0.072782 Iteration 4 Error: 0.031402 Align patch 7 18 left Iteration 1 Error: 1.066441 Iteration 2 Error: 0.248846 Iteration 3 Error: 0.064657 Iteration 4 Error: 0.024073 Align patch 8 17 left Iteration 1 Error: 0.755981 Iteration 2 Error: 0.215681 Iteration 3 Error: 0.082075 Iteration 4 Error: 0.020992 Align patch 9 16 left Iteration 1 Error: 0.925302 Iteration 2 Error: 0.108146 Iteration 3 Error: 0.031970 Align patch 10 15 left Iteration 1 Error: 0.726866 Iteration 2 Error: 0.161020 Iteration 3 Error: 0.046093 Align patch 11 14 left Iteration 1 Error: 0.660475 Iteration 2 Error: 0.116786 Iteration 3 Error: 0.038772 Align patch 12 13 left Iteration 1 Error: 0.627699 Iteration 2 Error: 0.169372 Iteration 3 Error: 0.055107 Iteration 4 Error: 0.026017 Align patch 13 12 left Iteration 1 Error: 0.771225 Iteration 2 Error: 0.187468 Iteration 3 Error: 0.066823 Iteration 4 Error: 0.018008 Align patch 14 11 left Iteration 1 Error: 0.826410 Iteration 2 Error: 0.311411 Iteration 3 Error: 0.060388 Iteration 4 Error: 0.021875 Align patch 15 10 left Iteration 1 Error: 0.518822 Iteration 2 Error: 0.182103 Iteration 3 Error: 0.065857 Iteration 4 Error: 0.024070 Align patch 16 9 left Iteration 1 Error: 1.164905 Iteration 2 Error: 0.316123 Iteration 3 Error: 0.119401 Iteration 4 Error: 0.069559 Iteration 5 Error: 0.033133 Align patch 17 8 left Iteration 1 Error: 0.955461 Iteration 2 Error: 0.308074 Iteration 3 Error: 0.125893 Iteration 4 Error: 0.045778 Align patch 18 7 left Iteration 1 Error: 0.908524 Iteration 2 Error: 0.218420 Iteration 3 Error: 0.055020 Iteration 4 Error: 0.024676 Align patch 19 6 left Iteration 1 Error: 1.021708 Iteration 2 Error: 0.244113 Iteration 3 Error: 0.058366 Iteration 4 Error: 0.017076 Align patch 20 5 left Iteration 1 Error: 1.124243 Iteration 2 Error: 0.111445 Iteration 3 Error: 0.036663 Align patch 21 4 left Iteration 1 Error: 0.719565 Iteration 2 Error: 0.208206 Iteration 3 Error: 0.095674 Iteration 4 Error: 0.042697 Align patch 22 3 left Iteration 1 Error: 0.913712 Iteration 2 Error: 0.214669 Iteration 3 Error: 0.099983 Iteration 4 Error: 0.037786 Align patch 23 2 left Iteration 1 Error: 0.993505 Iteration 2 Error: 0.224140 Iteration 3 Error: 0.163902 Iteration 4 Error: 0.054174 Iteration 5 Error: 0.054781 Align patch 23 2 left Iteration 1 Error: 0.598620 Iteration 2 Error: 0.063439 Iteration 3 Error: 0.024391 Align patch 24 1 left Iteration 1 Error: 0.761265 Iteration 2 Error: 0.161281 Iteration 3 Error: 0.076893 Iteration 4 Error: 0.023854 Align patch 25 0 left Iteration 1 Error: 0.819224 Iteration 2 Error: 0.138531 Iteration 3 Error: 0.048731 3D Fitting completed. Patch alignment time: 22.86(sec) Local motion has been corrected. Process thread exits. Computational time: 41.171223 sec Total time: 50.315964 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00003hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00003hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.553856s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00003hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.276059s ........................................ >>>>>>TIME<<<<<< FFT: 0.949064s Defocus_U Defocus_V Angle CCC 24828.11 25738.31 9.14 0.042198 Final Values Defocus_U Defocus_V Angle CCC 24853.11 25750.82 10.09 0.063647 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00003hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00003hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.994e-02 CC threshold: 0.734 Mean Std: 39.12 6.66 Num Hot pixels: 153 Hot pixel threshold: 79.05 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 3.671761 Iteration 2 Error: 0.660967 Iteration 3 Error: 0.169094 Iteration 4 Error: 0.056783 Iteration 5 Error: 0.025260 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.08 -0.14 ...... Frame ( 3) shift: -0.16 -0.27 ...... Frame ( 4) shift: -0.24 -0.41 ...... Frame ( 5) shift: -0.32 -0.55 ...... Frame ( 6) shift: -0.25 -0.58 ...... Frame ( 7) shift: -0.04 -0.50 ...... Frame ( 8) shift: 0.18 -0.42 ...... Frame ( 9) shift: 0.38 -0.31 ...... Frame ( 10) shift: 0.56 -0.17 ...... Frame ( 11) shift: 0.74 -0.03 ...... Frame ( 12) shift: 0.91 0.13 ...... Frame ( 13) shift: 1.08 0.31 ...... Frame ( 14) shift: 1.26 0.49 ...... Frame ( 15) shift: 1.41 0.66 ...... Frame ( 16) shift: 1.56 0.82 ...... Frame ( 17) shift: 1.71 0.99 ...... Frame ( 18) shift: 1.87 1.11 ...... Frame ( 19) shift: 2.04 1.18 ...... Frame ( 20) shift: 2.21 1.26 ...... Frame ( 21) shift: 2.39 1.35 ...... Frame ( 22) shift: 2.59 1.47 ...... Frame ( 23) shift: 2.79 1.59 ...... Frame ( 24) shift: 2.95 1.70 ...... Frame ( 25) shift: 3.07 1.80 ...... Frame ( 26) shift: 3.19 1.90 ...... Frame ( 27) shift: 3.36 2.01 ...... Frame ( 28) shift: 3.57 2.14 ...... Frame ( 29) shift: 3.78 2.28 ...... Frame ( 30) shift: 3.96 2.37 ...... Frame ( 31) shift: 4.13 2.43 ...... Frame ( 32) shift: 4.30 2.49 ...... Frame ( 33) shift: 4.50 2.59 ...... Frame ( 34) shift: 4.74 2.75 ...... Frame ( 35) shift: 4.98 2.90 ...... Frame ( 36) shift: 5.19 3.03 ...... Frame ( 37) shift: 5.37 3.12 ...... Frame ( 38) shift: 5.55 3.21 ...... Frame ( 39) shift: 5.73 3.31 ...... Frame ( 40) shift: 5.92 3.40 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.065632 Iteration 2 Error: 0.133256 Iteration 3 Error: 0.040957 Align patch 2 23 left Iteration 1 Error: 1.410397 Iteration 2 Error: 0.191588 Iteration 3 Error: 0.039757 Align patch 3 22 left Iteration 1 Error: 1.136856 Iteration 2 Error: 0.164684 Iteration 3 Error: 0.043274 Align patch 4 21 left Iteration 1 Error: 0.563636 Iteration 2 Error: 0.135034 Iteration 3 Error: 0.045602 Align patch 5 20 left Iteration 1 Error: 1.121238 Iteration 2 Error: 0.113447 Iteration 3 Error: 0.023517 Align patch 6 19 left Iteration 1 Error: 0.913231 Iteration 2 Error: 0.180877 Iteration 3 Error: 0.058103 Iteration 4 Error: 0.013632 Align patch 7 18 left Iteration 1 Error: 0.654925 Iteration 2 Error: 0.117720 Iteration 3 Error: 0.028624 Align patch 8 17 left Iteration 1 Error: 0.731231 Iteration 2 Error: 0.253014 Iteration 3 Error: 0.063959 Iteration 4 Error: 0.022219 Align patch 9 16 left Iteration 1 Error: 0.670412 Iteration 2 Error: 0.110751 Iteration 3 Error: 0.034295 Align patch 10 15 left Iteration 1 Error: 0.698563 Iteration 2 Error: 0.141973 Iteration 3 Error: 0.033453 Align patch 11 14 left Iteration 1 Error: 0.650163 Iteration 2 Error: 0.112596 Iteration 3 Error: 0.030131 Align patch 12 13 left Iteration 1 Error: 0.657206 Iteration 2 Error: 0.184466 Iteration 3 Error: 0.064678 Iteration 4 Error: 0.043705 Align patch 13 12 left Iteration 1 Error: 0.669094 Iteration 2 Error: 0.128561 Iteration 3 Error: 0.034190 Align patch 14 11 left Iteration 1 Error: 0.924589 Iteration 2 Error: 0.113479 Iteration 3 Error: 0.039076 Align patch 15 10 left Iteration 1 Error: 0.523635 Iteration 2 Error: 0.092002 Iteration 3 Error: 0.021282 Align patch 16 9 left Iteration 1 Error: 0.734472 Iteration 2 Error: 0.169745 Iteration 3 Error: 0.031415 Align patch 17 8 left Iteration 1 Error: 1.011935 Iteration 2 Error: 0.181971 Iteration 3 Error: 0.046115 Align patch 18 7 left Iteration 1 Error: 0.631209 Iteration 2 Error: 0.103508 Iteration 3 Error: 0.028217 Align patch 19 6 left Iteration 1 Error: 0.719316 Iteration 2 Error: 0.137812 Iteration 3 Error: 0.052364 Iteration 4 Error: 0.022629 Align patch 20 5 left Iteration 1 Error: 0.548378 Iteration 2 Error: 0.111527 Iteration 3 Error: 0.035255 Align patch 21 4 left Iteration 1 Error: 0.808718 Iteration 2 Error: 0.134660 Iteration 3 Error: 0.041745 Align patch 22 3 left Iteration 1 Error: 1.122587 Iteration 2 Error: 0.208448 Iteration 3 Error: 0.078307 Iteration 4 Error: 0.030164 Align patch 23 2 left Iteration 1 Error: 0.988091 Iteration 2 Error: 0.149473 Iteration 3 Error: 0.030766 Align patch 24 1 left Iteration 1 Error: 0.679255 Iteration 2 Error: 0.100169 Iteration 3 Error: 0.020336 Align patch 25 0 left Iteration 1 Error: 0.682636 Iteration 2 Error: 0.102657 Iteration 3 Error: 0.024556 3D Fitting completed. Patch alignment time: 19.30(sec) Local motion has been corrected. Process thread exits. Computational time: 35.059196 sec Total time: 43.111835 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00003hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00003hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.616285s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00003hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 5.217588s ........................................ >>>>>>TIME<<<<<< FFT: 1.335651s Defocus_U Defocus_V Angle CCC 27337.90 26669.93 88.86 0.051247 Final Values Defocus_U Defocus_V Angle CCC 27253.53 26701.33 88.86 0.075947 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00003hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00003hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.988e-02 CC threshold: 0.734 Mean Std: 39.50 6.67 Num Hot pixels: 152 Hot pixel threshold: 79.54 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.401546 Iteration 2 Error: 0.526149 Iteration 3 Error: 0.196596 Iteration 4 Error: 0.082401 Iteration 5 Error: 0.038758 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.03 -0.23 ...... Frame ( 3) shift: -0.06 -0.46 ...... Frame ( 4) shift: -0.09 -0.69 ...... Frame ( 5) shift: -0.13 -0.92 ...... Frame ( 6) shift: -0.09 -0.99 ...... Frame ( 7) shift: 0.02 -0.92 ...... Frame ( 8) shift: 0.13 -0.85 ...... Frame ( 9) shift: 0.25 -0.73 ...... Frame ( 10) shift: 0.39 -0.57 ...... Frame ( 11) shift: 0.54 -0.41 ...... Frame ( 12) shift: 0.75 -0.22 ...... Frame ( 13) shift: 1.04 -0.02 ...... Frame ( 14) shift: 1.32 0.19 ...... Frame ( 15) shift: 1.50 0.32 ...... Frame ( 16) shift: 1.58 0.38 ...... Frame ( 17) shift: 1.65 0.44 ...... Frame ( 18) shift: 1.75 0.54 ...... Frame ( 19) shift: 1.88 0.68 ...... Frame ( 20) shift: 2.01 0.82 ...... Frame ( 21) shift: 2.16 0.99 ...... Frame ( 22) shift: 2.33 1.18 ...... Frame ( 23) shift: 2.49 1.38 ...... Frame ( 24) shift: 2.66 1.53 ...... Frame ( 25) shift: 2.83 1.64 ...... Frame ( 26) shift: 3.01 1.75 ...... Frame ( 27) shift: 3.16 1.84 ...... Frame ( 28) shift: 3.28 1.93 ...... Frame ( 29) shift: 3.41 2.01 ...... Frame ( 30) shift: 3.52 2.12 ...... Frame ( 31) shift: 3.61 2.26 ...... Frame ( 32) shift: 3.70 2.40 ...... Frame ( 33) shift: 3.79 2.46 ...... Frame ( 34) shift: 3.89 2.44 ...... Frame ( 35) shift: 3.99 2.42 ...... Frame ( 36) shift: 4.09 2.47 ...... Frame ( 37) shift: 4.20 2.57 ...... Frame ( 38) shift: 4.31 2.68 ...... Frame ( 39) shift: 4.42 2.79 ...... Frame ( 40) shift: 4.53 2.90 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.950571 Iteration 2 Error: 0.257542 Iteration 3 Error: 0.074207 Iteration 4 Error: 0.038287 Align patch 2 23 left Iteration 1 Error: 1.118101 Iteration 2 Error: 0.229304 Iteration 3 Error: 0.063287 Iteration 4 Error: 0.027029 Align patch 3 22 left Iteration 1 Error: 1.286675 Iteration 2 Error: 0.426964 Iteration 3 Error: 0.103900 Iteration 4 Error: 0.057730 Iteration 5 Error: 0.027241 Align patch 4 21 left Iteration 1 Error: 1.398270 Iteration 2 Error: 0.274581 Iteration 3 Error: 0.100991 Iteration 4 Error: 0.031558 Align patch 5 20 left Iteration 1 Error: 0.920146 Iteration 2 Error: 0.210887 Iteration 3 Error: 0.099042 Iteration 4 Error: 0.045624 Align patch 6 19 left Iteration 1 Error: 1.373459 Iteration 2 Error: 0.237710 Iteration 3 Error: 0.101018 Iteration 4 Error: 0.043369 Align patch 7 18 left Iteration 1 Error: 1.385085 Iteration 2 Error: 0.406331 Iteration 3 Error: 0.134608 Iteration 4 Error: 0.084943 Iteration 5 Error: 0.034772 Align patch 8 17 left Iteration 1 Error: 0.862473 Iteration 2 Error: 0.148520 Iteration 3 Error: 0.044292 Align patch 9 16 left Iteration 1 Error: 1.041771 Iteration 2 Error: 0.248460 Iteration 3 Error: 0.075035 Iteration 4 Error: 0.031733 Align patch 10 15 left Iteration 1 Error: 0.645276 Iteration 2 Error: 0.171326 Iteration 3 Error: 0.062802 Iteration 4 Error: 0.029831 Align patch 11 14 left Iteration 1 Error: 1.297025 Iteration 2 Error: 0.258915 Iteration 3 Error: 0.064155 Iteration 4 Error: 0.031981 Align patch 12 13 left Iteration 1 Error: 0.920474 Iteration 2 Error: 0.174563 Iteration 3 Error: 0.057886 Iteration 4 Error: 0.030214 Align patch 13 12 left Iteration 1 Error: 0.896722 Iteration 2 Error: 0.264847 Iteration 3 Error: 0.116726 Iteration 4 Error: 0.082402 Iteration 5 Error: 0.038532 Align patch 14 11 left Iteration 1 Error: 0.655241 Iteration 2 Error: 0.199622 Iteration 3 Error: 0.038593 Align patch 15 10 left Iteration 1 Error: 0.810740 Iteration 2 Error: 0.379699 Iteration 3 Error: 0.143574 Iteration 4 Error: 0.070882 Iteration 5 Error: 0.033138 Align patch 16 9 left Iteration 1 Error: 0.744609 Iteration 2 Error: 0.141718 Iteration 3 Error: 0.031121 Align patch 17 8 left Iteration 1 Error: 0.662393 Iteration 2 Error: 0.290152 Iteration 3 Error: 0.151354 Iteration 4 Error: 0.063668 Iteration 5 Error: 0.025481 Align patch 18 7 left Iteration 1 Error: 0.759930 Iteration 2 Error: 0.149642 Iteration 3 Error: 0.041331 Align patch 19 6 left Iteration 1 Error: 0.618020 Iteration 2 Error: 0.139870 Iteration 3 Error: 0.026703 Align patch 20 5 left Iteration 1 Error: 1.116831 Iteration 2 Error: 0.156270 Iteration 3 Error: 0.070081 Iteration 4 Error: 0.020623 Align patch 21 4 left Iteration 1 Error: 1.469913 Iteration 2 Error: 0.263427 Iteration 3 Error: 0.149077 Iteration 4 Error: 0.070812 Iteration 5 Error: 0.040244 Align patch 22 3 left Iteration 1 Error: 0.789959 Iteration 2 Error: 0.140694 Iteration 3 Error: 0.049897 Align patch 23 2 left Iteration 1 Error: 0.957342 Iteration 2 Error: 0.249069 Iteration 3 Error: 0.100021 Iteration 4 Error: 0.044319 Align patch 24 1 left Iteration 1 Error: 0.914810 Iteration 2 Error: 0.125116 Iteration 3 Error: 0.050029 Iteration 4 Error: 0.014701 Align patch 25 0 left Iteration 1 Error: 1.022821 Iteration 2 Error: 0.192753 Iteration 3 Error: 0.102003 Iteration 4 Error: 0.048156 3D Fitting completed. Patch alignment time: 18.70(sec) Local motion has been corrected. Process thread exits. Computational time: 35.577122 sec Total time: 43.868973 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00003hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00003hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.642014s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00003hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 4.752958s ........................................ >>>>>>TIME<<<<<< FFT: 1.606456s Defocus_U Defocus_V Angle CCC 25630.88 24857.44 85.56 0.042363 Final Values Defocus_U Defocus_V Angle CCC 25627.85 24838.79 85.88 0.063824 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00004hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00004hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.342e-01 9.985e-02 CC threshold: 0.733 Mean Std: 41.20 6.81 Num Hot pixels: 167 Hot pixel threshold: 82.05 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 3.525503 Iteration 2 Error: 0.835757 Iteration 3 Error: 0.339532 Iteration 4 Error: 0.146513 Iteration 5 Error: 0.060892 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.23 -0.46 ...... Frame ( 3) shift: 0.45 -0.93 ...... Frame ( 4) shift: 0.68 -1.39 ...... Frame ( 5) shift: 0.90 -1.86 ...... Frame ( 6) shift: 1.15 -1.99 ...... Frame ( 7) shift: 1.42 -1.79 ...... Frame ( 8) shift: 1.69 -1.59 ...... Frame ( 9) shift: 1.96 -1.36 ...... Frame ( 10) shift: 2.25 -1.10 ...... Frame ( 11) shift: 2.54 -0.83 ...... Frame ( 12) shift: 2.75 -0.59 ...... Frame ( 13) shift: 2.87 -0.36 ...... Frame ( 14) shift: 3.00 -0.13 ...... Frame ( 15) shift: 3.19 0.05 ...... Frame ( 16) shift: 3.45 0.19 ...... Frame ( 17) shift: 3.71 0.32 ...... Frame ( 18) shift: 3.93 0.49 ...... Frame ( 19) shift: 4.10 0.70 ...... Frame ( 20) shift: 4.27 0.91 ...... Frame ( 21) shift: 4.42 1.09 ...... Frame ( 22) shift: 4.54 1.24 ...... Frame ( 23) shift: 4.66 1.39 ...... Frame ( 24) shift: 4.81 1.51 ...... Frame ( 25) shift: 4.99 1.61 ...... Frame ( 26) shift: 5.17 1.71 ...... Frame ( 27) shift: 5.44 1.85 ...... Frame ( 28) shift: 5.78 2.03 ...... Frame ( 29) shift: 6.13 2.21 ...... Frame ( 30) shift: 6.42 2.36 ...... Frame ( 31) shift: 6.67 2.47 ...... Frame ( 32) shift: 6.93 2.59 ...... Frame ( 33) shift: 7.10 2.66 ...... Frame ( 34) shift: 7.20 2.69 ...... Frame ( 35) shift: 7.30 2.72 ...... Frame ( 36) shift: 7.45 2.77 ...... Frame ( 37) shift: 7.66 2.81 ...... Frame ( 38) shift: 7.87 2.86 ...... Frame ( 39) shift: 8.08 2.91 ...... Frame ( 40) shift: 8.29 2.96 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.383039 Iteration 2 Error: 0.247251 Iteration 3 Error: 0.091935 Iteration 4 Error: 0.035801 Align patch 2 23 left Iteration 1 Error: 0.916370 Iteration 2 Error: 0.295862 Iteration 3 Error: 0.092340 Iteration 4 Error: 0.031429 Align patch 3 22 left Iteration 1 Error: 0.884967 Iteration 2 Error: 0.173375 Iteration 3 Error: 0.070797 Iteration 4 Error: 0.018836 Align patch 4 21 left Iteration 1 Error: 1.250596 Iteration 2 Error: 0.205090 Iteration 3 Error: 0.050320 Iteration 4 Error: 0.013987 Align patch 5 20 left Iteration 1 Error: 1.055481 Iteration 2 Error: 0.180614 Iteration 3 Error: 0.056777 Iteration 4 Error: 0.027102 Align patch 6 19 left Iteration 1 Error: 1.387433 Iteration 2 Error: 0.247117 Iteration 3 Error: 0.060045 Iteration 4 Error: 0.019427 Align patch 7 18 left Iteration 1 Error: 1.557064 Iteration 2 Error: 0.260064 Iteration 3 Error: 0.075340 Iteration 4 Error: 0.027632 Align patch 8 17 left Iteration 1 Error: 0.913532 Iteration 2 Error: 0.206909 Iteration 3 Error: 0.128877 Iteration 4 Error: 0.073110 Iteration 5 Error: 0.053294 Align patch 8 17 left Iteration 1 Error: 0.861071 Iteration 2 Error: 0.057941 Iteration 3 Error: 0.023231 Align patch 9 16 left Iteration 1 Error: 0.941854 Iteration 2 Error: 0.258339 Iteration 3 Error: 0.163106 Iteration 4 Error: 0.059597 Iteration 5 Error: 0.032551 Align patch 10 15 left Iteration 1 Error: 1.220003 Iteration 2 Error: 0.304012 Iteration 3 Error: 0.061295 Iteration 4 Error: 0.023814 Align patch 11 14 left Iteration 1 Error: 1.433379 Iteration 2 Error: 0.290140 Iteration 3 Error: 0.086937 Iteration 4 Error: 0.031226 Align patch 12 13 left Iteration 1 Error: 0.946501 Iteration 2 Error: 0.205372 Iteration 3 Error: 0.084079 Iteration 4 Error: 0.030129 Align patch 13 12 left Iteration 1 Error: 0.631896 Iteration 2 Error: 0.214190 Iteration 3 Error: 0.050637 Iteration 4 Error: 0.029797 Align patch 14 11 left Iteration 1 Error: 1.064866 Iteration 2 Error: 0.272625 Iteration 3 Error: 0.072659 Iteration 4 Error: 0.026866 Align patch 15 10 left Iteration 1 Error: 1.206400 Iteration 2 Error: 0.329061 Iteration 3 Error: 0.091291 Iteration 4 Error: 0.046027 Align patch 16 9 left Iteration 1 Error: 0.926839 Iteration 2 Error: 0.315029 Iteration 3 Error: 0.119236 Iteration 4 Error: 0.041421 Align patch 17 8 left Iteration 1 Error: 0.844230 Iteration 2 Error: 0.129080 Iteration 3 Error: 0.043678 Align patch 18 7 left Iteration 1 Error: 1.336553 Iteration 2 Error: 0.205949 Iteration 3 Error: 0.095043 Iteration 4 Error: 0.039868 Align patch 19 6 left Iteration 1 Error: 0.972942 Iteration 2 Error: 0.244060 Iteration 3 Error: 0.123329 Iteration 4 Error: 0.041583 Align patch 20 5 left Iteration 1 Error: 0.774621 Iteration 2 Error: 0.236810 Iteration 3 Error: 0.070029 Iteration 4 Error: 0.022483 Align patch 21 4 left Iteration 1 Error: 0.929175 Iteration 2 Error: 0.376231 Iteration 3 Error: 0.192990 Iteration 4 Error: 0.077909 Iteration 5 Error: 0.047613 Align patch 22 3 left Iteration 1 Error: 0.934012 Iteration 2 Error: 0.121995 Iteration 3 Error: 0.047587 Align patch 23 2 left Iteration 1 Error: 0.999295 Iteration 2 Error: 0.174520 Iteration 3 Error: 0.066638 Iteration 4 Error: 0.030619 Align patch 24 1 left Iteration 1 Error: 1.173206 Iteration 2 Error: 0.282546 Iteration 3 Error: 0.070026 Iteration 4 Error: 0.033055 Align patch 25 0 left Iteration 1 Error: 0.876583 Iteration 2 Error: 0.185627 Iteration 3 Error: 0.084330 Iteration 4 Error: 0.030493 3D Fitting completed. Patch alignment time: 21.96(sec) Local motion has been corrected. Process thread exits. Computational time: 42.090336 sec Total time: 50.161919 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00004hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00004hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.571252s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00004hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 4.131318s ........................................ >>>>>>TIME<<<<<< FFT: 1.491450s Defocus_U Defocus_V Angle CCC 22457.02 23367.20 7.12 0.043865 Final Values Defocus_U Defocus_V Angle CCC 22467.96 23368.77 7.43 0.073989 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00004hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00004hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.342e-01 9.983e-02 CC threshold: 0.733 Mean Std: 41.58 6.89 Num Hot pixels: 164 Hot pixel threshold: 82.94 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.943136 Iteration 2 Error: 0.683134 Iteration 3 Error: 0.312293 Iteration 4 Error: 0.130081 Iteration 5 Error: 0.059003 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.16 -0.42 ...... Frame ( 3) shift: 0.33 -0.83 ...... Frame ( 4) shift: 0.49 -1.25 ...... Frame ( 5) shift: 0.65 -1.66 ...... Frame ( 6) shift: 0.79 -1.82 ...... Frame ( 7) shift: 0.91 -1.74 ...... Frame ( 8) shift: 1.03 -1.65 ...... Frame ( 9) shift: 1.21 -1.49 ...... Frame ( 10) shift: 1.46 -1.28 ...... Frame ( 11) shift: 1.71 -1.06 ...... Frame ( 12) shift: 1.89 -0.86 ...... Frame ( 13) shift: 2.01 -0.69 ...... Frame ( 14) shift: 2.13 -0.51 ...... Frame ( 15) shift: 2.24 -0.36 ...... Frame ( 16) shift: 2.34 -0.25 ...... Frame ( 17) shift: 2.44 -0.14 ...... Frame ( 18) shift: 2.61 -0.07 ...... Frame ( 19) shift: 2.86 -0.06 ...... Frame ( 20) shift: 3.10 -0.04 ...... Frame ( 21) shift: 3.33 0.02 ...... Frame ( 22) shift: 3.53 0.12 ...... Frame ( 23) shift: 3.73 0.22 ...... Frame ( 24) shift: 3.95 0.32 ...... Frame ( 25) shift: 4.18 0.42 ...... Frame ( 26) shift: 4.41 0.53 ...... Frame ( 27) shift: 4.62 0.68 ...... Frame ( 28) shift: 4.82 0.88 ...... Frame ( 29) shift: 5.02 1.09 ...... Frame ( 30) shift: 5.25 1.31 ...... Frame ( 31) shift: 5.50 1.54 ...... Frame ( 32) shift: 5.76 1.77 ...... Frame ( 33) shift: 5.95 1.93 ...... Frame ( 34) shift: 6.09 2.02 ...... Frame ( 35) shift: 6.23 2.11 ...... Frame ( 36) shift: 6.37 2.16 ...... Frame ( 37) shift: 6.51 2.15 ...... Frame ( 38) shift: 6.65 2.15 ...... Frame ( 39) shift: 6.79 2.15 ...... Frame ( 40) shift: 6.93 2.15 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.556470 Iteration 2 Error: 0.296907 Iteration 3 Error: 0.142135 Iteration 4 Error: 0.092758 Iteration 5 Error: 0.059940 Align patch 1 24 left Iteration 1 Error: 1.446074 Iteration 2 Error: 0.153919 Iteration 3 Error: 0.041600 Align patch 2 23 left Iteration 1 Error: 1.044743 Iteration 2 Error: 0.283109 Iteration 3 Error: 0.095868 Iteration 4 Error: 0.056910 Iteration 5 Error: 0.015377 Align patch 3 22 left Iteration 1 Error: 0.687208 Iteration 2 Error: 0.192377 Iteration 3 Error: 0.093223 Iteration 4 Error: 0.034846 Align patch 4 21 left Iteration 1 Error: 0.973926 Iteration 2 Error: 0.238736 Iteration 3 Error: 0.074408 Iteration 4 Error: 0.035980 Align patch 5 20 left Iteration 1 Error: 1.241969 Iteration 2 Error: 0.398729 Iteration 3 Error: 0.127410 Iteration 4 Error: 0.037427 Align patch 6 19 left Iteration 1 Error: 1.222486 Iteration 2 Error: 0.304710 Iteration 3 Error: 0.100103 Iteration 4 Error: 0.052098 Iteration 5 Error: 0.041705 Align patch 7 18 left Iteration 1 Error: 1.614966 Iteration 2 Error: 0.313071 Iteration 3 Error: 0.094814 Iteration 4 Error: 0.028240 Align patch 8 17 left Iteration 1 Error: 0.951499 Iteration 2 Error: 0.210807 Iteration 3 Error: 0.064978 Iteration 4 Error: 0.018585 Align patch 9 16 left Iteration 1 Error: 0.773203 Iteration 2 Error: 0.137065 Iteration 3 Error: 0.047885 Align patch 10 15 left Iteration 1 Error: 0.995681 Iteration 2 Error: 0.215686 Iteration 3 Error: 0.052909 Iteration 4 Error: 0.019259 Align patch 11 14 left Iteration 1 Error: 1.110726 Iteration 2 Error: 0.185034 Iteration 3 Error: 0.074129 Iteration 4 Error: 0.037249 Align patch 12 13 left Iteration 1 Error: 1.559083 Iteration 2 Error: 0.484565 Iteration 3 Error: 0.216989 Iteration 4 Error: 0.097504 Iteration 5 Error: 0.057003 Align patch 12 13 left Iteration 1 Error: 1.624138 Iteration 2 Error: 0.252044 Iteration 3 Error: 0.074082 Iteration 4 Error: 0.023281 Align patch 13 12 left Iteration 1 Error: 1.533131 Iteration 2 Error: 0.317380 Iteration 3 Error: 0.120926 Iteration 4 Error: 0.040505 Align patch 14 11 left Iteration 1 Error: 1.029387 Iteration 2 Error: 0.227094 Iteration 3 Error: 0.083849 Iteration 4 Error: 0.032295 Align patch 15 10 left Iteration 1 Error: 0.771077 Iteration 2 Error: 0.220654 Iteration 3 Error: 0.059763 Iteration 4 Error: 0.027114 Align patch 16 9 left Iteration 1 Error: 1.220322 Iteration 2 Error: 0.404094 Iteration 3 Error: 0.197824 Iteration 4 Error: 0.087053 Iteration 5 Error: 0.050868 Align patch 16 9 left Iteration 1 Error: 0.851209 Iteration 2 Error: 0.200835 Iteration 3 Error: 0.069036 Iteration 4 Error: 0.032376 Align patch 17 8 left Iteration 1 Error: 0.991890 Iteration 2 Error: 0.300672 Iteration 3 Error: 0.091832 Iteration 4 Error: 0.053053 Iteration 5 Error: 0.030816 Align patch 18 7 left Iteration 1 Error: 1.294655 Iteration 2 Error: 0.457869 Iteration 3 Error: 0.131533 Iteration 4 Error: 0.064924 Iteration 5 Error: 0.033613 Align patch 19 6 left Iteration 1 Error: 1.260337 Iteration 2 Error: 0.119031 Iteration 3 Error: 0.023517 Align patch 20 5 left Iteration 1 Error: 0.715726 Iteration 2 Error: 0.138121 Iteration 3 Error: 0.039167 Align patch 21 4 left Iteration 1 Error: 1.046922 Iteration 2 Error: 0.261949 Iteration 3 Error: 0.089822 Iteration 4 Error: 0.041266 Align patch 22 3 left Iteration 1 Error: 1.274842 Iteration 2 Error: 0.309481 Iteration 3 Error: 0.084770 Iteration 4 Error: 0.033713 Align patch 23 2 left Iteration 1 Error: 1.072758 Iteration 2 Error: 0.209868 Iteration 3 Error: 0.085844 Iteration 4 Error: 0.028499 Align patch 24 1 left Iteration 1 Error: 0.767817 Iteration 2 Error: 0.156755 Iteration 3 Error: 0.051265 Iteration 4 Error: 0.031056 Align patch 25 0 left Iteration 1 Error: 0.918247 Iteration 2 Error: 0.164605 Iteration 3 Error: 0.066247 Iteration 4 Error: 0.023471 3D Fitting completed. Patch alignment time: 26.02(sec) Local motion has been corrected. Process thread exits. Computational time: 45.041229 sec Total time: 52.493469 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00004hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00004hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.804209s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00004hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.542177s ........................................ >>>>>>TIME<<<<<< FFT: 1.397459s Defocus_U Defocus_V Angle CCC 26582.02 27535.18 8.47 0.043347 Final Values Defocus_U Defocus_V Angle CCC 26605.48 27558.64 7.23 0.073427 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00004hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00004hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.342e-01 9.989e-02 CC threshold: 0.734 Mean Std: 42.09 6.89 Num Hot pixels: 166 Hot pixel threshold: 83.42 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 5.902883 Iteration 2 Error: 1.860766 Iteration 3 Error: 0.410155 Iteration 4 Error: 0.113827 Iteration 5 Error: 0.037958 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.02 -0.43 ...... Frame ( 3) shift: 0.03 -0.86 ...... Frame ( 4) shift: 0.05 -1.28 ...... Frame ( 5) shift: 0.06 -1.71 ...... Frame ( 6) shift: 0.14 -1.94 ...... Frame ( 7) shift: 0.28 -1.97 ...... Frame ( 8) shift: 0.42 -2.00 ...... Frame ( 9) shift: 0.63 -1.98 ...... Frame ( 10) shift: 0.93 -1.93 ...... Frame ( 11) shift: 1.22 -1.88 ...... Frame ( 12) shift: 1.50 -1.83 ...... Frame ( 13) shift: 1.76 -1.78 ...... Frame ( 14) shift: 2.02 -1.72 ...... Frame ( 15) shift: 2.30 -1.64 ...... Frame ( 16) shift: 2.59 -1.53 ...... Frame ( 17) shift: 2.88 -1.42 ...... Frame ( 18) shift: 3.12 -1.33 ...... Frame ( 19) shift: 3.31 -1.26 ...... Frame ( 20) shift: 3.49 -1.19 ...... Frame ( 21) shift: 3.73 -1.07 ...... Frame ( 22) shift: 4.02 -0.90 ...... Frame ( 23) shift: 4.30 -0.73 ...... Frame ( 24) shift: 4.58 -0.55 ...... Frame ( 25) shift: 4.85 -0.38 ...... Frame ( 26) shift: 5.11 -0.21 ...... Frame ( 27) shift: 5.35 0.01 ...... Frame ( 28) shift: 5.57 0.27 ...... Frame ( 29) shift: 5.79 0.54 ...... Frame ( 30) shift: 6.10 0.79 ...... Frame ( 31) shift: 6.50 1.04 ...... Frame ( 32) shift: 6.90 1.29 ...... Frame ( 33) shift: 7.21 1.50 ...... Frame ( 34) shift: 7.43 1.67 ...... Frame ( 35) shift: 7.65 1.85 ...... Frame ( 36) shift: 7.89 2.02 ...... Frame ( 37) shift: 8.16 2.19 ...... Frame ( 38) shift: 8.42 2.36 ...... Frame ( 39) shift: 8.68 2.53 ...... Frame ( 40) shift: 8.94 2.70 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.070291 Iteration 2 Error: 0.144353 Iteration 3 Error: 0.056524 Iteration 4 Error: 0.017848 Align patch 2 23 left Iteration 1 Error: 0.955180 Iteration 2 Error: 0.121628 Iteration 3 Error: 0.072273 Iteration 4 Error: 0.028499 Align patch 3 22 left Iteration 1 Error: 1.357159 Iteration 2 Error: 0.213158 Iteration 3 Error: 0.105071 Iteration 4 Error: 0.046122 Align patch 4 21 left Iteration 1 Error: 1.111183 Iteration 2 Error: 0.281925 Iteration 3 Error: 0.112812 Iteration 4 Error: 0.046769 Align patch 5 20 left Iteration 1 Error: 1.146402 Iteration 2 Error: 0.273461 Iteration 3 Error: 0.106701 Iteration 4 Error: 0.030153 Align patch 6 19 left Iteration 1 Error: 1.476085 Iteration 2 Error: 0.223531 Iteration 3 Error: 0.051742 Iteration 4 Error: 0.017960 Align patch 7 18 left Iteration 1 Error: 0.853388 Iteration 2 Error: 0.193625 Iteration 3 Error: 0.046012 Align patch 8 17 left Iteration 1 Error: 1.143520 Iteration 2 Error: 0.231573 Iteration 3 Error: 0.091509 Iteration 4 Error: 0.045852 Align patch 9 16 left Iteration 1 Error: 1.687573 Iteration 2 Error: 0.318977 Iteration 3 Error: 0.154103 Iteration 4 Error: 0.058813 Iteration 5 Error: 0.022791 Align patch 10 15 left Iteration 1 Error: 0.903183 Iteration 2 Error: 0.172089 Iteration 3 Error: 0.048263 Align patch 11 14 left Iteration 1 Error: 1.184543 Iteration 2 Error: 0.128343 Iteration 3 Error: 0.040760 Align patch 12 13 left Iteration 1 Error: 1.123521 Iteration 2 Error: 0.220696 Iteration 3 Error: 0.089308 Iteration 4 Error: 0.038568 Align patch 13 12 left Iteration 1 Error: 1.164127 Iteration 2 Error: 0.365039 Iteration 3 Error: 0.086310 Iteration 4 Error: 0.040654 Align patch 14 11 left Iteration 1 Error: 1.090998 Iteration 2 Error: 0.332955 Iteration 3 Error: 0.121236 Iteration 4 Error: 0.047394 Align patch 15 10 left Iteration 1 Error: 0.784338 Iteration 2 Error: 0.127889 Iteration 3 Error: 0.035644 Align patch 16 9 left Iteration 1 Error: 0.616551 Iteration 2 Error: 0.112865 Iteration 3 Error: 0.032044 Align patch 17 8 left Iteration 1 Error: 0.852175 Iteration 2 Error: 0.167104 Iteration 3 Error: 0.049901 Align patch 18 7 left Iteration 1 Error: 1.491135 Iteration 2 Error: 0.333954 Iteration 3 Error: 0.121079 Iteration 4 Error: 0.041741 Align patch 19 6 left Iteration 1 Error: 0.590120 Iteration 2 Error: 0.228566 Iteration 3 Error: 0.061393 Iteration 4 Error: 0.019215 Align patch 20 5 left Iteration 1 Error: 0.957872 Iteration 2 Error: 0.174858 Iteration 3 Error: 0.057002 Iteration 4 Error: 0.016996 Align patch 21 4 left Iteration 1 Error: 0.797665 Iteration 2 Error: 0.305363 Iteration 3 Error: 0.108856 Iteration 4 Error: 0.044894 Align patch 22 3 left Iteration 1 Error: 1.739876 Iteration 2 Error: 0.296056 Iteration 3 Error: 0.089196 Iteration 4 Error: 0.044069 Align patch 23 2 left Iteration 1 Error: 1.159163 Iteration 2 Error: 0.328371 Iteration 3 Error: 0.104214 Iteration 4 Error: 0.047307 Align patch 24 1 left Iteration 1 Error: 1.643642 Iteration 2 Error: 0.404141 Iteration 3 Error: 0.091824 Iteration 4 Error: 0.038825 Align patch 25 0 left Iteration 1 Error: 0.761161 Iteration 2 Error: 0.102850 Iteration 3 Error: 0.031057 3D Fitting completed. Patch alignment time: 17.51(sec) Local motion has been corrected. Process thread exits. Computational time: 33.189224 sec Total time: 40.389175 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00004hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00004hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.755720s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00004hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.202720s ........................................ >>>>>>TIME<<<<<< FFT: 1.087355s Defocus_U Defocus_V Angle CCC 23771.48 23263.67 89.80 0.048839 Final Values Defocus_U Defocus_V Angle CCC 23762.10 23276.18 88.86 0.078600 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00004hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00004hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.991e-02 CC threshold: 0.734 Mean Std: 42.39 6.92 Num Hot pixels: 162 Hot pixel threshold: 83.92 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.872706 Iteration 2 Error: 0.618116 Iteration 3 Error: 0.214392 Iteration 4 Error: 0.099436 Iteration 5 Error: 0.038876 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.05 -0.38 ...... Frame ( 3) shift: 0.10 -0.76 ...... Frame ( 4) shift: 0.15 -1.13 ...... Frame ( 5) shift: 0.19 -1.51 ...... Frame ( 6) shift: 0.33 -1.62 ...... Frame ( 7) shift: 0.56 -1.44 ...... Frame ( 8) shift: 0.79 -1.27 ...... Frame ( 9) shift: 0.97 -1.11 ...... Frame ( 10) shift: 1.12 -0.97 ...... Frame ( 11) shift: 1.27 -0.82 ...... Frame ( 12) shift: 1.45 -0.65 ...... Frame ( 13) shift: 1.65 -0.46 ...... Frame ( 14) shift: 1.86 -0.27 ...... Frame ( 15) shift: 1.99 -0.13 ...... Frame ( 16) shift: 2.05 -0.04 ...... Frame ( 17) shift: 2.10 0.04 ...... Frame ( 18) shift: 2.21 0.13 ...... Frame ( 19) shift: 2.37 0.21 ...... Frame ( 20) shift: 2.53 0.29 ...... Frame ( 21) shift: 2.66 0.36 ...... Frame ( 22) shift: 2.77 0.42 ...... Frame ( 23) shift: 2.88 0.49 ...... Frame ( 24) shift: 3.02 0.64 ...... Frame ( 25) shift: 3.20 0.87 ...... Frame ( 26) shift: 3.39 1.11 ...... Frame ( 27) shift: 3.55 1.27 ...... Frame ( 28) shift: 3.71 1.35 ...... Frame ( 29) shift: 3.86 1.44 ...... Frame ( 30) shift: 4.04 1.58 ...... Frame ( 31) shift: 4.25 1.78 ...... Frame ( 32) shift: 4.46 1.98 ...... Frame ( 33) shift: 4.68 2.15 ...... Frame ( 34) shift: 4.90 2.30 ...... Frame ( 35) shift: 5.12 2.45 ...... Frame ( 36) shift: 5.26 2.53 ...... Frame ( 37) shift: 5.32 2.55 ...... Frame ( 38) shift: 5.38 2.56 ...... Frame ( 39) shift: 5.43 2.58 ...... Frame ( 40) shift: 5.49 2.59 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.096497 Iteration 2 Error: 0.195284 Iteration 3 Error: 0.050844 Iteration 4 Error: 0.017921 Align patch 2 23 left Iteration 1 Error: 1.157372 Iteration 2 Error: 0.227132 Iteration 3 Error: 0.072863 Iteration 4 Error: 0.023152 Align patch 3 22 left Iteration 1 Error: 1.141886 Iteration 2 Error: 0.213203 Iteration 3 Error: 0.089132 Iteration 4 Error: 0.035119 Align patch 4 21 left Iteration 1 Error: 1.120628 Iteration 2 Error: 0.326955 Iteration 3 Error: 0.110239 Iteration 4 Error: 0.031840 Align patch 5 20 left Iteration 1 Error: 1.288728 Iteration 2 Error: 0.199402 Iteration 3 Error: 0.062138 Iteration 4 Error: 0.023470 Align patch 6 19 left Iteration 1 Error: 0.905973 Iteration 2 Error: 0.221671 Iteration 3 Error: 0.098846 Iteration 4 Error: 0.031184 Align patch 7 18 left Iteration 1 Error: 0.913047 Iteration 2 Error: 0.175456 Iteration 3 Error: 0.038402 Align patch 8 17 left Iteration 1 Error: 0.881714 Iteration 2 Error: 0.167821 Iteration 3 Error: 0.070864 Iteration 4 Error: 0.027262 Align patch 9 16 left Iteration 1 Error: 1.327817 Iteration 2 Error: 0.412454 Iteration 3 Error: 0.166403 Iteration 4 Error: 0.061555 Iteration 5 Error: 0.025755 Align patch 10 15 left Iteration 1 Error: 1.179633 Iteration 2 Error: 0.243179 Iteration 3 Error: 0.093090 Iteration 4 Error: 0.035610 Align patch 11 14 left Iteration 1 Error: 1.085008 Iteration 2 Error: 0.225221 Iteration 3 Error: 0.144860 Iteration 4 Error: 0.053786 Iteration 5 Error: 0.031371 Align patch 12 13 left Iteration 1 Error: 1.245321 Iteration 2 Error: 0.253357 Iteration 3 Error: 0.099117 Iteration 4 Error: 0.027541 Align patch 13 12 left Iteration 1 Error: 1.624228 Iteration 2 Error: 0.273258 Iteration 3 Error: 0.059016 Iteration 4 Error: 0.018610 Align patch 14 11 left Iteration 1 Error: 0.669436 Iteration 2 Error: 0.187815 Iteration 3 Error: 0.112827 Iteration 4 Error: 0.022239 Align patch 15 10 left Iteration 1 Error: 0.973928 Iteration 2 Error: 0.140735 Iteration 3 Error: 0.023340 Align patch 16 9 left Iteration 1 Error: 0.781361 Iteration 2 Error: 0.136279 Iteration 3 Error: 0.048332 Align patch 17 8 left Iteration 1 Error: 0.704491 Iteration 2 Error: 0.231431 Iteration 3 Error: 0.068070 Iteration 4 Error: 0.050978 Iteration 5 Error: 0.023066 Align patch 18 7 left Iteration 1 Error: 0.874021 Iteration 2 Error: 0.170885 Iteration 3 Error: 0.103493 Iteration 4 Error: 0.027747 Align patch 19 6 left Iteration 1 Error: 1.028844 Iteration 2 Error: 0.290926 Iteration 3 Error: 0.054406 Iteration 4 Error: 0.013516 Align patch 20 5 left Iteration 1 Error: 0.788929 Iteration 2 Error: 0.183937 Iteration 3 Error: 0.045240 Align patch 21 4 left Iteration 1 Error: 0.767509 Iteration 2 Error: 0.188543 Iteration 3 Error: 0.035229 Align patch 22 3 left Iteration 1 Error: 1.187000 Iteration 2 Error: 0.207142 Iteration 3 Error: 0.081155 Iteration 4 Error: 0.017224 Align patch 23 2 left Iteration 1 Error: 0.973823 Iteration 2 Error: 0.220383 Iteration 3 Error: 0.080213 Iteration 4 Error: 0.054075 Iteration 5 Error: 0.020443 Align patch 24 1 left Iteration 1 Error: 1.428576 Iteration 2 Error: 0.172051 Iteration 3 Error: 0.034812 Align patch 25 0 left Iteration 1 Error: 0.920065 Iteration 2 Error: 0.152172 Iteration 3 Error: 0.044475 3D Fitting completed. Patch alignment time: 19.38(sec) Local motion has been corrected. Process thread exits. Computational time: 36.050285 sec Total time: 44.840637 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00004hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00004hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.567788s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00004hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.790701s ........................................ >>>>>>TIME<<<<<< FFT: 1.005733s Defocus_U Defocus_V Angle CCC 28627.26 27853.48 85.02 0.041554 Final Values Defocus_U Defocus_V Angle CCC 28606.97 27858.20 85.02 0.069927 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00005hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00005hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.985e-02 CC threshold: 0.733 Mean Std: 40.29 6.72 Num Hot pixels: 151 Hot pixel threshold: 80.62 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 3.801157 Iteration 2 Error: 0.888325 Iteration 3 Error: 0.348525 Iteration 4 Error: 0.149877 Iteration 5 Error: 0.063833 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.14 -0.07 ...... Frame ( 3) shift: 0.27 -0.15 ...... Frame ( 4) shift: 0.41 -0.22 ...... Frame ( 5) shift: 0.54 -0.30 ...... Frame ( 6) shift: 0.70 -0.27 ...... Frame ( 7) shift: 0.89 -0.13 ...... Frame ( 8) shift: 1.07 0.01 ...... Frame ( 9) shift: 1.29 0.12 ...... Frame ( 10) shift: 1.52 0.22 ...... Frame ( 11) shift: 1.76 0.31 ...... Frame ( 12) shift: 1.97 0.43 ...... Frame ( 13) shift: 2.16 0.55 ...... Frame ( 14) shift: 2.34 0.67 ...... Frame ( 15) shift: 2.53 0.85 ...... Frame ( 16) shift: 2.72 1.07 ...... Frame ( 17) shift: 2.92 1.28 ...... Frame ( 18) shift: 3.12 1.49 ...... Frame ( 19) shift: 3.32 1.69 ...... Frame ( 20) shift: 3.53 1.89 ...... Frame ( 21) shift: 3.73 2.02 ...... Frame ( 22) shift: 3.93 2.08 ...... Frame ( 23) shift: 4.13 2.14 ...... Frame ( 24) shift: 4.30 2.25 ...... Frame ( 25) shift: 4.46 2.41 ...... Frame ( 26) shift: 4.62 2.57 ...... Frame ( 27) shift: 4.80 2.71 ...... Frame ( 28) shift: 5.00 2.82 ...... Frame ( 29) shift: 5.20 2.94 ...... Frame ( 30) shift: 5.41 3.06 ...... Frame ( 31) shift: 5.64 3.19 ...... Frame ( 32) shift: 5.86 3.32 ...... Frame ( 33) shift: 6.07 3.44 ...... Frame ( 34) shift: 6.25 3.55 ...... Frame ( 35) shift: 6.44 3.66 ...... Frame ( 36) shift: 6.66 3.78 ...... Frame ( 37) shift: 6.92 3.93 ...... Frame ( 38) shift: 7.17 4.08 ...... Frame ( 39) shift: 7.43 4.23 ...... Frame ( 40) shift: 7.68 4.38 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.742281 Iteration 2 Error: 0.254827 Iteration 3 Error: 0.115616 Iteration 4 Error: 0.058802 Iteration 5 Error: 0.023793 Align patch 2 23 left Iteration 1 Error: 1.304835 Iteration 2 Error: 0.176625 Iteration 3 Error: 0.059325 Iteration 4 Error: 0.026765 Align patch 3 22 left Iteration 1 Error: 1.100675 Iteration 2 Error: 0.281873 Iteration 3 Error: 0.073426 Iteration 4 Error: 0.039491 Align patch 4 21 left Iteration 1 Error: 1.094241 Iteration 2 Error: 0.298423 Iteration 3 Error: 0.124231 Iteration 4 Error: 0.052640 Iteration 5 Error: 0.027335 Align patch 5 20 left Iteration 1 Error: 1.053380 Iteration 2 Error: 0.215529 Iteration 3 Error: 0.078114 Iteration 4 Error: 0.028787 Align patch 6 19 left Iteration 1 Error: 1.976739 Iteration 2 Error: 0.334201 Iteration 3 Error: 0.071012 Iteration 4 Error: 0.025724 Align patch 7 18 left Iteration 1 Error: 0.733779 Iteration 2 Error: 0.203707 Iteration 3 Error: 0.091408 Iteration 4 Error: 0.031080 Align patch 8 17 left Iteration 1 Error: 1.069674 Iteration 2 Error: 0.268422 Iteration 3 Error: 0.083005 Iteration 4 Error: 0.033506 Align patch 9 16 left Iteration 1 Error: 1.042981 Iteration 2 Error: 0.300406 Iteration 3 Error: 0.124791 Iteration 4 Error: 0.032214 Align patch 10 15 left Iteration 1 Error: 0.628100 Iteration 2 Error: 0.193366 Iteration 3 Error: 0.037009 Align patch 11 14 left Iteration 1 Error: 1.128742 Iteration 2 Error: 0.326692 Iteration 3 Error: 0.126122 Iteration 4 Error: 0.039119 Align patch 12 13 left Iteration 1 Error: 1.085262 Iteration 2 Error: 0.241715 Iteration 3 Error: 0.053201 Iteration 4 Error: 0.026134 Align patch 13 12 left Iteration 1 Error: 1.099599 Iteration 2 Error: 0.294207 Iteration 3 Error: 0.087512 Iteration 4 Error: 0.043170 Align patch 14 11 left Iteration 1 Error: 0.783646 Iteration 2 Error: 0.189568 Iteration 3 Error: 0.078006 Iteration 4 Error: 0.025167 Align patch 15 10 left Iteration 1 Error: 0.885723 Iteration 2 Error: 0.161087 Iteration 3 Error: 0.070953 Iteration 4 Error: 0.020063 Align patch 16 9 left Iteration 1 Error: 0.880653 Iteration 2 Error: 0.343761 Iteration 3 Error: 0.103639 Iteration 4 Error: 0.046067 Align patch 17 8 left Iteration 1 Error: 0.699922 Iteration 2 Error: 0.212953 Iteration 3 Error: 0.079768 Iteration 4 Error: 0.053304 Iteration 5 Error: 0.018169 Align patch 18 7 left Iteration 1 Error: 1.627745 Iteration 2 Error: 0.443752 Iteration 3 Error: 0.139739 Iteration 4 Error: 0.052312 Iteration 5 Error: 0.023634 Align patch 19 6 left Iteration 1 Error: 1.163756 Iteration 2 Error: 0.220195 Iteration 3 Error: 0.056367 Iteration 4 Error: 0.035414 Align patch 20 5 left Iteration 1 Error: 0.855500 Iteration 2 Error: 0.231016 Iteration 3 Error: 0.124206 Iteration 4 Error: 0.043924 Align patch 21 4 left Iteration 1 Error: 1.116893 Iteration 2 Error: 0.201405 Iteration 3 Error: 0.068505 Iteration 4 Error: 0.032552 Align patch 22 3 left Iteration 1 Error: 0.976422 Iteration 2 Error: 0.259118 Iteration 3 Error: 0.075686 Iteration 4 Error: 0.023327 Align patch 23 2 left Iteration 1 Error: 0.806305 Iteration 2 Error: 0.248287 Iteration 3 Error: 0.089715 Iteration 4 Error: 0.060099 Iteration 5 Error: 0.035940 Align patch 24 1 left Iteration 1 Error: 1.187784 Iteration 2 Error: 0.322822 Iteration 3 Error: 0.126404 Iteration 4 Error: 0.055828 Iteration 5 Error: 0.030927 Align patch 25 0 left Iteration 1 Error: 0.860589 Iteration 2 Error: 0.152394 Iteration 3 Error: 0.051791 Iteration 4 Error: 0.017194 3D Fitting completed. Patch alignment time: 21.38(sec) Local motion has been corrected. Process thread exits. Computational time: 39.752132 sec Total time: 48.531998 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00005hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00005hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.572084s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00005hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 4.985125s ........................................ >>>>>>TIME<<<<<< FFT: 1.695153s Defocus_U Defocus_V Angle CCC 26367.24 27164.11 7.06 0.042270 Final Values Defocus_U Defocus_V Angle CCC 26379.68 27164.20 7.37 0.064681 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00005hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00005hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.992e-02 CC threshold: 0.734 Mean Std: 40.08 6.71 Num Hot pixels: 151 Hot pixel threshold: 80.36 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.919565 Iteration 2 Error: 0.628918 Iteration 3 Error: 0.231537 Iteration 4 Error: 0.087205 Iteration 5 Error: 0.037479 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.18 0.01 ...... Frame ( 3) shift: 0.35 0.01 ...... Frame ( 4) shift: 0.53 0.02 ...... Frame ( 5) shift: 0.70 0.02 ...... Frame ( 6) shift: 0.85 0.10 ...... Frame ( 7) shift: 0.97 0.26 ...... Frame ( 8) shift: 1.09 0.41 ...... Frame ( 9) shift: 1.27 0.57 ...... Frame ( 10) shift: 1.50 0.74 ...... Frame ( 11) shift: 1.73 0.90 ...... Frame ( 12) shift: 1.91 1.06 ...... Frame ( 13) shift: 2.05 1.20 ...... Frame ( 14) shift: 2.19 1.34 ...... Frame ( 15) shift: 2.35 1.47 ...... Frame ( 16) shift: 2.53 1.60 ...... Frame ( 17) shift: 2.70 1.72 ...... Frame ( 18) shift: 2.89 1.90 ...... Frame ( 19) shift: 3.08 2.11 ...... Frame ( 20) shift: 3.28 2.33 ...... Frame ( 21) shift: 3.47 2.49 ...... Frame ( 22) shift: 3.66 2.61 ...... Frame ( 23) shift: 3.85 2.72 ...... Frame ( 24) shift: 4.05 2.84 ...... Frame ( 25) shift: 4.26 2.94 ...... Frame ( 26) shift: 4.46 3.05 ...... Frame ( 27) shift: 4.60 3.13 ...... Frame ( 28) shift: 4.67 3.19 ...... Frame ( 29) shift: 4.74 3.24 ...... Frame ( 30) shift: 4.83 3.32 ...... Frame ( 31) shift: 4.96 3.42 ...... Frame ( 32) shift: 5.08 3.53 ...... Frame ( 33) shift: 5.23 3.60 ...... Frame ( 34) shift: 5.41 3.65 ...... Frame ( 35) shift: 5.59 3.70 ...... Frame ( 36) shift: 5.76 3.80 ...... Frame ( 37) shift: 5.93 3.95 ...... Frame ( 38) shift: 6.11 4.09 ...... Frame ( 39) shift: 6.28 4.24 ...... Frame ( 40) shift: 6.45 4.39 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.921080 Iteration 2 Error: 0.285379 Iteration 3 Error: 0.118755 Iteration 4 Error: 0.049848 Align patch 2 23 left Iteration 1 Error: 1.034617 Iteration 2 Error: 0.199669 Iteration 3 Error: 0.050057 Iteration 4 Error: 0.021215 Align patch 3 22 left Iteration 1 Error: 0.527152 Iteration 2 Error: 0.164893 Iteration 3 Error: 0.072447 Iteration 4 Error: 0.034000 Align patch 4 21 left Iteration 1 Error: 1.111901 Iteration 2 Error: 0.232146 Iteration 3 Error: 0.066835 Iteration 4 Error: 0.021646 Align patch 5 20 left Iteration 1 Error: 0.678441 Iteration 2 Error: 0.121725 Iteration 3 Error: 0.042490 Align patch 6 19 left Iteration 1 Error: 0.688564 Iteration 2 Error: 0.097514 Iteration 3 Error: 0.029388 Align patch 7 18 left Iteration 1 Error: 0.733132 Iteration 2 Error: 0.130145 Iteration 3 Error: 0.035820 Align patch 8 17 left Iteration 1 Error: 1.035737 Iteration 2 Error: 0.185241 Iteration 3 Error: 0.050098 Iteration 4 Error: 0.027742 Align patch 9 16 left Iteration 1 Error: 1.064917 Iteration 2 Error: 0.200768 Iteration 3 Error: 0.079043 Iteration 4 Error: 0.034864 Align patch 10 15 left Iteration 1 Error: 0.743167 Iteration 2 Error: 0.100796 Iteration 3 Error: 0.022195 Align patch 11 14 left Iteration 1 Error: 0.943612 Iteration 2 Error: 0.198449 Iteration 3 Error: 0.075170 Iteration 4 Error: 0.032062 Align patch 12 13 left Iteration 1 Error: 0.909161 Iteration 2 Error: 0.169922 Iteration 3 Error: 0.062098 Iteration 4 Error: 0.014320 Align patch 13 12 left Iteration 1 Error: 0.816813 Iteration 2 Error: 0.217703 Iteration 3 Error: 0.080827 Iteration 4 Error: 0.029527 Align patch 14 11 left Iteration 1 Error: 0.509577 Iteration 2 Error: 0.148491 Iteration 3 Error: 0.049796 Align patch 15 10 left Iteration 1 Error: 0.786122 Iteration 2 Error: 0.157291 Iteration 3 Error: 0.041385 Align patch 16 9 left Iteration 1 Error: 0.855399 Iteration 2 Error: 0.116267 Iteration 3 Error: 0.042401 Align patch 17 8 left Iteration 1 Error: 0.596077 Iteration 2 Error: 0.150188 Iteration 3 Error: 0.056065 Iteration 4 Error: 0.018391 Align patch 18 7 left Iteration 1 Error: 0.954064 Iteration 2 Error: 0.241146 Iteration 3 Error: 0.054876 Iteration 4 Error: 0.030808 Align patch 19 6 left Iteration 1 Error: 0.730686 Iteration 2 Error: 0.246154 Iteration 3 Error: 0.116349 Iteration 4 Error: 0.048510 Align patch 20 5 left Iteration 1 Error: 0.626941 Iteration 2 Error: 0.226959 Iteration 3 Error: 0.067448 Iteration 4 Error: 0.025309 Align patch 21 4 left Iteration 1 Error: 0.508967 Iteration 2 Error: 0.139709 Iteration 3 Error: 0.047299 Align patch 22 3 left Iteration 1 Error: 1.029395 Iteration 2 Error: 0.308663 Iteration 3 Error: 0.094066 Iteration 4 Error: 0.034507 Align patch 23 2 left Iteration 1 Error: 1.212450 Iteration 2 Error: 0.170726 Iteration 3 Error: 0.039370 Align patch 24 1 left Iteration 1 Error: 1.039151 Iteration 2 Error: 0.222710 Iteration 3 Error: 0.100728 Iteration 4 Error: 0.035666 Align patch 25 0 left Iteration 1 Error: 1.269730 Iteration 2 Error: 0.192462 Iteration 3 Error: 0.083347 Iteration 4 Error: 0.023073 3D Fitting completed. Patch alignment time: 20.69(sec) Local motion has been corrected. Process thread exits. Computational time: 39.301174 sec Total time: 49.007114 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00005hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00005hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 3.684908s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00005hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.220771s ........................................ >>>>>>TIME<<<<<< FFT: 1.435678s Defocus_U Defocus_V Angle CCC 25234.40 26121.12 5.99 0.046983 Final Values Defocus_U Defocus_V Angle CCC 25232.84 26116.43 5.67 0.073818 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00005hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00005hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.992e-02 CC threshold: 0.734 Mean Std: 41.23 6.82 Num Hot pixels: 173 Hot pixel threshold: 82.14 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.590055 Iteration 2 Error: 0.510587 Iteration 3 Error: 0.140339 Iteration 4 Error: 0.054848 Iteration 5 Error: 0.018041 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.09 0.01 ...... Frame ( 3) shift: 0.19 0.03 ...... Frame ( 4) shift: 0.28 0.04 ...... Frame ( 5) shift: 0.37 0.06 ...... Frame ( 6) shift: 0.51 0.21 ...... Frame ( 7) shift: 0.69 0.49 ...... Frame ( 8) shift: 0.86 0.77 ...... Frame ( 9) shift: 1.04 0.98 ...... Frame ( 10) shift: 1.21 1.11 ...... Frame ( 11) shift: 1.38 1.24 ...... Frame ( 12) shift: 1.53 1.35 ...... Frame ( 13) shift: 1.66 1.44 ...... Frame ( 14) shift: 1.79 1.53 ...... Frame ( 15) shift: 1.90 1.64 ...... Frame ( 16) shift: 1.99 1.75 ...... Frame ( 17) shift: 2.09 1.86 ...... Frame ( 18) shift: 2.17 1.95 ...... Frame ( 19) shift: 2.23 2.02 ...... Frame ( 20) shift: 2.29 2.08 ...... Frame ( 21) shift: 2.41 2.18 ...... Frame ( 22) shift: 2.58 2.32 ...... Frame ( 23) shift: 2.74 2.45 ...... Frame ( 24) shift: 2.89 2.52 ...... Frame ( 25) shift: 3.03 2.53 ...... Frame ( 26) shift: 3.17 2.55 ...... Frame ( 27) shift: 3.30 2.61 ...... Frame ( 28) shift: 3.43 2.72 ...... Frame ( 29) shift: 3.56 2.83 ...... Frame ( 30) shift: 3.67 2.93 ...... Frame ( 31) shift: 3.75 3.02 ...... Frame ( 32) shift: 3.84 3.11 ...... Frame ( 33) shift: 3.94 3.16 ...... Frame ( 34) shift: 4.06 3.18 ...... Frame ( 35) shift: 4.17 3.20 ...... Frame ( 36) shift: 4.30 3.24 ...... Frame ( 37) shift: 4.44 3.30 ...... Frame ( 38) shift: 4.58 3.35 ...... Frame ( 39) shift: 4.71 3.41 ...... Frame ( 40) shift: 4.85 3.46 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.717255 Iteration 2 Error: 0.101416 Iteration 3 Error: 0.022419 Align patch 2 23 left Iteration 1 Error: 0.678419 Iteration 2 Error: 0.192507 Iteration 3 Error: 0.065989 Iteration 4 Error: 0.020502 Align patch 3 22 left Iteration 1 Error: 1.003489 Iteration 2 Error: 0.157596 Iteration 3 Error: 0.033703 Align patch 4 21 left Iteration 1 Error: 0.650865 Iteration 2 Error: 0.140299 Iteration 3 Error: 0.050248 Iteration 4 Error: 0.015548 Align patch 5 20 left Iteration 1 Error: 1.003211 Iteration 2 Error: 0.154189 Iteration 3 Error: 0.054118 Iteration 4 Error: 0.022452 Align patch 6 19 left Iteration 1 Error: 1.225635 Iteration 2 Error: 0.284909 Iteration 3 Error: 0.060591 Iteration 4 Error: 0.025818 Align patch 7 18 left Iteration 1 Error: 0.812255 Iteration 2 Error: 0.199489 Iteration 3 Error: 0.065283 Iteration 4 Error: 0.039634 Align patch 8 17 left Iteration 1 Error: 1.010019 Iteration 2 Error: 0.147093 Iteration 3 Error: 0.041323 Align patch 9 16 left Iteration 1 Error: 0.978538 Iteration 2 Error: 0.215268 Iteration 3 Error: 0.061873 Iteration 4 Error: 0.024755 Align patch 10 15 left Iteration 1 Error: 1.377032 Iteration 2 Error: 0.265572 Iteration 3 Error: 0.079793 Iteration 4 Error: 0.024844 Align patch 11 14 left Iteration 1 Error: 0.577235 Iteration 2 Error: 0.133321 Iteration 3 Error: 0.033380 Align patch 12 13 left Iteration 1 Error: 0.565492 Iteration 2 Error: 0.095782 Iteration 3 Error: 0.025313 Align patch 13 12 left Iteration 1 Error: 0.698271 Iteration 2 Error: 0.195973 Iteration 3 Error: 0.052115 Iteration 4 Error: 0.021222 Align patch 14 11 left Iteration 1 Error: 0.891720 Iteration 2 Error: 0.278110 Iteration 3 Error: 0.109909 Iteration 4 Error: 0.047638 Align patch 15 10 left Iteration 1 Error: 0.970076 Iteration 2 Error: 0.101808 Iteration 3 Error: 0.035547 Align patch 16 9 left Iteration 1 Error: 1.056717 Iteration 2 Error: 0.161130 Iteration 3 Error: 0.049034 Align patch 17 8 left Iteration 1 Error: 0.640195 Iteration 2 Error: 0.164956 Iteration 3 Error: 0.051405 Iteration 4 Error: 0.027094 Align patch 18 7 left Iteration 1 Error: 0.643613 Iteration 2 Error: 0.128765 Iteration 3 Error: 0.042549 Align patch 19 6 left Iteration 1 Error: 0.619867 Iteration 2 Error: 0.205179 Iteration 3 Error: 0.059429 Iteration 4 Error: 0.032753 Align patch 20 5 left Iteration 1 Error: 0.613796 Iteration 2 Error: 0.141430 Iteration 3 Error: 0.026980 Align patch 21 4 left Iteration 1 Error: 0.807787 Iteration 2 Error: 0.145835 Iteration 3 Error: 0.061052 Iteration 4 Error: 0.019697 Align patch 22 3 left Iteration 1 Error: 0.959453 Iteration 2 Error: 0.151648 Iteration 3 Error: 0.038880 Align patch 23 2 left Iteration 1 Error: 0.696174 Iteration 2 Error: 0.144763 Iteration 3 Error: 0.045679 Align patch 24 1 left Iteration 1 Error: 0.991975 Iteration 2 Error: 0.132173 Iteration 3 Error: 0.027213 Align patch 25 0 left Iteration 1 Error: 0.808235 Iteration 2 Error: 0.186518 Iteration 3 Error: 0.055892 Iteration 4 Error: 0.018185 3D Fitting completed. Patch alignment time: 19.46(sec) Local motion has been corrected. Process thread exits. Computational time: 34.218300 sec Total time: 41.921780 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00005hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00005hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.564063s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00005hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.472527s ........................................ >>>>>>TIME<<<<<< FFT: 1.365463s Defocus_U Defocus_V Angle CCC 27546.93 26894.58 86.35 0.043559 Final Values Defocus_U Defocus_V Angle CCC 27546.93 26900.84 86.98 0.069872 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00005hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00005hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.993e-02 CC threshold: 0.734 Mean Std: 40.19 6.74 Num Hot pixels: 157 Hot pixel threshold: 80.61 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.921757 Iteration 2 Error: 0.423860 Iteration 3 Error: 0.127969 Iteration 4 Error: 0.043934 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.18 0.14 ...... Frame ( 3) shift: 0.37 0.28 ...... Frame ( 4) shift: 0.55 0.42 ...... Frame ( 5) shift: 0.73 0.56 ...... Frame ( 6) shift: 0.93 0.70 ...... Frame ( 7) shift: 1.15 0.85 ...... Frame ( 8) shift: 1.36 1.00 ...... Frame ( 9) shift: 1.54 1.15 ...... Frame ( 10) shift: 1.68 1.29 ...... Frame ( 11) shift: 1.82 1.44 ...... Frame ( 12) shift: 1.94 1.55 ...... Frame ( 13) shift: 2.05 1.63 ...... Frame ( 14) shift: 2.16 1.70 ...... Frame ( 15) shift: 2.29 1.80 ...... Frame ( 16) shift: 2.42 1.92 ...... Frame ( 17) shift: 2.56 2.05 ...... Frame ( 18) shift: 2.71 2.17 ...... Frame ( 19) shift: 2.87 2.27 ...... Frame ( 20) shift: 3.04 2.38 ...... Frame ( 21) shift: 3.19 2.46 ...... Frame ( 22) shift: 3.34 2.51 ...... Frame ( 23) shift: 3.48 2.56 ...... Frame ( 24) shift: 3.63 2.66 ...... Frame ( 25) shift: 3.78 2.82 ...... Frame ( 26) shift: 3.94 2.97 ...... Frame ( 27) shift: 4.04 3.05 ...... Frame ( 28) shift: 4.09 3.06 ...... Frame ( 29) shift: 4.15 3.07 ...... Frame ( 30) shift: 4.19 3.10 ...... Frame ( 31) shift: 4.23 3.16 ...... Frame ( 32) shift: 4.26 3.22 ...... Frame ( 33) shift: 4.33 3.26 ...... Frame ( 34) shift: 4.43 3.30 ...... Frame ( 35) shift: 4.53 3.33 ...... Frame ( 36) shift: 4.62 3.39 ...... Frame ( 37) shift: 4.70 3.48 ...... Frame ( 38) shift: 4.78 3.57 ...... Frame ( 39) shift: 4.86 3.66 ...... Frame ( 40) shift: 4.94 3.75 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.964809 Iteration 2 Error: 0.186620 Iteration 3 Error: 0.023165 Align patch 2 23 left Iteration 1 Error: 0.771540 Iteration 2 Error: 0.151970 Iteration 3 Error: 0.033779 Align patch 3 22 left Iteration 1 Error: 1.050726 Iteration 2 Error: 0.150217 Iteration 3 Error: 0.039943 Align patch 4 21 left Iteration 1 Error: 1.318667 Iteration 2 Error: 0.218403 Iteration 3 Error: 0.088734 Iteration 4 Error: 0.045106 Align patch 5 20 left Iteration 1 Error: 0.627312 Iteration 2 Error: 0.093904 Iteration 3 Error: 0.022528 Align patch 6 19 left Iteration 1 Error: 1.574137 Iteration 2 Error: 0.186719 Iteration 3 Error: 0.034058 Align patch 7 18 left Iteration 1 Error: 0.659689 Iteration 2 Error: 0.090898 Iteration 3 Error: 0.025487 Align patch 8 17 left Iteration 1 Error: 1.002285 Iteration 2 Error: 0.162922 Iteration 3 Error: 0.048064 Align patch 9 16 left Iteration 1 Error: 0.751648 Iteration 2 Error: 0.120288 Iteration 3 Error: 0.051319 Iteration 4 Error: 0.017516 Align patch 10 15 left Iteration 1 Error: 0.534506 Iteration 2 Error: 0.116304 Iteration 3 Error: 0.023390 Align patch 11 14 left Iteration 1 Error: 0.813200 Iteration 2 Error: 0.183706 Iteration 3 Error: 0.034122 Align patch 12 13 left Iteration 1 Error: 0.659932 Iteration 2 Error: 0.121218 Iteration 3 Error: 0.031958 Align patch 13 12 left Iteration 1 Error: 0.858081 Iteration 2 Error: 0.192670 Iteration 3 Error: 0.077392 Iteration 4 Error: 0.031059 Align patch 14 11 left Iteration 1 Error: 0.628901 Iteration 2 Error: 0.189433 Iteration 3 Error: 0.048585 Align patch 15 10 left Iteration 1 Error: 0.700051 Iteration 2 Error: 0.098835 Iteration 3 Error: 0.023918 Align patch 16 9 left Iteration 1 Error: 0.687151 Iteration 2 Error: 0.125842 Iteration 3 Error: 0.044396 Align patch 17 8 left Iteration 1 Error: 0.687941 Iteration 2 Error: 0.084562 Iteration 3 Error: 0.018510 Align patch 18 7 left Iteration 1 Error: 0.849096 Iteration 2 Error: 0.162677 Iteration 3 Error: 0.042767 Align patch 19 6 left Iteration 1 Error: 0.688431 Iteration 2 Error: 0.124734 Iteration 3 Error: 0.029273 Align patch 20 5 left Iteration 1 Error: 0.845612 Iteration 2 Error: 0.104153 Iteration 3 Error: 0.029509 Align patch 21 4 left Iteration 1 Error: 1.190076 Iteration 2 Error: 0.108478 Iteration 3 Error: 0.032200 Align patch 22 3 left Iteration 1 Error: 0.967970 Iteration 2 Error: 0.174299 Iteration 3 Error: 0.042890 Align patch 23 2 left Iteration 1 Error: 1.929304 Iteration 2 Error: 0.301799 Iteration 3 Error: 0.097151 Iteration 4 Error: 0.031750 Align patch 24 1 left Iteration 1 Error: 0.874875 Iteration 2 Error: 0.153640 Iteration 3 Error: 0.049539 Align patch 25 0 left Iteration 1 Error: 0.964254 Iteration 2 Error: 0.131954 Iteration 3 Error: 0.047765 3D Fitting completed. Patch alignment time: 19.23(sec) Local motion has been corrected. Process thread exits. Computational time: 36.436893 sec Total time: 44.688107 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00005hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00005hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.543179s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00005hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.048624s ........................................ >>>>>>TIME<<<<<< FFT: 1.075022s Defocus_U Defocus_V Angle CCC 28068.40 27373.09 83.05 0.040359 Final Values Defocus_U Defocus_V Angle CCC 28051.25 27418.49 83.36 0.063380 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00006hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00006hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 40.23 6.82 Num Hot pixels: 161 Hot pixel threshold: 81.13 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 3.458288 Iteration 2 Error: 0.565804 Iteration 3 Error: 0.086477 Iteration 4 Error: 0.022583 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.47 -0.69 ...... Frame ( 3) shift: -0.94 -1.39 ...... Frame ( 4) shift: -1.41 -2.08 ...... Frame ( 5) shift: -1.88 -2.78 ...... Frame ( 6) shift: -2.05 -3.12 ...... Frame ( 7) shift: -1.92 -3.13 ...... Frame ( 8) shift: -1.79 -3.14 ...... Frame ( 9) shift: -1.60 -3.05 ...... Frame ( 10) shift: -1.35 -2.86 ...... Frame ( 11) shift: -1.10 -2.68 ...... Frame ( 12) shift: -0.81 -2.52 ...... Frame ( 13) shift: -0.47 -2.38 ...... Frame ( 14) shift: -0.13 -2.25 ...... Frame ( 15) shift: 0.12 -2.14 ...... Frame ( 16) shift: 0.28 -2.07 ...... Frame ( 17) shift: 0.44 -2.00 ...... Frame ( 18) shift: 0.63 -1.92 ...... Frame ( 19) shift: 0.86 -1.84 ...... Frame ( 20) shift: 1.08 -1.75 ...... Frame ( 21) shift: 1.30 -1.69 ...... Frame ( 22) shift: 1.52 -1.64 ...... Frame ( 23) shift: 1.74 -1.59 ...... Frame ( 24) shift: 1.96 -1.52 ...... Frame ( 25) shift: 2.18 -1.44 ...... Frame ( 26) shift: 2.40 -1.35 ...... Frame ( 27) shift: 2.58 -1.28 ...... Frame ( 28) shift: 2.72 -1.23 ...... Frame ( 29) shift: 2.86 -1.18 ...... Frame ( 30) shift: 3.03 -1.14 ...... Frame ( 31) shift: 3.22 -1.13 ...... Frame ( 32) shift: 3.42 -1.11 ...... Frame ( 33) shift: 3.59 -1.06 ...... Frame ( 34) shift: 3.72 -0.98 ...... Frame ( 35) shift: 3.86 -0.90 ...... Frame ( 36) shift: 4.01 -0.80 ...... Frame ( 37) shift: 4.16 -0.69 ...... Frame ( 38) shift: 4.32 -0.59 ...... Frame ( 39) shift: 4.48 -0.48 ...... Frame ( 40) shift: 4.64 -0.37 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.642311 Iteration 2 Error: 0.203879 Iteration 3 Error: 0.038766 Align patch 2 23 left Iteration 1 Error: 1.586685 Iteration 2 Error: 0.166689 Iteration 3 Error: 0.021306 Align patch 3 22 left Iteration 1 Error: 1.180867 Iteration 2 Error: 0.178854 Iteration 3 Error: 0.025038 Align patch 4 21 left Iteration 1 Error: 1.033540 Iteration 2 Error: 0.121212 Iteration 3 Error: 0.020708 Align patch 5 20 left Iteration 1 Error: 0.953941 Iteration 2 Error: 0.105418 Iteration 3 Error: 0.011400 Align patch 6 19 left Iteration 1 Error: 1.206308 Iteration 2 Error: 0.117018 Iteration 3 Error: 0.015290 Align patch 7 18 left Iteration 1 Error: 0.889519 Iteration 2 Error: 0.113240 Iteration 3 Error: 0.033480 Align patch 8 17 left Iteration 1 Error: 0.746731 Iteration 2 Error: 0.108919 Iteration 3 Error: 0.033904 Align patch 9 16 left Iteration 1 Error: 0.816132 Iteration 2 Error: 0.123364 Iteration 3 Error: 0.027731 Align patch 10 15 left Iteration 1 Error: 0.832158 Iteration 2 Error: 0.058117 Iteration 3 Error: 0.010198 Align patch 11 14 left Iteration 1 Error: 0.691714 Iteration 2 Error: 0.096459 Iteration 3 Error: 0.019783 Align patch 12 13 left Iteration 1 Error: 0.842189 Iteration 2 Error: 0.104496 Iteration 3 Error: 0.023307 Align patch 13 12 left Iteration 1 Error: 0.622319 Iteration 2 Error: 0.082784 Iteration 3 Error: 0.020849 Align patch 14 11 left Iteration 1 Error: 0.762646 Iteration 2 Error: 0.104544 Iteration 3 Error: 0.030591 Align patch 15 10 left Iteration 1 Error: 0.725744 Iteration 2 Error: 0.058502 Iteration 3 Error: 0.012384 Align patch 16 9 left Iteration 1 Error: 0.721310 Iteration 2 Error: 0.084618 Iteration 3 Error: 0.013073 Align patch 17 8 left Iteration 1 Error: 0.680321 Iteration 2 Error: 0.147227 Iteration 3 Error: 0.019607 Align patch 18 7 left Iteration 1 Error: 1.060463 Iteration 2 Error: 0.094722 Iteration 3 Error: 0.024035 Align patch 19 6 left Iteration 1 Error: 0.484006 Iteration 2 Error: 0.060582 Iteration 3 Error: 0.015794 Align patch 20 5 left Iteration 1 Error: 0.682862 Iteration 2 Error: 0.111231 Iteration 3 Error: 0.024187 Align patch 21 4 left Iteration 1 Error: 0.788647 Iteration 2 Error: 0.124257 Iteration 3 Error: 0.029093 Align patch 22 3 left Iteration 1 Error: 0.563407 Iteration 2 Error: 0.056965 Iteration 3 Error: 0.008978 Align patch 23 2 left Iteration 1 Error: 0.548968 Iteration 2 Error: 0.067328 Iteration 3 Error: 0.013706 Align patch 24 1 left Iteration 1 Error: 0.901312 Iteration 2 Error: 0.092655 Iteration 3 Error: 0.021313 Align patch 25 0 left Iteration 1 Error: 0.935509 Iteration 2 Error: 0.108390 Iteration 3 Error: 0.028492 3D Fitting completed. Patch alignment time: 18.32(sec) Local motion has been corrected. Process thread exits. Computational time: 34.117050 sec Total time: 41.770096 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00006hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00006hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.580648s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00006hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 4.328414s ........................................ >>>>>>TIME<<<<<< FFT: 1.615654s Defocus_U Defocus_V Angle CCC 24775.40 25591.80 4.59 0.072283 Final Values Defocus_U Defocus_V Angle CCC 24773.84 25568.37 5.22 0.110967 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00006hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00006hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.342e-01 9.984e-02 CC threshold: 0.733 Mean Std: 42.36 6.91 Num Hot pixels: 172 Hot pixel threshold: 83.84 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.934083 Iteration 2 Error: 0.671660 Iteration 3 Error: 0.247408 Iteration 4 Error: 0.107105 Iteration 5 Error: 0.039389 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.15 -0.50 ...... Frame ( 3) shift: -0.30 -1.00 ...... Frame ( 4) shift: -0.45 -1.49 ...... Frame ( 5) shift: -0.60 -1.99 ...... Frame ( 6) shift: -0.58 -2.20 ...... Frame ( 7) shift: -0.40 -2.11 ...... Frame ( 8) shift: -0.21 -2.03 ...... Frame ( 9) shift: 0.06 -1.91 ...... Frame ( 10) shift: 0.42 -1.77 ...... Frame ( 11) shift: 0.79 -1.63 ...... Frame ( 12) shift: 1.07 -1.46 ...... Frame ( 13) shift: 1.27 -1.25 ...... Frame ( 14) shift: 1.47 -1.04 ...... Frame ( 15) shift: 1.66 -0.86 ...... Frame ( 16) shift: 1.83 -0.70 ...... Frame ( 17) shift: 1.99 -0.55 ...... Frame ( 18) shift: 2.17 -0.41 ...... Frame ( 19) shift: 2.35 -0.29 ...... Frame ( 20) shift: 2.53 -0.16 ...... Frame ( 21) shift: 2.75 -0.04 ...... Frame ( 22) shift: 3.01 0.07 ...... Frame ( 23) shift: 3.28 0.19 ...... Frame ( 24) shift: 3.49 0.31 ...... Frame ( 25) shift: 3.65 0.43 ...... Frame ( 26) shift: 3.80 0.54 ...... Frame ( 27) shift: 3.94 0.60 ...... Frame ( 28) shift: 4.05 0.59 ...... Frame ( 29) shift: 4.16 0.58 ...... Frame ( 30) shift: 4.31 0.63 ...... Frame ( 31) shift: 4.51 0.75 ...... Frame ( 32) shift: 4.70 0.87 ...... Frame ( 33) shift: 4.86 0.98 ...... Frame ( 34) shift: 4.97 1.09 ...... Frame ( 35) shift: 5.08 1.21 ...... Frame ( 36) shift: 5.21 1.29 ...... Frame ( 37) shift: 5.38 1.33 ...... Frame ( 38) shift: 5.55 1.38 ...... Frame ( 39) shift: 5.72 1.42 ...... Frame ( 40) shift: 5.89 1.47 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.979824 Iteration 2 Error: 0.250091 Iteration 3 Error: 0.053387 Iteration 4 Error: 0.014494 Align patch 2 23 left Iteration 1 Error: 1.399296 Iteration 2 Error: 0.311368 Iteration 3 Error: 0.079420 Iteration 4 Error: 0.048939 Align patch 3 22 left Iteration 1 Error: 0.720904 Iteration 2 Error: 0.203682 Iteration 3 Error: 0.038446 Align patch 4 21 left Iteration 1 Error: 1.593657 Iteration 2 Error: 0.323964 Iteration 3 Error: 0.095678 Iteration 4 Error: 0.039488 Align patch 5 20 left Iteration 1 Error: 1.213287 Iteration 2 Error: 0.321754 Iteration 3 Error: 0.166178 Iteration 4 Error: 0.049469 Align patch 6 19 left Iteration 1 Error: 1.220243 Iteration 2 Error: 0.230013 Iteration 3 Error: 0.065748 Iteration 4 Error: 0.023386 Align patch 7 18 left Iteration 1 Error: 1.097578 Iteration 2 Error: 0.255824 Iteration 3 Error: 0.064953 Iteration 4 Error: 0.027019 Align patch 8 17 left Iteration 1 Error: 1.006831 Iteration 2 Error: 0.228820 Iteration 3 Error: 0.099254 Iteration 4 Error: 0.040442 Align patch 9 16 left Iteration 1 Error: 1.212280 Iteration 2 Error: 0.160964 Iteration 3 Error: 0.031930 Align patch 10 15 left Iteration 1 Error: 1.573104 Iteration 2 Error: 0.193216 Iteration 3 Error: 0.069047 Iteration 4 Error: 0.031346 Align patch 11 14 left Iteration 1 Error: 0.800970 Iteration 2 Error: 0.214089 Iteration 3 Error: 0.062356 Iteration 4 Error: 0.028370 Align patch 12 13 left Iteration 1 Error: 0.671749 Iteration 2 Error: 0.153996 Iteration 3 Error: 0.046371 Align patch 13 12 left Iteration 1 Error: 0.873403 Iteration 2 Error: 0.211996 Iteration 3 Error: 0.086633 Iteration 4 Error: 0.026919 Align patch 14 11 left Iteration 1 Error: 0.938244 Iteration 2 Error: 0.163054 Iteration 3 Error: 0.071065 Iteration 4 Error: 0.025599 Align patch 15 10 left Iteration 1 Error: 1.015689 Iteration 2 Error: 0.408661 Iteration 3 Error: 0.128333 Iteration 4 Error: 0.084249 Iteration 5 Error: 0.027033 Align patch 16 9 left Iteration 1 Error: 1.008517 Iteration 2 Error: 0.172578 Iteration 3 Error: 0.076437 Iteration 4 Error: 0.026780 Align patch 17 8 left Iteration 1 Error: 0.826331 Iteration 2 Error: 0.125814 Iteration 3 Error: 0.033221 Align patch 18 7 left Iteration 1 Error: 0.674472 Iteration 2 Error: 0.129350 Iteration 3 Error: 0.048256 Align patch 19 6 left Iteration 1 Error: 1.287577 Iteration 2 Error: 0.216031 Iteration 3 Error: 0.085441 Iteration 4 Error: 0.029726 Align patch 20 5 left Iteration 1 Error: 1.258049 Iteration 2 Error: 0.351134 Iteration 3 Error: 0.117870 Iteration 4 Error: 0.064646 Iteration 5 Error: 0.026336 Align patch 21 4 left Iteration 1 Error: 0.966078 Iteration 2 Error: 0.169007 Iteration 3 Error: 0.046538 Align patch 22 3 left Iteration 1 Error: 1.165531 Iteration 2 Error: 0.231493 Iteration 3 Error: 0.096951 Iteration 4 Error: 0.040660 Align patch 23 2 left Iteration 1 Error: 0.766456 Iteration 2 Error: 0.139228 Iteration 3 Error: 0.041287 Align patch 24 1 left Iteration 1 Error: 1.064652 Iteration 2 Error: 0.194785 Iteration 3 Error: 0.051015 Iteration 4 Error: 0.018964 Align patch 25 0 left Iteration 1 Error: 1.025144 Iteration 2 Error: 0.165165 Iteration 3 Error: 0.044674 3D Fitting completed. Patch alignment time: 16.22(sec) Local motion has been corrected. Process thread exits. Computational time: 31.941841 sec Total time: 39.258377 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00006hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00006hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.842244s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00006hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 4.685522s ........................................ >>>>>>TIME<<<<<< FFT: 1.241866s Defocus_U Defocus_V Angle CCC 26632.81 27511.72 2.66 0.045385 Final Values Defocus_U Defocus_V Angle CCC 26634.37 27507.04 2.97 0.074693 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00006hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00006hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.342e-01 9.987e-02 CC threshold: 0.733 Mean Std: 42.24 6.90 Num Hot pixels: 178 Hot pixel threshold: 83.66 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 3.554981 Iteration 2 Error: 0.909002 Iteration 3 Error: 0.334974 Iteration 4 Error: 0.115344 Iteration 5 Error: 0.048223 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.26 -0.25 ...... Frame ( 3) shift: -0.51 -0.50 ...... Frame ( 4) shift: -0.77 -0.74 ...... Frame ( 5) shift: -1.02 -0.99 ...... Frame ( 6) shift: -1.03 -1.02 ...... Frame ( 7) shift: -0.80 -0.84 ...... Frame ( 8) shift: -0.56 -0.65 ...... Frame ( 9) shift: -0.30 -0.44 ...... Frame ( 10) shift: 0.00 -0.21 ...... Frame ( 11) shift: 0.30 0.02 ...... Frame ( 12) shift: 0.61 0.22 ...... Frame ( 13) shift: 0.92 0.41 ...... Frame ( 14) shift: 1.24 0.60 ...... Frame ( 15) shift: 1.58 0.78 ...... Frame ( 16) shift: 1.95 0.94 ...... Frame ( 17) shift: 2.33 1.10 ...... Frame ( 18) shift: 2.60 1.29 ...... Frame ( 19) shift: 2.76 1.52 ...... Frame ( 20) shift: 2.92 1.75 ...... Frame ( 21) shift: 3.07 1.95 ...... Frame ( 22) shift: 3.19 2.12 ...... Frame ( 23) shift: 3.31 2.29 ...... Frame ( 24) shift: 3.49 2.43 ...... Frame ( 25) shift: 3.74 2.53 ...... Frame ( 26) shift: 3.98 2.64 ...... Frame ( 27) shift: 4.18 2.74 ...... Frame ( 28) shift: 4.32 2.85 ...... Frame ( 29) shift: 4.46 2.96 ...... Frame ( 30) shift: 4.60 3.09 ...... Frame ( 31) shift: 4.74 3.22 ...... Frame ( 32) shift: 4.87 3.36 ...... Frame ( 33) shift: 5.01 3.48 ...... Frame ( 34) shift: 5.13 3.57 ...... Frame ( 35) shift: 5.26 3.67 ...... Frame ( 36) shift: 5.47 3.72 ...... Frame ( 37) shift: 5.77 3.74 ...... Frame ( 38) shift: 6.07 3.76 ...... Frame ( 39) shift: 6.36 3.78 ...... Frame ( 40) shift: 6.66 3.80 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.298929 Iteration 2 Error: 0.198212 Iteration 3 Error: 0.044567 Align patch 2 23 left Iteration 1 Error: 1.084327 Iteration 2 Error: 0.351097 Iteration 3 Error: 0.062969 Iteration 4 Error: 0.033145 Align patch 3 22 left Iteration 1 Error: 1.061422 Iteration 2 Error: 0.328197 Iteration 3 Error: 0.119261 Iteration 4 Error: 0.049605 Align patch 4 21 left Iteration 1 Error: 0.514422 Iteration 2 Error: 0.118921 Iteration 3 Error: 0.044861 Align patch 5 20 left Iteration 1 Error: 0.657541 Iteration 2 Error: 0.189297 Iteration 3 Error: 0.097579 Iteration 4 Error: 0.046985 Align patch 6 19 left Iteration 1 Error: 1.420589 Iteration 2 Error: 0.198968 Iteration 3 Error: 0.047501 Align patch 7 18 left Iteration 1 Error: 1.291211 Iteration 2 Error: 0.185123 Iteration 3 Error: 0.037920 Align patch 8 17 left Iteration 1 Error: 1.056487 Iteration 2 Error: 0.204879 Iteration 3 Error: 0.059114 Iteration 4 Error: 0.024780 Align patch 9 16 left Iteration 1 Error: 0.781889 Iteration 2 Error: 0.194157 Iteration 3 Error: 0.045651 Align patch 10 15 left Iteration 1 Error: 0.810266 Iteration 2 Error: 0.240046 Iteration 3 Error: 0.075567 Iteration 4 Error: 0.022581 Align patch 11 14 left Iteration 1 Error: 1.270066 Iteration 2 Error: 0.234216 Iteration 3 Error: 0.068456 Iteration 4 Error: 0.026254 Align patch 12 13 left Iteration 1 Error: 0.942527 Iteration 2 Error: 0.251718 Iteration 3 Error: 0.080091 Iteration 4 Error: 0.033338 Align patch 13 12 left Iteration 1 Error: 1.165659 Iteration 2 Error: 0.233921 Iteration 3 Error: 0.063419 Iteration 4 Error: 0.019481 Align patch 14 11 left Iteration 1 Error: 1.477624 Iteration 2 Error: 0.324475 Iteration 3 Error: 0.084889 Iteration 4 Error: 0.048904 Align patch 15 10 left Iteration 1 Error: 1.018227 Iteration 2 Error: 0.244176 Iteration 3 Error: 0.094366 Iteration 4 Error: 0.034827 Align patch 16 9 left Iteration 1 Error: 0.936596 Iteration 2 Error: 0.177795 Iteration 3 Error: 0.067108 Iteration 4 Error: 0.025821 Align patch 17 8 left Iteration 1 Error: 0.938330 Iteration 2 Error: 0.206775 Iteration 3 Error: 0.054461 Iteration 4 Error: 0.012951 Align patch 18 7 left Iteration 1 Error: 0.591119 Iteration 2 Error: 0.162113 Iteration 3 Error: 0.062857 Iteration 4 Error: 0.023809 Align patch 19 6 left Iteration 1 Error: 1.031526 Iteration 2 Error: 0.300385 Iteration 3 Error: 0.085618 Iteration 4 Error: 0.030073 Align patch 20 5 left Iteration 1 Error: 1.728230 Iteration 2 Error: 0.192014 Iteration 3 Error: 0.069008 Iteration 4 Error: 0.032522 Align patch 21 4 left Iteration 1 Error: 0.949468 Iteration 2 Error: 0.185546 Iteration 3 Error: 0.054258 Iteration 4 Error: 0.023321 Align patch 22 3 left Iteration 1 Error: 1.138684 Iteration 2 Error: 0.328010 Iteration 3 Error: 0.065220 Iteration 4 Error: 0.037512 Align patch 23 2 left Iteration 1 Error: 1.328596 Iteration 2 Error: 0.411056 Iteration 3 Error: 0.151440 Iteration 4 Error: 0.048377 Align patch 24 1 left Iteration 1 Error: 0.838581 Iteration 2 Error: 0.258497 Iteration 3 Error: 0.087389 Iteration 4 Error: 0.031261 Align patch 25 0 left Iteration 1 Error: 2.175259 Iteration 2 Error: 0.185062 Iteration 3 Error: 0.042753 3D Fitting completed. Patch alignment time: 13.56(sec) Local motion has been corrected. Process thread exits. Computational time: 23.489847 sec Total time: 29.685995 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00006hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00006hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.745062s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00006hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.694492s ........................................ >>>>>>TIME<<<<<< FFT: 1.181230s Defocus_U Defocus_V Angle CCC 24224.61 23544.92 89.20 0.045882 Final Values Defocus_U Defocus_V Angle CCC 24226.17 23555.87 89.20 0.077764 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00006hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00006hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.342e-01 9.988e-02 CC threshold: 0.734 Mean Std: 42.47 6.92 Num Hot pixels: 180 Hot pixel threshold: 83.98 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.998686 Iteration 2 Error: 0.641721 Iteration 3 Error: 0.212245 Iteration 4 Error: 0.086555 Iteration 5 Error: 0.032636 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.41 -0.45 ...... Frame ( 3) shift: -0.81 -0.90 ...... Frame ( 4) shift: -1.22 -1.35 ...... Frame ( 5) shift: -1.62 -1.80 ...... Frame ( 6) shift: -1.70 -1.98 ...... Frame ( 7) shift: -1.45 -1.88 ...... Frame ( 8) shift: -1.20 -1.78 ...... Frame ( 9) shift: -0.92 -1.61 ...... Frame ( 10) shift: -0.61 -1.36 ...... Frame ( 11) shift: -0.30 -1.12 ...... Frame ( 12) shift: -0.05 -0.94 ...... Frame ( 13) shift: 0.14 -0.81 ...... Frame ( 14) shift: 0.33 -0.69 ...... Frame ( 15) shift: 0.54 -0.54 ...... Frame ( 16) shift: 0.77 -0.35 ...... Frame ( 17) shift: 1.00 -0.17 ...... Frame ( 18) shift: 1.17 0.00 ...... Frame ( 19) shift: 1.30 0.17 ...... Frame ( 20) shift: 1.43 0.33 ...... Frame ( 21) shift: 1.59 0.47 ...... Frame ( 22) shift: 1.79 0.58 ...... Frame ( 23) shift: 1.99 0.69 ...... Frame ( 24) shift: 2.15 0.75 ...... Frame ( 25) shift: 2.26 0.77 ...... Frame ( 26) shift: 2.37 0.79 ...... Frame ( 27) shift: 2.48 0.86 ...... Frame ( 28) shift: 2.61 0.98 ...... Frame ( 29) shift: 2.73 1.11 ...... Frame ( 30) shift: 2.83 1.21 ...... Frame ( 31) shift: 2.90 1.28 ...... Frame ( 32) shift: 2.98 1.35 ...... Frame ( 33) shift: 3.10 1.42 ...... Frame ( 34) shift: 3.26 1.50 ...... Frame ( 35) shift: 3.43 1.57 ...... Frame ( 36) shift: 3.51 1.61 ...... Frame ( 37) shift: 3.52 1.62 ...... Frame ( 38) shift: 3.53 1.62 ...... Frame ( 39) shift: 3.54 1.62 ...... Frame ( 40) shift: 3.55 1.63 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.069824 Iteration 2 Error: 0.217451 Iteration 3 Error: 0.049460 Align patch 2 23 left Iteration 1 Error: 1.376500 Iteration 2 Error: 0.308006 Iteration 3 Error: 0.116346 Iteration 4 Error: 0.035270 Align patch 3 22 left Iteration 1 Error: 1.585437 Iteration 2 Error: 0.288268 Iteration 3 Error: 0.111651 Iteration 4 Error: 0.048169 Align patch 4 21 left Iteration 1 Error: 1.729057 Iteration 2 Error: 0.293514 Iteration 3 Error: 0.061116 Iteration 4 Error: 0.037932 Align patch 5 20 left Iteration 1 Error: 0.663066 Iteration 2 Error: 0.174733 Iteration 3 Error: 0.052083 Iteration 4 Error: 0.020798 Align patch 6 19 left Iteration 1 Error: 1.188545 Iteration 2 Error: 0.241712 Iteration 3 Error: 0.122013 Iteration 4 Error: 0.056464 Iteration 5 Error: 0.034066 Align patch 7 18 left Iteration 1 Error: 0.896827 Iteration 2 Error: 0.291795 Iteration 3 Error: 0.087751 Iteration 4 Error: 0.059481 Iteration 5 Error: 0.017712 Align patch 8 17 left Iteration 1 Error: 0.801020 Iteration 2 Error: 0.182100 Iteration 3 Error: 0.056346 Iteration 4 Error: 0.020119 Align patch 9 16 left Iteration 1 Error: 1.962497 Iteration 2 Error: 0.227861 Iteration 3 Error: 0.053430 Iteration 4 Error: 0.026103 Align patch 10 15 left Iteration 1 Error: 1.298655 Iteration 2 Error: 0.180919 Iteration 3 Error: 0.036924 Align patch 11 14 left Iteration 1 Error: 0.967538 Iteration 2 Error: 0.172619 Iteration 3 Error: 0.048829 Align patch 12 13 left Iteration 1 Error: 1.093893 Iteration 2 Error: 0.188826 Iteration 3 Error: 0.060398 Iteration 4 Error: 0.019501 Align patch 13 12 left Iteration 1 Error: 0.964728 Iteration 2 Error: 0.212605 Iteration 3 Error: 0.059932 Iteration 4 Error: 0.026851 Align patch 14 11 left Iteration 1 Error: 0.719694 Iteration 2 Error: 0.282811 Iteration 3 Error: 0.073553 Iteration 4 Error: 0.031275 Align patch 15 10 left Iteration 1 Error: 0.881841 Iteration 2 Error: 0.227212 Iteration 3 Error: 0.105877 Iteration 4 Error: 0.048986 Align patch 16 9 left Iteration 1 Error: 1.599437 Iteration 2 Error: 0.219334 Iteration 3 Error: 0.066116 Iteration 4 Error: 0.015871 Align patch 17 8 left Iteration 1 Error: 1.171311 Iteration 2 Error: 0.339339 Iteration 3 Error: 0.115618 Iteration 4 Error: 0.045486 Align patch 18 7 left Iteration 1 Error: 0.668735 Iteration 2 Error: 0.105363 Iteration 3 Error: 0.041095 Align patch 19 6 left Iteration 1 Error: 0.879232 Iteration 2 Error: 0.200767 Iteration 3 Error: 0.073973 Iteration 4 Error: 0.041965 Align patch 20 5 left Iteration 1 Error: 1.059545 Iteration 2 Error: 0.139905 Iteration 3 Error: 0.048022 Align patch 21 4 left Iteration 1 Error: 1.017103 Iteration 2 Error: 0.196911 Iteration 3 Error: 0.064514 Iteration 4 Error: 0.023447 Align patch 22 3 left Iteration 1 Error: 0.920160 Iteration 2 Error: 0.241742 Iteration 3 Error: 0.076441 Iteration 4 Error: 0.025248 Align patch 23 2 left Iteration 1 Error: 0.937827 Iteration 2 Error: 0.152756 Iteration 3 Error: 0.043349 Align patch 24 1 left Iteration 1 Error: 1.134269 Iteration 2 Error: 0.456526 Iteration 3 Error: 0.207322 Iteration 4 Error: 0.124184 Iteration 5 Error: 0.058483 Align patch 24 1 left Iteration 1 Error: 0.775995 Iteration 2 Error: 0.063124 Iteration 3 Error: 0.015369 Align patch 25 0 left Iteration 1 Error: 1.497573 Iteration 2 Error: 0.273018 Iteration 3 Error: 0.052307 Iteration 4 Error: 0.021501 3D Fitting completed. Patch alignment time: 13.73(sec) Local motion has been corrected. Process thread exits. Computational time: 23.889500 sec Total time: 29.586876 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00006hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00006hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.631475s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00006hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.379279s ........................................ >>>>>>TIME<<<<<< FFT: 0.960736s Defocus_U Defocus_V Angle CCC 27041.05 26248.04 88.14 0.045681 Final Values Defocus_U Defocus_V Angle CCC 27047.31 26254.29 88.77 0.073148 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00007hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00007hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.342e-01 9.983e-02 CC threshold: 0.733 Mean Std: 41.70 6.86 Num Hot pixels: 184 Hot pixel threshold: 82.84 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.382921 Iteration 2 Error: 0.498944 Iteration 3 Error: 0.198336 Iteration 4 Error: 0.071364 Iteration 5 Error: 0.031939 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.13 -0.10 ...... Frame ( 3) shift: 0.26 -0.20 ...... Frame ( 4) shift: 0.39 -0.30 ...... Frame ( 5) shift: 0.52 -0.40 ...... Frame ( 6) shift: 0.62 -0.36 ...... Frame ( 7) shift: 0.68 -0.17 ...... Frame ( 8) shift: 0.75 0.02 ...... Frame ( 9) shift: 0.86 0.21 ...... Frame ( 10) shift: 1.03 0.39 ...... Frame ( 11) shift: 1.19 0.58 ...... Frame ( 12) shift: 1.32 0.77 ...... Frame ( 13) shift: 1.41 0.97 ...... Frame ( 14) shift: 1.50 1.17 ...... Frame ( 15) shift: 1.62 1.37 ...... Frame ( 16) shift: 1.77 1.57 ...... Frame ( 17) shift: 1.92 1.77 ...... Frame ( 18) shift: 2.04 1.93 ...... Frame ( 19) shift: 2.15 2.05 ...... Frame ( 20) shift: 2.25 2.17 ...... Frame ( 21) shift: 2.37 2.32 ...... Frame ( 22) shift: 2.50 2.48 ...... Frame ( 23) shift: 2.64 2.65 ...... Frame ( 24) shift: 2.82 2.77 ...... Frame ( 25) shift: 3.06 2.86 ...... Frame ( 26) shift: 3.29 2.95 ...... Frame ( 27) shift: 3.49 3.06 ...... Frame ( 28) shift: 3.65 3.21 ...... Frame ( 29) shift: 3.82 3.36 ...... Frame ( 30) shift: 3.91 3.44 ...... Frame ( 31) shift: 3.95 3.46 ...... Frame ( 32) shift: 3.99 3.48 ...... Frame ( 33) shift: 4.01 3.53 ...... Frame ( 34) shift: 4.01 3.61 ...... Frame ( 35) shift: 4.02 3.69 ...... Frame ( 36) shift: 4.08 3.77 ...... Frame ( 37) shift: 4.20 3.83 ...... Frame ( 38) shift: 4.31 3.89 ...... Frame ( 39) shift: 4.43 3.96 ...... Frame ( 40) shift: 4.55 4.02 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.206982 Iteration 2 Error: 0.187208 Iteration 3 Error: 0.065587 Iteration 4 Error: 0.026573 Align patch 2 23 left Iteration 1 Error: 1.128062 Iteration 2 Error: 0.221820 Iteration 3 Error: 0.060278 Iteration 4 Error: 0.025843 Align patch 3 22 left Iteration 1 Error: 1.111791 Iteration 2 Error: 0.225849 Iteration 3 Error: 0.067301 Iteration 4 Error: 0.025000 Align patch 4 21 left Iteration 1 Error: 0.693532 Iteration 2 Error: 0.136628 Iteration 3 Error: 0.040673 Align patch 5 20 left Iteration 1 Error: 0.919170 Iteration 2 Error: 0.181128 Iteration 3 Error: 0.047711 Align patch 6 19 left Iteration 1 Error: 0.868353 Iteration 2 Error: 0.181587 Iteration 3 Error: 0.062871 Iteration 4 Error: 0.024086 Align patch 7 18 left Iteration 1 Error: 0.631874 Iteration 2 Error: 0.156193 Iteration 3 Error: 0.042376 Align patch 8 17 left Iteration 1 Error: 1.210806 Iteration 2 Error: 0.206842 Iteration 3 Error: 0.063376 Iteration 4 Error: 0.025261 Align patch 9 16 left Iteration 1 Error: 0.753781 Iteration 2 Error: 0.166535 Iteration 3 Error: 0.091934 Iteration 4 Error: 0.024398 Align patch 10 15 left Iteration 1 Error: 0.617228 Iteration 2 Error: 0.153183 Iteration 3 Error: 0.042316 Align patch 11 14 left Iteration 1 Error: 0.850826 Iteration 2 Error: 0.205709 Iteration 3 Error: 0.055651 Iteration 4 Error: 0.021249 Align patch 12 13 left Iteration 1 Error: 1.574677 Iteration 2 Error: 0.244681 Iteration 3 Error: 0.050037 Iteration 4 Error: 0.018278 Align patch 13 12 left Iteration 1 Error: 0.912759 Iteration 2 Error: 0.169198 Iteration 3 Error: 0.045355 Align patch 14 11 left Iteration 1 Error: 0.705373 Iteration 2 Error: 0.192065 Iteration 3 Error: 0.058236 Iteration 4 Error: 0.019318 Align patch 15 10 left Iteration 1 Error: 0.868625 Iteration 2 Error: 0.158952 Iteration 3 Error: 0.043909 Align patch 16 9 left Iteration 1 Error: 1.063022 Iteration 2 Error: 0.218671 Iteration 3 Error: 0.077513 Iteration 4 Error: 0.024753 Align patch 17 8 left Iteration 1 Error: 1.007868 Iteration 2 Error: 0.311205 Iteration 3 Error: 0.067325 Iteration 4 Error: 0.042451 Align patch 18 7 left Iteration 1 Error: 0.726142 Iteration 2 Error: 0.220505 Iteration 3 Error: 0.070410 Iteration 4 Error: 0.025081 Align patch 19 6 left Iteration 1 Error: 1.023668 Iteration 2 Error: 0.152813 Iteration 3 Error: 0.054615 Iteration 4 Error: 0.024582 Align patch 20 5 left Iteration 1 Error: 0.717419 Iteration 2 Error: 0.298038 Iteration 3 Error: 0.071342 Iteration 4 Error: 0.034148 Align patch 21 4 left Iteration 1 Error: 0.596170 Iteration 2 Error: 0.146208 Iteration 3 Error: 0.034093 Align patch 22 3 left Iteration 1 Error: 0.896148 Iteration 2 Error: 0.257678 Iteration 3 Error: 0.112571 Iteration 4 Error: 0.045761 Align patch 23 2 left Iteration 1 Error: 0.644028 Iteration 2 Error: 0.166668 Iteration 3 Error: 0.063059 Iteration 4 Error: 0.033716 Align patch 24 1 left Iteration 1 Error: 0.914128 Iteration 2 Error: 0.168244 Iteration 3 Error: 0.056079 Iteration 4 Error: 0.024608 Align patch 25 0 left Iteration 1 Error: 1.003125 Iteration 2 Error: 0.216408 Iteration 3 Error: 0.048783 3D Fitting completed. Patch alignment time: 13.36(sec) Local motion has been corrected. Process thread exits. Computational time: 23.524834 sec Total time: 28.520876 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00007hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00007hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.684155s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00007hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.989891s ........................................ >>>>>>TIME<<<<<< FFT: 1.245970s Defocus_U Defocus_V Angle CCC 25285.17 26128.92 4.10 0.044510 Final Values Defocus_U Defocus_V Angle CCC 25311.74 26121.12 4.10 0.072864 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00007hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00007hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.991e-02 CC threshold: 0.734 Mean Std: 41.67 6.88 Num Hot pixels: 190 Hot pixel threshold: 82.92 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.450391 Iteration 2 Error: 0.406724 Iteration 3 Error: 0.144925 Iteration 4 Error: 0.051516 Iteration 5 Error: 0.018920 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.18 0.13 ...... Frame ( 3) shift: 0.37 0.26 ...... Frame ( 4) shift: 0.55 0.39 ...... Frame ( 5) shift: 0.74 0.52 ...... Frame ( 6) shift: 0.86 0.61 ...... Frame ( 7) shift: 0.92 0.66 ...... Frame ( 8) shift: 0.98 0.71 ...... Frame ( 9) shift: 1.10 0.81 ...... Frame ( 10) shift: 1.29 0.98 ...... Frame ( 11) shift: 1.48 1.14 ...... Frame ( 12) shift: 1.63 1.30 ...... Frame ( 13) shift: 1.76 1.46 ...... Frame ( 14) shift: 1.88 1.62 ...... Frame ( 15) shift: 2.01 1.69 ...... Frame ( 16) shift: 2.15 1.68 ...... Frame ( 17) shift: 2.28 1.68 ...... Frame ( 18) shift: 2.43 1.75 ...... Frame ( 19) shift: 2.60 1.90 ...... Frame ( 20) shift: 2.76 2.05 ...... Frame ( 21) shift: 2.88 2.17 ...... Frame ( 22) shift: 2.95 2.28 ...... Frame ( 23) shift: 3.02 2.38 ...... Frame ( 24) shift: 3.11 2.43 ...... Frame ( 25) shift: 3.24 2.44 ...... Frame ( 26) shift: 3.36 2.45 ...... Frame ( 27) shift: 3.45 2.46 ...... Frame ( 28) shift: 3.51 2.50 ...... Frame ( 29) shift: 3.57 2.53 ...... Frame ( 30) shift: 3.61 2.59 ...... Frame ( 31) shift: 3.65 2.69 ...... Frame ( 32) shift: 3.69 2.78 ...... Frame ( 33) shift: 3.80 2.83 ...... Frame ( 34) shift: 3.97 2.85 ...... Frame ( 35) shift: 4.15 2.87 ...... Frame ( 36) shift: 4.28 2.94 ...... Frame ( 37) shift: 4.38 3.04 ...... Frame ( 38) shift: 4.49 3.15 ...... Frame ( 39) shift: 4.59 3.25 ...... Frame ( 40) shift: 4.69 3.36 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.830297 Iteration 2 Error: 0.232721 Iteration 3 Error: 0.067791 Iteration 4 Error: 0.029327 Align patch 2 23 left Iteration 1 Error: 1.418762 Iteration 2 Error: 0.153248 Iteration 3 Error: 0.037368 Align patch 3 22 left Iteration 1 Error: 0.761758 Iteration 2 Error: 0.116321 Iteration 3 Error: 0.040849 Align patch 4 21 left Iteration 1 Error: 0.756800 Iteration 2 Error: 0.166348 Iteration 3 Error: 0.059882 Iteration 4 Error: 0.028386 Align patch 5 20 left Iteration 1 Error: 0.670037 Iteration 2 Error: 0.120661 Iteration 3 Error: 0.041100 Align patch 6 19 left Iteration 1 Error: 0.788572 Iteration 2 Error: 0.119634 Iteration 3 Error: 0.026400 Align patch 7 18 left Iteration 1 Error: 0.816308 Iteration 2 Error: 0.172083 Iteration 3 Error: 0.079666 Iteration 4 Error: 0.035490 Align patch 8 17 left Iteration 1 Error: 0.850529 Iteration 2 Error: 0.175349 Iteration 3 Error: 0.047398 Align patch 9 16 left Iteration 1 Error: 0.974209 Iteration 2 Error: 0.254395 Iteration 3 Error: 0.107076 Iteration 4 Error: 0.043801 Align patch 10 15 left Iteration 1 Error: 1.301493 Iteration 2 Error: 0.175044 Iteration 3 Error: 0.043177 Align patch 11 14 left Iteration 1 Error: 1.016687 Iteration 2 Error: 0.153098 Iteration 3 Error: 0.053784 Iteration 4 Error: 0.024910 Align patch 12 13 left Iteration 1 Error: 1.008472 Iteration 2 Error: 0.238829 Iteration 3 Error: 0.055806 Iteration 4 Error: 0.027144 Align patch 13 12 left Iteration 1 Error: 0.733414 Iteration 2 Error: 0.157950 Iteration 3 Error: 0.060608 Iteration 4 Error: 0.026267 Align patch 14 11 left Iteration 1 Error: 0.641382 Iteration 2 Error: 0.155292 Iteration 3 Error: 0.069380 Iteration 4 Error: 0.052511 Iteration 5 Error: 0.032531 Align patch 15 10 left Iteration 1 Error: 0.894071 Iteration 2 Error: 0.175115 Iteration 3 Error: 0.050943 Iteration 4 Error: 0.018564 Align patch 16 9 left Iteration 1 Error: 1.047777 Iteration 2 Error: 0.146216 Iteration 3 Error: 0.057640 Iteration 4 Error: 0.024181 Align patch 17 8 left Iteration 1 Error: 1.328114 Iteration 2 Error: 0.188602 Iteration 3 Error: 0.086843 Iteration 4 Error: 0.022026 Align patch 18 7 left Iteration 1 Error: 0.847686 Iteration 2 Error: 0.172258 Iteration 3 Error: 0.056533 Iteration 4 Error: 0.027021 Align patch 19 6 left Iteration 1 Error: 0.724709 Iteration 2 Error: 0.185036 Iteration 3 Error: 0.049990 Align patch 20 5 left Iteration 1 Error: 1.026717 Iteration 2 Error: 0.260338 Iteration 3 Error: 0.097801 Iteration 4 Error: 0.036779 Align patch 21 4 left Iteration 1 Error: 0.865886 Iteration 2 Error: 0.225671 Iteration 3 Error: 0.068340 Iteration 4 Error: 0.024494 Align patch 22 3 left Iteration 1 Error: 1.102335 Iteration 2 Error: 0.312035 Iteration 3 Error: 0.091056 Iteration 4 Error: 0.030184 Align patch 23 2 left Iteration 1 Error: 0.869610 Iteration 2 Error: 0.333262 Iteration 3 Error: 0.141929 Iteration 4 Error: 0.066708 Iteration 5 Error: 0.046808 Align patch 24 1 left Iteration 1 Error: 1.404805 Iteration 2 Error: 0.187328 Iteration 3 Error: 0.035713 Align patch 25 0 left Iteration 1 Error: 1.200851 Iteration 2 Error: 0.164615 Iteration 3 Error: 0.038897 3D Fitting completed. Patch alignment time: 14.17(sec) Local motion has been corrected. Process thread exits. Computational time: 23.610136 sec Total time: 29.136480 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00007hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00007hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.780968s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00007hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.552077s ........................................ >>>>>>TIME<<<<<< FFT: 0.913445s Defocus_U Defocus_V Angle CCC 24185.57 25068.39 6.71 0.045568 Final Values Defocus_U Defocus_V Angle CCC 24190.28 25060.59 6.71 0.073553 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00007hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00007hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.995e-02 CC threshold: 0.734 Mean Std: 42.24 6.92 Num Hot pixels: 190 Hot pixel threshold: 83.73 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.624286 Iteration 2 Error: 0.288724 Iteration 3 Error: 0.082621 Iteration 4 Error: 0.032334 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.09 -0.09 ...... Frame ( 3) shift: 0.18 -0.18 ...... Frame ( 4) shift: 0.26 -0.27 ...... Frame ( 5) shift: 0.35 -0.36 ...... Frame ( 6) shift: 0.42 -0.34 ...... Frame ( 7) shift: 0.48 -0.21 ...... Frame ( 8) shift: 0.54 -0.09 ...... Frame ( 9) shift: 0.61 0.04 ...... Frame ( 10) shift: 0.69 0.17 ...... Frame ( 11) shift: 0.77 0.30 ...... Frame ( 12) shift: 0.84 0.49 ...... Frame ( 13) shift: 0.90 0.72 ...... Frame ( 14) shift: 0.96 0.95 ...... Frame ( 15) shift: 1.03 1.09 ...... Frame ( 16) shift: 1.14 1.13 ...... Frame ( 17) shift: 1.24 1.16 ...... Frame ( 18) shift: 1.25 1.25 ...... Frame ( 19) shift: 1.17 1.37 ...... Frame ( 20) shift: 1.08 1.50 ...... Frame ( 21) shift: 1.06 1.63 ...... Frame ( 22) shift: 1.09 1.75 ...... Frame ( 23) shift: 1.13 1.88 ...... Frame ( 24) shift: 1.18 1.98 ...... Frame ( 25) shift: 1.26 2.06 ...... Frame ( 26) shift: 1.34 2.14 ...... Frame ( 27) shift: 1.39 2.22 ...... Frame ( 28) shift: 1.40 2.31 ...... Frame ( 29) shift: 1.40 2.40 ...... Frame ( 30) shift: 1.47 2.48 ...... Frame ( 31) shift: 1.59 2.57 ...... Frame ( 32) shift: 1.72 2.66 ...... Frame ( 33) shift: 1.79 2.74 ...... Frame ( 34) shift: 1.81 2.80 ...... Frame ( 35) shift: 1.83 2.87 ...... Frame ( 36) shift: 1.85 2.90 ...... Frame ( 37) shift: 1.87 2.90 ...... Frame ( 38) shift: 1.89 2.89 ...... Frame ( 39) shift: 1.90 2.89 ...... Frame ( 40) shift: 1.92 2.88 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.109847 Iteration 2 Error: 0.161411 Iteration 3 Error: 0.052283 Iteration 4 Error: 0.016448 Align patch 2 23 left Iteration 1 Error: 0.975115 Iteration 2 Error: 0.147939 Iteration 3 Error: 0.035172 Align patch 3 22 left Iteration 1 Error: 1.152121 Iteration 2 Error: 0.192147 Iteration 3 Error: 0.051593 Iteration 4 Error: 0.021025 Align patch 4 21 left Iteration 1 Error: 0.945943 Iteration 2 Error: 0.153233 Iteration 3 Error: 0.036545 Align patch 5 20 left Iteration 1 Error: 1.071730 Iteration 2 Error: 0.187179 Iteration 3 Error: 0.053093 Iteration 4 Error: 0.015035 Align patch 6 19 left Iteration 1 Error: 0.700808 Iteration 2 Error: 0.113967 Iteration 3 Error: 0.049077 Align patch 7 18 left Iteration 1 Error: 1.116670 Iteration 2 Error: 0.208348 Iteration 3 Error: 0.059613 Iteration 4 Error: 0.025467 Align patch 8 17 left Iteration 1 Error: 1.009483 Iteration 2 Error: 0.259563 Iteration 3 Error: 0.083006 Iteration 4 Error: 0.031279 Align patch 9 16 left Iteration 1 Error: 0.729188 Iteration 2 Error: 0.125343 Iteration 3 Error: 0.044360 Align patch 10 15 left Iteration 1 Error: 0.945116 Iteration 2 Error: 0.097749 Iteration 3 Error: 0.015893 Align patch 11 14 left Iteration 1 Error: 0.722512 Iteration 2 Error: 0.080885 Iteration 3 Error: 0.029424 Align patch 12 13 left Iteration 1 Error: 0.881450 Iteration 2 Error: 0.116770 Iteration 3 Error: 0.050122 Iteration 4 Error: 0.015828 Align patch 13 12 left Iteration 1 Error: 0.565846 Iteration 2 Error: 0.127761 Iteration 3 Error: 0.029644 Align patch 14 11 left Iteration 1 Error: 1.228725 Iteration 2 Error: 0.116247 Iteration 3 Error: 0.022203 Align patch 15 10 left Iteration 1 Error: 0.615548 Iteration 2 Error: 0.091079 Iteration 3 Error: 0.025764 Align patch 16 9 left Iteration 1 Error: 0.658199 Iteration 2 Error: 0.162519 Iteration 3 Error: 0.043281 Align patch 17 8 left Iteration 1 Error: 0.710510 Iteration 2 Error: 0.077191 Iteration 3 Error: 0.022957 Align patch 18 7 left Iteration 1 Error: 1.072586 Iteration 2 Error: 0.196854 Iteration 3 Error: 0.054541 Iteration 4 Error: 0.013106 Align patch 19 6 left Iteration 1 Error: 1.037101 Iteration 2 Error: 0.155209 Iteration 3 Error: 0.040997 Align patch 20 5 left Iteration 1 Error: 1.218162 Iteration 2 Error: 0.130701 Iteration 3 Error: 0.034471 Align patch 21 4 left Iteration 1 Error: 0.685484 Iteration 2 Error: 0.126494 Iteration 3 Error: 0.035234 Align patch 22 3 left Iteration 1 Error: 0.626048 Iteration 2 Error: 0.155266 Iteration 3 Error: 0.043606 Align patch 23 2 left Iteration 1 Error: 0.806997 Iteration 2 Error: 0.089005 Iteration 3 Error: 0.022936 Align patch 24 1 left Iteration 1 Error: 0.943150 Iteration 2 Error: 0.160000 Iteration 3 Error: 0.039115 Align patch 25 0 left Iteration 1 Error: 0.820697 Iteration 2 Error: 0.095755 Iteration 3 Error: 0.027065 3D Fitting completed. Patch alignment time: 11.42(sec) Local motion has been corrected. Process thread exits. Computational time: 21.322882 sec Total time: 26.684282 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00007hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00007hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.527562s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00007hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.254341s ........................................ >>>>>>TIME<<<<<< FFT: 0.927042s Defocus_U Defocus_V Angle CCC 24841.80 24232.43 89.05 0.048193 Final Values Defocus_U Defocus_V Angle CCC 24869.91 24213.70 88.74 0.077413 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00007hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00007hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.991e-02 CC threshold: 0.734 Mean Std: 42.63 6.95 Num Hot pixels: 190 Hot pixel threshold: 84.33 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.632359 Iteration 2 Error: 0.267704 Iteration 3 Error: 0.075385 Iteration 4 Error: 0.018921 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.04 -0.07 ...... Frame ( 3) shift: 0.08 -0.13 ...... Frame ( 4) shift: 0.11 -0.20 ...... Frame ( 5) shift: 0.15 -0.26 ...... Frame ( 6) shift: 0.19 -0.25 ...... Frame ( 7) shift: 0.23 -0.16 ...... Frame ( 8) shift: 0.27 -0.07 ...... Frame ( 9) shift: 0.32 0.05 ...... Frame ( 10) shift: 0.37 0.18 ...... Frame ( 11) shift: 0.43 0.32 ...... Frame ( 12) shift: 0.46 0.46 ...... Frame ( 13) shift: 0.46 0.59 ...... Frame ( 14) shift: 0.46 0.73 ...... Frame ( 15) shift: 0.49 0.81 ...... Frame ( 16) shift: 0.54 0.83 ...... Frame ( 17) shift: 0.58 0.85 ...... Frame ( 18) shift: 0.63 0.90 ...... Frame ( 19) shift: 0.68 0.99 ...... Frame ( 20) shift: 0.72 1.08 ...... Frame ( 21) shift: 0.79 1.17 ...... Frame ( 22) shift: 0.89 1.26 ...... Frame ( 23) shift: 0.98 1.35 ...... Frame ( 24) shift: 1.04 1.46 ...... Frame ( 25) shift: 1.06 1.60 ...... Frame ( 26) shift: 1.08 1.74 ...... Frame ( 27) shift: 1.09 1.83 ...... Frame ( 28) shift: 1.10 1.88 ...... Frame ( 29) shift: 1.10 1.94 ...... Frame ( 30) shift: 1.18 1.98 ...... Frame ( 31) shift: 1.36 2.01 ...... Frame ( 32) shift: 1.53 2.05 ...... Frame ( 33) shift: 1.59 2.12 ...... Frame ( 34) shift: 1.54 2.22 ...... Frame ( 35) shift: 1.49 2.32 ...... Frame ( 36) shift: 1.52 2.39 ...... Frame ( 37) shift: 1.63 2.42 ...... Frame ( 38) shift: 1.75 2.46 ...... Frame ( 39) shift: 1.86 2.50 ...... Frame ( 40) shift: 1.98 2.54 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.867299 Iteration 2 Error: 0.086543 Iteration 3 Error: 0.027217 Align patch 2 23 left Iteration 1 Error: 0.725026 Iteration 2 Error: 0.160168 Iteration 3 Error: 0.034216 Align patch 3 22 left Iteration 1 Error: 0.792204 Iteration 2 Error: 0.161869 Iteration 3 Error: 0.049855 Align patch 4 21 left Iteration 1 Error: 1.199811 Iteration 2 Error: 0.165553 Iteration 3 Error: 0.058808 Iteration 4 Error: 0.022346 Align patch 5 20 left Iteration 1 Error: 1.002962 Iteration 2 Error: 0.169738 Iteration 3 Error: 0.045519 Align patch 6 19 left Iteration 1 Error: 0.872198 Iteration 2 Error: 0.143649 Iteration 3 Error: 0.035949 Align patch 7 18 left Iteration 1 Error: 0.614128 Iteration 2 Error: 0.131245 Iteration 3 Error: 0.052305 Iteration 4 Error: 0.015315 Align patch 8 17 left Iteration 1 Error: 0.602945 Iteration 2 Error: 0.096352 Iteration 3 Error: 0.030707 Align patch 9 16 left Iteration 1 Error: 0.791930 Iteration 2 Error: 0.133624 Iteration 3 Error: 0.050880 Iteration 4 Error: 0.022687 Align patch 10 15 left Iteration 1 Error: 0.918958 Iteration 2 Error: 0.148456 Iteration 3 Error: 0.039066 Align patch 11 14 left Iteration 1 Error: 0.865288 Iteration 2 Error: 0.160119 Iteration 3 Error: 0.044978 Align patch 12 13 left Iteration 1 Error: 0.924159 Iteration 2 Error: 0.102160 Iteration 3 Error: 0.018949 Align patch 13 12 left Iteration 1 Error: 0.784343 Iteration 2 Error: 0.121817 Iteration 3 Error: 0.036530 Align patch 14 11 left Iteration 1 Error: 0.990366 Iteration 2 Error: 0.128085 Iteration 3 Error: 0.032244 Align patch 15 10 left Iteration 1 Error: 0.714696 Iteration 2 Error: 0.126796 Iteration 3 Error: 0.040484 Align patch 16 9 left Iteration 1 Error: 0.933533 Iteration 2 Error: 0.186658 Iteration 3 Error: 0.040463 Align patch 17 8 left Iteration 1 Error: 0.739310 Iteration 2 Error: 0.174982 Iteration 3 Error: 0.053680 Iteration 4 Error: 0.016835 Align patch 18 7 left Iteration 1 Error: 0.859881 Iteration 2 Error: 0.115103 Iteration 3 Error: 0.022094 Align patch 19 6 left Iteration 1 Error: 0.922835 Iteration 2 Error: 0.173449 Iteration 3 Error: 0.037767 Align patch 20 5 left Iteration 1 Error: 0.564114 Iteration 2 Error: 0.091504 Iteration 3 Error: 0.025774 Align patch 21 4 left Iteration 1 Error: 0.816906 Iteration 2 Error: 0.146495 Iteration 3 Error: 0.033823 Align patch 22 3 left Iteration 1 Error: 0.610936 Iteration 2 Error: 0.120125 Iteration 3 Error: 0.020133 Align patch 23 2 left Iteration 1 Error: 1.117764 Iteration 2 Error: 0.149332 Iteration 3 Error: 0.047897 Align patch 24 1 left Iteration 1 Error: 1.382251 Iteration 2 Error: 0.182550 Iteration 3 Error: 0.053379 Iteration 4 Error: 0.016643 Align patch 25 0 left Iteration 1 Error: 0.764602 Iteration 2 Error: 0.208827 Iteration 3 Error: 0.077561 Iteration 4 Error: 0.028354 3D Fitting completed. Patch alignment time: 19.19(sec) Local motion has been corrected. Process thread exits. Computational time: 35.950493 sec Total time: 44.111881 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00007hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00007hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.157699s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00007hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.167136s ........................................ >>>>>>TIME<<<<<< FFT: 1.079765s Defocus_U Defocus_V Angle CCC 23917.70 24668.40 0.02 0.044377 Final Values Defocus_U Defocus_V Angle CCC 23920.83 24665.27 0.34 0.071353 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00008hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00008hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.990e-02 CC threshold: 0.734 Mean Std: 42.16 6.90 Num Hot pixels: 179 Hot pixel threshold: 83.59 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.516102 Iteration 2 Error: 0.443907 Iteration 3 Error: 0.131179 Iteration 4 Error: 0.046346 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.11 0.05 ...... Frame ( 3) shift: 0.22 0.10 ...... Frame ( 4) shift: 0.34 0.15 ...... Frame ( 5) shift: 0.45 0.20 ...... Frame ( 6) shift: 0.60 0.28 ...... Frame ( 7) shift: 0.80 0.41 ...... Frame ( 8) shift: 0.99 0.53 ...... Frame ( 9) shift: 1.18 0.67 ...... Frame ( 10) shift: 1.35 0.85 ...... Frame ( 11) shift: 1.52 1.02 ...... Frame ( 12) shift: 1.68 1.21 ...... Frame ( 13) shift: 1.80 1.42 ...... Frame ( 14) shift: 1.93 1.63 ...... Frame ( 15) shift: 2.07 1.74 ...... Frame ( 16) shift: 2.21 1.74 ...... Frame ( 17) shift: 2.36 1.75 ...... Frame ( 18) shift: 2.51 1.80 ...... Frame ( 19) shift: 2.65 1.90 ...... Frame ( 20) shift: 2.80 2.00 ...... Frame ( 21) shift: 2.95 2.08 ...... Frame ( 22) shift: 3.10 2.14 ...... Frame ( 23) shift: 3.26 2.19 ...... Frame ( 24) shift: 3.43 2.22 ...... Frame ( 25) shift: 3.63 2.23 ...... Frame ( 26) shift: 3.82 2.23 ...... Frame ( 27) shift: 3.94 2.25 ...... Frame ( 28) shift: 3.99 2.27 ...... Frame ( 29) shift: 4.04 2.29 ...... Frame ( 30) shift: 4.06 2.34 ...... Frame ( 31) shift: 4.04 2.42 ...... Frame ( 32) shift: 4.02 2.49 ...... Frame ( 33) shift: 4.06 2.53 ...... Frame ( 34) shift: 4.15 2.53 ...... Frame ( 35) shift: 4.25 2.54 ...... Frame ( 36) shift: 4.34 2.60 ...... Frame ( 37) shift: 4.42 2.72 ...... Frame ( 38) shift: 4.50 2.84 ...... Frame ( 39) shift: 4.58 2.96 ...... Frame ( 40) shift: 4.66 3.08 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.796100 Iteration 2 Error: 0.179197 Iteration 3 Error: 0.057694 Iteration 4 Error: 0.039347 Align patch 2 23 left Iteration 1 Error: 0.985608 Iteration 2 Error: 0.256788 Iteration 3 Error: 0.041083 Align patch 3 22 left Iteration 1 Error: 1.101984 Iteration 2 Error: 0.179432 Iteration 3 Error: 0.078528 Iteration 4 Error: 0.030516 Align patch 4 21 left Iteration 1 Error: 0.854661 Iteration 2 Error: 0.204252 Iteration 3 Error: 0.066348 Iteration 4 Error: 0.022317 Align patch 5 20 left Iteration 1 Error: 0.677333 Iteration 2 Error: 0.129980 Iteration 3 Error: 0.048723 Align patch 6 19 left Iteration 1 Error: 0.944511 Iteration 2 Error: 0.188064 Iteration 3 Error: 0.087813 Iteration 4 Error: 0.039306 Align patch 7 18 left Iteration 1 Error: 0.615168 Iteration 2 Error: 0.173591 Iteration 3 Error: 0.093140 Iteration 4 Error: 0.043365 Align patch 8 17 left Iteration 1 Error: 0.913371 Iteration 2 Error: 0.216740 Iteration 3 Error: 0.078643 Iteration 4 Error: 0.041762 Align patch 9 16 left Iteration 1 Error: 0.718153 Iteration 2 Error: 0.128971 Iteration 3 Error: 0.039884 Align patch 10 15 left Iteration 1 Error: 0.699846 Iteration 2 Error: 0.120131 Iteration 3 Error: 0.045566 Align patch 11 14 left Iteration 1 Error: 0.922699 Iteration 2 Error: 0.159042 Iteration 3 Error: 0.065413 Iteration 4 Error: 0.014842 Align patch 12 13 left Iteration 1 Error: 0.877189 Iteration 2 Error: 0.194510 Iteration 3 Error: 0.060556 Iteration 4 Error: 0.018969 Align patch 13 12 left Iteration 1 Error: 1.267591 Iteration 2 Error: 0.223479 Iteration 3 Error: 0.065297 Iteration 4 Error: 0.021415 Align patch 14 11 left Iteration 1 Error: 0.741762 Iteration 2 Error: 0.122605 Iteration 3 Error: 0.040203 Align patch 15 10 left Iteration 1 Error: 0.759896 Iteration 2 Error: 0.152137 Iteration 3 Error: 0.056267 Iteration 4 Error: 0.013298 Align patch 16 9 left Iteration 1 Error: 0.573700 Iteration 2 Error: 0.162614 Iteration 3 Error: 0.048843 Align patch 17 8 left Iteration 1 Error: 0.588055 Iteration 2 Error: 0.140628 Iteration 3 Error: 0.060038 Iteration 4 Error: 0.031458 Align patch 18 7 left Iteration 1 Error: 0.965504 Iteration 2 Error: 0.133763 Iteration 3 Error: 0.030140 Align patch 19 6 left Iteration 1 Error: 0.950624 Iteration 2 Error: 0.271980 Iteration 3 Error: 0.074576 Iteration 4 Error: 0.039332 Align patch 20 5 left Iteration 1 Error: 0.843942 Iteration 2 Error: 0.143582 Iteration 3 Error: 0.048153 Align patch 21 4 left Iteration 1 Error: 0.781381 Iteration 2 Error: 0.152828 Iteration 3 Error: 0.072285 Iteration 4 Error: 0.028677 Align patch 22 3 left Iteration 1 Error: 1.145907 Iteration 2 Error: 0.190667 Iteration 3 Error: 0.065842 Iteration 4 Error: 0.023479 Align patch 23 2 left Iteration 1 Error: 0.816134 Iteration 2 Error: 0.223835 Iteration 3 Error: 0.057671 Iteration 4 Error: 0.024100 Align patch 24 1 left Iteration 1 Error: 0.752693 Iteration 2 Error: 0.136358 Iteration 3 Error: 0.040687 Align patch 25 0 left Iteration 1 Error: 0.678950 Iteration 2 Error: 0.126621 Iteration 3 Error: 0.037329 3D Fitting completed. Patch alignment time: 17.61(sec) Local motion has been corrected. Process thread exits. Computational time: 36.156052 sec Total time: 45.330448 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00008hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00008hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.603037s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00008hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.404451s ........................................ >>>>>>TIME<<<<<< FFT: 1.422884s Defocus_U Defocus_V Angle CCC 25619.14 26384.77 6.58 0.046285 Final Values Defocus_U Defocus_V Angle CCC 25606.64 26397.27 7.20 0.073894 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00008hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00008hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.988e-02 CC threshold: 0.734 Mean Std: 42.42 6.93 Num Hot pixels: 180 Hot pixel threshold: 83.99 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.513315 Iteration 2 Error: 0.468763 Iteration 3 Error: 0.182094 Iteration 4 Error: 0.072752 Iteration 5 Error: 0.032905 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.00 -0.05 ...... Frame ( 3) shift: -0.01 -0.09 ...... Frame ( 4) shift: -0.01 -0.14 ...... Frame ( 5) shift: -0.02 -0.19 ...... Frame ( 6) shift: 0.10 -0.14 ...... Frame ( 7) shift: 0.33 0.01 ...... Frame ( 8) shift: 0.56 0.16 ...... Frame ( 9) shift: 0.77 0.34 ...... Frame ( 10) shift: 0.96 0.53 ...... Frame ( 11) shift: 1.14 0.72 ...... Frame ( 12) shift: 1.35 0.91 ...... Frame ( 13) shift: 1.58 1.09 ...... Frame ( 14) shift: 1.81 1.27 ...... Frame ( 15) shift: 2.00 1.43 ...... Frame ( 16) shift: 2.15 1.59 ...... Frame ( 17) shift: 2.31 1.74 ...... Frame ( 18) shift: 2.46 1.89 ...... Frame ( 19) shift: 2.59 2.03 ...... Frame ( 20) shift: 2.72 2.16 ...... Frame ( 21) shift: 2.85 2.28 ...... Frame ( 22) shift: 2.98 2.38 ...... Frame ( 23) shift: 3.11 2.49 ...... Frame ( 24) shift: 3.24 2.55 ...... Frame ( 25) shift: 3.35 2.57 ...... Frame ( 26) shift: 3.46 2.59 ...... Frame ( 27) shift: 3.53 2.60 ...... Frame ( 28) shift: 3.54 2.61 ...... Frame ( 29) shift: 3.55 2.62 ...... Frame ( 30) shift: 3.59 2.64 ...... Frame ( 31) shift: 3.65 2.68 ...... Frame ( 32) shift: 3.72 2.71 ...... Frame ( 33) shift: 3.87 2.75 ...... Frame ( 34) shift: 4.11 2.79 ...... Frame ( 35) shift: 4.35 2.83 ...... Frame ( 36) shift: 4.55 2.88 ...... Frame ( 37) shift: 4.71 2.93 ...... Frame ( 38) shift: 4.88 2.99 ...... Frame ( 39) shift: 5.04 3.04 ...... Frame ( 40) shift: 5.20 3.09 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.835900 Iteration 2 Error: 0.234685 Iteration 3 Error: 0.069780 Iteration 4 Error: 0.026169 Align patch 2 23 left Iteration 1 Error: 0.889615 Iteration 2 Error: 0.152960 Iteration 3 Error: 0.044630 Align patch 3 22 left Iteration 1 Error: 1.081670 Iteration 2 Error: 0.186027 Iteration 3 Error: 0.066162 Iteration 4 Error: 0.027962 Align patch 4 21 left Iteration 1 Error: 1.110143 Iteration 2 Error: 0.248443 Iteration 3 Error: 0.117972 Iteration 4 Error: 0.079185 Iteration 5 Error: 0.026721 Align patch 5 20 left Iteration 1 Error: 0.998342 Iteration 2 Error: 0.136770 Iteration 3 Error: 0.052582 Iteration 4 Error: 0.023667 Align patch 6 19 left Iteration 1 Error: 1.443000 Iteration 2 Error: 0.213721 Iteration 3 Error: 0.067845 Iteration 4 Error: 0.019965 Align patch 7 18 left Iteration 1 Error: 1.778825 Iteration 2 Error: 0.410285 Iteration 3 Error: 0.120307 Iteration 4 Error: 0.045795 Align patch 8 17 left Iteration 1 Error: 0.540987 Iteration 2 Error: 0.187598 Iteration 3 Error: 0.079330 Iteration 4 Error: 0.034899 Align patch 9 16 left Iteration 1 Error: 0.947567 Iteration 2 Error: 0.215269 Iteration 3 Error: 0.086156 Iteration 4 Error: 0.032121 Align patch 10 15 left Iteration 1 Error: 0.743451 Iteration 2 Error: 0.105574 Iteration 3 Error: 0.049601 Align patch 11 14 left Iteration 1 Error: 0.718209 Iteration 2 Error: 0.141271 Iteration 3 Error: 0.067540 Iteration 4 Error: 0.021714 Align patch 12 13 left Iteration 1 Error: 1.458114 Iteration 2 Error: 0.330754 Iteration 3 Error: 0.093645 Iteration 4 Error: 0.050774 Iteration 5 Error: 0.025458 Align patch 13 12 left Iteration 1 Error: 0.897950 Iteration 2 Error: 0.172289 Iteration 3 Error: 0.095966 Iteration 4 Error: 0.035338 Align patch 14 11 left Iteration 1 Error: 0.908803 Iteration 2 Error: 0.161973 Iteration 3 Error: 0.054811 Iteration 4 Error: 0.026562 Align patch 15 10 left Iteration 1 Error: 0.874869 Iteration 2 Error: 0.192553 Iteration 3 Error: 0.048401 Align patch 16 9 left Iteration 1 Error: 0.951509 Iteration 2 Error: 0.198411 Iteration 3 Error: 0.045058 Align patch 17 8 left Iteration 1 Error: 1.092060 Iteration 2 Error: 0.268503 Iteration 3 Error: 0.110588 Iteration 4 Error: 0.055134 Iteration 5 Error: 0.034500 Align patch 18 7 left Iteration 1 Error: 0.896529 Iteration 2 Error: 0.276895 Iteration 3 Error: 0.091028 Iteration 4 Error: 0.043534 Align patch 19 6 left Iteration 1 Error: 0.785088 Iteration 2 Error: 0.166382 Iteration 3 Error: 0.058590 Iteration 4 Error: 0.029299 Align patch 20 5 left Iteration 1 Error: 1.020954 Iteration 2 Error: 0.283482 Iteration 3 Error: 0.066207 Iteration 4 Error: 0.025718 Align patch 21 4 left Iteration 1 Error: 0.792025 Iteration 2 Error: 0.164364 Iteration 3 Error: 0.055001 Iteration 4 Error: 0.032353 Align patch 22 3 left Iteration 1 Error: 0.751200 Iteration 2 Error: 0.274993 Iteration 3 Error: 0.147077 Iteration 4 Error: 0.068565 Iteration 5 Error: 0.027602 Align patch 23 2 left Iteration 1 Error: 0.994294 Iteration 2 Error: 0.354138 Iteration 3 Error: 0.121669 Iteration 4 Error: 0.056808 Iteration 5 Error: 0.028190 Align patch 24 1 left Iteration 1 Error: 1.476749 Iteration 2 Error: 0.187479 Iteration 3 Error: 0.041995 Align patch 25 0 left Iteration 1 Error: 1.026250 Iteration 2 Error: 0.221596 Iteration 3 Error: 0.071775 Iteration 4 Error: 0.033308 3D Fitting completed. Patch alignment time: 18.97(sec) Local motion has been corrected. Process thread exits. Computational time: 31.839241 sec Total time: 40.197487 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00008hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00008hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.655342s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00008hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.110681s ........................................ >>>>>>TIME<<<<<< FFT: 1.417864s Defocus_U Defocus_V Angle CCC 28080.08 28908.20 3.68 0.038814 Final Values Defocus_U Defocus_V Angle CCC 28051.95 28908.22 3.37 0.064636 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00008hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00008hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.996e-02 CC threshold: 0.734 Mean Std: 42.25 6.90 Num Hot pixels: 184 Hot pixel threshold: 83.64 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.621589 Iteration 2 Error: 0.230938 Iteration 3 Error: 0.060415 Iteration 4 Error: 0.018161 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.05 0.15 ...... Frame ( 3) shift: 0.11 0.30 ...... Frame ( 4) shift: 0.16 0.44 ...... Frame ( 5) shift: 0.21 0.59 ...... Frame ( 6) shift: 0.27 0.72 ...... Frame ( 7) shift: 0.34 0.84 ...... Frame ( 8) shift: 0.40 0.96 ...... Frame ( 9) shift: 0.49 1.06 ...... Frame ( 10) shift: 0.61 1.15 ...... Frame ( 11) shift: 0.72 1.23 ...... Frame ( 12) shift: 0.78 1.32 ...... Frame ( 13) shift: 0.79 1.39 ...... Frame ( 14) shift: 0.79 1.46 ...... Frame ( 15) shift: 0.82 1.53 ...... Frame ( 16) shift: 0.89 1.59 ...... Frame ( 17) shift: 0.96 1.66 ...... Frame ( 18) shift: 0.99 1.71 ...... Frame ( 19) shift: 0.98 1.74 ...... Frame ( 20) shift: 0.98 1.78 ...... Frame ( 21) shift: 1.00 1.83 ...... Frame ( 22) shift: 1.06 1.90 ...... Frame ( 23) shift: 1.12 1.97 ...... Frame ( 24) shift: 1.16 2.05 ...... Frame ( 25) shift: 1.17 2.13 ...... Frame ( 26) shift: 1.19 2.22 ...... Frame ( 27) shift: 1.23 2.27 ...... Frame ( 28) shift: 1.28 2.29 ...... Frame ( 29) shift: 1.33 2.31 ...... Frame ( 30) shift: 1.39 2.33 ...... Frame ( 31) shift: 1.47 2.36 ...... Frame ( 32) shift: 1.55 2.39 ...... Frame ( 33) shift: 1.64 2.44 ...... Frame ( 34) shift: 1.73 2.51 ...... Frame ( 35) shift: 1.81 2.57 ...... Frame ( 36) shift: 1.89 2.62 ...... Frame ( 37) shift: 1.94 2.66 ...... Frame ( 38) shift: 1.99 2.69 ...... Frame ( 39) shift: 2.04 2.73 ...... Frame ( 40) shift: 2.10 2.76 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.940844 Iteration 2 Error: 0.093907 Iteration 3 Error: 0.026365 Align patch 2 23 left Iteration 1 Error: 0.747043 Iteration 2 Error: 0.218172 Iteration 3 Error: 0.083449 Iteration 4 Error: 0.041670 Align patch 3 22 left Iteration 1 Error: 1.568708 Iteration 2 Error: 0.311121 Iteration 3 Error: 0.081513 Iteration 4 Error: 0.021640 Align patch 4 21 left Iteration 1 Error: 0.780892 Iteration 2 Error: 0.120923 Iteration 3 Error: 0.021957 Align patch 5 20 left Iteration 1 Error: 0.801217 Iteration 2 Error: 0.126382 Iteration 3 Error: 0.042541 Align patch 6 19 left Iteration 1 Error: 0.811204 Iteration 2 Error: 0.129599 Iteration 3 Error: 0.037745 Align patch 7 18 left Iteration 1 Error: 0.562228 Iteration 2 Error: 0.105680 Iteration 3 Error: 0.036712 Align patch 8 17 left Iteration 1 Error: 0.675320 Iteration 2 Error: 0.101602 Iteration 3 Error: 0.028848 Align patch 9 16 left Iteration 1 Error: 0.918279 Iteration 2 Error: 0.180217 Iteration 3 Error: 0.039691 Align patch 10 15 left Iteration 1 Error: 0.665784 Iteration 2 Error: 0.123162 Iteration 3 Error: 0.039999 Align patch 11 14 left Iteration 1 Error: 0.554716 Iteration 2 Error: 0.069795 Iteration 3 Error: 0.018805 Align patch 12 13 left Iteration 1 Error: 0.722229 Iteration 2 Error: 0.102929 Iteration 3 Error: 0.027709 Align patch 13 12 left Iteration 1 Error: 0.990736 Iteration 2 Error: 0.249910 Iteration 3 Error: 0.070631 Iteration 4 Error: 0.030503 Align patch 14 11 left Iteration 1 Error: 0.605231 Iteration 2 Error: 0.180003 Iteration 3 Error: 0.077904 Iteration 4 Error: 0.037700 Align patch 15 10 left Iteration 1 Error: 0.671385 Iteration 2 Error: 0.132379 Iteration 3 Error: 0.050129 Iteration 4 Error: 0.014081 Align patch 16 9 left Iteration 1 Error: 0.721405 Iteration 2 Error: 0.134002 Iteration 3 Error: 0.048511 Align patch 17 8 left Iteration 1 Error: 0.638765 Iteration 2 Error: 0.104178 Iteration 3 Error: 0.042453 Align patch 18 7 left Iteration 1 Error: 0.508865 Iteration 2 Error: 0.084284 Iteration 3 Error: 0.024089 Align patch 19 6 left Iteration 1 Error: 0.953843 Iteration 2 Error: 0.108022 Iteration 3 Error: 0.023748 Align patch 20 5 left Iteration 1 Error: 1.092796 Iteration 2 Error: 0.074174 Iteration 3 Error: 0.016996 Align patch 21 4 left Iteration 1 Error: 1.167901 Iteration 2 Error: 0.214815 Iteration 3 Error: 0.049339 Align patch 22 3 left Iteration 1 Error: 0.704140 Iteration 2 Error: 0.128589 Iteration 3 Error: 0.034008 Align patch 23 2 left Iteration 1 Error: 0.517887 Iteration 2 Error: 0.112210 Iteration 3 Error: 0.032848 Align patch 24 1 left Iteration 1 Error: 0.934596 Iteration 2 Error: 0.168571 Iteration 3 Error: 0.044272 Align patch 25 0 left Iteration 1 Error: 0.853388 Iteration 2 Error: 0.117831 Iteration 3 Error: 0.029473 3D Fitting completed. Patch alignment time: 19.00(sec) Local motion has been corrected. Process thread exits. Computational time: 38.505089 sec Total time: 48.275909 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00008hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00008hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.566731s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00008hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.050391s ........................................ >>>>>>TIME<<<<<< FFT: 1.338643s Defocus_U Defocus_V Angle CCC 27972.68 27292.99 89.61 0.039329 Final Values Defocus_U Defocus_V Angle CCC 27303.95 27971.14 0.24 0.065677 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00008hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00008hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.997e-02 CC threshold: 0.734 Mean Std: 42.35 6.92 Num Hot pixels: 170 Hot pixel threshold: 83.88 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.130933 Iteration 2 Error: 0.363089 Iteration 3 Error: 0.101212 Iteration 4 Error: 0.030892 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.05 0.12 ...... Frame ( 3) shift: 0.10 0.24 ...... Frame ( 4) shift: 0.16 0.36 ...... Frame ( 5) shift: 0.21 0.48 ...... Frame ( 6) shift: 0.24 0.59 ...... Frame ( 7) shift: 0.27 0.67 ...... Frame ( 8) shift: 0.29 0.75 ...... Frame ( 9) shift: 0.35 0.86 ...... Frame ( 10) shift: 0.46 0.99 ...... Frame ( 11) shift: 0.57 1.12 ...... Frame ( 12) shift: 0.74 1.26 ...... Frame ( 13) shift: 0.97 1.41 ...... Frame ( 14) shift: 1.21 1.56 ...... Frame ( 15) shift: 1.37 1.68 ...... Frame ( 16) shift: 1.47 1.76 ...... Frame ( 17) shift: 1.56 1.85 ...... Frame ( 18) shift: 1.70 1.94 ...... Frame ( 19) shift: 1.88 2.03 ...... Frame ( 20) shift: 2.06 2.12 ...... Frame ( 21) shift: 2.18 2.19 ...... Frame ( 22) shift: 2.23 2.25 ...... Frame ( 23) shift: 2.28 2.30 ...... Frame ( 24) shift: 2.30 2.38 ...... Frame ( 25) shift: 2.30 2.49 ...... Frame ( 26) shift: 2.30 2.59 ...... Frame ( 27) shift: 2.37 2.67 ...... Frame ( 28) shift: 2.49 2.73 ...... Frame ( 29) shift: 2.61 2.80 ...... Frame ( 30) shift: 2.73 2.86 ...... Frame ( 31) shift: 2.84 2.94 ...... Frame ( 32) shift: 2.96 3.01 ...... Frame ( 33) shift: 3.06 3.06 ...... Frame ( 34) shift: 3.14 3.08 ...... Frame ( 35) shift: 3.23 3.10 ...... Frame ( 36) shift: 3.31 3.14 ...... Frame ( 37) shift: 3.40 3.21 ...... Frame ( 38) shift: 3.49 3.28 ...... Frame ( 39) shift: 3.58 3.35 ...... Frame ( 40) shift: 3.67 3.42 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.034337 Iteration 2 Error: 0.189011 Iteration 3 Error: 0.047848 Align patch 2 23 left Iteration 1 Error: 0.679751 Iteration 2 Error: 0.149600 Iteration 3 Error: 0.030742 Align patch 3 22 left Iteration 1 Error: 1.009696 Iteration 2 Error: 0.221184 Iteration 3 Error: 0.091343 Iteration 4 Error: 0.041871 Align patch 4 21 left Iteration 1 Error: 0.834715 Iteration 2 Error: 0.126028 Iteration 3 Error: 0.037291 Align patch 5 20 left Iteration 1 Error: 0.920532 Iteration 2 Error: 0.194576 Iteration 3 Error: 0.053847 Iteration 4 Error: 0.018066 Align patch 6 19 left Iteration 1 Error: 0.885904 Iteration 2 Error: 0.200400 Iteration 3 Error: 0.060629 Iteration 4 Error: 0.030593 Align patch 7 18 left Iteration 1 Error: 0.944104 Iteration 2 Error: 0.183427 Iteration 3 Error: 0.048649 Align patch 8 17 left Iteration 1 Error: 0.721576 Iteration 2 Error: 0.116821 Iteration 3 Error: 0.039796 Align patch 9 16 left Iteration 1 Error: 0.734420 Iteration 2 Error: 0.124324 Iteration 3 Error: 0.038569 Align patch 10 15 left Iteration 1 Error: 1.003420 Iteration 2 Error: 0.266304 Iteration 3 Error: 0.102913 Iteration 4 Error: 0.048554 Align patch 11 14 left Iteration 1 Error: 0.629111 Iteration 2 Error: 0.118873 Iteration 3 Error: 0.040106 Align patch 12 13 left Iteration 1 Error: 0.539176 Iteration 2 Error: 0.081897 Iteration 3 Error: 0.031476 Align patch 13 12 left Iteration 1 Error: 0.612412 Iteration 2 Error: 0.134021 Iteration 3 Error: 0.023839 Align patch 14 11 left Iteration 1 Error: 0.565310 Iteration 2 Error: 0.106980 Iteration 3 Error: 0.046301 Align patch 15 10 left Iteration 1 Error: 0.811606 Iteration 2 Error: 0.101902 Iteration 3 Error: 0.026189 Align patch 16 9 left Iteration 1 Error: 0.969542 Iteration 2 Error: 0.196597 Iteration 3 Error: 0.054150 Iteration 4 Error: 0.021589 Align patch 17 8 left Iteration 1 Error: 0.719615 Iteration 2 Error: 0.106018 Iteration 3 Error: 0.036393 Align patch 18 7 left Iteration 1 Error: 0.552585 Iteration 2 Error: 0.078096 Iteration 3 Error: 0.015721 Align patch 19 6 left Iteration 1 Error: 0.927709 Iteration 2 Error: 0.105390 Iteration 3 Error: 0.025076 Align patch 20 5 left Iteration 1 Error: 0.905573 Iteration 2 Error: 0.139247 Iteration 3 Error: 0.044083 Align patch 21 4 left Iteration 1 Error: 1.240699 Iteration 2 Error: 0.147323 Iteration 3 Error: 0.064419 Iteration 4 Error: 0.013497 Align patch 22 3 left Iteration 1 Error: 1.180980 Iteration 2 Error: 0.173766 Iteration 3 Error: 0.057163 Iteration 4 Error: 0.017398 Align patch 23 2 left Iteration 1 Error: 0.682364 Iteration 2 Error: 0.108499 Iteration 3 Error: 0.025214 Align patch 24 1 left Iteration 1 Error: 0.922075 Iteration 2 Error: 0.154047 Iteration 3 Error: 0.038644 Align patch 25 0 left Iteration 1 Error: 0.663554 Iteration 2 Error: 0.100587 Iteration 3 Error: 0.039442 3D Fitting completed. Patch alignment time: 19.06(sec) Local motion has been corrected. Process thread exits. Computational time: 35.468979 sec Total time: 44.613937 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00008hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00008hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.617320s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00008hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.327451s ........................................ >>>>>>TIME<<<<<< FFT: 1.376911s Defocus_U Defocus_V Angle CCC 29027.36 28238.27 83.95 0.041235 Final Values Defocus_U Defocus_V Angle CCC 29038.30 28230.45 85.52 0.070209 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00009hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00009hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.342e-01 9.986e-02 CC threshold: 0.733 Mean Std: 42.52 6.94 Num Hot pixels: 169 Hot pixel threshold: 84.13 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.659150 Iteration 2 Error: 0.549356 Iteration 3 Error: 0.234396 Iteration 4 Error: 0.097088 Iteration 5 Error: 0.041305 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.10 -0.35 ...... Frame ( 3) shift: 0.19 -0.70 ...... Frame ( 4) shift: 0.29 -1.06 ...... Frame ( 5) shift: 0.39 -1.41 ...... Frame ( 6) shift: 0.50 -1.50 ...... Frame ( 7) shift: 0.64 -1.32 ...... Frame ( 8) shift: 0.79 -1.14 ...... Frame ( 9) shift: 0.89 -0.97 ...... Frame ( 10) shift: 0.97 -0.79 ...... Frame ( 11) shift: 1.04 -0.61 ...... Frame ( 12) shift: 1.18 -0.37 ...... Frame ( 13) shift: 1.38 -0.06 ...... Frame ( 14) shift: 1.58 0.25 ...... Frame ( 15) shift: 1.78 0.49 ...... Frame ( 16) shift: 1.97 0.67 ...... Frame ( 17) shift: 2.17 0.85 ...... Frame ( 18) shift: 2.35 1.06 ...... Frame ( 19) shift: 2.52 1.30 ...... Frame ( 20) shift: 2.70 1.53 ...... Frame ( 21) shift: 2.84 1.69 ...... Frame ( 22) shift: 2.97 1.76 ...... Frame ( 23) shift: 3.09 1.83 ...... Frame ( 24) shift: 3.20 1.95 ...... Frame ( 25) shift: 3.28 2.11 ...... Frame ( 26) shift: 3.37 2.28 ...... Frame ( 27) shift: 3.48 2.37 ...... Frame ( 28) shift: 3.61 2.38 ...... Frame ( 29) shift: 3.74 2.40 ...... Frame ( 30) shift: 3.92 2.49 ...... Frame ( 31) shift: 4.14 2.64 ...... Frame ( 32) shift: 4.37 2.80 ...... Frame ( 33) shift: 4.54 2.96 ...... Frame ( 34) shift: 4.67 3.14 ...... Frame ( 35) shift: 4.79 3.31 ...... Frame ( 36) shift: 4.89 3.40 ...... Frame ( 37) shift: 4.96 3.41 ...... Frame ( 38) shift: 5.03 3.42 ...... Frame ( 39) shift: 5.10 3.44 ...... Frame ( 40) shift: 5.17 3.45 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.512110 Iteration 2 Error: 0.169967 Iteration 3 Error: 0.038567 Align patch 2 23 left Iteration 1 Error: 0.847374 Iteration 2 Error: 0.214127 Iteration 3 Error: 0.071036 Iteration 4 Error: 0.027893 Align patch 3 22 left Iteration 1 Error: 1.518271 Iteration 2 Error: 0.340561 Iteration 3 Error: 0.123427 Iteration 4 Error: 0.047945 Align patch 4 21 left Iteration 1 Error: 1.401793 Iteration 2 Error: 0.141174 Iteration 3 Error: 0.061336 Iteration 4 Error: 0.019944 Align patch 5 20 left Iteration 1 Error: 0.912525 Iteration 2 Error: 0.206971 Iteration 3 Error: 0.083238 Iteration 4 Error: 0.021438 Align patch 6 19 left Iteration 1 Error: 1.254990 Iteration 2 Error: 0.157249 Iteration 3 Error: 0.046499 Align patch 7 18 left Iteration 1 Error: 0.778549 Iteration 2 Error: 0.189496 Iteration 3 Error: 0.107459 Iteration 4 Error: 0.043894 Align patch 8 17 left Iteration 1 Error: 1.324213 Iteration 2 Error: 0.262659 Iteration 3 Error: 0.083516 Iteration 4 Error: 0.025760 Align patch 9 16 left Iteration 1 Error: 0.959674 Iteration 2 Error: 0.336089 Iteration 3 Error: 0.076665 Iteration 4 Error: 0.021425 Align patch 10 15 left Iteration 1 Error: 1.093339 Iteration 2 Error: 0.182050 Iteration 3 Error: 0.056670 Iteration 4 Error: 0.020244 Align patch 11 14 left Iteration 1 Error: 1.152763 Iteration 2 Error: 0.235297 Iteration 3 Error: 0.130622 Iteration 4 Error: 0.052772 Iteration 5 Error: 0.025935 Align patch 12 13 left Iteration 1 Error: 0.859409 Iteration 2 Error: 0.364112 Iteration 3 Error: 0.124247 Iteration 4 Error: 0.048562 Align patch 13 12 left Iteration 1 Error: 1.123374 Iteration 2 Error: 0.212408 Iteration 3 Error: 0.097166 Iteration 4 Error: 0.026048 Align patch 14 11 left Iteration 1 Error: 1.110423 Iteration 2 Error: 0.204605 Iteration 3 Error: 0.048245 Align patch 15 10 left Iteration 1 Error: 0.841978 Iteration 2 Error: 0.307828 Iteration 3 Error: 0.050508 Iteration 4 Error: 0.014886 Align patch 16 9 left Iteration 1 Error: 1.243279 Iteration 2 Error: 0.165147 Iteration 3 Error: 0.036954 Align patch 17 8 left Iteration 1 Error: 1.032856 Iteration 2 Error: 0.153363 Iteration 3 Error: 0.048567 Align patch 18 7 left Iteration 1 Error: 0.762350 Iteration 2 Error: 0.159308 Iteration 3 Error: 0.042543 Align patch 19 6 left Iteration 1 Error: 0.659615 Iteration 2 Error: 0.177735 Iteration 3 Error: 0.071857 Iteration 4 Error: 0.040095 Align patch 20 5 left Iteration 1 Error: 0.956955 Iteration 2 Error: 0.170289 Iteration 3 Error: 0.076060 Iteration 4 Error: 0.025582 Align patch 21 4 left Iteration 1 Error: 1.214690 Iteration 2 Error: 0.247701 Iteration 3 Error: 0.065154 Iteration 4 Error: 0.020427 Align patch 22 3 left Iteration 1 Error: 0.717676 Iteration 2 Error: 0.132697 Iteration 3 Error: 0.039282 Align patch 23 2 left Iteration 1 Error: 0.856927 Iteration 2 Error: 0.158129 Iteration 3 Error: 0.044174 Align patch 24 1 left Iteration 1 Error: 0.690324 Iteration 2 Error: 0.126252 Iteration 3 Error: 0.035148 Align patch 25 0 left Iteration 1 Error: 1.086698 Iteration 2 Error: 0.211834 Iteration 3 Error: 0.068159 Iteration 4 Error: 0.030330 3D Fitting completed. Patch alignment time: 19.43(sec) Local motion has been corrected. Process thread exits. Computational time: 34.621117 sec Total time: 42.700680 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00009hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00009hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.583403s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00009hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.916769s ........................................ >>>>>>TIME<<<<<< FFT: 1.249534s Defocus_U Defocus_V Angle CCC 24867.19 25703.12 8.85 0.048782 Final Values Defocus_U Defocus_V Angle CCC 24856.24 25701.57 8.54 0.081935 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00009hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00009hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.995e-02 CC threshold: 0.734 Mean Std: 42.21 6.93 Num Hot pixels: 184 Hot pixel threshold: 83.80 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.190562 Iteration 2 Error: 0.397500 Iteration 3 Error: 0.114292 Iteration 4 Error: 0.043900 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.12 -0.24 ...... Frame ( 3) shift: 0.23 -0.48 ...... Frame ( 4) shift: 0.35 -0.72 ...... Frame ( 5) shift: 0.46 -0.97 ...... Frame ( 6) shift: 0.56 -1.10 ...... Frame ( 7) shift: 0.65 -1.14 ...... Frame ( 8) shift: 0.74 -1.17 ...... Frame ( 9) shift: 0.82 -1.12 ...... Frame ( 10) shift: 0.90 -0.97 ...... Frame ( 11) shift: 0.97 -0.82 ...... Frame ( 12) shift: 1.03 -0.68 ...... Frame ( 13) shift: 1.05 -0.56 ...... Frame ( 14) shift: 1.08 -0.43 ...... Frame ( 15) shift: 1.13 -0.31 ...... Frame ( 16) shift: 1.22 -0.19 ...... Frame ( 17) shift: 1.30 -0.07 ...... Frame ( 18) shift: 1.46 0.08 ...... Frame ( 19) shift: 1.70 0.25 ...... Frame ( 20) shift: 1.94 0.43 ...... Frame ( 21) shift: 2.15 0.60 ...... Frame ( 22) shift: 2.33 0.76 ...... Frame ( 23) shift: 2.51 0.93 ...... Frame ( 24) shift: 2.62 1.02 ...... Frame ( 25) shift: 2.64 1.05 ...... Frame ( 26) shift: 2.67 1.07 ...... Frame ( 27) shift: 2.69 1.12 ...... Frame ( 28) shift: 2.71 1.19 ...... Frame ( 29) shift: 2.74 1.26 ...... Frame ( 30) shift: 2.75 1.33 ...... Frame ( 31) shift: 2.76 1.40 ...... Frame ( 32) shift: 2.77 1.47 ...... Frame ( 33) shift: 2.86 1.51 ...... Frame ( 34) shift: 3.03 1.54 ...... Frame ( 35) shift: 3.19 1.56 ...... Frame ( 36) shift: 3.34 1.64 ...... Frame ( 37) shift: 3.46 1.76 ...... Frame ( 38) shift: 3.59 1.89 ...... Frame ( 39) shift: 3.72 2.01 ...... Frame ( 40) shift: 3.85 2.13 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.703776 Iteration 2 Error: 0.118895 Iteration 3 Error: 0.027310 Align patch 2 23 left Iteration 1 Error: 1.354546 Iteration 2 Error: 0.146316 Iteration 3 Error: 0.034844 Align patch 3 22 left Iteration 1 Error: 1.098452 Iteration 2 Error: 0.230646 Iteration 3 Error: 0.053691 Iteration 4 Error: 0.024128 Align patch 4 21 left Iteration 1 Error: 0.992991 Iteration 2 Error: 0.204888 Iteration 3 Error: 0.056285 Iteration 4 Error: 0.028199 Align patch 5 20 left Iteration 1 Error: 1.023099 Iteration 2 Error: 0.211338 Iteration 3 Error: 0.048697 Align patch 6 19 left Iteration 1 Error: 0.470301 Iteration 2 Error: 0.097642 Iteration 3 Error: 0.034931 Align patch 7 18 left Iteration 1 Error: 1.472509 Iteration 2 Error: 0.092804 Iteration 3 Error: 0.027140 Align patch 8 17 left Iteration 1 Error: 1.390802 Iteration 2 Error: 0.257598 Iteration 3 Error: 0.078114 Iteration 4 Error: 0.037318 Align patch 9 16 left Iteration 1 Error: 0.929327 Iteration 2 Error: 0.180527 Iteration 3 Error: 0.042292 Align patch 10 15 left Iteration 1 Error: 1.002075 Iteration 2 Error: 0.143833 Iteration 3 Error: 0.031701 Align patch 11 14 left Iteration 1 Error: 0.616353 Iteration 2 Error: 0.164894 Iteration 3 Error: 0.041454 Align patch 12 13 left Iteration 1 Error: 0.539877 Iteration 2 Error: 0.066353 Iteration 3 Error: 0.020892 Align patch 13 12 left Iteration 1 Error: 0.970218 Iteration 2 Error: 0.181212 Iteration 3 Error: 0.060388 Iteration 4 Error: 0.033193 Align patch 14 11 left Iteration 1 Error: 0.683574 Iteration 2 Error: 0.169854 Iteration 3 Error: 0.042834 Align patch 15 10 left Iteration 1 Error: 1.059064 Iteration 2 Error: 0.176423 Iteration 3 Error: 0.065882 Iteration 4 Error: 0.037562 Align patch 16 9 left Iteration 1 Error: 0.757183 Iteration 2 Error: 0.142647 Iteration 3 Error: 0.041705 Align patch 17 8 left Iteration 1 Error: 0.953599 Iteration 2 Error: 0.119283 Iteration 3 Error: 0.026860 Align patch 18 7 left Iteration 1 Error: 0.771010 Iteration 2 Error: 0.152573 Iteration 3 Error: 0.033600 Align patch 19 6 left Iteration 1 Error: 0.780280 Iteration 2 Error: 0.168975 Iteration 3 Error: 0.052583 Iteration 4 Error: 0.018507 Align patch 20 5 left Iteration 1 Error: 1.101188 Iteration 2 Error: 0.181884 Iteration 3 Error: 0.041959 Align patch 21 4 left Iteration 1 Error: 0.531851 Iteration 2 Error: 0.179987 Iteration 3 Error: 0.078440 Iteration 4 Error: 0.037681 Align patch 22 3 left Iteration 1 Error: 0.666296 Iteration 2 Error: 0.076249 Iteration 3 Error: 0.022934 Align patch 23 2 left Iteration 1 Error: 0.677103 Iteration 2 Error: 0.119559 Iteration 3 Error: 0.022682 Align patch 24 1 left Iteration 1 Error: 0.806930 Iteration 2 Error: 0.100099 Iteration 3 Error: 0.031438 Align patch 25 0 left Iteration 1 Error: 0.882206 Iteration 2 Error: 0.168922 Iteration 3 Error: 0.049572 3D Fitting completed. Patch alignment time: 19.22(sec) Local motion has been corrected. Process thread exits. Computational time: 38.375103 sec Total time: 46.196808 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00009hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00009hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.557884s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00009hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.281650s ........................................ >>>>>>TIME<<<<<< FFT: 1.407868s Defocus_U Defocus_V Angle CCC 22697.27 23544.93 7.64 0.048890 Final Values Defocus_U Defocus_V Angle CCC 22680.06 23574.64 7.96 0.080280 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00009hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00009hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.342e-01 9.989e-02 CC threshold: 0.734 Mean Std: 42.50 6.94 Num Hot pixels: 175 Hot pixel threshold: 84.14 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 3.066652 Iteration 2 Error: 0.810093 Iteration 3 Error: 0.390958 Iteration 4 Error: 0.162985 Iteration 5 Error: 0.070911 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.13 -0.15 ...... Frame ( 3) shift: 0.25 -0.31 ...... Frame ( 4) shift: 0.38 -0.46 ...... Frame ( 5) shift: 0.51 -0.62 ...... Frame ( 6) shift: 0.61 -0.62 ...... Frame ( 7) shift: 0.67 -0.47 ...... Frame ( 8) shift: 0.73 -0.32 ...... Frame ( 9) shift: 0.80 -0.18 ...... Frame ( 10) shift: 0.88 -0.07 ...... Frame ( 11) shift: 0.95 0.04 ...... Frame ( 12) shift: 0.97 0.13 ...... Frame ( 13) shift: 0.93 0.19 ...... Frame ( 14) shift: 0.90 0.25 ...... Frame ( 15) shift: 0.97 0.34 ...... Frame ( 16) shift: 1.16 0.45 ...... Frame ( 17) shift: 1.35 0.56 ...... Frame ( 18) shift: 1.53 0.62 ...... Frame ( 19) shift: 1.70 0.64 ...... Frame ( 20) shift: 1.88 0.66 ...... Frame ( 21) shift: 2.24 0.78 ...... Frame ( 22) shift: 2.80 0.98 ...... Frame ( 23) shift: 3.37 1.19 ...... Frame ( 24) shift: 3.70 1.38 ...... Frame ( 25) shift: 3.80 1.55 ...... Frame ( 26) shift: 3.91 1.73 ...... Frame ( 27) shift: 4.11 1.86 ...... Frame ( 28) shift: 4.41 1.96 ...... Frame ( 29) shift: 4.70 2.06 ...... Frame ( 30) shift: 5.10 2.29 ...... Frame ( 31) shift: 5.59 2.63 ...... Frame ( 32) shift: 6.09 2.98 ...... Frame ( 33) shift: 6.29 3.24 ...... Frame ( 34) shift: 6.19 3.43 ...... Frame ( 35) shift: 6.10 3.61 ...... Frame ( 36) shift: 5.98 3.72 ...... Frame ( 37) shift: 5.84 3.74 ...... Frame ( 38) shift: 5.69 3.76 ...... Frame ( 39) shift: 5.55 3.78 ...... Frame ( 40) shift: 5.41 3.81 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.307661 Iteration 2 Error: 0.476264 Iteration 3 Error: 0.106842 Iteration 4 Error: 0.049845 Align patch 2 23 left Iteration 1 Error: 1.070227 Iteration 2 Error: 0.187240 Iteration 3 Error: 0.072694 Iteration 4 Error: 0.020695 Align patch 3 22 left Iteration 1 Error: 1.162542 Iteration 2 Error: 0.177448 Iteration 3 Error: 0.055198 Iteration 4 Error: 0.028944 Align patch 4 21 left Iteration 1 Error: 1.489375 Iteration 2 Error: 0.324072 Iteration 3 Error: 0.095385 Iteration 4 Error: 0.031805 Align patch 5 20 left Iteration 1 Error: 1.115676 Iteration 2 Error: 0.161326 Iteration 3 Error: 0.049793 Align patch 6 19 left Iteration 1 Error: 1.664342 Iteration 2 Error: 0.239697 Iteration 3 Error: 0.070901 Iteration 4 Error: 0.033868 Align patch 7 18 left Iteration 1 Error: 1.238397 Iteration 2 Error: 0.222602 Iteration 3 Error: 0.072987 Iteration 4 Error: 0.027947 Align patch 8 17 left Iteration 1 Error: 0.952144 Iteration 2 Error: 0.227026 Iteration 3 Error: 0.062293 Iteration 4 Error: 0.019252 Align patch 9 16 left Iteration 1 Error: 0.639498 Iteration 2 Error: 0.135367 Iteration 3 Error: 0.057016 Iteration 4 Error: 0.020864 Align patch 10 15 left Iteration 1 Error: 0.969911 Iteration 2 Error: 0.324923 Iteration 3 Error: 0.135274 Iteration 4 Error: 0.061091 Iteration 5 Error: 0.025000 Align patch 11 14 left Iteration 1 Error: 0.983329 Iteration 2 Error: 0.170633 Iteration 3 Error: 0.049839 Align patch 12 13 left Iteration 1 Error: 1.097694 Iteration 2 Error: 0.213920 Iteration 3 Error: 0.068415 Iteration 4 Error: 0.025006 Align patch 13 12 left Iteration 1 Error: 0.707494 Iteration 2 Error: 0.200096 Iteration 3 Error: 0.063594 Iteration 4 Error: 0.027197 Align patch 14 11 left Iteration 1 Error: 0.634967 Iteration 2 Error: 0.199087 Iteration 3 Error: 0.052528 Iteration 4 Error: 0.025022 Align patch 15 10 left Iteration 1 Error: 1.705118 Iteration 2 Error: 0.413295 Iteration 3 Error: 0.129340 Iteration 4 Error: 0.040060 Align patch 16 9 left Iteration 1 Error: 0.813233 Iteration 2 Error: 0.191552 Iteration 3 Error: 0.049574 Align patch 17 8 left Iteration 1 Error: 1.584145 Iteration 2 Error: 0.362464 Iteration 3 Error: 0.102775 Iteration 4 Error: 0.052351 Iteration 5 Error: 0.026266 Align patch 18 7 left Iteration 1 Error: 1.291565 Iteration 2 Error: 0.353160 Iteration 3 Error: 0.109310 Iteration 4 Error: 0.058509 Iteration 5 Error: 0.027233 Align patch 19 6 left Iteration 1 Error: 1.127166 Iteration 2 Error: 0.277105 Iteration 3 Error: 0.092152 Iteration 4 Error: 0.039778 Align patch 20 5 left Iteration 1 Error: 0.985434 Iteration 2 Error: 0.215362 Iteration 3 Error: 0.081335 Iteration 4 Error: 0.036891 Align patch 21 4 left Iteration 1 Error: 1.177963 Iteration 2 Error: 0.305931 Iteration 3 Error: 0.093305 Iteration 4 Error: 0.026788 Align patch 22 3 left Iteration 1 Error: 1.256657 Iteration 2 Error: 0.151583 Iteration 3 Error: 0.037802 Align patch 23 2 left Iteration 1 Error: 1.107237 Iteration 2 Error: 0.362782 Iteration 3 Error: 0.058883 Iteration 4 Error: 0.026402 Align patch 24 1 left Iteration 1 Error: 1.419539 Iteration 2 Error: 0.408808 Iteration 3 Error: 0.105720 Iteration 4 Error: 0.067248 Iteration 5 Error: 0.027842 Align patch 25 0 left Iteration 1 Error: 1.090705 Iteration 2 Error: 0.288908 Iteration 3 Error: 0.074359 Iteration 4 Error: 0.027609 3D Fitting completed. Patch alignment time: 21.64(sec) Local motion has been corrected. Process thread exits. Computational time: 35.483448 sec Total time: 44.093872 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00009hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00009hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.585217s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00009hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.999190s ........................................ >>>>>>TIME<<<<<< FFT: 1.312608s Defocus_U Defocus_V Angle CCC 23755.90 23099.58 89.99 0.048982 Final Values Defocus_U Defocus_V Angle CCC 23763.70 23110.53 89.99 0.084715 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00009hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00009hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.995e-02 CC threshold: 0.734 Mean Std: 41.37 6.87 Num Hot pixels: 182 Hot pixel threshold: 82.57 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.562958 Iteration 2 Error: 0.258085 Iteration 3 Error: 0.059134 Iteration 4 Error: 0.019545 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.25 -0.56 ...... Frame ( 3) shift: 0.50 -1.11 ...... Frame ( 4) shift: 0.75 -1.67 ...... Frame ( 5) shift: 1.00 -2.22 ...... Frame ( 6) shift: 1.21 -2.53 ...... Frame ( 7) shift: 1.39 -2.59 ...... Frame ( 8) shift: 1.57 -2.65 ...... Frame ( 9) shift: 1.73 -2.68 ...... Frame ( 10) shift: 1.87 -2.67 ...... Frame ( 11) shift: 2.00 -2.66 ...... Frame ( 12) shift: 2.14 -2.59 ...... Frame ( 13) shift: 2.27 -2.46 ...... Frame ( 14) shift: 2.41 -2.33 ...... Frame ( 15) shift: 2.56 -2.26 ...... Frame ( 16) shift: 2.71 -2.26 ...... Frame ( 17) shift: 2.86 -2.25 ...... Frame ( 18) shift: 2.95 -2.26 ...... Frame ( 19) shift: 2.98 -2.29 ...... Frame ( 20) shift: 3.01 -2.31 ...... Frame ( 21) shift: 3.03 -2.32 ...... Frame ( 22) shift: 3.05 -2.30 ...... Frame ( 23) shift: 3.07 -2.29 ...... Frame ( 24) shift: 3.12 -2.23 ...... Frame ( 25) shift: 3.22 -2.13 ...... Frame ( 26) shift: 3.31 -2.02 ...... Frame ( 27) shift: 3.40 -1.98 ...... Frame ( 28) shift: 3.47 -1.99 ...... Frame ( 29) shift: 3.54 -1.99 ...... Frame ( 30) shift: 3.60 -1.96 ...... Frame ( 31) shift: 3.64 -1.90 ...... Frame ( 32) shift: 3.68 -1.83 ...... Frame ( 33) shift: 3.72 -1.79 ...... Frame ( 34) shift: 3.77 -1.76 ...... Frame ( 35) shift: 3.81 -1.74 ...... Frame ( 36) shift: 3.85 -1.74 ...... Frame ( 37) shift: 3.88 -1.76 ...... Frame ( 38) shift: 3.91 -1.78 ...... Frame ( 39) shift: 3.95 -1.81 ...... Frame ( 40) shift: 3.98 -1.83 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.815816 Iteration 2 Error: 0.244975 Iteration 3 Error: 0.049648 Align patch 2 23 left Iteration 1 Error: 1.348395 Iteration 2 Error: 0.131677 Iteration 3 Error: 0.040768 Align patch 3 22 left Iteration 1 Error: 1.589230 Iteration 2 Error: 0.212722 Iteration 3 Error: 0.091502 Iteration 4 Error: 0.033021 Align patch 4 21 left Iteration 1 Error: 0.973999 Iteration 2 Error: 0.326115 Iteration 3 Error: 0.142291 Iteration 4 Error: 0.049658 Align patch 5 20 left Iteration 1 Error: 4.229171 Iteration 2 Error: 0.648811 Iteration 3 Error: 0.307929 Iteration 4 Error: 0.066498 Iteration 5 Error: 0.030032 Align patch 6 19 left Iteration 1 Error: 1.484707 Iteration 2 Error: 0.284620 Iteration 3 Error: 0.093329 Iteration 4 Error: 0.029941 Align patch 7 18 left Iteration 1 Error: 0.895326 Iteration 2 Error: 0.096359 Iteration 3 Error: 0.017057 Align patch 8 17 left Iteration 1 Error: 1.171190 Iteration 2 Error: 0.203530 Iteration 3 Error: 0.051135 Iteration 4 Error: 0.025365 Align patch 9 16 left Iteration 1 Error: 1.378693 Iteration 2 Error: 0.299147 Iteration 3 Error: 0.089185 Iteration 4 Error: 0.035338 Align patch 10 15 left Iteration 1 Error: 1.800745 Iteration 2 Error: 0.645203 Iteration 3 Error: 0.207957 Iteration 4 Error: 0.070141 Iteration 5 Error: 0.020001 Align patch 11 14 left Iteration 1 Error: 1.294023 Iteration 2 Error: 0.108435 Iteration 3 Error: 0.032579 Align patch 12 13 left Iteration 1 Error: 0.937467 Iteration 2 Error: 0.161768 Iteration 3 Error: 0.052451 Iteration 4 Error: 0.022896 Align patch 13 12 left Iteration 1 Error: 0.703609 Iteration 2 Error: 0.127419 Iteration 3 Error: 0.021167 Align patch 14 11 left Iteration 1 Error: 0.761084 Iteration 2 Error: 0.168634 Iteration 3 Error: 0.061323 Iteration 4 Error: 0.028677 Align patch 15 10 left Iteration 1 Error: 1.222734 Iteration 2 Error: 0.279582 Iteration 3 Error: 0.067072 Iteration 4 Error: 0.035743 Align patch 16 9 left Iteration 1 Error: 1.228334 Iteration 2 Error: 0.181460 Iteration 3 Error: 0.057144 Iteration 4 Error: 0.023436 Align patch 17 8 left Iteration 1 Error: 0.736755 Iteration 2 Error: 0.126149 Iteration 3 Error: 0.027456 Align patch 18 7 left Iteration 1 Error: 0.641725 Iteration 2 Error: 0.072318 Iteration 3 Error: 0.019085 Align patch 19 6 left Iteration 1 Error: 0.856001 Iteration 2 Error: 0.101277 Iteration 3 Error: 0.022523 Align patch 20 5 left Iteration 1 Error: 0.773540 Iteration 2 Error: 0.127981 Iteration 3 Error: 0.045291 Align patch 21 4 left Iteration 1 Error: 1.008792 Iteration 2 Error: 0.212298 Iteration 3 Error: 0.081765 Iteration 4 Error: 0.016519 Align patch 22 3 left Iteration 1 Error: 1.098151 Iteration 2 Error: 0.157242 Iteration 3 Error: 0.030967 Align patch 23 2 left Iteration 1 Error: 1.394794 Iteration 2 Error: 0.283195 Iteration 3 Error: 0.033562 Align patch 24 1 left Iteration 1 Error: 1.248276 Iteration 2 Error: 0.143695 Iteration 3 Error: 0.022145 Align patch 25 0 left Iteration 1 Error: 1.131833 Iteration 2 Error: 0.176663 Iteration 3 Error: 0.052552 Iteration 4 Error: 0.013342 3D Fitting completed. Patch alignment time: 19.65(sec) Local motion has been corrected. Process thread exits. Computational time: 37.842854 sec Total time: 44.968433 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00009hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00009hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.565733s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00009hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 4.088541s ........................................ >>>>>>TIME<<<<<< FFT: 1.464535s Defocus_U Defocus_V Angle CCC 28484.38 27710.93 89.68 0.040815 Final Values Defocus_U Defocus_V Angle CCC 28465.62 27732.87 89.68 0.063760 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00010hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00010hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.996e-02 CC threshold: 0.734 Mean Std: 40.49 6.79 Num Hot pixels: 159 Hot pixel threshold: 81.24 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.423643 Iteration 2 Error: 0.372708 Iteration 3 Error: 0.096607 Iteration 4 Error: 0.034234 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.02 -0.10 ...... Frame ( 3) shift: -0.04 -0.20 ...... Frame ( 4) shift: -0.06 -0.30 ...... Frame ( 5) shift: -0.09 -0.40 ...... Frame ( 6) shift: -0.08 -0.34 ...... Frame ( 7) shift: -0.04 -0.12 ...... Frame ( 8) shift: -0.00 0.09 ...... Frame ( 9) shift: 0.08 0.26 ...... Frame ( 10) shift: 0.21 0.36 ...... Frame ( 11) shift: 0.34 0.47 ...... Frame ( 12) shift: 0.43 0.60 ...... Frame ( 13) shift: 0.49 0.74 ...... Frame ( 14) shift: 0.55 0.88 ...... Frame ( 15) shift: 0.65 1.02 ...... Frame ( 16) shift: 0.81 1.16 ...... Frame ( 17) shift: 0.96 1.30 ...... Frame ( 18) shift: 1.07 1.43 ...... Frame ( 19) shift: 1.14 1.53 ...... Frame ( 20) shift: 1.21 1.64 ...... Frame ( 21) shift: 1.33 1.78 ...... Frame ( 22) shift: 1.49 1.94 ...... Frame ( 23) shift: 1.65 2.10 ...... Frame ( 24) shift: 1.77 2.24 ...... Frame ( 25) shift: 1.86 2.36 ...... Frame ( 26) shift: 1.94 2.48 ...... Frame ( 27) shift: 2.04 2.57 ...... Frame ( 28) shift: 2.15 2.61 ...... Frame ( 29) shift: 2.26 2.65 ...... Frame ( 30) shift: 2.38 2.75 ...... Frame ( 31) shift: 2.49 2.90 ...... Frame ( 32) shift: 2.61 3.05 ...... Frame ( 33) shift: 2.72 3.18 ...... Frame ( 34) shift: 2.82 3.29 ...... Frame ( 35) shift: 2.93 3.41 ...... Frame ( 36) shift: 2.99 3.49 ...... Frame ( 37) shift: 3.02 3.54 ...... Frame ( 38) shift: 3.05 3.59 ...... Frame ( 39) shift: 3.08 3.64 ...... Frame ( 40) shift: 3.11 3.69 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.903362 Iteration 2 Error: 0.200353 Iteration 3 Error: 0.060870 Iteration 4 Error: 0.024742 Align patch 2 23 left Iteration 1 Error: 1.370409 Iteration 2 Error: 0.252188 Iteration 3 Error: 0.075703 Iteration 4 Error: 0.035040 Align patch 3 22 left Iteration 1 Error: 0.811576 Iteration 2 Error: 0.082348 Iteration 3 Error: 0.021928 Align patch 4 21 left Iteration 1 Error: 0.770466 Iteration 2 Error: 0.061940 Iteration 3 Error: 0.012730 Align patch 5 20 left Iteration 1 Error: 0.527062 Iteration 2 Error: 0.106801 Iteration 3 Error: 0.017712 Align patch 6 19 left Iteration 1 Error: 0.905349 Iteration 2 Error: 0.086595 Iteration 3 Error: 0.029825 Align patch 7 18 left Iteration 1 Error: 0.931882 Iteration 2 Error: 0.189310 Iteration 3 Error: 0.061746 Iteration 4 Error: 0.026868 Align patch 8 17 left Iteration 1 Error: 0.964696 Iteration 2 Error: 0.124425 Iteration 3 Error: 0.033010 Align patch 9 16 left Iteration 1 Error: 0.459746 Iteration 2 Error: 0.111501 Iteration 3 Error: 0.016974 Align patch 10 15 left Iteration 1 Error: 0.598547 Iteration 2 Error: 0.095785 Iteration 3 Error: 0.016286 Align patch 11 14 left Iteration 1 Error: 0.708828 Iteration 2 Error: 0.077561 Iteration 3 Error: 0.027778 Align patch 12 13 left Iteration 1 Error: 0.648143 Iteration 2 Error: 0.248713 Iteration 3 Error: 0.129472 Iteration 4 Error: 0.061552 Iteration 5 Error: 0.031995 Align patch 13 12 left Iteration 1 Error: 0.603963 Iteration 2 Error: 0.115245 Iteration 3 Error: 0.039104 Align patch 14 11 left Iteration 1 Error: 0.764469 Iteration 2 Error: 0.119008 Iteration 3 Error: 0.038631 Align patch 15 10 left Iteration 1 Error: 0.612858 Iteration 2 Error: 0.113195 Iteration 3 Error: 0.028042 Align patch 16 9 left Iteration 1 Error: 1.354930 Iteration 2 Error: 0.156544 Iteration 3 Error: 0.038206 Align patch 17 8 left Iteration 1 Error: 1.013275 Iteration 2 Error: 0.124680 Iteration 3 Error: 0.028291 Align patch 18 7 left Iteration 1 Error: 0.901191 Iteration 2 Error: 0.116072 Iteration 3 Error: 0.026644 Align patch 19 6 left Iteration 1 Error: 0.676897 Iteration 2 Error: 0.072340 Iteration 3 Error: 0.016999 Align patch 20 5 left Iteration 1 Error: 0.691131 Iteration 2 Error: 0.148831 Iteration 3 Error: 0.027963 Align patch 21 4 left Iteration 1 Error: 0.945653 Iteration 2 Error: 0.104417 Iteration 3 Error: 0.034378 Align patch 22 3 left Iteration 1 Error: 0.603088 Iteration 2 Error: 0.141959 Iteration 3 Error: 0.041986 Align patch 23 2 left Iteration 1 Error: 0.658997 Iteration 2 Error: 0.121109 Iteration 3 Error: 0.029367 Align patch 24 1 left Iteration 1 Error: 1.013070 Iteration 2 Error: 0.121232 Iteration 3 Error: 0.018172 Align patch 25 0 left Iteration 1 Error: 0.957432 Iteration 2 Error: 0.122345 Iteration 3 Error: 0.054561 Iteration 4 Error: 0.027217 3D Fitting completed. Patch alignment time: 17.98(sec) Local motion has been corrected. Process thread exits. Computational time: 29.479904 sec Total time: 36.425617 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00010hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00010hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.572048s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00010hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.087653s ........................................ >>>>>>TIME<<<<<< FFT: 1.087305s Defocus_U Defocus_V Angle CCC 26974.61 27705.08 5.70 0.051181 Final Values Defocus_U Defocus_V Angle CCC 26976.18 27694.14 5.70 0.080125 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00010hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00010hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 39.89 6.75 Num Hot pixels: 166 Hot pixel threshold: 80.41 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.480348 Iteration 2 Error: 0.385347 Iteration 3 Error: 0.096688 Iteration 4 Error: 0.034042 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.03 -0.15 ...... Frame ( 3) shift: -0.07 -0.30 ...... Frame ( 4) shift: -0.10 -0.45 ...... Frame ( 5) shift: -0.13 -0.61 ...... Frame ( 6) shift: -0.06 -0.63 ...... Frame ( 7) shift: 0.12 -0.54 ...... Frame ( 8) shift: 0.29 -0.44 ...... Frame ( 9) shift: 0.46 -0.33 ...... Frame ( 10) shift: 0.60 -0.19 ...... Frame ( 11) shift: 0.75 -0.05 ...... Frame ( 12) shift: 0.90 0.09 ...... Frame ( 13) shift: 1.04 0.23 ...... Frame ( 14) shift: 1.19 0.37 ...... Frame ( 15) shift: 1.32 0.53 ...... Frame ( 16) shift: 1.44 0.70 ...... Frame ( 17) shift: 1.56 0.87 ...... Frame ( 18) shift: 1.69 1.03 ...... Frame ( 19) shift: 1.82 1.19 ...... Frame ( 20) shift: 1.95 1.35 ...... Frame ( 21) shift: 2.08 1.49 ...... Frame ( 22) shift: 2.21 1.62 ...... Frame ( 23) shift: 2.34 1.75 ...... Frame ( 24) shift: 2.47 1.85 ...... Frame ( 25) shift: 2.59 1.90 ...... Frame ( 26) shift: 2.71 1.96 ...... Frame ( 27) shift: 2.81 1.97 ...... Frame ( 28) shift: 2.87 1.94 ...... Frame ( 29) shift: 2.93 1.90 ...... Frame ( 30) shift: 3.01 1.94 ...... Frame ( 31) shift: 3.10 2.06 ...... Frame ( 32) shift: 3.19 2.17 ...... Frame ( 33) shift: 3.31 2.28 ...... Frame ( 34) shift: 3.46 2.40 ...... Frame ( 35) shift: 3.62 2.51 ...... Frame ( 36) shift: 3.75 2.60 ...... Frame ( 37) shift: 3.85 2.67 ...... Frame ( 38) shift: 3.95 2.74 ...... Frame ( 39) shift: 4.06 2.82 ...... Frame ( 40) shift: 4.16 2.89 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.971644 Iteration 2 Error: 0.101400 Iteration 3 Error: 0.024910 Align patch 2 23 left Iteration 1 Error: 1.143005 Iteration 2 Error: 0.102493 Iteration 3 Error: 0.019013 Align patch 3 22 left Iteration 1 Error: 0.965685 Iteration 2 Error: 0.160071 Iteration 3 Error: 0.038566 Align patch 4 21 left Iteration 1 Error: 0.656207 Iteration 2 Error: 0.131081 Iteration 3 Error: 0.027550 Align patch 5 20 left Iteration 1 Error: 0.510084 Iteration 2 Error: 0.110382 Iteration 3 Error: 0.032480 Align patch 6 19 left Iteration 1 Error: 0.467907 Iteration 2 Error: 0.081460 Iteration 3 Error: 0.016671 Align patch 7 18 left Iteration 1 Error: 0.823177 Iteration 2 Error: 0.115151 Iteration 3 Error: 0.029666 Align patch 8 17 left Iteration 1 Error: 0.844459 Iteration 2 Error: 0.143738 Iteration 3 Error: 0.050129 Iteration 4 Error: 0.016027 Align patch 9 16 left Iteration 1 Error: 0.508544 Iteration 2 Error: 0.062210 Iteration 3 Error: 0.015807 Align patch 10 15 left Iteration 1 Error: 0.429360 Iteration 2 Error: 0.088814 Iteration 3 Error: 0.021273 Align patch 11 14 left Iteration 1 Error: 0.598443 Iteration 2 Error: 0.068869 Iteration 3 Error: 0.022467 Align patch 12 13 left Iteration 1 Error: 0.963395 Iteration 2 Error: 0.137152 Iteration 3 Error: 0.038236 Align patch 13 12 left Iteration 1 Error: 0.651676 Iteration 2 Error: 0.104854 Iteration 3 Error: 0.024897 Align patch 14 11 left Iteration 1 Error: 0.816776 Iteration 2 Error: 0.131019 Iteration 3 Error: 0.029510 Align patch 15 10 left Iteration 1 Error: 0.771153 Iteration 2 Error: 0.144686 Iteration 3 Error: 0.036498 Align patch 16 9 left Iteration 1 Error: 0.439789 Iteration 2 Error: 0.079139 Iteration 3 Error: 0.025317 Align patch 17 8 left Iteration 1 Error: 0.420753 Iteration 2 Error: 0.068388 Iteration 3 Error: 0.011679 Align patch 18 7 left Iteration 1 Error: 0.589751 Iteration 2 Error: 0.130473 Iteration 3 Error: 0.026039 Align patch 19 6 left Iteration 1 Error: 0.735800 Iteration 2 Error: 0.111579 Iteration 3 Error: 0.027710 Align patch 20 5 left Iteration 1 Error: 0.765393 Iteration 2 Error: 0.145328 Iteration 3 Error: 0.048201 Align patch 21 4 left Iteration 1 Error: 0.753024 Iteration 2 Error: 0.107341 Iteration 3 Error: 0.030554 Align patch 22 3 left Iteration 1 Error: 0.601498 Iteration 2 Error: 0.090282 Iteration 3 Error: 0.013257 Align patch 23 2 left Iteration 1 Error: 0.500806 Iteration 2 Error: 0.096567 Iteration 3 Error: 0.025928 Align patch 24 1 left Iteration 1 Error: 0.935773 Iteration 2 Error: 0.213136 Iteration 3 Error: 0.069141 Iteration 4 Error: 0.029960 Align patch 25 0 left Iteration 1 Error: 0.613611 Iteration 2 Error: 0.139465 Iteration 3 Error: 0.031447 3D Fitting completed. Patch alignment time: 18.53(sec) Local motion has been corrected. Process thread exits. Computational time: 34.395947 sec Total time: 43.065056 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00010hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00010hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.969599s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00010hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.279549s ........................................ >>>>>>TIME<<<<<< FFT: 1.609210s Defocus_U Defocus_V Angle CCC 25191.41 26089.85 7.58 0.058944 Final Values Defocus_U Defocus_V Angle CCC 25178.91 26096.10 7.58 0.091240 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00010hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00010hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.989e-02 CC threshold: 0.734 Mean Std: 41.33 6.84 Num Hot pixels: 176 Hot pixel threshold: 82.34 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.118920 Iteration 2 Error: 0.314745 Iteration 3 Error: 0.074690 Iteration 4 Error: 0.029333 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.15 0.15 ...... Frame ( 3) shift: 0.30 0.30 ...... Frame ( 4) shift: 0.46 0.45 ...... Frame ( 5) shift: 0.61 0.60 ...... Frame ( 6) shift: 0.73 0.72 ...... Frame ( 7) shift: 0.82 0.81 ...... Frame ( 8) shift: 0.91 0.91 ...... Frame ( 9) shift: 1.02 1.01 ...... Frame ( 10) shift: 1.14 1.12 ...... Frame ( 11) shift: 1.25 1.24 ...... Frame ( 12) shift: 1.34 1.34 ...... Frame ( 13) shift: 1.39 1.44 ...... Frame ( 14) shift: 1.43 1.53 ...... Frame ( 15) shift: 1.49 1.63 ...... Frame ( 16) shift: 1.55 1.74 ...... Frame ( 17) shift: 1.61 1.85 ...... Frame ( 18) shift: 1.70 1.96 ...... Frame ( 19) shift: 1.83 2.08 ...... Frame ( 20) shift: 1.96 2.20 ...... Frame ( 21) shift: 2.05 2.28 ...... Frame ( 22) shift: 2.10 2.32 ...... Frame ( 23) shift: 2.14 2.35 ...... Frame ( 24) shift: 2.23 2.37 ...... Frame ( 25) shift: 2.37 2.38 ...... Frame ( 26) shift: 2.51 2.38 ...... Frame ( 27) shift: 2.60 2.42 ...... Frame ( 28) shift: 2.63 2.48 ...... Frame ( 29) shift: 2.66 2.55 ...... Frame ( 30) shift: 2.70 2.56 ...... Frame ( 31) shift: 2.73 2.53 ...... Frame ( 32) shift: 2.77 2.50 ...... Frame ( 33) shift: 2.85 2.50 ...... Frame ( 34) shift: 2.98 2.53 ...... Frame ( 35) shift: 3.10 2.56 ...... Frame ( 36) shift: 3.19 2.63 ...... Frame ( 37) shift: 3.25 2.72 ...... Frame ( 38) shift: 3.31 2.81 ...... Frame ( 39) shift: 3.37 2.90 ...... Frame ( 40) shift: 3.43 2.99 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.273943 Iteration 2 Error: 0.278377 Iteration 3 Error: 0.068820 Iteration 4 Error: 0.020149 Align patch 2 23 left Iteration 1 Error: 1.525210 Iteration 2 Error: 0.185196 Iteration 3 Error: 0.049682 Align patch 3 22 left Iteration 1 Error: 0.906256 Iteration 2 Error: 0.157442 Iteration 3 Error: 0.042599 Align patch 4 21 left Iteration 1 Error: 0.565021 Iteration 2 Error: 0.070815 Iteration 3 Error: 0.017456 Align patch 5 20 left Iteration 1 Error: 0.649737 Iteration 2 Error: 0.186759 Iteration 3 Error: 0.064627 Iteration 4 Error: 0.022483 Align patch 6 19 left Iteration 1 Error: 0.864051 Iteration 2 Error: 0.100682 Iteration 3 Error: 0.020564 Align patch 7 18 left Iteration 1 Error: 1.573537 Iteration 2 Error: 0.219725 Iteration 3 Error: 0.064734 Iteration 4 Error: 0.013692 Align patch 8 17 left Iteration 1 Error: 0.765265 Iteration 2 Error: 0.142645 Iteration 3 Error: 0.048702 Align patch 9 16 left Iteration 1 Error: 0.627088 Iteration 2 Error: 0.161311 Iteration 3 Error: 0.042970 Align patch 10 15 left Iteration 1 Error: 0.823630 Iteration 2 Error: 0.177441 Iteration 3 Error: 0.059066 Iteration 4 Error: 0.016726 Align patch 11 14 left Iteration 1 Error: 0.831320 Iteration 2 Error: 0.164789 Iteration 3 Error: 0.046585 Align patch 12 13 left Iteration 1 Error: 1.339723 Iteration 2 Error: 0.179078 Iteration 3 Error: 0.043725 Align patch 13 12 left Iteration 1 Error: 0.761662 Iteration 2 Error: 0.222251 Iteration 3 Error: 0.036702 Align patch 14 11 left Iteration 1 Error: 0.946766 Iteration 2 Error: 0.139741 Iteration 3 Error: 0.035703 Align patch 15 10 left Iteration 1 Error: 0.852929 Iteration 2 Error: 0.123618 Iteration 3 Error: 0.026021 Align patch 16 9 left Iteration 1 Error: 1.010963 Iteration 2 Error: 0.157870 Iteration 3 Error: 0.044799 Align patch 17 8 left Iteration 1 Error: 0.849671 Iteration 2 Error: 0.130291 Iteration 3 Error: 0.046087 Align patch 18 7 left Iteration 1 Error: 0.853522 Iteration 2 Error: 0.125359 Iteration 3 Error: 0.032560 Align patch 19 6 left Iteration 1 Error: 0.856819 Iteration 2 Error: 0.205327 Iteration 3 Error: 0.045330 Align patch 20 5 left Iteration 1 Error: 1.443075 Iteration 2 Error: 0.200332 Iteration 3 Error: 0.068905 Iteration 4 Error: 0.024865 Align patch 21 4 left Iteration 1 Error: 0.937898 Iteration 2 Error: 0.221321 Iteration 3 Error: 0.056409 Iteration 4 Error: 0.023838 Align patch 22 3 left Iteration 1 Error: 1.337078 Iteration 2 Error: 0.177958 Iteration 3 Error: 0.072374 Iteration 4 Error: 0.023264 Align patch 23 2 left Iteration 1 Error: 0.895336 Iteration 2 Error: 0.159168 Iteration 3 Error: 0.029538 Align patch 24 1 left Iteration 1 Error: 1.104670 Iteration 2 Error: 0.211355 Iteration 3 Error: 0.046126 Align patch 25 0 left Iteration 1 Error: 1.443805 Iteration 2 Error: 0.208846 Iteration 3 Error: 0.027478 3D Fitting completed. Patch alignment time: 19.27(sec) Local motion has been corrected. Process thread exits. Computational time: 36.466305 sec Total time: 44.822338 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00010hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00010hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.608222s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00010hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 4.785210s ........................................ >>>>>>TIME<<<<<< FFT: 1.577189s Defocus_U Defocus_V Angle CCC 27396.51 26779.30 84.90 0.042901 Final Values Defocus_U Defocus_V Angle CCC 27426.19 26755.86 85.84 0.066988 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00010hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00010hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.996e-02 CC threshold: 0.734 Mean Std: 41.08 6.82 Num Hot pixels: 161 Hot pixel threshold: 82.02 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.664085 Iteration 2 Error: 0.238146 Iteration 3 Error: 0.056050 Iteration 4 Error: 0.014160 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.03 -0.01 ...... Frame ( 3) shift: 0.05 -0.02 ...... Frame ( 4) shift: 0.08 -0.03 ...... Frame ( 5) shift: 0.11 -0.04 ...... Frame ( 6) shift: 0.21 0.03 ...... Frame ( 7) shift: 0.38 0.17 ...... Frame ( 8) shift: 0.56 0.30 ...... Frame ( 9) shift: 0.69 0.44 ...... Frame ( 10) shift: 0.78 0.57 ...... Frame ( 11) shift: 0.87 0.70 ...... Frame ( 12) shift: 0.97 0.79 ...... Frame ( 13) shift: 1.08 0.83 ...... Frame ( 14) shift: 1.18 0.88 ...... Frame ( 15) shift: 1.27 0.94 ...... Frame ( 16) shift: 1.35 1.02 ...... Frame ( 17) shift: 1.43 1.09 ...... Frame ( 18) shift: 1.52 1.18 ...... Frame ( 19) shift: 1.64 1.27 ...... Frame ( 20) shift: 1.76 1.36 ...... Frame ( 21) shift: 1.84 1.44 ...... Frame ( 22) shift: 1.89 1.51 ...... Frame ( 23) shift: 1.94 1.58 ...... Frame ( 24) shift: 1.96 1.60 ...... Frame ( 25) shift: 1.96 1.59 ...... Frame ( 26) shift: 1.96 1.58 ...... Frame ( 27) shift: 1.99 1.57 ...... Frame ( 28) shift: 2.05 1.57 ...... Frame ( 29) shift: 2.11 1.58 ...... Frame ( 30) shift: 2.16 1.57 ...... Frame ( 31) shift: 2.18 1.56 ...... Frame ( 32) shift: 2.20 1.55 ...... Frame ( 33) shift: 2.19 1.57 ...... Frame ( 34) shift: 2.16 1.62 ...... Frame ( 35) shift: 2.13 1.67 ...... Frame ( 36) shift: 2.12 1.70 ...... Frame ( 37) shift: 2.14 1.73 ...... Frame ( 38) shift: 2.17 1.76 ...... Frame ( 39) shift: 2.19 1.79 ...... Frame ( 40) shift: 2.21 1.82 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.045079 Iteration 2 Error: 0.258808 Iteration 3 Error: 0.086367 Iteration 4 Error: 0.040252 Align patch 2 23 left Iteration 1 Error: 0.856830 Iteration 2 Error: 0.180530 Iteration 3 Error: 0.048865 Align patch 3 22 left Iteration 1 Error: 0.685774 Iteration 2 Error: 0.159416 Iteration 3 Error: 0.042208 Align patch 4 21 left Iteration 1 Error: 0.982833 Iteration 2 Error: 0.227127 Iteration 3 Error: 0.055635 Iteration 4 Error: 0.017178 Align patch 5 20 left Iteration 1 Error: 0.769801 Iteration 2 Error: 0.123773 Iteration 3 Error: 0.037425 Align patch 6 19 left Iteration 1 Error: 0.660310 Iteration 2 Error: 0.142579 Iteration 3 Error: 0.054352 Iteration 4 Error: 0.027622 Align patch 7 18 left Iteration 1 Error: 1.075356 Iteration 2 Error: 0.127392 Iteration 3 Error: 0.028661 Align patch 8 17 left Iteration 1 Error: 0.732701 Iteration 2 Error: 0.134691 Iteration 3 Error: 0.044187 Align patch 9 16 left Iteration 1 Error: 0.915130 Iteration 2 Error: 0.341651 Iteration 3 Error: 0.122982 Iteration 4 Error: 0.046585 Align patch 10 15 left Iteration 1 Error: 0.632201 Iteration 2 Error: 0.075695 Iteration 3 Error: 0.034874 Align patch 11 14 left Iteration 1 Error: 0.699922 Iteration 2 Error: 0.105252 Iteration 3 Error: 0.017407 Align patch 12 13 left Iteration 1 Error: 0.816366 Iteration 2 Error: 0.156388 Iteration 3 Error: 0.035793 Align patch 13 12 left Iteration 1 Error: 0.732167 Iteration 2 Error: 0.088447 Iteration 3 Error: 0.021112 Align patch 14 11 left Iteration 1 Error: 0.556164 Iteration 2 Error: 0.109600 Iteration 3 Error: 0.022473 Align patch 15 10 left Iteration 1 Error: 0.665122 Iteration 2 Error: 0.178102 Iteration 3 Error: 0.047927 Align patch 16 9 left Iteration 1 Error: 0.592789 Iteration 2 Error: 0.126070 Iteration 3 Error: 0.042008 Align patch 17 8 left Iteration 1 Error: 0.685116 Iteration 2 Error: 0.272808 Iteration 3 Error: 0.070918 Iteration 4 Error: 0.024638 Align patch 18 7 left Iteration 1 Error: 0.698903 Iteration 2 Error: 0.168739 Iteration 3 Error: 0.043014 Align patch 19 6 left Iteration 1 Error: 0.749394 Iteration 2 Error: 0.145641 Iteration 3 Error: 0.031697 Align patch 20 5 left Iteration 1 Error: 1.071130 Iteration 2 Error: 0.124810 Iteration 3 Error: 0.040294 Align patch 21 4 left Iteration 1 Error: 0.601653 Iteration 2 Error: 0.134159 Iteration 3 Error: 0.034799 Align patch 22 3 left Iteration 1 Error: 0.581803 Iteration 2 Error: 0.121824 Iteration 3 Error: 0.026970 Align patch 23 2 left Iteration 1 Error: 0.685583 Iteration 2 Error: 0.084908 Iteration 3 Error: 0.018130 Align patch 24 1 left Iteration 1 Error: 0.869112 Iteration 2 Error: 0.155023 Iteration 3 Error: 0.058433 Iteration 4 Error: 0.012178 Align patch 25 0 left Iteration 1 Error: 0.736012 Iteration 2 Error: 0.135602 Iteration 3 Error: 0.035205 3D Fitting completed. Patch alignment time: 19.12(sec) Local motion has been corrected. Process thread exits. Computational time: 32.322075 sec Total time: 41.999699 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00010hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00010hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.753294s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00010hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.137980s ........................................ >>>>>>TIME<<<<<< FFT: 1.483920s Defocus_U Defocus_V Angle CCC 28097.74 27289.04 84.05 0.039051 Final Values Defocus_U Defocus_V Angle CCC 28080.54 27293.74 84.05 0.062909 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00011hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00011hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.355e-01 1.007e-01 CC threshold: 0.740 Mean Std: 12.08 9.90 Num Hot pixels: 425 Hot pixel threshold: 71.48 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.471466 Iteration 2 Error: 0.328040 Iteration 3 Error: 0.040562 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.03 -0.20 ...... Frame ( 3) shift: -0.05 -0.41 ...... Frame ( 4) shift: -0.08 -0.61 ...... Frame ( 5) shift: -0.11 -0.82 ...... Frame ( 6) shift: -0.05 -0.90 ...... Frame ( 7) shift: 0.08 -0.85 ...... Frame ( 8) shift: 0.22 -0.80 ...... Frame ( 9) shift: 0.35 -0.69 ...... Frame ( 10) shift: 0.49 -0.51 ...... Frame ( 11) shift: 0.63 -0.34 ...... Frame ( 12) shift: 0.74 -0.17 ...... Frame ( 13) shift: 0.83 -0.00 ...... Frame ( 14) shift: 0.92 0.17 ...... Frame ( 15) shift: 1.03 0.32 ...... Frame ( 16) shift: 1.17 0.45 ...... Frame ( 17) shift: 1.30 0.58 ...... Frame ( 18) shift: 1.42 0.68 ...... Frame ( 19) shift: 1.51 0.75 ...... Frame ( 20) shift: 1.61 0.82 ...... Frame ( 21) shift: 1.70 0.91 ...... Frame ( 22) shift: 1.77 1.01 ...... Frame ( 23) shift: 1.83 1.11 ...... Frame ( 24) shift: 1.94 1.22 ...... Frame ( 25) shift: 2.09 1.35 ...... Frame ( 26) shift: 2.23 1.48 ...... Frame ( 27) shift: 2.37 1.59 ...... Frame ( 28) shift: 2.50 1.66 ...... Frame ( 29) shift: 2.63 1.74 ...... Frame ( 30) shift: 2.72 1.81 ...... Frame ( 31) shift: 2.77 1.87 ...... Frame ( 32) shift: 2.82 1.93 ...... Frame ( 33) shift: 2.85 2.01 ...... Frame ( 34) shift: 2.87 2.11 ...... Frame ( 35) shift: 2.90 2.21 ...... Frame ( 36) shift: 2.95 2.31 ...... Frame ( 37) shift: 3.03 2.40 ...... Frame ( 38) shift: 3.12 2.50 ...... Frame ( 39) shift: 3.20 2.59 ...... Frame ( 40) shift: 3.28 2.68 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.467239 Iteration 2 Error: 0.185254 Iteration 3 Error: 0.027194 Align patch 2 23 left Iteration 1 Error: 1.922092 Iteration 2 Error: 0.167078 Iteration 3 Error: 0.041502 Align patch 3 22 left Iteration 1 Error: 0.535644 Iteration 2 Error: 0.175095 Iteration 3 Error: 0.054173 Iteration 4 Error: 0.020316 Align patch 4 21 left Iteration 1 Error: 0.323017 Iteration 2 Error: 0.116221 Iteration 3 Error: 0.041454 Align patch 5 20 left Iteration 1 Error: 0.377455 Iteration 2 Error: 0.129606 Iteration 3 Error: 0.035762 Align patch 6 19 left Iteration 1 Error: 1.511739 Iteration 2 Error: 0.048053 Align patch 7 18 left Iteration 1 Error: 0.811210 Iteration 2 Error: 0.148065 Iteration 3 Error: 0.026095 Align patch 8 17 left Iteration 1 Error: 1.600627 Iteration 2 Error: 0.193088 Iteration 3 Error: 0.017418 Align patch 9 16 left Iteration 1 Error: 0.465267 Iteration 2 Error: 0.167711 Iteration 3 Error: 0.043594 Align patch 10 15 left Iteration 1 Error: 0.548908 Iteration 2 Error: 0.163134 Iteration 3 Error: 0.040190 Align patch 11 14 left Iteration 1 Error: 1.741258 Iteration 2 Error: 0.140440 Iteration 3 Error: 0.021563 Align patch 12 13 left Iteration 1 Error: 1.465142 Iteration 2 Error: 0.080677 Iteration 3 Error: 0.005529 Align patch 13 12 left Iteration 1 Error: 1.425275 Iteration 2 Error: 0.066963 Iteration 3 Error: 0.004870 Align patch 14 11 left Iteration 1 Error: 0.995538 Iteration 2 Error: 0.125223 Iteration 3 Error: 0.023113 Align patch 15 10 left Iteration 1 Error: 1.402541 Iteration 2 Error: 0.320050 Iteration 3 Error: 0.070894 Iteration 4 Error: 0.019008 Align patch 16 9 left Iteration 1 Error: 2.215957 Iteration 2 Error: 0.207516 Iteration 3 Error: 0.009577 Align patch 17 8 left Iteration 1 Error: 1.481414 Iteration 2 Error: 0.180981 Iteration 3 Error: 0.041310 Align patch 18 7 left Iteration 1 Error: 1.508255 Iteration 2 Error: 0.076756 Iteration 3 Error: 0.003460 Align patch 19 6 left Iteration 1 Error: 1.792393 Iteration 2 Error: 0.103418 Iteration 3 Error: 0.011385 Align patch 20 5 left Iteration 1 Error: 0.452104 Iteration 2 Error: 0.035365 Align patch 21 4 left Iteration 1 Error: 1.247576 Iteration 2 Error: 0.114524 Iteration 3 Error: 0.009357 Align patch 22 3 left Iteration 1 Error: 1.886732 Iteration 2 Error: 0.160289 Iteration 3 Error: 0.021520 Align patch 23 2 left Iteration 1 Error: 1.753921 Iteration 2 Error: 0.071506 Iteration 3 Error: 0.012252 Align patch 24 1 left Iteration 1 Error: 0.739190 Iteration 2 Error: 0.123310 Iteration 3 Error: 0.025545 Align patch 25 0 left Iteration 1 Error: 1.018894 Iteration 2 Error: 0.118134 Iteration 3 Error: 0.020906 3D Fitting completed. Patch alignment time: 18.74(sec) Local motion has been corrected. Process thread exits. Computational time: 30.394787 sec Total time: 46.054966 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00011hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00011hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.599144s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00011hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.308516s ........................................ >>>>>>TIME<<<<<< FFT: 1.232342s Defocus_U Defocus_V Angle CCC 22738.23 23586.00 10.57 0.004959 Final Values Defocus_U Defocus_V Angle CCC 22716.34 23614.15 10.88 0.028492 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00011hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00011hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.359e-01 1.010e-01 CC threshold: 0.742 Mean Std: 10.37 8.50 Num Hot pixels: 5222 Hot pixel threshold: 61.36 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.266937 Iteration 2 Error: 0.209763 Iteration 3 Error: 0.013890 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.00 -0.16 ...... Frame ( 3) shift: 0.01 -0.33 ...... Frame ( 4) shift: 0.01 -0.49 ...... Frame ( 5) shift: 0.02 -0.66 ...... Frame ( 6) shift: 0.04 -0.72 ...... Frame ( 7) shift: 0.08 -0.69 ...... Frame ( 8) shift: 0.13 -0.65 ...... Frame ( 9) shift: 0.18 -0.58 ...... Frame ( 10) shift: 0.24 -0.46 ...... Frame ( 11) shift: 0.30 -0.34 ...... Frame ( 12) shift: 0.39 -0.19 ...... Frame ( 13) shift: 0.52 -0.02 ...... Frame ( 14) shift: 0.65 0.14 ...... Frame ( 15) shift: 0.78 0.37 ...... Frame ( 16) shift: 0.92 0.65 ...... Frame ( 17) shift: 1.05 0.93 ...... Frame ( 18) shift: 1.16 1.13 ...... Frame ( 19) shift: 1.24 1.24 ...... Frame ( 20) shift: 1.31 1.36 ...... Frame ( 21) shift: 1.37 1.43 ...... Frame ( 22) shift: 1.40 1.47 ...... Frame ( 23) shift: 1.43 1.50 ...... Frame ( 24) shift: 1.50 1.56 ...... Frame ( 25) shift: 1.60 1.63 ...... Frame ( 26) shift: 1.70 1.70 ...... Frame ( 27) shift: 1.77 1.76 ...... Frame ( 28) shift: 1.83 1.83 ...... Frame ( 29) shift: 1.88 1.89 ...... Frame ( 30) shift: 1.96 1.95 ...... Frame ( 31) shift: 2.08 2.00 ...... Frame ( 32) shift: 2.19 2.06 ...... Frame ( 33) shift: 2.28 2.11 ...... Frame ( 34) shift: 2.35 2.15 ...... Frame ( 35) shift: 2.42 2.20 ...... Frame ( 36) shift: 2.47 2.27 ...... Frame ( 37) shift: 2.50 2.36 ...... Frame ( 38) shift: 2.54 2.46 ...... Frame ( 39) shift: 2.57 2.55 ...... Frame ( 40) shift: 2.61 2.64 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.958507 Iteration 2 Error: 0.058741 Iteration 3 Error: 0.005412 Align patch 2 23 left Iteration 1 Error: 0.782139 Iteration 2 Error: 0.092095 Iteration 3 Error: 0.014199 Align patch 3 22 left Iteration 1 Error: 0.440475 Iteration 2 Error: 0.073823 Iteration 3 Error: 0.013681 Align patch 4 21 left Iteration 1 Error: 0.320249 Iteration 2 Error: 0.074391 Iteration 3 Error: 0.025051 Align patch 5 20 left Iteration 1 Error: 0.560152 Iteration 2 Error: 0.156505 Iteration 3 Error: 0.040110 Align patch 6 19 left Iteration 1 Error: 1.677780 Iteration 2 Error: 0.089343 Iteration 3 Error: 0.005247 Align patch 7 18 left Iteration 1 Error: 0.926706 Iteration 2 Error: 0.068139 Iteration 3 Error: 0.005323 Align patch 8 17 left Iteration 1 Error: 0.555736 Iteration 2 Error: 0.091168 Iteration 3 Error: 0.008162 Align patch 9 16 left Iteration 1 Error: 0.880574 Iteration 2 Error: 0.205166 Iteration 3 Error: 0.059447 Iteration 4 Error: 0.013547 Align patch 10 15 left Iteration 1 Error: 0.504893 Iteration 2 Error: 0.149022 Iteration 3 Error: 0.045699 Align patch 11 14 left Iteration 1 Error: 1.784940 Iteration 2 Error: 0.111260 Iteration 3 Error: 0.005926 Align patch 12 13 left Iteration 1 Error: 1.988923 Iteration 2 Error: 0.126424 Iteration 3 Error: 0.005045 Align patch 13 12 left Iteration 1 Error: 1.083754 Iteration 2 Error: 0.083014 Iteration 3 Error: 0.006076 Align patch 14 11 left Iteration 1 Error: 1.613934 Iteration 2 Error: 0.310134 Iteration 3 Error: 0.075415 Iteration 4 Error: 0.020126 Align patch 15 10 left Iteration 1 Error: 0.729291 Iteration 2 Error: 0.141770 Iteration 3 Error: 0.029528 Align patch 16 9 left Iteration 1 Error: 1.410713 Iteration 2 Error: 0.068907 Iteration 3 Error: 0.007323 Align patch 17 8 left Iteration 1 Error: 1.122156 Iteration 2 Error: 0.116578 Iteration 3 Error: 0.011829 Align patch 18 7 left Iteration 1 Error: 1.075787 Iteration 2 Error: 0.074833 Iteration 3 Error: 0.006227 Align patch 19 6 left Iteration 1 Error: 0.977686 Iteration 2 Error: 0.063908 Iteration 3 Error: 0.004058 Align patch 20 5 left Iteration 1 Error: 1.102574 Iteration 2 Error: 0.079575 Iteration 3 Error: 0.007961 Align patch 21 4 left Iteration 1 Error: 1.017549 Iteration 2 Error: 0.087079 Iteration 3 Error: 0.009652 Align patch 22 3 left Iteration 1 Error: 1.708601 Iteration 2 Error: 0.099372 Iteration 3 Error: 0.012360 Align patch 23 2 left Iteration 1 Error: 1.361672 Iteration 2 Error: 0.095916 Iteration 3 Error: 0.011461 Align patch 24 1 left Iteration 1 Error: 1.516782 Iteration 2 Error: 0.116989 Iteration 3 Error: 0.012908 Align patch 25 0 left Iteration 1 Error: 0.906455 Iteration 2 Error: 0.087121 Iteration 3 Error: 0.014825 3D Fitting completed. Patch alignment time: 19.56(sec) Local motion has been corrected. Process thread exits. Computational time: 31.408081 sec Total time: 41.213650 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00011hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00011hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.577997s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00011hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.827347s ........................................ >>>>>>TIME<<<<<< FFT: 1.201409s Defocus_U Defocus_V Angle CCC 24722.65 25531.26 10.35 -0.005548 Final Values Defocus_U Defocus_V Angle CCC 24683.61 25517.23 10.66 0.010821 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00011hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00011hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.357e-01 1.008e-01 CC threshold: 0.741 Mean Std: 11.57 10.41 Num Hot pixels: 267 Hot pixel threshold: 74.03 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.361094 Iteration 2 Error: 0.332009 Iteration 3 Error: 0.081833 Iteration 4 Error: 0.025761 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.01 -0.19 ...... Frame ( 3) shift: -0.01 -0.38 ...... Frame ( 4) shift: -0.02 -0.58 ...... Frame ( 5) shift: -0.03 -0.77 ...... Frame ( 6) shift: 0.03 -0.84 ...... Frame ( 7) shift: 0.16 -0.78 ...... Frame ( 8) shift: 0.29 -0.73 ...... Frame ( 9) shift: 0.46 -0.63 ...... Frame ( 10) shift: 0.67 -0.50 ...... Frame ( 11) shift: 0.87 -0.37 ...... Frame ( 12) shift: 1.04 -0.25 ...... Frame ( 13) shift: 1.16 -0.14 ...... Frame ( 14) shift: 1.29 -0.03 ...... Frame ( 15) shift: 1.40 0.11 ...... Frame ( 16) shift: 1.51 0.26 ...... Frame ( 17) shift: 1.62 0.41 ...... Frame ( 18) shift: 1.72 0.54 ...... Frame ( 19) shift: 1.81 0.64 ...... Frame ( 20) shift: 1.90 0.74 ...... Frame ( 21) shift: 1.98 0.82 ...... Frame ( 22) shift: 2.07 0.89 ...... Frame ( 23) shift: 2.16 0.96 ...... Frame ( 24) shift: 2.26 1.02 ...... Frame ( 25) shift: 2.37 1.06 ...... Frame ( 26) shift: 2.48 1.11 ...... Frame ( 27) shift: 2.55 1.17 ...... Frame ( 28) shift: 2.58 1.24 ...... Frame ( 29) shift: 2.61 1.32 ...... Frame ( 30) shift: 2.66 1.37 ...... Frame ( 31) shift: 2.71 1.41 ...... Frame ( 32) shift: 2.76 1.45 ...... Frame ( 33) shift: 2.78 1.47 ...... Frame ( 34) shift: 2.77 1.49 ...... Frame ( 35) shift: 2.76 1.50 ...... Frame ( 36) shift: 2.79 1.50 ...... Frame ( 37) shift: 2.85 1.49 ...... Frame ( 38) shift: 2.91 1.48 ...... Frame ( 39) shift: 2.97 1.47 ...... Frame ( 40) shift: 3.03 1.46 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.247817 Iteration 2 Error: 0.137185 Iteration 3 Error: 0.011463 Align patch 2 23 left Iteration 1 Error: 0.901836 Iteration 2 Error: 0.122951 Iteration 3 Error: 0.017079 Align patch 3 22 left Iteration 1 Error: 0.556488 Iteration 2 Error: 0.125953 Iteration 3 Error: 0.024620 Align patch 4 21 left Iteration 1 Error: 0.417348 Iteration 2 Error: 0.147753 Iteration 3 Error: 0.052021 Iteration 4 Error: 0.019419 Align patch 5 20 left Iteration 1 Error: 0.520479 Iteration 2 Error: 0.098942 Iteration 3 Error: 0.028314 Align patch 6 19 left Iteration 1 Error: 1.594714 Iteration 2 Error: 0.221082 Iteration 3 Error: 0.032992 Align patch 7 18 left Iteration 1 Error: 1.286061 Iteration 2 Error: 0.175168 Iteration 3 Error: 0.023742 Align patch 8 17 left Iteration 1 Error: 1.178823 Iteration 2 Error: 0.107520 Iteration 3 Error: 0.014007 Align patch 9 16 left Iteration 1 Error: 0.391318 Iteration 2 Error: 0.107381 Iteration 3 Error: 0.028997 Align patch 10 15 left Iteration 1 Error: 0.660908 Iteration 2 Error: 0.178126 Iteration 3 Error: 0.055548 Iteration 4 Error: 0.015570 Align patch 11 14 left Iteration 1 Error: 1.834121 Iteration 2 Error: 0.129325 Iteration 3 Error: 0.005685 Align patch 12 13 left Iteration 1 Error: 1.269900 Iteration 2 Error: 0.098474 Iteration 3 Error: 0.007155 Align patch 13 12 left Iteration 1 Error: 1.582260 Iteration 2 Error: 0.133554 Iteration 3 Error: 0.027013 Align patch 14 11 left Iteration 1 Error: 7.615975 Iteration 2 Error: 1.317272 Iteration 3 Error: 0.507876 Iteration 4 Error: 0.230745 Iteration 5 Error: 0.126391 Align patch 14 11 left Iteration 1 Error: 4.494380 Iteration 2 Error: 0.369106 Iteration 3 Error: 0.074508 Iteration 4 Error: 0.019779 Align patch 15 10 left Iteration 1 Error: 0.651026 Iteration 2 Error: 0.150049 Iteration 3 Error: 0.063732 Iteration 4 Error: 0.015367 Align patch 16 9 left Iteration 1 Error: 2.119694 Iteration 2 Error: 0.069206 Iteration 3 Error: 0.004929 Align patch 17 8 left Iteration 1 Error: 3.365718 Iteration 2 Error: 0.345389 Iteration 3 Error: 0.131322 Iteration 4 Error: 0.037222 Align patch 18 7 left Iteration 1 Error: 1.918345 Iteration 2 Error: 0.138597 Iteration 3 Error: 0.012615 Align patch 19 6 left Iteration 1 Error: 2.352757 Iteration 2 Error: 0.149275 Iteration 3 Error: 0.019314 Align patch 20 5 left Iteration 1 Error: 2.371688 Iteration 2 Error: 0.232564 Iteration 3 Error: 0.048163 Align patch 21 4 left Iteration 1 Error: 2.828351 Iteration 2 Error: 0.100739 Iteration 3 Error: 0.011265 Align patch 22 3 left Iteration 1 Error: 42.038082 Iteration 2 Error: 36.176758 Iteration 3 Error: 34.990814 Iteration 4 Error: 30.902447 Iteration 5 Error: 19.414545 Align patch 22 3 left Iteration 1 Error: 4.697376 Iteration 2 Error: 0.129330 Iteration 3 Error: 0.020066 Align patch 23 2 left Iteration 1 Error: 1.951446 Iteration 2 Error: 0.096368 Iteration 3 Error: 0.008727 Align patch 24 1 left Iteration 1 Error: 2.018851 Iteration 2 Error: 0.165451 Iteration 3 Error: 0.041057 Align patch 25 0 left Iteration 1 Error: 1.744210 Iteration 2 Error: 0.205886 Iteration 3 Error: 0.058399 Iteration 4 Error: 0.022943 3D Fitting completed. Patch alignment time: 21.85(sec) Local motion has been corrected. Process thread exits. Computational time: 34.798962 sec Total time: 42.976074 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00011hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00011hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.657020s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00011hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 4.226842s ........................................ >>>>>>TIME<<<<<< FFT: 1.302950s Defocus_U Defocus_V Angle CCC 23753.96 24285.21 3.94 -0.002961 Final Values Defocus_U Defocus_V Angle CCC 23764.91 24293.04 5.51 0.011324 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00011hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00011hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.362e-01 1.012e-01 CC threshold: 0.743 Mean Std: 11.02 9.53 Num Hot pixels: 901 Hot pixel threshold: 68.18 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.758074 Iteration 2 Error: 0.214043 Iteration 3 Error: 0.026986 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.05 -0.21 ...... Frame ( 3) shift: -0.10 -0.42 ...... Frame ( 4) shift: -0.16 -0.63 ...... Frame ( 5) shift: -0.21 -0.84 ...... Frame ( 6) shift: -0.19 -0.91 ...... Frame ( 7) shift: -0.12 -0.85 ...... Frame ( 8) shift: -0.04 -0.79 ...... Frame ( 9) shift: 0.05 -0.72 ...... Frame ( 10) shift: 0.16 -0.66 ...... Frame ( 11) shift: 0.26 -0.59 ...... Frame ( 12) shift: 0.37 -0.50 ...... Frame ( 13) shift: 0.48 -0.40 ...... Frame ( 14) shift: 0.59 -0.29 ...... Frame ( 15) shift: 0.66 -0.20 ...... Frame ( 16) shift: 0.67 -0.12 ...... Frame ( 17) shift: 0.68 -0.04 ...... Frame ( 18) shift: 0.73 0.03 ...... Frame ( 19) shift: 0.81 0.10 ...... Frame ( 20) shift: 0.90 0.18 ...... Frame ( 21) shift: 0.98 0.23 ...... Frame ( 22) shift: 1.06 0.28 ...... Frame ( 23) shift: 1.14 0.33 ...... Frame ( 24) shift: 1.24 0.38 ...... Frame ( 25) shift: 1.34 0.43 ...... Frame ( 26) shift: 1.45 0.48 ...... Frame ( 27) shift: 1.51 0.53 ...... Frame ( 28) shift: 1.54 0.59 ...... Frame ( 29) shift: 1.57 0.65 ...... Frame ( 30) shift: 1.60 0.70 ...... Frame ( 31) shift: 1.63 0.77 ...... Frame ( 32) shift: 1.67 0.83 ...... Frame ( 33) shift: 1.67 0.86 ...... Frame ( 34) shift: 1.64 0.88 ...... Frame ( 35) shift: 1.61 0.89 ...... Frame ( 36) shift: 1.61 0.92 ...... Frame ( 37) shift: 1.64 0.95 ...... Frame ( 38) shift: 1.66 0.98 ...... Frame ( 39) shift: 1.69 1.01 ...... Frame ( 40) shift: 1.72 1.04 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.523761 Iteration 2 Error: 0.083425 Iteration 3 Error: 0.007486 Align patch 2 23 left Iteration 1 Error: 1.595170 Iteration 2 Error: 0.197302 Iteration 3 Error: 0.029905 Align patch 3 22 left Iteration 1 Error: 0.505902 Iteration 2 Error: 0.093751 Iteration 3 Error: 0.021452 Align patch 4 21 left Iteration 1 Error: 0.242417 Iteration 2 Error: 0.042760 Align patch 5 20 left Iteration 1 Error: 0.525558 Iteration 2 Error: 0.166790 Iteration 3 Error: 0.054441 Iteration 4 Error: 0.017657 Align patch 6 19 left Iteration 1 Error: 1.374161 Iteration 2 Error: 0.107247 Iteration 3 Error: 0.012860 Align patch 7 18 left Iteration 1 Error: 0.946364 Iteration 2 Error: 0.132601 Iteration 3 Error: 0.016460 Align patch 8 17 left Iteration 1 Error: 1.988470 Iteration 2 Error: 0.388304 Iteration 3 Error: 0.089702 Iteration 4 Error: 0.019335 Align patch 9 16 left Iteration 1 Error: 0.240147 Iteration 2 Error: 0.052088 Iteration 3 Error: 0.011827 Align patch 10 15 left Iteration 1 Error: 0.574514 Iteration 2 Error: 0.141268 Iteration 3 Error: 0.034815 Align patch 11 14 left Iteration 1 Error: 1.827513 Iteration 2 Error: 0.094747 Iteration 3 Error: 0.009937 Align patch 12 13 left Iteration 1 Error: 1.035315 Iteration 2 Error: 0.163132 Iteration 3 Error: 0.020198 Align patch 13 12 left Iteration 1 Error: 0.991617 Iteration 2 Error: 0.105097 Iteration 3 Error: 0.014734 Align patch 14 11 left Iteration 1 Error: 1.305584 Iteration 2 Error: 0.229493 Iteration 3 Error: 0.051765 Iteration 4 Error: 0.012842 Align patch 15 10 left Iteration 1 Error: 0.799007 Iteration 2 Error: 0.120239 Iteration 3 Error: 0.022038 Align patch 16 9 left Iteration 1 Error: 1.146979 Iteration 2 Error: 0.078676 Iteration 3 Error: 0.006890 Align patch 17 8 left Iteration 1 Error: 0.910756 Iteration 2 Error: 0.068275 Iteration 3 Error: 0.005878 Align patch 18 7 left Iteration 1 Error: 1.338487 Iteration 2 Error: 0.043301 Align patch 19 6 left Iteration 1 Error: 1.340608 Iteration 2 Error: 0.064959 Iteration 3 Error: 0.006237 Align patch 20 5 left Iteration 1 Error: 1.659033 Iteration 2 Error: 0.068126 Iteration 3 Error: 0.004570 Align patch 21 4 left Iteration 1 Error: 1.331099 Iteration 2 Error: 0.076901 Iteration 3 Error: 0.004218 Align patch 22 3 left Iteration 1 Error: 1.340091 Iteration 2 Error: 0.087254 Iteration 3 Error: 0.004530 Align patch 23 2 left Iteration 1 Error: 1.311850 Iteration 2 Error: 0.100189 Iteration 3 Error: 0.015315 Align patch 24 1 left Iteration 1 Error: 1.611361 Iteration 2 Error: 0.108475 Iteration 3 Error: 0.011376 Align patch 25 0 left Iteration 1 Error: 2.723907 Iteration 2 Error: 0.100506 Iteration 3 Error: 0.006409 3D Fitting completed. Patch alignment time: 18.50(sec) Local motion has been corrected. Process thread exits. Computational time: 32.286777 sec Total time: 41.342072 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00011hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00011hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.599091s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00011hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 4.096509s ........................................ >>>>>>TIME<<<<<< FFT: 1.341715s Defocus_U Defocus_V Angle CCC 25273.44 24519.53 89.52 -0.009919 Final Values Defocus_U Defocus_V Angle CCC 25275.01 24521.09 89.52 0.005148 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00012hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00012hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.993e-02 CC threshold: 0.734 Mean Std: 41.93 6.90 Num Hot pixels: 223 Hot pixel threshold: 83.31 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.368167 Iteration 2 Error: 0.351499 Iteration 3 Error: 0.064888 Iteration 4 Error: 0.025211 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.07 -0.04 ...... Frame ( 3) shift: 0.14 -0.07 ...... Frame ( 4) shift: 0.21 -0.11 ...... Frame ( 5) shift: 0.28 -0.14 ...... Frame ( 6) shift: 0.36 -0.13 ...... Frame ( 7) shift: 0.44 -0.06 ...... Frame ( 8) shift: 0.53 0.01 ...... Frame ( 9) shift: 0.59 0.09 ...... Frame ( 10) shift: 0.63 0.18 ...... Frame ( 11) shift: 0.66 0.27 ...... Frame ( 12) shift: 0.74 0.38 ...... Frame ( 13) shift: 0.85 0.50 ...... Frame ( 14) shift: 0.96 0.61 ...... Frame ( 15) shift: 1.01 0.75 ...... Frame ( 16) shift: 0.98 0.89 ...... Frame ( 17) shift: 0.96 1.04 ...... Frame ( 18) shift: 0.96 1.18 ...... Frame ( 19) shift: 0.99 1.31 ...... Frame ( 20) shift: 1.02 1.45 ...... Frame ( 21) shift: 1.05 1.50 ...... Frame ( 22) shift: 1.09 1.48 ...... Frame ( 23) shift: 1.13 1.46 ...... Frame ( 24) shift: 1.21 1.49 ...... Frame ( 25) shift: 1.31 1.59 ...... Frame ( 26) shift: 1.41 1.68 ...... Frame ( 27) shift: 1.45 1.77 ...... Frame ( 28) shift: 1.41 1.85 ...... Frame ( 29) shift: 1.37 1.94 ...... Frame ( 30) shift: 1.42 2.03 ...... Frame ( 31) shift: 1.55 2.13 ...... Frame ( 32) shift: 1.68 2.24 ...... Frame ( 33) shift: 1.76 2.30 ...... Frame ( 34) shift: 1.77 2.34 ...... Frame ( 35) shift: 1.78 2.37 ...... Frame ( 36) shift: 1.80 2.41 ...... Frame ( 37) shift: 1.82 2.46 ...... Frame ( 38) shift: 1.85 2.50 ...... Frame ( 39) shift: 1.87 2.55 ...... Frame ( 40) shift: 1.89 2.59 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.870652 Iteration 2 Error: 0.219686 Iteration 3 Error: 0.053895 Iteration 4 Error: 0.023294 Align patch 2 23 left Iteration 1 Error: 1.276441 Iteration 2 Error: 0.170803 Iteration 3 Error: 0.042429 Align patch 3 22 left Iteration 1 Error: 0.951199 Iteration 2 Error: 0.169444 Iteration 3 Error: 0.036464 Align patch 4 21 left Iteration 1 Error: 0.645541 Iteration 2 Error: 0.252215 Iteration 3 Error: 0.106363 Iteration 4 Error: 0.046503 Align patch 5 20 left Iteration 1 Error: 0.617733 Iteration 2 Error: 0.124634 Iteration 3 Error: 0.031732 Align patch 6 19 left Iteration 1 Error: 0.786472 Iteration 2 Error: 0.257169 Iteration 3 Error: 0.104080 Iteration 4 Error: 0.037638 Align patch 7 18 left Iteration 1 Error: 0.852734 Iteration 2 Error: 0.150138 Iteration 3 Error: 0.067506 Iteration 4 Error: 0.021407 Align patch 8 17 left Iteration 1 Error: 0.973116 Iteration 2 Error: 0.168567 Iteration 3 Error: 0.048332 Align patch 9 16 left Iteration 1 Error: 0.844727 Iteration 2 Error: 0.124504 Iteration 3 Error: 0.053287 Iteration 4 Error: 0.021188 Align patch 10 15 left Iteration 1 Error: 0.878631 Iteration 2 Error: 0.110571 Iteration 3 Error: 0.036548 Align patch 11 14 left Iteration 1 Error: 0.758479 Iteration 2 Error: 0.211511 Iteration 3 Error: 0.114544 Iteration 4 Error: 0.044436 Align patch 12 13 left Iteration 1 Error: 0.641292 Iteration 2 Error: 0.096409 Iteration 3 Error: 0.027092 Align patch 13 12 left Iteration 1 Error: 0.701527 Iteration 2 Error: 0.325519 Iteration 3 Error: 0.162959 Iteration 4 Error: 0.071528 Iteration 5 Error: 0.046372 Align patch 14 11 left Iteration 1 Error: 0.831570 Iteration 2 Error: 0.123272 Iteration 3 Error: 0.028271 Align patch 15 10 left Iteration 1 Error: 1.143849 Iteration 2 Error: 0.157165 Iteration 3 Error: 0.045265 Align patch 16 9 left Iteration 1 Error: 0.991281 Iteration 2 Error: 0.179427 Iteration 3 Error: 0.045295 Align patch 17 8 left Iteration 1 Error: 1.110846 Iteration 2 Error: 0.199407 Iteration 3 Error: 0.061944 Iteration 4 Error: 0.025115 Align patch 18 7 left Iteration 1 Error: 0.828359 Iteration 2 Error: 0.193438 Iteration 3 Error: 0.056799 Iteration 4 Error: 0.021743 Align patch 19 6 left Iteration 1 Error: 0.727973 Iteration 2 Error: 0.122676 Iteration 3 Error: 0.033460 Align patch 20 5 left Iteration 1 Error: 1.162309 Iteration 2 Error: 0.173353 Iteration 3 Error: 0.034430 Align patch 21 4 left Iteration 1 Error: 1.043968 Iteration 2 Error: 0.177129 Iteration 3 Error: 0.031558 Align patch 22 3 left Iteration 1 Error: 0.939881 Iteration 2 Error: 0.141963 Iteration 3 Error: 0.024518 Align patch 23 2 left Iteration 1 Error: 0.591211 Iteration 2 Error: 0.126691 Iteration 3 Error: 0.039830 Align patch 24 1 left Iteration 1 Error: 0.910371 Iteration 2 Error: 0.146223 Iteration 3 Error: 0.038774 Align patch 25 0 left Iteration 1 Error: 1.261912 Iteration 2 Error: 0.167322 Iteration 3 Error: 0.035832 3D Fitting completed. Patch alignment time: 17.38(sec) Local motion has been corrected. Process thread exits. Computational time: 29.798405 sec Total time: 39.079639 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00012hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00012hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.679899s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00012hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.196651s ........................................ >>>>>>TIME<<<<<< FFT: 1.276777s Defocus_U Defocus_V Angle CCC 26611.33 27345.70 10.16 0.042629 Final Values Defocus_U Defocus_V Angle CCC 26586.32 27364.46 12.03 0.065134 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00012hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00012hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.992e-02 CC threshold: 0.734 Mean Std: 41.43 6.87 Num Hot pixels: 182 Hot pixel threshold: 82.67 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.472854 Iteration 2 Error: 0.302764 Iteration 3 Error: 0.078788 Iteration 4 Error: 0.021702 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.08 0.02 ...... Frame ( 3) shift: 0.15 0.04 ...... Frame ( 4) shift: 0.23 0.06 ...... Frame ( 5) shift: 0.31 0.08 ...... Frame ( 6) shift: 0.38 0.14 ...... Frame ( 7) shift: 0.44 0.23 ...... Frame ( 8) shift: 0.51 0.33 ...... Frame ( 9) shift: 0.59 0.41 ...... Frame ( 10) shift: 0.71 0.47 ...... Frame ( 11) shift: 0.82 0.54 ...... Frame ( 12) shift: 0.85 0.63 ...... Frame ( 13) shift: 0.79 0.75 ...... Frame ( 14) shift: 0.73 0.87 ...... Frame ( 15) shift: 0.73 0.97 ...... Frame ( 16) shift: 0.78 1.05 ...... Frame ( 17) shift: 0.84 1.14 ...... Frame ( 18) shift: 0.90 1.22 ...... Frame ( 19) shift: 0.97 1.29 ...... Frame ( 20) shift: 1.03 1.36 ...... Frame ( 21) shift: 1.15 1.41 ...... Frame ( 22) shift: 1.31 1.45 ...... Frame ( 23) shift: 1.47 1.49 ...... Frame ( 24) shift: 1.55 1.56 ...... Frame ( 25) shift: 1.57 1.65 ...... Frame ( 26) shift: 1.58 1.74 ...... Frame ( 27) shift: 1.61 1.82 ...... Frame ( 28) shift: 1.66 1.88 ...... Frame ( 29) shift: 1.72 1.95 ...... Frame ( 30) shift: 1.76 2.00 ...... Frame ( 31) shift: 1.79 2.03 ...... Frame ( 32) shift: 1.83 2.07 ...... Frame ( 33) shift: 1.87 2.10 ...... Frame ( 34) shift: 1.91 2.11 ...... Frame ( 35) shift: 1.96 2.13 ...... Frame ( 36) shift: 2.01 2.17 ...... Frame ( 37) shift: 2.07 2.21 ...... Frame ( 38) shift: 2.12 2.26 ...... Frame ( 39) shift: 2.18 2.31 ...... Frame ( 40) shift: 2.23 2.35 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.841871 Iteration 2 Error: 0.267624 Iteration 3 Error: 0.047002 Align patch 2 23 left Iteration 1 Error: 0.747943 Iteration 2 Error: 0.118963 Iteration 3 Error: 0.032174 Align patch 3 22 left Iteration 1 Error: 1.111320 Iteration 2 Error: 0.173622 Iteration 3 Error: 0.053940 Iteration 4 Error: 0.025444 Align patch 4 21 left Iteration 1 Error: 0.966491 Iteration 2 Error: 0.143421 Iteration 3 Error: 0.037495 Align patch 5 20 left Iteration 1 Error: 0.502326 Iteration 2 Error: 0.094018 Iteration 3 Error: 0.023482 Align patch 6 19 left Iteration 1 Error: 0.901679 Iteration 2 Error: 0.138872 Iteration 3 Error: 0.037068 Align patch 7 18 left Iteration 1 Error: 0.682814 Iteration 2 Error: 0.221550 Iteration 3 Error: 0.043264 Align patch 8 17 left Iteration 1 Error: 0.555840 Iteration 2 Error: 0.127753 Iteration 3 Error: 0.032912 Align patch 9 16 left Iteration 1 Error: 0.672737 Iteration 2 Error: 0.177689 Iteration 3 Error: 0.068121 Iteration 4 Error: 0.015105 Align patch 10 15 left Iteration 1 Error: 1.108495 Iteration 2 Error: 0.120729 Iteration 3 Error: 0.041385 Align patch 11 14 left Iteration 1 Error: 0.897843 Iteration 2 Error: 0.149657 Iteration 3 Error: 0.024347 Align patch 12 13 left Iteration 1 Error: 0.929493 Iteration 2 Error: 0.157368 Iteration 3 Error: 0.025370 Align patch 13 12 left Iteration 1 Error: 0.668234 Iteration 2 Error: 0.117272 Iteration 3 Error: 0.044477 Align patch 14 11 left Iteration 1 Error: 0.572619 Iteration 2 Error: 0.112735 Iteration 3 Error: 0.023435 Align patch 15 10 left Iteration 1 Error: 0.956131 Iteration 2 Error: 0.194008 Iteration 3 Error: 0.043021 Align patch 16 9 left Iteration 1 Error: 0.690517 Iteration 2 Error: 0.138340 Iteration 3 Error: 0.040071 Align patch 17 8 left Iteration 1 Error: 0.615994 Iteration 2 Error: 0.160693 Iteration 3 Error: 0.034391 Align patch 18 7 left Iteration 1 Error: 0.977459 Iteration 2 Error: 0.133476 Iteration 3 Error: 0.035471 Align patch 19 6 left Iteration 1 Error: 0.763536 Iteration 2 Error: 0.120639 Iteration 3 Error: 0.032522 Align patch 20 5 left Iteration 1 Error: 0.799490 Iteration 2 Error: 0.104208 Iteration 3 Error: 0.033019 Align patch 21 4 left Iteration 1 Error: 0.715455 Iteration 2 Error: 0.111873 Iteration 3 Error: 0.026084 Align patch 22 3 left Iteration 1 Error: 0.849300 Iteration 2 Error: 0.132477 Iteration 3 Error: 0.026972 Align patch 23 2 left Iteration 1 Error: 0.615912 Iteration 2 Error: 0.138209 Iteration 3 Error: 0.033164 Align patch 24 1 left Iteration 1 Error: 1.221337 Iteration 2 Error: 0.165894 Iteration 3 Error: 0.038542 Align patch 25 0 left Iteration 1 Error: 1.034977 Iteration 2 Error: 0.113853 Iteration 3 Error: 0.029440 3D Fitting completed. Patch alignment time: 16.11(sec) Local motion has been corrected. Process thread exits. Computational time: 30.522062 sec Total time: 38.764744 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00012hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00012hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.569969s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00012hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.402803s ........................................ >>>>>>TIME<<<<<< FFT: 1.533895s Defocus_U Defocus_V Angle CCC 25101.57 26003.91 2.80 0.043846 Final Values Defocus_U Defocus_V Angle CCC 25090.63 25992.97 2.80 0.067446 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00012hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00012hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.997e-02 CC threshold: 0.734 Mean Std: 41.82 6.90 Num Hot pixels: 207 Hot pixel threshold: 83.21 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.340495 Iteration 2 Error: 0.214277 Iteration 3 Error: 0.039235 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.05 -0.06 ...... Frame ( 3) shift: 0.10 -0.12 ...... Frame ( 4) shift: 0.14 -0.18 ...... Frame ( 5) shift: 0.19 -0.24 ...... Frame ( 6) shift: 0.23 -0.23 ...... Frame ( 7) shift: 0.24 -0.14 ...... Frame ( 8) shift: 0.26 -0.05 ...... Frame ( 9) shift: 0.28 0.06 ...... Frame ( 10) shift: 0.29 0.20 ...... Frame ( 11) shift: 0.30 0.34 ...... Frame ( 12) shift: 0.28 0.45 ...... Frame ( 13) shift: 0.22 0.54 ...... Frame ( 14) shift: 0.16 0.62 ...... Frame ( 15) shift: 0.16 0.75 ...... Frame ( 16) shift: 0.20 0.92 ...... Frame ( 17) shift: 0.24 1.09 ...... Frame ( 18) shift: 0.25 1.22 ...... Frame ( 19) shift: 0.24 1.30 ...... Frame ( 20) shift: 0.24 1.38 ...... Frame ( 21) shift: 0.24 1.47 ...... Frame ( 22) shift: 0.27 1.56 ...... Frame ( 23) shift: 0.30 1.65 ...... Frame ( 24) shift: 0.33 1.70 ...... Frame ( 25) shift: 0.35 1.73 ...... Frame ( 26) shift: 0.38 1.76 ...... Frame ( 27) shift: 0.40 1.78 ...... Frame ( 28) shift: 0.40 1.81 ...... Frame ( 29) shift: 0.40 1.83 ...... Frame ( 30) shift: 0.41 1.87 ...... Frame ( 31) shift: 0.43 1.93 ...... Frame ( 32) shift: 0.46 1.99 ...... Frame ( 33) shift: 0.49 2.05 ...... Frame ( 34) shift: 0.52 2.12 ...... Frame ( 35) shift: 0.56 2.19 ...... Frame ( 36) shift: 0.59 2.26 ...... Frame ( 37) shift: 0.62 2.36 ...... Frame ( 38) shift: 0.65 2.45 ...... Frame ( 39) shift: 0.68 2.54 ...... Frame ( 40) shift: 0.71 2.63 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.833900 Iteration 2 Error: 0.126041 Iteration 3 Error: 0.027417 Align patch 2 23 left Iteration 1 Error: 0.958816 Iteration 2 Error: 0.190999 Iteration 3 Error: 0.048266 Align patch 3 22 left Iteration 1 Error: 1.001785 Iteration 2 Error: 0.134350 Iteration 3 Error: 0.025829 Align patch 4 21 left Iteration 1 Error: 0.855683 Iteration 2 Error: 0.090696 Iteration 3 Error: 0.016290 Align patch 5 20 left Iteration 1 Error: 0.856818 Iteration 2 Error: 0.071519 Iteration 3 Error: 0.018273 Align patch 6 19 left Iteration 1 Error: 1.328960 Iteration 2 Error: 0.167399 Iteration 3 Error: 0.052961 Iteration 4 Error: 0.023861 Align patch 7 18 left Iteration 1 Error: 0.959557 Iteration 2 Error: 0.194902 Iteration 3 Error: 0.047695 Align patch 8 17 left Iteration 1 Error: 0.660014 Iteration 2 Error: 0.168195 Iteration 3 Error: 0.039799 Align patch 9 16 left Iteration 1 Error: 0.478539 Iteration 2 Error: 0.084310 Iteration 3 Error: 0.021992 Align patch 10 15 left Iteration 1 Error: 0.748563 Iteration 2 Error: 0.087694 Iteration 3 Error: 0.016242 Align patch 11 14 left Iteration 1 Error: 0.692189 Iteration 2 Error: 0.167586 Iteration 3 Error: 0.031641 Align patch 12 13 left Iteration 1 Error: 0.737270 Iteration 2 Error: 0.122616 Iteration 3 Error: 0.025978 Align patch 13 12 left Iteration 1 Error: 0.629375 Iteration 2 Error: 0.115895 Iteration 3 Error: 0.044734 Align patch 14 11 left Iteration 1 Error: 0.808624 Iteration 2 Error: 0.153267 Iteration 3 Error: 0.040700 Align patch 15 10 left Iteration 1 Error: 0.398541 Iteration 2 Error: 0.081151 Iteration 3 Error: 0.018269 Align patch 16 9 left Iteration 1 Error: 0.630035 Iteration 2 Error: 0.088846 Iteration 3 Error: 0.030177 Align patch 17 8 left Iteration 1 Error: 0.636917 Iteration 2 Error: 0.130019 Iteration 3 Error: 0.036631 Align patch 18 7 left Iteration 1 Error: 0.675067 Iteration 2 Error: 0.082475 Iteration 3 Error: 0.025283 Align patch 19 6 left Iteration 1 Error: 0.764747 Iteration 2 Error: 0.088581 Iteration 3 Error: 0.020396 Align patch 20 5 left Iteration 1 Error: 0.608711 Iteration 2 Error: 0.116392 Iteration 3 Error: 0.025526 Align patch 21 4 left Iteration 1 Error: 0.560887 Iteration 2 Error: 0.109794 Iteration 3 Error: 0.017934 Align patch 22 3 left Iteration 1 Error: 0.951133 Iteration 2 Error: 0.118947 Iteration 3 Error: 0.021008 Align patch 23 2 left Iteration 1 Error: 0.714577 Iteration 2 Error: 0.100663 Iteration 3 Error: 0.027028 Align patch 24 1 left Iteration 1 Error: 0.584167 Iteration 2 Error: 0.102627 Iteration 3 Error: 0.029870 Align patch 25 0 left Iteration 1 Error: 0.966042 Iteration 2 Error: 0.230409 Iteration 3 Error: 0.074667 Iteration 4 Error: 0.022196 3D Fitting completed. Patch alignment time: 18.47(sec) Local motion has been corrected. Process thread exits. Computational time: 33.159428 sec Total time: 41.022697 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00012hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00012hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.154185s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00012hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.613576s ........................................ >>>>>>TIME<<<<<< FFT: 1.280439s Defocus_U Defocus_V Angle CCC 25416.02 24771.49 84.75 0.042464 Final Values Defocus_U Defocus_V Angle CCC 25412.90 24774.62 85.38 0.067529 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00012hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00012hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.989e-02 CC threshold: 0.734 Mean Std: 41.67 6.88 Num Hot pixels: 197 Hot pixel threshold: 82.95 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.445387 Iteration 2 Error: 0.150220 Iteration 3 Error: 0.030600 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.09 0.16 ...... Frame ( 3) shift: 0.18 0.32 ...... Frame ( 4) shift: 0.26 0.49 ...... Frame ( 5) shift: 0.35 0.65 ...... Frame ( 6) shift: 0.39 0.77 ...... Frame ( 7) shift: 0.37 0.86 ...... Frame ( 8) shift: 0.35 0.95 ...... Frame ( 9) shift: 0.33 1.03 ...... Frame ( 10) shift: 0.30 1.10 ...... Frame ( 11) shift: 0.28 1.17 ...... Frame ( 12) shift: 0.30 1.27 ...... Frame ( 13) shift: 0.36 1.38 ...... Frame ( 14) shift: 0.42 1.49 ...... Frame ( 15) shift: 0.46 1.60 ...... Frame ( 16) shift: 0.47 1.73 ...... Frame ( 17) shift: 0.47 1.85 ...... Frame ( 18) shift: 0.46 1.93 ...... Frame ( 19) shift: 0.42 1.97 ...... Frame ( 20) shift: 0.38 2.01 ...... Frame ( 21) shift: 0.39 2.07 ...... Frame ( 22) shift: 0.46 2.14 ...... Frame ( 23) shift: 0.52 2.20 ...... Frame ( 24) shift: 0.55 2.23 ...... Frame ( 25) shift: 0.54 2.23 ...... Frame ( 26) shift: 0.53 2.22 ...... Frame ( 27) shift: 0.53 2.22 ...... Frame ( 28) shift: 0.55 2.23 ...... Frame ( 29) shift: 0.56 2.24 ...... Frame ( 30) shift: 0.56 2.25 ...... Frame ( 31) shift: 0.53 2.25 ...... Frame ( 32) shift: 0.51 2.25 ...... Frame ( 33) shift: 0.52 2.23 ...... Frame ( 34) shift: 0.56 2.21 ...... Frame ( 35) shift: 0.60 2.18 ...... Frame ( 36) shift: 0.63 2.20 ...... Frame ( 37) shift: 0.64 2.28 ...... Frame ( 38) shift: 0.66 2.36 ...... Frame ( 39) shift: 0.67 2.44 ...... Frame ( 40) shift: 0.69 2.52 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.073685 Iteration 2 Error: 0.238423 Iteration 3 Error: 0.044791 Align patch 2 23 left Iteration 1 Error: 0.575389 Iteration 2 Error: 0.098502 Iteration 3 Error: 0.020718 Align patch 3 22 left Iteration 1 Error: 0.952120 Iteration 2 Error: 0.079614 Iteration 3 Error: 0.021378 Align patch 4 21 left Iteration 1 Error: 0.712083 Iteration 2 Error: 0.137882 Iteration 3 Error: 0.035864 Align patch 5 20 left Iteration 1 Error: 0.746815 Iteration 2 Error: 0.117877 Iteration 3 Error: 0.050559 Iteration 4 Error: 0.023160 Align patch 6 19 left Iteration 1 Error: 1.455556 Iteration 2 Error: 0.180496 Iteration 3 Error: 0.036025 Align patch 7 18 left Iteration 1 Error: 1.247412 Iteration 2 Error: 0.121315 Iteration 3 Error: 0.035280 Align patch 8 17 left Iteration 1 Error: 1.080772 Iteration 2 Error: 0.142667 Iteration 3 Error: 0.061313 Iteration 4 Error: 0.014143 Align patch 9 16 left Iteration 1 Error: 1.113870 Iteration 2 Error: 0.102951 Iteration 3 Error: 0.022696 Align patch 10 15 left Iteration 1 Error: 0.493015 Iteration 2 Error: 0.096874 Iteration 3 Error: 0.025354 Align patch 11 14 left Iteration 1 Error: 0.863630 Iteration 2 Error: 0.135599 Iteration 3 Error: 0.033368 Align patch 12 13 left Iteration 1 Error: 0.547076 Iteration 2 Error: 0.064215 Iteration 3 Error: 0.014863 Align patch 13 12 left Iteration 1 Error: 0.819040 Iteration 2 Error: 0.151982 Iteration 3 Error: 0.032337 Align patch 14 11 left Iteration 1 Error: 0.669606 Iteration 2 Error: 0.093620 Iteration 3 Error: 0.029868 Align patch 15 10 left Iteration 1 Error: 0.805385 Iteration 2 Error: 0.236771 Iteration 3 Error: 0.054918 Iteration 4 Error: 0.021528 Align patch 16 9 left Iteration 1 Error: 0.849248 Iteration 2 Error: 0.124296 Iteration 3 Error: 0.029245 Align patch 17 8 left Iteration 1 Error: 0.668706 Iteration 2 Error: 0.134016 Iteration 3 Error: 0.033754 Align patch 18 7 left Iteration 1 Error: 0.686316 Iteration 2 Error: 0.146878 Iteration 3 Error: 0.031734 Align patch 19 6 left Iteration 1 Error: 0.874189 Iteration 2 Error: 0.147964 Iteration 3 Error: 0.033806 Align patch 20 5 left Iteration 1 Error: 0.849469 Iteration 2 Error: 0.116767 Iteration 3 Error: 0.035011 Align patch 21 4 left Iteration 1 Error: 0.857808 Iteration 2 Error: 0.120859 Iteration 3 Error: 0.023809 Align patch 22 3 left Iteration 1 Error: 1.382882 Iteration 2 Error: 0.131703 Iteration 3 Error: 0.031743 Align patch 23 2 left Iteration 1 Error: 1.077277 Iteration 2 Error: 0.105584 Iteration 3 Error: 0.029784 Align patch 24 1 left Iteration 1 Error: 1.262831 Iteration 2 Error: 0.203262 Iteration 3 Error: 0.031544 Align patch 25 0 left Iteration 1 Error: 0.982161 Iteration 2 Error: 0.132413 Iteration 3 Error: 0.044239 3D Fitting completed. Patch alignment time: 14.57(sec) Local motion has been corrected. Process thread exits. Computational time: 30.196653 sec Total time: 39.628544 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00012hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00012hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.445494s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00012hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.783227s ........................................ >>>>>>TIME<<<<<< FFT: 1.436896s Defocus_U Defocus_V Angle CCC 29117.23 28316.41 84.64 0.036185 Final Values Defocus_U Defocus_V Angle CCC 29146.92 28302.35 85.58 0.058450 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00013hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00013hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.992e-02 CC threshold: 0.734 Mean Std: 42.57 6.94 Num Hot pixels: 202 Hot pixel threshold: 84.24 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.283025 Iteration 2 Error: 0.620939 Iteration 3 Error: 0.141666 Iteration 4 Error: 0.055777 Iteration 5 Error: 0.018937 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.08 -0.06 ...... Frame ( 3) shift: -0.15 -0.12 ...... Frame ( 4) shift: -0.23 -0.18 ...... Frame ( 5) shift: -0.31 -0.24 ...... Frame ( 6) shift: -0.30 -0.24 ...... Frame ( 7) shift: -0.19 -0.17 ...... Frame ( 8) shift: -0.09 -0.11 ...... Frame ( 9) shift: 0.05 -0.02 ...... Frame ( 10) shift: 0.24 0.08 ...... Frame ( 11) shift: 0.42 0.18 ...... Frame ( 12) shift: 0.64 0.36 ...... Frame ( 13) shift: 0.87 0.61 ...... Frame ( 14) shift: 1.11 0.86 ...... Frame ( 15) shift: 1.32 1.02 ...... Frame ( 16) shift: 1.50 1.09 ...... Frame ( 17) shift: 1.69 1.15 ...... Frame ( 18) shift: 1.86 1.24 ...... Frame ( 19) shift: 2.01 1.36 ...... Frame ( 20) shift: 2.15 1.47 ...... Frame ( 21) shift: 2.28 1.52 ...... Frame ( 22) shift: 2.40 1.50 ...... Frame ( 23) shift: 2.51 1.48 ...... Frame ( 24) shift: 2.64 1.52 ...... Frame ( 25) shift: 2.78 1.61 ...... Frame ( 26) shift: 2.93 1.70 ...... Frame ( 27) shift: 3.04 1.77 ...... Frame ( 28) shift: 3.10 1.83 ...... Frame ( 29) shift: 3.16 1.88 ...... Frame ( 30) shift: 3.25 1.96 ...... Frame ( 31) shift: 3.37 2.06 ...... Frame ( 32) shift: 3.48 2.17 ...... Frame ( 33) shift: 3.54 2.24 ...... Frame ( 34) shift: 3.54 2.28 ...... Frame ( 35) shift: 3.54 2.33 ...... Frame ( 36) shift: 3.61 2.40 ...... Frame ( 37) shift: 3.74 2.50 ...... Frame ( 38) shift: 3.87 2.60 ...... Frame ( 39) shift: 4.01 2.71 ...... Frame ( 40) shift: 4.14 2.81 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.284486 Iteration 2 Error: 0.161976 Iteration 3 Error: 0.048154 Align patch 2 23 left Iteration 1 Error: 1.380063 Iteration 2 Error: 0.214594 Iteration 3 Error: 0.044696 Align patch 3 22 left Iteration 1 Error: 1.268103 Iteration 2 Error: 0.198650 Iteration 3 Error: 0.071579 Iteration 4 Error: 0.025409 Align patch 4 21 left Iteration 1 Error: 0.905774 Iteration 2 Error: 0.228282 Iteration 3 Error: 0.069994 Iteration 4 Error: 0.037063 Align patch 5 20 left Iteration 1 Error: 0.751610 Iteration 2 Error: 0.202025 Iteration 3 Error: 0.088456 Iteration 4 Error: 0.033576 Align patch 6 19 left Iteration 1 Error: 0.828008 Iteration 2 Error: 0.179716 Iteration 3 Error: 0.055456 Iteration 4 Error: 0.023169 Align patch 7 18 left Iteration 1 Error: 1.145758 Iteration 2 Error: 0.210683 Iteration 3 Error: 0.080032 Iteration 4 Error: 0.027833 Align patch 8 17 left Iteration 1 Error: 0.834194 Iteration 2 Error: 0.165575 Iteration 3 Error: 0.038638 Align patch 9 16 left Iteration 1 Error: 1.234246 Iteration 2 Error: 0.264716 Iteration 3 Error: 0.073607 Iteration 4 Error: 0.031771 Align patch 10 15 left Iteration 1 Error: 0.927965 Iteration 2 Error: 0.170471 Iteration 3 Error: 0.056610 Iteration 4 Error: 0.017657 Align patch 11 14 left Iteration 1 Error: 0.970470 Iteration 2 Error: 0.123480 Iteration 3 Error: 0.060661 Iteration 4 Error: 0.015957 Align patch 12 13 left Iteration 1 Error: 0.932322 Iteration 2 Error: 0.092477 Iteration 3 Error: 0.019424 Align patch 13 12 left Iteration 1 Error: 0.688199 Iteration 2 Error: 0.161219 Iteration 3 Error: 0.058059 Iteration 4 Error: 0.023458 Align patch 14 11 left Iteration 1 Error: 0.769222 Iteration 2 Error: 0.143938 Iteration 3 Error: 0.034289 Align patch 15 10 left Iteration 1 Error: 0.979468 Iteration 2 Error: 0.195465 Iteration 3 Error: 0.060822 Iteration 4 Error: 0.021028 Align patch 16 9 left Iteration 1 Error: 0.844254 Iteration 2 Error: 0.112627 Iteration 3 Error: 0.035644 Align patch 17 8 left Iteration 1 Error: 1.428993 Iteration 2 Error: 0.347194 Iteration 3 Error: 0.143697 Iteration 4 Error: 0.063939 Iteration 5 Error: 0.024745 Align patch 18 7 left Iteration 1 Error: 1.468404 Iteration 2 Error: 0.267704 Iteration 3 Error: 0.037343 Align patch 19 6 left Iteration 1 Error: 0.633730 Iteration 2 Error: 0.158058 Iteration 3 Error: 0.040996 Align patch 20 5 left Iteration 1 Error: 1.107206 Iteration 2 Error: 0.154530 Iteration 3 Error: 0.047557 Align patch 21 4 left Iteration 1 Error: 1.031512 Iteration 2 Error: 0.154550 Iteration 3 Error: 0.078696 Iteration 4 Error: 0.031131 Align patch 22 3 left Iteration 1 Error: 0.874175 Iteration 2 Error: 0.193059 Iteration 3 Error: 0.094091 Iteration 4 Error: 0.029705 Align patch 23 2 left Iteration 1 Error: 0.632613 Iteration 2 Error: 0.132074 Iteration 3 Error: 0.046006 Align patch 24 1 left Iteration 1 Error: 0.935332 Iteration 2 Error: 0.230761 Iteration 3 Error: 0.044541 Align patch 25 0 left Iteration 1 Error: 1.058567 Iteration 2 Error: 0.191402 Iteration 3 Error: 0.046241 3D Fitting completed. Patch alignment time: 21.82(sec) Local motion has been corrected. Process thread exits. Computational time: 39.049484 sec Total time: 47.339352 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00013hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00013hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.603496s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00013hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 4.867104s ........................................ >>>>>>TIME<<<<<< FFT: 1.631480s Defocus_U Defocus_V Angle CCC 25378.91 26117.19 6.81 0.045251 Final Values Defocus_U Defocus_V Angle CCC 25394.52 26114.08 8.07 0.072917 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00013hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00013hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.993e-02 CC threshold: 0.734 Mean Std: 42.38 6.95 Num Hot pixels: 195 Hot pixel threshold: 84.07 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.546922 Iteration 2 Error: 0.454334 Iteration 3 Error: 0.199297 Iteration 4 Error: 0.060754 Iteration 5 Error: 0.023697 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.02 -0.15 ...... Frame ( 3) shift: -0.03 -0.30 ...... Frame ( 4) shift: -0.05 -0.45 ...... Frame ( 5) shift: -0.06 -0.60 ...... Frame ( 6) shift: 0.04 -0.61 ...... Frame ( 7) shift: 0.25 -0.50 ...... Frame ( 8) shift: 0.46 -0.39 ...... Frame ( 9) shift: 0.68 -0.21 ...... Frame ( 10) shift: 0.90 0.04 ...... Frame ( 11) shift: 1.13 0.28 ...... Frame ( 12) shift: 1.33 0.48 ...... Frame ( 13) shift: 1.51 0.62 ...... Frame ( 14) shift: 1.68 0.76 ...... Frame ( 15) shift: 1.84 0.91 ...... Frame ( 16) shift: 1.98 1.09 ...... Frame ( 17) shift: 2.11 1.26 ...... Frame ( 18) shift: 2.23 1.41 ...... Frame ( 19) shift: 2.32 1.52 ...... Frame ( 20) shift: 2.40 1.64 ...... Frame ( 21) shift: 2.57 1.74 ...... Frame ( 22) shift: 2.80 1.84 ...... Frame ( 23) shift: 3.04 1.93 ...... Frame ( 24) shift: 3.18 1.97 ...... Frame ( 25) shift: 3.23 1.95 ...... Frame ( 26) shift: 3.28 1.92 ...... Frame ( 27) shift: 3.37 1.95 ...... Frame ( 28) shift: 3.48 2.02 ...... Frame ( 29) shift: 3.60 2.09 ...... Frame ( 30) shift: 3.72 2.14 ...... Frame ( 31) shift: 3.85 2.17 ...... Frame ( 32) shift: 3.98 2.20 ...... Frame ( 33) shift: 4.08 2.23 ...... Frame ( 34) shift: 4.15 2.26 ...... Frame ( 35) shift: 4.23 2.29 ...... Frame ( 36) shift: 4.34 2.32 ...... Frame ( 37) shift: 4.49 2.36 ...... Frame ( 38) shift: 4.65 2.39 ...... Frame ( 39) shift: 4.80 2.43 ...... Frame ( 40) shift: 4.96 2.46 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.573642 Iteration 2 Error: 0.217902 Iteration 3 Error: 0.049462 Align patch 2 23 left Iteration 1 Error: 1.881760 Iteration 2 Error: 0.232912 Iteration 3 Error: 0.034707 Align patch 3 22 left Iteration 1 Error: 0.686112 Iteration 2 Error: 0.123136 Iteration 3 Error: 0.047664 Align patch 4 21 left Iteration 1 Error: 0.741951 Iteration 2 Error: 0.143794 Iteration 3 Error: 0.045466 Align patch 5 20 left Iteration 1 Error: 1.177776 Iteration 2 Error: 0.180635 Iteration 3 Error: 0.050493 Iteration 4 Error: 0.016725 Align patch 6 19 left Iteration 1 Error: 1.090515 Iteration 2 Error: 0.261952 Iteration 3 Error: 0.087550 Iteration 4 Error: 0.031816 Align patch 7 18 left Iteration 1 Error: 1.713940 Iteration 2 Error: 0.314632 Iteration 3 Error: 0.091535 Iteration 4 Error: 0.042118 Align patch 8 17 left Iteration 1 Error: 0.622016 Iteration 2 Error: 0.115107 Iteration 3 Error: 0.070301 Iteration 4 Error: 0.025263 Align patch 9 16 left Iteration 1 Error: 0.922106 Iteration 2 Error: 0.189005 Iteration 3 Error: 0.068428 Iteration 4 Error: 0.027199 Align patch 10 15 left Iteration 1 Error: 0.846524 Iteration 2 Error: 0.179418 Iteration 3 Error: 0.080391 Iteration 4 Error: 0.034103 Align patch 11 14 left Iteration 1 Error: 1.148198 Iteration 2 Error: 0.140631 Iteration 3 Error: 0.040364 Align patch 12 13 left Iteration 1 Error: 0.994984 Iteration 2 Error: 0.212760 Iteration 3 Error: 0.075314 Iteration 4 Error: 0.029256 Align patch 13 12 left Iteration 1 Error: 0.967436 Iteration 2 Error: 0.244408 Iteration 3 Error: 0.069106 Iteration 4 Error: 0.055165 Iteration 5 Error: 0.026697 Align patch 14 11 left Iteration 1 Error: 1.086056 Iteration 2 Error: 0.159828 Iteration 3 Error: 0.073080 Iteration 4 Error: 0.017794 Align patch 15 10 left Iteration 1 Error: 0.655401 Iteration 2 Error: 0.178526 Iteration 3 Error: 0.044465 Align patch 16 9 left Iteration 1 Error: 0.941096 Iteration 2 Error: 0.225434 Iteration 3 Error: 0.097013 Iteration 4 Error: 0.030725 Align patch 17 8 left Iteration 1 Error: 0.818626 Iteration 2 Error: 0.154946 Iteration 3 Error: 0.063387 Iteration 4 Error: 0.018054 Align patch 18 7 left Iteration 1 Error: 0.833331 Iteration 2 Error: 0.183406 Iteration 3 Error: 0.043918 Align patch 19 6 left Iteration 1 Error: 0.597007 Iteration 2 Error: 0.114835 Iteration 3 Error: 0.020043 Align patch 20 5 left Iteration 1 Error: 1.633496 Iteration 2 Error: 0.215798 Iteration 3 Error: 0.060760 Iteration 4 Error: 0.026289 Align patch 21 4 left Iteration 1 Error: 1.051105 Iteration 2 Error: 0.188368 Iteration 3 Error: 0.058428 Iteration 4 Error: 0.021303 Align patch 22 3 left Iteration 1 Error: 0.714848 Iteration 2 Error: 0.251448 Iteration 3 Error: 0.042666 Align patch 23 2 left Iteration 1 Error: 1.069185 Iteration 2 Error: 0.170441 Iteration 3 Error: 0.065784 Iteration 4 Error: 0.023737 Align patch 24 1 left Iteration 1 Error: 0.706842 Iteration 2 Error: 0.143876 Iteration 3 Error: 0.037246 Align patch 25 0 left Iteration 1 Error: 0.984240 Iteration 2 Error: 0.156050 Iteration 3 Error: 0.026984 3D Fitting completed. Patch alignment time: 17.63(sec) Local motion has been corrected. Process thread exits. Computational time: 35.308163 sec Total time: 43.350147 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00013hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00013hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.856387s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00013hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.923445s ........................................ >>>>>>TIME<<<<<< FFT: 1.426064s Defocus_U Defocus_V Angle CCC 24125.01 24961.03 5.10 0.050443 Final Values Defocus_U Defocus_V Angle CCC 24107.82 24940.71 6.66 0.082100 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00013hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00013hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.989e-02 CC threshold: 0.734 Mean Std: 42.68 6.95 Num Hot pixels: 175 Hot pixel threshold: 84.38 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.577610 Iteration 2 Error: 0.217302 Iteration 3 Error: 0.039215 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.06 0.15 ...... Frame ( 3) shift: 0.12 0.30 ...... Frame ( 4) shift: 0.18 0.45 ...... Frame ( 5) shift: 0.24 0.59 ...... Frame ( 6) shift: 0.31 0.69 ...... Frame ( 7) shift: 0.38 0.74 ...... Frame ( 8) shift: 0.46 0.78 ...... Frame ( 9) shift: 0.56 0.85 ...... Frame ( 10) shift: 0.67 0.95 ...... Frame ( 11) shift: 0.77 1.05 ...... Frame ( 12) shift: 0.87 1.13 ...... Frame ( 13) shift: 0.94 1.18 ...... Frame ( 14) shift: 1.02 1.23 ...... Frame ( 15) shift: 1.10 1.30 ...... Frame ( 16) shift: 1.18 1.38 ...... Frame ( 17) shift: 1.25 1.46 ...... Frame ( 18) shift: 1.31 1.51 ...... Frame ( 19) shift: 1.34 1.52 ...... Frame ( 20) shift: 1.37 1.53 ...... Frame ( 21) shift: 1.41 1.54 ...... Frame ( 22) shift: 1.46 1.57 ...... Frame ( 23) shift: 1.52 1.60 ...... Frame ( 24) shift: 1.55 1.62 ...... Frame ( 25) shift: 1.57 1.65 ...... Frame ( 26) shift: 1.59 1.67 ...... Frame ( 27) shift: 1.65 1.67 ...... Frame ( 28) shift: 1.76 1.64 ...... Frame ( 29) shift: 1.87 1.61 ...... Frame ( 30) shift: 1.90 1.57 ...... Frame ( 31) shift: 1.84 1.51 ...... Frame ( 32) shift: 1.78 1.46 ...... Frame ( 33) shift: 1.82 1.44 ...... Frame ( 34) shift: 1.98 1.47 ...... Frame ( 35) shift: 2.14 1.50 ...... Frame ( 36) shift: 2.31 1.53 ...... Frame ( 37) shift: 2.48 1.55 ...... Frame ( 38) shift: 2.66 1.58 ...... Frame ( 39) shift: 2.83 1.60 ...... Frame ( 40) shift: 3.01 1.63 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.005904 Iteration 2 Error: 0.157359 Iteration 3 Error: 0.032387 Align patch 2 23 left Iteration 1 Error: 0.841731 Iteration 2 Error: 0.097909 Iteration 3 Error: 0.023024 Align patch 3 22 left Iteration 1 Error: 0.679862 Iteration 2 Error: 0.130176 Iteration 3 Error: 0.044568 Align patch 4 21 left Iteration 1 Error: 0.931868 Iteration 2 Error: 0.220761 Iteration 3 Error: 0.066940 Iteration 4 Error: 0.035625 Align patch 5 20 left Iteration 1 Error: 0.502171 Iteration 2 Error: 0.062109 Iteration 3 Error: 0.022350 Align patch 6 19 left Iteration 1 Error: 1.222860 Iteration 2 Error: 0.130939 Iteration 3 Error: 0.038579 Align patch 7 18 left Iteration 1 Error: 0.788372 Iteration 2 Error: 0.125677 Iteration 3 Error: 0.038934 Align patch 8 17 left Iteration 1 Error: 0.790507 Iteration 2 Error: 0.144581 Iteration 3 Error: 0.033197 Align patch 9 16 left Iteration 1 Error: 0.562522 Iteration 2 Error: 0.134756 Iteration 3 Error: 0.047113 Align patch 10 15 left Iteration 1 Error: 0.500704 Iteration 2 Error: 0.115043 Iteration 3 Error: 0.026743 Align patch 11 14 left Iteration 1 Error: 0.408082 Iteration 2 Error: 0.113494 Iteration 3 Error: 0.024050 Align patch 12 13 left Iteration 1 Error: 0.823717 Iteration 2 Error: 0.103064 Iteration 3 Error: 0.027281 Align patch 13 12 left Iteration 1 Error: 0.673036 Iteration 2 Error: 0.063121 Iteration 3 Error: 0.020035 Align patch 14 11 left Iteration 1 Error: 0.843159 Iteration 2 Error: 0.103093 Iteration 3 Error: 0.029612 Align patch 15 10 left Iteration 1 Error: 0.975685 Iteration 2 Error: 0.176586 Iteration 3 Error: 0.072613 Iteration 4 Error: 0.035095 Align patch 16 9 left Iteration 1 Error: 1.047420 Iteration 2 Error: 0.323669 Iteration 3 Error: 0.100255 Iteration 4 Error: 0.032824 Align patch 17 8 left Iteration 1 Error: 0.719576 Iteration 2 Error: 0.146044 Iteration 3 Error: 0.061941 Iteration 4 Error: 0.015920 Align patch 18 7 left Iteration 1 Error: 1.478826 Iteration 2 Error: 0.211045 Iteration 3 Error: 0.042108 Align patch 19 6 left Iteration 1 Error: 0.896768 Iteration 2 Error: 0.172695 Iteration 3 Error: 0.044570 Align patch 20 5 left Iteration 1 Error: 1.116645 Iteration 2 Error: 0.312100 Iteration 3 Error: 0.084864 Iteration 4 Error: 0.032003 Align patch 21 4 left Iteration 1 Error: 0.801789 Iteration 2 Error: 0.123908 Iteration 3 Error: 0.020702 Align patch 22 3 left Iteration 1 Error: 0.442112 Iteration 2 Error: 0.126619 Iteration 3 Error: 0.020587 Align patch 23 2 left Iteration 1 Error: 0.722992 Iteration 2 Error: 0.120078 Iteration 3 Error: 0.024430 Align patch 24 1 left Iteration 1 Error: 0.602484 Iteration 2 Error: 0.177596 Iteration 3 Error: 0.057006 Iteration 4 Error: 0.024973 Align patch 25 0 left Iteration 1 Error: 0.919834 Iteration 2 Error: 0.152935 Iteration 3 Error: 0.036543 3D Fitting completed. Patch alignment time: 19.44(sec) Local motion has been corrected. Process thread exits. Computational time: 35.641109 sec Total time: 43.326439 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00013hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00013hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.592547s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00013hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.894363s ........................................ >>>>>>TIME<<<<<< FFT: 1.457346s Defocus_U Defocus_V Angle CCC 22585.94 23187.52 0.85 0.039163 Final Values Defocus_U Defocus_V Angle CCC 22592.20 23196.90 1.16 0.066852 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00013hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00013hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.991e-02 CC threshold: 0.734 Mean Std: 42.39 6.94 Num Hot pixels: 177 Hot pixel threshold: 84.01 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.311686 Iteration 2 Error: 0.352421 Iteration 3 Error: 0.134008 Iteration 4 Error: 0.043009 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.10 0.03 ...... Frame ( 3) shift: 0.21 0.05 ...... Frame ( 4) shift: 0.31 0.08 ...... Frame ( 5) shift: 0.41 0.10 ...... Frame ( 6) shift: 0.51 0.15 ...... Frame ( 7) shift: 0.61 0.21 ...... Frame ( 8) shift: 0.71 0.27 ...... Frame ( 9) shift: 0.86 0.40 ...... Frame ( 10) shift: 1.08 0.61 ...... Frame ( 11) shift: 1.29 0.81 ...... Frame ( 12) shift: 1.49 0.93 ...... Frame ( 13) shift: 1.68 0.98 ...... Frame ( 14) shift: 1.86 1.03 ...... Frame ( 15) shift: 1.99 1.14 ...... Frame ( 16) shift: 2.07 1.31 ...... Frame ( 17) shift: 2.16 1.49 ...... Frame ( 18) shift: 2.30 1.65 ...... Frame ( 19) shift: 2.51 1.82 ...... Frame ( 20) shift: 2.71 1.99 ...... Frame ( 21) shift: 2.85 2.11 ...... Frame ( 22) shift: 2.93 2.20 ...... Frame ( 23) shift: 3.01 2.28 ...... Frame ( 24) shift: 3.05 2.35 ...... Frame ( 25) shift: 3.06 2.41 ...... Frame ( 26) shift: 3.07 2.47 ...... Frame ( 27) shift: 3.15 2.54 ...... Frame ( 28) shift: 3.30 2.62 ...... Frame ( 29) shift: 3.45 2.70 ...... Frame ( 30) shift: 3.49 2.71 ...... Frame ( 31) shift: 3.40 2.66 ...... Frame ( 32) shift: 3.32 2.60 ...... Frame ( 33) shift: 3.30 2.59 ...... Frame ( 34) shift: 3.35 2.62 ...... Frame ( 35) shift: 3.40 2.64 ...... Frame ( 36) shift: 3.43 2.69 ...... Frame ( 37) shift: 3.45 2.76 ...... Frame ( 38) shift: 3.46 2.82 ...... Frame ( 39) shift: 3.47 2.89 ...... Frame ( 40) shift: 3.48 2.96 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.298706 Iteration 2 Error: 0.233117 Iteration 3 Error: 0.066082 Iteration 4 Error: 0.018074 Align patch 2 23 left Iteration 1 Error: 0.762022 Iteration 2 Error: 0.109090 Iteration 3 Error: 0.026777 Align patch 3 22 left Iteration 1 Error: 1.378537 Iteration 2 Error: 0.244677 Iteration 3 Error: 0.058166 Iteration 4 Error: 0.020937 Align patch 4 21 left Iteration 1 Error: 0.975719 Iteration 2 Error: 0.283050 Iteration 3 Error: 0.150018 Iteration 4 Error: 0.050759 Iteration 5 Error: 0.042644 Align patch 5 20 left Iteration 1 Error: 1.257639 Iteration 2 Error: 0.171523 Iteration 3 Error: 0.044013 Align patch 6 19 left Iteration 1 Error: 0.767705 Iteration 2 Error: 0.122693 Iteration 3 Error: 0.030119 Align patch 7 18 left Iteration 1 Error: 1.052576 Iteration 2 Error: 0.234974 Iteration 3 Error: 0.050803 Iteration 4 Error: 0.017592 Align patch 8 17 left Iteration 1 Error: 0.903661 Iteration 2 Error: 0.162239 Iteration 3 Error: 0.042197 Align patch 9 16 left Iteration 1 Error: 0.888772 Iteration 2 Error: 0.219390 Iteration 3 Error: 0.087256 Iteration 4 Error: 0.037501 Align patch 10 15 left Iteration 1 Error: 0.986581 Iteration 2 Error: 0.256217 Iteration 3 Error: 0.090957 Iteration 4 Error: 0.037755 Align patch 11 14 left Iteration 1 Error: 0.683238 Iteration 2 Error: 0.113755 Iteration 3 Error: 0.025225 Align patch 12 13 left Iteration 1 Error: 1.023937 Iteration 2 Error: 0.165928 Iteration 3 Error: 0.064819 Iteration 4 Error: 0.018274 Align patch 13 12 left Iteration 1 Error: 0.783375 Iteration 2 Error: 0.178579 Iteration 3 Error: 0.066154 Iteration 4 Error: 0.021466 Align patch 14 11 left Iteration 1 Error: 1.209890 Iteration 2 Error: 0.191610 Iteration 3 Error: 0.055284 Iteration 4 Error: 0.019794 Align patch 15 10 left Iteration 1 Error: 1.147906 Iteration 2 Error: 0.183820 Iteration 3 Error: 0.054877 Iteration 4 Error: 0.015470 Align patch 16 9 left Iteration 1 Error: 0.817384 Iteration 2 Error: 0.116453 Iteration 3 Error: 0.058826 Iteration 4 Error: 0.024371 Align patch 17 8 left Iteration 1 Error: 0.738104 Iteration 2 Error: 0.302350 Iteration 3 Error: 0.133753 Iteration 4 Error: 0.067734 Iteration 5 Error: 0.037213 Align patch 18 7 left Iteration 1 Error: 0.776866 Iteration 2 Error: 0.153787 Iteration 3 Error: 0.052440 Iteration 4 Error: 0.020719 Align patch 19 6 left Iteration 1 Error: 0.854687 Iteration 2 Error: 0.251153 Iteration 3 Error: 0.078005 Iteration 4 Error: 0.029459 Align patch 20 5 left Iteration 1 Error: 0.639100 Iteration 2 Error: 0.207621 Iteration 3 Error: 0.041730 Align patch 21 4 left Iteration 1 Error: 0.843178 Iteration 2 Error: 0.134818 Iteration 3 Error: 0.030767 Align patch 22 3 left Iteration 1 Error: 1.477547 Iteration 2 Error: 0.338773 Iteration 3 Error: 0.101987 Iteration 4 Error: 0.053028 Iteration 5 Error: 0.017005 Align patch 23 2 left Iteration 1 Error: 0.573096 Iteration 2 Error: 0.089338 Iteration 3 Error: 0.030784 Align patch 24 1 left Iteration 1 Error: 0.760758 Iteration 2 Error: 0.138457 Iteration 3 Error: 0.056728 Iteration 4 Error: 0.024787 Align patch 25 0 left Iteration 1 Error: 0.916096 Iteration 2 Error: 0.244069 Iteration 3 Error: 0.071753 Iteration 4 Error: 0.030514 3D Fitting completed. Patch alignment time: 19.48(sec) Local motion has been corrected. Process thread exits. Computational time: 35.443428 sec Total time: 42.093666 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00013hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00013hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.132761s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00013hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.626355s ........................................ >>>>>>TIME<<<<<< FFT: 1.526978s Defocus_U Defocus_V Angle CCC 26209.40 25494.07 89.50 0.044962 Final Values Defocus_U Defocus_V Angle CCC 26237.53 25494.10 87.94 0.070734 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00014hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00014hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.991e-02 CC threshold: 0.734 Mean Std: 42.97 6.99 Num Hot pixels: 227 Hot pixel threshold: 84.90 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.628658 Iteration 2 Error: 0.400275 Iteration 3 Error: 0.111652 Iteration 4 Error: 0.039818 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.12 -0.21 ...... Frame ( 3) shift: 0.23 -0.42 ...... Frame ( 4) shift: 0.35 -0.62 ...... Frame ( 5) shift: 0.46 -0.83 ...... Frame ( 6) shift: 0.55 -0.89 ...... Frame ( 7) shift: 0.62 -0.80 ...... Frame ( 8) shift: 0.69 -0.71 ...... Frame ( 9) shift: 0.75 -0.62 ...... Frame ( 10) shift: 0.80 -0.53 ...... Frame ( 11) shift: 0.86 -0.45 ...... Frame ( 12) shift: 0.88 -0.32 ...... Frame ( 13) shift: 0.87 -0.15 ...... Frame ( 14) shift: 0.86 0.03 ...... Frame ( 15) shift: 0.96 0.20 ...... Frame ( 16) shift: 1.17 0.39 ...... Frame ( 17) shift: 1.38 0.57 ...... Frame ( 18) shift: 1.54 0.71 ...... Frame ( 19) shift: 1.65 0.82 ...... Frame ( 20) shift: 1.76 0.92 ...... Frame ( 21) shift: 1.86 1.03 ...... Frame ( 22) shift: 1.95 1.13 ...... Frame ( 23) shift: 2.04 1.23 ...... Frame ( 24) shift: 2.15 1.33 ...... Frame ( 25) shift: 2.29 1.44 ...... Frame ( 26) shift: 2.42 1.55 ...... Frame ( 27) shift: 2.51 1.63 ...... Frame ( 28) shift: 2.54 1.69 ...... Frame ( 29) shift: 2.58 1.74 ...... Frame ( 30) shift: 2.60 1.80 ...... Frame ( 31) shift: 2.62 1.87 ...... Frame ( 32) shift: 2.64 1.93 ...... Frame ( 33) shift: 2.65 2.01 ...... Frame ( 34) shift: 2.65 2.08 ...... Frame ( 35) shift: 2.65 2.16 ...... Frame ( 36) shift: 2.68 2.19 ...... Frame ( 37) shift: 2.73 2.18 ...... Frame ( 38) shift: 2.78 2.16 ...... Frame ( 39) shift: 2.83 2.14 ...... Frame ( 40) shift: 2.88 2.13 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.480344 Iteration 2 Error: 0.293285 Iteration 3 Error: 0.089324 Iteration 4 Error: 0.048585 Align patch 2 23 left Iteration 1 Error: 1.219914 Iteration 2 Error: 0.165633 Iteration 3 Error: 0.050121 Iteration 4 Error: 0.025853 Align patch 3 22 left Iteration 1 Error: 1.329830 Iteration 2 Error: 0.257367 Iteration 3 Error: 0.039883 Align patch 4 21 left Iteration 1 Error: 1.078384 Iteration 2 Error: 0.304857 Iteration 3 Error: 0.149613 Iteration 4 Error: 0.073729 Iteration 5 Error: 0.031796 Align patch 5 20 left Iteration 1 Error: 0.915060 Iteration 2 Error: 0.172986 Iteration 3 Error: 0.041696 Align patch 6 19 left Iteration 1 Error: 0.811036 Iteration 2 Error: 0.186072 Iteration 3 Error: 0.062684 Iteration 4 Error: 0.018699 Align patch 7 18 left Iteration 1 Error: 0.837930 Iteration 2 Error: 0.164564 Iteration 3 Error: 0.064001 Iteration 4 Error: 0.038634 Align patch 8 17 left Iteration 1 Error: 0.551345 Iteration 2 Error: 0.082788 Iteration 3 Error: 0.028879 Align patch 9 16 left Iteration 1 Error: 0.809619 Iteration 2 Error: 0.160977 Iteration 3 Error: 0.038110 Align patch 10 15 left Iteration 1 Error: 0.762646 Iteration 2 Error: 0.137461 Iteration 3 Error: 0.025056 Align patch 11 14 left Iteration 1 Error: 0.920526 Iteration 2 Error: 0.182076 Iteration 3 Error: 0.042178 Align patch 12 13 left Iteration 1 Error: 1.049543 Iteration 2 Error: 0.150143 Iteration 3 Error: 0.041098 Align patch 13 12 left Iteration 1 Error: 0.928027 Iteration 2 Error: 0.193499 Iteration 3 Error: 0.103039 Iteration 4 Error: 0.033172 Align patch 14 11 left Iteration 1 Error: 0.971578 Iteration 2 Error: 0.161479 Iteration 3 Error: 0.040323 Align patch 15 10 left Iteration 1 Error: 0.741766 Iteration 2 Error: 0.158700 Iteration 3 Error: 0.047795 Align patch 16 9 left Iteration 1 Error: 0.859906 Iteration 2 Error: 0.125834 Iteration 3 Error: 0.039744 Align patch 17 8 left Iteration 1 Error: 1.092314 Iteration 2 Error: 0.233632 Iteration 3 Error: 0.054410 Iteration 4 Error: 0.017914 Align patch 18 7 left Iteration 1 Error: 0.756956 Iteration 2 Error: 0.109693 Iteration 3 Error: 0.032625 Align patch 19 6 left Iteration 1 Error: 0.698590 Iteration 2 Error: 0.196145 Iteration 3 Error: 0.060579 Iteration 4 Error: 0.031408 Align patch 20 5 left Iteration 1 Error: 1.073817 Iteration 2 Error: 0.218762 Iteration 3 Error: 0.047012 Align patch 21 4 left Iteration 1 Error: 0.920241 Iteration 2 Error: 0.212084 Iteration 3 Error: 0.074249 Iteration 4 Error: 0.039520 Align patch 22 3 left Iteration 1 Error: 1.007372 Iteration 2 Error: 0.239867 Iteration 3 Error: 0.105365 Iteration 4 Error: 0.032438 Align patch 23 2 left Iteration 1 Error: 0.849800 Iteration 2 Error: 0.128868 Iteration 3 Error: 0.035210 Align patch 24 1 left Iteration 1 Error: 0.849692 Iteration 2 Error: 0.113240 Iteration 3 Error: 0.057732 Iteration 4 Error: 0.011923 Align patch 25 0 left Iteration 1 Error: 0.690458 Iteration 2 Error: 0.191033 Iteration 3 Error: 0.067965 Iteration 4 Error: 0.025631 3D Fitting completed. Patch alignment time: 18.66(sec) Local motion has been corrected. Process thread exits. Computational time: 34.473278 sec Total time: 42.615688 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00014hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00014hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.589232s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00014hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.302179s ........................................ >>>>>>TIME<<<<<< FFT: 1.210976s Defocus_U Defocus_V Angle CCC 22509.76 23357.44 6.22 0.044567 Final Values Defocus_U Defocus_V Angle CCC 22508.19 23352.76 6.85 0.075187 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00014hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00014hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.997e-02 CC threshold: 0.734 Mean Std: 42.78 6.97 Num Hot pixels: 201 Hot pixel threshold: 84.60 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.058482 Iteration 2 Error: 0.358946 Iteration 3 Error: 0.108042 Iteration 4 Error: 0.035664 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.18 -0.13 ...... Frame ( 3) shift: 0.37 -0.26 ...... Frame ( 4) shift: 0.55 -0.39 ...... Frame ( 5) shift: 0.74 -0.51 ...... Frame ( 6) shift: 0.87 -0.53 ...... Frame ( 7) shift: 0.95 -0.43 ...... Frame ( 8) shift: 1.03 -0.33 ...... Frame ( 9) shift: 1.09 -0.21 ...... Frame ( 10) shift: 1.13 -0.07 ...... Frame ( 11) shift: 1.16 0.08 ...... Frame ( 12) shift: 1.23 0.22 ...... Frame ( 13) shift: 1.32 0.36 ...... Frame ( 14) shift: 1.41 0.51 ...... Frame ( 15) shift: 1.49 0.65 ...... Frame ( 16) shift: 1.55 0.80 ...... Frame ( 17) shift: 1.61 0.95 ...... Frame ( 18) shift: 1.66 1.07 ...... Frame ( 19) shift: 1.70 1.16 ...... Frame ( 20) shift: 1.73 1.25 ...... Frame ( 21) shift: 1.79 1.33 ...... Frame ( 22) shift: 1.88 1.40 ...... Frame ( 23) shift: 1.97 1.47 ...... Frame ( 24) shift: 2.04 1.58 ...... Frame ( 25) shift: 2.11 1.71 ...... Frame ( 26) shift: 2.18 1.85 ...... Frame ( 27) shift: 2.24 1.99 ...... Frame ( 28) shift: 2.28 2.14 ...... Frame ( 29) shift: 2.31 2.29 ...... Frame ( 30) shift: 2.38 2.37 ...... Frame ( 31) shift: 2.48 2.38 ...... Frame ( 32) shift: 2.58 2.39 ...... Frame ( 33) shift: 2.67 2.42 ...... Frame ( 34) shift: 2.73 2.46 ...... Frame ( 35) shift: 2.80 2.50 ...... Frame ( 36) shift: 2.92 2.56 ...... Frame ( 37) shift: 3.10 2.63 ...... Frame ( 38) shift: 3.28 2.70 ...... Frame ( 39) shift: 3.45 2.78 ...... Frame ( 40) shift: 3.63 2.85 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.188760 Iteration 2 Error: 0.184298 Iteration 3 Error: 0.061264 Iteration 4 Error: 0.021628 Align patch 2 23 left Iteration 1 Error: 0.971883 Iteration 2 Error: 0.214940 Iteration 3 Error: 0.075187 Iteration 4 Error: 0.034109 Align patch 3 22 left Iteration 1 Error: 0.843048 Iteration 2 Error: 0.177945 Iteration 3 Error: 0.055001 Iteration 4 Error: 0.022274 Align patch 4 21 left Iteration 1 Error: 0.958178 Iteration 2 Error: 0.228866 Iteration 3 Error: 0.040518 Align patch 5 20 left Iteration 1 Error: 0.794762 Iteration 2 Error: 0.134760 Iteration 3 Error: 0.030184 Align patch 6 19 left Iteration 1 Error: 1.264715 Iteration 2 Error: 0.231928 Iteration 3 Error: 0.096473 Iteration 4 Error: 0.042648 Align patch 7 18 left Iteration 1 Error: 0.776912 Iteration 2 Error: 0.149653 Iteration 3 Error: 0.072129 Iteration 4 Error: 0.029011 Align patch 8 17 left Iteration 1 Error: 0.719519 Iteration 2 Error: 0.228461 Iteration 3 Error: 0.066406 Iteration 4 Error: 0.030815 Align patch 9 16 left Iteration 1 Error: 0.917206 Iteration 2 Error: 0.130632 Iteration 3 Error: 0.030303 Align patch 10 15 left Iteration 1 Error: 1.131805 Iteration 2 Error: 0.173117 Iteration 3 Error: 0.052387 Iteration 4 Error: 0.018700 Align patch 11 14 left Iteration 1 Error: 0.727202 Iteration 2 Error: 0.168361 Iteration 3 Error: 0.038930 Align patch 12 13 left Iteration 1 Error: 0.960541 Iteration 2 Error: 0.181636 Iteration 3 Error: 0.056394 Iteration 4 Error: 0.034346 Align patch 13 12 left Iteration 1 Error: 1.374988 Iteration 2 Error: 0.232077 Iteration 3 Error: 0.078760 Iteration 4 Error: 0.039772 Align patch 14 11 left Iteration 1 Error: 0.709271 Iteration 2 Error: 0.153129 Iteration 3 Error: 0.054665 Iteration 4 Error: 0.023736 Align patch 15 10 left Iteration 1 Error: 1.276458 Iteration 2 Error: 0.150856 Iteration 3 Error: 0.063228 Iteration 4 Error: 0.018633 Align patch 16 9 left Iteration 1 Error: 0.937863 Iteration 2 Error: 0.123112 Iteration 3 Error: 0.037769 Align patch 17 8 left Iteration 1 Error: 1.022770 Iteration 2 Error: 0.225925 Iteration 3 Error: 0.056681 Iteration 4 Error: 0.017576 Align patch 18 7 left Iteration 1 Error: 0.805386 Iteration 2 Error: 0.144680 Iteration 3 Error: 0.064526 Iteration 4 Error: 0.023913 Align patch 19 6 left Iteration 1 Error: 0.971044 Iteration 2 Error: 0.207955 Iteration 3 Error: 0.058625 Iteration 4 Error: 0.019815 Align patch 20 5 left Iteration 1 Error: 0.892390 Iteration 2 Error: 0.217382 Iteration 3 Error: 0.039235 Align patch 21 4 left Iteration 1 Error: 0.797573 Iteration 2 Error: 0.160780 Iteration 3 Error: 0.026415 Align patch 22 3 left Iteration 1 Error: 0.604899 Iteration 2 Error: 0.168891 Iteration 3 Error: 0.065189 Iteration 4 Error: 0.030386 Align patch 23 2 left Iteration 1 Error: 0.878408 Iteration 2 Error: 0.184547 Iteration 3 Error: 0.046407 Align patch 24 1 left Iteration 1 Error: 0.874035 Iteration 2 Error: 0.309676 Iteration 3 Error: 0.107777 Iteration 4 Error: 0.035117 Align patch 25 0 left Iteration 1 Error: 0.927363 Iteration 2 Error: 0.217804 Iteration 3 Error: 0.046096 3D Fitting completed. Patch alignment time: 18.94(sec) Local motion has been corrected. Process thread exits. Computational time: 31.248590 sec Total time: 39.463459 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00014hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00014hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.595941s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00014hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.828376s ........................................ >>>>>>TIME<<<<<< FFT: 1.448826s Defocus_U Defocus_V Angle CCC 25880.86 26869.14 7.32 0.050452 Final Values Defocus_U Defocus_V Angle CCC 25882.42 26867.58 7.32 0.081217 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00014hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00014hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.995e-02 CC threshold: 0.734 Mean Std: 43.32 7.02 Num Hot pixels: 195 Hot pixel threshold: 85.46 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.470781 Iteration 2 Error: 0.271174 Iteration 3 Error: 0.059530 Iteration 4 Error: 0.020116 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.06 -0.28 ...... Frame ( 3) shift: 0.12 -0.56 ...... Frame ( 4) shift: 0.18 -0.84 ...... Frame ( 5) shift: 0.24 -1.12 ...... Frame ( 6) shift: 0.29 -1.22 ...... Frame ( 7) shift: 0.33 -1.13 ...... Frame ( 8) shift: 0.37 -1.05 ...... Frame ( 9) shift: 0.40 -0.93 ...... Frame ( 10) shift: 0.43 -0.78 ...... Frame ( 11) shift: 0.46 -0.64 ...... Frame ( 12) shift: 0.49 -0.50 ...... Frame ( 13) shift: 0.52 -0.37 ...... Frame ( 14) shift: 0.56 -0.23 ...... Frame ( 15) shift: 0.58 -0.09 ...... Frame ( 16) shift: 0.59 0.06 ...... Frame ( 17) shift: 0.61 0.21 ...... Frame ( 18) shift: 0.66 0.33 ...... Frame ( 19) shift: 0.74 0.44 ...... Frame ( 20) shift: 0.82 0.54 ...... Frame ( 21) shift: 0.91 0.64 ...... Frame ( 22) shift: 1.01 0.74 ...... Frame ( 23) shift: 1.10 0.83 ...... Frame ( 24) shift: 1.16 0.91 ...... Frame ( 25) shift: 1.18 0.97 ...... Frame ( 26) shift: 1.19 1.03 ...... Frame ( 27) shift: 1.23 1.07 ...... Frame ( 28) shift: 1.29 1.11 ...... Frame ( 29) shift: 1.34 1.15 ...... Frame ( 30) shift: 1.39 1.19 ...... Frame ( 31) shift: 1.43 1.22 ...... Frame ( 32) shift: 1.47 1.26 ...... Frame ( 33) shift: 1.52 1.30 ...... Frame ( 34) shift: 1.58 1.33 ...... Frame ( 35) shift: 1.64 1.37 ...... Frame ( 36) shift: 1.66 1.39 ...... Frame ( 37) shift: 1.63 1.39 ...... Frame ( 38) shift: 1.61 1.39 ...... Frame ( 39) shift: 1.58 1.40 ...... Frame ( 40) shift: 1.55 1.40 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.269775 Iteration 2 Error: 0.198191 Iteration 3 Error: 0.079786 Iteration 4 Error: 0.021401 Align patch 2 23 left Iteration 1 Error: 1.434690 Iteration 2 Error: 0.388908 Iteration 3 Error: 0.093277 Iteration 4 Error: 0.033779 Align patch 3 22 left Iteration 1 Error: 0.981665 Iteration 2 Error: 0.163418 Iteration 3 Error: 0.047269 Align patch 4 21 left Iteration 1 Error: 1.031511 Iteration 2 Error: 0.137565 Iteration 3 Error: 0.044549 Align patch 5 20 left Iteration 1 Error: 0.933227 Iteration 2 Error: 0.201011 Iteration 3 Error: 0.051477 Iteration 4 Error: 0.021687 Align patch 6 19 left Iteration 1 Error: 1.008636 Iteration 2 Error: 0.195002 Iteration 3 Error: 0.055425 Iteration 4 Error: 0.013127 Align patch 7 18 left Iteration 1 Error: 1.128781 Iteration 2 Error: 0.163948 Iteration 3 Error: 0.042086 Align patch 8 17 left Iteration 1 Error: 0.769635 Iteration 2 Error: 0.105703 Iteration 3 Error: 0.025631 Align patch 9 16 left Iteration 1 Error: 0.725091 Iteration 2 Error: 0.159591 Iteration 3 Error: 0.053119 Iteration 4 Error: 0.019845 Align patch 10 15 left Iteration 1 Error: 0.745743 Iteration 2 Error: 0.156680 Iteration 3 Error: 0.040653 Align patch 11 14 left Iteration 1 Error: 0.830171 Iteration 2 Error: 0.161631 Iteration 3 Error: 0.045186 Align patch 12 13 left Iteration 1 Error: 0.953883 Iteration 2 Error: 0.172977 Iteration 3 Error: 0.062952 Iteration 4 Error: 0.015512 Align patch 13 12 left Iteration 1 Error: 0.949065 Iteration 2 Error: 0.145947 Iteration 3 Error: 0.034237 Align patch 14 11 left Iteration 1 Error: 1.270856 Iteration 2 Error: 0.235465 Iteration 3 Error: 0.054440 Iteration 4 Error: 0.015028 Align patch 15 10 left Iteration 1 Error: 1.001392 Iteration 2 Error: 0.205883 Iteration 3 Error: 0.048004 Align patch 16 9 left Iteration 1 Error: 0.601273 Iteration 2 Error: 0.187622 Iteration 3 Error: 0.049807 Align patch 17 8 left Iteration 1 Error: 0.886050 Iteration 2 Error: 0.114010 Iteration 3 Error: 0.027479 Align patch 18 7 left Iteration 1 Error: 0.667103 Iteration 2 Error: 0.110505 Iteration 3 Error: 0.034279 Align patch 19 6 left Iteration 1 Error: 0.792763 Iteration 2 Error: 0.176154 Iteration 3 Error: 0.052838 Iteration 4 Error: 0.026478 Align patch 20 5 left Iteration 1 Error: 1.110443 Iteration 2 Error: 0.145218 Iteration 3 Error: 0.057685 Iteration 4 Error: 0.022069 Align patch 21 4 left Iteration 1 Error: 0.640609 Iteration 2 Error: 0.078224 Iteration 3 Error: 0.027396 Align patch 22 3 left Iteration 1 Error: 0.962482 Iteration 2 Error: 0.177110 Iteration 3 Error: 0.037621 Align patch 23 2 left Iteration 1 Error: 0.723717 Iteration 2 Error: 0.118693 Iteration 3 Error: 0.027590 Align patch 24 1 left Iteration 1 Error: 1.008903 Iteration 2 Error: 0.210633 Iteration 3 Error: 0.030763 Align patch 25 0 left Iteration 1 Error: 0.677638 Iteration 2 Error: 0.065408 Iteration 3 Error: 0.017921 3D Fitting completed. Patch alignment time: 20.34(sec) Local motion has been corrected. Process thread exits. Computational time: 36.150669 sec Total time: 44.262062 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00014hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00014hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.587650s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00014hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.730295s ........................................ >>>>>>TIME<<<<<< FFT: 1.706590s Defocus_U Defocus_V Angle CCC 25796.74 26504.09 1.35 0.047476 Final Values Defocus_U Defocus_V Angle CCC 25804.55 26502.54 2.29 0.074993 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00014hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00014hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 1.000e-01 CC threshold: 0.734 Mean Std: 42.84 6.98 Num Hot pixels: 201 Hot pixel threshold: 84.73 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.326755 Iteration 2 Error: 0.178454 Iteration 3 Error: 0.038731 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.10 -0.25 ...... Frame ( 3) shift: 0.20 -0.49 ...... Frame ( 4) shift: 0.30 -0.74 ...... Frame ( 5) shift: 0.40 -0.98 ...... Frame ( 6) shift: 0.47 -1.04 ...... Frame ( 7) shift: 0.51 -0.91 ...... Frame ( 8) shift: 0.56 -0.78 ...... Frame ( 9) shift: 0.60 -0.65 ...... Frame ( 10) shift: 0.63 -0.52 ...... Frame ( 11) shift: 0.66 -0.38 ...... Frame ( 12) shift: 0.70 -0.28 ...... Frame ( 13) shift: 0.75 -0.22 ...... Frame ( 14) shift: 0.80 -0.16 ...... Frame ( 15) shift: 0.78 -0.06 ...... Frame ( 16) shift: 0.70 0.07 ...... Frame ( 17) shift: 0.63 0.21 ...... Frame ( 18) shift: 0.58 0.31 ...... Frame ( 19) shift: 0.58 0.38 ...... Frame ( 20) shift: 0.57 0.45 ...... Frame ( 21) shift: 0.56 0.55 ...... Frame ( 22) shift: 0.55 0.67 ...... Frame ( 23) shift: 0.55 0.80 ...... Frame ( 24) shift: 0.58 0.87 ...... Frame ( 25) shift: 0.67 0.87 ...... Frame ( 26) shift: 0.75 0.88 ...... Frame ( 27) shift: 0.83 0.84 ...... Frame ( 28) shift: 0.91 0.77 ...... Frame ( 29) shift: 0.99 0.70 ...... Frame ( 30) shift: 1.03 0.68 ...... Frame ( 31) shift: 1.04 0.71 ...... Frame ( 32) shift: 1.05 0.75 ...... Frame ( 33) shift: 1.10 0.81 ...... Frame ( 34) shift: 1.20 0.89 ...... Frame ( 35) shift: 1.29 0.98 ...... Frame ( 36) shift: 1.36 1.02 ...... Frame ( 37) shift: 1.40 1.02 ...... Frame ( 38) shift: 1.44 1.01 ...... Frame ( 39) shift: 1.48 1.01 ...... Frame ( 40) shift: 1.53 1.00 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.142168 Iteration 2 Error: 0.181699 Iteration 3 Error: 0.034607 Align patch 2 23 left Iteration 1 Error: 1.509349 Iteration 2 Error: 0.272984 Iteration 3 Error: 0.084180 Iteration 4 Error: 0.032139 Align patch 3 22 left Iteration 1 Error: 0.991081 Iteration 2 Error: 0.102789 Iteration 3 Error: 0.032823 Align patch 4 21 left Iteration 1 Error: 0.752801 Iteration 2 Error: 0.114619 Iteration 3 Error: 0.026870 Align patch 5 20 left Iteration 1 Error: 0.696741 Iteration 2 Error: 0.197235 Iteration 3 Error: 0.047080 Align patch 6 19 left Iteration 1 Error: 0.816969 Iteration 2 Error: 0.175890 Iteration 3 Error: 0.040626 Align patch 7 18 left Iteration 1 Error: 1.231065 Iteration 2 Error: 0.248469 Iteration 3 Error: 0.056038 Iteration 4 Error: 0.017273 Align patch 8 17 left Iteration 1 Error: 1.435937 Iteration 2 Error: 0.189977 Iteration 3 Error: 0.048585 Align patch 9 16 left Iteration 1 Error: 0.746110 Iteration 2 Error: 0.161127 Iteration 3 Error: 0.057930 Iteration 4 Error: 0.013084 Align patch 10 15 left Iteration 1 Error: 1.027951 Iteration 2 Error: 0.166203 Iteration 3 Error: 0.045438 Align patch 11 14 left Iteration 1 Error: 0.846390 Iteration 2 Error: 0.137832 Iteration 3 Error: 0.038688 Align patch 12 13 left Iteration 1 Error: 0.499467 Iteration 2 Error: 0.070353 Iteration 3 Error: 0.018394 Align patch 13 12 left Iteration 1 Error: 0.868629 Iteration 2 Error: 0.144697 Iteration 3 Error: 0.037239 Align patch 14 11 left Iteration 1 Error: 0.752256 Iteration 2 Error: 0.152051 Iteration 3 Error: 0.045995 Align patch 15 10 left Iteration 1 Error: 0.760245 Iteration 2 Error: 0.128975 Iteration 3 Error: 0.034832 Align patch 16 9 left Iteration 1 Error: 0.661168 Iteration 2 Error: 0.102558 Iteration 3 Error: 0.019396 Align patch 17 8 left Iteration 1 Error: 0.744045 Iteration 2 Error: 0.135644 Iteration 3 Error: 0.060544 Iteration 4 Error: 0.023011 Align patch 18 7 left Iteration 1 Error: 0.818988 Iteration 2 Error: 0.106599 Iteration 3 Error: 0.025567 Align patch 19 6 left Iteration 1 Error: 0.687800 Iteration 2 Error: 0.123019 Iteration 3 Error: 0.036307 Align patch 20 5 left Iteration 1 Error: 0.903113 Iteration 2 Error: 0.183060 Iteration 3 Error: 0.062345 Iteration 4 Error: 0.024476 Align patch 21 4 left Iteration 1 Error: 0.744074 Iteration 2 Error: 0.120515 Iteration 3 Error: 0.029781 Align patch 22 3 left Iteration 1 Error: 1.001825 Iteration 2 Error: 0.285812 Iteration 3 Error: 0.055159 Iteration 4 Error: 0.019705 Align patch 23 2 left Iteration 1 Error: 0.765165 Iteration 2 Error: 0.148716 Iteration 3 Error: 0.041696 Align patch 24 1 left Iteration 1 Error: 1.224151 Iteration 2 Error: 0.223085 Iteration 3 Error: 0.053859 Iteration 4 Error: 0.022820 Align patch 25 0 left Iteration 1 Error: 1.229678 Iteration 2 Error: 0.178684 Iteration 3 Error: 0.018147 3D Fitting completed. Patch alignment time: 16.63(sec) Local motion has been corrected. Process thread exits. Computational time: 27.291634 sec Total time: 35.223743 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00014hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00014hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.762431s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00014hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.782526s ........................................ >>>>>>TIME<<<<<< FFT: 1.015382s Defocus_U Defocus_V Angle CCC 26662.11 27388.67 1.40 0.044952 Final Values Defocus_U Defocus_V Angle CCC 26658.98 27398.05 1.72 0.075627 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00015hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00015hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.997e-02 CC threshold: 0.734 Mean Std: 40.57 6.79 Num Hot pixels: 182 Hot pixel threshold: 81.30 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.950127 Iteration 2 Error: 0.416505 Iteration 3 Error: 0.096058 Iteration 4 Error: 0.042262 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.01 -0.01 ...... Frame ( 3) shift: 0.02 -0.03 ...... Frame ( 4) shift: 0.03 -0.04 ...... Frame ( 5) shift: 0.03 -0.06 ...... Frame ( 6) shift: 0.09 0.00 ...... Frame ( 7) shift: 0.18 0.14 ...... Frame ( 8) shift: 0.27 0.28 ...... Frame ( 9) shift: 0.42 0.40 ...... Frame ( 10) shift: 0.63 0.51 ...... Frame ( 11) shift: 0.84 0.61 ...... Frame ( 12) shift: 1.02 0.71 ...... Frame ( 13) shift: 1.17 0.81 ...... Frame ( 14) shift: 1.32 0.90 ...... Frame ( 15) shift: 1.41 0.99 ...... Frame ( 16) shift: 1.45 1.07 ...... Frame ( 17) shift: 1.48 1.15 ...... Frame ( 18) shift: 1.54 1.30 ...... Frame ( 19) shift: 1.61 1.50 ...... Frame ( 20) shift: 1.68 1.70 ...... Frame ( 21) shift: 1.79 1.83 ...... Frame ( 22) shift: 1.91 1.87 ...... Frame ( 23) shift: 2.04 1.92 ...... Frame ( 24) shift: 2.18 1.98 ...... Frame ( 25) shift: 2.31 2.05 ...... Frame ( 26) shift: 2.45 2.13 ...... Frame ( 27) shift: 2.55 2.21 ...... Frame ( 28) shift: 2.61 2.30 ...... Frame ( 29) shift: 2.66 2.40 ...... Frame ( 30) shift: 2.70 2.44 ...... Frame ( 31) shift: 2.71 2.44 ...... Frame ( 32) shift: 2.72 2.44 ...... Frame ( 33) shift: 2.76 2.47 ...... Frame ( 34) shift: 2.82 2.51 ...... Frame ( 35) shift: 2.89 2.55 ...... Frame ( 36) shift: 2.97 2.60 ...... Frame ( 37) shift: 3.08 2.65 ...... Frame ( 38) shift: 3.20 2.70 ...... Frame ( 39) shift: 3.31 2.75 ...... Frame ( 40) shift: 3.42 2.80 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.912068 Iteration 2 Error: 0.376150 Iteration 3 Error: 0.120722 Iteration 4 Error: 0.060862 Iteration 5 Error: 0.022851 Align patch 2 23 left Iteration 1 Error: 0.996303 Iteration 2 Error: 0.215001 Iteration 3 Error: 0.067742 Iteration 4 Error: 0.027361 Align patch 3 22 left Iteration 1 Error: 0.785490 Iteration 2 Error: 0.231414 Iteration 3 Error: 0.102947 Iteration 4 Error: 0.040905 Align patch 4 21 left Iteration 1 Error: 1.209957 Iteration 2 Error: 0.179135 Iteration 3 Error: 0.032371 Align patch 5 20 left Iteration 1 Error: 1.006805 Iteration 2 Error: 0.227667 Iteration 3 Error: 0.077626 Iteration 4 Error: 0.022123 Align patch 6 19 left Iteration 1 Error: 0.523852 Iteration 2 Error: 0.132118 Iteration 3 Error: 0.045197 Align patch 7 18 left Iteration 1 Error: 0.848309 Iteration 2 Error: 0.115498 Iteration 3 Error: 0.025434 Align patch 8 17 left Iteration 1 Error: 1.187088 Iteration 2 Error: 0.250876 Iteration 3 Error: 0.080635 Iteration 4 Error: 0.033343 Align patch 9 16 left Iteration 1 Error: 0.907799 Iteration 2 Error: 0.121040 Iteration 3 Error: 0.038252 Align patch 10 15 left Iteration 1 Error: 0.375878 Iteration 2 Error: 0.081878 Iteration 3 Error: 0.018951 Align patch 11 14 left Iteration 1 Error: 1.080398 Iteration 2 Error: 0.111963 Iteration 3 Error: 0.059810 Iteration 4 Error: 0.016517 Align patch 12 13 left Iteration 1 Error: 0.555981 Iteration 2 Error: 0.123079 Iteration 3 Error: 0.038865 Align patch 13 12 left Iteration 1 Error: 0.794004 Iteration 2 Error: 0.154494 Iteration 3 Error: 0.078927 Iteration 4 Error: 0.021479 Align patch 14 11 left Iteration 1 Error: 0.545561 Iteration 2 Error: 0.118503 Iteration 3 Error: 0.045228 Align patch 15 10 left Iteration 1 Error: 0.740989 Iteration 2 Error: 0.130109 Iteration 3 Error: 0.037734 Align patch 16 9 left Iteration 1 Error: 0.649195 Iteration 2 Error: 0.152046 Iteration 3 Error: 0.038892 Align patch 17 8 left Iteration 1 Error: 0.890639 Iteration 2 Error: 0.131465 Iteration 3 Error: 0.038623 Align patch 18 7 left Iteration 1 Error: 0.694430 Iteration 2 Error: 0.126413 Iteration 3 Error: 0.039543 Align patch 19 6 left Iteration 1 Error: 0.526873 Iteration 2 Error: 0.088338 Iteration 3 Error: 0.023253 Align patch 20 5 left Iteration 1 Error: 0.935921 Iteration 2 Error: 0.361543 Iteration 3 Error: 0.072746 Iteration 4 Error: 0.050229 Iteration 5 Error: 0.015667 Align patch 21 4 left Iteration 1 Error: 0.732423 Iteration 2 Error: 0.212144 Iteration 3 Error: 0.062535 Iteration 4 Error: 0.019834 Align patch 22 3 left Iteration 1 Error: 0.713758 Iteration 2 Error: 0.218887 Iteration 3 Error: 0.067349 Iteration 4 Error: 0.021615 Align patch 23 2 left Iteration 1 Error: 0.447849 Iteration 2 Error: 0.112626 Iteration 3 Error: 0.024369 Align patch 24 1 left Iteration 1 Error: 0.656804 Iteration 2 Error: 0.110323 Iteration 3 Error: 0.017346 Align patch 25 0 left Iteration 1 Error: 1.021276 Iteration 2 Error: 0.204858 Iteration 3 Error: 0.053338 Iteration 4 Error: 0.017728 3D Fitting completed. Patch alignment time: 13.06(sec) Local motion has been corrected. Process thread exits. Computational time: 23.348860 sec Total time: 28.936069 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00015hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00015hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.784206s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00015hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.728938s ........................................ >>>>>>TIME<<<<<< FFT: 1.045519s Defocus_U Defocus_V Angle CCC 27490.25 28255.88 8.18 0.039293 Final Values Defocus_U Defocus_V Angle CCC 27482.44 28282.45 8.50 0.061223 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00015hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00015hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.991e-02 CC threshold: 0.734 Mean Std: 39.91 6.71 Num Hot pixels: 201 Hot pixel threshold: 80.18 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.909685 Iteration 2 Error: 0.630947 Iteration 3 Error: 0.151330 Iteration 4 Error: 0.064243 Iteration 5 Error: 0.027995 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.00 -0.05 ...... Frame ( 3) shift: 0.01 -0.09 ...... Frame ( 4) shift: 0.01 -0.14 ...... Frame ( 5) shift: 0.02 -0.19 ...... Frame ( 6) shift: 0.09 -0.20 ...... Frame ( 7) shift: 0.22 -0.19 ...... Frame ( 8) shift: 0.35 -0.17 ...... Frame ( 9) shift: 0.46 -0.10 ...... Frame ( 10) shift: 0.57 0.04 ...... Frame ( 11) shift: 0.68 0.18 ...... Frame ( 12) shift: 0.81 0.31 ...... Frame ( 13) shift: 0.98 0.42 ...... Frame ( 14) shift: 1.14 0.54 ...... Frame ( 15) shift: 1.25 0.66 ...... Frame ( 16) shift: 1.32 0.76 ...... Frame ( 17) shift: 1.39 0.87 ...... Frame ( 18) shift: 1.49 0.99 ...... Frame ( 19) shift: 1.62 1.13 ...... Frame ( 20) shift: 1.76 1.27 ...... Frame ( 21) shift: 1.95 1.44 ...... Frame ( 22) shift: 2.18 1.64 ...... Frame ( 23) shift: 2.42 1.85 ...... Frame ( 24) shift: 2.57 1.96 ...... Frame ( 25) shift: 2.64 1.98 ...... Frame ( 26) shift: 2.71 2.00 ...... Frame ( 27) shift: 2.81 2.05 ...... Frame ( 28) shift: 2.93 2.13 ...... Frame ( 29) shift: 3.05 2.21 ...... Frame ( 30) shift: 3.16 2.30 ...... Frame ( 31) shift: 3.25 2.40 ...... Frame ( 32) shift: 3.34 2.50 ...... Frame ( 33) shift: 3.34 2.58 ...... Frame ( 34) shift: 3.26 2.65 ...... Frame ( 35) shift: 3.17 2.72 ...... Frame ( 36) shift: 3.17 2.77 ...... Frame ( 37) shift: 3.25 2.81 ...... Frame ( 38) shift: 3.33 2.85 ...... Frame ( 39) shift: 3.41 2.89 ...... Frame ( 40) shift: 3.50 2.93 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.881430 Iteration 2 Error: 0.332830 Iteration 3 Error: 0.111495 Iteration 4 Error: 0.049369 Align patch 2 23 left Iteration 1 Error: 1.099152 Iteration 2 Error: 0.162350 Iteration 3 Error: 0.071156 Iteration 4 Error: 0.033502 Align patch 3 22 left Iteration 1 Error: 1.147825 Iteration 2 Error: 0.302127 Iteration 3 Error: 0.176946 Iteration 4 Error: 0.046006 Align patch 4 21 left Iteration 1 Error: 0.762596 Iteration 2 Error: 0.141460 Iteration 3 Error: 0.033886 Align patch 5 20 left Iteration 1 Error: 0.973995 Iteration 2 Error: 0.295694 Iteration 3 Error: 0.046899 Align patch 6 19 left Iteration 1 Error: 1.193030 Iteration 2 Error: 0.198540 Iteration 3 Error: 0.070520 Iteration 4 Error: 0.035016 Align patch 7 18 left Iteration 1 Error: 0.965840 Iteration 2 Error: 0.230988 Iteration 3 Error: 0.049590 Align patch 8 17 left Iteration 1 Error: 0.808345 Iteration 2 Error: 0.193078 Iteration 3 Error: 0.090090 Iteration 4 Error: 0.038266 Align patch 9 16 left Iteration 1 Error: 0.782206 Iteration 2 Error: 0.243465 Iteration 3 Error: 0.099908 Iteration 4 Error: 0.051226 Iteration 5 Error: 0.019384 Align patch 10 15 left Iteration 1 Error: 0.801752 Iteration 2 Error: 0.363135 Iteration 3 Error: 0.151880 Iteration 4 Error: 0.064073 Iteration 5 Error: 0.024637 Align patch 11 14 left Iteration 1 Error: 0.727747 Iteration 2 Error: 0.164326 Iteration 3 Error: 0.051389 Iteration 4 Error: 0.019863 Align patch 12 13 left Iteration 1 Error: 0.920154 Iteration 2 Error: 0.185907 Iteration 3 Error: 0.039720 Align patch 13 12 left Iteration 1 Error: 0.622717 Iteration 2 Error: 0.119004 Iteration 3 Error: 0.030683 Align patch 14 11 left Iteration 1 Error: 0.824108 Iteration 2 Error: 0.141143 Iteration 3 Error: 0.044409 Align patch 15 10 left Iteration 1 Error: 0.783256 Iteration 2 Error: 0.105229 Iteration 3 Error: 0.040956 Align patch 16 9 left Iteration 1 Error: 0.806767 Iteration 2 Error: 0.297267 Iteration 3 Error: 0.109562 Iteration 4 Error: 0.045940 Align patch 17 8 left Iteration 1 Error: 0.655047 Iteration 2 Error: 0.256255 Iteration 3 Error: 0.062982 Iteration 4 Error: 0.024875 Align patch 18 7 left Iteration 1 Error: 0.985226 Iteration 2 Error: 0.189663 Iteration 3 Error: 0.072890 Iteration 4 Error: 0.026922 Align patch 19 6 left Iteration 1 Error: 0.930610 Iteration 2 Error: 0.404834 Iteration 3 Error: 0.182049 Iteration 4 Error: 0.086663 Iteration 5 Error: 0.041941 Align patch 20 5 left Iteration 1 Error: 0.726463 Iteration 2 Error: 0.244227 Iteration 3 Error: 0.110788 Iteration 4 Error: 0.053459 Iteration 5 Error: 0.025552 Align patch 21 4 left Iteration 1 Error: 0.901490 Iteration 2 Error: 0.142748 Iteration 3 Error: 0.067578 Iteration 4 Error: 0.023845 Align patch 22 3 left Iteration 1 Error: 1.160367 Iteration 2 Error: 0.195846 Iteration 3 Error: 0.051509 Iteration 4 Error: 0.017154 Align patch 23 2 left Iteration 1 Error: 1.204477 Iteration 2 Error: 0.225031 Iteration 3 Error: 0.071630 Iteration 4 Error: 0.020067 Align patch 24 1 left Iteration 1 Error: 0.993318 Iteration 2 Error: 0.221609 Iteration 3 Error: 0.064371 Iteration 4 Error: 0.020734 Align patch 25 0 left Iteration 1 Error: 1.000852 Iteration 2 Error: 0.248428 Iteration 3 Error: 0.060140 Iteration 4 Error: 0.016774 3D Fitting completed. Patch alignment time: 14.61(sec) Local motion has been corrected. Process thread exits. Computational time: 23.457594 sec Total time: 29.078600 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00015hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00015hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.660328s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00015hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.668514s ........................................ >>>>>>TIME<<<<<< FFT: 0.956790s Defocus_U Defocus_V Angle CCC 26423.81 27341.81 8.11 0.039600 Final Values Defocus_U Defocus_V Angle CCC 26405.07 27329.35 9.05 0.059341 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00015hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00015hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.992e-02 CC threshold: 0.734 Mean Std: 41.04 6.83 Num Hot pixels: 201 Hot pixel threshold: 82.01 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.630070 Iteration 2 Error: 0.255547 Iteration 3 Error: 0.063238 Iteration 4 Error: 0.019775 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.06 0.05 ...... Frame ( 3) shift: -0.11 0.11 ...... Frame ( 4) shift: -0.17 0.16 ...... Frame ( 5) shift: -0.22 0.22 ...... Frame ( 6) shift: -0.17 0.29 ...... Frame ( 7) shift: -0.02 0.37 ...... Frame ( 8) shift: 0.13 0.45 ...... Frame ( 9) shift: 0.27 0.55 ...... Frame ( 10) shift: 0.39 0.66 ...... Frame ( 11) shift: 0.51 0.78 ...... Frame ( 12) shift: 0.61 0.90 ...... Frame ( 13) shift: 0.69 1.03 ...... Frame ( 14) shift: 0.77 1.17 ...... Frame ( 15) shift: 0.85 1.24 ...... Frame ( 16) shift: 0.95 1.24 ...... Frame ( 17) shift: 1.04 1.25 ...... Frame ( 18) shift: 1.12 1.30 ...... Frame ( 19) shift: 1.18 1.40 ...... Frame ( 20) shift: 1.25 1.50 ...... Frame ( 21) shift: 1.39 1.60 ...... Frame ( 22) shift: 1.61 1.70 ...... Frame ( 23) shift: 1.83 1.80 ...... Frame ( 24) shift: 1.92 1.85 ...... Frame ( 25) shift: 1.87 1.84 ...... Frame ( 26) shift: 1.81 1.84 ...... Frame ( 27) shift: 1.79 1.86 ...... Frame ( 28) shift: 1.80 1.92 ...... Frame ( 29) shift: 1.81 1.97 ...... Frame ( 30) shift: 1.84 2.00 ...... Frame ( 31) shift: 1.88 1.99 ...... Frame ( 32) shift: 1.93 1.99 ...... Frame ( 33) shift: 1.93 1.96 ...... Frame ( 34) shift: 1.86 1.92 ...... Frame ( 35) shift: 1.80 1.87 ...... Frame ( 36) shift: 1.84 1.88 ...... Frame ( 37) shift: 1.99 1.93 ...... Frame ( 38) shift: 2.13 1.98 ...... Frame ( 39) shift: 2.27 2.04 ...... Frame ( 40) shift: 2.42 2.09 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.248894 Iteration 2 Error: 0.258161 Iteration 3 Error: 0.086596 Iteration 4 Error: 0.039848 Align patch 2 23 left Iteration 1 Error: 1.142923 Iteration 2 Error: 0.279945 Iteration 3 Error: 0.087731 Iteration 4 Error: 0.052335 Iteration 5 Error: 0.020213 Align patch 3 22 left Iteration 1 Error: 1.008041 Iteration 2 Error: 0.264455 Iteration 3 Error: 0.088341 Iteration 4 Error: 0.034141 Align patch 4 21 left Iteration 1 Error: 0.750272 Iteration 2 Error: 0.161108 Iteration 3 Error: 0.041502 Align patch 5 20 left Iteration 1 Error: 0.691887 Iteration 2 Error: 0.125560 Iteration 3 Error: 0.024167 Align patch 6 19 left Iteration 1 Error: 1.004491 Iteration 2 Error: 0.169399 Iteration 3 Error: 0.048838 Align patch 7 18 left Iteration 1 Error: 1.480310 Iteration 2 Error: 0.539052 Iteration 3 Error: 0.200675 Iteration 4 Error: 0.152651 Iteration 5 Error: 0.073397 Align patch 7 18 left Iteration 1 Error: 1.251992 Iteration 2 Error: 0.152154 Iteration 3 Error: 0.024469 Align patch 8 17 left Iteration 1 Error: 1.131910 Iteration 2 Error: 0.246013 Iteration 3 Error: 0.081600 Iteration 4 Error: 0.029971 Align patch 9 16 left Iteration 1 Error: 0.796201 Iteration 2 Error: 0.088572 Iteration 3 Error: 0.030539 Align patch 10 15 left Iteration 1 Error: 0.989598 Iteration 2 Error: 0.342192 Iteration 3 Error: 0.158941 Iteration 4 Error: 0.069599 Iteration 5 Error: 0.032329 Align patch 11 14 left Iteration 1 Error: 1.092800 Iteration 2 Error: 0.170497 Iteration 3 Error: 0.063703 Iteration 4 Error: 0.015138 Align patch 12 13 left Iteration 1 Error: 1.102912 Iteration 2 Error: 0.223720 Iteration 3 Error: 0.078095 Iteration 4 Error: 0.032507 Align patch 13 12 left Iteration 1 Error: 0.948175 Iteration 2 Error: 0.344444 Iteration 3 Error: 0.120085 Iteration 4 Error: 0.078485 Iteration 5 Error: 0.035314 Align patch 14 11 left Iteration 1 Error: 0.660076 Iteration 2 Error: 0.145980 Iteration 3 Error: 0.042559 Align patch 15 10 left Iteration 1 Error: 0.663257 Iteration 2 Error: 0.075098 Iteration 3 Error: 0.012228 Align patch 16 9 left Iteration 1 Error: 0.843978 Iteration 2 Error: 0.141477 Iteration 3 Error: 0.036596 Align patch 17 8 left Iteration 1 Error: 0.446620 Iteration 2 Error: 0.097056 Iteration 3 Error: 0.028634 Align patch 18 7 left Iteration 1 Error: 0.463385 Iteration 2 Error: 0.086248 Iteration 3 Error: 0.026481 Align patch 19 6 left Iteration 1 Error: 0.619497 Iteration 2 Error: 0.096943 Iteration 3 Error: 0.032203 Align patch 20 5 left Iteration 1 Error: 0.585398 Iteration 2 Error: 0.127585 Iteration 3 Error: 0.046251 Align patch 21 4 left Iteration 1 Error: 0.569689 Iteration 2 Error: 0.124210 Iteration 3 Error: 0.025346 Align patch 22 3 left Iteration 1 Error: 0.566156 Iteration 2 Error: 0.077587 Iteration 3 Error: 0.019358 Align patch 23 2 left Iteration 1 Error: 0.744729 Iteration 2 Error: 0.164100 Iteration 3 Error: 0.056009 Iteration 4 Error: 0.017723 Align patch 24 1 left Iteration 1 Error: 0.753867 Iteration 2 Error: 0.098506 Iteration 3 Error: 0.022759 Align patch 25 0 left Iteration 1 Error: 0.725861 Iteration 2 Error: 0.178547 Iteration 3 Error: 0.040596 3D Fitting completed. Patch alignment time: 14.06(sec) Local motion has been corrected. Process thread exits. Computational time: 23.129154 sec Total time: 29.977680 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00015hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00015hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.726657s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00015hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.386830s ........................................ >>>>>>TIME<<<<<< FFT: 0.924138s Defocus_U Defocus_V Angle CCC 27546.94 27062.54 87.01 0.038819 Final Values Defocus_U Defocus_V Angle CCC 27037.54 27534.44 0.47 0.059862 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00015hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00015hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.993e-02 CC threshold: 0.734 Mean Std: 40.56 6.78 Num Hot pixels: 198 Hot pixel threshold: 81.24 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.880882 Iteration 2 Error: 0.322667 Iteration 3 Error: 0.082128 Iteration 4 Error: 0.024361 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.10 0.04 ...... Frame ( 3) shift: 0.21 0.08 ...... Frame ( 4) shift: 0.31 0.12 ...... Frame ( 5) shift: 0.42 0.16 ...... Frame ( 6) shift: 0.55 0.22 ...... Frame ( 7) shift: 0.69 0.32 ...... Frame ( 8) shift: 0.84 0.41 ...... Frame ( 9) shift: 0.94 0.46 ...... Frame ( 10) shift: 0.99 0.48 ...... Frame ( 11) shift: 1.04 0.49 ...... Frame ( 12) shift: 1.10 0.55 ...... Frame ( 13) shift: 1.17 0.67 ...... Frame ( 14) shift: 1.23 0.79 ...... Frame ( 15) shift: 1.36 0.90 ...... Frame ( 16) shift: 1.55 1.02 ...... Frame ( 17) shift: 1.74 1.14 ...... Frame ( 18) shift: 1.84 1.20 ...... Frame ( 19) shift: 1.87 1.18 ...... Frame ( 20) shift: 1.90 1.16 ...... Frame ( 21) shift: 1.99 1.21 ...... Frame ( 22) shift: 2.13 1.32 ...... Frame ( 23) shift: 2.27 1.43 ...... Frame ( 24) shift: 2.39 1.51 ...... Frame ( 25) shift: 2.48 1.58 ...... Frame ( 26) shift: 2.58 1.64 ...... Frame ( 27) shift: 2.64 1.70 ...... Frame ( 28) shift: 2.65 1.77 ...... Frame ( 29) shift: 2.67 1.84 ...... Frame ( 30) shift: 2.75 1.89 ...... Frame ( 31) shift: 2.88 1.93 ...... Frame ( 32) shift: 3.01 1.97 ...... Frame ( 33) shift: 3.08 2.01 ...... Frame ( 34) shift: 3.09 2.07 ...... Frame ( 35) shift: 3.10 2.12 ...... Frame ( 36) shift: 3.11 2.16 ...... Frame ( 37) shift: 3.11 2.19 ...... Frame ( 38) shift: 3.11 2.22 ...... Frame ( 39) shift: 3.12 2.25 ...... Frame ( 40) shift: 3.12 2.28 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.582597 Iteration 2 Error: 0.115313 Iteration 3 Error: 0.039608 Align patch 2 23 left Iteration 1 Error: 0.805516 Iteration 2 Error: 0.081093 Iteration 3 Error: 0.025634 Align patch 3 22 left Iteration 1 Error: 1.364382 Iteration 2 Error: 0.211810 Iteration 3 Error: 0.046088 Align patch 4 21 left Iteration 1 Error: 1.147472 Iteration 2 Error: 0.131690 Iteration 3 Error: 0.031094 Align patch 5 20 left Iteration 1 Error: 0.606570 Iteration 2 Error: 0.088389 Iteration 3 Error: 0.027312 Align patch 6 19 left Iteration 1 Error: 0.618358 Iteration 2 Error: 0.077774 Iteration 3 Error: 0.022932 Align patch 7 18 left Iteration 1 Error: 0.628403 Iteration 2 Error: 0.152987 Iteration 3 Error: 0.038941 Align patch 8 17 left Iteration 1 Error: 0.568297 Iteration 2 Error: 0.103857 Iteration 3 Error: 0.024856 Align patch 9 16 left Iteration 1 Error: 0.675084 Iteration 2 Error: 0.115772 Iteration 3 Error: 0.032196 Align patch 10 15 left Iteration 1 Error: 0.762230 Iteration 2 Error: 0.196297 Iteration 3 Error: 0.036296 Align patch 11 14 left Iteration 1 Error: 0.560662 Iteration 2 Error: 0.185994 Iteration 3 Error: 0.054908 Iteration 4 Error: 0.022326 Align patch 12 13 left Iteration 1 Error: 0.857134 Iteration 2 Error: 0.129604 Iteration 3 Error: 0.025065 Align patch 13 12 left Iteration 1 Error: 0.668278 Iteration 2 Error: 0.160074 Iteration 3 Error: 0.080649 Iteration 4 Error: 0.024122 Align patch 14 11 left Iteration 1 Error: 0.977442 Iteration 2 Error: 0.147583 Iteration 3 Error: 0.042029 Align patch 15 10 left Iteration 1 Error: 0.634623 Iteration 2 Error: 0.129917 Iteration 3 Error: 0.025119 Align patch 16 9 left Iteration 1 Error: 0.835107 Iteration 2 Error: 0.178381 Iteration 3 Error: 0.045213 Align patch 17 8 left Iteration 1 Error: 0.789749 Iteration 2 Error: 0.226813 Iteration 3 Error: 0.057924 Iteration 4 Error: 0.016753 Align patch 18 7 left Iteration 1 Error: 0.611284 Iteration 2 Error: 0.120296 Iteration 3 Error: 0.038132 Align patch 19 6 left Iteration 1 Error: 0.640866 Iteration 2 Error: 0.160177 Iteration 3 Error: 0.044953 Align patch 20 5 left Iteration 1 Error: 0.989538 Iteration 2 Error: 0.158844 Iteration 3 Error: 0.030456 Align patch 21 4 left Iteration 1 Error: 0.915914 Iteration 2 Error: 0.179643 Iteration 3 Error: 0.053489 Iteration 4 Error: 0.016825 Align patch 22 3 left Iteration 1 Error: 1.182189 Iteration 2 Error: 0.252116 Iteration 3 Error: 0.060048 Iteration 4 Error: 0.022080 Align patch 23 2 left Iteration 1 Error: 1.338470 Iteration 2 Error: 0.327262 Iteration 3 Error: 0.104351 Iteration 4 Error: 0.047616 Align patch 24 1 left Iteration 1 Error: 0.773722 Iteration 2 Error: 0.169807 Iteration 3 Error: 0.051254 Iteration 4 Error: 0.013094 Align patch 25 0 left Iteration 1 Error: 1.024071 Iteration 2 Error: 0.172399 Iteration 3 Error: 0.046105 3D Fitting completed. Patch alignment time: 12.97(sec) Local motion has been corrected. Process thread exits. Computational time: 21.857735 sec Total time: 27.048529 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00015hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00015hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.648999s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00015hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.222734s ........................................ >>>>>>TIME<<<<<< FFT: 0.850486s Defocus_U Defocus_V Angle CCC 28580.09 27935.53 84.83 0.035361 Final Values Defocus_U Defocus_V Angle CCC 28545.70 27944.93 83.90 0.053798 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00016hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00016hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.987e-02 CC threshold: 0.734 Mean Std: 43.60 7.04 Num Hot pixels: 182 Hot pixel threshold: 85.82 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.938661 Iteration 2 Error: 0.432018 Iteration 3 Error: 0.122641 Iteration 4 Error: 0.044151 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.15 -0.31 ...... Frame ( 3) shift: -0.30 -0.62 ...... Frame ( 4) shift: -0.44 -0.93 ...... Frame ( 5) shift: -0.59 -1.23 ...... Frame ( 6) shift: -0.66 -1.39 ...... Frame ( 7) shift: -0.63 -1.40 ...... Frame ( 8) shift: -0.61 -1.40 ...... Frame ( 9) shift: -0.52 -1.33 ...... Frame ( 10) shift: -0.36 -1.20 ...... Frame ( 11) shift: -0.20 -1.06 ...... Frame ( 12) shift: -0.03 -0.89 ...... Frame ( 13) shift: 0.15 -0.69 ...... Frame ( 14) shift: 0.33 -0.50 ...... Frame ( 15) shift: 0.50 -0.33 ...... Frame ( 16) shift: 0.66 -0.21 ...... Frame ( 17) shift: 0.83 -0.08 ...... Frame ( 18) shift: 0.94 0.01 ...... Frame ( 19) shift: 1.01 0.06 ...... Frame ( 20) shift: 1.08 0.12 ...... Frame ( 21) shift: 1.18 0.17 ...... Frame ( 22) shift: 1.32 0.23 ...... Frame ( 23) shift: 1.46 0.30 ...... Frame ( 24) shift: 1.55 0.36 ...... Frame ( 25) shift: 1.59 0.43 ...... Frame ( 26) shift: 1.63 0.49 ...... Frame ( 27) shift: 1.72 0.55 ...... Frame ( 28) shift: 1.85 0.59 ...... Frame ( 29) shift: 1.98 0.63 ...... Frame ( 30) shift: 2.10 0.70 ...... Frame ( 31) shift: 2.21 0.79 ...... Frame ( 32) shift: 2.33 0.88 ...... Frame ( 33) shift: 2.43 0.93 ...... Frame ( 34) shift: 2.51 0.94 ...... Frame ( 35) shift: 2.59 0.95 ...... Frame ( 36) shift: 2.66 0.99 ...... Frame ( 37) shift: 2.71 1.06 ...... Frame ( 38) shift: 2.77 1.12 ...... Frame ( 39) shift: 2.82 1.19 ...... Frame ( 40) shift: 2.88 1.25 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.067439 Iteration 2 Error: 0.238493 Iteration 3 Error: 0.062543 Iteration 4 Error: 0.026762 Align patch 2 23 left Iteration 1 Error: 1.225635 Iteration 2 Error: 0.131407 Iteration 3 Error: 0.032497 Align patch 3 22 left Iteration 1 Error: 1.741562 Iteration 2 Error: 0.197337 Iteration 3 Error: 0.073124 Iteration 4 Error: 0.023360 Align patch 4 21 left Iteration 1 Error: 1.301140 Iteration 2 Error: 0.281796 Iteration 3 Error: 0.047810 Align patch 5 20 left Iteration 1 Error: 1.112363 Iteration 2 Error: 0.379837 Iteration 3 Error: 0.103632 Iteration 4 Error: 0.040270 Align patch 6 19 left Iteration 1 Error: 0.755463 Iteration 2 Error: 0.179482 Iteration 3 Error: 0.043217 Align patch 7 18 left Iteration 1 Error: 0.877511 Iteration 2 Error: 0.160110 Iteration 3 Error: 0.050015 Iteration 4 Error: 0.017472 Align patch 8 17 left Iteration 1 Error: 0.982650 Iteration 2 Error: 0.143854 Iteration 3 Error: 0.050498 Iteration 4 Error: 0.020501 Align patch 9 16 left Iteration 1 Error: 1.000085 Iteration 2 Error: 0.325044 Iteration 3 Error: 0.114755 Iteration 4 Error: 0.038616 Align patch 10 15 left Iteration 1 Error: 1.026604 Iteration 2 Error: 0.225729 Iteration 3 Error: 0.071805 Iteration 4 Error: 0.028369 Align patch 11 14 left Iteration 1 Error: 0.771910 Iteration 2 Error: 0.211979 Iteration 3 Error: 0.092028 Iteration 4 Error: 0.033261 Align patch 12 13 left Iteration 1 Error: 1.247807 Iteration 2 Error: 0.166111 Iteration 3 Error: 0.055213 Iteration 4 Error: 0.013991 Align patch 13 12 left Iteration 1 Error: 0.704782 Iteration 2 Error: 0.131836 Iteration 3 Error: 0.042178 Align patch 14 11 left Iteration 1 Error: 0.832915 Iteration 2 Error: 0.175605 Iteration 3 Error: 0.044117 Align patch 15 10 left Iteration 1 Error: 0.781333 Iteration 2 Error: 0.312491 Iteration 3 Error: 0.171407 Iteration 4 Error: 0.075442 Iteration 5 Error: 0.042081 Align patch 16 9 left Iteration 1 Error: 0.853232 Iteration 2 Error: 0.169735 Iteration 3 Error: 0.050067 Iteration 4 Error: 0.025529 Align patch 17 8 left Iteration 1 Error: 1.223824 Iteration 2 Error: 0.255682 Iteration 3 Error: 0.072760 Iteration 4 Error: 0.024149 Align patch 18 7 left Iteration 1 Error: 0.823716 Iteration 2 Error: 0.249621 Iteration 3 Error: 0.060704 Iteration 4 Error: 0.037534 Align patch 19 6 left Iteration 1 Error: 0.890686 Iteration 2 Error: 0.168490 Iteration 3 Error: 0.044652 Align patch 20 5 left Iteration 1 Error: 0.816140 Iteration 2 Error: 0.315866 Iteration 3 Error: 0.073672 Iteration 4 Error: 0.030193 Align patch 21 4 left Iteration 1 Error: 0.886133 Iteration 2 Error: 0.252872 Iteration 3 Error: 0.073944 Iteration 4 Error: 0.031925 Align patch 22 3 left Iteration 1 Error: 1.327938 Iteration 2 Error: 0.145565 Iteration 3 Error: 0.032517 Align patch 23 2 left Iteration 1 Error: 0.872269 Iteration 2 Error: 0.238112 Iteration 3 Error: 0.099590 Iteration 4 Error: 0.050766 Iteration 5 Error: 0.020872 Align patch 24 1 left Iteration 1 Error: 0.823408 Iteration 2 Error: 0.253809 Iteration 3 Error: 0.052282 Iteration 4 Error: 0.018273 Align patch 25 0 left Iteration 1 Error: 1.110327 Iteration 2 Error: 0.158234 Iteration 3 Error: 0.044404 3D Fitting completed. Patch alignment time: 14.19(sec) Local motion has been corrected. Process thread exits. Computational time: 23.382208 sec Total time: 28.716700 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00016hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00016hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.735643s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00016hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.900689s ........................................ >>>>>>TIME<<<<<< FFT: 0.903525s Defocus_U Defocus_V Angle CCC 26498.05 27345.70 6.70 0.045028 Final Values Defocus_U Defocus_V Angle CCC 26533.96 27350.44 7.01 0.069692 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00016hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00016hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.997e-02 CC threshold: 0.734 Mean Std: 43.28 7.05 Num Hot pixels: 217 Hot pixel threshold: 85.56 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.737453 Iteration 2 Error: 0.264961 Iteration 3 Error: 0.055721 Iteration 4 Error: 0.017021 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.03 -0.24 ...... Frame ( 3) shift: 0.05 -0.49 ...... Frame ( 4) shift: 0.08 -0.73 ...... Frame ( 5) shift: 0.10 -0.98 ...... Frame ( 6) shift: 0.16 -1.09 ...... Frame ( 7) shift: 0.24 -1.07 ...... Frame ( 8) shift: 0.32 -1.05 ...... Frame ( 9) shift: 0.39 -1.02 ...... Frame ( 10) shift: 0.47 -0.98 ...... Frame ( 11) shift: 0.54 -0.94 ...... Frame ( 12) shift: 0.63 -0.89 ...... Frame ( 13) shift: 0.73 -0.84 ...... Frame ( 14) shift: 0.83 -0.80 ...... Frame ( 15) shift: 0.88 -0.75 ...... Frame ( 16) shift: 0.86 -0.69 ...... Frame ( 17) shift: 0.84 -0.64 ...... Frame ( 18) shift: 0.90 -0.56 ...... Frame ( 19) shift: 1.04 -0.47 ...... Frame ( 20) shift: 1.18 -0.38 ...... Frame ( 21) shift: 1.26 -0.30 ...... Frame ( 22) shift: 1.30 -0.23 ...... Frame ( 23) shift: 1.34 -0.16 ...... Frame ( 24) shift: 1.43 -0.10 ...... Frame ( 25) shift: 1.56 -0.06 ...... Frame ( 26) shift: 1.69 -0.02 ...... Frame ( 27) shift: 1.82 0.02 ...... Frame ( 28) shift: 1.93 0.06 ...... Frame ( 29) shift: 2.05 0.11 ...... Frame ( 30) shift: 2.17 0.16 ...... Frame ( 31) shift: 2.29 0.21 ...... Frame ( 32) shift: 2.41 0.26 ...... Frame ( 33) shift: 2.49 0.27 ...... Frame ( 34) shift: 2.51 0.22 ...... Frame ( 35) shift: 2.53 0.17 ...... Frame ( 36) shift: 2.62 0.17 ...... Frame ( 37) shift: 2.77 0.20 ...... Frame ( 38) shift: 2.93 0.24 ...... Frame ( 39) shift: 3.08 0.27 ...... Frame ( 40) shift: 3.23 0.31 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.026449 Iteration 2 Error: 0.206595 Iteration 3 Error: 0.037167 Align patch 2 23 left Iteration 1 Error: 1.274107 Iteration 2 Error: 0.207713 Iteration 3 Error: 0.049288 Align patch 3 22 left Iteration 1 Error: 1.156984 Iteration 2 Error: 0.133950 Iteration 3 Error: 0.023381 Align patch 4 21 left Iteration 1 Error: 0.797748 Iteration 2 Error: 0.131599 Iteration 3 Error: 0.032788 Align patch 5 20 left Iteration 1 Error: 1.176858 Iteration 2 Error: 0.107272 Iteration 3 Error: 0.027290 Align patch 6 19 left Iteration 1 Error: 0.693985 Iteration 2 Error: 0.134603 Iteration 3 Error: 0.035634 Align patch 7 18 left Iteration 1 Error: 0.686492 Iteration 2 Error: 0.114395 Iteration 3 Error: 0.024017 Align patch 8 17 left Iteration 1 Error: 0.577765 Iteration 2 Error: 0.065774 Iteration 3 Error: 0.012475 Align patch 9 16 left Iteration 1 Error: 1.205372 Iteration 2 Error: 0.130990 Iteration 3 Error: 0.035806 Align patch 10 15 left Iteration 1 Error: 0.707919 Iteration 2 Error: 0.158144 Iteration 3 Error: 0.028805 Align patch 11 14 left Iteration 1 Error: 0.704015 Iteration 2 Error: 0.176637 Iteration 3 Error: 0.057388 Iteration 4 Error: 0.024178 Align patch 12 13 left Iteration 1 Error: 0.702304 Iteration 2 Error: 0.084366 Iteration 3 Error: 0.014821 Align patch 13 12 left Iteration 1 Error: 1.025272 Iteration 2 Error: 0.115051 Iteration 3 Error: 0.026291 Align patch 14 11 left Iteration 1 Error: 0.787735 Iteration 2 Error: 0.168872 Iteration 3 Error: 0.062239 Iteration 4 Error: 0.024702 Align patch 15 10 left Iteration 1 Error: 0.670244 Iteration 2 Error: 0.101619 Iteration 3 Error: 0.024182 Align patch 16 9 left Iteration 1 Error: 0.810124 Iteration 2 Error: 0.134597 Iteration 3 Error: 0.032312 Align patch 17 8 left Iteration 1 Error: 0.916132 Iteration 2 Error: 0.093703 Iteration 3 Error: 0.016967 Align patch 18 7 left Iteration 1 Error: 1.125349 Iteration 2 Error: 0.273945 Iteration 3 Error: 0.046535 Align patch 19 6 left Iteration 1 Error: 1.153494 Iteration 2 Error: 0.366495 Iteration 3 Error: 0.117734 Iteration 4 Error: 0.037294 Align patch 20 5 left Iteration 1 Error: 0.706611 Iteration 2 Error: 0.093191 Iteration 3 Error: 0.020035 Align patch 21 4 left Iteration 1 Error: 1.125436 Iteration 2 Error: 0.160377 Iteration 3 Error: 0.033423 Align patch 22 3 left Iteration 1 Error: 1.428200 Iteration 2 Error: 0.137406 Iteration 3 Error: 0.039676 Align patch 23 2 left Iteration 1 Error: 1.448243 Iteration 2 Error: 0.157760 Iteration 3 Error: 0.049917 Align patch 24 1 left Iteration 1 Error: 0.582969 Iteration 2 Error: 0.099929 Iteration 3 Error: 0.022530 Align patch 25 0 left Iteration 1 Error: 0.725377 Iteration 2 Error: 0.174696 Iteration 3 Error: 0.039933 3D Fitting completed. Patch alignment time: 17.27(sec) Local motion has been corrected. Process thread exits. Computational time: 32.583229 sec Total time: 41.031204 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00016hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00016hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.629084s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00016hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.923398s ........................................ >>>>>>TIME<<<<<< FFT: 1.804298s Defocus_U Defocus_V Angle CCC 28425.78 29285.16 6.79 0.044708 Final Values Defocus_U Defocus_V Angle CCC 28421.08 29274.23 6.48 0.074567 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00016hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00016hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.989e-02 CC threshold: 0.734 Mean Std: 43.15 6.98 Num Hot pixels: 205 Hot pixel threshold: 85.05 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.398694 Iteration 2 Error: 0.498898 Iteration 3 Error: 0.138383 Iteration 4 Error: 0.060457 Iteration 5 Error: 0.027573 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.26 -0.22 ...... Frame ( 3) shift: -0.51 -0.43 ...... Frame ( 4) shift: -0.77 -0.65 ...... Frame ( 5) shift: -1.02 -0.87 ...... Frame ( 6) shift: -1.07 -0.92 ...... Frame ( 7) shift: -0.90 -0.80 ...... Frame ( 8) shift: -0.74 -0.68 ...... Frame ( 9) shift: -0.52 -0.52 ...... Frame ( 10) shift: -0.26 -0.34 ...... Frame ( 11) shift: 0.00 -0.15 ...... Frame ( 12) shift: 0.21 0.02 ...... Frame ( 13) shift: 0.37 0.18 ...... Frame ( 14) shift: 0.52 0.35 ...... Frame ( 15) shift: 0.67 0.48 ...... Frame ( 16) shift: 0.80 0.58 ...... Frame ( 17) shift: 0.94 0.69 ...... Frame ( 18) shift: 1.07 0.76 ...... Frame ( 19) shift: 1.21 0.79 ...... Frame ( 20) shift: 1.34 0.83 ...... Frame ( 21) shift: 1.45 0.92 ...... Frame ( 22) shift: 1.53 1.07 ...... Frame ( 23) shift: 1.62 1.22 ...... Frame ( 24) shift: 1.66 1.32 ...... Frame ( 25) shift: 1.67 1.37 ...... Frame ( 26) shift: 1.69 1.42 ...... Frame ( 27) shift: 1.76 1.49 ...... Frame ( 28) shift: 1.88 1.59 ...... Frame ( 29) shift: 2.01 1.68 ...... Frame ( 30) shift: 2.10 1.77 ...... Frame ( 31) shift: 2.16 1.86 ...... Frame ( 32) shift: 2.21 1.94 ...... Frame ( 33) shift: 2.28 2.00 ...... Frame ( 34) shift: 2.37 2.04 ...... Frame ( 35) shift: 2.46 2.09 ...... Frame ( 36) shift: 2.53 2.11 ...... Frame ( 37) shift: 2.61 2.13 ...... Frame ( 38) shift: 2.68 2.14 ...... Frame ( 39) shift: 2.75 2.15 ...... Frame ( 40) shift: 2.82 2.17 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.669403 Iteration 2 Error: 0.274027 Iteration 3 Error: 0.103687 Iteration 4 Error: 0.036384 Align patch 2 23 left Iteration 1 Error: 0.829278 Iteration 2 Error: 0.180678 Iteration 3 Error: 0.062134 Iteration 4 Error: 0.025254 Align patch 3 22 left Iteration 1 Error: 0.956002 Iteration 2 Error: 0.188991 Iteration 3 Error: 0.037566 Align patch 4 21 left Iteration 1 Error: 1.000284 Iteration 2 Error: 0.149218 Iteration 3 Error: 0.070653 Iteration 4 Error: 0.019801 Align patch 5 20 left Iteration 1 Error: 0.955811 Iteration 2 Error: 0.171926 Iteration 3 Error: 0.054247 Iteration 4 Error: 0.022171 Align patch 6 19 left Iteration 1 Error: 0.871523 Iteration 2 Error: 0.088473 Iteration 3 Error: 0.039190 Align patch 7 18 left Iteration 1 Error: 0.872614 Iteration 2 Error: 0.096045 Iteration 3 Error: 0.050686 Iteration 4 Error: 0.016464 Align patch 8 17 left Iteration 1 Error: 0.953181 Iteration 2 Error: 0.246887 Iteration 3 Error: 0.043234 Align patch 9 16 left Iteration 1 Error: 0.843684 Iteration 2 Error: 0.284380 Iteration 3 Error: 0.089561 Iteration 4 Error: 0.040416 Align patch 10 15 left Iteration 1 Error: 1.271325 Iteration 2 Error: 0.226889 Iteration 3 Error: 0.079929 Iteration 4 Error: 0.020150 Align patch 11 14 left Iteration 1 Error: 1.392577 Iteration 2 Error: 0.190361 Iteration 3 Error: 0.106330 Iteration 4 Error: 0.027583 Align patch 12 13 left Iteration 1 Error: 0.722556 Iteration 2 Error: 0.154739 Iteration 3 Error: 0.043331 Align patch 13 12 left Iteration 1 Error: 0.731498 Iteration 2 Error: 0.131031 Iteration 3 Error: 0.047397 Align patch 14 11 left Iteration 1 Error: 0.956571 Iteration 2 Error: 0.162546 Iteration 3 Error: 0.047107 Align patch 15 10 left Iteration 1 Error: 0.940760 Iteration 2 Error: 0.215043 Iteration 3 Error: 0.092015 Iteration 4 Error: 0.041664 Align patch 16 9 left Iteration 1 Error: 1.034007 Iteration 2 Error: 0.276624 Iteration 3 Error: 0.055252 Iteration 4 Error: 0.036936 Align patch 17 8 left Iteration 1 Error: 0.639684 Iteration 2 Error: 0.096018 Iteration 3 Error: 0.029183 Align patch 18 7 left Iteration 1 Error: 1.008419 Iteration 2 Error: 0.252264 Iteration 3 Error: 0.066386 Iteration 4 Error: 0.037849 Align patch 19 6 left Iteration 1 Error: 0.802090 Iteration 2 Error: 0.157236 Iteration 3 Error: 0.050899 Iteration 4 Error: 0.017844 Align patch 20 5 left Iteration 1 Error: 0.636270 Iteration 2 Error: 0.121014 Iteration 3 Error: 0.063869 Iteration 4 Error: 0.020505 Align patch 21 4 left Iteration 1 Error: 1.034458 Iteration 2 Error: 0.375704 Iteration 3 Error: 0.114188 Iteration 4 Error: 0.053750 Iteration 5 Error: 0.022068 Align patch 22 3 left Iteration 1 Error: 0.874776 Iteration 2 Error: 0.091549 Iteration 3 Error: 0.018511 Align patch 23 2 left Iteration 1 Error: 0.843490 Iteration 2 Error: 0.277039 Iteration 3 Error: 0.085456 Iteration 4 Error: 0.033231 Align patch 24 1 left Iteration 1 Error: 0.590720 Iteration 2 Error: 0.154493 Iteration 3 Error: 0.043909 Align patch 25 0 left Iteration 1 Error: 1.040734 Iteration 2 Error: 0.176909 Iteration 3 Error: 0.047130 3D Fitting completed. Patch alignment time: 19.11(sec) Local motion has been corrected. Process thread exits. Computational time: 37.442284 sec Total time: 55.008022 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00016hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00016hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.893805s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00016hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.965099s ........................................ >>>>>>TIME<<<<<< FFT: 1.337810s Defocus_U Defocus_V Angle CCC 27611.35 27013.65 87.50 0.044503 Final Values Defocus_U Defocus_V Angle CCC 27029.30 27576.95 1.59 0.073387 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00016hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00016hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.992e-02 CC threshold: 0.734 Mean Std: 42.72 6.97 Num Hot pixels: 217 Hot pixel threshold: 84.53 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.150719 Iteration 2 Error: 0.391032 Iteration 3 Error: 0.118321 Iteration 4 Error: 0.044398 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.06 -0.26 ...... Frame ( 3) shift: -0.13 -0.52 ...... Frame ( 4) shift: -0.19 -0.78 ...... Frame ( 5) shift: -0.26 -1.04 ...... Frame ( 6) shift: -0.21 -1.15 ...... Frame ( 7) shift: -0.03 -1.12 ...... Frame ( 8) shift: 0.14 -1.08 ...... Frame ( 9) shift: 0.28 -0.99 ...... Frame ( 10) shift: 0.37 -0.83 ...... Frame ( 11) shift: 0.47 -0.68 ...... Frame ( 12) shift: 0.61 -0.53 ...... Frame ( 13) shift: 0.80 -0.37 ...... Frame ( 14) shift: 0.99 -0.22 ...... Frame ( 15) shift: 1.17 -0.06 ...... Frame ( 16) shift: 1.33 0.09 ...... Frame ( 17) shift: 1.49 0.25 ...... Frame ( 18) shift: 1.67 0.38 ...... Frame ( 19) shift: 1.87 0.48 ...... Frame ( 20) shift: 2.06 0.58 ...... Frame ( 21) shift: 2.19 0.67 ...... Frame ( 22) shift: 2.26 0.76 ...... Frame ( 23) shift: 2.32 0.85 ...... Frame ( 24) shift: 2.40 0.93 ...... Frame ( 25) shift: 2.50 1.02 ...... Frame ( 26) shift: 2.60 1.10 ...... Frame ( 27) shift: 2.67 1.15 ...... Frame ( 28) shift: 2.71 1.15 ...... Frame ( 29) shift: 2.76 1.15 ...... Frame ( 30) shift: 2.79 1.15 ...... Frame ( 31) shift: 2.82 1.15 ...... Frame ( 32) shift: 2.84 1.15 ...... Frame ( 33) shift: 2.96 1.17 ...... Frame ( 34) shift: 3.15 1.21 ...... Frame ( 35) shift: 3.35 1.25 ...... Frame ( 36) shift: 3.48 1.28 ...... Frame ( 37) shift: 3.56 1.29 ...... Frame ( 38) shift: 3.64 1.31 ...... Frame ( 39) shift: 3.72 1.33 ...... Frame ( 40) shift: 3.79 1.34 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.917230 Iteration 2 Error: 0.111822 Iteration 3 Error: 0.031398 Align patch 2 23 left Iteration 1 Error: 0.606094 Iteration 2 Error: 0.116987 Iteration 3 Error: 0.027447 Align patch 3 22 left Iteration 1 Error: 1.314855 Iteration 2 Error: 0.177450 Iteration 3 Error: 0.050686 Iteration 4 Error: 0.020986 Align patch 4 21 left Iteration 1 Error: 1.133443 Iteration 2 Error: 0.132173 Iteration 3 Error: 0.037945 Align patch 5 20 left Iteration 1 Error: 1.113086 Iteration 2 Error: 0.180467 Iteration 3 Error: 0.036955 Align patch 6 19 left Iteration 1 Error: 1.042434 Iteration 2 Error: 0.097350 Iteration 3 Error: 0.022982 Align patch 7 18 left Iteration 1 Error: 0.706332 Iteration 2 Error: 0.121734 Iteration 3 Error: 0.034855 Align patch 8 17 left Iteration 1 Error: 1.073724 Iteration 2 Error: 0.256996 Iteration 3 Error: 0.103044 Iteration 4 Error: 0.060185 Iteration 5 Error: 0.032402 Align patch 9 16 left Iteration 1 Error: 0.758004 Iteration 2 Error: 0.167487 Iteration 3 Error: 0.067650 Iteration 4 Error: 0.024858 Align patch 10 15 left Iteration 1 Error: 0.647451 Iteration 2 Error: 0.138880 Iteration 3 Error: 0.032444 Align patch 11 14 left Iteration 1 Error: 0.973037 Iteration 2 Error: 0.190092 Iteration 3 Error: 0.055747 Iteration 4 Error: 0.024887 Align patch 12 13 left Iteration 1 Error: 0.717499 Iteration 2 Error: 0.155032 Iteration 3 Error: 0.048785 Align patch 13 12 left Iteration 1 Error: 0.847523 Iteration 2 Error: 0.149952 Iteration 3 Error: 0.048827 Align patch 14 11 left Iteration 1 Error: 1.037803 Iteration 2 Error: 0.104729 Iteration 3 Error: 0.028746 Align patch 15 10 left Iteration 1 Error: 0.603068 Iteration 2 Error: 0.090285 Iteration 3 Error: 0.019401 Align patch 16 9 left Iteration 1 Error: 1.238426 Iteration 2 Error: 0.125230 Iteration 3 Error: 0.042405 Align patch 17 8 left Iteration 1 Error: 0.956515 Iteration 2 Error: 0.122531 Iteration 3 Error: 0.035772 Align patch 18 7 left Iteration 1 Error: 0.634951 Iteration 2 Error: 0.166352 Iteration 3 Error: 0.063768 Iteration 4 Error: 0.016932 Align patch 19 6 left Iteration 1 Error: 0.702365 Iteration 2 Error: 0.185071 Iteration 3 Error: 0.075269 Iteration 4 Error: 0.031063 Align patch 20 5 left Iteration 1 Error: 0.854894 Iteration 2 Error: 0.217519 Iteration 3 Error: 0.057486 Iteration 4 Error: 0.020674 Align patch 21 4 left Iteration 1 Error: 0.870539 Iteration 2 Error: 0.146218 Iteration 3 Error: 0.023374 Align patch 22 3 left Iteration 1 Error: 0.868386 Iteration 2 Error: 0.127725 Iteration 3 Error: 0.040651 Align patch 23 2 left Iteration 1 Error: 1.035134 Iteration 2 Error: 0.153336 Iteration 3 Error: 0.073432 Iteration 4 Error: 0.023449 Align patch 24 1 left Iteration 1 Error: 0.883374 Iteration 2 Error: 0.205703 Iteration 3 Error: 0.052824 Iteration 4 Error: 0.025821 Align patch 25 0 left Iteration 1 Error: 0.747559 Iteration 2 Error: 0.159946 Iteration 3 Error: 0.057403 Iteration 4 Error: 0.028000 3D Fitting completed. Patch alignment time: 19.68(sec) Local motion has been corrected. Process thread exits. Computational time: 35.816448 sec Total time: 44.251938 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00016hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00016hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.582310s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00016hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.902301s ........................................ >>>>>>TIME<<<<<< FFT: 1.329275s Defocus_U Defocus_V Angle CCC 29084.13 28287.11 84.48 0.041587 Final Values Defocus_U Defocus_V Angle CCC 29071.62 28299.62 84.48 0.068070 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00017hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00017hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.987e-02 CC threshold: 0.734 Mean Std: 41.88 6.88 Num Hot pixels: 194 Hot pixel threshold: 83.18 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.596752 Iteration 2 Error: 0.304010 Iteration 3 Error: 0.083833 Iteration 4 Error: 0.033606 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.09 -0.05 ...... Frame ( 3) shift: 0.19 -0.11 ...... Frame ( 4) shift: 0.28 -0.16 ...... Frame ( 5) shift: 0.37 -0.21 ...... Frame ( 6) shift: 0.49 -0.19 ...... Frame ( 7) shift: 0.64 -0.09 ...... Frame ( 8) shift: 0.79 0.02 ...... Frame ( 9) shift: 0.89 0.11 ...... Frame ( 10) shift: 0.94 0.19 ...... Frame ( 11) shift: 1.00 0.27 ...... Frame ( 12) shift: 1.07 0.38 ...... Frame ( 13) shift: 1.17 0.50 ...... Frame ( 14) shift: 1.27 0.62 ...... Frame ( 15) shift: 1.36 0.73 ...... Frame ( 16) shift: 1.46 0.81 ...... Frame ( 17) shift: 1.55 0.89 ...... Frame ( 18) shift: 1.62 0.95 ...... Frame ( 19) shift: 1.67 0.98 ...... Frame ( 20) shift: 1.72 1.01 ...... Frame ( 21) shift: 1.82 1.07 ...... Frame ( 22) shift: 1.96 1.16 ...... Frame ( 23) shift: 2.10 1.25 ...... Frame ( 24) shift: 2.21 1.31 ...... Frame ( 25) shift: 2.30 1.35 ...... Frame ( 26) shift: 2.39 1.39 ...... Frame ( 27) shift: 2.50 1.40 ...... Frame ( 28) shift: 2.62 1.37 ...... Frame ( 29) shift: 2.75 1.35 ...... Frame ( 30) shift: 2.82 1.38 ...... Frame ( 31) shift: 2.83 1.47 ...... Frame ( 32) shift: 2.85 1.55 ...... Frame ( 33) shift: 2.89 1.55 ...... Frame ( 34) shift: 2.95 1.45 ...... Frame ( 35) shift: 3.01 1.36 ...... Frame ( 36) shift: 3.11 1.32 ...... Frame ( 37) shift: 3.24 1.36 ...... Frame ( 38) shift: 3.38 1.39 ...... Frame ( 39) shift: 3.51 1.43 ...... Frame ( 40) shift: 3.64 1.46 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.741306 Iteration 2 Error: 0.240107 Iteration 3 Error: 0.053964 Iteration 4 Error: 0.013464 Align patch 2 23 left Iteration 1 Error: 0.896372 Iteration 2 Error: 0.163965 Iteration 3 Error: 0.070109 Iteration 4 Error: 0.027386 Align patch 3 22 left Iteration 1 Error: 1.670398 Iteration 2 Error: 0.273698 Iteration 3 Error: 0.069116 Iteration 4 Error: 0.038783 Align patch 4 21 left Iteration 1 Error: 1.176539 Iteration 2 Error: 0.281474 Iteration 3 Error: 0.124279 Iteration 4 Error: 0.039666 Align patch 5 20 left Iteration 1 Error: 0.947389 Iteration 2 Error: 0.193365 Iteration 3 Error: 0.049873 Align patch 6 19 left Iteration 1 Error: 1.689897 Iteration 2 Error: 0.223217 Iteration 3 Error: 0.068071 Iteration 4 Error: 0.021139 Align patch 7 18 left Iteration 1 Error: 0.573537 Iteration 2 Error: 0.201228 Iteration 3 Error: 0.058755 Iteration 4 Error: 0.029095 Align patch 8 17 left Iteration 1 Error: 0.764814 Iteration 2 Error: 0.109249 Iteration 3 Error: 0.049352 Align patch 9 16 left Iteration 1 Error: 0.666872 Iteration 2 Error: 0.103793 Iteration 3 Error: 0.023944 Align patch 10 15 left Iteration 1 Error: 0.987101 Iteration 2 Error: 0.222898 Iteration 3 Error: 0.084835 Iteration 4 Error: 0.023251 Align patch 11 14 left Iteration 1 Error: 1.109928 Iteration 2 Error: 0.122990 Iteration 3 Error: 0.034739 Align patch 12 13 left Iteration 1 Error: 1.014958 Iteration 2 Error: 0.180527 Iteration 3 Error: 0.055587 Iteration 4 Error: 0.018881 Align patch 13 12 left Iteration 1 Error: 0.936375 Iteration 2 Error: 0.136095 Iteration 3 Error: 0.028614 Align patch 14 11 left Iteration 1 Error: 0.999165 Iteration 2 Error: 0.197655 Iteration 3 Error: 0.044991 Align patch 15 10 left Iteration 1 Error: 1.314818 Iteration 2 Error: 0.233737 Iteration 3 Error: 0.054128 Iteration 4 Error: 0.019106 Align patch 16 9 left Iteration 1 Error: 0.759944 Iteration 2 Error: 0.113428 Iteration 3 Error: 0.025301 Align patch 17 8 left Iteration 1 Error: 0.514466 Iteration 2 Error: 0.083723 Iteration 3 Error: 0.025541 Align patch 18 7 left Iteration 1 Error: 0.715954 Iteration 2 Error: 0.142500 Iteration 3 Error: 0.044436 Align patch 19 6 left Iteration 1 Error: 1.467675 Iteration 2 Error: 0.191383 Iteration 3 Error: 0.050483 Iteration 4 Error: 0.029721 Align patch 20 5 left Iteration 1 Error: 1.018512 Iteration 2 Error: 0.216941 Iteration 3 Error: 0.058476 Iteration 4 Error: 0.017765 Align patch 21 4 left Iteration 1 Error: 0.683527 Iteration 2 Error: 0.109086 Iteration 3 Error: 0.028742 Align patch 22 3 left Iteration 1 Error: 0.766645 Iteration 2 Error: 0.171783 Iteration 3 Error: 0.046547 Align patch 23 2 left Iteration 1 Error: 0.989421 Iteration 2 Error: 0.182574 Iteration 3 Error: 0.031514 Align patch 24 1 left Iteration 1 Error: 0.623312 Iteration 2 Error: 0.106248 Iteration 3 Error: 0.044160 Align patch 25 0 left Iteration 1 Error: 1.055648 Iteration 2 Error: 0.172910 Iteration 3 Error: 0.032669 3D Fitting completed. Patch alignment time: 18.96(sec) Local motion has been corrected. Process thread exits. Computational time: 34.528839 sec Total time: 46.472889 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00017hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00017hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.828964s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00017hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 4.197702s ........................................ >>>>>>TIME<<<<<< FFT: 1.399041s Defocus_U Defocus_V Angle CCC 24105.46 24785.16 8.89 0.044297 Final Values Defocus_U Defocus_V Angle CCC 24108.62 24778.95 9.83 0.071605 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00017hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00017hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.991e-02 CC threshold: 0.734 Mean Std: 41.44 6.85 Num Hot pixels: 203 Hot pixel threshold: 82.56 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.492066 Iteration 2 Error: 0.252662 Iteration 3 Error: 0.075203 Iteration 4 Error: 0.028149 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.11 0.03 ...... Frame ( 3) shift: 0.22 0.07 ...... Frame ( 4) shift: 0.33 0.10 ...... Frame ( 5) shift: 0.45 0.14 ...... Frame ( 6) shift: 0.56 0.19 ...... Frame ( 7) shift: 0.68 0.27 ...... Frame ( 8) shift: 0.80 0.35 ...... Frame ( 9) shift: 0.90 0.42 ...... Frame ( 10) shift: 0.99 0.49 ...... Frame ( 11) shift: 1.07 0.56 ...... Frame ( 12) shift: 1.14 0.60 ...... Frame ( 13) shift: 1.20 0.60 ...... Frame ( 14) shift: 1.25 0.61 ...... Frame ( 15) shift: 1.30 0.65 ...... Frame ( 16) shift: 1.35 0.74 ...... Frame ( 17) shift: 1.40 0.82 ...... Frame ( 18) shift: 1.46 0.91 ...... Frame ( 19) shift: 1.54 1.01 ...... Frame ( 20) shift: 1.62 1.11 ...... Frame ( 21) shift: 1.69 1.18 ...... Frame ( 22) shift: 1.74 1.21 ...... Frame ( 23) shift: 1.79 1.24 ...... Frame ( 24) shift: 1.89 1.29 ...... Frame ( 25) shift: 2.04 1.37 ...... Frame ( 26) shift: 2.19 1.45 ...... Frame ( 27) shift: 2.28 1.49 ...... Frame ( 28) shift: 2.32 1.49 ...... Frame ( 29) shift: 2.35 1.48 ...... Frame ( 30) shift: 2.43 1.51 ...... Frame ( 31) shift: 2.54 1.56 ...... Frame ( 32) shift: 2.66 1.61 ...... Frame ( 33) shift: 2.71 1.63 ...... Frame ( 34) shift: 2.71 1.62 ...... Frame ( 35) shift: 2.71 1.61 ...... Frame ( 36) shift: 2.72 1.59 ...... Frame ( 37) shift: 2.75 1.56 ...... Frame ( 38) shift: 2.78 1.53 ...... Frame ( 39) shift: 2.81 1.50 ...... Frame ( 40) shift: 2.84 1.47 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.621691 Iteration 2 Error: 0.156807 Iteration 3 Error: 0.052861 Iteration 4 Error: 0.020673 Align patch 2 23 left Iteration 1 Error: 1.569683 Iteration 2 Error: 0.138752 Iteration 3 Error: 0.045721 Align patch 3 22 left Iteration 1 Error: 1.208566 Iteration 2 Error: 0.196694 Iteration 3 Error: 0.064224 Iteration 4 Error: 0.012919 Align patch 4 21 left Iteration 1 Error: 1.018725 Iteration 2 Error: 0.231016 Iteration 3 Error: 0.080352 Iteration 4 Error: 0.030592 Align patch 5 20 left Iteration 1 Error: 0.597084 Iteration 2 Error: 0.091915 Iteration 3 Error: 0.026414 Align patch 6 19 left Iteration 1 Error: 1.098048 Iteration 2 Error: 0.112646 Iteration 3 Error: 0.025644 Align patch 7 18 left Iteration 1 Error: 0.669782 Iteration 2 Error: 0.135095 Iteration 3 Error: 0.024545 Align patch 8 17 left Iteration 1 Error: 0.656689 Iteration 2 Error: 0.140435 Iteration 3 Error: 0.050418 Iteration 4 Error: 0.017616 Align patch 9 16 left Iteration 1 Error: 0.718784 Iteration 2 Error: 0.118109 Iteration 3 Error: 0.031177 Align patch 10 15 left Iteration 1 Error: 0.740559 Iteration 2 Error: 0.127406 Iteration 3 Error: 0.023822 Align patch 11 14 left Iteration 1 Error: 0.901155 Iteration 2 Error: 0.166392 Iteration 3 Error: 0.048057 Align patch 12 13 left Iteration 1 Error: 0.843142 Iteration 2 Error: 0.213022 Iteration 3 Error: 0.048437 Align patch 13 12 left Iteration 1 Error: 0.574423 Iteration 2 Error: 0.100611 Iteration 3 Error: 0.037652 Align patch 14 11 left Iteration 1 Error: 1.096107 Iteration 2 Error: 0.215705 Iteration 3 Error: 0.053252 Iteration 4 Error: 0.016869 Align patch 15 10 left Iteration 1 Error: 0.682370 Iteration 2 Error: 0.204925 Iteration 3 Error: 0.047972 Align patch 16 9 left Iteration 1 Error: 1.088593 Iteration 2 Error: 0.120898 Iteration 3 Error: 0.027182 Align patch 17 8 left Iteration 1 Error: 0.796221 Iteration 2 Error: 0.207775 Iteration 3 Error: 0.059117 Iteration 4 Error: 0.017261 Align patch 18 7 left Iteration 1 Error: 0.760605 Iteration 2 Error: 0.131990 Iteration 3 Error: 0.028289 Align patch 19 6 left Iteration 1 Error: 0.722451 Iteration 2 Error: 0.152148 Iteration 3 Error: 0.053212 Iteration 4 Error: 0.018355 Align patch 20 5 left Iteration 1 Error: 1.428069 Iteration 2 Error: 0.191415 Iteration 3 Error: 0.066162 Iteration 4 Error: 0.013788 Align patch 21 4 left Iteration 1 Error: 1.170927 Iteration 2 Error: 0.229286 Iteration 3 Error: 0.068836 Iteration 4 Error: 0.040101 Align patch 22 3 left Iteration 1 Error: 1.070103 Iteration 2 Error: 0.129450 Iteration 3 Error: 0.037774 Align patch 23 2 left Iteration 1 Error: 0.684681 Iteration 2 Error: 0.113860 Iteration 3 Error: 0.019182 Align patch 24 1 left Iteration 1 Error: 0.607570 Iteration 2 Error: 0.162206 Iteration 3 Error: 0.047077 Align patch 25 0 left Iteration 1 Error: 1.608791 Iteration 2 Error: 0.209926 Iteration 3 Error: 0.043896 3D Fitting completed. Patch alignment time: 18.72(sec) Local motion has been corrected. Process thread exits. Computational time: 37.514885 sec Total time: 45.850662 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00017hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00017hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.570253s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00017hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.302615s ........................................ >>>>>>TIME<<<<<< FFT: 1.495433s Defocus_U Defocus_V Angle CCC 23539.06 24394.53 4.98 0.038387 Final Values Defocus_U Defocus_V Angle CCC 23539.06 24407.03 4.67 0.062828 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00017hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00017hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.997e-02 CC threshold: 0.734 Mean Std: 42.23 6.92 Num Hot pixels: 183 Hot pixel threshold: 83.73 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.154178 Iteration 2 Error: 0.222491 Iteration 3 Error: 0.050013 Iteration 4 Error: 0.020301 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.02 -0.00 ...... Frame ( 3) shift: -0.05 -0.00 ...... Frame ( 4) shift: -0.07 -0.00 ...... Frame ( 5) shift: -0.10 -0.01 ...... Frame ( 6) shift: -0.09 0.06 ...... Frame ( 7) shift: -0.05 0.19 ...... Frame ( 8) shift: -0.00 0.32 ...... Frame ( 9) shift: 0.06 0.43 ...... Frame ( 10) shift: 0.12 0.52 ...... Frame ( 11) shift: 0.19 0.60 ...... Frame ( 12) shift: 0.25 0.69 ...... Frame ( 13) shift: 0.28 0.77 ...... Frame ( 14) shift: 0.32 0.85 ...... Frame ( 15) shift: 0.36 0.92 ...... Frame ( 16) shift: 0.39 0.97 ...... Frame ( 17) shift: 0.42 1.03 ...... Frame ( 18) shift: 0.44 1.11 ...... Frame ( 19) shift: 0.44 1.23 ...... Frame ( 20) shift: 0.44 1.35 ...... Frame ( 21) shift: 0.49 1.45 ...... Frame ( 22) shift: 0.57 1.52 ...... Frame ( 23) shift: 0.66 1.60 ...... Frame ( 24) shift: 0.70 1.68 ...... Frame ( 25) shift: 0.72 1.75 ...... Frame ( 26) shift: 0.73 1.83 ...... Frame ( 27) shift: 0.78 1.84 ...... Frame ( 28) shift: 0.85 1.79 ...... Frame ( 29) shift: 0.93 1.74 ...... Frame ( 30) shift: 0.99 1.78 ...... Frame ( 31) shift: 1.05 1.90 ...... Frame ( 32) shift: 1.11 2.02 ...... Frame ( 33) shift: 1.10 2.08 ...... Frame ( 34) shift: 1.02 2.10 ...... Frame ( 35) shift: 0.95 2.11 ...... Frame ( 36) shift: 0.94 2.10 ...... Frame ( 37) shift: 1.00 2.05 ...... Frame ( 38) shift: 1.07 2.01 ...... Frame ( 39) shift: 1.13 1.96 ...... Frame ( 40) shift: 1.20 1.91 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.161368 Iteration 2 Error: 0.241444 Iteration 3 Error: 0.075704 Iteration 4 Error: 0.031661 Align patch 2 23 left Iteration 1 Error: 1.682696 Iteration 2 Error: 0.165978 Iteration 3 Error: 0.050968 Iteration 4 Error: 0.026937 Align patch 3 22 left Iteration 1 Error: 1.182411 Iteration 2 Error: 0.207517 Iteration 3 Error: 0.079376 Iteration 4 Error: 0.031167 Align patch 4 21 left Iteration 1 Error: 0.831642 Iteration 2 Error: 0.145878 Iteration 3 Error: 0.051900 Iteration 4 Error: 0.022055 Align patch 5 20 left Iteration 1 Error: 0.691805 Iteration 2 Error: 0.111948 Iteration 3 Error: 0.026570 Align patch 6 19 left Iteration 1 Error: 0.556494 Iteration 2 Error: 0.151737 Iteration 3 Error: 0.038543 Align patch 7 18 left Iteration 1 Error: 0.866770 Iteration 2 Error: 0.104920 Iteration 3 Error: 0.032427 Align patch 8 17 left Iteration 1 Error: 0.579589 Iteration 2 Error: 0.146799 Iteration 3 Error: 0.035495 Align patch 9 16 left Iteration 1 Error: 0.904850 Iteration 2 Error: 0.094579 Iteration 3 Error: 0.027489 Align patch 10 15 left Iteration 1 Error: 0.699154 Iteration 2 Error: 0.130009 Iteration 3 Error: 0.039866 Align patch 11 14 left Iteration 1 Error: 1.011041 Iteration 2 Error: 0.411803 Iteration 3 Error: 0.118065 Iteration 4 Error: 0.041411 Align patch 12 13 left Iteration 1 Error: 0.822990 Iteration 2 Error: 0.244275 Iteration 3 Error: 0.057034 Iteration 4 Error: 0.019686 Align patch 13 12 left Iteration 1 Error: 0.716109 Iteration 2 Error: 0.111546 Iteration 3 Error: 0.036926 Align patch 14 11 left Iteration 1 Error: 0.606216 Iteration 2 Error: 0.123513 Iteration 3 Error: 0.034593 Align patch 15 10 left Iteration 1 Error: 0.545335 Iteration 2 Error: 0.170996 Iteration 3 Error: 0.048632 Align patch 16 9 left Iteration 1 Error: 0.639623 Iteration 2 Error: 0.123616 Iteration 3 Error: 0.040119 Align patch 17 8 left Iteration 1 Error: 0.595770 Iteration 2 Error: 0.102227 Iteration 3 Error: 0.026462 Align patch 18 7 left Iteration 1 Error: 1.023685 Iteration 2 Error: 0.177956 Iteration 3 Error: 0.065270 Iteration 4 Error: 0.019724 Align patch 19 6 left Iteration 1 Error: 0.607965 Iteration 2 Error: 0.091284 Iteration 3 Error: 0.022628 Align patch 20 5 left Iteration 1 Error: 0.992294 Iteration 2 Error: 0.098959 Iteration 3 Error: 0.031982 Align patch 21 4 left Iteration 1 Error: 0.584185 Iteration 2 Error: 0.070463 Iteration 3 Error: 0.020685 Align patch 22 3 left Iteration 1 Error: 0.841762 Iteration 2 Error: 0.122705 Iteration 3 Error: 0.021601 Align patch 23 2 left Iteration 1 Error: 1.279857 Iteration 2 Error: 0.198373 Iteration 3 Error: 0.057876 Iteration 4 Error: 0.025579 Align patch 24 1 left Iteration 1 Error: 0.801496 Iteration 2 Error: 0.145888 Iteration 3 Error: 0.046548 Align patch 25 0 left Iteration 1 Error: 0.986736 Iteration 2 Error: 0.143430 Iteration 3 Error: 0.035313 3D Fitting completed. Patch alignment time: 17.75(sec) Local motion has been corrected. Process thread exits. Computational time: 35.722027 sec Total time: 46.295700 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00017hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00017hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 3.006888s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00017hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.915150s ........................................ >>>>>>TIME<<<<<< FFT: 1.399035s Defocus_U Defocus_V Angle CCC 23791.01 24396.53 2.03 0.041344 Final Values Defocus_U Defocus_V Angle CCC 23792.57 24391.84 1.71 0.065561 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00017hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00017hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.993e-02 CC threshold: 0.734 Mean Std: 41.53 6.87 Num Hot pixels: 183 Hot pixel threshold: 82.74 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.324003 Iteration 2 Error: 0.219485 Iteration 3 Error: 0.056721 Iteration 4 Error: 0.017631 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.00 0.03 ...... Frame ( 3) shift: -0.00 0.05 ...... Frame ( 4) shift: -0.01 0.08 ...... Frame ( 5) shift: -0.01 0.11 ...... Frame ( 6) shift: 0.02 0.18 ...... Frame ( 7) shift: 0.07 0.31 ...... Frame ( 8) shift: 0.12 0.45 ...... Frame ( 9) shift: 0.19 0.56 ...... Frame ( 10) shift: 0.29 0.67 ...... Frame ( 11) shift: 0.39 0.78 ...... Frame ( 12) shift: 0.43 0.92 ...... Frame ( 13) shift: 0.43 1.09 ...... Frame ( 14) shift: 0.42 1.26 ...... Frame ( 15) shift: 0.47 1.35 ...... Frame ( 16) shift: 0.56 1.35 ...... Frame ( 17) shift: 0.66 1.35 ...... Frame ( 18) shift: 0.73 1.37 ...... Frame ( 19) shift: 0.78 1.40 ...... Frame ( 20) shift: 0.83 1.43 ...... Frame ( 21) shift: 0.87 1.47 ...... Frame ( 22) shift: 0.90 1.54 ...... Frame ( 23) shift: 0.94 1.60 ...... Frame ( 24) shift: 0.97 1.65 ...... Frame ( 25) shift: 0.99 1.70 ...... Frame ( 26) shift: 1.00 1.74 ...... Frame ( 27) shift: 1.05 1.81 ...... Frame ( 28) shift: 1.11 1.89 ...... Frame ( 29) shift: 1.18 1.97 ...... Frame ( 30) shift: 1.21 2.02 ...... Frame ( 31) shift: 1.19 2.05 ...... Frame ( 32) shift: 1.18 2.07 ...... Frame ( 33) shift: 1.22 2.11 ...... Frame ( 34) shift: 1.29 2.16 ...... Frame ( 35) shift: 1.36 2.22 ...... Frame ( 36) shift: 1.41 2.26 ...... Frame ( 37) shift: 1.45 2.27 ...... Frame ( 38) shift: 1.48 2.29 ...... Frame ( 39) shift: 1.52 2.30 ...... Frame ( 40) shift: 1.55 2.32 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.208827 Iteration 2 Error: 0.311332 Iteration 3 Error: 0.090121 Iteration 4 Error: 0.036089 Align patch 2 23 left Iteration 1 Error: 1.452008 Iteration 2 Error: 0.174015 Iteration 3 Error: 0.054430 Iteration 4 Error: 0.023360 Align patch 3 22 left Iteration 1 Error: 0.887426 Iteration 2 Error: 0.149612 Iteration 3 Error: 0.079291 Iteration 4 Error: 0.022707 Align patch 4 21 left Iteration 1 Error: 1.000090 Iteration 2 Error: 0.148308 Iteration 3 Error: 0.020459 Align patch 5 20 left Iteration 1 Error: 0.759881 Iteration 2 Error: 0.100486 Iteration 3 Error: 0.033329 Align patch 6 19 left Iteration 1 Error: 1.101379 Iteration 2 Error: 0.185542 Iteration 3 Error: 0.044089 Align patch 7 18 left Iteration 1 Error: 0.800389 Iteration 2 Error: 0.139997 Iteration 3 Error: 0.036163 Align patch 8 17 left Iteration 1 Error: 0.926841 Iteration 2 Error: 0.176128 Iteration 3 Error: 0.042530 Align patch 9 16 left Iteration 1 Error: 0.692422 Iteration 2 Error: 0.085436 Iteration 3 Error: 0.023278 Align patch 10 15 left Iteration 1 Error: 0.926980 Iteration 2 Error: 0.176466 Iteration 3 Error: 0.046813 Align patch 11 14 left Iteration 1 Error: 0.510204 Iteration 2 Error: 0.092944 Iteration 3 Error: 0.020953 Align patch 12 13 left Iteration 1 Error: 1.049118 Iteration 2 Error: 0.158728 Iteration 3 Error: 0.039974 Align patch 13 12 left Iteration 1 Error: 0.939996 Iteration 2 Error: 0.222272 Iteration 3 Error: 0.044106 Align patch 14 11 left Iteration 1 Error: 0.921909 Iteration 2 Error: 0.206422 Iteration 3 Error: 0.049638 Align patch 15 10 left Iteration 1 Error: 0.694240 Iteration 2 Error: 0.160032 Iteration 3 Error: 0.030926 Align patch 16 9 left Iteration 1 Error: 1.208469 Iteration 2 Error: 0.197054 Iteration 3 Error: 0.058010 Iteration 4 Error: 0.017164 Align patch 17 8 left Iteration 1 Error: 1.166291 Iteration 2 Error: 0.190083 Iteration 3 Error: 0.029269 Align patch 18 7 left Iteration 1 Error: 0.692408 Iteration 2 Error: 0.147360 Iteration 3 Error: 0.036696 Align patch 19 6 left Iteration 1 Error: 0.870504 Iteration 2 Error: 0.147001 Iteration 3 Error: 0.039044 Align patch 20 5 left Iteration 1 Error: 0.517598 Iteration 2 Error: 0.107775 Iteration 3 Error: 0.018747 Align patch 21 4 left Iteration 1 Error: 0.751233 Iteration 2 Error: 0.099756 Iteration 3 Error: 0.033356 Align patch 22 3 left Iteration 1 Error: 0.883843 Iteration 2 Error: 0.121864 Iteration 3 Error: 0.028738 Align patch 23 2 left Iteration 1 Error: 0.935882 Iteration 2 Error: 0.204081 Iteration 3 Error: 0.042755 Align patch 24 1 left Iteration 1 Error: 0.796627 Iteration 2 Error: 0.126689 Iteration 3 Error: 0.019710 Align patch 25 0 left Iteration 1 Error: 0.708152 Iteration 2 Error: 0.081082 Iteration 3 Error: 0.018503 3D Fitting completed. Patch alignment time: 18.60(sec) Local motion has been corrected. Process thread exits. Computational time: 34.244541 sec Total time: 44.127563 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00017hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00017hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.595163s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00017hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.948122s ........................................ >>>>>>TIME<<<<<< FFT: 1.472863s Defocus_U Defocus_V Angle CCC 27855.55 27046.90 88.28 0.040579 Final Values Defocus_U Defocus_V Angle CCC 27855.56 27050.04 88.28 0.065195 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00018hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00018hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.992e-02 CC threshold: 0.734 Mean Std: 42.67 6.96 Num Hot pixels: 217 Hot pixel threshold: 84.45 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.291890 Iteration 2 Error: 0.510357 Iteration 3 Error: 0.165067 Iteration 4 Error: 0.056461 Iteration 5 Error: 0.029186 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.03 -0.17 ...... Frame ( 3) shift: -0.07 -0.34 ...... Frame ( 4) shift: -0.10 -0.51 ...... Frame ( 5) shift: -0.14 -0.69 ...... Frame ( 6) shift: -0.11 -0.71 ...... Frame ( 7) shift: -0.01 -0.58 ...... Frame ( 8) shift: 0.08 -0.46 ...... Frame ( 9) shift: 0.21 -0.30 ...... Frame ( 10) shift: 0.38 -0.10 ...... Frame ( 11) shift: 0.55 0.10 ...... Frame ( 12) shift: 0.67 0.24 ...... Frame ( 13) shift: 0.75 0.33 ...... Frame ( 14) shift: 0.83 0.41 ...... Frame ( 15) shift: 0.97 0.50 ...... Frame ( 16) shift: 1.17 0.59 ...... Frame ( 17) shift: 1.36 0.69 ...... Frame ( 18) shift: 1.54 0.75 ...... Frame ( 19) shift: 1.70 0.78 ...... Frame ( 20) shift: 1.87 0.81 ...... Frame ( 21) shift: 1.97 0.83 ...... Frame ( 22) shift: 2.01 0.82 ...... Frame ( 23) shift: 2.06 0.82 ...... Frame ( 24) shift: 2.12 0.84 ...... Frame ( 25) shift: 2.22 0.89 ...... Frame ( 26) shift: 2.31 0.94 ...... Frame ( 27) shift: 2.44 1.06 ...... Frame ( 28) shift: 2.62 1.26 ...... Frame ( 29) shift: 2.80 1.46 ...... Frame ( 30) shift: 2.94 1.61 ...... Frame ( 31) shift: 3.02 1.71 ...... Frame ( 32) shift: 3.11 1.80 ...... Frame ( 33) shift: 3.19 1.85 ...... Frame ( 34) shift: 3.28 1.86 ...... Frame ( 35) shift: 3.37 1.86 ...... Frame ( 36) shift: 3.49 1.91 ...... Frame ( 37) shift: 3.63 2.01 ...... Frame ( 38) shift: 3.78 2.11 ...... Frame ( 39) shift: 3.92 2.21 ...... Frame ( 40) shift: 4.07 2.31 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.858175 Iteration 2 Error: 0.207303 Iteration 3 Error: 0.064968 Iteration 4 Error: 0.036919 Align patch 2 23 left Iteration 1 Error: 0.939173 Iteration 2 Error: 0.163063 Iteration 3 Error: 0.033027 Align patch 3 22 left Iteration 1 Error: 1.407811 Iteration 2 Error: 0.250970 Iteration 3 Error: 0.054964 Iteration 4 Error: 0.019453 Align patch 4 21 left Iteration 1 Error: 0.711864 Iteration 2 Error: 0.125178 Iteration 3 Error: 0.023235 Align patch 5 20 left Iteration 1 Error: 0.688162 Iteration 2 Error: 0.178007 Iteration 3 Error: 0.046157 Align patch 6 19 left Iteration 1 Error: 0.765914 Iteration 2 Error: 0.127492 Iteration 3 Error: 0.039701 Align patch 7 18 left Iteration 1 Error: 1.350216 Iteration 2 Error: 0.294545 Iteration 3 Error: 0.099540 Iteration 4 Error: 0.040605 Align patch 8 17 left Iteration 1 Error: 0.875011 Iteration 2 Error: 0.158715 Iteration 3 Error: 0.056793 Iteration 4 Error: 0.016171 Align patch 9 16 left Iteration 1 Error: 0.626520 Iteration 2 Error: 0.146789 Iteration 3 Error: 0.065816 Iteration 4 Error: 0.023295 Align patch 10 15 left Iteration 1 Error: 0.737740 Iteration 2 Error: 0.123208 Iteration 3 Error: 0.037076 Align patch 11 14 left Iteration 1 Error: 0.750332 Iteration 2 Error: 0.126037 Iteration 3 Error: 0.044166 Align patch 12 13 left Iteration 1 Error: 0.705438 Iteration 2 Error: 0.247568 Iteration 3 Error: 0.088691 Iteration 4 Error: 0.043458 Align patch 13 12 left Iteration 1 Error: 0.894786 Iteration 2 Error: 0.291317 Iteration 3 Error: 0.138043 Iteration 4 Error: 0.036527 Align patch 14 11 left Iteration 1 Error: 0.786500 Iteration 2 Error: 0.146749 Iteration 3 Error: 0.078708 Iteration 4 Error: 0.034547 Align patch 15 10 left Iteration 1 Error: 0.726806 Iteration 2 Error: 0.105077 Iteration 3 Error: 0.037336 Align patch 16 9 left Iteration 1 Error: 1.166136 Iteration 2 Error: 0.478586 Iteration 3 Error: 0.091143 Iteration 4 Error: 0.039024 Align patch 17 8 left Iteration 1 Error: 1.652011 Iteration 2 Error: 0.429754 Iteration 3 Error: 0.092693 Iteration 4 Error: 0.059546 Iteration 5 Error: 0.017708 Align patch 18 7 left Iteration 1 Error: 0.695725 Iteration 2 Error: 0.136075 Iteration 3 Error: 0.033604 Align patch 19 6 left Iteration 1 Error: 0.654660 Iteration 2 Error: 0.203585 Iteration 3 Error: 0.072469 Iteration 4 Error: 0.026622 Align patch 20 5 left Iteration 1 Error: 0.439719 Iteration 2 Error: 0.083910 Iteration 3 Error: 0.048909 Align patch 21 4 left Iteration 1 Error: 0.852585 Iteration 2 Error: 0.189486 Iteration 3 Error: 0.041835 Align patch 22 3 left Iteration 1 Error: 0.787796 Iteration 2 Error: 0.170925 Iteration 3 Error: 0.049285 Align patch 23 2 left Iteration 1 Error: 0.781654 Iteration 2 Error: 0.196217 Iteration 3 Error: 0.073000 Iteration 4 Error: 0.029095 Align patch 24 1 left Iteration 1 Error: 0.771806 Iteration 2 Error: 0.122959 Iteration 3 Error: 0.039285 Align patch 25 0 left Iteration 1 Error: 0.742333 Iteration 2 Error: 0.169546 Iteration 3 Error: 0.073759 Iteration 4 Error: 0.032842 3D Fitting completed. Patch alignment time: 19.51(sec) Local motion has been corrected. Process thread exits. Computational time: 34.242653 sec Total time: 44.268200 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00018hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00018hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.564035s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00018hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.339401s ........................................ >>>>>>TIME<<<<<< FFT: 1.367121s Defocus_U Defocus_V Angle CCC 25121.09 25816.41 6.90 0.047957 Final Values Defocus_U Defocus_V Angle CCC 25139.84 25785.16 5.65 0.076248 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00018hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00018hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.995e-02 CC threshold: 0.734 Mean Std: 42.71 6.96 Num Hot pixels: 227 Hot pixel threshold: 84.48 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.375870 Iteration 2 Error: 0.490524 Iteration 3 Error: 0.150339 Iteration 4 Error: 0.054043 Iteration 5 Error: 0.024020 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.13 -0.21 ...... Frame ( 3) shift: -0.26 -0.42 ...... Frame ( 4) shift: -0.39 -0.63 ...... Frame ( 5) shift: -0.52 -0.84 ...... Frame ( 6) shift: -0.49 -0.88 ...... Frame ( 7) shift: -0.31 -0.77 ...... Frame ( 8) shift: -0.12 -0.65 ...... Frame ( 9) shift: 0.08 -0.48 ...... Frame ( 10) shift: 0.29 -0.24 ...... Frame ( 11) shift: 0.50 -0.01 ...... Frame ( 12) shift: 0.71 0.17 ...... Frame ( 13) shift: 0.92 0.29 ...... Frame ( 14) shift: 1.13 0.41 ...... Frame ( 15) shift: 1.30 0.53 ...... Frame ( 16) shift: 1.43 0.67 ...... Frame ( 17) shift: 1.56 0.80 ...... Frame ( 18) shift: 1.65 0.89 ...... Frame ( 19) shift: 1.71 0.95 ...... Frame ( 20) shift: 1.77 1.01 ...... Frame ( 21) shift: 1.87 1.04 ...... Frame ( 22) shift: 2.02 1.05 ...... Frame ( 23) shift: 2.17 1.05 ...... Frame ( 24) shift: 2.32 1.11 ...... Frame ( 25) shift: 2.45 1.23 ...... Frame ( 26) shift: 2.58 1.35 ...... Frame ( 27) shift: 2.71 1.43 ...... Frame ( 28) shift: 2.83 1.48 ...... Frame ( 29) shift: 2.96 1.52 ...... Frame ( 30) shift: 3.02 1.54 ...... Frame ( 31) shift: 3.03 1.53 ...... Frame ( 32) shift: 3.03 1.52 ...... Frame ( 33) shift: 3.11 1.57 ...... Frame ( 34) shift: 3.25 1.67 ...... Frame ( 35) shift: 3.40 1.78 ...... Frame ( 36) shift: 3.55 1.82 ...... Frame ( 37) shift: 3.69 1.82 ...... Frame ( 38) shift: 3.84 1.81 ...... Frame ( 39) shift: 3.98 1.81 ...... Frame ( 40) shift: 4.13 1.80 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.829659 Iteration 2 Error: 0.124688 Iteration 3 Error: 0.035806 Align patch 2 23 left Iteration 1 Error: 0.821498 Iteration 2 Error: 0.143460 Iteration 3 Error: 0.044280 Align patch 3 22 left Iteration 1 Error: 0.839419 Iteration 2 Error: 0.150249 Iteration 3 Error: 0.033041 Align patch 4 21 left Iteration 1 Error: 1.207006 Iteration 2 Error: 0.194180 Iteration 3 Error: 0.044425 Align patch 5 20 left Iteration 1 Error: 0.863105 Iteration 2 Error: 0.219176 Iteration 3 Error: 0.057373 Iteration 4 Error: 0.036474 Align patch 6 19 left Iteration 1 Error: 1.344611 Iteration 2 Error: 0.213416 Iteration 3 Error: 0.087447 Iteration 4 Error: 0.017661 Align patch 7 18 left Iteration 1 Error: 1.382591 Iteration 2 Error: 0.195481 Iteration 3 Error: 0.058798 Iteration 4 Error: 0.015022 Align patch 8 17 left Iteration 1 Error: 0.654868 Iteration 2 Error: 0.076000 Iteration 3 Error: 0.025174 Align patch 9 16 left Iteration 1 Error: 0.953923 Iteration 2 Error: 0.187882 Iteration 3 Error: 0.050203 Iteration 4 Error: 0.019835 Align patch 10 15 left Iteration 1 Error: 0.902278 Iteration 2 Error: 0.150508 Iteration 3 Error: 0.056923 Iteration 4 Error: 0.028940 Align patch 11 14 left Iteration 1 Error: 1.242307 Iteration 2 Error: 0.381720 Iteration 3 Error: 0.170394 Iteration 4 Error: 0.069400 Iteration 5 Error: 0.044698 Align patch 12 13 left Iteration 1 Error: 1.404995 Iteration 2 Error: 0.449399 Iteration 3 Error: 0.123427 Iteration 4 Error: 0.058427 Iteration 5 Error: 0.021542 Align patch 13 12 left Iteration 1 Error: 0.885781 Iteration 2 Error: 0.101920 Iteration 3 Error: 0.039765 Align patch 14 11 left Iteration 1 Error: 0.719298 Iteration 2 Error: 0.166017 Iteration 3 Error: 0.087673 Iteration 4 Error: 0.042502 Align patch 15 10 left Iteration 1 Error: 1.132782 Iteration 2 Error: 0.280836 Iteration 3 Error: 0.091984 Iteration 4 Error: 0.037201 Align patch 16 9 left Iteration 1 Error: 0.698755 Iteration 2 Error: 0.143435 Iteration 3 Error: 0.062171 Iteration 4 Error: 0.018151 Align patch 17 8 left Iteration 1 Error: 0.681109 Iteration 2 Error: 0.116070 Iteration 3 Error: 0.041793 Align patch 18 7 left Iteration 1 Error: 0.680079 Iteration 2 Error: 0.199325 Iteration 3 Error: 0.084823 Iteration 4 Error: 0.030595 Align patch 19 6 left Iteration 1 Error: 1.121758 Iteration 2 Error: 0.170492 Iteration 3 Error: 0.049869 Align patch 20 5 left Iteration 1 Error: 1.179507 Iteration 2 Error: 0.266862 Iteration 3 Error: 0.071742 Iteration 4 Error: 0.029664 Align patch 21 4 left Iteration 1 Error: 0.729129 Iteration 2 Error: 0.158919 Iteration 3 Error: 0.040774 Align patch 22 3 left Iteration 1 Error: 0.669341 Iteration 2 Error: 0.130217 Iteration 3 Error: 0.045148 Align patch 23 2 left Iteration 1 Error: 0.747029 Iteration 2 Error: 0.255983 Iteration 3 Error: 0.071838 Iteration 4 Error: 0.036512 Align patch 24 1 left Iteration 1 Error: 0.927764 Iteration 2 Error: 0.247630 Iteration 3 Error: 0.062269 Iteration 4 Error: 0.023772 Align patch 25 0 left Iteration 1 Error: 0.764639 Iteration 2 Error: 0.184906 Iteration 3 Error: 0.061552 Iteration 4 Error: 0.022844 3D Fitting completed. Patch alignment time: 18.87(sec) Local motion has been corrected. Process thread exits. Computational time: 33.568985 sec Total time: 40.896000 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00018hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00018hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.760230s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00018hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.464559s ........................................ >>>>>>TIME<<<<<< FFT: 1.219611s Defocus_U Defocus_V Angle CCC 27339.79 28230.53 2.55 0.042227 Final Values Defocus_U Defocus_V Angle CCC 27350.74 28241.61 2.55 0.069798 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00018hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00018hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.987e-02 CC threshold: 0.733 Mean Std: 42.02 7.03 Num Hot pixels: 182 Hot pixel threshold: 84.19 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.907415 Iteration 2 Error: 0.370735 Iteration 3 Error: 0.122170 Iteration 4 Error: 0.043475 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.02 0.13 ...... Frame ( 3) shift: 0.04 0.26 ...... Frame ( 4) shift: 0.06 0.39 ...... Frame ( 5) shift: 0.07 0.52 ...... Frame ( 6) shift: 0.12 0.65 ...... Frame ( 7) shift: 0.21 0.78 ...... Frame ( 8) shift: 0.29 0.92 ...... Frame ( 9) shift: 0.36 1.09 ...... Frame ( 10) shift: 0.41 1.31 ...... Frame ( 11) shift: 0.47 1.54 ...... Frame ( 12) shift: 0.48 1.72 ...... Frame ( 13) shift: 0.45 1.85 ...... Frame ( 14) shift: 0.42 1.99 ...... Frame ( 15) shift: 0.41 2.17 ...... Frame ( 16) shift: 0.41 2.39 ...... Frame ( 17) shift: 0.42 2.60 ...... Frame ( 18) shift: 0.44 2.73 ...... Frame ( 19) shift: 0.49 2.77 ...... Frame ( 20) shift: 0.54 2.81 ...... Frame ( 21) shift: 0.53 2.85 ...... Frame ( 22) shift: 0.45 2.88 ...... Frame ( 23) shift: 0.38 2.92 ...... Frame ( 24) shift: 0.34 3.00 ...... Frame ( 25) shift: 0.35 3.11 ...... Frame ( 26) shift: 0.36 3.23 ...... Frame ( 27) shift: 0.35 3.30 ...... Frame ( 28) shift: 0.34 3.32 ...... Frame ( 29) shift: 0.32 3.35 ...... Frame ( 30) shift: 0.27 3.42 ...... Frame ( 31) shift: 0.20 3.54 ...... Frame ( 32) shift: 0.12 3.67 ...... Frame ( 33) shift: 0.02 3.71 ...... Frame ( 34) shift: -0.10 3.68 ...... Frame ( 35) shift: -0.23 3.65 ...... Frame ( 36) shift: -0.28 3.67 ...... Frame ( 37) shift: -0.27 3.75 ...... Frame ( 38) shift: -0.26 3.82 ...... Frame ( 39) shift: -0.25 3.90 ...... Frame ( 40) shift: -0.23 3.97 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.041719 Iteration 2 Error: 0.191217 Iteration 3 Error: 0.032505 Align patch 2 23 left Iteration 1 Error: 0.827795 Iteration 2 Error: 0.184970 Iteration 3 Error: 0.031480 Align patch 3 22 left Iteration 1 Error: 0.914197 Iteration 2 Error: 0.137120 Iteration 3 Error: 0.041939 Align patch 4 21 left Iteration 1 Error: 1.379770 Iteration 2 Error: 0.331450 Iteration 3 Error: 0.168298 Iteration 4 Error: 0.075620 Iteration 5 Error: 0.045379 Align patch 5 20 left Iteration 1 Error: 3.891991 Iteration 2 Error: 1.349883 Iteration 3 Error: 1.439185 Iteration 4 Error: 0.684941 Iteration 5 Error: 0.575737 Align patch 5 20 left Iteration 1 Error: 3.692543 Iteration 2 Error: 1.209932 Iteration 3 Error: 0.684172 Iteration 4 Error: 0.383720 Iteration 5 Error: 0.266794 Align patch 6 19 left Iteration 1 Error: 0.737186 Iteration 2 Error: 0.089118 Iteration 3 Error: 0.035258 Align patch 7 18 left Iteration 1 Error: 1.181257 Iteration 2 Error: 0.336961 Iteration 3 Error: 0.066449 Iteration 4 Error: 0.029757 Align patch 8 17 left Iteration 1 Error: 2.558477 Iteration 2 Error: 1.323900 Iteration 3 Error: 1.246875 Iteration 4 Error: 0.739783 Iteration 5 Error: 0.399755 Align patch 8 17 left Iteration 1 Error: 3.722987 Iteration 2 Error: 1.051608 Iteration 3 Error: 0.502404 Iteration 4 Error: 0.228656 Iteration 5 Error: 0.127855 Align patch 9 16 left Iteration 1 Error: 4.843960 Iteration 2 Error: 6.797609 Iteration 3 Error: 3.725110 Iteration 4 Error: 1.945615 Iteration 5 Error: 0.994133 Align patch 9 16 left Iteration 1 Error: 5.073249 Iteration 2 Error: 2.004520 Iteration 3 Error: 1.190720 Iteration 4 Error: 0.868150 Iteration 5 Error: 0.648420 Align patch 10 15 left Iteration 1 Error: 4.134151 Iteration 2 Error: 1.127037 Iteration 3 Error: 0.788377 Iteration 4 Error: 0.555902 Iteration 5 Error: 0.372651 Align patch 10 15 left Iteration 1 Error: 4.794854 Iteration 2 Error: 1.318148 Iteration 3 Error: 0.797789 Iteration 4 Error: 0.514212 Iteration 5 Error: 0.361718 Align patch 11 14 left Iteration 1 Error: 1.415200 Iteration 2 Error: 0.253188 Iteration 3 Error: 0.070117 Iteration 4 Error: 0.025957 Align patch 12 13 left Iteration 1 Error: 1.296364 Iteration 2 Error: 0.192823 Iteration 3 Error: 0.073413 Iteration 4 Error: 0.022081 Align patch 13 12 left Iteration 1 Error: 0.966386 Iteration 2 Error: 0.267403 Iteration 3 Error: 0.130742 Iteration 4 Error: 0.059334 Iteration 5 Error: 0.043068 Align patch 14 11 left Iteration 1 Error: 6.043159 Iteration 2 Error: 2.933426 Iteration 3 Error: 0.797088 Iteration 4 Error: 0.683543 Iteration 5 Error: 0.676916 Align patch 14 11 left Iteration 1 Error: 4.450057 Iteration 2 Error: 1.320799 Iteration 3 Error: 0.975623 Iteration 4 Error: 0.676514 Iteration 5 Error: 0.481244 Align patch 15 10 left Iteration 1 Error: 6.709151 Iteration 2 Error: 2.503607 Iteration 3 Error: 2.404093 Iteration 4 Error: 1.658439 Iteration 5 Error: 0.721856 Align patch 15 10 left Iteration 1 Error: 6.223637 Iteration 2 Error: 2.718477 Iteration 3 Error: 1.266786 Iteration 4 Error: 0.747524 Iteration 5 Error: 0.531529 Align patch 16 9 left Iteration 1 Error: 1.186481 Iteration 2 Error: 0.215705 Iteration 3 Error: 0.059042 Iteration 4 Error: 0.023497 Align patch 17 8 left Iteration 1 Error: 0.999679 Iteration 2 Error: 0.169352 Iteration 3 Error: 0.036714 Align patch 18 7 left Iteration 1 Error: 1.367945 Iteration 2 Error: 0.168188 Iteration 3 Error: 0.044073 Align patch 19 6 left Iteration 1 Error: 1.010674 Iteration 2 Error: 0.302805 Iteration 3 Error: 0.052826 Iteration 4 Error: 0.029378 Align patch 20 5 left Iteration 1 Error: 1.741850 Iteration 2 Error: 0.863647 Iteration 3 Error: 0.550258 Iteration 4 Error: 0.272104 Iteration 5 Error: 0.181373 Align patch 20 5 left Iteration 1 Error: 3.120629 Iteration 2 Error: 0.680697 Iteration 3 Error: 0.177406 Iteration 4 Error: 0.062738 Iteration 5 Error: 0.025970 Align patch 21 4 left Iteration 1 Error: 1.810449 Iteration 2 Error: 0.290567 Iteration 3 Error: 0.067657 Iteration 4 Error: 0.022396 Align patch 22 3 left Iteration 1 Error: 1.652732 Iteration 2 Error: 0.372827 Iteration 3 Error: 0.081012 Iteration 4 Error: 0.027438 Align patch 23 2 left Iteration 1 Error: 1.620280 Iteration 2 Error: 0.306037 Iteration 3 Error: 0.085151 Iteration 4 Error: 0.018973 Align patch 24 1 left Iteration 1 Error: 1.538009 Iteration 2 Error: 0.479704 Iteration 3 Error: 0.135081 Iteration 4 Error: 0.053272 Iteration 5 Error: 0.035071 Align patch 25 0 left Iteration 1 Error: 2.410542 Iteration 2 Error: 0.570868 Iteration 3 Error: 0.210594 Iteration 4 Error: 0.088081 Iteration 5 Error: 0.050988 Align patch 25 0 left Iteration 1 Error: 2.440345 Iteration 2 Error: 0.325009 Iteration 3 Error: 0.048992 3D Fitting completed. Patch alignment time: 30.46(sec) Local motion has been corrected. Process thread exits. Computational time: 48.234516 sec Total time: 55.785393 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00018hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00018hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.646614s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00018hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.241667s ........................................ >>>>>>TIME<<<<<< FFT: 1.465668s Defocus_U Defocus_V Angle CCC 27652.42 26999.97 86.62 0.039390 Final Values Defocus_U Defocus_V Angle CCC 27661.79 26965.59 85.99 0.065767 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00018hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00018hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.988e-02 CC threshold: 0.734 Mean Std: 42.44 6.93 Num Hot pixels: 214 Hot pixel threshold: 84.03 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.199368 Iteration 2 Error: 0.408184 Iteration 3 Error: 0.127257 Iteration 4 Error: 0.062479 Iteration 5 Error: 0.026119 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.11 -0.06 ...... Frame ( 3) shift: -0.22 -0.13 ...... Frame ( 4) shift: -0.32 -0.19 ...... Frame ( 5) shift: -0.43 -0.26 ...... Frame ( 6) shift: -0.39 -0.21 ...... Frame ( 7) shift: -0.21 -0.05 ...... Frame ( 8) shift: -0.02 0.12 ...... Frame ( 9) shift: 0.14 0.27 ...... Frame ( 10) shift: 0.28 0.42 ...... Frame ( 11) shift: 0.42 0.57 ...... Frame ( 12) shift: 0.57 0.69 ...... Frame ( 13) shift: 0.73 0.79 ...... Frame ( 14) shift: 0.89 0.89 ...... Frame ( 15) shift: 1.06 1.00 ...... Frame ( 16) shift: 1.24 1.13 ...... Frame ( 17) shift: 1.41 1.26 ...... Frame ( 18) shift: 1.55 1.39 ...... Frame ( 19) shift: 1.65 1.52 ...... Frame ( 20) shift: 1.75 1.66 ...... Frame ( 21) shift: 1.83 1.76 ...... Frame ( 22) shift: 1.92 1.83 ...... Frame ( 23) shift: 2.00 1.90 ...... Frame ( 24) shift: 2.08 2.00 ...... Frame ( 25) shift: 2.17 2.12 ...... Frame ( 26) shift: 2.26 2.25 ...... Frame ( 27) shift: 2.38 2.31 ...... Frame ( 28) shift: 2.52 2.31 ...... Frame ( 29) shift: 2.67 2.31 ...... Frame ( 30) shift: 2.77 2.32 ...... Frame ( 31) shift: 2.84 2.36 ...... Frame ( 32) shift: 2.90 2.40 ...... Frame ( 33) shift: 2.96 2.47 ...... Frame ( 34) shift: 3.01 2.58 ...... Frame ( 35) shift: 3.07 2.68 ...... Frame ( 36) shift: 3.11 2.69 ...... Frame ( 37) shift: 3.14 2.58 ...... Frame ( 38) shift: 3.17 2.47 ...... Frame ( 39) shift: 3.20 2.36 ...... Frame ( 40) shift: 3.24 2.26 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.007514 Iteration 2 Error: 0.187600 Iteration 3 Error: 0.054165 Iteration 4 Error: 0.025280 Align patch 2 23 left Iteration 1 Error: 0.918169 Iteration 2 Error: 0.192118 Iteration 3 Error: 0.069601 Iteration 4 Error: 0.034947 Align patch 3 22 left Iteration 1 Error: 1.079572 Iteration 2 Error: 0.145988 Iteration 3 Error: 0.043507 Align patch 4 21 left Iteration 1 Error: 0.796859 Iteration 2 Error: 0.280878 Iteration 3 Error: 0.144071 Iteration 4 Error: 0.074373 Iteration 5 Error: 0.039071 Align patch 5 20 left Iteration 1 Error: 1.692958 Iteration 2 Error: 0.307937 Iteration 3 Error: 0.073312 Iteration 4 Error: 0.029296 Align patch 6 19 left Iteration 1 Error: 0.938050 Iteration 2 Error: 0.138649 Iteration 3 Error: 0.033439 Align patch 7 18 left Iteration 1 Error: 0.779158 Iteration 2 Error: 0.115808 Iteration 3 Error: 0.031387 Align patch 8 17 left Iteration 1 Error: 0.657153 Iteration 2 Error: 0.178110 Iteration 3 Error: 0.062198 Iteration 4 Error: 0.031852 Align patch 9 16 left Iteration 1 Error: 0.793400 Iteration 2 Error: 0.188802 Iteration 3 Error: 0.052946 Iteration 4 Error: 0.034904 Align patch 10 15 left Iteration 1 Error: 0.974422 Iteration 2 Error: 0.164661 Iteration 3 Error: 0.044621 Align patch 11 14 left Iteration 1 Error: 0.716299 Iteration 2 Error: 0.114120 Iteration 3 Error: 0.030638 Align patch 12 13 left Iteration 1 Error: 0.838351 Iteration 2 Error: 0.166400 Iteration 3 Error: 0.061005 Iteration 4 Error: 0.025414 Align patch 13 12 left Iteration 1 Error: 1.086326 Iteration 2 Error: 0.151777 Iteration 3 Error: 0.039373 Align patch 14 11 left Iteration 1 Error: 0.669886 Iteration 2 Error: 0.212038 Iteration 3 Error: 0.068579 Iteration 4 Error: 0.027234 Align patch 15 10 left Iteration 1 Error: 0.905751 Iteration 2 Error: 0.203077 Iteration 3 Error: 0.049213 Align patch 16 9 left Iteration 1 Error: 1.075609 Iteration 2 Error: 0.253599 Iteration 3 Error: 0.062143 Iteration 4 Error: 0.023500 Align patch 17 8 left Iteration 1 Error: 0.741004 Iteration 2 Error: 0.220604 Iteration 3 Error: 0.086751 Iteration 4 Error: 0.040579 Align patch 18 7 left Iteration 1 Error: 0.813955 Iteration 2 Error: 0.151767 Iteration 3 Error: 0.072993 Iteration 4 Error: 0.020393 Align patch 19 6 left Iteration 1 Error: 1.475335 Iteration 2 Error: 0.320887 Iteration 3 Error: 0.115061 Iteration 4 Error: 0.044766 Align patch 20 5 left Iteration 1 Error: 0.989507 Iteration 2 Error: 0.193776 Iteration 3 Error: 0.059384 Iteration 4 Error: 0.027788 Align patch 21 4 left Iteration 1 Error: 0.687853 Iteration 2 Error: 0.270469 Iteration 3 Error: 0.067836 Iteration 4 Error: 0.038120 Align patch 22 3 left Iteration 1 Error: 0.988090 Iteration 2 Error: 0.262523 Iteration 3 Error: 0.059019 Iteration 4 Error: 0.023220 Align patch 23 2 left Iteration 1 Error: 0.806188 Iteration 2 Error: 0.180917 Iteration 3 Error: 0.050041 Iteration 4 Error: 0.024789 Align patch 24 1 left Iteration 1 Error: 0.903795 Iteration 2 Error: 0.317143 Iteration 3 Error: 0.186400 Iteration 4 Error: 0.074942 Iteration 5 Error: 0.046190 Align patch 25 0 left Iteration 1 Error: 0.832658 Iteration 2 Error: 0.199755 Iteration 3 Error: 0.076599 Iteration 4 Error: 0.032164 3D Fitting completed. Patch alignment time: 20.63(sec) Local motion has been corrected. Process thread exits. Computational time: 40.455109 sec Total time: 48.197468 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00018hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00018hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.626981s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00018hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.663383s ........................................ >>>>>>TIME<<<<<< FFT: 1.324986s Defocus_U Defocus_V Angle CCC 27908.21 27197.27 86.04 0.044224 Final Values Defocus_U Defocus_V Angle CCC 27895.67 27197.35 84.48 0.071124 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00019hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00019hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.993e-02 CC threshold: 0.734 Mean Std: 42.85 6.98 Num Hot pixels: 207 Hot pixel threshold: 84.73 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.605004 Iteration 2 Error: 0.296196 Iteration 3 Error: 0.080208 Iteration 4 Error: 0.031383 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.04 -0.19 ...... Frame ( 3) shift: 0.08 -0.38 ...... Frame ( 4) shift: 0.13 -0.57 ...... Frame ( 5) shift: 0.17 -0.76 ...... Frame ( 6) shift: 0.26 -0.78 ...... Frame ( 7) shift: 0.41 -0.64 ...... Frame ( 8) shift: 0.56 -0.50 ...... Frame ( 9) shift: 0.67 -0.40 ...... Frame ( 10) shift: 0.73 -0.32 ...... Frame ( 11) shift: 0.80 -0.25 ...... Frame ( 12) shift: 0.85 -0.12 ...... Frame ( 13) shift: 0.89 0.07 ...... Frame ( 14) shift: 0.93 0.26 ...... Frame ( 15) shift: 0.99 0.42 ...... Frame ( 16) shift: 1.08 0.56 ...... Frame ( 17) shift: 1.16 0.70 ...... Frame ( 18) shift: 1.25 0.83 ...... Frame ( 19) shift: 1.33 0.93 ...... Frame ( 20) shift: 1.42 1.04 ...... Frame ( 21) shift: 1.48 1.12 ...... Frame ( 22) shift: 1.53 1.19 ...... Frame ( 23) shift: 1.58 1.25 ...... Frame ( 24) shift: 1.59 1.29 ...... Frame ( 25) shift: 1.57 1.31 ...... Frame ( 26) shift: 1.54 1.34 ...... Frame ( 27) shift: 1.59 1.32 ...... Frame ( 28) shift: 1.72 1.27 ...... Frame ( 29) shift: 1.85 1.22 ...... Frame ( 30) shift: 1.92 1.26 ...... Frame ( 31) shift: 1.92 1.40 ...... Frame ( 32) shift: 1.93 1.54 ...... Frame ( 33) shift: 1.97 1.64 ...... Frame ( 34) shift: 2.07 1.70 ...... Frame ( 35) shift: 2.16 1.76 ...... Frame ( 36) shift: 2.24 1.82 ...... Frame ( 37) shift: 2.30 1.88 ...... Frame ( 38) shift: 2.37 1.95 ...... Frame ( 39) shift: 2.43 2.01 ...... Frame ( 40) shift: 2.50 2.07 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.883692 Iteration 2 Error: 0.213688 Iteration 3 Error: 0.091971 Iteration 4 Error: 0.032453 Align patch 2 23 left Iteration 1 Error: 0.792225 Iteration 2 Error: 0.142238 Iteration 3 Error: 0.041114 Align patch 3 22 left Iteration 1 Error: 0.740851 Iteration 2 Error: 0.220068 Iteration 3 Error: 0.057603 Iteration 4 Error: 0.026869 Align patch 4 21 left Iteration 1 Error: 0.837212 Iteration 2 Error: 0.236826 Iteration 3 Error: 0.077028 Iteration 4 Error: 0.037231 Align patch 5 20 left Iteration 1 Error: 1.216029 Iteration 2 Error: 0.167910 Iteration 3 Error: 0.057618 Iteration 4 Error: 0.021989 Align patch 6 19 left Iteration 1 Error: 0.956113 Iteration 2 Error: 0.186932 Iteration 3 Error: 0.054231 Iteration 4 Error: 0.022202 Align patch 7 18 left Iteration 1 Error: 0.741546 Iteration 2 Error: 0.147981 Iteration 3 Error: 0.042099 Align patch 8 17 left Iteration 1 Error: 0.850534 Iteration 2 Error: 0.186537 Iteration 3 Error: 0.061544 Iteration 4 Error: 0.031101 Align patch 9 16 left Iteration 1 Error: 0.806963 Iteration 2 Error: 0.222310 Iteration 3 Error: 0.045721 Align patch 10 15 left Iteration 1 Error: 1.094061 Iteration 2 Error: 0.145801 Iteration 3 Error: 0.042127 Align patch 11 14 left Iteration 1 Error: 0.720793 Iteration 2 Error: 0.120767 Iteration 3 Error: 0.029436 Align patch 12 13 left Iteration 1 Error: 1.020463 Iteration 2 Error: 0.278441 Iteration 3 Error: 0.067804 Iteration 4 Error: 0.027656 Align patch 13 12 left Iteration 1 Error: 0.512290 Iteration 2 Error: 0.093237 Iteration 3 Error: 0.043487 Align patch 14 11 left Iteration 1 Error: 0.745009 Iteration 2 Error: 0.170232 Iteration 3 Error: 0.078543 Iteration 4 Error: 0.041479 Align patch 15 10 left Iteration 1 Error: 0.848432 Iteration 2 Error: 0.232312 Iteration 3 Error: 0.065080 Iteration 4 Error: 0.022354 Align patch 16 9 left Iteration 1 Error: 0.743744 Iteration 2 Error: 0.209575 Iteration 3 Error: 0.080699 Iteration 4 Error: 0.029749 Align patch 17 8 left Iteration 1 Error: 0.657084 Iteration 2 Error: 0.152720 Iteration 3 Error: 0.031092 Align patch 18 7 left Iteration 1 Error: 0.820728 Iteration 2 Error: 0.133006 Iteration 3 Error: 0.032651 Align patch 19 6 left Iteration 1 Error: 0.923240 Iteration 2 Error: 0.160556 Iteration 3 Error: 0.051626 Iteration 4 Error: 0.018035 Align patch 20 5 left Iteration 1 Error: 0.760338 Iteration 2 Error: 0.094797 Iteration 3 Error: 0.029776 Align patch 21 4 left Iteration 1 Error: 0.947806 Iteration 2 Error: 0.179434 Iteration 3 Error: 0.042540 Align patch 22 3 left Iteration 1 Error: 0.729813 Iteration 2 Error: 0.128513 Iteration 3 Error: 0.035155 Align patch 23 2 left Iteration 1 Error: 0.771732 Iteration 2 Error: 0.153267 Iteration 3 Error: 0.051404 Iteration 4 Error: 0.015440 Align patch 24 1 left Iteration 1 Error: 0.748716 Iteration 2 Error: 0.096117 Iteration 3 Error: 0.032556 Align patch 25 0 left Iteration 1 Error: 1.208633 Iteration 2 Error: 0.145838 Iteration 3 Error: 0.024347 3D Fitting completed. Patch alignment time: 17.77(sec) Local motion has been corrected. Process thread exits. Computational time: 31.684614 sec Total time: 40.277603 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00019hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00019hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.555570s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00019hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.068145s ........................................ >>>>>>TIME<<<<<< FFT: 1.432089s Defocus_U Defocus_V Angle CCC 22726.48 23523.81 6.41 0.042599 Final Values Defocus_U Defocus_V Angle CCC 22723.31 23561.46 6.73 0.073688 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00019hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00019hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.993e-02 CC threshold: 0.734 Mean Std: 42.57 6.95 Num Hot pixels: 211 Hot pixel threshold: 84.26 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.179526 Iteration 2 Error: 0.214024 Iteration 3 Error: 0.046135 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.10 -0.07 ...... Frame ( 3) shift: 0.19 -0.14 ...... Frame ( 4) shift: 0.29 -0.21 ...... Frame ( 5) shift: 0.39 -0.27 ...... Frame ( 6) shift: 0.39 -0.24 ...... Frame ( 7) shift: 0.31 -0.10 ...... Frame ( 8) shift: 0.22 0.05 ...... Frame ( 9) shift: 0.20 0.15 ...... Frame ( 10) shift: 0.25 0.22 ...... Frame ( 11) shift: 0.30 0.30 ...... Frame ( 12) shift: 0.33 0.37 ...... Frame ( 13) shift: 0.34 0.44 ...... Frame ( 14) shift: 0.34 0.51 ...... Frame ( 15) shift: 0.40 0.61 ...... Frame ( 16) shift: 0.50 0.74 ...... Frame ( 17) shift: 0.60 0.87 ...... Frame ( 18) shift: 0.64 0.93 ...... Frame ( 19) shift: 0.62 0.93 ...... Frame ( 20) shift: 0.60 0.92 ...... Frame ( 21) shift: 0.60 0.97 ...... Frame ( 22) shift: 0.63 1.06 ...... Frame ( 23) shift: 0.65 1.15 ...... Frame ( 24) shift: 0.63 1.23 ...... Frame ( 25) shift: 0.57 1.29 ...... Frame ( 26) shift: 0.50 1.34 ...... Frame ( 27) shift: 0.51 1.40 ...... Frame ( 28) shift: 0.57 1.47 ...... Frame ( 29) shift: 0.64 1.53 ...... Frame ( 30) shift: 0.68 1.61 ...... Frame ( 31) shift: 0.70 1.70 ...... Frame ( 32) shift: 0.71 1.80 ...... Frame ( 33) shift: 0.77 1.88 ...... Frame ( 34) shift: 0.87 1.94 ...... Frame ( 35) shift: 0.98 2.00 ...... Frame ( 36) shift: 1.06 2.04 ...... Frame ( 37) shift: 1.10 2.06 ...... Frame ( 38) shift: 1.15 2.08 ...... Frame ( 39) shift: 1.20 2.10 ...... Frame ( 40) shift: 1.25 2.12 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.305107 Iteration 2 Error: 0.215572 Iteration 3 Error: 0.054213 Iteration 4 Error: 0.022048 Align patch 2 23 left Iteration 1 Error: 1.033844 Iteration 2 Error: 0.172224 Iteration 3 Error: 0.055023 Iteration 4 Error: 0.019019 Align patch 3 22 left Iteration 1 Error: 1.056511 Iteration 2 Error: 0.131278 Iteration 3 Error: 0.023648 Align patch 4 21 left Iteration 1 Error: 0.593499 Iteration 2 Error: 0.096313 Iteration 3 Error: 0.028203 Align patch 5 20 left Iteration 1 Error: 0.871509 Iteration 2 Error: 0.183169 Iteration 3 Error: 0.059400 Iteration 4 Error: 0.013435 Align patch 6 19 left Iteration 1 Error: 0.850687 Iteration 2 Error: 0.163801 Iteration 3 Error: 0.033489 Align patch 7 18 left Iteration 1 Error: 0.623052 Iteration 2 Error: 0.187139 Iteration 3 Error: 0.039442 Align patch 8 17 left Iteration 1 Error: 0.830127 Iteration 2 Error: 0.110536 Iteration 3 Error: 0.030244 Align patch 9 16 left Iteration 1 Error: 0.723390 Iteration 2 Error: 0.122627 Iteration 3 Error: 0.026657 Align patch 10 15 left Iteration 1 Error: 0.700690 Iteration 2 Error: 0.079310 Iteration 3 Error: 0.019655 Align patch 11 14 left Iteration 1 Error: 0.832881 Iteration 2 Error: 0.233344 Iteration 3 Error: 0.055977 Iteration 4 Error: 0.025363 Align patch 12 13 left Iteration 1 Error: 0.671768 Iteration 2 Error: 0.162627 Iteration 3 Error: 0.038186 Align patch 13 12 left Iteration 1 Error: 0.714256 Iteration 2 Error: 0.097294 Iteration 3 Error: 0.037700 Align patch 14 11 left Iteration 1 Error: 1.162032 Iteration 2 Error: 0.164937 Iteration 3 Error: 0.056050 Iteration 4 Error: 0.018642 Align patch 15 10 left Iteration 1 Error: 1.074474 Iteration 2 Error: 0.139249 Iteration 3 Error: 0.028377 Align patch 16 9 left Iteration 1 Error: 0.803582 Iteration 2 Error: 0.149062 Iteration 3 Error: 0.037418 Align patch 17 8 left Iteration 1 Error: 0.716807 Iteration 2 Error: 0.101384 Iteration 3 Error: 0.031386 Align patch 18 7 left Iteration 1 Error: 0.838028 Iteration 2 Error: 0.359015 Iteration 3 Error: 0.095191 Iteration 4 Error: 0.055428 Iteration 5 Error: 0.013435 Align patch 19 6 left Iteration 1 Error: 0.859798 Iteration 2 Error: 0.243248 Iteration 3 Error: 0.069248 Iteration 4 Error: 0.025101 Align patch 20 5 left Iteration 1 Error: 0.931121 Iteration 2 Error: 0.204254 Iteration 3 Error: 0.047142 Align patch 21 4 left Iteration 1 Error: 0.700080 Iteration 2 Error: 0.128105 Iteration 3 Error: 0.040132 Align patch 22 3 left Iteration 1 Error: 0.873713 Iteration 2 Error: 0.178532 Iteration 3 Error: 0.060944 Iteration 4 Error: 0.018435 Align patch 23 2 left Iteration 1 Error: 0.862964 Iteration 2 Error: 0.207043 Iteration 3 Error: 0.035224 Align patch 24 1 left Iteration 1 Error: 0.599720 Iteration 2 Error: 0.116390 Iteration 3 Error: 0.039916 Align patch 25 0 left Iteration 1 Error: 1.326206 Iteration 2 Error: 0.162824 Iteration 3 Error: 0.040317 3D Fitting completed. Patch alignment time: 15.94(sec) Local motion has been corrected. Process thread exits. Computational time: 32.509098 sec Total time: 40.758904 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00019hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00019hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.581203s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00019hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.389254s ........................................ >>>>>>TIME<<<<<< FFT: 1.723261s Defocus_U Defocus_V Angle CCC 27017.55 27869.18 8.79 0.040877 Final Values Defocus_U Defocus_V Angle CCC 27008.17 27900.45 8.79 0.066759 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00019hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00019hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.995e-02 CC threshold: 0.734 Mean Std: 42.81 6.97 Num Hot pixels: 201 Hot pixel threshold: 84.64 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.161134 Iteration 2 Error: 0.241724 Iteration 3 Error: 0.057692 Iteration 4 Error: 0.019253 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.17 -0.08 ...... Frame ( 3) shift: 0.35 -0.16 ...... Frame ( 4) shift: 0.52 -0.24 ...... Frame ( 5) shift: 0.70 -0.31 ...... Frame ( 6) shift: 0.75 -0.33 ...... Frame ( 7) shift: 0.69 -0.27 ...... Frame ( 8) shift: 0.62 -0.22 ...... Frame ( 9) shift: 0.63 -0.11 ...... Frame ( 10) shift: 0.70 0.05 ...... Frame ( 11) shift: 0.77 0.21 ...... Frame ( 12) shift: 0.80 0.33 ...... Frame ( 13) shift: 0.78 0.40 ...... Frame ( 14) shift: 0.77 0.48 ...... Frame ( 15) shift: 0.80 0.60 ...... Frame ( 16) shift: 0.88 0.78 ...... Frame ( 17) shift: 0.95 0.96 ...... Frame ( 18) shift: 1.01 1.08 ...... Frame ( 19) shift: 1.05 1.15 ...... Frame ( 20) shift: 1.09 1.22 ...... Frame ( 21) shift: 1.16 1.32 ...... Frame ( 22) shift: 1.28 1.44 ...... Frame ( 23) shift: 1.39 1.57 ...... Frame ( 24) shift: 1.46 1.64 ...... Frame ( 25) shift: 1.47 1.66 ...... Frame ( 26) shift: 1.48 1.68 ...... Frame ( 27) shift: 1.47 1.68 ...... Frame ( 28) shift: 1.46 1.64 ...... Frame ( 29) shift: 1.44 1.61 ...... Frame ( 30) shift: 1.46 1.61 ...... Frame ( 31) shift: 1.51 1.66 ...... Frame ( 32) shift: 1.56 1.71 ...... Frame ( 33) shift: 1.64 1.74 ...... Frame ( 34) shift: 1.74 1.77 ...... Frame ( 35) shift: 1.83 1.79 ...... Frame ( 36) shift: 1.88 1.81 ...... Frame ( 37) shift: 1.89 1.82 ...... Frame ( 38) shift: 1.89 1.83 ...... Frame ( 39) shift: 1.89 1.84 ...... Frame ( 40) shift: 1.90 1.85 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.004508 Iteration 2 Error: 0.224446 Iteration 3 Error: 0.047473 Align patch 2 23 left Iteration 1 Error: 0.913066 Iteration 2 Error: 0.138158 Iteration 3 Error: 0.044808 Align patch 3 22 left Iteration 1 Error: 1.086783 Iteration 2 Error: 0.143429 Iteration 3 Error: 0.051200 Iteration 4 Error: 0.019142 Align patch 4 21 left Iteration 1 Error: 1.167635 Iteration 2 Error: 0.223446 Iteration 3 Error: 0.066567 Iteration 4 Error: 0.017103 Align patch 5 20 left Iteration 1 Error: 0.744940 Iteration 2 Error: 0.093103 Iteration 3 Error: 0.024073 Align patch 6 19 left Iteration 1 Error: 0.851712 Iteration 2 Error: 0.112686 Iteration 3 Error: 0.023774 Align patch 7 18 left Iteration 1 Error: 0.954667 Iteration 2 Error: 0.183865 Iteration 3 Error: 0.061132 Iteration 4 Error: 0.024481 Align patch 8 17 left Iteration 1 Error: 1.204495 Iteration 2 Error: 0.169047 Iteration 3 Error: 0.052486 Iteration 4 Error: 0.019253 Align patch 9 16 left Iteration 1 Error: 0.822676 Iteration 2 Error: 0.253776 Iteration 3 Error: 0.064210 Iteration 4 Error: 0.023537 Align patch 10 15 left Iteration 1 Error: 0.652345 Iteration 2 Error: 0.089246 Iteration 3 Error: 0.019677 Align patch 11 14 left Iteration 1 Error: 0.915733 Iteration 2 Error: 0.214967 Iteration 3 Error: 0.062189 Iteration 4 Error: 0.020676 Align patch 12 13 left Iteration 1 Error: 0.886269 Iteration 2 Error: 0.115873 Iteration 3 Error: 0.033204 Align patch 13 12 left Iteration 1 Error: 0.687632 Iteration 2 Error: 0.124375 Iteration 3 Error: 0.036233 Align patch 14 11 left Iteration 1 Error: 0.763519 Iteration 2 Error: 0.166684 Iteration 3 Error: 0.043737 Align patch 15 10 left Iteration 1 Error: 0.690636 Iteration 2 Error: 0.190330 Iteration 3 Error: 0.064762 Iteration 4 Error: 0.019493 Align patch 16 9 left Iteration 1 Error: 0.831756 Iteration 2 Error: 0.172768 Iteration 3 Error: 0.040266 Align patch 17 8 left Iteration 1 Error: 1.080575 Iteration 2 Error: 0.147781 Iteration 3 Error: 0.052102 Iteration 4 Error: 0.024422 Align patch 18 7 left Iteration 1 Error: 0.547343 Iteration 2 Error: 0.133939 Iteration 3 Error: 0.031345 Align patch 19 6 left Iteration 1 Error: 0.597815 Iteration 2 Error: 0.112251 Iteration 3 Error: 0.025718 Align patch 20 5 left Iteration 1 Error: 0.739705 Iteration 2 Error: 0.199936 Iteration 3 Error: 0.066638 Iteration 4 Error: 0.021467 Align patch 21 4 left Iteration 1 Error: 1.019700 Iteration 2 Error: 0.122605 Iteration 3 Error: 0.043313 Align patch 22 3 left Iteration 1 Error: 1.670691 Iteration 2 Error: 0.133166 Iteration 3 Error: 0.052334 Iteration 4 Error: 0.011711 Align patch 23 2 left Iteration 1 Error: 0.857392 Iteration 2 Error: 0.130095 Iteration 3 Error: 0.035401 Align patch 24 1 left Iteration 1 Error: 0.758358 Iteration 2 Error: 0.143870 Iteration 3 Error: 0.027484 Align patch 25 0 left Iteration 1 Error: 1.023590 Iteration 2 Error: 0.204684 Iteration 3 Error: 0.046185 3D Fitting completed. Patch alignment time: 19.70(sec) Local motion has been corrected. Process thread exits. Computational time: 33.874397 sec Total time: 42.365402 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00019hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00019hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.579032s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00019hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.753951s ........................................ >>>>>>TIME<<<<<< FFT: 1.522706s Defocus_U Defocus_V Angle CCC 26871.11 26218.76 89.33 0.041910 Final Values Defocus_U Defocus_V Angle CCC 26871.11 26218.76 89.02 0.066345 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00019hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00019hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.996e-02 CC threshold: 0.734 Mean Std: 40.28 6.79 Num Hot pixels: 180 Hot pixel threshold: 81.03 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.575911 Iteration 2 Error: 0.515884 Iteration 3 Error: 0.098256 Iteration 4 Error: 0.035728 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.13 -0.07 ...... Frame ( 3) shift: 0.25 -0.13 ...... Frame ( 4) shift: 0.38 -0.20 ...... Frame ( 5) shift: 0.51 -0.26 ...... Frame ( 6) shift: 0.59 -0.18 ...... Frame ( 7) shift: 0.63 0.04 ...... Frame ( 8) shift: 0.67 0.27 ...... Frame ( 9) shift: 0.68 0.52 ...... Frame ( 10) shift: 0.67 0.82 ...... Frame ( 11) shift: 0.66 1.11 ...... Frame ( 12) shift: 0.63 1.39 ...... Frame ( 13) shift: 0.60 1.67 ...... Frame ( 14) shift: 0.57 1.94 ...... Frame ( 15) shift: 0.53 2.19 ...... Frame ( 16) shift: 0.46 2.42 ...... Frame ( 17) shift: 0.40 2.66 ...... Frame ( 18) shift: 0.40 2.86 ...... Frame ( 19) shift: 0.47 3.03 ...... Frame ( 20) shift: 0.54 3.20 ...... Frame ( 21) shift: 0.58 3.37 ...... Frame ( 22) shift: 0.58 3.55 ...... Frame ( 23) shift: 0.59 3.74 ...... Frame ( 24) shift: 0.58 3.89 ...... Frame ( 25) shift: 0.54 4.00 ...... Frame ( 26) shift: 0.51 4.12 ...... Frame ( 27) shift: 0.52 4.21 ...... Frame ( 28) shift: 0.58 4.27 ...... Frame ( 29) shift: 0.65 4.34 ...... Frame ( 30) shift: 0.70 4.38 ...... Frame ( 31) shift: 0.75 4.41 ...... Frame ( 32) shift: 0.81 4.44 ...... Frame ( 33) shift: 0.84 4.48 ...... Frame ( 34) shift: 0.85 4.51 ...... Frame ( 35) shift: 0.86 4.55 ...... Frame ( 36) shift: 0.86 4.63 ...... Frame ( 37) shift: 0.83 4.77 ...... Frame ( 38) shift: 0.81 4.91 ...... Frame ( 39) shift: 0.78 5.05 ...... Frame ( 40) shift: 0.75 5.18 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.162014 Iteration 2 Error: 0.185062 Iteration 3 Error: 0.033068 Align patch 2 23 left Iteration 1 Error: 0.940346 Iteration 2 Error: 0.228745 Iteration 3 Error: 0.048368 Align patch 3 22 left Iteration 1 Error: 0.860570 Iteration 2 Error: 0.185565 Iteration 3 Error: 0.052871 Iteration 4 Error: 0.018199 Align patch 4 21 left Iteration 1 Error: 0.856530 Iteration 2 Error: 0.253423 Iteration 3 Error: 0.094647 Iteration 4 Error: 0.028960 Align patch 5 20 left Iteration 1 Error: 1.360568 Iteration 2 Error: 0.198454 Iteration 3 Error: 0.052864 Iteration 4 Error: 0.019236 Align patch 6 19 left Iteration 1 Error: 0.698678 Iteration 2 Error: 0.167245 Iteration 3 Error: 0.039222 Align patch 7 18 left Iteration 1 Error: 1.057111 Iteration 2 Error: 0.186419 Iteration 3 Error: 0.063899 Iteration 4 Error: 0.015084 Align patch 8 17 left Iteration 1 Error: 0.631089 Iteration 2 Error: 0.137554 Iteration 3 Error: 0.054691 Iteration 4 Error: 0.018593 Align patch 9 16 left Iteration 1 Error: 0.649150 Iteration 2 Error: 0.122166 Iteration 3 Error: 0.033207 Align patch 10 15 left Iteration 1 Error: 0.671993 Iteration 2 Error: 0.169207 Iteration 3 Error: 0.029325 Align patch 11 14 left Iteration 1 Error: 0.789184 Iteration 2 Error: 0.099457 Iteration 3 Error: 0.021916 Align patch 12 13 left Iteration 1 Error: 0.754893 Iteration 2 Error: 0.101829 Iteration 3 Error: 0.017772 Align patch 13 12 left Iteration 1 Error: 0.677615 Iteration 2 Error: 0.130705 Iteration 3 Error: 0.036574 Align patch 14 11 left Iteration 1 Error: 0.583628 Iteration 2 Error: 0.083774 Iteration 3 Error: 0.026692 Align patch 15 10 left Iteration 1 Error: 0.557827 Iteration 2 Error: 0.080933 Iteration 3 Error: 0.023010 Align patch 16 9 left Iteration 1 Error: 1.574223 Iteration 2 Error: 0.244346 Iteration 3 Error: 0.057465 Iteration 4 Error: 0.019717 Align patch 17 8 left Iteration 1 Error: 1.257158 Iteration 2 Error: 0.221730 Iteration 3 Error: 0.077470 Iteration 4 Error: 0.028442 Align patch 18 7 left Iteration 1 Error: 0.989022 Iteration 2 Error: 0.135430 Iteration 3 Error: 0.036646 Align patch 19 6 left Iteration 1 Error: 1.318953 Iteration 2 Error: 0.153218 Iteration 3 Error: 0.044471 Align patch 20 5 left Iteration 1 Error: 0.827318 Iteration 2 Error: 0.173315 Iteration 3 Error: 0.036591 Align patch 21 4 left Iteration 1 Error: 1.751741 Iteration 2 Error: 0.266190 Iteration 3 Error: 0.049963 Align patch 22 3 left Iteration 1 Error: 1.398322 Iteration 2 Error: 0.219515 Iteration 3 Error: 0.061587 Iteration 4 Error: 0.016354 Align patch 23 2 left Iteration 1 Error: 1.101980 Iteration 2 Error: 0.244357 Iteration 3 Error: 0.043895 Align patch 24 1 left Iteration 1 Error: 0.780298 Iteration 2 Error: 0.247324 Iteration 3 Error: 0.035880 Align patch 25 0 left Iteration 1 Error: 0.942857 Iteration 2 Error: 0.123042 Iteration 3 Error: 0.032079 3D Fitting completed. Patch alignment time: 15.49(sec) Local motion has been corrected. Process thread exits. Computational time: 32.898697 sec Total time: 41.320202 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00019hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00019hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.704680s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00019hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.086829s ........................................ >>>>>>TIME<<<<<< FFT: 1.568410s Defocus_U Defocus_V Angle CCC 28597.70 27800.80 87.18 0.047044 Final Values Defocus_U Defocus_V Angle CCC 28611.77 27808.62 88.44 0.077015 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00020hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00020hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.996e-02 CC threshold: 0.734 Mean Std: 41.96 6.90 Num Hot pixels: 196 Hot pixel threshold: 83.38 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.565798 Iteration 2 Error: 0.272435 Iteration 3 Error: 0.055537 Iteration 4 Error: 0.019230 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.03 -0.06 ...... Frame ( 3) shift: 0.07 -0.12 ...... Frame ( 4) shift: 0.10 -0.18 ...... Frame ( 5) shift: 0.13 -0.24 ...... Frame ( 6) shift: 0.20 -0.26 ...... Frame ( 7) shift: 0.29 -0.23 ...... Frame ( 8) shift: 0.38 -0.20 ...... Frame ( 9) shift: 0.44 -0.19 ...... Frame ( 10) shift: 0.47 -0.21 ...... Frame ( 11) shift: 0.49 -0.23 ...... Frame ( 12) shift: 0.56 -0.15 ...... Frame ( 13) shift: 0.67 0.03 ...... Frame ( 14) shift: 0.78 0.20 ...... Frame ( 15) shift: 0.90 0.33 ...... Frame ( 16) shift: 1.01 0.40 ...... Frame ( 17) shift: 1.13 0.47 ...... Frame ( 18) shift: 1.22 0.52 ...... Frame ( 19) shift: 1.28 0.55 ...... Frame ( 20) shift: 1.35 0.58 ...... Frame ( 21) shift: 1.42 0.62 ...... Frame ( 22) shift: 1.51 0.66 ...... Frame ( 23) shift: 1.60 0.70 ...... Frame ( 24) shift: 1.68 0.74 ...... Frame ( 25) shift: 1.74 0.80 ...... Frame ( 26) shift: 1.80 0.86 ...... Frame ( 27) shift: 1.91 0.88 ...... Frame ( 28) shift: 2.05 0.86 ...... Frame ( 29) shift: 2.20 0.84 ...... Frame ( 30) shift: 2.26 0.87 ...... Frame ( 31) shift: 2.26 0.96 ...... Frame ( 32) shift: 2.25 1.04 ...... Frame ( 33) shift: 2.26 1.11 ...... Frame ( 34) shift: 2.28 1.17 ...... Frame ( 35) shift: 2.30 1.22 ...... Frame ( 36) shift: 2.40 1.23 ...... Frame ( 37) shift: 2.58 1.20 ...... Frame ( 38) shift: 2.75 1.18 ...... Frame ( 39) shift: 2.93 1.15 ...... Frame ( 40) shift: 3.11 1.12 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.938084 Iteration 2 Error: 0.170590 Iteration 3 Error: 0.035255 Align patch 2 23 left Iteration 1 Error: 0.870519 Iteration 2 Error: 0.174964 Iteration 3 Error: 0.044162 Align patch 3 22 left Iteration 1 Error: 0.689941 Iteration 2 Error: 0.128222 Iteration 3 Error: 0.027524 Align patch 4 21 left Iteration 1 Error: 0.658091 Iteration 2 Error: 0.146689 Iteration 3 Error: 0.026405 Align patch 5 20 left Iteration 1 Error: 0.637505 Iteration 2 Error: 0.116760 Iteration 3 Error: 0.029958 Align patch 6 19 left Iteration 1 Error: 0.575736 Iteration 2 Error: 0.066356 Iteration 3 Error: 0.018026 Align patch 7 18 left Iteration 1 Error: 0.724472 Iteration 2 Error: 0.161464 Iteration 3 Error: 0.029046 Align patch 8 17 left Iteration 1 Error: 1.000514 Iteration 2 Error: 0.180718 Iteration 3 Error: 0.036130 Align patch 9 16 left Iteration 1 Error: 0.835956 Iteration 2 Error: 0.134753 Iteration 3 Error: 0.043090 Align patch 10 15 left Iteration 1 Error: 1.168416 Iteration 2 Error: 0.362659 Iteration 3 Error: 0.079517 Iteration 4 Error: 0.040781 Align patch 11 14 left Iteration 1 Error: 1.332492 Iteration 2 Error: 0.264638 Iteration 3 Error: 0.116932 Iteration 4 Error: 0.050734 Iteration 5 Error: 0.027370 Align patch 12 13 left Iteration 1 Error: 0.644743 Iteration 2 Error: 0.170315 Iteration 3 Error: 0.039666 Align patch 13 12 left Iteration 1 Error: 0.725878 Iteration 2 Error: 0.109250 Iteration 3 Error: 0.034187 Align patch 14 11 left Iteration 1 Error: 1.158811 Iteration 2 Error: 0.150786 Iteration 3 Error: 0.037140 Align patch 15 10 left Iteration 1 Error: 0.844020 Iteration 2 Error: 0.148672 Iteration 3 Error: 0.024466 Align patch 16 9 left Iteration 1 Error: 0.831796 Iteration 2 Error: 0.142187 Iteration 3 Error: 0.036466 Align patch 17 8 left Iteration 1 Error: 0.708499 Iteration 2 Error: 0.161750 Iteration 3 Error: 0.055478 Iteration 4 Error: 0.022327 Align patch 18 7 left Iteration 1 Error: 0.666595 Iteration 2 Error: 0.082788 Iteration 3 Error: 0.015545 Align patch 19 6 left Iteration 1 Error: 0.800341 Iteration 2 Error: 0.149532 Iteration 3 Error: 0.060141 Iteration 4 Error: 0.026462 Align patch 20 5 left Iteration 1 Error: 0.616147 Iteration 2 Error: 0.133969 Iteration 3 Error: 0.031123 Align patch 21 4 left Iteration 1 Error: 0.853237 Iteration 2 Error: 0.106283 Iteration 3 Error: 0.032793 Align patch 22 3 left Iteration 1 Error: 0.477250 Iteration 2 Error: 0.088495 Iteration 3 Error: 0.026075 Align patch 23 2 left Iteration 1 Error: 0.753342 Iteration 2 Error: 0.107133 Iteration 3 Error: 0.028307 Align patch 24 1 left Iteration 1 Error: 0.837817 Iteration 2 Error: 0.099535 Iteration 3 Error: 0.024624 Align patch 25 0 left Iteration 1 Error: 1.046647 Iteration 2 Error: 0.199655 Iteration 3 Error: 0.030701 3D Fitting completed. Patch alignment time: 16.92(sec) Local motion has been corrected. Process thread exits. Computational time: 37.153194 sec Total time: 45.341923 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00020hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00020hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.567933s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00020hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.228593s ........................................ >>>>>>TIME<<<<<< FFT: 1.393113s Defocus_U Defocus_V Angle CCC 26148.44 26945.31 4.08 0.044325 Final Values Defocus_U Defocus_V Angle CCC 26164.07 26917.20 5.02 0.069291 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00020hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00020hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.989e-02 CC threshold: 0.734 Mean Std: 42.04 6.90 Num Hot pixels: 206 Hot pixel threshold: 83.43 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.601900 Iteration 2 Error: 0.471112 Iteration 3 Error: 0.170202 Iteration 4 Error: 0.060618 Iteration 5 Error: 0.026986 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.08 0.20 ...... Frame ( 3) shift: 0.17 0.40 ...... Frame ( 4) shift: 0.25 0.60 ...... Frame ( 5) shift: 0.33 0.79 ...... Frame ( 6) shift: 0.43 0.93 ...... Frame ( 7) shift: 0.56 0.99 ...... Frame ( 8) shift: 0.69 1.05 ...... Frame ( 9) shift: 0.81 1.12 ...... Frame ( 10) shift: 0.93 1.17 ...... Frame ( 11) shift: 1.05 1.23 ...... Frame ( 12) shift: 1.21 1.34 ...... Frame ( 13) shift: 1.40 1.48 ...... Frame ( 14) shift: 1.59 1.63 ...... Frame ( 15) shift: 1.74 1.75 ...... Frame ( 16) shift: 1.85 1.85 ...... Frame ( 17) shift: 1.95 1.94 ...... Frame ( 18) shift: 2.09 2.05 ...... Frame ( 19) shift: 2.26 2.16 ...... Frame ( 20) shift: 2.44 2.28 ...... Frame ( 21) shift: 2.61 2.41 ...... Frame ( 22) shift: 2.78 2.55 ...... Frame ( 23) shift: 2.95 2.69 ...... Frame ( 24) shift: 3.09 2.79 ...... Frame ( 25) shift: 3.18 2.87 ...... Frame ( 26) shift: 3.28 2.94 ...... Frame ( 27) shift: 3.38 3.04 ...... Frame ( 28) shift: 3.49 3.16 ...... Frame ( 29) shift: 3.60 3.28 ...... Frame ( 30) shift: 3.71 3.37 ...... Frame ( 31) shift: 3.80 3.43 ...... Frame ( 32) shift: 3.90 3.48 ...... Frame ( 33) shift: 4.02 3.56 ...... Frame ( 34) shift: 4.18 3.64 ...... Frame ( 35) shift: 4.33 3.73 ...... Frame ( 36) shift: 4.47 3.85 ...... Frame ( 37) shift: 4.57 4.01 ...... Frame ( 38) shift: 4.68 4.17 ...... Frame ( 39) shift: 4.79 4.33 ...... Frame ( 40) shift: 4.90 4.49 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.171839 Iteration 2 Error: 0.211612 Iteration 3 Error: 0.048239 Align patch 2 23 left Iteration 1 Error: 0.726152 Iteration 2 Error: 0.170532 Iteration 3 Error: 0.051365 Iteration 4 Error: 0.020394 Align patch 3 22 left Iteration 1 Error: 1.074330 Iteration 2 Error: 0.128145 Iteration 3 Error: 0.044309 Align patch 4 21 left Iteration 1 Error: 1.081307 Iteration 2 Error: 0.206545 Iteration 3 Error: 0.073861 Iteration 4 Error: 0.029625 Align patch 5 20 left Iteration 1 Error: 0.829966 Iteration 2 Error: 0.249858 Iteration 3 Error: 0.093035 Iteration 4 Error: 0.035684 Align patch 6 19 left Iteration 1 Error: 1.204005 Iteration 2 Error: 0.199935 Iteration 3 Error: 0.039454 Align patch 7 18 left Iteration 1 Error: 0.864455 Iteration 2 Error: 0.267577 Iteration 3 Error: 0.096826 Iteration 4 Error: 0.040599 Align patch 8 17 left Iteration 1 Error: 1.743214 Iteration 2 Error: 0.310819 Iteration 3 Error: 0.056081 Iteration 4 Error: 0.033994 Align patch 9 16 left Iteration 1 Error: 1.025339 Iteration 2 Error: 0.331419 Iteration 3 Error: 0.103717 Iteration 4 Error: 0.043227 Align patch 10 15 left Iteration 1 Error: 1.041463 Iteration 2 Error: 0.311148 Iteration 3 Error: 0.110510 Iteration 4 Error: 0.041263 Align patch 11 14 left Iteration 1 Error: 1.155450 Iteration 2 Error: 0.226986 Iteration 3 Error: 0.075442 Iteration 4 Error: 0.031799 Align patch 12 13 left Iteration 1 Error: 1.203947 Iteration 2 Error: 0.287568 Iteration 3 Error: 0.122719 Iteration 4 Error: 0.030695 Align patch 13 12 left Iteration 1 Error: 0.837375 Iteration 2 Error: 0.274829 Iteration 3 Error: 0.126234 Iteration 4 Error: 0.069254 Iteration 5 Error: 0.035319 Align patch 14 11 left Iteration 1 Error: 0.969393 Iteration 2 Error: 0.159957 Iteration 3 Error: 0.034196 Align patch 15 10 left Iteration 1 Error: 0.767485 Iteration 2 Error: 0.139053 Iteration 3 Error: 0.060570 Iteration 4 Error: 0.026612 Align patch 16 9 left Iteration 1 Error: 1.102762 Iteration 2 Error: 0.259345 Iteration 3 Error: 0.054950 Iteration 4 Error: 0.032670 Align patch 17 8 left Iteration 1 Error: 1.074734 Iteration 2 Error: 0.172995 Iteration 3 Error: 0.062525 Iteration 4 Error: 0.034783 Align patch 18 7 left Iteration 1 Error: 1.150996 Iteration 2 Error: 0.330117 Iteration 3 Error: 0.123468 Iteration 4 Error: 0.063089 Iteration 5 Error: 0.030284 Align patch 19 6 left Iteration 1 Error: 1.259196 Iteration 2 Error: 0.343231 Iteration 3 Error: 0.070255 Iteration 4 Error: 0.026768 Align patch 20 5 left Iteration 1 Error: 0.488875 Iteration 2 Error: 0.109220 Iteration 3 Error: 0.049673 Align patch 21 4 left Iteration 1 Error: 1.157460 Iteration 2 Error: 0.231046 Iteration 3 Error: 0.159968 Iteration 4 Error: 0.041241 Align patch 22 3 left Iteration 1 Error: 1.597443 Iteration 2 Error: 0.229891 Iteration 3 Error: 0.088676 Iteration 4 Error: 0.033287 Align patch 23 2 left Iteration 1 Error: 1.249191 Iteration 2 Error: 0.226200 Iteration 3 Error: 0.062799 Iteration 4 Error: 0.021574 Align patch 24 1 left Iteration 1 Error: 0.627787 Iteration 2 Error: 0.131826 Iteration 3 Error: 0.044048 Align patch 25 0 left Iteration 1 Error: 0.972592 Iteration 2 Error: 0.099939 Iteration 3 Error: 0.029396 3D Fitting completed. Patch alignment time: 16.61(sec) Local motion has been corrected. Process thread exits. Computational time: 34.810013 sec Total time: 44.132870 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00020hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00020hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.624060s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00020hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.844084s ........................................ >>>>>>TIME<<<<<< FFT: 1.542202s Defocus_U Defocus_V Angle CCC 28197.25 29091.83 7.13 0.042750 Final Values Defocus_U Defocus_V Angle CCC 28194.14 29060.62 8.08 0.071047 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00020hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00020hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.995e-02 CC threshold: 0.734 Mean Std: 41.52 6.86 Num Hot pixels: 204 Hot pixel threshold: 82.67 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.506999 Iteration 2 Error: 0.331362 Iteration 3 Error: 0.072228 Iteration 4 Error: 0.026275 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.32 0.02 ...... Frame ( 3) shift: 0.64 0.05 ...... Frame ( 4) shift: 0.96 0.07 ...... Frame ( 5) shift: 1.28 0.09 ...... Frame ( 6) shift: 1.54 0.16 ...... Frame ( 7) shift: 1.75 0.29 ...... Frame ( 8) shift: 1.96 0.41 ...... Frame ( 9) shift: 2.11 0.54 ...... Frame ( 10) shift: 2.20 0.68 ...... Frame ( 11) shift: 2.28 0.83 ...... Frame ( 12) shift: 2.35 0.95 ...... Frame ( 13) shift: 2.40 1.04 ...... Frame ( 14) shift: 2.45 1.13 ...... Frame ( 15) shift: 2.52 1.24 ...... Frame ( 16) shift: 2.62 1.38 ...... Frame ( 17) shift: 2.71 1.52 ...... Frame ( 18) shift: 2.78 1.64 ...... Frame ( 19) shift: 2.82 1.73 ...... Frame ( 20) shift: 2.87 1.82 ...... Frame ( 21) shift: 2.92 1.90 ...... Frame ( 22) shift: 2.99 1.96 ...... Frame ( 23) shift: 3.05 2.03 ...... Frame ( 24) shift: 3.10 2.10 ...... Frame ( 25) shift: 3.13 2.17 ...... Frame ( 26) shift: 3.17 2.24 ...... Frame ( 27) shift: 3.18 2.29 ...... Frame ( 28) shift: 3.18 2.33 ...... Frame ( 29) shift: 3.17 2.38 ...... Frame ( 30) shift: 3.19 2.41 ...... Frame ( 31) shift: 3.21 2.45 ...... Frame ( 32) shift: 3.24 2.48 ...... Frame ( 33) shift: 3.30 2.51 ...... Frame ( 34) shift: 3.39 2.55 ...... Frame ( 35) shift: 3.48 2.58 ...... Frame ( 36) shift: 3.55 2.61 ...... Frame ( 37) shift: 3.60 2.66 ...... Frame ( 38) shift: 3.66 2.70 ...... Frame ( 39) shift: 3.71 2.74 ...... Frame ( 40) shift: 3.76 2.78 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.801452 Iteration 2 Error: 0.105620 Iteration 3 Error: 0.029841 Align patch 2 23 left Iteration 1 Error: 0.788949 Iteration 2 Error: 0.092564 Iteration 3 Error: 0.033007 Align patch 3 22 left Iteration 1 Error: 0.602019 Iteration 2 Error: 0.096736 Iteration 3 Error: 0.025590 Align patch 4 21 left Iteration 1 Error: 0.923634 Iteration 2 Error: 0.126395 Iteration 3 Error: 0.027537 Align patch 5 20 left Iteration 1 Error: 0.597760 Iteration 2 Error: 0.092265 Iteration 3 Error: 0.024515 Align patch 6 19 left Iteration 1 Error: 0.658226 Iteration 2 Error: 0.199876 Iteration 3 Error: 0.051469 Iteration 4 Error: 0.021376 Align patch 7 18 left Iteration 1 Error: 0.636488 Iteration 2 Error: 0.136250 Iteration 3 Error: 0.030364 Align patch 8 17 left Iteration 1 Error: 0.754364 Iteration 2 Error: 0.086408 Iteration 3 Error: 0.017684 Align patch 9 16 left Iteration 1 Error: 0.946466 Iteration 2 Error: 0.196908 Iteration 3 Error: 0.068521 Iteration 4 Error: 0.028785 Align patch 10 15 left Iteration 1 Error: 0.789248 Iteration 2 Error: 0.101912 Iteration 3 Error: 0.039966 Align patch 11 14 left Iteration 1 Error: 0.631835 Iteration 2 Error: 0.111797 Iteration 3 Error: 0.030154 Align patch 12 13 left Iteration 1 Error: 0.682057 Iteration 2 Error: 0.140297 Iteration 3 Error: 0.061663 Iteration 4 Error: 0.018572 Align patch 13 12 left Iteration 1 Error: 0.730236 Iteration 2 Error: 0.175681 Iteration 3 Error: 0.043176 Align patch 14 11 left Iteration 1 Error: 0.685614 Iteration 2 Error: 0.240153 Iteration 3 Error: 0.058959 Iteration 4 Error: 0.018771 Align patch 15 10 left Iteration 1 Error: 0.617501 Iteration 2 Error: 0.125472 Iteration 3 Error: 0.036274 Align patch 16 9 left Iteration 1 Error: 0.788906 Iteration 2 Error: 0.138507 Iteration 3 Error: 0.038847 Align patch 17 8 left Iteration 1 Error: 0.560323 Iteration 2 Error: 0.104624 Iteration 3 Error: 0.034975 Align patch 18 7 left Iteration 1 Error: 0.702110 Iteration 2 Error: 0.092796 Iteration 3 Error: 0.036116 Align patch 19 6 left Iteration 1 Error: 0.877642 Iteration 2 Error: 0.097263 Iteration 3 Error: 0.021527 Align patch 20 5 left Iteration 1 Error: 1.039234 Iteration 2 Error: 0.081140 Iteration 3 Error: 0.024407 Align patch 21 4 left Iteration 1 Error: 0.496320 Iteration 2 Error: 0.093025 Iteration 3 Error: 0.031768 Align patch 22 3 left Iteration 1 Error: 0.726169 Iteration 2 Error: 0.105357 Iteration 3 Error: 0.026538 Align patch 23 2 left Iteration 1 Error: 0.977488 Iteration 2 Error: 0.140782 Iteration 3 Error: 0.029259 Align patch 24 1 left Iteration 1 Error: 1.511755 Iteration 2 Error: 0.251252 Iteration 3 Error: 0.039419 Align patch 25 0 left Iteration 1 Error: 1.597177 Iteration 2 Error: 0.246100 Iteration 3 Error: 0.042939 3D Fitting completed. Patch alignment time: 16.48(sec) Local motion has been corrected. Process thread exits. Computational time: 31.295368 sec Total time: 38.145348 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00020hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00020hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.559119s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00020hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.322671s ........................................ >>>>>>TIME<<<<<< FFT: 1.169105s Defocus_U Defocus_V Angle CCC 26291.02 25677.73 87.11 0.049012 Final Values Defocus_U Defocus_V Angle CCC 26291.02 25683.98 88.06 0.076633 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00020hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00020hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.994e-02 CC threshold: 0.734 Mean Std: 41.47 6.86 Num Hot pixels: 204 Hot pixel threshold: 82.63 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.107978 Iteration 2 Error: 0.395338 Iteration 3 Error: 0.099930 Iteration 4 Error: 0.030521 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.06 0.00 ...... Frame ( 3) shift: 0.12 0.01 ...... Frame ( 4) shift: 0.18 0.01 ...... Frame ( 5) shift: 0.23 0.02 ...... Frame ( 6) shift: 0.29 0.03 ...... Frame ( 7) shift: 0.35 0.04 ...... Frame ( 8) shift: 0.41 0.05 ...... Frame ( 9) shift: 0.48 0.09 ...... Frame ( 10) shift: 0.55 0.15 ...... Frame ( 11) shift: 0.63 0.21 ...... Frame ( 12) shift: 0.71 0.29 ...... Frame ( 13) shift: 0.80 0.38 ...... Frame ( 14) shift: 0.88 0.47 ...... Frame ( 15) shift: 0.97 0.50 ...... Frame ( 16) shift: 1.06 0.46 ...... Frame ( 17) shift: 1.14 0.42 ...... Frame ( 18) shift: 1.25 0.43 ...... Frame ( 19) shift: 1.36 0.47 ...... Frame ( 20) shift: 1.48 0.51 ...... Frame ( 21) shift: 1.58 0.55 ...... Frame ( 22) shift: 1.67 0.60 ...... Frame ( 23) shift: 1.76 0.65 ...... Frame ( 24) shift: 1.89 0.76 ...... Frame ( 25) shift: 2.05 0.92 ...... Frame ( 26) shift: 2.21 1.08 ...... Frame ( 27) shift: 2.38 1.20 ...... Frame ( 28) shift: 2.54 1.30 ...... Frame ( 29) shift: 2.70 1.39 ...... Frame ( 30) shift: 2.82 1.46 ...... Frame ( 31) shift: 2.91 1.51 ...... Frame ( 32) shift: 3.00 1.56 ...... Frame ( 33) shift: 3.10 1.65 ...... Frame ( 34) shift: 3.21 1.78 ...... Frame ( 35) shift: 3.32 1.92 ...... Frame ( 36) shift: 3.41 1.99 ...... Frame ( 37) shift: 3.47 2.01 ...... Frame ( 38) shift: 3.53 2.04 ...... Frame ( 39) shift: 3.59 2.06 ...... Frame ( 40) shift: 3.65 2.08 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.861597 Iteration 2 Error: 0.160314 Iteration 3 Error: 0.074719 Iteration 4 Error: 0.024359 Align patch 2 23 left Iteration 1 Error: 0.797341 Iteration 2 Error: 0.160176 Iteration 3 Error: 0.041775 Align patch 3 22 left Iteration 1 Error: 0.953886 Iteration 2 Error: 0.215588 Iteration 3 Error: 0.062803 Iteration 4 Error: 0.015490 Align patch 4 21 left Iteration 1 Error: 0.881328 Iteration 2 Error: 0.180634 Iteration 3 Error: 0.075181 Iteration 4 Error: 0.031196 Align patch 5 20 left Iteration 1 Error: 0.736088 Iteration 2 Error: 0.183005 Iteration 3 Error: 0.073626 Iteration 4 Error: 0.030861 Align patch 6 19 left Iteration 1 Error: 1.212190 Iteration 2 Error: 0.253493 Iteration 3 Error: 0.069980 Iteration 4 Error: 0.052994 Iteration 5 Error: 0.029338 Align patch 7 18 left Iteration 1 Error: 0.872368 Iteration 2 Error: 0.277797 Iteration 3 Error: 0.108828 Iteration 4 Error: 0.083587 Iteration 5 Error: 0.029972 Align patch 8 17 left Iteration 1 Error: 0.906032 Iteration 2 Error: 0.136145 Iteration 3 Error: 0.038195 Align patch 9 16 left Iteration 1 Error: 1.056690 Iteration 2 Error: 0.183432 Iteration 3 Error: 0.028522 Align patch 10 15 left Iteration 1 Error: 0.649618 Iteration 2 Error: 0.127643 Iteration 3 Error: 0.042382 Align patch 11 14 left Iteration 1 Error: 0.853687 Iteration 2 Error: 0.181032 Iteration 3 Error: 0.041256 Align patch 12 13 left Iteration 1 Error: 0.426011 Iteration 2 Error: 0.105132 Iteration 3 Error: 0.031748 Align patch 13 12 left Iteration 1 Error: 0.847440 Iteration 2 Error: 0.103968 Iteration 3 Error: 0.030722 Align patch 14 11 left Iteration 1 Error: 0.730584 Iteration 2 Error: 0.167456 Iteration 3 Error: 0.055702 Iteration 4 Error: 0.022416 Align patch 15 10 left Iteration 1 Error: 0.668322 Iteration 2 Error: 0.139484 Iteration 3 Error: 0.050764 Iteration 4 Error: 0.012729 Align patch 16 9 left Iteration 1 Error: 0.652213 Iteration 2 Error: 0.138754 Iteration 3 Error: 0.044132 Align patch 17 8 left Iteration 1 Error: 0.419836 Iteration 2 Error: 0.069643 Iteration 3 Error: 0.024358 Align patch 18 7 left Iteration 1 Error: 0.738297 Iteration 2 Error: 0.105324 Iteration 3 Error: 0.034897 Align patch 19 6 left Iteration 1 Error: 0.814654 Iteration 2 Error: 0.152162 Iteration 3 Error: 0.045145 Align patch 20 5 left Iteration 1 Error: 1.190685 Iteration 2 Error: 0.207098 Iteration 3 Error: 0.041085 Align patch 21 4 left Iteration 1 Error: 0.815457 Iteration 2 Error: 0.149775 Iteration 3 Error: 0.055773 Iteration 4 Error: 0.012146 Align patch 22 3 left Iteration 1 Error: 1.360832 Iteration 2 Error: 0.249907 Iteration 3 Error: 0.044148 Align patch 23 2 left Iteration 1 Error: 1.143895 Iteration 2 Error: 0.136708 Iteration 3 Error: 0.024030 Align patch 24 1 left Iteration 1 Error: 0.644772 Iteration 2 Error: 0.134623 Iteration 3 Error: 0.034548 Align patch 25 0 left Iteration 1 Error: 0.582433 Iteration 2 Error: 0.086251 Iteration 3 Error: 0.018116 3D Fitting completed. Patch alignment time: 16.60(sec) Local motion has been corrected. Process thread exits. Computational time: 32.331902 sec Total time: 40.567856 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00020hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00020hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.577804s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00020hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.702183s ........................................ >>>>>>TIME<<<<<< FFT: 1.399127s Defocus_U Defocus_V Angle CCC 25078.17 24308.62 88.06 0.045567 Final Values Defocus_U Defocus_V Angle CCC 25106.27 24302.40 89.63 0.072232 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00021hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00021hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.991e-02 CC threshold: 0.734 Mean Std: 39.65 6.69 Num Hot pixels: 192 Hot pixel threshold: 79.79 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.793126 Iteration 2 Error: 0.360839 Iteration 3 Error: 0.107126 Iteration 4 Error: 0.031227 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.13 -0.06 ...... Frame ( 3) shift: -0.26 -0.11 ...... Frame ( 4) shift: -0.39 -0.17 ...... Frame ( 5) shift: -0.52 -0.22 ...... Frame ( 6) shift: -0.52 -0.22 ...... Frame ( 7) shift: -0.40 -0.15 ...... Frame ( 8) shift: -0.27 -0.08 ...... Frame ( 9) shift: -0.16 -0.02 ...... Frame ( 10) shift: -0.06 0.02 ...... Frame ( 11) shift: 0.04 0.07 ...... Frame ( 12) shift: 0.22 0.17 ...... Frame ( 13) shift: 0.47 0.31 ...... Frame ( 14) shift: 0.73 0.46 ...... Frame ( 15) shift: 0.89 0.60 ...... Frame ( 16) shift: 0.94 0.74 ...... Frame ( 17) shift: 1.00 0.87 ...... Frame ( 18) shift: 1.11 0.99 ...... Frame ( 19) shift: 1.27 1.09 ...... Frame ( 20) shift: 1.43 1.19 ...... Frame ( 21) shift: 1.56 1.26 ...... Frame ( 22) shift: 1.65 1.30 ...... Frame ( 23) shift: 1.75 1.34 ...... Frame ( 24) shift: 1.84 1.38 ...... Frame ( 25) shift: 1.93 1.42 ...... Frame ( 26) shift: 2.01 1.46 ...... Frame ( 27) shift: 2.10 1.47 ...... Frame ( 28) shift: 2.19 1.47 ...... Frame ( 29) shift: 2.28 1.46 ...... Frame ( 30) shift: 2.37 1.48 ...... Frame ( 31) shift: 2.45 1.53 ...... Frame ( 32) shift: 2.54 1.58 ...... Frame ( 33) shift: 2.64 1.55 ...... Frame ( 34) shift: 2.75 1.45 ...... Frame ( 35) shift: 2.86 1.34 ...... Frame ( 36) shift: 2.97 1.31 ...... Frame ( 37) shift: 3.09 1.33 ...... Frame ( 38) shift: 3.20 1.36 ...... Frame ( 39) shift: 3.32 1.39 ...... Frame ( 40) shift: 3.44 1.42 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.819159 Iteration 2 Error: 0.103680 Iteration 3 Error: 0.025142 Align patch 2 23 left Iteration 1 Error: 1.593132 Iteration 2 Error: 0.219012 Iteration 3 Error: 0.067527 Iteration 4 Error: 0.019238 Align patch 3 22 left Iteration 1 Error: 0.736452 Iteration 2 Error: 0.231185 Iteration 3 Error: 0.051014 Iteration 4 Error: 0.008916 Align patch 4 21 left Iteration 1 Error: 0.850490 Iteration 2 Error: 0.130075 Iteration 3 Error: 0.046926 Align patch 5 20 left Iteration 1 Error: 0.766293 Iteration 2 Error: 0.130745 Iteration 3 Error: 0.050944 Iteration 4 Error: 0.016354 Align patch 6 19 left Iteration 1 Error: 0.543380 Iteration 2 Error: 0.132805 Iteration 3 Error: 0.043442 Align patch 7 18 left Iteration 1 Error: 1.008947 Iteration 2 Error: 0.131162 Iteration 3 Error: 0.037295 Align patch 8 17 left Iteration 1 Error: 0.731793 Iteration 2 Error: 0.163161 Iteration 3 Error: 0.036189 Align patch 9 16 left Iteration 1 Error: 1.429516 Iteration 2 Error: 0.256060 Iteration 3 Error: 0.081456 Iteration 4 Error: 0.033654 Align patch 10 15 left Iteration 1 Error: 0.967636 Iteration 2 Error: 0.144811 Iteration 3 Error: 0.032071 Align patch 11 14 left Iteration 1 Error: 0.598254 Iteration 2 Error: 0.113028 Iteration 3 Error: 0.032244 Align patch 12 13 left Iteration 1 Error: 0.734933 Iteration 2 Error: 0.200175 Iteration 3 Error: 0.040023 Align patch 13 12 left Iteration 1 Error: 0.931517 Iteration 2 Error: 0.121834 Iteration 3 Error: 0.033998 Align patch 14 11 left Iteration 1 Error: 0.650302 Iteration 2 Error: 0.077132 Iteration 3 Error: 0.016530 Align patch 15 10 left Iteration 1 Error: 0.885709 Iteration 2 Error: 0.234769 Iteration 3 Error: 0.062147 Iteration 4 Error: 0.021966 Align patch 16 9 left Iteration 1 Error: 0.743959 Iteration 2 Error: 0.187911 Iteration 3 Error: 0.058377 Iteration 4 Error: 0.018385 Align patch 17 8 left Iteration 1 Error: 0.749384 Iteration 2 Error: 0.195093 Iteration 3 Error: 0.057266 Iteration 4 Error: 0.016584 Align patch 18 7 left Iteration 1 Error: 0.886972 Iteration 2 Error: 0.127998 Iteration 3 Error: 0.058598 Iteration 4 Error: 0.043606 Align patch 19 6 left Iteration 1 Error: 0.524852 Iteration 2 Error: 0.077264 Iteration 3 Error: 0.020713 Align patch 20 5 left Iteration 1 Error: 0.742896 Iteration 2 Error: 0.131150 Iteration 3 Error: 0.042269 Align patch 21 4 left Iteration 1 Error: 0.598738 Iteration 2 Error: 0.148368 Iteration 3 Error: 0.036317 Align patch 22 3 left Iteration 1 Error: 0.703469 Iteration 2 Error: 0.200138 Iteration 3 Error: 0.041808 Align patch 23 2 left Iteration 1 Error: 0.778313 Iteration 2 Error: 0.265523 Iteration 3 Error: 0.079530 Iteration 4 Error: 0.027622 Align patch 24 1 left Iteration 1 Error: 0.931192 Iteration 2 Error: 0.173064 Iteration 3 Error: 0.047650 Align patch 25 0 left Iteration 1 Error: 0.837979 Iteration 2 Error: 0.169973 Iteration 3 Error: 0.047190 3D Fitting completed. Patch alignment time: 20.04(sec) Local motion has been corrected. Process thread exits. Computational time: 36.676704 sec Total time: 44.843723 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00021hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00021hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.616692s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00021hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.519331s ........................................ >>>>>>TIME<<<<<< FFT: 1.485662s Defocus_U Defocus_V Angle CCC 27203.13 27843.79 8.81 0.039327 Final Values Defocus_U Defocus_V Angle CCC 27209.39 27821.93 9.44 0.059640 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00021hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00021hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 38.47 6.62 Num Hot pixels: 206 Hot pixel threshold: 78.19 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.873035 Iteration 2 Error: 0.345284 Iteration 3 Error: 0.070806 Iteration 4 Error: 0.020267 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.06 -0.24 ...... Frame ( 3) shift: -0.11 -0.49 ...... Frame ( 4) shift: -0.17 -0.73 ...... Frame ( 5) shift: -0.23 -0.97 ...... Frame ( 6) shift: -0.20 -1.05 ...... Frame ( 7) shift: -0.10 -0.97 ...... Frame ( 8) shift: 0.01 -0.89 ...... Frame ( 9) shift: 0.14 -0.75 ...... Frame ( 10) shift: 0.31 -0.57 ...... Frame ( 11) shift: 0.47 -0.38 ...... Frame ( 12) shift: 0.61 -0.26 ...... Frame ( 13) shift: 0.73 -0.21 ...... Frame ( 14) shift: 0.84 -0.16 ...... Frame ( 15) shift: 0.95 -0.09 ...... Frame ( 16) shift: 1.04 -0.02 ...... Frame ( 17) shift: 1.14 0.06 ...... Frame ( 18) shift: 1.24 0.13 ...... Frame ( 19) shift: 1.35 0.20 ...... Frame ( 20) shift: 1.46 0.27 ...... Frame ( 21) shift: 1.60 0.33 ...... Frame ( 22) shift: 1.79 0.37 ...... Frame ( 23) shift: 1.97 0.42 ...... Frame ( 24) shift: 2.13 0.46 ...... Frame ( 25) shift: 2.26 0.49 ...... Frame ( 26) shift: 2.40 0.53 ...... Frame ( 27) shift: 2.48 0.50 ...... Frame ( 28) shift: 2.51 0.40 ...... Frame ( 29) shift: 2.53 0.30 ...... Frame ( 30) shift: 2.55 0.27 ...... Frame ( 31) shift: 2.56 0.33 ...... Frame ( 32) shift: 2.58 0.39 ...... Frame ( 33) shift: 2.61 0.45 ...... Frame ( 34) shift: 2.67 0.52 ...... Frame ( 35) shift: 2.72 0.59 ...... Frame ( 36) shift: 2.81 0.70 ...... Frame ( 37) shift: 2.92 0.84 ...... Frame ( 38) shift: 3.03 0.99 ...... Frame ( 39) shift: 3.15 1.13 ...... Frame ( 40) shift: 3.26 1.28 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.038670 Iteration 2 Error: 0.150308 Iteration 3 Error: 0.032491 Align patch 2 23 left Iteration 1 Error: 1.273427 Iteration 2 Error: 0.154295 Iteration 3 Error: 0.033115 Align patch 3 22 left Iteration 1 Error: 1.013348 Iteration 2 Error: 0.132077 Iteration 3 Error: 0.031182 Align patch 4 21 left Iteration 1 Error: 1.167029 Iteration 2 Error: 0.105000 Iteration 3 Error: 0.026077 Align patch 5 20 left Iteration 1 Error: 0.924630 Iteration 2 Error: 0.086965 Iteration 3 Error: 0.021540 Align patch 6 19 left Iteration 1 Error: 0.694154 Iteration 2 Error: 0.116321 Iteration 3 Error: 0.021069 Align patch 7 18 left Iteration 1 Error: 0.713188 Iteration 2 Error: 0.094445 Iteration 3 Error: 0.026775 Align patch 8 17 left Iteration 1 Error: 0.650652 Iteration 2 Error: 0.098818 Iteration 3 Error: 0.025983 Align patch 9 16 left Iteration 1 Error: 1.023004 Iteration 2 Error: 0.238822 Iteration 3 Error: 0.042478 Align patch 10 15 left Iteration 1 Error: 0.666089 Iteration 2 Error: 0.112433 Iteration 3 Error: 0.028219 Align patch 11 14 left Iteration 1 Error: 0.718899 Iteration 2 Error: 0.099412 Iteration 3 Error: 0.034180 Align patch 12 13 left Iteration 1 Error: 0.512222 Iteration 2 Error: 0.103648 Iteration 3 Error: 0.026065 Align patch 13 12 left Iteration 1 Error: 0.529380 Iteration 2 Error: 0.159859 Iteration 3 Error: 0.044397 Align patch 14 11 left Iteration 1 Error: 0.724223 Iteration 2 Error: 0.093583 Iteration 3 Error: 0.025655 Align patch 15 10 left Iteration 1 Error: 0.534893 Iteration 2 Error: 0.056701 Iteration 3 Error: 0.009755 Align patch 16 9 left Iteration 1 Error: 0.814733 Iteration 2 Error: 0.162496 Iteration 3 Error: 0.034449 Align patch 17 8 left Iteration 1 Error: 0.643313 Iteration 2 Error: 0.068770 Iteration 3 Error: 0.012951 Align patch 18 7 left Iteration 1 Error: 0.788178 Iteration 2 Error: 0.124679 Iteration 3 Error: 0.040614 Align patch 19 6 left Iteration 1 Error: 0.506405 Iteration 2 Error: 0.089154 Iteration 3 Error: 0.019643 Align patch 20 5 left Iteration 1 Error: 0.851659 Iteration 2 Error: 0.128605 Iteration 3 Error: 0.035888 Align patch 21 4 left Iteration 1 Error: 0.960072 Iteration 2 Error: 0.141225 Iteration 3 Error: 0.031991 Align patch 22 3 left Iteration 1 Error: 0.695379 Iteration 2 Error: 0.141128 Iteration 3 Error: 0.032793 Align patch 23 2 left Iteration 1 Error: 0.737421 Iteration 2 Error: 0.193295 Iteration 3 Error: 0.050314 Iteration 4 Error: 0.013839 Align patch 24 1 left Iteration 1 Error: 1.013896 Iteration 2 Error: 0.174340 Iteration 3 Error: 0.033684 Align patch 25 0 left Iteration 1 Error: 0.505304 Iteration 2 Error: 0.078613 Iteration 3 Error: 0.020857 3D Fitting completed. Patch alignment time: 19.24(sec) Local motion has been corrected. Process thread exits. Computational time: 35.722878 sec Total time: 44.523209 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00021hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00021hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.607655s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00021hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.260709s ........................................ >>>>>>TIME<<<<<< FFT: 1.475253s Defocus_U Defocus_V Angle CCC 27537.12 28458.99 8.59 0.042018 Final Values Defocus_U Defocus_V Angle CCC 27515.23 28502.78 9.54 0.059751 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00021hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00021hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.987e-02 CC threshold: 0.734 Mean Std: 40.05 6.73 Num Hot pixels: 191 Hot pixel threshold: 80.41 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.942454 Iteration 2 Error: 0.364937 Iteration 3 Error: 0.093228 Iteration 4 Error: 0.034406 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.05 0.11 ...... Frame ( 3) shift: 0.09 0.21 ...... Frame ( 4) shift: 0.14 0.32 ...... Frame ( 5) shift: 0.19 0.43 ...... Frame ( 6) shift: 0.22 0.53 ...... Frame ( 7) shift: 0.23 0.62 ...... Frame ( 8) shift: 0.24 0.72 ...... Frame ( 9) shift: 0.29 0.87 ...... Frame ( 10) shift: 0.40 1.07 ...... Frame ( 11) shift: 0.50 1.28 ...... Frame ( 12) shift: 0.61 1.43 ...... Frame ( 13) shift: 0.72 1.52 ...... Frame ( 14) shift: 0.83 1.62 ...... Frame ( 15) shift: 0.92 1.72 ...... Frame ( 16) shift: 1.01 1.82 ...... Frame ( 17) shift: 1.09 1.93 ...... Frame ( 18) shift: 1.16 2.04 ...... Frame ( 19) shift: 1.23 2.17 ...... Frame ( 20) shift: 1.30 2.29 ...... Frame ( 21) shift: 1.35 2.39 ...... Frame ( 22) shift: 1.39 2.48 ...... Frame ( 23) shift: 1.42 2.56 ...... Frame ( 24) shift: 1.48 2.60 ...... Frame ( 25) shift: 1.57 2.59 ...... Frame ( 26) shift: 1.66 2.58 ...... Frame ( 27) shift: 1.77 2.59 ...... Frame ( 28) shift: 1.89 2.61 ...... Frame ( 29) shift: 2.01 2.63 ...... Frame ( 30) shift: 2.09 2.68 ...... Frame ( 31) shift: 2.13 2.76 ...... Frame ( 32) shift: 2.18 2.84 ...... Frame ( 33) shift: 2.21 2.92 ...... Frame ( 34) shift: 2.22 2.99 ...... Frame ( 35) shift: 2.24 3.07 ...... Frame ( 36) shift: 2.30 3.16 ...... Frame ( 37) shift: 2.40 3.27 ...... Frame ( 38) shift: 2.51 3.37 ...... Frame ( 39) shift: 2.61 3.48 ...... Frame ( 40) shift: 2.71 3.58 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.695195 Iteration 2 Error: 0.117978 Iteration 3 Error: 0.033676 Align patch 2 23 left Iteration 1 Error: 1.022586 Iteration 2 Error: 0.361375 Iteration 3 Error: 0.118864 Iteration 4 Error: 0.031559 Align patch 3 22 left Iteration 1 Error: 0.785088 Iteration 2 Error: 0.159503 Iteration 3 Error: 0.092377 Iteration 4 Error: 0.018897 Align patch 4 21 left Iteration 1 Error: 0.853613 Iteration 2 Error: 0.176916 Iteration 3 Error: 0.039902 Align patch 5 20 left Iteration 1 Error: 0.835984 Iteration 2 Error: 0.094424 Iteration 3 Error: 0.041073 Align patch 6 19 left Iteration 1 Error: 0.863523 Iteration 2 Error: 0.124869 Iteration 3 Error: 0.034789 Align patch 7 18 left Iteration 1 Error: 0.564248 Iteration 2 Error: 0.186752 Iteration 3 Error: 0.061524 Iteration 4 Error: 0.023715 Align patch 8 17 left Iteration 1 Error: 0.806350 Iteration 2 Error: 0.166274 Iteration 3 Error: 0.063867 Iteration 4 Error: 0.014970 Align patch 9 16 left Iteration 1 Error: 0.725685 Iteration 2 Error: 0.095012 Iteration 3 Error: 0.023963 Align patch 10 15 left Iteration 1 Error: 0.531901 Iteration 2 Error: 0.082383 Iteration 3 Error: 0.014706 Align patch 11 14 left Iteration 1 Error: 0.978563 Iteration 2 Error: 0.159836 Iteration 3 Error: 0.042410 Align patch 12 13 left Iteration 1 Error: 0.990639 Iteration 2 Error: 0.136759 Iteration 3 Error: 0.062729 Iteration 4 Error: 0.020154 Align patch 13 12 left Iteration 1 Error: 0.525797 Iteration 2 Error: 0.131381 Iteration 3 Error: 0.046092 Align patch 14 11 left Iteration 1 Error: 0.571993 Iteration 2 Error: 0.128329 Iteration 3 Error: 0.040425 Align patch 15 10 left Iteration 1 Error: 0.587513 Iteration 2 Error: 0.189079 Iteration 3 Error: 0.047188 Align patch 16 9 left Iteration 1 Error: 1.086795 Iteration 2 Error: 0.157162 Iteration 3 Error: 0.084585 Iteration 4 Error: 0.030173 Align patch 17 8 left Iteration 1 Error: 0.720810 Iteration 2 Error: 0.257141 Iteration 3 Error: 0.077250 Iteration 4 Error: 0.043438 Align patch 18 7 left Iteration 1 Error: 0.719908 Iteration 2 Error: 0.209801 Iteration 3 Error: 0.100006 Iteration 4 Error: 0.056821 Iteration 5 Error: 0.029363 Align patch 19 6 left Iteration 1 Error: 0.580112 Iteration 2 Error: 0.227520 Iteration 3 Error: 0.049772 Align patch 20 5 left Iteration 1 Error: 0.963313 Iteration 2 Error: 0.169622 Iteration 3 Error: 0.046624 Align patch 21 4 left Iteration 1 Error: 1.096402 Iteration 2 Error: 0.188826 Iteration 3 Error: 0.055009 Iteration 4 Error: 0.021430 Align patch 22 3 left Iteration 1 Error: 0.731547 Iteration 2 Error: 0.192955 Iteration 3 Error: 0.033897 Align patch 23 2 left Iteration 1 Error: 0.744897 Iteration 2 Error: 0.153319 Iteration 3 Error: 0.050706 Iteration 4 Error: 0.017867 Align patch 24 1 left Iteration 1 Error: 1.364307 Iteration 2 Error: 0.206984 Iteration 3 Error: 0.040861 Align patch 25 0 left Iteration 1 Error: 0.969562 Iteration 2 Error: 0.230358 Iteration 3 Error: 0.065759 Iteration 4 Error: 0.029572 3D Fitting completed. Patch alignment time: 20.02(sec) Local motion has been corrected. Process thread exits. Computational time: 31.748802 sec Total time: 41.565018 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00021hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00021hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.593063s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00021hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.042288s ........................................ >>>>>>TIME<<<<<< FFT: 1.089402s Defocus_U Defocus_V Angle CCC 27160.17 26503.92 84.57 0.042495 Final Values Defocus_U Defocus_V Angle CCC 27132.04 26478.94 87.80 0.062898 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00021hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00021hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.990e-02 CC threshold: 0.734 Mean Std: 39.09 6.64 Num Hot pixels: 194 Hot pixel threshold: 78.94 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.130463 Iteration 2 Error: 0.472064 Iteration 3 Error: 0.151579 Iteration 4 Error: 0.048061 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.01 0.02 ...... Frame ( 3) shift: -0.02 0.05 ...... Frame ( 4) shift: -0.03 0.07 ...... Frame ( 5) shift: -0.04 0.09 ...... Frame ( 6) shift: 0.05 0.18 ...... Frame ( 7) shift: 0.24 0.34 ...... Frame ( 8) shift: 0.44 0.50 ...... Frame ( 9) shift: 0.57 0.64 ...... Frame ( 10) shift: 0.64 0.75 ...... Frame ( 11) shift: 0.71 0.86 ...... Frame ( 12) shift: 0.83 0.99 ...... Frame ( 13) shift: 1.02 1.13 ...... Frame ( 14) shift: 1.21 1.28 ...... Frame ( 15) shift: 1.35 1.44 ...... Frame ( 16) shift: 1.44 1.62 ...... Frame ( 17) shift: 1.53 1.79 ...... Frame ( 18) shift: 1.63 1.95 ...... Frame ( 19) shift: 1.74 2.09 ...... Frame ( 20) shift: 1.84 2.23 ...... Frame ( 21) shift: 1.92 2.36 ...... Frame ( 22) shift: 1.96 2.48 ...... Frame ( 23) shift: 2.01 2.60 ...... Frame ( 24) shift: 2.10 2.66 ...... Frame ( 25) shift: 2.22 2.67 ...... Frame ( 26) shift: 2.34 2.68 ...... Frame ( 27) shift: 2.40 2.74 ...... Frame ( 28) shift: 2.40 2.84 ...... Frame ( 29) shift: 2.40 2.94 ...... Frame ( 30) shift: 2.50 3.02 ...... Frame ( 31) shift: 2.70 3.09 ...... Frame ( 32) shift: 2.91 3.15 ...... Frame ( 33) shift: 3.05 3.13 ...... Frame ( 34) shift: 3.13 3.02 ...... Frame ( 35) shift: 3.21 2.91 ...... Frame ( 36) shift: 3.29 2.89 ...... Frame ( 37) shift: 3.38 2.95 ...... Frame ( 38) shift: 3.47 3.01 ...... Frame ( 39) shift: 3.56 3.08 ...... Frame ( 40) shift: 3.64 3.14 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.793579 Iteration 2 Error: 0.223390 Iteration 3 Error: 0.096456 Iteration 4 Error: 0.047714 Align patch 2 23 left Iteration 1 Error: 0.955608 Iteration 2 Error: 0.217975 Iteration 3 Error: 0.083090 Iteration 4 Error: 0.023394 Align patch 3 22 left Iteration 1 Error: 1.560165 Iteration 2 Error: 0.378340 Iteration 3 Error: 0.109753 Iteration 4 Error: 0.045061 Align patch 4 21 left Iteration 1 Error: 1.021947 Iteration 2 Error: 0.190290 Iteration 3 Error: 0.048132 Align patch 5 20 left Iteration 1 Error: 0.791749 Iteration 2 Error: 0.209319 Iteration 3 Error: 0.047857 Align patch 6 19 left Iteration 1 Error: 0.857976 Iteration 2 Error: 0.100518 Iteration 3 Error: 0.031544 Align patch 7 18 left Iteration 1 Error: 0.877268 Iteration 2 Error: 0.172263 Iteration 3 Error: 0.081471 Iteration 4 Error: 0.037615 Align patch 8 17 left Iteration 1 Error: 0.766236 Iteration 2 Error: 0.142393 Iteration 3 Error: 0.056483 Iteration 4 Error: 0.019622 Align patch 9 16 left Iteration 1 Error: 0.872152 Iteration 2 Error: 0.217328 Iteration 3 Error: 0.090965 Iteration 4 Error: 0.035695 Align patch 10 15 left Iteration 1 Error: 0.675953 Iteration 2 Error: 0.153125 Iteration 3 Error: 0.041551 Align patch 11 14 left Iteration 1 Error: 0.717350 Iteration 2 Error: 0.130721 Iteration 3 Error: 0.040634 Align patch 12 13 left Iteration 1 Error: 0.908045 Iteration 2 Error: 0.271813 Iteration 3 Error: 0.130514 Iteration 4 Error: 0.077290 Iteration 5 Error: 0.041249 Align patch 13 12 left Iteration 1 Error: 0.873645 Iteration 2 Error: 0.164191 Iteration 3 Error: 0.053402 Iteration 4 Error: 0.015124 Align patch 14 11 left Iteration 1 Error: 0.818923 Iteration 2 Error: 0.177601 Iteration 3 Error: 0.044191 Align patch 15 10 left Iteration 1 Error: 0.676201 Iteration 2 Error: 0.097819 Iteration 3 Error: 0.033101 Align patch 16 9 left Iteration 1 Error: 0.954703 Iteration 2 Error: 0.236428 Iteration 3 Error: 0.052294 Iteration 4 Error: 0.019383 Align patch 17 8 left Iteration 1 Error: 0.517554 Iteration 2 Error: 0.102430 Iteration 3 Error: 0.015354 Align patch 18 7 left Iteration 1 Error: 0.587880 Iteration 2 Error: 0.087046 Iteration 3 Error: 0.020429 Align patch 19 6 left Iteration 1 Error: 1.387700 Iteration 2 Error: 0.164107 Iteration 3 Error: 0.039735 Align patch 20 5 left Iteration 1 Error: 0.939674 Iteration 2 Error: 0.167194 Iteration 3 Error: 0.069812 Iteration 4 Error: 0.020332 Align patch 21 4 left Iteration 1 Error: 0.820680 Iteration 2 Error: 0.182420 Iteration 3 Error: 0.063696 Iteration 4 Error: 0.020800 Align patch 22 3 left Iteration 1 Error: 0.538109 Iteration 2 Error: 0.104884 Iteration 3 Error: 0.021393 Align patch 23 2 left Iteration 1 Error: 0.866077 Iteration 2 Error: 0.157579 Iteration 3 Error: 0.044313 Align patch 24 1 left Iteration 1 Error: 0.753631 Iteration 2 Error: 0.134488 Iteration 3 Error: 0.036049 Align patch 25 0 left Iteration 1 Error: 0.974526 Iteration 2 Error: 0.171377 Iteration 3 Error: 0.032608 3D Fitting completed. Patch alignment time: 15.90(sec) Local motion has been corrected. Process thread exits. Computational time: 32.712296 sec Total time: 42.537148 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00021hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00021hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.403129s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00021hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 4.008245s ........................................ >>>>>>TIME<<<<<< FFT: 1.354311s Defocus_U Defocus_V Angle CCC 29444.86 28844.33 77.89 0.029455 Final Values Defocus_U Defocus_V Angle CCC 29437.04 28852.14 77.27 0.046640 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00022hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00022hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 41.66 6.88 Num Hot pixels: 208 Hot pixel threshold: 82.96 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.526911 Iteration 2 Error: 0.235954 Iteration 3 Error: 0.067373 Iteration 4 Error: 0.018188 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.10 -0.37 ...... Frame ( 3) shift: 0.20 -0.75 ...... Frame ( 4) shift: 0.31 -1.12 ...... Frame ( 5) shift: 0.41 -1.50 ...... Frame ( 6) shift: 0.52 -1.66 ...... Frame ( 7) shift: 0.65 -1.60 ...... Frame ( 8) shift: 0.77 -1.55 ...... Frame ( 9) shift: 0.87 -1.49 ...... Frame ( 10) shift: 0.96 -1.43 ...... Frame ( 11) shift: 1.04 -1.36 ...... Frame ( 12) shift: 1.14 -1.30 ...... Frame ( 13) shift: 1.25 -1.23 ...... Frame ( 14) shift: 1.36 -1.17 ...... Frame ( 15) shift: 1.47 -1.08 ...... Frame ( 16) shift: 1.57 -0.97 ...... Frame ( 17) shift: 1.66 -0.87 ...... Frame ( 18) shift: 1.74 -0.78 ...... Frame ( 19) shift: 1.78 -0.71 ...... Frame ( 20) shift: 1.82 -0.63 ...... Frame ( 21) shift: 1.88 -0.57 ...... Frame ( 22) shift: 1.95 -0.50 ...... Frame ( 23) shift: 2.02 -0.44 ...... Frame ( 24) shift: 2.13 -0.38 ...... Frame ( 25) shift: 2.27 -0.33 ...... Frame ( 26) shift: 2.42 -0.27 ...... Frame ( 27) shift: 2.51 -0.21 ...... Frame ( 28) shift: 2.54 -0.14 ...... Frame ( 29) shift: 2.58 -0.08 ...... Frame ( 30) shift: 2.57 -0.03 ...... Frame ( 31) shift: 2.51 0.01 ...... Frame ( 32) shift: 2.46 0.04 ...... Frame ( 33) shift: 2.47 0.07 ...... Frame ( 34) shift: 2.53 0.09 ...... Frame ( 35) shift: 2.59 0.11 ...... Frame ( 36) shift: 2.67 0.15 ...... Frame ( 37) shift: 2.77 0.19 ...... Frame ( 38) shift: 2.86 0.24 ...... Frame ( 39) shift: 2.96 0.29 ...... Frame ( 40) shift: 3.05 0.33 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.503183 Iteration 2 Error: 0.084376 Iteration 3 Error: 0.034970 Align patch 2 23 left Iteration 1 Error: 0.490762 Iteration 2 Error: 0.115572 Iteration 3 Error: 0.024370 Align patch 3 22 left Iteration 1 Error: 0.691576 Iteration 2 Error: 0.098980 Iteration 3 Error: 0.022993 Align patch 4 21 left Iteration 1 Error: 0.658160 Iteration 2 Error: 0.136623 Iteration 3 Error: 0.038961 Align patch 5 20 left Iteration 1 Error: 0.733369 Iteration 2 Error: 0.152330 Iteration 3 Error: 0.031524 Align patch 6 19 left Iteration 1 Error: 0.923043 Iteration 2 Error: 0.215754 Iteration 3 Error: 0.046299 Align patch 7 18 left Iteration 1 Error: 0.769634 Iteration 2 Error: 0.087435 Iteration 3 Error: 0.030268 Align patch 8 17 left Iteration 1 Error: 0.978194 Iteration 2 Error: 0.113404 Iteration 3 Error: 0.037622 Align patch 9 16 left Iteration 1 Error: 0.895207 Iteration 2 Error: 0.135916 Iteration 3 Error: 0.044088 Align patch 10 15 left Iteration 1 Error: 0.797970 Iteration 2 Error: 0.152901 Iteration 3 Error: 0.059262 Iteration 4 Error: 0.029897 Align patch 11 14 left Iteration 1 Error: 0.547186 Iteration 2 Error: 0.096998 Iteration 3 Error: 0.031153 Align patch 12 13 left Iteration 1 Error: 0.507262 Iteration 2 Error: 0.096958 Iteration 3 Error: 0.025510 Align patch 13 12 left Iteration 1 Error: 0.753534 Iteration 2 Error: 0.119482 Iteration 3 Error: 0.049222 Align patch 14 11 left Iteration 1 Error: 0.743400 Iteration 2 Error: 0.173394 Iteration 3 Error: 0.028480 Align patch 15 10 left Iteration 1 Error: 0.687566 Iteration 2 Error: 0.145143 Iteration 3 Error: 0.041850 Align patch 16 9 left Iteration 1 Error: 0.910126 Iteration 2 Error: 0.129463 Iteration 3 Error: 0.040140 Align patch 17 8 left Iteration 1 Error: 0.748048 Iteration 2 Error: 0.162229 Iteration 3 Error: 0.037251 Align patch 18 7 left Iteration 1 Error: 0.685510 Iteration 2 Error: 0.156005 Iteration 3 Error: 0.030846 Align patch 19 6 left Iteration 1 Error: 0.833691 Iteration 2 Error: 0.093654 Iteration 3 Error: 0.020453 Align patch 20 5 left Iteration 1 Error: 0.515555 Iteration 2 Error: 0.073090 Iteration 3 Error: 0.025865 Align patch 21 4 left Iteration 1 Error: 0.484987 Iteration 2 Error: 0.057095 Iteration 3 Error: 0.011022 Align patch 22 3 left Iteration 1 Error: 0.666175 Iteration 2 Error: 0.112641 Iteration 3 Error: 0.023443 Align patch 23 2 left Iteration 1 Error: 0.653979 Iteration 2 Error: 0.088056 Iteration 3 Error: 0.020317 Align patch 24 1 left Iteration 1 Error: 0.707998 Iteration 2 Error: 0.105987 Iteration 3 Error: 0.028496 Align patch 25 0 left Iteration 1 Error: 0.487503 Iteration 2 Error: 0.071102 Iteration 3 Error: 0.014326 3D Fitting completed. Patch alignment time: 16.60(sec) Local motion has been corrected. Process thread exits. Computational time: 36.281166 sec Total time: 51.174179 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00022hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00022hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.558526s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00022hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 4.225685s ........................................ >>>>>>TIME<<<<<< FFT: 1.484168s Defocus_U Defocus_V Angle CCC 17986.33 18775.39 9.37 0.041156 Final Values Defocus_U Defocus_V Angle CCC 17998.83 18766.02 9.37 0.071414 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00022hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00022hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.993e-02 CC threshold: 0.734 Mean Std: 42.06 6.92 Num Hot pixels: 214 Hot pixel threshold: 83.55 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.454788 Iteration 2 Error: 0.276028 Iteration 3 Error: 0.077758 Iteration 4 Error: 0.032230 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.16 -0.29 ...... Frame ( 3) shift: 0.33 -0.58 ...... Frame ( 4) shift: 0.49 -0.87 ...... Frame ( 5) shift: 0.66 -1.17 ...... Frame ( 6) shift: 0.77 -1.30 ...... Frame ( 7) shift: 0.83 -1.27 ...... Frame ( 8) shift: 0.89 -1.24 ...... Frame ( 9) shift: 0.98 -1.12 ...... Frame ( 10) shift: 1.09 -0.92 ...... Frame ( 11) shift: 1.20 -0.72 ...... Frame ( 12) shift: 1.27 -0.53 ...... Frame ( 13) shift: 1.29 -0.34 ...... Frame ( 14) shift: 1.30 -0.15 ...... Frame ( 15) shift: 1.38 -0.05 ...... Frame ( 16) shift: 1.51 -0.03 ...... Frame ( 17) shift: 1.64 -0.01 ...... Frame ( 18) shift: 1.74 0.05 ...... Frame ( 19) shift: 1.82 0.15 ...... Frame ( 20) shift: 1.90 0.25 ...... Frame ( 21) shift: 1.98 0.33 ...... Frame ( 22) shift: 2.09 0.38 ...... Frame ( 23) shift: 2.19 0.44 ...... Frame ( 24) shift: 2.27 0.49 ...... Frame ( 25) shift: 2.35 0.55 ...... Frame ( 26) shift: 2.42 0.60 ...... Frame ( 27) shift: 2.51 0.63 ...... Frame ( 28) shift: 2.61 0.63 ...... Frame ( 29) shift: 2.72 0.64 ...... Frame ( 30) shift: 2.79 0.63 ...... Frame ( 31) shift: 2.82 0.62 ...... Frame ( 32) shift: 2.85 0.60 ...... Frame ( 33) shift: 2.88 0.60 ...... Frame ( 34) shift: 2.91 0.61 ...... Frame ( 35) shift: 2.95 0.63 ...... Frame ( 36) shift: 2.99 0.64 ...... Frame ( 37) shift: 3.06 0.65 ...... Frame ( 38) shift: 3.12 0.67 ...... Frame ( 39) shift: 3.18 0.68 ...... Frame ( 40) shift: 3.25 0.69 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.762319 Iteration 2 Error: 0.262784 Iteration 3 Error: 0.058839 Iteration 4 Error: 0.016540 Align patch 2 23 left Iteration 1 Error: 0.895989 Iteration 2 Error: 0.145811 Iteration 3 Error: 0.038264 Align patch 3 22 left Iteration 1 Error: 1.143852 Iteration 2 Error: 0.133360 Iteration 3 Error: 0.042505 Align patch 4 21 left Iteration 1 Error: 1.581902 Iteration 2 Error: 0.229866 Iteration 3 Error: 0.097502 Iteration 4 Error: 0.042081 Align patch 5 20 left Iteration 1 Error: 0.862520 Iteration 2 Error: 0.145761 Iteration 3 Error: 0.035855 Align patch 6 19 left Iteration 1 Error: 0.959278 Iteration 2 Error: 0.189582 Iteration 3 Error: 0.025440 Align patch 7 18 left Iteration 1 Error: 0.934901 Iteration 2 Error: 0.155706 Iteration 3 Error: 0.035042 Align patch 8 17 left Iteration 1 Error: 1.318977 Iteration 2 Error: 0.315236 Iteration 3 Error: 0.063777 Iteration 4 Error: 0.032664 Align patch 9 16 left Iteration 1 Error: 1.039600 Iteration 2 Error: 0.140081 Iteration 3 Error: 0.070557 Iteration 4 Error: 0.021955 Align patch 10 15 left Iteration 1 Error: 0.601956 Iteration 2 Error: 0.220841 Iteration 3 Error: 0.057940 Iteration 4 Error: 0.024862 Align patch 11 14 left Iteration 1 Error: 1.080559 Iteration 2 Error: 0.176558 Iteration 3 Error: 0.067667 Iteration 4 Error: 0.030118 Align patch 12 13 left Iteration 1 Error: 0.825831 Iteration 2 Error: 0.224846 Iteration 3 Error: 0.066948 Iteration 4 Error: 0.025264 Align patch 13 12 left Iteration 1 Error: 0.736036 Iteration 2 Error: 0.114021 Iteration 3 Error: 0.044545 Align patch 14 11 left Iteration 1 Error: 0.498552 Iteration 2 Error: 0.127618 Iteration 3 Error: 0.030793 Align patch 15 10 left Iteration 1 Error: 0.642399 Iteration 2 Error: 0.212236 Iteration 3 Error: 0.052727 Iteration 4 Error: 0.013041 Align patch 16 9 left Iteration 1 Error: 0.915599 Iteration 2 Error: 0.240183 Iteration 3 Error: 0.071065 Iteration 4 Error: 0.024435 Align patch 17 8 left Iteration 1 Error: 0.638890 Iteration 2 Error: 0.145847 Iteration 3 Error: 0.040695 Align patch 18 7 left Iteration 1 Error: 0.507670 Iteration 2 Error: 0.151374 Iteration 3 Error: 0.046211 Align patch 19 6 left Iteration 1 Error: 0.569762 Iteration 2 Error: 0.117816 Iteration 3 Error: 0.041876 Align patch 20 5 left Iteration 1 Error: 1.283618 Iteration 2 Error: 0.179535 Iteration 3 Error: 0.043567 Align patch 21 4 left Iteration 1 Error: 0.834121 Iteration 2 Error: 0.102347 Iteration 3 Error: 0.022826 Align patch 22 3 left Iteration 1 Error: 1.139065 Iteration 2 Error: 0.146492 Iteration 3 Error: 0.033686 Align patch 23 2 left Iteration 1 Error: 1.096925 Iteration 2 Error: 0.165271 Iteration 3 Error: 0.041997 Align patch 24 1 left Iteration 1 Error: 0.726817 Iteration 2 Error: 0.134788 Iteration 3 Error: 0.040802 Align patch 25 0 left Iteration 1 Error: 1.722340 Iteration 2 Error: 0.195931 Iteration 3 Error: 0.040496 3D Fitting completed. Patch alignment time: 17.42(sec) Local motion has been corrected. Process thread exits. Computational time: 31.075792 sec Total time: 50.193039 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00022hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00022hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.592626s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00022hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.834081s ........................................ >>>>>>TIME<<<<<< FFT: 1.075117s Defocus_U Defocus_V Angle CCC 21494.14 22361.33 6.84 0.043746 Final Values Defocus_U Defocus_V Angle CCC 21495.71 22372.27 6.53 0.073328 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00022hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00022hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.997e-02 CC threshold: 0.734 Mean Std: 42.46 6.94 Num Hot pixels: 201 Hot pixel threshold: 84.12 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.600167 Iteration 2 Error: 0.317587 Iteration 3 Error: 0.081489 Iteration 4 Error: 0.026730 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.05 -0.30 ...... Frame ( 3) shift: -0.10 -0.60 ...... Frame ( 4) shift: -0.16 -0.90 ...... Frame ( 5) shift: -0.21 -1.20 ...... Frame ( 6) shift: -0.16 -1.32 ...... Frame ( 7) shift: -0.01 -1.27 ...... Frame ( 8) shift: 0.14 -1.21 ...... Frame ( 9) shift: 0.29 -1.12 ...... Frame ( 10) shift: 0.44 -1.01 ...... Frame ( 11) shift: 0.58 -0.89 ...... Frame ( 12) shift: 0.70 -0.78 ...... Frame ( 13) shift: 0.79 -0.68 ...... Frame ( 14) shift: 0.89 -0.58 ...... Frame ( 15) shift: 0.99 -0.53 ...... Frame ( 16) shift: 1.11 -0.51 ...... Frame ( 17) shift: 1.22 -0.49 ...... Frame ( 18) shift: 1.32 -0.43 ...... Frame ( 19) shift: 1.41 -0.33 ...... Frame ( 20) shift: 1.50 -0.23 ...... Frame ( 21) shift: 1.57 -0.17 ...... Frame ( 22) shift: 1.62 -0.15 ...... Frame ( 23) shift: 1.67 -0.13 ...... Frame ( 24) shift: 1.76 -0.09 ...... Frame ( 25) shift: 1.87 -0.04 ...... Frame ( 26) shift: 1.98 0.01 ...... Frame ( 27) shift: 2.06 0.08 ...... Frame ( 28) shift: 2.11 0.15 ...... Frame ( 29) shift: 2.16 0.23 ...... Frame ( 30) shift: 2.22 0.29 ...... Frame ( 31) shift: 2.28 0.34 ...... Frame ( 32) shift: 2.34 0.39 ...... Frame ( 33) shift: 2.39 0.41 ...... Frame ( 34) shift: 2.43 0.41 ...... Frame ( 35) shift: 2.47 0.40 ...... Frame ( 36) shift: 2.53 0.44 ...... Frame ( 37) shift: 2.63 0.52 ...... Frame ( 38) shift: 2.72 0.60 ...... Frame ( 39) shift: 2.82 0.68 ...... Frame ( 40) shift: 2.91 0.76 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.772274 Iteration 2 Error: 0.231444 Iteration 3 Error: 0.095509 Iteration 4 Error: 0.037426 Align patch 2 23 left Iteration 1 Error: 0.727446 Iteration 2 Error: 0.185596 Iteration 3 Error: 0.083884 Iteration 4 Error: 0.033520 Align patch 3 22 left Iteration 1 Error: 1.041159 Iteration 2 Error: 0.180014 Iteration 3 Error: 0.034882 Align patch 4 21 left Iteration 1 Error: 1.810452 Iteration 2 Error: 0.189307 Iteration 3 Error: 0.025902 Align patch 5 20 left Iteration 1 Error: 0.753373 Iteration 2 Error: 0.156503 Iteration 3 Error: 0.030568 Align patch 6 19 left Iteration 1 Error: 0.758880 Iteration 2 Error: 0.208921 Iteration 3 Error: 0.053388 Iteration 4 Error: 0.020545 Align patch 7 18 left Iteration 1 Error: 1.111241 Iteration 2 Error: 0.137222 Iteration 3 Error: 0.032053 Align patch 8 17 left Iteration 1 Error: 0.862903 Iteration 2 Error: 0.216842 Iteration 3 Error: 0.070157 Iteration 4 Error: 0.029082 Align patch 9 16 left Iteration 1 Error: 1.093814 Iteration 2 Error: 0.154437 Iteration 3 Error: 0.077025 Iteration 4 Error: 0.029800 Align patch 10 15 left Iteration 1 Error: 0.871021 Iteration 2 Error: 0.176720 Iteration 3 Error: 0.064776 Iteration 4 Error: 0.031955 Align patch 11 14 left Iteration 1 Error: 0.519088 Iteration 2 Error: 0.091332 Iteration 3 Error: 0.020309 Align patch 12 13 left Iteration 1 Error: 0.668685 Iteration 2 Error: 0.164988 Iteration 3 Error: 0.047393 Align patch 13 12 left Iteration 1 Error: 0.596692 Iteration 2 Error: 0.115675 Iteration 3 Error: 0.039828 Align patch 14 11 left Iteration 1 Error: 1.031551 Iteration 2 Error: 0.213425 Iteration 3 Error: 0.062169 Iteration 4 Error: 0.019075 Align patch 15 10 left Iteration 1 Error: 0.775938 Iteration 2 Error: 0.123616 Iteration 3 Error: 0.030783 Align patch 16 9 left Iteration 1 Error: 0.851000 Iteration 2 Error: 0.260561 Iteration 3 Error: 0.058910 Iteration 4 Error: 0.018334 Align patch 17 8 left Iteration 1 Error: 0.639850 Iteration 2 Error: 0.109047 Iteration 3 Error: 0.030815 Align patch 18 7 left Iteration 1 Error: 0.612924 Iteration 2 Error: 0.152189 Iteration 3 Error: 0.054233 Iteration 4 Error: 0.016423 Align patch 19 6 left Iteration 1 Error: 1.125420 Iteration 2 Error: 0.180180 Iteration 3 Error: 0.046716 Align patch 20 5 left Iteration 1 Error: 0.840731 Iteration 2 Error: 0.117865 Iteration 3 Error: 0.027752 Align patch 21 4 left Iteration 1 Error: 0.609691 Iteration 2 Error: 0.116979 Iteration 3 Error: 0.027096 Align patch 22 3 left Iteration 1 Error: 0.556970 Iteration 2 Error: 0.193150 Iteration 3 Error: 0.064432 Iteration 4 Error: 0.031861 Align patch 23 2 left Iteration 1 Error: 0.698383 Iteration 2 Error: 0.091007 Iteration 3 Error: 0.030234 Align patch 24 1 left Iteration 1 Error: 0.940919 Iteration 2 Error: 0.125904 Iteration 3 Error: 0.017429 Align patch 25 0 left Iteration 1 Error: 0.666943 Iteration 2 Error: 0.128353 Iteration 3 Error: 0.057194 Iteration 4 Error: 0.022231 3D Fitting completed. Patch alignment time: 12.89(sec) Local motion has been corrected. Process thread exits. Computational time: 22.798782 sec Total time: 40.223789 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00022hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00022hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.710100s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00022hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.554884s ........................................ >>>>>>TIME<<<<<< FFT: 1.002076s Defocus_U Defocus_V Angle CCC 19318.38 19947.28 0.14 0.043415 Final Values Defocus_U Defocus_V Angle CCC 19329.27 19927.01 0.14 0.077462 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00022hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00022hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.993e-02 CC threshold: 0.734 Mean Std: 41.69 6.88 Num Hot pixels: 180 Hot pixel threshold: 82.99 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.365642 Iteration 2 Error: 0.265278 Iteration 3 Error: 0.065569 Iteration 4 Error: 0.013198 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.01 -0.30 ...... Frame ( 3) shift: 0.02 -0.61 ...... Frame ( 4) shift: 0.04 -0.91 ...... Frame ( 5) shift: 0.05 -1.22 ...... Frame ( 6) shift: 0.08 -1.34 ...... Frame ( 7) shift: 0.12 -1.27 ...... Frame ( 8) shift: 0.17 -1.21 ...... Frame ( 9) shift: 0.29 -1.13 ...... Frame ( 10) shift: 0.49 -1.04 ...... Frame ( 11) shift: 0.70 -0.95 ...... Frame ( 12) shift: 0.81 -0.87 ...... Frame ( 13) shift: 0.83 -0.79 ...... Frame ( 14) shift: 0.86 -0.71 ...... Frame ( 15) shift: 0.89 -0.63 ...... Frame ( 16) shift: 0.93 -0.54 ...... Frame ( 17) shift: 0.97 -0.45 ...... Frame ( 18) shift: 0.98 -0.37 ...... Frame ( 19) shift: 0.95 -0.31 ...... Frame ( 20) shift: 0.92 -0.25 ...... Frame ( 21) shift: 0.96 -0.20 ...... Frame ( 22) shift: 1.08 -0.16 ...... Frame ( 23) shift: 1.20 -0.13 ...... Frame ( 24) shift: 1.30 -0.07 ...... Frame ( 25) shift: 1.37 0.00 ...... Frame ( 26) shift: 1.45 0.08 ...... Frame ( 27) shift: 1.53 0.14 ...... Frame ( 28) shift: 1.61 0.18 ...... Frame ( 29) shift: 1.69 0.23 ...... Frame ( 30) shift: 1.79 0.26 ...... Frame ( 31) shift: 1.91 0.27 ...... Frame ( 32) shift: 2.03 0.29 ...... Frame ( 33) shift: 2.10 0.34 ...... Frame ( 34) shift: 2.12 0.44 ...... Frame ( 35) shift: 2.14 0.53 ...... Frame ( 36) shift: 2.17 0.58 ...... Frame ( 37) shift: 2.22 0.58 ...... Frame ( 38) shift: 2.27 0.59 ...... Frame ( 39) shift: 2.32 0.59 ...... Frame ( 40) shift: 2.38 0.59 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.533732 Iteration 2 Error: 0.122644 Iteration 3 Error: 0.016113 Align patch 2 23 left Iteration 1 Error: 0.720086 Iteration 2 Error: 0.224148 Iteration 3 Error: 0.083672 Iteration 4 Error: 0.038069 Align patch 3 22 left Iteration 1 Error: 1.149521 Iteration 2 Error: 0.167605 Iteration 3 Error: 0.035567 Align patch 4 21 left Iteration 1 Error: 0.814746 Iteration 2 Error: 0.119197 Iteration 3 Error: 0.020509 Align patch 5 20 left Iteration 1 Error: 0.784925 Iteration 2 Error: 0.143351 Iteration 3 Error: 0.061146 Iteration 4 Error: 0.022441 Align patch 6 19 left Iteration 1 Error: 0.683593 Iteration 2 Error: 0.109580 Iteration 3 Error: 0.029442 Align patch 7 18 left Iteration 1 Error: 0.901677 Iteration 2 Error: 0.175903 Iteration 3 Error: 0.052360 Iteration 4 Error: 0.018781 Align patch 8 17 left Iteration 1 Error: 1.130381 Iteration 2 Error: 0.161540 Iteration 3 Error: 0.051693 Iteration 4 Error: 0.024128 Align patch 9 16 left Iteration 1 Error: 0.792633 Iteration 2 Error: 0.139417 Iteration 3 Error: 0.045603 Align patch 10 15 left Iteration 1 Error: 0.636826 Iteration 2 Error: 0.093155 Iteration 3 Error: 0.030719 Align patch 11 14 left Iteration 1 Error: 0.540980 Iteration 2 Error: 0.121126 Iteration 3 Error: 0.030097 Align patch 12 13 left Iteration 1 Error: 0.907508 Iteration 2 Error: 0.154088 Iteration 3 Error: 0.036082 Align patch 13 12 left Iteration 1 Error: 0.921002 Iteration 2 Error: 0.171647 Iteration 3 Error: 0.047819 Align patch 14 11 left Iteration 1 Error: 0.769775 Iteration 2 Error: 0.160750 Iteration 3 Error: 0.050889 Iteration 4 Error: 0.018054 Align patch 15 10 left Iteration 1 Error: 0.563461 Iteration 2 Error: 0.093458 Iteration 3 Error: 0.027446 Align patch 16 9 left Iteration 1 Error: 0.703387 Iteration 2 Error: 0.108123 Iteration 3 Error: 0.036205 Align patch 17 8 left Iteration 1 Error: 0.715350 Iteration 2 Error: 0.114538 Iteration 3 Error: 0.032505 Align patch 18 7 left Iteration 1 Error: 0.646525 Iteration 2 Error: 0.119498 Iteration 3 Error: 0.023133 Align patch 19 6 left Iteration 1 Error: 1.072867 Iteration 2 Error: 0.108378 Iteration 3 Error: 0.020092 Align patch 20 5 left Iteration 1 Error: 0.666248 Iteration 2 Error: 0.093340 Iteration 3 Error: 0.019110 Align patch 21 4 left Iteration 1 Error: 0.779738 Iteration 2 Error: 0.120285 Iteration 3 Error: 0.032933 Align patch 22 3 left Iteration 1 Error: 0.776240 Iteration 2 Error: 0.130162 Iteration 3 Error: 0.032947 Align patch 23 2 left Iteration 1 Error: 0.873633 Iteration 2 Error: 0.181653 Iteration 3 Error: 0.051952 Iteration 4 Error: 0.017691 Align patch 24 1 left Iteration 1 Error: 0.637025 Iteration 2 Error: 0.117498 Iteration 3 Error: 0.036279 Align patch 25 0 left Iteration 1 Error: 0.700092 Iteration 2 Error: 0.092087 Iteration 3 Error: 0.019542 3D Fitting completed. Patch alignment time: 10.91(sec) Local motion has been corrected. Process thread exits. Computational time: 20.263187 sec Total time: 38.990479 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00022hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00022hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.685850s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00022hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.726778s ........................................ >>>>>>TIME<<<<<< FFT: 0.845074s Defocus_U Defocus_V Angle CCC 22996.09 23691.41 0.27 0.043112 Final Values Defocus_U Defocus_V Angle CCC 23005.47 23694.53 0.27 0.069984 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00023hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00023hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.998e-02 CC threshold: 0.734 Mean Std: 41.30 6.85 Num Hot pixels: 219 Hot pixel threshold: 82.38 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.298655 Iteration 2 Error: 0.248019 Iteration 3 Error: 0.063252 Iteration 4 Error: 0.020476 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.11 -0.03 ...... Frame ( 3) shift: 0.22 -0.07 ...... Frame ( 4) shift: 0.34 -0.10 ...... Frame ( 5) shift: 0.45 -0.14 ...... Frame ( 6) shift: 0.54 -0.12 ...... Frame ( 7) shift: 0.61 -0.05 ...... Frame ( 8) shift: 0.68 0.02 ...... Frame ( 9) shift: 0.72 0.07 ...... Frame ( 10) shift: 0.74 0.09 ...... Frame ( 11) shift: 0.76 0.11 ...... Frame ( 12) shift: 0.83 0.17 ...... Frame ( 13) shift: 0.94 0.25 ...... Frame ( 14) shift: 1.06 0.33 ...... Frame ( 15) shift: 1.17 0.43 ...... Frame ( 16) shift: 1.28 0.56 ...... Frame ( 17) shift: 1.39 0.68 ...... Frame ( 18) shift: 1.50 0.75 ...... Frame ( 19) shift: 1.61 0.76 ...... Frame ( 20) shift: 1.72 0.77 ...... Frame ( 21) shift: 1.80 0.81 ...... Frame ( 22) shift: 1.86 0.86 ...... Frame ( 23) shift: 1.91 0.92 ...... Frame ( 24) shift: 1.95 0.96 ...... Frame ( 25) shift: 1.96 1.00 ...... Frame ( 26) shift: 1.98 1.03 ...... Frame ( 27) shift: 2.01 1.05 ...... Frame ( 28) shift: 2.06 1.05 ...... Frame ( 29) shift: 2.11 1.06 ...... Frame ( 30) shift: 2.16 1.06 ...... Frame ( 31) shift: 2.20 1.07 ...... Frame ( 32) shift: 2.25 1.07 ...... Frame ( 33) shift: 2.30 1.12 ...... Frame ( 34) shift: 2.38 1.19 ...... Frame ( 35) shift: 2.45 1.26 ...... Frame ( 36) shift: 2.50 1.30 ...... Frame ( 37) shift: 2.54 1.28 ...... Frame ( 38) shift: 2.57 1.27 ...... Frame ( 39) shift: 2.60 1.25 ...... Frame ( 40) shift: 2.63 1.24 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.864336 Iteration 2 Error: 0.118976 Iteration 3 Error: 0.032467 Align patch 2 23 left Iteration 1 Error: 0.754617 Iteration 2 Error: 0.249619 Iteration 3 Error: 0.064107 Iteration 4 Error: 0.017444 Align patch 3 22 left Iteration 1 Error: 0.932714 Iteration 2 Error: 0.171191 Iteration 3 Error: 0.053861 Iteration 4 Error: 0.015840 Align patch 4 21 left Iteration 1 Error: 1.026076 Iteration 2 Error: 0.135876 Iteration 3 Error: 0.028919 Align patch 5 20 left Iteration 1 Error: 0.533863 Iteration 2 Error: 0.056486 Iteration 3 Error: 0.013694 Align patch 6 19 left Iteration 1 Error: 0.730310 Iteration 2 Error: 0.091698 Iteration 3 Error: 0.025201 Align patch 7 18 left Iteration 1 Error: 0.510431 Iteration 2 Error: 0.093623 Iteration 3 Error: 0.022114 Align patch 8 17 left Iteration 1 Error: 0.790052 Iteration 2 Error: 0.188091 Iteration 3 Error: 0.036007 Align patch 9 16 left Iteration 1 Error: 0.713704 Iteration 2 Error: 0.136929 Iteration 3 Error: 0.038763 Align patch 10 15 left Iteration 1 Error: 0.766702 Iteration 2 Error: 0.116817 Iteration 3 Error: 0.046791 Align patch 11 14 left Iteration 1 Error: 0.446305 Iteration 2 Error: 0.056852 Iteration 3 Error: 0.011705 Align patch 12 13 left Iteration 1 Error: 0.558454 Iteration 2 Error: 0.090763 Iteration 3 Error: 0.026659 Align patch 13 12 left Iteration 1 Error: 0.584757 Iteration 2 Error: 0.087337 Iteration 3 Error: 0.030342 Align patch 14 11 left Iteration 1 Error: 0.473728 Iteration 2 Error: 0.079641 Iteration 3 Error: 0.028929 Align patch 15 10 left Iteration 1 Error: 0.941611 Iteration 2 Error: 0.158236 Iteration 3 Error: 0.028844 Align patch 16 9 left Iteration 1 Error: 0.697484 Iteration 2 Error: 0.114371 Iteration 3 Error: 0.032402 Align patch 17 8 left Iteration 1 Error: 0.590475 Iteration 2 Error: 0.089535 Iteration 3 Error: 0.017493 Align patch 18 7 left Iteration 1 Error: 0.851792 Iteration 2 Error: 0.157625 Iteration 3 Error: 0.050613 Iteration 4 Error: 0.012464 Align patch 19 6 left Iteration 1 Error: 0.736769 Iteration 2 Error: 0.117070 Iteration 3 Error: 0.033924 Align patch 20 5 left Iteration 1 Error: 1.370962 Iteration 2 Error: 0.122419 Iteration 3 Error: 0.026387 Align patch 21 4 left Iteration 1 Error: 0.936927 Iteration 2 Error: 0.114974 Iteration 3 Error: 0.026946 Align patch 22 3 left Iteration 1 Error: 1.013541 Iteration 2 Error: 0.170907 Iteration 3 Error: 0.031421 Align patch 23 2 left Iteration 1 Error: 0.870133 Iteration 2 Error: 0.133951 Iteration 3 Error: 0.027415 Align patch 24 1 left Iteration 1 Error: 0.738484 Iteration 2 Error: 0.144669 Iteration 3 Error: 0.048309 Align patch 25 0 left Iteration 1 Error: 0.842487 Iteration 2 Error: 0.109475 Iteration 3 Error: 0.022649 3D Fitting completed. Patch alignment time: 13.23(sec) Local motion has been corrected. Process thread exits. Computational time: 22.281065 sec Total time: 28.208000 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00023hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00023hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.600032s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00023hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.687186s ........................................ >>>>>>TIME<<<<<< FFT: 1.183557s Defocus_U Defocus_V Angle CCC 19890.62 20703.12 11.17 0.038489 Final Values Defocus_U Defocus_V Angle CCC 19893.73 20715.66 11.48 0.066418 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00023hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00023hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 38.91 6.69 Num Hot pixels: 196 Hot pixel threshold: 79.04 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.468319 Iteration 2 Error: 0.226631 Iteration 3 Error: 0.055661 Iteration 4 Error: 0.017004 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.00 0.12 ...... Frame ( 3) shift: 0.01 0.23 ...... Frame ( 4) shift: 0.01 0.35 ...... Frame ( 5) shift: 0.02 0.46 ...... Frame ( 6) shift: 0.05 0.53 ...... Frame ( 7) shift: 0.10 0.54 ...... Frame ( 8) shift: 0.16 0.56 ...... Frame ( 9) shift: 0.24 0.58 ...... Frame ( 10) shift: 0.35 0.61 ...... Frame ( 11) shift: 0.46 0.65 ...... Frame ( 12) shift: 0.56 0.71 ...... Frame ( 13) shift: 0.66 0.82 ...... Frame ( 14) shift: 0.77 0.92 ...... Frame ( 15) shift: 0.88 1.00 ...... Frame ( 16) shift: 1.00 1.06 ...... Frame ( 17) shift: 1.12 1.11 ...... Frame ( 18) shift: 1.24 1.19 ...... Frame ( 19) shift: 1.37 1.29 ...... Frame ( 20) shift: 1.49 1.39 ...... Frame ( 21) shift: 1.59 1.45 ...... Frame ( 22) shift: 1.66 1.48 ...... Frame ( 23) shift: 1.74 1.50 ...... Frame ( 24) shift: 1.82 1.49 ...... Frame ( 25) shift: 1.91 1.44 ...... Frame ( 26) shift: 2.00 1.40 ...... Frame ( 27) shift: 2.04 1.43 ...... Frame ( 28) shift: 2.03 1.54 ...... Frame ( 29) shift: 2.01 1.64 ...... Frame ( 30) shift: 2.01 1.68 ...... Frame ( 31) shift: 2.01 1.64 ...... Frame ( 32) shift: 2.01 1.60 ...... Frame ( 33) shift: 2.05 1.57 ...... Frame ( 34) shift: 2.14 1.55 ...... Frame ( 35) shift: 2.22 1.52 ...... Frame ( 36) shift: 2.28 1.54 ...... Frame ( 37) shift: 2.31 1.60 ...... Frame ( 38) shift: 2.34 1.67 ...... Frame ( 39) shift: 2.36 1.73 ...... Frame ( 40) shift: 2.39 1.79 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.561581 Iteration 2 Error: 0.131562 Iteration 3 Error: 0.037098 Align patch 2 23 left Iteration 1 Error: 0.627555 Iteration 2 Error: 0.146838 Iteration 3 Error: 0.044729 Align patch 3 22 left Iteration 1 Error: 0.702996 Iteration 2 Error: 0.130234 Iteration 3 Error: 0.014776 Align patch 4 21 left Iteration 1 Error: 0.942963 Iteration 2 Error: 0.150279 Iteration 3 Error: 0.028215 Align patch 5 20 left Iteration 1 Error: 1.111068 Iteration 2 Error: 0.176531 Iteration 3 Error: 0.044087 Align patch 6 19 left Iteration 1 Error: 0.710627 Iteration 2 Error: 0.149145 Iteration 3 Error: 0.034253 Align patch 7 18 left Iteration 1 Error: 0.806047 Iteration 2 Error: 0.091672 Iteration 3 Error: 0.025238 Align patch 8 17 left Iteration 1 Error: 0.500951 Iteration 2 Error: 0.093433 Iteration 3 Error: 0.013126 Align patch 9 16 left Iteration 1 Error: 0.916262 Iteration 2 Error: 0.098548 Iteration 3 Error: 0.031784 Align patch 10 15 left Iteration 1 Error: 0.805676 Iteration 2 Error: 0.178969 Iteration 3 Error: 0.045317 Align patch 11 14 left Iteration 1 Error: 0.795088 Iteration 2 Error: 0.148063 Iteration 3 Error: 0.030519 Align patch 12 13 left Iteration 1 Error: 0.579042 Iteration 2 Error: 0.100693 Iteration 3 Error: 0.020515 Align patch 13 12 left Iteration 1 Error: 0.578948 Iteration 2 Error: 0.083514 Iteration 3 Error: 0.013857 Align patch 14 11 left Iteration 1 Error: 0.995633 Iteration 2 Error: 0.142887 Iteration 3 Error: 0.045261 Align patch 15 10 left Iteration 1 Error: 0.795125 Iteration 2 Error: 0.104677 Iteration 3 Error: 0.017986 Align patch 16 9 left Iteration 1 Error: 0.940229 Iteration 2 Error: 0.145466 Iteration 3 Error: 0.040408 Align patch 17 8 left Iteration 1 Error: 0.771096 Iteration 2 Error: 0.091187 Iteration 3 Error: 0.019224 Align patch 18 7 left Iteration 1 Error: 0.735850 Iteration 2 Error: 0.102504 Iteration 3 Error: 0.020565 Align patch 19 6 left Iteration 1 Error: 0.818030 Iteration 2 Error: 0.069685 Iteration 3 Error: 0.017525 Align patch 20 5 left Iteration 1 Error: 0.692555 Iteration 2 Error: 0.120876 Iteration 3 Error: 0.018963 Align patch 21 4 left Iteration 1 Error: 0.819198 Iteration 2 Error: 0.151446 Iteration 3 Error: 0.048206 Align patch 22 3 left Iteration 1 Error: 0.939222 Iteration 2 Error: 0.139079 Iteration 3 Error: 0.048762 Align patch 23 2 left Iteration 1 Error: 0.587609 Iteration 2 Error: 0.107175 Iteration 3 Error: 0.024838 Align patch 24 1 left Iteration 1 Error: 0.637722 Iteration 2 Error: 0.137665 Iteration 3 Error: 0.028317 Align patch 25 0 left Iteration 1 Error: 0.838466 Iteration 2 Error: 0.190795 Iteration 3 Error: 0.044127 3D Fitting completed. Patch alignment time: 11.40(sec) Local motion has been corrected. Process thread exits. Computational time: 21.169994 sec Total time: 27.131958 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00023hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00023hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.775378s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00023hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.204743s ........................................ >>>>>>TIME<<<<<< FFT: 0.949687s Defocus_U Defocus_V Angle CCC 18972.63 19824.24 7.68 0.034555 Final Values Defocus_U Defocus_V Angle CCC 18949.18 19835.19 7.68 0.056555 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00023hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00023hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.992e-02 CC threshold: 0.734 Mean Std: 41.19 6.83 Num Hot pixels: 211 Hot pixel threshold: 82.17 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.480509 Iteration 2 Error: 0.259466 Iteration 3 Error: 0.062521 Iteration 4 Error: 0.017066 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.10 0.09 ...... Frame ( 3) shift: 0.21 0.17 ...... Frame ( 4) shift: 0.31 0.26 ...... Frame ( 5) shift: 0.41 0.35 ...... Frame ( 6) shift: 0.53 0.44 ...... Frame ( 7) shift: 0.66 0.55 ...... Frame ( 8) shift: 0.78 0.67 ...... Frame ( 9) shift: 0.83 0.78 ...... Frame ( 10) shift: 0.81 0.90 ...... Frame ( 11) shift: 0.78 1.02 ...... Frame ( 12) shift: 0.79 1.10 ...... Frame ( 13) shift: 0.85 1.15 ...... Frame ( 14) shift: 0.90 1.19 ...... Frame ( 15) shift: 0.98 1.17 ...... Frame ( 16) shift: 1.09 1.11 ...... Frame ( 17) shift: 1.20 1.04 ...... Frame ( 18) shift: 1.29 0.99 ...... Frame ( 19) shift: 1.35 0.97 ...... Frame ( 20) shift: 1.40 0.94 ...... Frame ( 21) shift: 1.42 0.96 ...... Frame ( 22) shift: 1.40 1.01 ...... Frame ( 23) shift: 1.38 1.06 ...... Frame ( 24) shift: 1.43 1.13 ...... Frame ( 25) shift: 1.55 1.22 ...... Frame ( 26) shift: 1.67 1.31 ...... Frame ( 27) shift: 1.76 1.37 ...... Frame ( 28) shift: 1.81 1.41 ...... Frame ( 29) shift: 1.87 1.44 ...... Frame ( 30) shift: 1.91 1.53 ...... Frame ( 31) shift: 1.96 1.68 ...... Frame ( 32) shift: 2.00 1.82 ...... Frame ( 33) shift: 2.03 1.93 ...... Frame ( 34) shift: 2.05 2.02 ...... Frame ( 35) shift: 2.06 2.10 ...... Frame ( 36) shift: 2.09 2.17 ...... Frame ( 37) shift: 2.14 2.21 ...... Frame ( 38) shift: 2.19 2.26 ...... Frame ( 39) shift: 2.24 2.30 ...... Frame ( 40) shift: 2.29 2.35 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.435662 Iteration 2 Error: 0.364205 Iteration 3 Error: 0.148995 Iteration 4 Error: 0.073583 Iteration 5 Error: 0.045536 Align patch 2 23 left Iteration 1 Error: 1.068970 Iteration 2 Error: 0.162530 Iteration 3 Error: 0.039279 Align patch 3 22 left Iteration 1 Error: 0.625486 Iteration 2 Error: 0.156266 Iteration 3 Error: 0.047507 Align patch 4 21 left Iteration 1 Error: 0.504376 Iteration 2 Error: 0.082259 Iteration 3 Error: 0.016309 Align patch 5 20 left Iteration 1 Error: 0.678703 Iteration 2 Error: 0.128242 Iteration 3 Error: 0.029870 Align patch 6 19 left Iteration 1 Error: 1.005366 Iteration 2 Error: 0.133439 Iteration 3 Error: 0.053069 Iteration 4 Error: 0.013204 Align patch 7 18 left Iteration 1 Error: 0.812254 Iteration 2 Error: 0.126664 Iteration 3 Error: 0.048867 Align patch 8 17 left Iteration 1 Error: 0.929783 Iteration 2 Error: 0.177253 Iteration 3 Error: 0.069586 Iteration 4 Error: 0.017438 Align patch 9 16 left Iteration 1 Error: 0.722656 Iteration 2 Error: 0.229215 Iteration 3 Error: 0.082430 Iteration 4 Error: 0.033060 Align patch 10 15 left Iteration 1 Error: 0.619453 Iteration 2 Error: 0.134061 Iteration 3 Error: 0.069195 Iteration 4 Error: 0.025856 Align patch 11 14 left Iteration 1 Error: 0.798393 Iteration 2 Error: 0.148577 Iteration 3 Error: 0.034523 Align patch 12 13 left Iteration 1 Error: 0.857589 Iteration 2 Error: 0.116556 Iteration 3 Error: 0.023591 Align patch 13 12 left Iteration 1 Error: 0.951616 Iteration 2 Error: 0.086537 Iteration 3 Error: 0.026267 Align patch 14 11 left Iteration 1 Error: 0.896749 Iteration 2 Error: 0.190951 Iteration 3 Error: 0.053666 Iteration 4 Error: 0.024728 Align patch 15 10 left Iteration 1 Error: 0.648679 Iteration 2 Error: 0.170467 Iteration 3 Error: 0.056905 Iteration 4 Error: 0.013836 Align patch 16 9 left Iteration 1 Error: 0.684824 Iteration 2 Error: 0.075490 Iteration 3 Error: 0.023494 Align patch 17 8 left Iteration 1 Error: 0.712673 Iteration 2 Error: 0.124029 Iteration 3 Error: 0.029400 Align patch 18 7 left Iteration 1 Error: 0.823937 Iteration 2 Error: 0.126844 Iteration 3 Error: 0.031836 Align patch 19 6 left Iteration 1 Error: 0.613889 Iteration 2 Error: 0.065431 Iteration 3 Error: 0.020838 Align patch 20 5 left Iteration 1 Error: 0.526653 Iteration 2 Error: 0.084285 Iteration 3 Error: 0.019412 Align patch 21 4 left Iteration 1 Error: 0.599878 Iteration 2 Error: 0.094041 Iteration 3 Error: 0.029679 Align patch 22 3 left Iteration 1 Error: 0.597701 Iteration 2 Error: 0.078166 Iteration 3 Error: 0.023076 Align patch 23 2 left Iteration 1 Error: 0.766307 Iteration 2 Error: 0.126399 Iteration 3 Error: 0.034511 Align patch 24 1 left Iteration 1 Error: 1.145565 Iteration 2 Error: 0.091311 Iteration 3 Error: 0.018215 Align patch 25 0 left Iteration 1 Error: 0.685233 Iteration 2 Error: 0.106123 Iteration 3 Error: 0.027362 3D Fitting completed. Patch alignment time: 11.21(sec) Local motion has been corrected. Process thread exits. Computational time: 20.864763 sec Total time: 27.306595 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00023hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00023hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.730343s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00023hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.497394s ........................................ >>>>>>TIME<<<<<< FFT: 0.910064s Defocus_U Defocus_V Angle CCC 21964.89 21339.84 89.85 0.041528 Final Values Defocus_U Defocus_V Angle CCC 21352.35 21971.14 1.11 0.068004 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00023hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00023hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.002e-01 CC threshold: 0.736 Mean Std: 32.25 6.59 Num Hot pixels: 135 Hot pixel threshold: 71.80 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.893746 Iteration 2 Error: 0.208884 Iteration 3 Error: 0.036860 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.14 0.11 ...... Frame ( 3) shift: 0.28 0.22 ...... Frame ( 4) shift: 0.42 0.33 ...... Frame ( 5) shift: 0.56 0.44 ...... Frame ( 6) shift: 0.65 0.56 ...... Frame ( 7) shift: 0.69 0.68 ...... Frame ( 8) shift: 0.73 0.80 ...... Frame ( 9) shift: 0.82 0.89 ...... Frame ( 10) shift: 0.96 0.95 ...... Frame ( 11) shift: 1.10 1.02 ...... Frame ( 12) shift: 1.26 1.09 ...... Frame ( 13) shift: 1.44 1.17 ...... Frame ( 14) shift: 1.62 1.25 ...... Frame ( 15) shift: 1.69 1.33 ...... Frame ( 16) shift: 1.65 1.43 ...... Frame ( 17) shift: 1.61 1.52 ...... Frame ( 18) shift: 1.54 1.59 ...... Frame ( 19) shift: 1.43 1.63 ...... Frame ( 20) shift: 1.33 1.67 ...... Frame ( 21) shift: 1.29 1.74 ...... Frame ( 22) shift: 1.30 1.85 ...... Frame ( 23) shift: 1.31 1.96 ...... Frame ( 24) shift: 1.34 2.08 ...... Frame ( 25) shift: 1.39 2.23 ...... Frame ( 26) shift: 1.45 2.37 ...... Frame ( 27) shift: 1.50 2.50 ...... Frame ( 28) shift: 1.55 2.62 ...... Frame ( 29) shift: 1.60 2.73 ...... Frame ( 30) shift: 1.61 2.83 ...... Frame ( 31) shift: 1.57 2.91 ...... Frame ( 32) shift: 1.54 2.98 ...... Frame ( 33) shift: 1.55 3.08 ...... Frame ( 34) shift: 1.60 3.20 ...... Frame ( 35) shift: 1.65 3.32 ...... Frame ( 36) shift: 1.67 3.41 ...... Frame ( 37) shift: 1.67 3.47 ...... Frame ( 38) shift: 1.67 3.53 ...... Frame ( 39) shift: 1.66 3.58 ...... Frame ( 40) shift: 1.66 3.64 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.653478 Iteration 2 Error: 0.100480 Iteration 3 Error: 0.022291 Align patch 2 23 left Iteration 1 Error: 0.627825 Iteration 2 Error: 0.108541 Iteration 3 Error: 0.033372 Align patch 3 22 left Iteration 1 Error: 0.759770 Iteration 2 Error: 0.074415 Iteration 3 Error: 0.013814 Align patch 4 21 left Iteration 1 Error: 0.920049 Iteration 2 Error: 0.133089 Iteration 3 Error: 0.021188 Align patch 5 20 left Iteration 1 Error: 1.074203 Iteration 2 Error: 0.204358 Iteration 3 Error: 0.045437 Align patch 6 19 left Iteration 1 Error: 0.851996 Iteration 2 Error: 0.117003 Iteration 3 Error: 0.019270 Align patch 7 18 left Iteration 1 Error: 0.656290 Iteration 2 Error: 0.080051 Iteration 3 Error: 0.014284 Align patch 8 17 left Iteration 1 Error: 0.426691 Iteration 2 Error: 0.046877 Align patch 9 16 left Iteration 1 Error: 0.378387 Iteration 2 Error: 0.069678 Iteration 3 Error: 0.014274 Align patch 10 15 left Iteration 1 Error: 0.766614 Iteration 2 Error: 0.099633 Iteration 3 Error: 0.024988 Align patch 11 14 left Iteration 1 Error: 1.087316 Iteration 2 Error: 0.148724 Iteration 3 Error: 0.024146 Align patch 12 13 left Iteration 1 Error: 0.723857 Iteration 2 Error: 0.125122 Iteration 3 Error: 0.025020 Align patch 13 12 left Iteration 1 Error: 0.628734 Iteration 2 Error: 0.062934 Iteration 3 Error: 0.009311 Align patch 14 11 left Iteration 1 Error: 0.813019 Iteration 2 Error: 0.117175 Iteration 3 Error: 0.017362 Align patch 15 10 left Iteration 1 Error: 0.861412 Iteration 2 Error: 0.078647 Iteration 3 Error: 0.017810 Align patch 16 9 left Iteration 1 Error: 0.764734 Iteration 2 Error: 0.124240 Iteration 3 Error: 0.031762 Align patch 17 8 left Iteration 1 Error: 0.841376 Iteration 2 Error: 0.104408 Iteration 3 Error: 0.017782 Align patch 18 7 left Iteration 1 Error: 0.375341 Iteration 2 Error: 0.050195 Iteration 3 Error: 0.008662 Align patch 19 6 left Iteration 1 Error: 0.484060 Iteration 2 Error: 0.100747 Iteration 3 Error: 0.026909 Align patch 20 5 left Iteration 1 Error: 0.986119 Iteration 2 Error: 0.095860 Iteration 3 Error: 0.021890 Align patch 21 4 left Iteration 1 Error: 0.769411 Iteration 2 Error: 0.112454 Iteration 3 Error: 0.022168 Align patch 22 3 left Iteration 1 Error: 0.851759 Iteration 2 Error: 0.155216 Iteration 3 Error: 0.041481 Align patch 23 2 left Iteration 1 Error: 0.414910 Iteration 2 Error: 0.089319 Iteration 3 Error: 0.019677 Align patch 24 1 left Iteration 1 Error: 0.835644 Iteration 2 Error: 0.112393 Iteration 3 Error: 0.021554 Align patch 25 0 left Iteration 1 Error: 0.571160 Iteration 2 Error: 0.111472 Iteration 3 Error: 0.022988 3D Fitting completed. Patch alignment time: 12.53(sec) Local motion has been corrected. Process thread exits. Computational time: 21.662504 sec Total time: 27.759373 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00023hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00023hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.655376s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00023hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.143651s ........................................ >>>>>>TIME<<<<<< FFT: 0.938343s Defocus_U Defocus_V Angle CCC 22658.21 23587.90 6.17 0.038441 Final Values Defocus_U Defocus_V Angle CCC 22616.03 23545.72 8.67 0.053854 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00024hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00024hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.991e-02 CC threshold: 0.734 Mean Std: 41.43 6.85 Num Hot pixels: 209 Hot pixel threshold: 82.51 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.478183 Iteration 2 Error: 0.637328 Iteration 3 Error: 0.211911 Iteration 4 Error: 0.093866 Iteration 5 Error: 0.039279 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.04 -0.05 ...... Frame ( 3) shift: 0.07 -0.10 ...... Frame ( 4) shift: 0.11 -0.15 ...... Frame ( 5) shift: 0.14 -0.20 ...... Frame ( 6) shift: 0.21 -0.13 ...... Frame ( 7) shift: 0.32 0.08 ...... Frame ( 8) shift: 0.43 0.28 ...... Frame ( 9) shift: 0.58 0.45 ...... Frame ( 10) shift: 0.79 0.59 ...... Frame ( 11) shift: 1.00 0.73 ...... Frame ( 12) shift: 1.23 0.87 ...... Frame ( 13) shift: 1.49 1.01 ...... Frame ( 14) shift: 1.76 1.16 ...... Frame ( 15) shift: 2.00 1.28 ...... Frame ( 16) shift: 2.23 1.38 ...... Frame ( 17) shift: 2.47 1.48 ...... Frame ( 18) shift: 2.63 1.56 ...... Frame ( 19) shift: 2.72 1.61 ...... Frame ( 20) shift: 2.81 1.66 ...... Frame ( 21) shift: 2.95 1.78 ...... Frame ( 22) shift: 3.14 1.96 ...... Frame ( 23) shift: 3.33 2.13 ...... Frame ( 24) shift: 3.47 2.26 ...... Frame ( 25) shift: 3.56 2.32 ...... Frame ( 26) shift: 3.66 2.39 ...... Frame ( 27) shift: 3.78 2.49 ...... Frame ( 28) shift: 3.93 2.62 ...... Frame ( 29) shift: 4.09 2.75 ...... Frame ( 30) shift: 4.20 2.84 ...... Frame ( 31) shift: 4.27 2.88 ...... Frame ( 32) shift: 4.34 2.92 ...... Frame ( 33) shift: 4.42 2.97 ...... Frame ( 34) shift: 4.52 3.01 ...... Frame ( 35) shift: 4.63 3.05 ...... Frame ( 36) shift: 4.74 3.09 ...... Frame ( 37) shift: 4.87 3.13 ...... Frame ( 38) shift: 5.00 3.17 ...... Frame ( 39) shift: 5.13 3.22 ...... Frame ( 40) shift: 5.26 3.26 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.378813 Iteration 2 Error: 0.202771 Iteration 3 Error: 0.083784 Iteration 4 Error: 0.035558 Align patch 2 23 left Iteration 1 Error: 0.691377 Iteration 2 Error: 0.200884 Iteration 3 Error: 0.067887 Iteration 4 Error: 0.036614 Align patch 3 22 left Iteration 1 Error: 0.735855 Iteration 2 Error: 0.157803 Iteration 3 Error: 0.055745 Iteration 4 Error: 0.022974 Align patch 4 21 left Iteration 1 Error: 1.052613 Iteration 2 Error: 0.289608 Iteration 3 Error: 0.072717 Iteration 4 Error: 0.040219 Align patch 5 20 left Iteration 1 Error: 1.170804 Iteration 2 Error: 0.506238 Iteration 3 Error: 0.249913 Iteration 4 Error: 0.105857 Iteration 5 Error: 0.050273 Align patch 5 20 left Iteration 1 Error: 0.681525 Iteration 2 Error: 0.104408 Iteration 3 Error: 0.014785 Align patch 6 19 left Iteration 1 Error: 0.898545 Iteration 2 Error: 0.105740 Iteration 3 Error: 0.043768 Align patch 7 18 left Iteration 1 Error: 1.659621 Iteration 2 Error: 0.324244 Iteration 3 Error: 0.139420 Iteration 4 Error: 0.054155 Iteration 5 Error: 0.034985 Align patch 8 17 left Iteration 1 Error: 0.966893 Iteration 2 Error: 0.279429 Iteration 3 Error: 0.097200 Iteration 4 Error: 0.042860 Align patch 9 16 left Iteration 1 Error: 0.726059 Iteration 2 Error: 0.186551 Iteration 3 Error: 0.039858 Align patch 10 15 left Iteration 1 Error: 0.986858 Iteration 2 Error: 0.235980 Iteration 3 Error: 0.071283 Iteration 4 Error: 0.033339 Align patch 11 14 left Iteration 1 Error: 0.637573 Iteration 2 Error: 0.148502 Iteration 3 Error: 0.040133 Align patch 12 13 left Iteration 1 Error: 0.739800 Iteration 2 Error: 0.203070 Iteration 3 Error: 0.060002 Iteration 4 Error: 0.023252 Align patch 13 12 left Iteration 1 Error: 1.176016 Iteration 2 Error: 0.232102 Iteration 3 Error: 0.090156 Iteration 4 Error: 0.037183 Align patch 14 11 left Iteration 1 Error: 1.170727 Iteration 2 Error: 0.331282 Iteration 3 Error: 0.115331 Iteration 4 Error: 0.047890 Align patch 15 10 left Iteration 1 Error: 0.733987 Iteration 2 Error: 0.093390 Iteration 3 Error: 0.027504 Align patch 16 9 left Iteration 1 Error: 0.879323 Iteration 2 Error: 0.170314 Iteration 3 Error: 0.044653 Align patch 17 8 left Iteration 1 Error: 0.744062 Iteration 2 Error: 0.174803 Iteration 3 Error: 0.055518 Iteration 4 Error: 0.019939 Align patch 18 7 left Iteration 1 Error: 0.700027 Iteration 2 Error: 0.105297 Iteration 3 Error: 0.031657 Align patch 19 6 left Iteration 1 Error: 1.075951 Iteration 2 Error: 0.227514 Iteration 3 Error: 0.055551 Iteration 4 Error: 0.018613 Align patch 20 5 left Iteration 1 Error: 0.628755 Iteration 2 Error: 0.117105 Iteration 3 Error: 0.050759 Iteration 4 Error: 0.019203 Align patch 21 4 left Iteration 1 Error: 0.691181 Iteration 2 Error: 0.131963 Iteration 3 Error: 0.037566 Align patch 22 3 left Iteration 1 Error: 0.728057 Iteration 2 Error: 0.253266 Iteration 3 Error: 0.095648 Iteration 4 Error: 0.050257 Iteration 5 Error: 0.021797 Align patch 23 2 left Iteration 1 Error: 0.791827 Iteration 2 Error: 0.169717 Iteration 3 Error: 0.069124 Iteration 4 Error: 0.032151 Align patch 24 1 left Iteration 1 Error: 0.922099 Iteration 2 Error: 0.245215 Iteration 3 Error: 0.048437 Align patch 25 0 left Iteration 1 Error: 0.795404 Iteration 2 Error: 0.137118 Iteration 3 Error: 0.044624 3D Fitting completed. Patch alignment time: 15.20(sec) Local motion has been corrected. Process thread exits. Computational time: 26.981779 sec Total time: 34.415138 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00024hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00024hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.591224s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00024hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.705874s ........................................ >>>>>>TIME<<<<<< FFT: 0.915952s Defocus_U Defocus_V Angle CCC 18554.70 19359.39 8.52 0.040198 Final Values Defocus_U Defocus_V Angle CCC 18564.03 19334.43 7.27 0.069972 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00024hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00024hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 37.32 6.84 Num Hot pixels: 164 Hot pixel threshold: 78.36 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.910969 Iteration 2 Error: 0.634777 Iteration 3 Error: 0.181847 Iteration 4 Error: 0.070485 Iteration 5 Error: 0.028647 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.39 -0.42 ...... Frame ( 3) shift: -0.78 -0.85 ...... Frame ( 4) shift: -1.16 -1.27 ...... Frame ( 5) shift: -1.55 -1.70 ...... Frame ( 6) shift: -1.72 -1.92 ...... Frame ( 7) shift: -1.68 -1.92 ...... Frame ( 8) shift: -1.63 -1.93 ...... Frame ( 9) shift: -1.47 -1.86 ...... Frame ( 10) shift: -1.21 -1.70 ...... Frame ( 11) shift: -0.94 -1.55 ...... Frame ( 12) shift: -0.69 -1.40 ...... Frame ( 13) shift: -0.44 -1.26 ...... Frame ( 14) shift: -0.19 -1.11 ...... Frame ( 15) shift: 0.03 -0.95 ...... Frame ( 16) shift: 0.23 -0.76 ...... Frame ( 17) shift: 0.42 -0.57 ...... Frame ( 18) shift: 0.58 -0.41 ...... Frame ( 19) shift: 0.72 -0.27 ...... Frame ( 20) shift: 0.85 -0.14 ...... Frame ( 21) shift: 0.98 0.00 ...... Frame ( 22) shift: 1.13 0.15 ...... Frame ( 23) shift: 1.28 0.30 ...... Frame ( 24) shift: 1.46 0.47 ...... Frame ( 25) shift: 1.66 0.66 ...... Frame ( 26) shift: 1.87 0.84 ...... Frame ( 27) shift: 2.00 1.01 ...... Frame ( 28) shift: 2.04 1.15 ...... Frame ( 29) shift: 2.09 1.28 ...... Frame ( 30) shift: 2.16 1.45 ...... Frame ( 31) shift: 2.27 1.65 ...... Frame ( 32) shift: 2.37 1.86 ...... Frame ( 33) shift: 2.46 2.02 ...... Frame ( 34) shift: 2.54 2.15 ...... Frame ( 35) shift: 2.63 2.28 ...... Frame ( 36) shift: 2.73 2.38 ...... Frame ( 37) shift: 2.86 2.45 ...... Frame ( 38) shift: 2.99 2.52 ...... Frame ( 39) shift: 3.13 2.59 ...... Frame ( 40) shift: 3.26 2.66 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.156552 Iteration 2 Error: 0.156652 Iteration 3 Error: 0.047121 Align patch 2 23 left Iteration 1 Error: 2.059375 Iteration 2 Error: 0.580125 Iteration 3 Error: 0.261737 Iteration 4 Error: 0.145955 Iteration 5 Error: 0.061666 Align patch 2 23 left Iteration 1 Error: 2.445805 Iteration 2 Error: 0.513209 Iteration 3 Error: 0.138882 Iteration 4 Error: 0.050621 Iteration 5 Error: 0.018446 Align patch 3 22 left Iteration 1 Error: 4.062197 Iteration 2 Error: 1.870461 Iteration 3 Error: 0.641080 Iteration 4 Error: 0.341280 Iteration 5 Error: 0.236970 Align patch 3 22 left Iteration 1 Error: 3.354587 Iteration 2 Error: 0.874435 Iteration 3 Error: 0.294512 Iteration 4 Error: 0.145523 Iteration 5 Error: 0.077556 Align patch 4 21 left Iteration 1 Error: 1.474293 Iteration 2 Error: 0.347070 Iteration 3 Error: 0.148335 Iteration 4 Error: 0.062334 Iteration 5 Error: 0.026882 Align patch 5 20 left Iteration 1 Error: 1.264317 Iteration 2 Error: 0.340998 Iteration 3 Error: 0.109899 Iteration 4 Error: 0.060634 Iteration 5 Error: 0.032358 Align patch 6 19 left Iteration 1 Error: 0.672270 Iteration 2 Error: 0.184700 Iteration 3 Error: 0.044562 Align patch 7 18 left Iteration 1 Error: 1.366236 Iteration 2 Error: 0.280464 Iteration 3 Error: 0.108268 Iteration 4 Error: 0.042457 Align patch 8 17 left Iteration 1 Error: 1.901053 Iteration 2 Error: 0.648091 Iteration 3 Error: 0.285305 Iteration 4 Error: 0.155242 Iteration 5 Error: 0.096336 Align patch 8 17 left Iteration 1 Error: 3.178732 Iteration 2 Error: 0.559485 Iteration 3 Error: 0.151457 Iteration 4 Error: 0.055743 Iteration 5 Error: 0.017582 Align patch 9 16 left Iteration 1 Error: 2.225987 Iteration 2 Error: 0.971677 Iteration 3 Error: 0.324453 Iteration 4 Error: 0.197723 Iteration 5 Error: 0.138648 Align patch 9 16 left Iteration 1 Error: 2.901507 Iteration 2 Error: 0.616930 Iteration 3 Error: 0.120659 Iteration 4 Error: 0.038776 Align patch 10 15 left Iteration 1 Error: 1.004698 Iteration 2 Error: 0.187173 Iteration 3 Error: 0.054030 Iteration 4 Error: 0.018007 Align patch 11 14 left Iteration 1 Error: 0.687609 Iteration 2 Error: 0.134174 Iteration 3 Error: 0.037180 Align patch 12 13 left Iteration 1 Error: 0.740762 Iteration 2 Error: 0.110003 Iteration 3 Error: 0.038408 Align patch 13 12 left Iteration 1 Error: 1.090452 Iteration 2 Error: 0.196321 Iteration 3 Error: 0.051090 Iteration 4 Error: 0.015239 Align patch 14 11 left Iteration 1 Error: 1.007216 Iteration 2 Error: 0.176554 Iteration 3 Error: 0.044283 Align patch 15 10 left Iteration 1 Error: 0.741826 Iteration 2 Error: 0.089580 Iteration 3 Error: 0.022803 Align patch 16 9 left Iteration 1 Error: 0.497679 Iteration 2 Error: 0.122431 Iteration 3 Error: 0.028189 Align patch 17 8 left Iteration 1 Error: 0.568695 Iteration 2 Error: 0.095361 Iteration 3 Error: 0.019606 Align patch 18 7 left Iteration 1 Error: 0.667704 Iteration 2 Error: 0.084599 Iteration 3 Error: 0.016997 Align patch 19 6 left Iteration 1 Error: 0.733872 Iteration 2 Error: 0.121577 Iteration 3 Error: 0.026523 Align patch 20 5 left Iteration 1 Error: 0.762138 Iteration 2 Error: 0.115605 Iteration 3 Error: 0.032822 Align patch 21 4 left Iteration 1 Error: 1.384820 Iteration 2 Error: 0.256507 Iteration 3 Error: 0.060476 Iteration 4 Error: 0.019257 Align patch 22 3 left Iteration 1 Error: 1.619544 Iteration 2 Error: 0.243287 Iteration 3 Error: 0.043786 Align patch 23 2 left Iteration 1 Error: 1.027102 Iteration 2 Error: 0.148816 Iteration 3 Error: 0.049010 Align patch 24 1 left Iteration 1 Error: 0.954551 Iteration 2 Error: 0.141597 Iteration 3 Error: 0.038635 Align patch 25 0 left Iteration 1 Error: 0.777871 Iteration 2 Error: 0.134934 Iteration 3 Error: 0.040476 3D Fitting completed. Patch alignment time: 19.16(sec) Local motion has been corrected. Process thread exits. Computational time: 30.769478 sec Total time: 38.567921 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00024hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00024hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.571535s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00024hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.631366s ........................................ >>>>>>TIME<<<<<< FFT: 0.931807s Defocus_U Defocus_V Angle CCC 20029.29 20912.13 8.32 0.045471 Final Values Defocus_U Defocus_V Angle CCC 20019.92 20912.14 8.63 0.075550 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00024hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00024hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.342e-01 9.986e-02 CC threshold: 0.733 Mean Std: 41.39 6.84 Num Hot pixels: 199 Hot pixel threshold: 82.42 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.630737 Iteration 2 Error: 0.484530 Iteration 3 Error: 0.155445 Iteration 4 Error: 0.066893 Iteration 5 Error: 0.029174 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.04 -0.04 ...... Frame ( 3) shift: -0.08 -0.08 ...... Frame ( 4) shift: -0.11 -0.12 ...... Frame ( 5) shift: -0.15 -0.16 ...... Frame ( 6) shift: -0.18 -0.19 ...... Frame ( 7) shift: -0.19 -0.22 ...... Frame ( 8) shift: -0.21 -0.24 ...... Frame ( 9) shift: -0.13 -0.24 ...... Frame ( 10) shift: 0.05 -0.20 ...... Frame ( 11) shift: 0.23 -0.16 ...... Frame ( 12) shift: 0.45 -0.10 ...... Frame ( 13) shift: 0.70 -0.03 ...... Frame ( 14) shift: 0.95 0.04 ...... Frame ( 15) shift: 1.22 0.15 ...... Frame ( 16) shift: 1.51 0.30 ...... Frame ( 17) shift: 1.79 0.45 ...... Frame ( 18) shift: 1.97 0.53 ...... Frame ( 19) shift: 2.05 0.52 ...... Frame ( 20) shift: 2.12 0.52 ...... Frame ( 21) shift: 2.20 0.57 ...... Frame ( 22) shift: 2.27 0.69 ...... Frame ( 23) shift: 2.35 0.82 ...... Frame ( 24) shift: 2.43 0.90 ...... Frame ( 25) shift: 2.51 0.95 ...... Frame ( 26) shift: 2.59 0.99 ...... Frame ( 27) shift: 2.64 1.08 ...... Frame ( 28) shift: 2.63 1.20 ...... Frame ( 29) shift: 2.63 1.33 ...... Frame ( 30) shift: 2.67 1.44 ...... Frame ( 31) shift: 2.75 1.53 ...... Frame ( 32) shift: 2.83 1.63 ...... Frame ( 33) shift: 2.92 1.70 ...... Frame ( 34) shift: 3.02 1.74 ...... Frame ( 35) shift: 3.11 1.78 ...... Frame ( 36) shift: 3.21 1.79 ...... Frame ( 37) shift: 3.30 1.78 ...... Frame ( 38) shift: 3.40 1.76 ...... Frame ( 39) shift: 3.49 1.75 ...... Frame ( 40) shift: 3.58 1.73 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.247191 Iteration 2 Error: 0.204823 Iteration 3 Error: 0.089949 Iteration 4 Error: 0.036955 Align patch 2 23 left Iteration 1 Error: 1.572182 Iteration 2 Error: 0.340511 Iteration 3 Error: 0.095085 Iteration 4 Error: 0.042778 Align patch 3 22 left Iteration 1 Error: 0.943014 Iteration 2 Error: 0.212188 Iteration 3 Error: 0.083100 Iteration 4 Error: 0.029210 Align patch 4 21 left Iteration 1 Error: 1.030869 Iteration 2 Error: 0.200900 Iteration 3 Error: 0.060102 Iteration 4 Error: 0.013831 Align patch 5 20 left Iteration 1 Error: 1.227564 Iteration 2 Error: 0.159971 Iteration 3 Error: 0.039001 Align patch 6 19 left Iteration 1 Error: 0.857077 Iteration 2 Error: 0.167951 Iteration 3 Error: 0.048772 Align patch 7 18 left Iteration 1 Error: 1.277011 Iteration 2 Error: 0.284842 Iteration 3 Error: 0.125600 Iteration 4 Error: 0.059344 Iteration 5 Error: 0.031720 Align patch 8 17 left Iteration 1 Error: 1.685954 Iteration 2 Error: 0.284785 Iteration 3 Error: 0.078166 Iteration 4 Error: 0.027446 Align patch 9 16 left Iteration 1 Error: 1.127258 Iteration 2 Error: 0.271591 Iteration 3 Error: 0.077785 Iteration 4 Error: 0.024621 Align patch 10 15 left Iteration 1 Error: 0.727049 Iteration 2 Error: 0.276539 Iteration 3 Error: 0.100528 Iteration 4 Error: 0.030760 Align patch 11 14 left Iteration 1 Error: 0.784440 Iteration 2 Error: 0.233932 Iteration 3 Error: 0.080901 Iteration 4 Error: 0.023227 Align patch 12 13 left Iteration 1 Error: 1.134328 Iteration 2 Error: 0.370911 Iteration 3 Error: 0.125373 Iteration 4 Error: 0.049250 Align patch 13 12 left Iteration 1 Error: 0.897210 Iteration 2 Error: 0.224135 Iteration 3 Error: 0.073859 Iteration 4 Error: 0.032996 Align patch 14 11 left Iteration 1 Error: 0.552429 Iteration 2 Error: 0.075658 Iteration 3 Error: 0.036673 Align patch 15 10 left Iteration 1 Error: 0.898030 Iteration 2 Error: 0.155472 Iteration 3 Error: 0.064747 Iteration 4 Error: 0.034724 Align patch 16 9 left Iteration 1 Error: 0.931592 Iteration 2 Error: 0.175612 Iteration 3 Error: 0.065145 Iteration 4 Error: 0.022357 Align patch 17 8 left Iteration 1 Error: 0.699756 Iteration 2 Error: 0.160222 Iteration 3 Error: 0.041409 Align patch 18 7 left Iteration 1 Error: 0.689499 Iteration 2 Error: 0.185831 Iteration 3 Error: 0.064858 Iteration 4 Error: 0.026208 Align patch 19 6 left Iteration 1 Error: 0.859324 Iteration 2 Error: 0.196762 Iteration 3 Error: 0.059593 Iteration 4 Error: 0.034110 Align patch 20 5 left Iteration 1 Error: 0.819217 Iteration 2 Error: 0.177738 Iteration 3 Error: 0.094925 Iteration 4 Error: 0.026805 Align patch 21 4 left Iteration 1 Error: 0.987605 Iteration 2 Error: 0.158649 Iteration 3 Error: 0.045344 Align patch 22 3 left Iteration 1 Error: 0.990106 Iteration 2 Error: 0.202551 Iteration 3 Error: 0.030258 Align patch 23 2 left Iteration 1 Error: 0.832911 Iteration 2 Error: 0.126493 Iteration 3 Error: 0.026650 Align patch 24 1 left Iteration 1 Error: 1.233035 Iteration 2 Error: 0.196232 Iteration 3 Error: 0.083398 Iteration 4 Error: 0.038679 Align patch 25 0 left Iteration 1 Error: 1.021643 Iteration 2 Error: 0.167517 Iteration 3 Error: 0.048940 3D Fitting completed. Patch alignment time: 16.34(sec) Local motion has been corrected. Process thread exits. Computational time: 27.717424 sec Total time: 35.674889 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00024hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00024hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.716582s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00024hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.655865s ........................................ >>>>>>TIME<<<<<< FFT: 1.015807s Defocus_U Defocus_V Angle CCC 20744.19 20154.29 89.79 0.036457 Final Values Defocus_U Defocus_V Angle CCC 20144.94 20759.84 1.35 0.063658 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00025hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00025hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.995e-02 CC threshold: 0.734 Mean Std: 42.14 6.90 Num Hot pixels: 200 Hot pixel threshold: 83.56 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.521209 Iteration 2 Error: 0.297080 Iteration 3 Error: 0.068392 Iteration 4 Error: 0.021128 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.22 -0.03 ...... Frame ( 3) shift: 0.44 -0.06 ...... Frame ( 4) shift: 0.65 -0.10 ...... Frame ( 5) shift: 0.87 -0.13 ...... Frame ( 6) shift: 1.01 -0.14 ...... Frame ( 7) shift: 1.06 -0.13 ...... Frame ( 8) shift: 1.12 -0.13 ...... Frame ( 9) shift: 1.13 -0.05 ...... Frame ( 10) shift: 1.10 0.11 ...... Frame ( 11) shift: 1.08 0.27 ...... Frame ( 12) shift: 1.14 0.37 ...... Frame ( 13) shift: 1.31 0.41 ...... Frame ( 14) shift: 1.47 0.46 ...... Frame ( 15) shift: 1.60 0.53 ...... Frame ( 16) shift: 1.70 0.63 ...... Frame ( 17) shift: 1.80 0.74 ...... Frame ( 18) shift: 1.86 0.82 ...... Frame ( 19) shift: 1.88 0.89 ...... Frame ( 20) shift: 1.90 0.95 ...... Frame ( 21) shift: 1.93 1.00 ...... Frame ( 22) shift: 1.96 1.05 ...... Frame ( 23) shift: 1.99 1.11 ...... Frame ( 24) shift: 2.04 1.18 ...... Frame ( 25) shift: 2.09 1.28 ...... Frame ( 26) shift: 2.15 1.38 ...... Frame ( 27) shift: 2.16 1.45 ...... Frame ( 28) shift: 2.11 1.47 ...... Frame ( 29) shift: 2.07 1.49 ...... Frame ( 30) shift: 2.12 1.55 ...... Frame ( 31) shift: 2.26 1.64 ...... Frame ( 32) shift: 2.40 1.72 ...... Frame ( 33) shift: 2.49 1.73 ...... Frame ( 34) shift: 2.53 1.66 ...... Frame ( 35) shift: 2.57 1.59 ...... Frame ( 36) shift: 2.65 1.59 ...... Frame ( 37) shift: 2.78 1.65 ...... Frame ( 38) shift: 2.92 1.71 ...... Frame ( 39) shift: 3.05 1.78 ...... Frame ( 40) shift: 3.18 1.84 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.153847 Iteration 2 Error: 0.203389 Iteration 3 Error: 0.070649 Iteration 4 Error: 0.023916 Align patch 2 23 left Iteration 1 Error: 1.537358 Iteration 2 Error: 0.245925 Iteration 3 Error: 0.051307 Iteration 4 Error: 0.018134 Align patch 3 22 left Iteration 1 Error: 1.486610 Iteration 2 Error: 0.275321 Iteration 3 Error: 0.066021 Iteration 4 Error: 0.029515 Align patch 4 21 left Iteration 1 Error: 0.900666 Iteration 2 Error: 0.174352 Iteration 3 Error: 0.052197 Iteration 4 Error: 0.025288 Align patch 5 20 left Iteration 1 Error: 0.545705 Iteration 2 Error: 0.104649 Iteration 3 Error: 0.022603 Align patch 6 19 left Iteration 1 Error: 1.326221 Iteration 2 Error: 0.231202 Iteration 3 Error: 0.073426 Iteration 4 Error: 0.025125 Align patch 7 18 left Iteration 1 Error: 0.735544 Iteration 2 Error: 0.099861 Iteration 3 Error: 0.032947 Align patch 8 17 left Iteration 1 Error: 1.203475 Iteration 2 Error: 0.200443 Iteration 3 Error: 0.136797 Iteration 4 Error: 0.044923 Align patch 9 16 left Iteration 1 Error: 1.230397 Iteration 2 Error: 0.215639 Iteration 3 Error: 0.062739 Iteration 4 Error: 0.021410 Align patch 10 15 left Iteration 1 Error: 0.728696 Iteration 2 Error: 0.172050 Iteration 3 Error: 0.047017 Align patch 11 14 left Iteration 1 Error: 0.861372 Iteration 2 Error: 0.154542 Iteration 3 Error: 0.041479 Align patch 12 13 left Iteration 1 Error: 0.808998 Iteration 2 Error: 0.132698 Iteration 3 Error: 0.043984 Align patch 13 12 left Iteration 1 Error: 1.000284 Iteration 2 Error: 0.098928 Iteration 3 Error: 0.037840 Align patch 14 11 left Iteration 1 Error: 0.778503 Iteration 2 Error: 0.135085 Iteration 3 Error: 0.027913 Align patch 15 10 left Iteration 1 Error: 1.195005 Iteration 2 Error: 0.146898 Iteration 3 Error: 0.036577 Align patch 16 9 left Iteration 1 Error: 1.275922 Iteration 2 Error: 0.155020 Iteration 3 Error: 0.043782 Align patch 17 8 left Iteration 1 Error: 0.693824 Iteration 2 Error: 0.109104 Iteration 3 Error: 0.022448 Align patch 18 7 left Iteration 1 Error: 0.670152 Iteration 2 Error: 0.119401 Iteration 3 Error: 0.029787 Align patch 19 6 left Iteration 1 Error: 0.880765 Iteration 2 Error: 0.181034 Iteration 3 Error: 0.059612 Iteration 4 Error: 0.018231 Align patch 20 5 left Iteration 1 Error: 0.774624 Iteration 2 Error: 0.099163 Iteration 3 Error: 0.026415 Align patch 21 4 left Iteration 1 Error: 1.011017 Iteration 2 Error: 0.161278 Iteration 3 Error: 0.031024 Align patch 22 3 left Iteration 1 Error: 1.089231 Iteration 2 Error: 0.170311 Iteration 3 Error: 0.054535 Iteration 4 Error: 0.014909 Align patch 23 2 left Iteration 1 Error: 1.109362 Iteration 2 Error: 0.209848 Iteration 3 Error: 0.034321 Align patch 24 1 left Iteration 1 Error: 0.827836 Iteration 2 Error: 0.124746 Iteration 3 Error: 0.035680 Align patch 25 0 left Iteration 1 Error: 0.652697 Iteration 2 Error: 0.090000 Iteration 3 Error: 0.023485 3D Fitting completed. Patch alignment time: 14.09(sec) Local motion has been corrected. Process thread exits. Computational time: 24.416731 sec Total time: 31.237638 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00025hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00025hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.586479s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00025hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.972660s ........................................ >>>>>>TIME<<<<<< FFT: 1.170572s Defocus_U Defocus_V Angle CCC 17910.13 18640.78 6.04 0.039848 Final Values Defocus_U Defocus_V Angle CCC 17900.74 18659.54 5.72 0.070665 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00025hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00025hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 39.98 6.79 Num Hot pixels: 179 Hot pixel threshold: 80.72 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.537658 Iteration 2 Error: 0.296023 Iteration 3 Error: 0.085031 Iteration 4 Error: 0.026275 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.40 -0.09 ...... Frame ( 3) shift: 0.80 -0.18 ...... Frame ( 4) shift: 1.20 -0.27 ...... Frame ( 5) shift: 1.60 -0.37 ...... Frame ( 6) shift: 1.85 -0.40 ...... Frame ( 7) shift: 1.97 -0.38 ...... Frame ( 8) shift: 2.08 -0.36 ...... Frame ( 9) shift: 2.22 -0.31 ...... Frame ( 10) shift: 2.40 -0.25 ...... Frame ( 11) shift: 2.57 -0.19 ...... Frame ( 12) shift: 2.69 -0.09 ...... Frame ( 13) shift: 2.76 0.04 ...... Frame ( 14) shift: 2.83 0.18 ...... Frame ( 15) shift: 2.90 0.31 ...... Frame ( 16) shift: 2.96 0.43 ...... Frame ( 17) shift: 3.02 0.54 ...... Frame ( 18) shift: 3.10 0.64 ...... Frame ( 19) shift: 3.20 0.72 ...... Frame ( 20) shift: 3.30 0.79 ...... Frame ( 21) shift: 3.40 0.85 ...... Frame ( 22) shift: 3.50 0.88 ...... Frame ( 23) shift: 3.60 0.92 ...... Frame ( 24) shift: 3.71 0.96 ...... Frame ( 25) shift: 3.84 1.03 ...... Frame ( 26) shift: 3.96 1.09 ...... Frame ( 27) shift: 4.08 1.14 ...... Frame ( 28) shift: 4.19 1.18 ...... Frame ( 29) shift: 4.30 1.22 ...... Frame ( 30) shift: 4.44 1.26 ...... Frame ( 31) shift: 4.60 1.28 ...... Frame ( 32) shift: 4.76 1.31 ...... Frame ( 33) shift: 4.90 1.31 ...... Frame ( 34) shift: 5.02 1.28 ...... Frame ( 35) shift: 5.14 1.25 ...... Frame ( 36) shift: 5.24 1.25 ...... Frame ( 37) shift: 5.31 1.29 ...... Frame ( 38) shift: 5.38 1.32 ...... Frame ( 39) shift: 5.44 1.36 ...... Frame ( 40) shift: 5.51 1.39 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.561436 Iteration 2 Error: 0.087245 Iteration 3 Error: 0.026807 Align patch 2 23 left Iteration 1 Error: 0.630742 Iteration 2 Error: 0.088566 Iteration 3 Error: 0.017967 Align patch 3 22 left Iteration 1 Error: 0.764748 Iteration 2 Error: 0.109359 Iteration 3 Error: 0.040022 Align patch 4 21 left Iteration 1 Error: 0.925125 Iteration 2 Error: 0.194349 Iteration 3 Error: 0.056041 Iteration 4 Error: 0.019495 Align patch 5 20 left Iteration 1 Error: 0.727264 Iteration 2 Error: 0.113441 Iteration 3 Error: 0.025201 Align patch 6 19 left Iteration 1 Error: 0.547138 Iteration 2 Error: 0.096970 Iteration 3 Error: 0.021935 Align patch 7 18 left Iteration 1 Error: 0.654971 Iteration 2 Error: 0.089532 Iteration 3 Error: 0.019008 Align patch 8 17 left Iteration 1 Error: 1.239704 Iteration 2 Error: 0.182789 Iteration 3 Error: 0.045156 Align patch 9 16 left Iteration 1 Error: 0.743538 Iteration 2 Error: 0.125547 Iteration 3 Error: 0.031394 Align patch 10 15 left Iteration 1 Error: 0.464072 Iteration 2 Error: 0.058473 Iteration 3 Error: 0.017311 Align patch 11 14 left Iteration 1 Error: 0.693156 Iteration 2 Error: 0.162137 Iteration 3 Error: 0.039563 Align patch 12 13 left Iteration 1 Error: 0.681798 Iteration 2 Error: 0.150413 Iteration 3 Error: 0.027839 Align patch 13 12 left Iteration 1 Error: 0.596863 Iteration 2 Error: 0.099753 Iteration 3 Error: 0.024172 Align patch 14 11 left Iteration 1 Error: 0.645383 Iteration 2 Error: 0.133392 Iteration 3 Error: 0.030601 Align patch 15 10 left Iteration 1 Error: 0.561684 Iteration 2 Error: 0.075878 Iteration 3 Error: 0.028996 Align patch 16 9 left Iteration 1 Error: 0.832017 Iteration 2 Error: 0.103075 Iteration 3 Error: 0.026782 Align patch 17 8 left Iteration 1 Error: 0.967791 Iteration 2 Error: 0.120340 Iteration 3 Error: 0.032556 Align patch 18 7 left Iteration 1 Error: 0.403260 Iteration 2 Error: 0.076684 Iteration 3 Error: 0.019583 Align patch 19 6 left Iteration 1 Error: 0.638364 Iteration 2 Error: 0.093751 Iteration 3 Error: 0.026884 Align patch 20 5 left Iteration 1 Error: 1.119563 Iteration 2 Error: 0.152443 Iteration 3 Error: 0.044521 Align patch 21 4 left Iteration 1 Error: 0.830992 Iteration 2 Error: 0.119849 Iteration 3 Error: 0.031248 Align patch 22 3 left Iteration 1 Error: 0.763379 Iteration 2 Error: 0.091877 Iteration 3 Error: 0.017140 Align patch 23 2 left Iteration 1 Error: 0.916779 Iteration 2 Error: 0.168903 Iteration 3 Error: 0.028871 Align patch 24 1 left Iteration 1 Error: 0.706430 Iteration 2 Error: 0.128674 Iteration 3 Error: 0.040018 Align patch 25 0 left Iteration 1 Error: 1.090388 Iteration 2 Error: 0.149978 Iteration 3 Error: 0.036959 3D Fitting completed. Patch alignment time: 13.10(sec) Local motion has been corrected. Process thread exits. Computational time: 23.506130 sec Total time: 30.719419 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00025hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00025hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.799667s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00025hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.090096s ........................................ >>>>>>TIME<<<<<< FFT: 0.931309s Defocus_U Defocus_V Angle CCC 20904.25 21791.06 5.43 0.051977 Final Values Defocus_U Defocus_V Angle CCC 20901.12 21812.94 5.43 0.085537 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00025hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00025hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.994e-02 CC threshold: 0.734 Mean Std: 41.92 6.88 Num Hot pixels: 188 Hot pixel threshold: 83.20 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.733477 Iteration 2 Error: 0.262685 Iteration 3 Error: 0.061095 Iteration 4 Error: 0.025106 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.14 -0.18 ...... Frame ( 3) shift: 0.27 -0.36 ...... Frame ( 4) shift: 0.41 -0.54 ...... Frame ( 5) shift: 0.54 -0.72 ...... Frame ( 6) shift: 0.61 -0.74 ...... Frame ( 7) shift: 0.60 -0.61 ...... Frame ( 8) shift: 0.60 -0.47 ...... Frame ( 9) shift: 0.60 -0.31 ...... Frame ( 10) shift: 0.61 -0.14 ...... Frame ( 11) shift: 0.61 0.04 ...... Frame ( 12) shift: 0.64 0.23 ...... Frame ( 13) shift: 0.70 0.42 ...... Frame ( 14) shift: 0.76 0.62 ...... Frame ( 15) shift: 0.78 0.80 ...... Frame ( 16) shift: 0.75 0.98 ...... Frame ( 17) shift: 0.72 1.15 ...... Frame ( 18) shift: 0.68 1.29 ...... Frame ( 19) shift: 0.62 1.40 ...... Frame ( 20) shift: 0.56 1.51 ...... Frame ( 21) shift: 0.56 1.58 ...... Frame ( 22) shift: 0.60 1.61 ...... Frame ( 23) shift: 0.65 1.64 ...... Frame ( 24) shift: 0.69 1.72 ...... Frame ( 25) shift: 0.71 1.84 ...... Frame ( 26) shift: 0.73 1.96 ...... Frame ( 27) shift: 0.77 2.00 ...... Frame ( 28) shift: 0.82 1.99 ...... Frame ( 29) shift: 0.88 1.97 ...... Frame ( 30) shift: 0.88 2.00 ...... Frame ( 31) shift: 0.81 2.09 ...... Frame ( 32) shift: 0.75 2.18 ...... Frame ( 33) shift: 0.72 2.21 ...... Frame ( 34) shift: 0.73 2.17 ...... Frame ( 35) shift: 0.74 2.14 ...... Frame ( 36) shift: 0.77 2.10 ...... Frame ( 37) shift: 0.83 2.07 ...... Frame ( 38) shift: 0.89 2.04 ...... Frame ( 39) shift: 0.94 2.00 ...... Frame ( 40) shift: 1.00 1.97 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.503997 Iteration 2 Error: 0.103758 Iteration 3 Error: 0.021501 Align patch 2 23 left Iteration 1 Error: 1.875588 Iteration 2 Error: 0.348705 Iteration 3 Error: 0.054336 Iteration 4 Error: 0.014443 Align patch 3 22 left Iteration 1 Error: 1.401998 Iteration 2 Error: 0.237840 Iteration 3 Error: 0.060821 Iteration 4 Error: 0.035637 Align patch 4 21 left Iteration 1 Error: 0.985418 Iteration 2 Error: 0.257158 Iteration 3 Error: 0.038824 Align patch 5 20 left Iteration 1 Error: 0.745630 Iteration 2 Error: 0.129807 Iteration 3 Error: 0.032452 Align patch 6 19 left Iteration 1 Error: 0.642866 Iteration 2 Error: 0.117624 Iteration 3 Error: 0.033593 Align patch 7 18 left Iteration 1 Error: 0.741226 Iteration 2 Error: 0.132812 Iteration 3 Error: 0.040852 Align patch 8 17 left Iteration 1 Error: 0.808156 Iteration 2 Error: 0.146409 Iteration 3 Error: 0.069178 Iteration 4 Error: 0.023656 Align patch 9 16 left Iteration 1 Error: 1.283677 Iteration 2 Error: 0.243975 Iteration 3 Error: 0.078443 Iteration 4 Error: 0.023801 Align patch 10 15 left Iteration 1 Error: 0.634735 Iteration 2 Error: 0.139550 Iteration 3 Error: 0.037118 Align patch 11 14 left Iteration 1 Error: 0.601472 Iteration 2 Error: 0.093279 Iteration 3 Error: 0.027418 Align patch 12 13 left Iteration 1 Error: 0.739555 Iteration 2 Error: 0.205539 Iteration 3 Error: 0.062631 Iteration 4 Error: 0.022644 Align patch 13 12 left Iteration 1 Error: 1.105624 Iteration 2 Error: 0.187680 Iteration 3 Error: 0.050020 Iteration 4 Error: 0.020810 Align patch 14 11 left Iteration 1 Error: 0.693280 Iteration 2 Error: 0.158718 Iteration 3 Error: 0.045569 Align patch 15 10 left Iteration 1 Error: 1.168128 Iteration 2 Error: 0.217702 Iteration 3 Error: 0.049501 Align patch 16 9 left Iteration 1 Error: 0.902981 Iteration 2 Error: 0.159516 Iteration 3 Error: 0.044740 Align patch 17 8 left Iteration 1 Error: 1.245330 Iteration 2 Error: 0.151706 Iteration 3 Error: 0.048292 Align patch 18 7 left Iteration 1 Error: 0.657355 Iteration 2 Error: 0.118006 Iteration 3 Error: 0.025241 Align patch 19 6 left Iteration 1 Error: 0.811982 Iteration 2 Error: 0.132157 Iteration 3 Error: 0.033217 Align patch 20 5 left Iteration 1 Error: 0.897965 Iteration 2 Error: 0.223087 Iteration 3 Error: 0.060304 Iteration 4 Error: 0.016774 Align patch 21 4 left Iteration 1 Error: 0.891450 Iteration 2 Error: 0.154865 Iteration 3 Error: 0.035417 Align patch 22 3 left Iteration 1 Error: 0.738091 Iteration 2 Error: 0.189171 Iteration 3 Error: 0.064963 Iteration 4 Error: 0.017709 Align patch 23 2 left Iteration 1 Error: 0.576351 Iteration 2 Error: 0.106099 Iteration 3 Error: 0.036731 Align patch 24 1 left Iteration 1 Error: 0.602862 Iteration 2 Error: 0.073251 Iteration 3 Error: 0.023351 Align patch 25 0 left Iteration 1 Error: 0.739372 Iteration 2 Error: 0.185096 Iteration 3 Error: 0.055786 Iteration 4 Error: 0.019350 3D Fitting completed. Patch alignment time: 13.80(sec) Local motion has been corrected. Process thread exits. Computational time: 25.688595 sec Total time: 42.396252 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00025hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00025hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.754729s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00025hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.913183s ........................................ >>>>>>TIME<<<<<< FFT: 1.014764s Defocus_U Defocus_V Angle CCC 23050.82 22418.00 88.58 0.041444 Final Values Defocus_U Defocus_V Angle CCC 23078.96 22430.51 88.89 0.069280 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00025hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00025hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.999e-02 CC threshold: 0.734 Mean Std: 41.51 6.86 Num Hot pixels: 188 Hot pixel threshold: 82.65 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.098925 Iteration 2 Error: 0.105091 Iteration 3 Error: 0.021716 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.16 -0.05 ...... Frame ( 3) shift: 0.33 -0.10 ...... Frame ( 4) shift: 0.49 -0.16 ...... Frame ( 5) shift: 0.66 -0.21 ...... Frame ( 6) shift: 0.80 -0.21 ...... Frame ( 7) shift: 0.91 -0.17 ...... Frame ( 8) shift: 1.02 -0.13 ...... Frame ( 9) shift: 1.13 -0.05 ...... Frame ( 10) shift: 1.22 0.04 ...... Frame ( 11) shift: 1.31 0.14 ...... Frame ( 12) shift: 1.35 0.22 ...... Frame ( 13) shift: 1.33 0.26 ...... Frame ( 14) shift: 1.32 0.30 ...... Frame ( 15) shift: 1.30 0.38 ...... Frame ( 16) shift: 1.29 0.50 ...... Frame ( 17) shift: 1.28 0.62 ...... Frame ( 18) shift: 1.29 0.67 ...... Frame ( 19) shift: 1.31 0.65 ...... Frame ( 20) shift: 1.34 0.64 ...... Frame ( 21) shift: 1.35 0.63 ...... Frame ( 22) shift: 1.37 0.64 ...... Frame ( 23) shift: 1.39 0.65 ...... Frame ( 24) shift: 1.39 0.64 ...... Frame ( 25) shift: 1.38 0.62 ...... Frame ( 26) shift: 1.37 0.59 ...... Frame ( 27) shift: 1.39 0.61 ...... Frame ( 28) shift: 1.44 0.66 ...... Frame ( 29) shift: 1.49 0.72 ...... Frame ( 30) shift: 1.51 0.78 ...... Frame ( 31) shift: 1.52 0.85 ...... Frame ( 32) shift: 1.53 0.92 ...... Frame ( 33) shift: 1.53 0.93 ...... Frame ( 34) shift: 1.53 0.88 ...... Frame ( 35) shift: 1.52 0.83 ...... Frame ( 36) shift: 1.55 0.80 ...... Frame ( 37) shift: 1.62 0.80 ...... Frame ( 38) shift: 1.68 0.80 ...... Frame ( 39) shift: 1.75 0.80 ...... Frame ( 40) shift: 1.81 0.80 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.048038 Iteration 2 Error: 0.105317 Iteration 3 Error: 0.020990 Align patch 2 23 left Iteration 1 Error: 1.290952 Iteration 2 Error: 0.185536 Iteration 3 Error: 0.073178 Iteration 4 Error: 0.019083 Align patch 3 22 left Iteration 1 Error: 0.896750 Iteration 2 Error: 0.157545 Iteration 3 Error: 0.036070 Align patch 4 21 left Iteration 1 Error: 0.678888 Iteration 2 Error: 0.125996 Iteration 3 Error: 0.018607 Align patch 5 20 left Iteration 1 Error: 0.670040 Iteration 2 Error: 0.088090 Iteration 3 Error: 0.029024 Align patch 6 19 left Iteration 1 Error: 0.696705 Iteration 2 Error: 0.148724 Iteration 3 Error: 0.033462 Align patch 7 18 left Iteration 1 Error: 0.714078 Iteration 2 Error: 0.097125 Iteration 3 Error: 0.020637 Align patch 8 17 left Iteration 1 Error: 0.749340 Iteration 2 Error: 0.187095 Iteration 3 Error: 0.030578 Align patch 9 16 left Iteration 1 Error: 0.835586 Iteration 2 Error: 0.230567 Iteration 3 Error: 0.033391 Align patch 10 15 left Iteration 1 Error: 0.916196 Iteration 2 Error: 0.172223 Iteration 3 Error: 0.036599 Align patch 11 14 left Iteration 1 Error: 0.915365 Iteration 2 Error: 0.226720 Iteration 3 Error: 0.065419 Iteration 4 Error: 0.021249 Align patch 12 13 left Iteration 1 Error: 0.687363 Iteration 2 Error: 0.111386 Iteration 3 Error: 0.025884 Align patch 13 12 left Iteration 1 Error: 0.641207 Iteration 2 Error: 0.097747 Iteration 3 Error: 0.027110 Align patch 14 11 left Iteration 1 Error: 0.618264 Iteration 2 Error: 0.090714 Iteration 3 Error: 0.026108 Align patch 15 10 left Iteration 1 Error: 0.588636 Iteration 2 Error: 0.127547 Iteration 3 Error: 0.052212 Iteration 4 Error: 0.032370 Align patch 16 9 left Iteration 1 Error: 0.545587 Iteration 2 Error: 0.108544 Iteration 3 Error: 0.036411 Align patch 17 8 left Iteration 1 Error: 0.649154 Iteration 2 Error: 0.127252 Iteration 3 Error: 0.030239 Align patch 18 7 left Iteration 1 Error: 0.555436 Iteration 2 Error: 0.124779 Iteration 3 Error: 0.040603 Align patch 19 6 left Iteration 1 Error: 0.833575 Iteration 2 Error: 0.136257 Iteration 3 Error: 0.025687 Align patch 20 5 left Iteration 1 Error: 0.927952 Iteration 2 Error: 0.121314 Iteration 3 Error: 0.023415 Align patch 21 4 left Iteration 1 Error: 0.682514 Iteration 2 Error: 0.096519 Iteration 3 Error: 0.024510 Align patch 22 3 left Iteration 1 Error: 1.122321 Iteration 2 Error: 0.141702 Iteration 3 Error: 0.028702 Align patch 23 2 left Iteration 1 Error: 0.991206 Iteration 2 Error: 0.089348 Iteration 3 Error: 0.033395 Align patch 24 1 left Iteration 1 Error: 0.778980 Iteration 2 Error: 0.091575 Iteration 3 Error: 0.034821 Align patch 25 0 left Iteration 1 Error: 0.992253 Iteration 2 Error: 0.167571 Iteration 3 Error: 0.029398 3D Fitting completed. Patch alignment time: 13.60(sec) Local motion has been corrected. Process thread exits. Computational time: 23.049133 sec Total time: 29.786226 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00025hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00025hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.663973s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00025hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.615603s ........................................ >>>>>>TIME<<<<<< FFT: 0.924029s Defocus_U Defocus_V Angle CCC 18820.33 19589.86 2.44 0.035196 Final Values Defocus_U Defocus_V Angle CCC 18828.15 19616.44 2.75 0.062431 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00026hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00026hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.355e-01 1.007e-01 CC threshold: 0.740 Mean Std: 17.55 14.18 Num Hot pixels: 20 Hot pixel threshold: 102.61 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.062024 Iteration 2 Error: 0.228608 Iteration 3 Error: 0.068543 Iteration 4 Error: 0.020525 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.06 -0.10 ...... Frame ( 3) shift: -0.12 -0.21 ...... Frame ( 4) shift: -0.18 -0.31 ...... Frame ( 5) shift: -0.25 -0.41 ...... Frame ( 6) shift: -0.25 -0.43 ...... Frame ( 7) shift: -0.20 -0.35 ...... Frame ( 8) shift: -0.15 -0.27 ...... Frame ( 9) shift: -0.07 -0.16 ...... Frame ( 10) shift: 0.02 -0.02 ...... Frame ( 11) shift: 0.11 0.12 ...... Frame ( 12) shift: 0.21 0.26 ...... Frame ( 13) shift: 0.33 0.40 ...... Frame ( 14) shift: 0.44 0.55 ...... Frame ( 15) shift: 0.52 0.68 ...... Frame ( 16) shift: 0.57 0.79 ...... Frame ( 17) shift: 0.61 0.89 ...... Frame ( 18) shift: 0.67 0.99 ...... Frame ( 19) shift: 0.75 1.07 ...... Frame ( 20) shift: 0.82 1.15 ...... Frame ( 21) shift: 0.87 1.24 ...... Frame ( 22) shift: 0.90 1.32 ...... Frame ( 23) shift: 0.92 1.41 ...... Frame ( 24) shift: 0.98 1.50 ...... Frame ( 25) shift: 1.06 1.59 ...... Frame ( 26) shift: 1.15 1.69 ...... Frame ( 27) shift: 1.23 1.79 ...... Frame ( 28) shift: 1.28 1.89 ...... Frame ( 29) shift: 1.34 1.99 ...... Frame ( 30) shift: 1.41 2.10 ...... Frame ( 31) shift: 1.50 2.22 ...... Frame ( 32) shift: 1.58 2.35 ...... Frame ( 33) shift: 1.64 2.44 ...... Frame ( 34) shift: 1.66 2.51 ...... Frame ( 35) shift: 1.68 2.57 ...... Frame ( 36) shift: 1.71 2.64 ...... Frame ( 37) shift: 1.72 2.71 ...... Frame ( 38) shift: 1.74 2.78 ...... Frame ( 39) shift: 1.76 2.85 ...... Frame ( 40) shift: 1.78 2.92 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.964540 Iteration 2 Error: 0.196039 Iteration 3 Error: 0.062662 Iteration 4 Error: 0.023388 Align patch 2 23 left Iteration 1 Error: 0.697183 Iteration 2 Error: 0.196971 Iteration 3 Error: 0.052092 Iteration 4 Error: 0.021813 Align patch 3 22 left Iteration 1 Error: 0.779931 Iteration 2 Error: 0.120455 Iteration 3 Error: 0.038243 Align patch 4 21 left Iteration 1 Error: 0.716331 Iteration 2 Error: 0.257339 Iteration 3 Error: 0.089759 Iteration 4 Error: 0.031869 Align patch 5 20 left Iteration 1 Error: 0.503079 Iteration 2 Error: 0.130114 Iteration 3 Error: 0.033629 Align patch 6 19 left Iteration 1 Error: 1.051127 Iteration 2 Error: 0.294786 Iteration 3 Error: 0.097083 Iteration 4 Error: 0.048810 Align patch 7 18 left Iteration 1 Error: 0.930367 Iteration 2 Error: 0.209411 Iteration 3 Error: 0.065468 Iteration 4 Error: 0.025745 Align patch 8 17 left Iteration 1 Error: 0.734400 Iteration 2 Error: 0.217741 Iteration 3 Error: 0.076973 Iteration 4 Error: 0.029571 Align patch 9 16 left Iteration 1 Error: 0.769540 Iteration 2 Error: 0.286274 Iteration 3 Error: 0.123928 Iteration 4 Error: 0.056243 Iteration 5 Error: 0.025244 Align patch 10 15 left Iteration 1 Error: 0.439843 Iteration 2 Error: 0.050601 Iteration 3 Error: 0.011357 Align patch 11 14 left Iteration 1 Error: 0.758376 Iteration 2 Error: 0.133950 Iteration 3 Error: 0.026330 Align patch 12 13 left Iteration 1 Error: 1.116788 Iteration 2 Error: 0.401510 Iteration 3 Error: 0.128029 Iteration 4 Error: 0.052562 Iteration 5 Error: 0.020849 Align patch 13 12 left Iteration 1 Error: 0.837572 Iteration 2 Error: 0.256557 Iteration 3 Error: 0.072692 Iteration 4 Error: 0.027127 Align patch 14 11 left Iteration 1 Error: 0.669632 Iteration 2 Error: 0.106677 Iteration 3 Error: 0.020341 Align patch 15 10 left Iteration 1 Error: 0.991720 Iteration 2 Error: 0.115984 Iteration 3 Error: 0.016286 Align patch 16 9 left Iteration 1 Error: 1.247300 Iteration 2 Error: 0.240845 Iteration 3 Error: 0.068544 Iteration 4 Error: 0.025575 Align patch 17 8 left Iteration 1 Error: 1.442277 Iteration 2 Error: 0.219286 Iteration 3 Error: 0.045406 Align patch 18 7 left Iteration 1 Error: 0.931655 Iteration 2 Error: 0.142223 Iteration 3 Error: 0.022138 Align patch 19 6 left Iteration 1 Error: 0.960331 Iteration 2 Error: 0.042936 Align patch 20 5 left Iteration 1 Error: 0.767989 Iteration 2 Error: 0.041769 Align patch 21 4 left Iteration 1 Error: 0.472748 Iteration 2 Error: 0.140513 Iteration 3 Error: 0.043543 Align patch 22 3 left Iteration 1 Error: 1.577645 Iteration 2 Error: 0.140068 Iteration 3 Error: 0.017117 Align patch 23 2 left Iteration 1 Error: 1.276205 Iteration 2 Error: 0.210897 Iteration 3 Error: 0.044528 Align patch 24 1 left Iteration 1 Error: 5.010064 Iteration 2 Error: 0.276719 Iteration 3 Error: 0.065132 Iteration 4 Error: 0.022840 Align patch 25 0 left Iteration 1 Error: 1.014341 Iteration 2 Error: 0.041212 3D Fitting completed. Patch alignment time: 12.94(sec) Local motion has been corrected. Process thread exits. Computational time: 22.688614 sec Total time: 29.427647 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00026hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00026hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.557262s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00026hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.601839s ........................................ >>>>>>TIME<<<<<< FFT: 0.939969s Defocus_U Defocus_V Angle CCC 18193.34 18837.91 10.69 -0.003584 Final Values Defocus_U Defocus_V Angle CCC 18177.71 18822.29 12.90 0.008821 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00026hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00026hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.359e-01 1.010e-01 CC threshold: 0.742 Mean Std: 14.82 12.83 Num Hot pixels: 24 Hot pixel threshold: 91.78 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.446232 Iteration 2 Error: 0.225697 Iteration 3 Error: 0.047256 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.16 -0.38 ...... Frame ( 3) shift: -0.31 -0.77 ...... Frame ( 4) shift: -0.47 -1.15 ...... Frame ( 5) shift: -0.62 -1.54 ...... Frame ( 6) shift: -0.70 -1.74 ...... Frame ( 7) shift: -0.69 -1.78 ...... Frame ( 8) shift: -0.68 -1.81 ...... Frame ( 9) shift: -0.63 -1.79 ...... Frame ( 10) shift: -0.56 -1.71 ...... Frame ( 11) shift: -0.48 -1.64 ...... Frame ( 12) shift: -0.42 -1.57 ...... Frame ( 13) shift: -0.37 -1.50 ...... Frame ( 14) shift: -0.32 -1.43 ...... Frame ( 15) shift: -0.24 -1.35 ...... Frame ( 16) shift: -0.13 -1.27 ...... Frame ( 17) shift: -0.03 -1.18 ...... Frame ( 18) shift: 0.06 -1.11 ...... Frame ( 19) shift: 0.14 -1.04 ...... Frame ( 20) shift: 0.21 -0.98 ...... Frame ( 21) shift: 0.27 -0.90 ...... Frame ( 22) shift: 0.30 -0.80 ...... Frame ( 23) shift: 0.32 -0.70 ...... Frame ( 24) shift: 0.36 -0.62 ...... Frame ( 25) shift: 0.41 -0.56 ...... Frame ( 26) shift: 0.46 -0.50 ...... Frame ( 27) shift: 0.50 -0.42 ...... Frame ( 28) shift: 0.53 -0.33 ...... Frame ( 29) shift: 0.55 -0.24 ...... Frame ( 30) shift: 0.58 -0.18 ...... Frame ( 31) shift: 0.61 -0.13 ...... Frame ( 32) shift: 0.64 -0.08 ...... Frame ( 33) shift: 0.68 -0.03 ...... Frame ( 34) shift: 0.73 0.03 ...... Frame ( 35) shift: 0.78 0.09 ...... Frame ( 36) shift: 0.83 0.16 ...... Frame ( 37) shift: 0.86 0.22 ...... Frame ( 38) shift: 0.90 0.29 ...... Frame ( 39) shift: 0.94 0.35 ...... Frame ( 40) shift: 0.98 0.42 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.000277 Iteration 2 Error: 0.214402 Iteration 3 Error: 0.064560 Iteration 4 Error: 0.017606 Align patch 2 23 left Iteration 1 Error: 1.474534 Iteration 2 Error: 0.355524 Iteration 3 Error: 0.063501 Iteration 4 Error: 0.022342 Align patch 3 22 left Iteration 1 Error: 1.819455 Iteration 2 Error: 0.435988 Iteration 3 Error: 0.079144 Iteration 4 Error: 0.023674 Align patch 4 21 left Iteration 1 Error: 0.835223 Iteration 2 Error: 0.386860 Iteration 3 Error: 0.179381 Iteration 4 Error: 0.083242 Iteration 5 Error: 0.038466 Align patch 5 20 left Iteration 1 Error: 0.950900 Iteration 2 Error: 0.429897 Iteration 3 Error: 0.223464 Iteration 4 Error: 0.102922 Iteration 5 Error: 0.053202 Align patch 5 20 left Iteration 1 Error: 0.606575 Iteration 2 Error: 0.262815 Iteration 3 Error: 0.122162 Iteration 4 Error: 0.054073 Iteration 5 Error: 0.025162 Align patch 6 19 left Iteration 1 Error: 1.058179 Iteration 2 Error: 0.262234 Iteration 3 Error: 0.052347 Iteration 4 Error: 0.009043 Align patch 7 18 left Iteration 1 Error: 0.493993 Iteration 2 Error: 0.077855 Iteration 3 Error: 0.013981 Align patch 8 17 left Iteration 1 Error: 0.802536 Iteration 2 Error: 0.185779 Iteration 3 Error: 0.044030 Align patch 9 16 left Iteration 1 Error: 0.824440 Iteration 2 Error: 0.229704 Iteration 3 Error: 0.064953 Iteration 4 Error: 0.022025 Align patch 10 15 left Iteration 1 Error: 0.967517 Iteration 2 Error: 0.249309 Iteration 3 Error: 0.081646 Iteration 4 Error: 0.027162 Align patch 11 14 left Iteration 1 Error: 0.648457 Iteration 2 Error: 0.119593 Iteration 3 Error: 0.017377 Align patch 12 13 left Iteration 1 Error: 0.601255 Iteration 2 Error: 0.105683 Iteration 3 Error: 0.023783 Align patch 13 12 left Iteration 1 Error: 0.485988 Iteration 2 Error: 0.069155 Iteration 3 Error: 0.012883 Align patch 14 11 left Iteration 1 Error: 0.901870 Iteration 2 Error: 0.101586 Iteration 3 Error: 0.009696 Align patch 15 10 left Iteration 1 Error: 1.240934 Iteration 2 Error: 0.215337 Iteration 3 Error: 0.039722 Align patch 16 9 left Iteration 1 Error: 1.582351 Iteration 2 Error: 0.135454 Iteration 3 Error: 0.015305 Align patch 17 8 left Iteration 1 Error: 1.425747 Iteration 2 Error: 0.185318 Iteration 3 Error: 0.027567 Align patch 18 7 left Iteration 1 Error: 1.214346 Iteration 2 Error: 0.144051 Iteration 3 Error: 0.031796 Align patch 19 6 left Iteration 1 Error: 1.217661 Iteration 2 Error: 0.184496 Iteration 3 Error: 0.041587 Align patch 20 5 left Iteration 1 Error: 1.452248 Iteration 2 Error: 0.146591 Iteration 3 Error: 0.023721 Align patch 21 4 left Iteration 1 Error: 2.040478 Iteration 2 Error: 0.148403 Iteration 3 Error: 0.017014 Align patch 22 3 left Iteration 1 Error: 1.383959 Iteration 2 Error: 0.126833 Iteration 3 Error: 0.031219 Align patch 23 2 left Iteration 1 Error: 1.018589 Iteration 2 Error: 0.113902 Iteration 3 Error: 0.026275 Align patch 24 1 left Iteration 1 Error: 1.687943 Iteration 2 Error: 0.074280 Iteration 3 Error: 0.007042 Align patch 25 0 left Iteration 1 Error: 0.839350 Iteration 2 Error: 0.028809 3D Fitting completed. Patch alignment time: 12.84(sec) Local motion has been corrected. Process thread exits. Computational time: 28.243385 sec Total time: 36.362297 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00026hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00026hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.743106s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00026hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.322710s ........................................ >>>>>>TIME<<<<<< FFT: 1.135461s Defocus_U Defocus_V Angle CCC 22733.56 22207.84 86.06 -0.012803 Final Values Defocus_U Defocus_V Angle CCC 22738.20 22196.95 86.06 -0.002564 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00026hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00026hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.360e-01 1.011e-01 CC threshold: 0.743 Mean Std: 17.91 14.37 Num Hot pixels: 25 Hot pixel threshold: 104.11 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.330589 Iteration 2 Error: 0.150548 Iteration 3 Error: 0.021607 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.06 -0.27 ...... Frame ( 3) shift: -0.11 -0.53 ...... Frame ( 4) shift: -0.17 -0.80 ...... Frame ( 5) shift: -0.23 -1.06 ...... Frame ( 6) shift: -0.26 -1.18 ...... Frame ( 7) shift: -0.27 -1.14 ...... Frame ( 8) shift: -0.28 -1.10 ...... Frame ( 9) shift: -0.27 -1.04 ...... Frame ( 10) shift: -0.26 -0.96 ...... Frame ( 11) shift: -0.25 -0.88 ...... Frame ( 12) shift: -0.21 -0.79 ...... Frame ( 13) shift: -0.15 -0.70 ...... Frame ( 14) shift: -0.08 -0.60 ...... Frame ( 15) shift: -0.06 -0.52 ...... Frame ( 16) shift: -0.07 -0.44 ...... Frame ( 17) shift: -0.08 -0.36 ...... Frame ( 18) shift: -0.09 -0.29 ...... Frame ( 19) shift: -0.09 -0.24 ...... Frame ( 20) shift: -0.09 -0.19 ...... Frame ( 21) shift: -0.06 -0.13 ...... Frame ( 22) shift: 0.00 -0.06 ...... Frame ( 23) shift: 0.06 0.02 ...... Frame ( 24) shift: 0.13 0.08 ...... Frame ( 25) shift: 0.20 0.15 ...... Frame ( 26) shift: 0.27 0.21 ...... Frame ( 27) shift: 0.30 0.27 ...... Frame ( 28) shift: 0.30 0.32 ...... Frame ( 29) shift: 0.30 0.38 ...... Frame ( 30) shift: 0.34 0.42 ...... Frame ( 31) shift: 0.42 0.44 ...... Frame ( 32) shift: 0.49 0.46 ...... Frame ( 33) shift: 0.54 0.53 ...... Frame ( 34) shift: 0.57 0.65 ...... Frame ( 35) shift: 0.60 0.77 ...... Frame ( 36) shift: 0.63 0.86 ...... Frame ( 37) shift: 0.66 0.91 ...... Frame ( 38) shift: 0.70 0.96 ...... Frame ( 39) shift: 0.73 1.00 ...... Frame ( 40) shift: 0.77 1.05 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.745961 Iteration 2 Error: 0.170511 Iteration 3 Error: 0.044944 Align patch 2 23 left Iteration 1 Error: 0.811419 Iteration 2 Error: 0.157316 Iteration 3 Error: 0.049182 Align patch 3 22 left Iteration 1 Error: 0.757890 Iteration 2 Error: 0.155852 Iteration 3 Error: 0.062860 Iteration 4 Error: 0.013026 Align patch 4 21 left Iteration 1 Error: 0.477174 Iteration 2 Error: 0.152571 Iteration 3 Error: 0.047774 Align patch 5 20 left Iteration 1 Error: 0.285480 Iteration 2 Error: 0.049867 Align patch 6 19 left Iteration 1 Error: 1.051613 Iteration 2 Error: 0.250820 Iteration 3 Error: 0.065257 Iteration 4 Error: 0.021564 Align patch 7 18 left Iteration 1 Error: 0.822154 Iteration 2 Error: 0.176710 Iteration 3 Error: 0.035636 Align patch 8 17 left Iteration 1 Error: 0.601535 Iteration 2 Error: 0.241754 Iteration 3 Error: 0.096985 Iteration 4 Error: 0.039626 Align patch 9 16 left Iteration 1 Error: 0.731894 Iteration 2 Error: 0.294350 Iteration 3 Error: 0.136228 Iteration 4 Error: 0.064379 Iteration 5 Error: 0.030771 Align patch 10 15 left Iteration 1 Error: 0.517256 Iteration 2 Error: 0.060159 Iteration 3 Error: 0.013270 Align patch 11 14 left Iteration 1 Error: 0.703338 Iteration 2 Error: 0.085268 Iteration 3 Error: 0.007465 Align patch 12 13 left Iteration 1 Error: 0.771230 Iteration 2 Error: 0.062806 Iteration 3 Error: 0.006685 Align patch 13 12 left Iteration 1 Error: 0.606492 Iteration 2 Error: 0.104857 Iteration 3 Error: 0.022989 Align patch 14 11 left Iteration 1 Error: 0.859073 Iteration 2 Error: 0.096529 Iteration 3 Error: 0.016238 Align patch 15 10 left Iteration 1 Error: 0.937741 Iteration 2 Error: 0.079652 Iteration 3 Error: 0.010906 Align patch 16 9 left Iteration 1 Error: 0.805590 Iteration 2 Error: 0.145803 Iteration 3 Error: 0.023517 Align patch 17 8 left Iteration 1 Error: 1.226584 Iteration 2 Error: 0.145672 Iteration 3 Error: 0.024182 Align patch 18 7 left Iteration 1 Error: 0.540539 Iteration 2 Error: 0.033200 Align patch 19 6 left Iteration 1 Error: 2.452587 Iteration 2 Error: 0.291861 Iteration 3 Error: 0.073203 Iteration 4 Error: 0.018509 Align patch 20 5 left Iteration 1 Error: 1.112132 Iteration 2 Error: 0.114055 Iteration 3 Error: 0.025831 Align patch 21 4 left Iteration 1 Error: 2.011589 Iteration 2 Error: 0.271271 Iteration 3 Error: 0.098758 Iteration 4 Error: 0.037921 Align patch 22 3 left Iteration 1 Error: 0.896284 Iteration 2 Error: 0.127649 Iteration 3 Error: 0.007384 Align patch 23 2 left Iteration 1 Error: 1.177381 Iteration 2 Error: 0.069338 Iteration 3 Error: 0.011690 Align patch 24 1 left Iteration 1 Error: 2.330306 Iteration 2 Error: 0.430080 Iteration 3 Error: 0.160986 Iteration 4 Error: 0.080377 Iteration 5 Error: 0.031379 Align patch 25 0 left Iteration 1 Error: 41.452641 Iteration 2 Error: 25.588827 Iteration 3 Error: 0.295131 Iteration 4 Error: 0.150791 Iteration 5 Error: 0.102586 Align patch 25 0 left Iteration 1 Error: 3.909147 Iteration 2 Error: 0.413111 Iteration 3 Error: 0.150151 Iteration 4 Error: 0.052632 Iteration 5 Error: 0.021167 3D Fitting completed. Patch alignment time: 15.20(sec) Local motion has been corrected. Process thread exits. Computational time: 28.306343 sec Total time: 36.230980 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00026hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00026hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.857480s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00026hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.870615s ........................................ >>>>>>TIME<<<<<< FFT: 1.104124s Defocus_U Defocus_V Angle CCC 20132.89 19628.92 87.60 -0.010038 Final Values Defocus_U Defocus_V Angle CCC 20103.20 19636.76 86.66 -0.000106 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00027hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00027hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.997e-02 CC threshold: 0.734 Mean Std: 38.63 6.60 Num Hot pixels: 180 Hot pixel threshold: 78.21 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.879773 Iteration 2 Error: 0.428839 Iteration 3 Error: 0.088508 Iteration 4 Error: 0.038204 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.16 -0.12 ...... Frame ( 3) shift: -0.31 -0.24 ...... Frame ( 4) shift: -0.47 -0.36 ...... Frame ( 5) shift: -0.63 -0.48 ...... Frame ( 6) shift: -0.66 -0.51 ...... Frame ( 7) shift: -0.57 -0.46 ...... Frame ( 8) shift: -0.48 -0.40 ...... Frame ( 9) shift: -0.33 -0.33 ...... Frame ( 10) shift: -0.11 -0.23 ...... Frame ( 11) shift: 0.10 -0.13 ...... Frame ( 12) shift: 0.27 -0.01 ...... Frame ( 13) shift: 0.38 0.11 ...... Frame ( 14) shift: 0.49 0.23 ...... Frame ( 15) shift: 0.67 0.33 ...... Frame ( 16) shift: 0.91 0.41 ...... Frame ( 17) shift: 1.16 0.49 ...... Frame ( 18) shift: 1.33 0.59 ...... Frame ( 19) shift: 1.41 0.71 ...... Frame ( 20) shift: 1.49 0.83 ...... Frame ( 21) shift: 1.53 0.88 ...... Frame ( 22) shift: 1.52 0.86 ...... Frame ( 23) shift: 1.51 0.84 ...... Frame ( 24) shift: 1.55 0.87 ...... Frame ( 25) shift: 1.66 0.95 ...... Frame ( 26) shift: 1.76 1.02 ...... Frame ( 27) shift: 1.82 1.10 ...... Frame ( 28) shift: 1.82 1.17 ...... Frame ( 29) shift: 1.83 1.25 ...... Frame ( 30) shift: 1.87 1.29 ...... Frame ( 31) shift: 1.93 1.30 ...... Frame ( 32) shift: 2.00 1.31 ...... Frame ( 33) shift: 2.10 1.31 ...... Frame ( 34) shift: 2.23 1.29 ...... Frame ( 35) shift: 2.37 1.28 ...... Frame ( 36) shift: 2.49 1.32 ...... Frame ( 37) shift: 2.59 1.41 ...... Frame ( 38) shift: 2.69 1.51 ...... Frame ( 39) shift: 2.79 1.61 ...... Frame ( 40) shift: 2.89 1.71 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.892382 Iteration 2 Error: 0.169288 Iteration 3 Error: 0.064624 Iteration 4 Error: 0.014888 Align patch 2 23 left Iteration 1 Error: 1.088755 Iteration 2 Error: 0.212412 Iteration 3 Error: 0.058839 Iteration 4 Error: 0.011401 Align patch 3 22 left Iteration 1 Error: 0.837510 Iteration 2 Error: 0.104526 Iteration 3 Error: 0.027589 Align patch 4 21 left Iteration 1 Error: 0.983803 Iteration 2 Error: 0.237182 Iteration 3 Error: 0.056568 Iteration 4 Error: 0.022885 Align patch 5 20 left Iteration 1 Error: 0.731625 Iteration 2 Error: 0.134000 Iteration 3 Error: 0.088827 Iteration 4 Error: 0.033638 Align patch 6 19 left Iteration 1 Error: 0.529148 Iteration 2 Error: 0.158531 Iteration 3 Error: 0.064839 Iteration 4 Error: 0.029815 Align patch 7 18 left Iteration 1 Error: 0.679364 Iteration 2 Error: 0.143750 Iteration 3 Error: 0.056896 Iteration 4 Error: 0.031149 Align patch 8 17 left Iteration 1 Error: 0.767100 Iteration 2 Error: 0.160095 Iteration 3 Error: 0.053602 Iteration 4 Error: 0.027530 Align patch 9 16 left Iteration 1 Error: 1.013386 Iteration 2 Error: 0.177734 Iteration 3 Error: 0.019840 Align patch 10 15 left Iteration 1 Error: 0.794240 Iteration 2 Error: 0.152568 Iteration 3 Error: 0.051963 Iteration 4 Error: 0.021822 Align patch 11 14 left Iteration 1 Error: 0.715207 Iteration 2 Error: 0.213664 Iteration 3 Error: 0.058419 Iteration 4 Error: 0.019965 Align patch 12 13 left Iteration 1 Error: 1.002199 Iteration 2 Error: 0.139394 Iteration 3 Error: 0.041470 Align patch 13 12 left Iteration 1 Error: 0.673097 Iteration 2 Error: 0.107523 Iteration 3 Error: 0.028286 Align patch 14 11 left Iteration 1 Error: 0.756704 Iteration 2 Error: 0.183417 Iteration 3 Error: 0.031214 Align patch 15 10 left Iteration 1 Error: 0.747951 Iteration 2 Error: 0.173276 Iteration 3 Error: 0.042427 Align patch 16 9 left Iteration 1 Error: 0.679438 Iteration 2 Error: 0.082238 Iteration 3 Error: 0.025376 Align patch 17 8 left Iteration 1 Error: 0.948334 Iteration 2 Error: 0.132636 Iteration 3 Error: 0.050040 Iteration 4 Error: 0.016845 Align patch 18 7 left Iteration 1 Error: 0.708074 Iteration 2 Error: 0.181679 Iteration 3 Error: 0.070130 Iteration 4 Error: 0.037403 Align patch 19 6 left Iteration 1 Error: 0.951064 Iteration 2 Error: 0.131757 Iteration 3 Error: 0.022720 Align patch 20 5 left Iteration 1 Error: 0.589912 Iteration 2 Error: 0.207592 Iteration 3 Error: 0.046869 Align patch 21 4 left Iteration 1 Error: 0.589318 Iteration 2 Error: 0.139208 Iteration 3 Error: 0.043420 Align patch 22 3 left Iteration 1 Error: 1.420428 Iteration 2 Error: 0.266372 Iteration 3 Error: 0.062701 Iteration 4 Error: 0.028076 Align patch 23 2 left Iteration 1 Error: 1.377812 Iteration 2 Error: 0.252562 Iteration 3 Error: 0.060475 Iteration 4 Error: 0.021819 Align patch 24 1 left Iteration 1 Error: 0.846584 Iteration 2 Error: 0.258005 Iteration 3 Error: 0.069337 Iteration 4 Error: 0.026069 Align patch 25 0 left Iteration 1 Error: 0.959905 Iteration 2 Error: 0.189729 Iteration 3 Error: 0.040319 3D Fitting completed. Patch alignment time: 11.92(sec) Local motion has been corrected. Process thread exits. Computational time: 24.712688 sec Total time: 36.889538 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00027hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00027hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.716141s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00027hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.683632s ........................................ >>>>>>TIME<<<<<< FFT: 1.056324s Defocus_U Defocus_V Angle CCC 20685.55 21435.55 5.68 0.034048 Final Values Defocus_U Defocus_V Angle CCC 20701.17 21448.06 5.06 0.051623 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00027hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00027hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.999e-02 CC threshold: 0.734 Mean Std: 37.30 6.48 Num Hot pixels: 184 Hot pixel threshold: 76.19 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.363034 Iteration 2 Error: 0.256904 Iteration 3 Error: 0.066092 Iteration 4 Error: 0.014558 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.03 -0.21 ...... Frame ( 3) shift: 0.06 -0.41 ...... Frame ( 4) shift: 0.10 -0.62 ...... Frame ( 5) shift: 0.13 -0.83 ...... Frame ( 6) shift: 0.17 -0.92 ...... Frame ( 7) shift: 0.23 -0.90 ...... Frame ( 8) shift: 0.29 -0.88 ...... Frame ( 9) shift: 0.38 -0.84 ...... Frame ( 10) shift: 0.48 -0.78 ...... Frame ( 11) shift: 0.58 -0.73 ...... Frame ( 12) shift: 0.68 -0.64 ...... Frame ( 13) shift: 0.77 -0.53 ...... Frame ( 14) shift: 0.86 -0.41 ...... Frame ( 15) shift: 0.97 -0.30 ...... Frame ( 16) shift: 1.10 -0.19 ...... Frame ( 17) shift: 1.22 -0.08 ...... Frame ( 18) shift: 1.37 0.02 ...... Frame ( 19) shift: 1.55 0.13 ...... Frame ( 20) shift: 1.72 0.23 ...... Frame ( 21) shift: 1.80 0.33 ...... Frame ( 22) shift: 1.80 0.41 ...... Frame ( 23) shift: 1.80 0.50 ...... Frame ( 24) shift: 1.85 0.54 ...... Frame ( 25) shift: 1.95 0.54 ...... Frame ( 26) shift: 2.06 0.53 ...... Frame ( 27) shift: 2.10 0.55 ...... Frame ( 28) shift: 2.08 0.60 ...... Frame ( 29) shift: 2.06 0.64 ...... Frame ( 30) shift: 2.08 0.70 ...... Frame ( 31) shift: 2.15 0.79 ...... Frame ( 32) shift: 2.22 0.88 ...... Frame ( 33) shift: 2.28 0.90 ...... Frame ( 34) shift: 2.32 0.86 ...... Frame ( 35) shift: 2.35 0.83 ...... Frame ( 36) shift: 2.41 0.81 ...... Frame ( 37) shift: 2.48 0.82 ...... Frame ( 38) shift: 2.55 0.83 ...... Frame ( 39) shift: 2.62 0.84 ...... Frame ( 40) shift: 2.69 0.85 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.918638 Iteration 2 Error: 0.321090 Iteration 3 Error: 0.085934 Iteration 4 Error: 0.041980 Align patch 2 23 left Iteration 1 Error: 0.923906 Iteration 2 Error: 0.262325 Iteration 3 Error: 0.058132 Iteration 4 Error: 0.014561 Align patch 3 22 left Iteration 1 Error: 0.935739 Iteration 2 Error: 0.144052 Iteration 3 Error: 0.040556 Align patch 4 21 left Iteration 1 Error: 0.726552 Iteration 2 Error: 0.124361 Iteration 3 Error: 0.034999 Align patch 5 20 left Iteration 1 Error: 1.556554 Iteration 2 Error: 0.271321 Iteration 3 Error: 0.085923 Iteration 4 Error: 0.025456 Align patch 6 19 left Iteration 1 Error: 0.888538 Iteration 2 Error: 0.256790 Iteration 3 Error: 0.070882 Iteration 4 Error: 0.031995 Align patch 7 18 left Iteration 1 Error: 0.815289 Iteration 2 Error: 0.143958 Iteration 3 Error: 0.024825 Align patch 8 17 left Iteration 1 Error: 0.603441 Iteration 2 Error: 0.120337 Iteration 3 Error: 0.038852 Align patch 9 16 left Iteration 1 Error: 0.713970 Iteration 2 Error: 0.135986 Iteration 3 Error: 0.035915 Align patch 10 15 left Iteration 1 Error: 0.594837 Iteration 2 Error: 0.128239 Iteration 3 Error: 0.039399 Align patch 11 14 left Iteration 1 Error: 0.655016 Iteration 2 Error: 0.121906 Iteration 3 Error: 0.034593 Align patch 12 13 left Iteration 1 Error: 0.523185 Iteration 2 Error: 0.114478 Iteration 3 Error: 0.033215 Align patch 13 12 left Iteration 1 Error: 0.992886 Iteration 2 Error: 0.130833 Iteration 3 Error: 0.025627 Align patch 14 11 left Iteration 1 Error: 0.913469 Iteration 2 Error: 0.198320 Iteration 3 Error: 0.065573 Iteration 4 Error: 0.016522 Align patch 15 10 left Iteration 1 Error: 0.884951 Iteration 2 Error: 0.160731 Iteration 3 Error: 0.073731 Iteration 4 Error: 0.027475 Align patch 16 9 left Iteration 1 Error: 0.833887 Iteration 2 Error: 0.160456 Iteration 3 Error: 0.035117 Align patch 17 8 left Iteration 1 Error: 0.738631 Iteration 2 Error: 0.099679 Iteration 3 Error: 0.043355 Align patch 18 7 left Iteration 1 Error: 0.838270 Iteration 2 Error: 0.165099 Iteration 3 Error: 0.041822 Align patch 19 6 left Iteration 1 Error: 0.661544 Iteration 2 Error: 0.115010 Iteration 3 Error: 0.032677 Align patch 20 5 left Iteration 1 Error: 0.966146 Iteration 2 Error: 0.148184 Iteration 3 Error: 0.066903 Iteration 4 Error: 0.015235 Align patch 21 4 left Iteration 1 Error: 0.799169 Iteration 2 Error: 0.171648 Iteration 3 Error: 0.044330 Align patch 22 3 left Iteration 1 Error: 0.957589 Iteration 2 Error: 0.071921 Iteration 3 Error: 0.018405 Align patch 23 2 left Iteration 1 Error: 0.715277 Iteration 2 Error: 0.172872 Iteration 3 Error: 0.037153 Align patch 24 1 left Iteration 1 Error: 0.993783 Iteration 2 Error: 0.213651 Iteration 3 Error: 0.063214 Iteration 4 Error: 0.016026 Align patch 25 0 left Iteration 1 Error: 0.791115 Iteration 2 Error: 0.159201 Iteration 3 Error: 0.033296 3D Fitting completed. Patch alignment time: 12.19(sec) Local motion has been corrected. Process thread exits. Computational time: 20.897789 sec Total time: 28.391615 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00027hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00027hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.796807s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00027hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.342239s ........................................ >>>>>>TIME<<<<<< FFT: 0.998898s Defocus_U Defocus_V Angle CCC 20064.48 20752.00 17.44 0.026635 Final Values Defocus_U Defocus_V Angle CCC 20047.20 20750.58 23.77 0.038595 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00027hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00027hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.999e-02 CC threshold: 0.734 Mean Std: 39.34 6.65 Num Hot pixels: 209 Hot pixel threshold: 79.26 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.779746 Iteration 2 Error: 0.353526 Iteration 3 Error: 0.081209 Iteration 4 Error: 0.029988 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.09 -0.03 ...... Frame ( 3) shift: -0.19 -0.06 ...... Frame ( 4) shift: -0.28 -0.09 ...... Frame ( 5) shift: -0.37 -0.12 ...... Frame ( 6) shift: -0.41 -0.12 ...... Frame ( 7) shift: -0.38 -0.09 ...... Frame ( 8) shift: -0.35 -0.06 ...... Frame ( 9) shift: -0.23 0.01 ...... Frame ( 10) shift: -0.00 0.13 ...... Frame ( 11) shift: 0.22 0.25 ...... Frame ( 12) shift: 0.43 0.37 ...... Frame ( 13) shift: 0.64 0.50 ...... Frame ( 14) shift: 0.84 0.63 ...... Frame ( 15) shift: 0.99 0.77 ...... Frame ( 16) shift: 1.09 0.93 ...... Frame ( 17) shift: 1.19 1.09 ...... Frame ( 18) shift: 1.27 1.20 ...... Frame ( 19) shift: 1.35 1.28 ...... Frame ( 20) shift: 1.43 1.36 ...... Frame ( 21) shift: 1.54 1.42 ...... Frame ( 22) shift: 1.68 1.46 ...... Frame ( 23) shift: 1.82 1.50 ...... Frame ( 24) shift: 1.89 1.55 ...... Frame ( 25) shift: 1.89 1.60 ...... Frame ( 26) shift: 1.88 1.65 ...... Frame ( 27) shift: 1.90 1.70 ...... Frame ( 28) shift: 1.94 1.75 ...... Frame ( 29) shift: 1.98 1.80 ...... Frame ( 30) shift: 2.02 1.87 ...... Frame ( 31) shift: 2.05 1.95 ...... Frame ( 32) shift: 2.08 2.04 ...... Frame ( 33) shift: 2.09 2.13 ...... Frame ( 34) shift: 2.09 2.22 ...... Frame ( 35) shift: 2.08 2.32 ...... Frame ( 36) shift: 2.13 2.38 ...... Frame ( 37) shift: 2.22 2.42 ...... Frame ( 38) shift: 2.31 2.45 ...... Frame ( 39) shift: 2.40 2.49 ...... Frame ( 40) shift: 2.50 2.52 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.748683 Iteration 2 Error: 0.143402 Iteration 3 Error: 0.055254 Iteration 4 Error: 0.030461 Align patch 2 23 left Iteration 1 Error: 1.129620 Iteration 2 Error: 0.313503 Iteration 3 Error: 0.107578 Iteration 4 Error: 0.034979 Align patch 3 22 left Iteration 1 Error: 0.794982 Iteration 2 Error: 0.157395 Iteration 3 Error: 0.056961 Iteration 4 Error: 0.020337 Align patch 4 21 left Iteration 1 Error: 1.305348 Iteration 2 Error: 0.324732 Iteration 3 Error: 0.068904 Iteration 4 Error: 0.035840 Align patch 5 20 left Iteration 1 Error: 0.526715 Iteration 2 Error: 0.128135 Iteration 3 Error: 0.052351 Iteration 4 Error: 0.023223 Align patch 6 19 left Iteration 1 Error: 0.991844 Iteration 2 Error: 0.127408 Iteration 3 Error: 0.038641 Align patch 7 18 left Iteration 1 Error: 0.987095 Iteration 2 Error: 0.130579 Iteration 3 Error: 0.019899 Align patch 8 17 left Iteration 1 Error: 0.617813 Iteration 2 Error: 0.199388 Iteration 3 Error: 0.099657 Iteration 4 Error: 0.050662 Iteration 5 Error: 0.022650 Align patch 9 16 left Iteration 1 Error: 0.918489 Iteration 2 Error: 0.145944 Iteration 3 Error: 0.031483 Align patch 10 15 left Iteration 1 Error: 0.678725 Iteration 2 Error: 0.111716 Iteration 3 Error: 0.029305 Align patch 11 14 left Iteration 1 Error: 0.640645 Iteration 2 Error: 0.111976 Iteration 3 Error: 0.027799 Align patch 12 13 left Iteration 1 Error: 0.686738 Iteration 2 Error: 0.123885 Iteration 3 Error: 0.036121 Align patch 13 12 left Iteration 1 Error: 0.609910 Iteration 2 Error: 0.133610 Iteration 3 Error: 0.053809 Iteration 4 Error: 0.019025 Align patch 14 11 left Iteration 1 Error: 0.858095 Iteration 2 Error: 0.121069 Iteration 3 Error: 0.034339 Align patch 15 10 left Iteration 1 Error: 1.086734 Iteration 2 Error: 0.172297 Iteration 3 Error: 0.041233 Align patch 16 9 left Iteration 1 Error: 0.520016 Iteration 2 Error: 0.054063 Iteration 3 Error: 0.012826 Align patch 17 8 left Iteration 1 Error: 0.712143 Iteration 2 Error: 0.152575 Iteration 3 Error: 0.023525 Align patch 18 7 left Iteration 1 Error: 0.832677 Iteration 2 Error: 0.148907 Iteration 3 Error: 0.046666 Align patch 19 6 left Iteration 1 Error: 0.665629 Iteration 2 Error: 0.246463 Iteration 3 Error: 0.133585 Iteration 4 Error: 0.061980 Iteration 5 Error: 0.029627 Align patch 20 5 left Iteration 1 Error: 0.752573 Iteration 2 Error: 0.168983 Iteration 3 Error: 0.054294 Iteration 4 Error: 0.013446 Align patch 21 4 left Iteration 1 Error: 0.729441 Iteration 2 Error: 0.138719 Iteration 3 Error: 0.052209 Iteration 4 Error: 0.027279 Align patch 22 3 left Iteration 1 Error: 0.813993 Iteration 2 Error: 0.152449 Iteration 3 Error: 0.053448 Iteration 4 Error: 0.019434 Align patch 23 2 left Iteration 1 Error: 0.612666 Iteration 2 Error: 0.102853 Iteration 3 Error: 0.031898 Align patch 24 1 left Iteration 1 Error: 0.847267 Iteration 2 Error: 0.178103 Iteration 3 Error: 0.043936 Align patch 25 0 left Iteration 1 Error: 0.696231 Iteration 2 Error: 0.170202 Iteration 3 Error: 0.061837 Iteration 4 Error: 0.024677 3D Fitting completed. Patch alignment time: 11.79(sec) Local motion has been corrected. Process thread exits. Computational time: 21.927008 sec Total time: 28.708138 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00027hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00027hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.660124s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00027hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.297855s ........................................ >>>>>>TIME<<<<<< FFT: 0.951018s Defocus_U Defocus_V Angle CCC 17820.33 18332.05 0.64 0.029957 Final Values Defocus_U Defocus_V Angle CCC 17817.21 18322.68 1.90 0.048424 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00027hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00027hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.995e-02 CC threshold: 0.734 Mean Std: 38.21 6.57 Num Hot pixels: 199 Hot pixel threshold: 77.63 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.183058 Iteration 2 Error: 0.209023 Iteration 3 Error: 0.046336 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.08 -0.17 ...... Frame ( 3) shift: -0.17 -0.33 ...... Frame ( 4) shift: -0.25 -0.50 ...... Frame ( 5) shift: -0.34 -0.67 ...... Frame ( 6) shift: -0.39 -0.75 ...... Frame ( 7) shift: -0.41 -0.74 ...... Frame ( 8) shift: -0.42 -0.72 ...... Frame ( 9) shift: -0.39 -0.64 ...... Frame ( 10) shift: -0.33 -0.50 ...... Frame ( 11) shift: -0.26 -0.35 ...... Frame ( 12) shift: -0.17 -0.25 ...... Frame ( 13) shift: -0.08 -0.18 ...... Frame ( 14) shift: 0.02 -0.11 ...... Frame ( 15) shift: 0.08 0.00 ...... Frame ( 16) shift: 0.10 0.15 ...... Frame ( 17) shift: 0.13 0.31 ...... Frame ( 18) shift: 0.17 0.42 ...... Frame ( 19) shift: 0.24 0.49 ...... Frame ( 20) shift: 0.30 0.56 ...... Frame ( 21) shift: 0.39 0.60 ...... Frame ( 22) shift: 0.49 0.62 ...... Frame ( 23) shift: 0.60 0.63 ...... Frame ( 24) shift: 0.63 0.70 ...... Frame ( 25) shift: 0.59 0.81 ...... Frame ( 26) shift: 0.55 0.92 ...... Frame ( 27) shift: 0.58 1.00 ...... Frame ( 28) shift: 0.69 1.07 ...... Frame ( 29) shift: 0.80 1.14 ...... Frame ( 30) shift: 0.85 1.13 ...... Frame ( 31) shift: 0.85 1.05 ...... Frame ( 32) shift: 0.84 0.98 ...... Frame ( 33) shift: 0.86 1.00 ...... Frame ( 34) shift: 0.91 1.12 ...... Frame ( 35) shift: 0.96 1.25 ...... Frame ( 36) shift: 0.98 1.32 ...... Frame ( 37) shift: 0.99 1.33 ...... Frame ( 38) shift: 1.00 1.34 ...... Frame ( 39) shift: 1.01 1.35 ...... Frame ( 40) shift: 1.02 1.35 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.086510 Iteration 2 Error: 0.159513 Iteration 3 Error: 0.075198 Iteration 4 Error: 0.021175 Align patch 2 23 left Iteration 1 Error: 1.195275 Iteration 2 Error: 0.224161 Iteration 3 Error: 0.063141 Iteration 4 Error: 0.031531 Align patch 3 22 left Iteration 1 Error: 0.908708 Iteration 2 Error: 0.133750 Iteration 3 Error: 0.054857 Iteration 4 Error: 0.024932 Align patch 4 21 left Iteration 1 Error: 0.890443 Iteration 2 Error: 0.144364 Iteration 3 Error: 0.033779 Align patch 5 20 left Iteration 1 Error: 0.747269 Iteration 2 Error: 0.119592 Iteration 3 Error: 0.040977 Align patch 6 19 left Iteration 1 Error: 0.687206 Iteration 2 Error: 0.108525 Iteration 3 Error: 0.028910 Align patch 7 18 left Iteration 1 Error: 0.560214 Iteration 2 Error: 0.133267 Iteration 3 Error: 0.040552 Align patch 8 17 left Iteration 1 Error: 0.777330 Iteration 2 Error: 0.171685 Iteration 3 Error: 0.057023 Iteration 4 Error: 0.019501 Align patch 9 16 left Iteration 1 Error: 0.690442 Iteration 2 Error: 0.135512 Iteration 3 Error: 0.043726 Align patch 10 15 left Iteration 1 Error: 0.796740 Iteration 2 Error: 0.095345 Iteration 3 Error: 0.044713 Align patch 11 14 left Iteration 1 Error: 1.033931 Iteration 2 Error: 0.211269 Iteration 3 Error: 0.059926 Iteration 4 Error: 0.017740 Align patch 12 13 left Iteration 1 Error: 0.781084 Iteration 2 Error: 0.149214 Iteration 3 Error: 0.037106 Align patch 13 12 left Iteration 1 Error: 0.782027 Iteration 2 Error: 0.140684 Iteration 3 Error: 0.030111 Align patch 14 11 left Iteration 1 Error: 0.716133 Iteration 2 Error: 0.112415 Iteration 3 Error: 0.025545 Align patch 15 10 left Iteration 1 Error: 0.917684 Iteration 2 Error: 0.175201 Iteration 3 Error: 0.067331 Iteration 4 Error: 0.023879 Align patch 16 9 left Iteration 1 Error: 0.887044 Iteration 2 Error: 0.131136 Iteration 3 Error: 0.058848 Iteration 4 Error: 0.013342 Align patch 17 8 left Iteration 1 Error: 0.848816 Iteration 2 Error: 0.126423 Iteration 3 Error: 0.031316 Align patch 18 7 left Iteration 1 Error: 0.580373 Iteration 2 Error: 0.105526 Iteration 3 Error: 0.021692 Align patch 19 6 left Iteration 1 Error: 0.674914 Iteration 2 Error: 0.165389 Iteration 3 Error: 0.063837 Iteration 4 Error: 0.028587 Align patch 20 5 left Iteration 1 Error: 0.643789 Iteration 2 Error: 0.101378 Iteration 3 Error: 0.025777 Align patch 21 4 left Iteration 1 Error: 0.846789 Iteration 2 Error: 0.121296 Iteration 3 Error: 0.029433 Align patch 22 3 left Iteration 1 Error: 0.853131 Iteration 2 Error: 0.147337 Iteration 3 Error: 0.039839 Align patch 23 2 left Iteration 1 Error: 1.257013 Iteration 2 Error: 0.135008 Iteration 3 Error: 0.021266 Align patch 24 1 left Iteration 1 Error: 0.606655 Iteration 2 Error: 0.125638 Iteration 3 Error: 0.027098 Align patch 25 0 left Iteration 1 Error: 0.906631 Iteration 2 Error: 0.136915 Iteration 3 Error: 0.043493 3D Fitting completed. Patch alignment time: 10.86(sec) Local motion has been corrected. Process thread exits. Computational time: 22.983421 sec Total time: 30.798950 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00027hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00027hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.700642s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00027hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 4.174245s ........................................ >>>>>>TIME<<<<<< FFT: 1.085125s Defocus_U Defocus_V Angle CCC 21906.07 22664.33 3.12 0.031252 Final Values Defocus_U Defocus_V Angle CCC 21945.18 22490.98 1.56 0.046577 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00028hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00028hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.734 Mean Std: 41.90 6.89 Num Hot pixels: 194 Hot pixel threshold: 83.25 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.145788 Iteration 2 Error: 0.234118 Iteration 3 Error: 0.059369 Iteration 4 Error: 0.016585 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.02 -0.28 ...... Frame ( 3) shift: 0.04 -0.55 ...... Frame ( 4) shift: 0.06 -0.83 ...... Frame ( 5) shift: 0.08 -1.10 ...... Frame ( 6) shift: 0.13 -1.23 ...... Frame ( 7) shift: 0.20 -1.20 ...... Frame ( 8) shift: 0.28 -1.18 ...... Frame ( 9) shift: 0.33 -1.08 ...... Frame ( 10) shift: 0.35 -0.92 ...... Frame ( 11) shift: 0.37 -0.76 ...... Frame ( 12) shift: 0.37 -0.66 ...... Frame ( 13) shift: 0.36 -0.63 ...... Frame ( 14) shift: 0.34 -0.59 ...... Frame ( 15) shift: 0.34 -0.51 ...... Frame ( 16) shift: 0.36 -0.40 ...... Frame ( 17) shift: 0.38 -0.28 ...... Frame ( 18) shift: 0.43 -0.19 ...... Frame ( 19) shift: 0.50 -0.12 ...... Frame ( 20) shift: 0.57 -0.05 ...... Frame ( 21) shift: 0.66 0.01 ...... Frame ( 22) shift: 0.75 0.06 ...... Frame ( 23) shift: 0.85 0.11 ...... Frame ( 24) shift: 0.96 0.18 ...... Frame ( 25) shift: 1.09 0.27 ...... Frame ( 26) shift: 1.21 0.36 ...... Frame ( 27) shift: 1.27 0.42 ...... Frame ( 28) shift: 1.27 0.45 ...... Frame ( 29) shift: 1.26 0.47 ...... Frame ( 30) shift: 1.28 0.55 ...... Frame ( 31) shift: 1.34 0.66 ...... Frame ( 32) shift: 1.39 0.78 ...... Frame ( 33) shift: 1.45 0.85 ...... Frame ( 34) shift: 1.52 0.86 ...... Frame ( 35) shift: 1.59 0.88 ...... Frame ( 36) shift: 1.63 0.90 ...... Frame ( 37) shift: 1.62 0.92 ...... Frame ( 38) shift: 1.62 0.94 ...... Frame ( 39) shift: 1.62 0.96 ...... Frame ( 40) shift: 1.62 0.99 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.231256 Iteration 2 Error: 0.111171 Iteration 3 Error: 0.029119 Align patch 2 23 left Iteration 1 Error: 0.686379 Iteration 2 Error: 0.151087 Iteration 3 Error: 0.035181 Align patch 3 22 left Iteration 1 Error: 0.788630 Iteration 2 Error: 0.249188 Iteration 3 Error: 0.048678 Align patch 4 21 left Iteration 1 Error: 0.787558 Iteration 2 Error: 0.095705 Iteration 3 Error: 0.020477 Align patch 5 20 left Iteration 1 Error: 1.550545 Iteration 2 Error: 0.172414 Iteration 3 Error: 0.052681 Iteration 4 Error: 0.022539 Align patch 6 19 left Iteration 1 Error: 0.714722 Iteration 2 Error: 0.122191 Iteration 3 Error: 0.046731 Align patch 7 18 left Iteration 1 Error: 0.730365 Iteration 2 Error: 0.144790 Iteration 3 Error: 0.082547 Iteration 4 Error: 0.029539 Align patch 8 17 left Iteration 1 Error: 0.928757 Iteration 2 Error: 0.131171 Iteration 3 Error: 0.066792 Iteration 4 Error: 0.028068 Align patch 9 16 left Iteration 1 Error: 0.589577 Iteration 2 Error: 0.135339 Iteration 3 Error: 0.029522 Align patch 10 15 left Iteration 1 Error: 1.489633 Iteration 2 Error: 0.227907 Iteration 3 Error: 0.033700 Align patch 11 14 left Iteration 1 Error: 0.490538 Iteration 2 Error: 0.063287 Iteration 3 Error: 0.022752 Align patch 12 13 left Iteration 1 Error: 1.052000 Iteration 2 Error: 0.170061 Iteration 3 Error: 0.053033 Iteration 4 Error: 0.021181 Align patch 13 12 left Iteration 1 Error: 0.741563 Iteration 2 Error: 0.153148 Iteration 3 Error: 0.032969 Align patch 14 11 left Iteration 1 Error: 0.677719 Iteration 2 Error: 0.183776 Iteration 3 Error: 0.045314 Align patch 15 10 left Iteration 1 Error: 0.658518 Iteration 2 Error: 0.180373 Iteration 3 Error: 0.065751 Iteration 4 Error: 0.020929 Align patch 16 9 left Iteration 1 Error: 1.127316 Iteration 2 Error: 0.169832 Iteration 3 Error: 0.033166 Align patch 17 8 left Iteration 1 Error: 0.644666 Iteration 2 Error: 0.148907 Iteration 3 Error: 0.031845 Align patch 18 7 left Iteration 1 Error: 0.623513 Iteration 2 Error: 0.161120 Iteration 3 Error: 0.047332 Align patch 19 6 left Iteration 1 Error: 0.777836 Iteration 2 Error: 0.123423 Iteration 3 Error: 0.033417 Align patch 20 5 left Iteration 1 Error: 1.101426 Iteration 2 Error: 0.130148 Iteration 3 Error: 0.037292 Align patch 21 4 left Iteration 1 Error: 0.956304 Iteration 2 Error: 0.110540 Iteration 3 Error: 0.023836 Align patch 22 3 left Iteration 1 Error: 0.739609 Iteration 2 Error: 0.154524 Iteration 3 Error: 0.029012 Align patch 23 2 left Iteration 1 Error: 0.657217 Iteration 2 Error: 0.145546 Iteration 3 Error: 0.041711 Align patch 24 1 left Iteration 1 Error: 0.849917 Iteration 2 Error: 0.161141 Iteration 3 Error: 0.027680 Align patch 25 0 left Iteration 1 Error: 0.971679 Iteration 2 Error: 0.193040 Iteration 3 Error: 0.056254 Iteration 4 Error: 0.016867 3D Fitting completed. Patch alignment time: 12.78(sec) Local motion has been corrected. Process thread exits. Computational time: 26.242428 sec Total time: 33.564487 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00028hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00028hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.619868s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00028hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.525767s ........................................ >>>>>>TIME<<<<<< FFT: 1.130495s Defocus_U Defocus_V Angle CCC 19306.64 20126.98 9.52 0.039834 Final Values Defocus_U Defocus_V Angle CCC 19314.48 20128.57 9.52 0.069723 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00028hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00028hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.994e-02 CC threshold: 0.734 Mean Std: 42.14 6.92 Num Hot pixels: 199 Hot pixel threshold: 83.63 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.229346 Iteration 2 Error: 0.274641 Iteration 3 Error: 0.082519 Iteration 4 Error: 0.024913 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.20 -0.19 ...... Frame ( 3) shift: 0.41 -0.39 ...... Frame ( 4) shift: 0.61 -0.58 ...... Frame ( 5) shift: 0.81 -0.77 ...... Frame ( 6) shift: 0.96 -0.83 ...... Frame ( 7) shift: 1.04 -0.74 ...... Frame ( 8) shift: 1.13 -0.66 ...... Frame ( 9) shift: 1.17 -0.55 ...... Frame ( 10) shift: 1.15 -0.41 ...... Frame ( 11) shift: 1.14 -0.27 ...... Frame ( 12) shift: 1.17 -0.14 ...... Frame ( 13) shift: 1.25 -0.00 ...... Frame ( 14) shift: 1.33 0.13 ...... Frame ( 15) shift: 1.37 0.23 ...... Frame ( 16) shift: 1.38 0.30 ...... Frame ( 17) shift: 1.39 0.37 ...... Frame ( 18) shift: 1.38 0.44 ...... Frame ( 19) shift: 1.37 0.50 ...... Frame ( 20) shift: 1.36 0.57 ...... Frame ( 21) shift: 1.39 0.62 ...... Frame ( 22) shift: 1.46 0.67 ...... Frame ( 23) shift: 1.53 0.71 ...... Frame ( 24) shift: 1.60 0.76 ...... Frame ( 25) shift: 1.67 0.83 ...... Frame ( 26) shift: 1.74 0.90 ...... Frame ( 27) shift: 1.82 0.98 ...... Frame ( 28) shift: 1.90 1.08 ...... Frame ( 29) shift: 1.98 1.17 ...... Frame ( 30) shift: 2.05 1.24 ...... Frame ( 31) shift: 2.09 1.28 ...... Frame ( 32) shift: 2.14 1.33 ...... Frame ( 33) shift: 2.16 1.39 ...... Frame ( 34) shift: 2.13 1.49 ...... Frame ( 35) shift: 2.11 1.58 ...... Frame ( 36) shift: 2.12 1.64 ...... Frame ( 37) shift: 2.16 1.67 ...... Frame ( 38) shift: 2.20 1.69 ...... Frame ( 39) shift: 2.24 1.72 ...... Frame ( 40) shift: 2.28 1.74 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.611145 Iteration 2 Error: 0.342973 Iteration 3 Error: 0.072400 Iteration 4 Error: 0.033526 Align patch 2 23 left Iteration 1 Error: 0.929359 Iteration 2 Error: 0.335068 Iteration 3 Error: 0.143617 Iteration 4 Error: 0.063520 Iteration 5 Error: 0.026791 Align patch 3 22 left Iteration 1 Error: 1.167894 Iteration 2 Error: 0.181963 Iteration 3 Error: 0.041758 Align patch 4 21 left Iteration 1 Error: 0.780970 Iteration 2 Error: 0.105844 Iteration 3 Error: 0.030036 Align patch 5 20 left Iteration 1 Error: 0.838300 Iteration 2 Error: 0.136340 Iteration 3 Error: 0.078176 Iteration 4 Error: 0.037357 Align patch 6 19 left Iteration 1 Error: 1.265354 Iteration 2 Error: 0.339535 Iteration 3 Error: 0.185097 Iteration 4 Error: 0.081127 Iteration 5 Error: 0.065174 Align patch 6 19 left Iteration 1 Error: 1.117991 Iteration 2 Error: 0.186711 Iteration 3 Error: 0.029868 Align patch 7 18 left Iteration 1 Error: 0.920985 Iteration 2 Error: 0.263924 Iteration 3 Error: 0.090634 Iteration 4 Error: 0.035802 Align patch 8 17 left Iteration 1 Error: 0.757579 Iteration 2 Error: 0.175702 Iteration 3 Error: 0.069829 Iteration 4 Error: 0.033512 Align patch 9 16 left Iteration 1 Error: 0.904549 Iteration 2 Error: 0.223131 Iteration 3 Error: 0.056288 Iteration 4 Error: 0.045377 Align patch 10 15 left Iteration 1 Error: 0.747808 Iteration 2 Error: 0.135520 Iteration 3 Error: 0.035601 Align patch 11 14 left Iteration 1 Error: 0.819571 Iteration 2 Error: 0.108330 Iteration 3 Error: 0.025561 Align patch 12 13 left Iteration 1 Error: 0.486531 Iteration 2 Error: 0.070476 Iteration 3 Error: 0.018591 Align patch 13 12 left Iteration 1 Error: 0.703859 Iteration 2 Error: 0.229715 Iteration 3 Error: 0.068902 Iteration 4 Error: 0.025260 Align patch 14 11 left Iteration 1 Error: 0.642101 Iteration 2 Error: 0.123069 Iteration 3 Error: 0.042153 Align patch 15 10 left Iteration 1 Error: 0.907879 Iteration 2 Error: 0.195934 Iteration 3 Error: 0.068507 Iteration 4 Error: 0.018438 Align patch 16 9 left Iteration 1 Error: 0.983810 Iteration 2 Error: 0.127665 Iteration 3 Error: 0.034717 Align patch 17 8 left Iteration 1 Error: 0.767382 Iteration 2 Error: 0.108363 Iteration 3 Error: 0.032337 Align patch 18 7 left Iteration 1 Error: 0.807471 Iteration 2 Error: 0.118595 Iteration 3 Error: 0.039220 Align patch 19 6 left Iteration 1 Error: 0.731071 Iteration 2 Error: 0.110436 Iteration 3 Error: 0.046440 Align patch 20 5 left Iteration 1 Error: 0.798068 Iteration 2 Error: 0.135786 Iteration 3 Error: 0.025174 Align patch 21 4 left Iteration 1 Error: 0.897155 Iteration 2 Error: 0.182141 Iteration 3 Error: 0.069177 Iteration 4 Error: 0.026265 Align patch 22 3 left Iteration 1 Error: 0.802977 Iteration 2 Error: 0.126010 Iteration 3 Error: 0.050838 Iteration 4 Error: 0.016244 Align patch 23 2 left Iteration 1 Error: 0.826005 Iteration 2 Error: 0.126296 Iteration 3 Error: 0.037448 Align patch 24 1 left Iteration 1 Error: 1.242136 Iteration 2 Error: 0.195917 Iteration 3 Error: 0.055152 Iteration 4 Error: 0.022420 Align patch 25 0 left Iteration 1 Error: 0.667960 Iteration 2 Error: 0.179854 Iteration 3 Error: 0.063951 Iteration 4 Error: 0.028295 3D Fitting completed. Patch alignment time: 17.30(sec) Local motion has been corrected. Process thread exits. Computational time: 32.726376 sec Total time: 43.751949 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00028hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00028hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.595264s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00028hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.024907s ........................................ >>>>>>TIME<<<<<< FFT: 1.049564s Defocus_U Defocus_V Angle CCC 17837.89 18740.23 6.78 0.038251 Final Values Defocus_U Defocus_V Angle CCC 17847.27 18743.36 6.78 0.068329 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00028hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00028hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.989e-02 CC threshold: 0.734 Mean Std: 40.71 8.46 Num Hot pixels: 105 Hot pixel threshold: 91.45 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.173762 Iteration 2 Error: 0.135577 Iteration 3 Error: 0.028412 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.04 -0.16 ...... Frame ( 3) shift: 0.08 -0.31 ...... Frame ( 4) shift: 0.12 -0.47 ...... Frame ( 5) shift: 0.17 -0.62 ...... Frame ( 6) shift: 0.16 -0.76 ...... Frame ( 7) shift: 0.10 -0.90 ...... Frame ( 8) shift: 0.04 -1.03 ...... Frame ( 9) shift: 0.04 -1.12 ...... Frame ( 10) shift: 0.10 -1.16 ...... Frame ( 11) shift: 0.15 -1.21 ...... Frame ( 12) shift: 0.19 -1.24 ...... Frame ( 13) shift: 0.20 -1.25 ...... Frame ( 14) shift: 0.22 -1.25 ...... Frame ( 15) shift: 0.23 -1.28 ...... Frame ( 16) shift: 0.23 -1.33 ...... Frame ( 17) shift: 0.23 -1.39 ...... Frame ( 18) shift: 0.23 -1.44 ...... Frame ( 19) shift: 0.23 -1.50 ...... Frame ( 20) shift: 0.23 -1.56 ...... Frame ( 21) shift: 0.22 -1.61 ...... Frame ( 22) shift: 0.20 -1.65 ...... Frame ( 23) shift: 0.18 -1.68 ...... Frame ( 24) shift: 0.19 -1.72 ...... Frame ( 25) shift: 0.21 -1.75 ...... Frame ( 26) shift: 0.24 -1.78 ...... Frame ( 27) shift: 0.23 -1.79 ...... Frame ( 28) shift: 0.21 -1.79 ...... Frame ( 29) shift: 0.18 -1.78 ...... Frame ( 30) shift: 0.17 -1.81 ...... Frame ( 31) shift: 0.17 -1.87 ...... Frame ( 32) shift: 0.18 -1.93 ...... Frame ( 33) shift: 0.16 -1.97 ...... Frame ( 34) shift: 0.12 -1.99 ...... Frame ( 35) shift: 0.08 -2.00 ...... Frame ( 36) shift: 0.07 -2.03 ...... Frame ( 37) shift: 0.08 -2.07 ...... Frame ( 38) shift: 0.09 -2.11 ...... Frame ( 39) shift: 0.10 -2.16 ...... Frame ( 40) shift: 0.11 -2.20 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.254388 Iteration 2 Error: 0.295693 Iteration 3 Error: 0.064907 Iteration 4 Error: 0.017702 Align patch 2 23 left Iteration 1 Error: 1.543289 Iteration 2 Error: 0.364677 Iteration 3 Error: 0.107224 Iteration 4 Error: 0.051135 Iteration 5 Error: 0.024573 Align patch 3 22 left Iteration 1 Error: 1.597346 Iteration 2 Error: 0.533446 Iteration 3 Error: 0.292627 Iteration 4 Error: 0.164981 Iteration 5 Error: 0.111302 Align patch 3 22 left Iteration 1 Error: 3.457108 Iteration 2 Error: 0.976069 Iteration 3 Error: 0.381518 Iteration 4 Error: 0.146931 Iteration 5 Error: 0.067081 Align patch 4 21 left Iteration 1 Error: 1.651781 Iteration 2 Error: 0.394177 Iteration 3 Error: 0.077060 Iteration 4 Error: 0.026771 Align patch 5 20 left Iteration 1 Error: 1.162313 Iteration 2 Error: 0.046843 Align patch 6 19 left Iteration 1 Error: 1.467454 Iteration 2 Error: 0.337870 Iteration 3 Error: 0.091263 Iteration 4 Error: 0.035365 Align patch 7 18 left Iteration 1 Error: 1.290102 Iteration 2 Error: 0.553843 Iteration 3 Error: 0.189227 Iteration 4 Error: 0.117980 Iteration 5 Error: 0.060425 Align patch 7 18 left Iteration 1 Error: 2.321217 Iteration 2 Error: 0.575876 Iteration 3 Error: 0.116517 Iteration 4 Error: 0.039666 Align patch 8 17 left Iteration 1 Error: 3.488997 Iteration 2 Error: 1.493169 Iteration 3 Error: 0.675199 Iteration 4 Error: 0.396947 Iteration 5 Error: 0.256127 Align patch 8 17 left Iteration 1 Error: 4.380682 Iteration 2 Error: 1.059819 Iteration 3 Error: 0.293059 Iteration 4 Error: 0.129814 Iteration 5 Error: 0.045730 Align patch 9 16 left Iteration 1 Error: 8.901732 Iteration 2 Error: 2.528142 Iteration 3 Error: 2.423799 Iteration 4 Error: 1.257426 Iteration 5 Error: 0.483080 Align patch 9 16 left Iteration 1 Error: 2.801831 Iteration 2 Error: 0.432084 Iteration 3 Error: 0.129797 Iteration 4 Error: 0.055993 Iteration 5 Error: 0.024978 Align patch 10 15 left Iteration 1 Error: 0.864066 Iteration 2 Error: 0.076905 Iteration 3 Error: 0.008121 Align patch 11 14 left Iteration 1 Error: 1.448936 Iteration 2 Error: 0.328700 Iteration 3 Error: 0.069829 Iteration 4 Error: 0.034558 Align patch 12 13 left Iteration 1 Error: 2.366530 Iteration 2 Error: 1.005090 Iteration 3 Error: 0.391294 Iteration 4 Error: 0.165240 Iteration 5 Error: 0.062253 Align patch 12 13 left Iteration 1 Error: 2.611662 Iteration 2 Error: 0.457642 Iteration 3 Error: 0.099084 Iteration 4 Error: 0.034813 Align patch 13 12 left Iteration 1 Error: 6.408396 Iteration 2 Error: 2.365615 Iteration 3 Error: 1.304670 Iteration 4 Error: 0.590737 Iteration 5 Error: 0.427369 Align patch 13 12 left Iteration 1 Error: 4.756301 Iteration 2 Error: 0.779682 Iteration 3 Error: 0.223657 Iteration 4 Error: 0.081097 Iteration 5 Error: 0.035321 Align patch 14 11 left Iteration 1 Error: 4.731301 Iteration 2 Error: 2.122469 Iteration 3 Error: 0.851164 Iteration 4 Error: 2.292713 Iteration 5 Error: 2.072364 Align patch 14 11 left Iteration 1 Error: 5.093234 Iteration 2 Error: 1.855836 Iteration 3 Error: 1.110720 Iteration 4 Error: 0.623518 Iteration 5 Error: 0.318430 Align patch 15 10 left Iteration 1 Error: 6.926558 Iteration 2 Error: 6.263445 Iteration 3 Error: 2.607321 Iteration 4 Error: 0.860610 Iteration 5 Error: 2.462892 Align patch 15 10 left Iteration 1 Error: 4.549474 Iteration 2 Error: 1.273893 Iteration 3 Error: 0.874296 Iteration 4 Error: 0.536351 Iteration 5 Error: 0.289598 Align patch 16 9 left Iteration 1 Error: 1.381419 Iteration 2 Error: 0.279022 Iteration 3 Error: 0.067158 Iteration 4 Error: 0.023757 Align patch 17 8 left Iteration 1 Error: 1.050612 Iteration 2 Error: 0.273904 Iteration 3 Error: 0.061286 Iteration 4 Error: 0.016958 Align patch 18 7 left Iteration 1 Error: 1.938724 Iteration 2 Error: 0.437917 Iteration 3 Error: 0.173282 Iteration 4 Error: 0.071539 Iteration 5 Error: 0.047314 Align patch 19 6 left Iteration 1 Error: 3.714620 Iteration 2 Error: 0.980555 Iteration 3 Error: 1.500686 Iteration 4 Error: 0.805090 Iteration 5 Error: 0.833266 Align patch 19 6 left Iteration 1 Error: 3.369538 Iteration 2 Error: 0.898915 Iteration 3 Error: 0.317456 Iteration 4 Error: 0.131245 Iteration 5 Error: 0.056953 Align patch 20 5 left Iteration 1 Error: 2.274040 Iteration 2 Error: 1.156140 Iteration 3 Error: 0.471716 Iteration 4 Error: 0.478117 Iteration 5 Error: 0.424353 Align patch 20 5 left Iteration 1 Error: 3.516954 Iteration 2 Error: 1.086496 Iteration 3 Error: 0.562762 Iteration 4 Error: 0.220491 Iteration 5 Error: 0.115599 Align patch 21 4 left Iteration 1 Error: 1.216074 Iteration 2 Error: 0.279935 Iteration 3 Error: 0.044112 Align patch 22 3 left Iteration 1 Error: 1.055970 Iteration 2 Error: 0.205880 Iteration 3 Error: 0.031263 Align patch 23 2 left Iteration 1 Error: 1.217177 Iteration 2 Error: 0.219685 Iteration 3 Error: 0.038830 Align patch 24 1 left Iteration 1 Error: 1.377691 Iteration 2 Error: 0.316129 Iteration 3 Error: 0.109419 Iteration 4 Error: 0.036191 Align patch 25 0 left Iteration 1 Error: 1.123726 Iteration 2 Error: 0.327630 Iteration 3 Error: 0.096600 Iteration 4 Error: 0.054194 Iteration 5 Error: 0.025828 3D Fitting completed. Patch alignment time: 28.16(sec) Local motion has been corrected. Process thread exits. Computational time: 42.060616 sec Total time: 49.526672 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00028hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00028hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.619062s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00028hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.794755s ........................................ >>>>>>TIME<<<<<< FFT: 0.988659s Defocus_U Defocus_V Angle CCC 16746.10 17328.14 0.59 0.032680 Final Values Defocus_U Defocus_V Angle CCC 16758.60 17328.14 0.28 0.061544 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00028hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00028hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 41.92 6.91 Num Hot pixels: 214 Hot pixel threshold: 83.36 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.201253 Iteration 2 Error: 0.289124 Iteration 3 Error: 0.066774 Iteration 4 Error: 0.016937 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.08 -0.16 ...... Frame ( 3) shift: 0.16 -0.33 ...... Frame ( 4) shift: 0.23 -0.49 ...... Frame ( 5) shift: 0.31 -0.65 ...... Frame ( 6) shift: 0.34 -0.70 ...... Frame ( 7) shift: 0.32 -0.64 ...... Frame ( 8) shift: 0.31 -0.58 ...... Frame ( 9) shift: 0.30 -0.50 ...... Frame ( 10) shift: 0.31 -0.40 ...... Frame ( 11) shift: 0.31 -0.31 ...... Frame ( 12) shift: 0.35 -0.19 ...... Frame ( 13) shift: 0.41 -0.05 ...... Frame ( 14) shift: 0.46 0.09 ...... Frame ( 15) shift: 0.52 0.19 ...... Frame ( 16) shift: 0.56 0.27 ...... Frame ( 17) shift: 0.61 0.35 ...... Frame ( 18) shift: 0.65 0.45 ...... Frame ( 19) shift: 0.69 0.58 ...... Frame ( 20) shift: 0.74 0.71 ...... Frame ( 21) shift: 0.82 0.82 ...... Frame ( 22) shift: 0.92 0.90 ...... Frame ( 23) shift: 1.03 0.98 ...... Frame ( 24) shift: 1.07 1.05 ...... Frame ( 25) shift: 1.05 1.11 ...... Frame ( 26) shift: 1.03 1.17 ...... Frame ( 27) shift: 1.04 1.25 ...... Frame ( 28) shift: 1.10 1.35 ...... Frame ( 29) shift: 1.15 1.46 ...... Frame ( 30) shift: 1.18 1.53 ...... Frame ( 31) shift: 1.20 1.56 ...... Frame ( 32) shift: 1.22 1.60 ...... Frame ( 33) shift: 1.25 1.63 ...... Frame ( 34) shift: 1.31 1.66 ...... Frame ( 35) shift: 1.36 1.69 ...... Frame ( 36) shift: 1.42 1.71 ...... Frame ( 37) shift: 1.46 1.74 ...... Frame ( 38) shift: 1.51 1.76 ...... Frame ( 39) shift: 1.56 1.78 ...... Frame ( 40) shift: 1.61 1.80 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.694045 Iteration 2 Error: 0.145989 Iteration 3 Error: 0.025840 Align patch 2 23 left Iteration 1 Error: 0.825836 Iteration 2 Error: 0.126416 Iteration 3 Error: 0.034732 Align patch 3 22 left Iteration 1 Error: 0.621798 Iteration 2 Error: 0.090604 Iteration 3 Error: 0.024587 Align patch 4 21 left Iteration 1 Error: 0.825965 Iteration 2 Error: 0.108785 Iteration 3 Error: 0.033920 Align patch 5 20 left Iteration 1 Error: 0.768732 Iteration 2 Error: 0.166353 Iteration 3 Error: 0.065804 Iteration 4 Error: 0.012832 Align patch 6 19 left Iteration 1 Error: 0.958645 Iteration 2 Error: 0.121494 Iteration 3 Error: 0.048257 Align patch 7 18 left Iteration 1 Error: 0.617129 Iteration 2 Error: 0.133026 Iteration 3 Error: 0.041742 Align patch 8 17 left Iteration 1 Error: 0.641611 Iteration 2 Error: 0.107737 Iteration 3 Error: 0.019965 Align patch 9 16 left Iteration 1 Error: 0.682911 Iteration 2 Error: 0.092620 Iteration 3 Error: 0.018939 Align patch 10 15 left Iteration 1 Error: 0.512951 Iteration 2 Error: 0.076732 Iteration 3 Error: 0.031932 Align patch 11 14 left Iteration 1 Error: 0.595476 Iteration 2 Error: 0.098006 Iteration 3 Error: 0.027259 Align patch 12 13 left Iteration 1 Error: 0.634134 Iteration 2 Error: 0.051388 Iteration 3 Error: 0.019338 Align patch 13 12 left Iteration 1 Error: 0.683910 Iteration 2 Error: 0.086246 Iteration 3 Error: 0.024426 Align patch 14 11 left Iteration 1 Error: 0.610955 Iteration 2 Error: 0.097584 Iteration 3 Error: 0.024692 Align patch 15 10 left Iteration 1 Error: 0.787034 Iteration 2 Error: 0.129470 Iteration 3 Error: 0.036865 Align patch 16 9 left Iteration 1 Error: 0.693237 Iteration 2 Error: 0.083170 Iteration 3 Error: 0.018974 Align patch 17 8 left Iteration 1 Error: 0.780694 Iteration 2 Error: 0.108483 Iteration 3 Error: 0.030961 Align patch 18 7 left Iteration 1 Error: 0.491887 Iteration 2 Error: 0.114670 Iteration 3 Error: 0.023614 Align patch 19 6 left Iteration 1 Error: 0.711599 Iteration 2 Error: 0.115457 Iteration 3 Error: 0.033986 Align patch 20 5 left Iteration 1 Error: 0.797287 Iteration 2 Error: 0.170762 Iteration 3 Error: 0.051271 Iteration 4 Error: 0.018148 Align patch 21 4 left Iteration 1 Error: 0.537473 Iteration 2 Error: 0.080973 Iteration 3 Error: 0.021481 Align patch 22 3 left Iteration 1 Error: 1.148161 Iteration 2 Error: 0.137927 Iteration 3 Error: 0.020750 Align patch 23 2 left Iteration 1 Error: 0.886058 Iteration 2 Error: 0.194976 Iteration 3 Error: 0.043670 Align patch 24 1 left Iteration 1 Error: 0.741300 Iteration 2 Error: 0.147327 Iteration 3 Error: 0.028466 Align patch 25 0 left Iteration 1 Error: 0.809718 Iteration 2 Error: 0.158616 Iteration 3 Error: 0.032472 3D Fitting completed. Patch alignment time: 15.98(sec) Local motion has been corrected. Process thread exits. Computational time: 32.160969 sec Total time: 39.415707 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00028hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00028hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.752378s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00028hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.891436s ........................................ >>>>>>TIME<<<<<< FFT: 1.209392s Defocus_U Defocus_V Angle CCC 14132.81 14875.00 2.41 0.065727 Final Values Defocus_U Defocus_V Angle CCC 14128.12 14882.82 1.16 0.103917 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00029hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00029hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 1.000e-01 CC threshold: 0.734 Mean Std: 40.32 6.75 Num Hot pixels: 200 Hot pixel threshold: 80.83 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.735629 Iteration 2 Error: 0.280115 Iteration 3 Error: 0.073498 Iteration 4 Error: 0.021696 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.15 -0.03 ...... Frame ( 3) shift: 0.30 -0.07 ...... Frame ( 4) shift: 0.45 -0.10 ...... Frame ( 5) shift: 0.60 -0.14 ...... Frame ( 6) shift: 0.72 -0.10 ...... Frame ( 7) shift: 0.79 -0.00 ...... Frame ( 8) shift: 0.87 0.10 ...... Frame ( 9) shift: 0.99 0.17 ...... Frame ( 10) shift: 1.16 0.21 ...... Frame ( 11) shift: 1.32 0.24 ...... Frame ( 12) shift: 1.45 0.31 ...... Frame ( 13) shift: 1.53 0.40 ...... Frame ( 14) shift: 1.62 0.50 ...... Frame ( 15) shift: 1.73 0.59 ...... Frame ( 16) shift: 1.86 0.67 ...... Frame ( 17) shift: 1.99 0.76 ...... Frame ( 18) shift: 2.09 0.79 ...... Frame ( 19) shift: 2.17 0.76 ...... Frame ( 20) shift: 2.25 0.72 ...... Frame ( 21) shift: 2.31 0.69 ...... Frame ( 22) shift: 2.35 0.66 ...... Frame ( 23) shift: 2.39 0.63 ...... Frame ( 24) shift: 2.49 0.65 ...... Frame ( 25) shift: 2.64 0.72 ...... Frame ( 26) shift: 2.79 0.79 ...... Frame ( 27) shift: 2.89 0.84 ...... Frame ( 28) shift: 2.92 0.86 ...... Frame ( 29) shift: 2.95 0.89 ...... Frame ( 30) shift: 3.02 0.94 ...... Frame ( 31) shift: 3.12 1.01 ...... Frame ( 32) shift: 3.22 1.09 ...... Frame ( 33) shift: 3.29 1.11 ...... Frame ( 34) shift: 3.32 1.07 ...... Frame ( 35) shift: 3.34 1.03 ...... Frame ( 36) shift: 3.40 1.05 ...... Frame ( 37) shift: 3.49 1.13 ...... Frame ( 38) shift: 3.58 1.21 ...... Frame ( 39) shift: 3.67 1.29 ...... Frame ( 40) shift: 3.76 1.38 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.639978 Iteration 2 Error: 0.106371 Iteration 3 Error: 0.030507 Align patch 2 23 left Iteration 1 Error: 1.124941 Iteration 2 Error: 0.142208 Iteration 3 Error: 0.029689 Align patch 3 22 left Iteration 1 Error: 0.683648 Iteration 2 Error: 0.137968 Iteration 3 Error: 0.053279 Iteration 4 Error: 0.019940 Align patch 4 21 left Iteration 1 Error: 0.977333 Iteration 2 Error: 0.136128 Iteration 3 Error: 0.053142 Iteration 4 Error: 0.014080 Align patch 5 20 left Iteration 1 Error: 1.219793 Iteration 2 Error: 0.244365 Iteration 3 Error: 0.074703 Iteration 4 Error: 0.019423 Align patch 6 19 left Iteration 1 Error: 0.816712 Iteration 2 Error: 0.141139 Iteration 3 Error: 0.032292 Align patch 7 18 left Iteration 1 Error: 0.681815 Iteration 2 Error: 0.228271 Iteration 3 Error: 0.044129 Align patch 8 17 left Iteration 1 Error: 0.423270 Iteration 2 Error: 0.059847 Iteration 3 Error: 0.011568 Align patch 9 16 left Iteration 1 Error: 0.885368 Iteration 2 Error: 0.192909 Iteration 3 Error: 0.055479 Iteration 4 Error: 0.016806 Align patch 10 15 left Iteration 1 Error: 0.603405 Iteration 2 Error: 0.098144 Iteration 3 Error: 0.021068 Align patch 11 14 left Iteration 1 Error: 0.711286 Iteration 2 Error: 0.113971 Iteration 3 Error: 0.030086 Align patch 12 13 left Iteration 1 Error: 0.623661 Iteration 2 Error: 0.088082 Iteration 3 Error: 0.024401 Align patch 13 12 left Iteration 1 Error: 0.718863 Iteration 2 Error: 0.071021 Iteration 3 Error: 0.017076 Align patch 14 11 left Iteration 1 Error: 0.931217 Iteration 2 Error: 0.187691 Iteration 3 Error: 0.034366 Align patch 15 10 left Iteration 1 Error: 0.783027 Iteration 2 Error: 0.144331 Iteration 3 Error: 0.029261 Align patch 16 9 left Iteration 1 Error: 0.972340 Iteration 2 Error: 0.146548 Iteration 3 Error: 0.042487 Align patch 17 8 left Iteration 1 Error: 0.726650 Iteration 2 Error: 0.109288 Iteration 3 Error: 0.027650 Align patch 18 7 left Iteration 1 Error: 0.812115 Iteration 2 Error: 0.152767 Iteration 3 Error: 0.044885 Align patch 19 6 left Iteration 1 Error: 0.554780 Iteration 2 Error: 0.112401 Iteration 3 Error: 0.036987 Align patch 20 5 left Iteration 1 Error: 0.791388 Iteration 2 Error: 0.234834 Iteration 3 Error: 0.095985 Iteration 4 Error: 0.045663 Align patch 21 4 left Iteration 1 Error: 0.578073 Iteration 2 Error: 0.171297 Iteration 3 Error: 0.042212 Align patch 22 3 left Iteration 1 Error: 0.762088 Iteration 2 Error: 0.228171 Iteration 3 Error: 0.053678 Iteration 4 Error: 0.022149 Align patch 23 2 left Iteration 1 Error: 0.613888 Iteration 2 Error: 0.132405 Iteration 3 Error: 0.025797 Align patch 24 1 left Iteration 1 Error: 1.008527 Iteration 2 Error: 0.137127 Iteration 3 Error: 0.032965 Align patch 25 0 left Iteration 1 Error: 1.072212 Iteration 2 Error: 0.134482 Iteration 3 Error: 0.017682 3D Fitting completed. Patch alignment time: 16.79(sec) Local motion has been corrected. Process thread exits. Computational time: 33.170521 sec Total time: 42.236107 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00029hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00029hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.658060s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00029hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.573361s ........................................ >>>>>>TIME<<<<<< FFT: 1.190065s Defocus_U Defocus_V Angle CCC 15744.14 16513.68 9.01 0.048593 Final Values Defocus_U Defocus_V Angle CCC 15740.96 16529.36 8.39 0.078515 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00029hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00029hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.997e-02 CC threshold: 0.734 Mean Std: 39.47 6.67 Num Hot pixels: 189 Hot pixel threshold: 79.48 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.726719 Iteration 2 Error: 0.377464 Iteration 3 Error: 0.120351 Iteration 4 Error: 0.047650 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.13 0.04 ...... Frame ( 3) shift: 0.25 0.07 ...... Frame ( 4) shift: 0.38 0.11 ...... Frame ( 5) shift: 0.51 0.14 ...... Frame ( 6) shift: 0.61 0.18 ...... Frame ( 7) shift: 0.69 0.22 ...... Frame ( 8) shift: 0.76 0.26 ...... Frame ( 9) shift: 0.83 0.35 ...... Frame ( 10) shift: 0.87 0.48 ...... Frame ( 11) shift: 0.92 0.61 ...... Frame ( 12) shift: 1.02 0.68 ...... Frame ( 13) shift: 1.15 0.71 ...... Frame ( 14) shift: 1.29 0.74 ...... Frame ( 15) shift: 1.45 0.79 ...... Frame ( 16) shift: 1.62 0.85 ...... Frame ( 17) shift: 1.80 0.91 ...... Frame ( 18) shift: 1.96 1.02 ...... Frame ( 19) shift: 2.10 1.17 ...... Frame ( 20) shift: 2.24 1.32 ...... Frame ( 21) shift: 2.36 1.43 ...... Frame ( 22) shift: 2.45 1.51 ...... Frame ( 23) shift: 2.55 1.58 ...... Frame ( 24) shift: 2.63 1.64 ...... Frame ( 25) shift: 2.71 1.68 ...... Frame ( 26) shift: 2.78 1.72 ...... Frame ( 27) shift: 2.83 1.77 ...... Frame ( 28) shift: 2.84 1.84 ...... Frame ( 29) shift: 2.85 1.90 ...... Frame ( 30) shift: 2.91 1.93 ...... Frame ( 31) shift: 3.01 1.93 ...... Frame ( 32) shift: 3.11 1.93 ...... Frame ( 33) shift: 3.17 1.94 ...... Frame ( 34) shift: 3.20 1.97 ...... Frame ( 35) shift: 3.23 2.00 ...... Frame ( 36) shift: 3.28 2.05 ...... Frame ( 37) shift: 3.37 2.13 ...... Frame ( 38) shift: 3.45 2.20 ...... Frame ( 39) shift: 3.53 2.28 ...... Frame ( 40) shift: 3.62 2.36 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.236487 Iteration 2 Error: 0.167017 Iteration 3 Error: 0.049253 Align patch 2 23 left Iteration 1 Error: 0.764717 Iteration 2 Error: 0.120409 Iteration 3 Error: 0.048691 Align patch 3 22 left Iteration 1 Error: 1.780565 Iteration 2 Error: 0.333861 Iteration 3 Error: 0.096539 Iteration 4 Error: 0.041507 Align patch 4 21 left Iteration 1 Error: 1.178490 Iteration 2 Error: 0.162616 Iteration 3 Error: 0.021427 Align patch 5 20 left Iteration 1 Error: 1.140279 Iteration 2 Error: 0.244303 Iteration 3 Error: 0.064677 Iteration 4 Error: 0.027660 Align patch 6 19 left Iteration 1 Error: 0.862150 Iteration 2 Error: 0.172728 Iteration 3 Error: 0.092027 Iteration 4 Error: 0.046608 Align patch 7 18 left Iteration 1 Error: 0.818474 Iteration 2 Error: 0.121186 Iteration 3 Error: 0.026402 Align patch 8 17 left Iteration 1 Error: 0.856100 Iteration 2 Error: 0.142822 Iteration 3 Error: 0.037689 Align patch 9 16 left Iteration 1 Error: 1.114236 Iteration 2 Error: 0.123160 Iteration 3 Error: 0.031638 Align patch 10 15 left Iteration 1 Error: 0.921994 Iteration 2 Error: 0.166442 Iteration 3 Error: 0.038807 Align patch 11 14 left Iteration 1 Error: 0.958815 Iteration 2 Error: 0.124818 Iteration 3 Error: 0.045935 Align patch 12 13 left Iteration 1 Error: 0.646535 Iteration 2 Error: 0.142043 Iteration 3 Error: 0.057236 Iteration 4 Error: 0.017853 Align patch 13 12 left Iteration 1 Error: 0.894410 Iteration 2 Error: 0.096873 Iteration 3 Error: 0.039184 Align patch 14 11 left Iteration 1 Error: 0.773851 Iteration 2 Error: 0.164335 Iteration 3 Error: 0.054750 Iteration 4 Error: 0.015409 Align patch 15 10 left Iteration 1 Error: 1.144098 Iteration 2 Error: 0.235171 Iteration 3 Error: 0.056700 Iteration 4 Error: 0.016829 Align patch 16 9 left Iteration 1 Error: 0.873313 Iteration 2 Error: 0.147483 Iteration 3 Error: 0.051986 Iteration 4 Error: 0.020262 Align patch 17 8 left Iteration 1 Error: 0.806505 Iteration 2 Error: 0.125548 Iteration 3 Error: 0.043003 Align patch 18 7 left Iteration 1 Error: 0.792760 Iteration 2 Error: 0.184771 Iteration 3 Error: 0.070722 Iteration 4 Error: 0.024045 Align patch 19 6 left Iteration 1 Error: 1.026323 Iteration 2 Error: 0.182339 Iteration 3 Error: 0.038655 Align patch 20 5 left Iteration 1 Error: 0.671451 Iteration 2 Error: 0.173156 Iteration 3 Error: 0.032791 Align patch 21 4 left Iteration 1 Error: 0.640376 Iteration 2 Error: 0.129414 Iteration 3 Error: 0.030084 Align patch 22 3 left Iteration 1 Error: 0.980346 Iteration 2 Error: 0.187222 Iteration 3 Error: 0.051950 Iteration 4 Error: 0.018414 Align patch 23 2 left Iteration 1 Error: 1.134738 Iteration 2 Error: 0.203622 Iteration 3 Error: 0.067134 Iteration 4 Error: 0.026281 Align patch 24 1 left Iteration 1 Error: 0.934179 Iteration 2 Error: 0.105416 Iteration 3 Error: 0.023797 Align patch 25 0 left Iteration 1 Error: 0.611200 Iteration 2 Error: 0.117645 Iteration 3 Error: 0.024181 3D Fitting completed. Patch alignment time: 16.74(sec) Local motion has been corrected. Process thread exits. Computational time: 31.418133 sec Total time: 39.975502 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00029hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00029hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.590968s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00029hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.102427s ........................................ >>>>>>TIME<<<<<< FFT: 1.113621s Defocus_U Defocus_V Angle CCC 15257.82 16054.71 6.00 0.045609 Final Values Defocus_U Defocus_V Angle CCC 15251.58 16057.84 6.00 0.071156 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00029hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00029hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.996e-02 CC threshold: 0.734 Mean Std: 40.64 6.78 Num Hot pixels: 187 Hot pixel threshold: 81.32 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.466563 Iteration 2 Error: 0.183710 Iteration 3 Error: 0.047195 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.14 0.06 ...... Frame ( 3) shift: 0.28 0.13 ...... Frame ( 4) shift: 0.42 0.19 ...... Frame ( 5) shift: 0.56 0.26 ...... Frame ( 6) shift: 0.68 0.34 ...... Frame ( 7) shift: 0.77 0.45 ...... Frame ( 8) shift: 0.86 0.56 ...... Frame ( 9) shift: 0.94 0.66 ...... Frame ( 10) shift: 1.01 0.77 ...... Frame ( 11) shift: 1.09 0.88 ...... Frame ( 12) shift: 1.12 0.94 ...... Frame ( 13) shift: 1.12 0.96 ...... Frame ( 14) shift: 1.11 0.98 ...... Frame ( 15) shift: 1.15 0.98 ...... Frame ( 16) shift: 1.22 0.98 ...... Frame ( 17) shift: 1.29 0.97 ...... Frame ( 18) shift: 1.40 0.97 ...... Frame ( 19) shift: 1.54 0.98 ...... Frame ( 20) shift: 1.68 0.99 ...... Frame ( 21) shift: 1.78 1.02 ...... Frame ( 22) shift: 1.82 1.08 ...... Frame ( 23) shift: 1.86 1.13 ...... Frame ( 24) shift: 1.91 1.15 ...... Frame ( 25) shift: 1.97 1.13 ...... Frame ( 26) shift: 2.02 1.10 ...... Frame ( 27) shift: 2.06 1.09 ...... Frame ( 28) shift: 2.07 1.10 ...... Frame ( 29) shift: 2.08 1.10 ...... Frame ( 30) shift: 2.12 1.12 ...... Frame ( 31) shift: 2.19 1.15 ...... Frame ( 32) shift: 2.26 1.17 ...... Frame ( 33) shift: 2.34 1.19 ...... Frame ( 34) shift: 2.44 1.20 ...... Frame ( 35) shift: 2.54 1.21 ...... Frame ( 36) shift: 2.60 1.24 ...... Frame ( 37) shift: 2.62 1.28 ...... Frame ( 38) shift: 2.64 1.33 ...... Frame ( 39) shift: 2.66 1.37 ...... Frame ( 40) shift: 2.68 1.41 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.920035 Iteration 2 Error: 0.205791 Iteration 3 Error: 0.076950 Iteration 4 Error: 0.036381 Align patch 2 23 left Iteration 1 Error: 1.245370 Iteration 2 Error: 0.287273 Iteration 3 Error: 0.064788 Iteration 4 Error: 0.025201 Align patch 3 22 left Iteration 1 Error: 0.650341 Iteration 2 Error: 0.169123 Iteration 3 Error: 0.031709 Align patch 4 21 left Iteration 1 Error: 0.423185 Iteration 2 Error: 0.087488 Iteration 3 Error: 0.017866 Align patch 5 20 left Iteration 1 Error: 0.759537 Iteration 2 Error: 0.126269 Iteration 3 Error: 0.024475 Align patch 6 19 left Iteration 1 Error: 0.877727 Iteration 2 Error: 0.147063 Iteration 3 Error: 0.047360 Align patch 7 18 left Iteration 1 Error: 0.540890 Iteration 2 Error: 0.085353 Iteration 3 Error: 0.019366 Align patch 8 17 left Iteration 1 Error: 1.051745 Iteration 2 Error: 0.151855 Iteration 3 Error: 0.052170 Iteration 4 Error: 0.012996 Align patch 9 16 left Iteration 1 Error: 0.592692 Iteration 2 Error: 0.181352 Iteration 3 Error: 0.060903 Iteration 4 Error: 0.022894 Align patch 10 15 left Iteration 1 Error: 0.903105 Iteration 2 Error: 0.128032 Iteration 3 Error: 0.030237 Align patch 11 14 left Iteration 1 Error: 0.864150 Iteration 2 Error: 0.364490 Iteration 3 Error: 0.165305 Iteration 4 Error: 0.074200 Iteration 5 Error: 0.034213 Align patch 12 13 left Iteration 1 Error: 0.916831 Iteration 2 Error: 0.249779 Iteration 3 Error: 0.050069 Iteration 4 Error: 0.022719 Align patch 13 12 left Iteration 1 Error: 0.830684 Iteration 2 Error: 0.245354 Iteration 3 Error: 0.050388 Iteration 4 Error: 0.023797 Align patch 14 11 left Iteration 1 Error: 0.876344 Iteration 2 Error: 0.142232 Iteration 3 Error: 0.054831 Iteration 4 Error: 0.013928 Align patch 15 10 left Iteration 1 Error: 1.026867 Iteration 2 Error: 0.131305 Iteration 3 Error: 0.037098 Align patch 16 9 left Iteration 1 Error: 1.076375 Iteration 2 Error: 0.196912 Iteration 3 Error: 0.058391 Iteration 4 Error: 0.015021 Align patch 17 8 left Iteration 1 Error: 0.810995 Iteration 2 Error: 0.082760 Iteration 3 Error: 0.020689 Align patch 18 7 left Iteration 1 Error: 0.663058 Iteration 2 Error: 0.133746 Iteration 3 Error: 0.029765 Align patch 19 6 left Iteration 1 Error: 0.711455 Iteration 2 Error: 0.096010 Iteration 3 Error: 0.019076 Align patch 20 5 left Iteration 1 Error: 0.752262 Iteration 2 Error: 0.127737 Iteration 3 Error: 0.021550 Align patch 21 4 left Iteration 1 Error: 0.711632 Iteration 2 Error: 0.124977 Iteration 3 Error: 0.021135 Align patch 22 3 left Iteration 1 Error: 0.961907 Iteration 2 Error: 0.161843 Iteration 3 Error: 0.037025 Align patch 23 2 left Iteration 1 Error: 0.626606 Iteration 2 Error: 0.166963 Iteration 3 Error: 0.049158 Align patch 24 1 left Iteration 1 Error: 0.771736 Iteration 2 Error: 0.182658 Iteration 3 Error: 0.029247 Align patch 25 0 left Iteration 1 Error: 0.974468 Iteration 2 Error: 0.192436 Iteration 3 Error: 0.039983 3D Fitting completed. Patch alignment time: 13.38(sec) Local motion has been corrected. Process thread exits. Computational time: 28.050880 sec Total time: 35.672836 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00029hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00029hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.589407s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00029hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.317079s ........................................ >>>>>>TIME<<<<<< FFT: 0.980015s Defocus_U Defocus_V Angle CCC 16388.64 16970.74 0.26 0.040370 Final Values Defocus_U Defocus_V Angle CCC 16380.80 16972.32 0.57 0.068974 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00029hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00029hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.997e-02 CC threshold: 0.734 Mean Std: 39.86 6.71 Num Hot pixels: 195 Hot pixel threshold: 80.09 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.635022 Iteration 2 Error: 0.243634 Iteration 3 Error: 0.065331 Iteration 4 Error: 0.021607 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.00 0.14 ...... Frame ( 3) shift: -0.01 0.28 ...... Frame ( 4) shift: -0.01 0.41 ...... Frame ( 5) shift: -0.02 0.55 ...... Frame ( 6) shift: 0.03 0.67 ...... Frame ( 7) shift: 0.13 0.77 ...... Frame ( 8) shift: 0.23 0.88 ...... Frame ( 9) shift: 0.33 0.95 ...... Frame ( 10) shift: 0.45 0.99 ...... Frame ( 11) shift: 0.56 1.03 ...... Frame ( 12) shift: 0.67 1.08 ...... Frame ( 13) shift: 0.78 1.16 ...... Frame ( 14) shift: 0.88 1.23 ...... Frame ( 15) shift: 0.93 1.30 ...... Frame ( 16) shift: 0.92 1.38 ...... Frame ( 17) shift: 0.90 1.47 ...... Frame ( 18) shift: 0.97 1.54 ...... Frame ( 19) shift: 1.11 1.61 ...... Frame ( 20) shift: 1.26 1.68 ...... Frame ( 21) shift: 1.36 1.75 ...... Frame ( 22) shift: 1.43 1.82 ...... Frame ( 23) shift: 1.49 1.89 ...... Frame ( 24) shift: 1.55 1.95 ...... Frame ( 25) shift: 1.59 1.99 ...... Frame ( 26) shift: 1.64 2.03 ...... Frame ( 27) shift: 1.69 2.10 ...... Frame ( 28) shift: 1.75 2.19 ...... Frame ( 29) shift: 1.81 2.28 ...... Frame ( 30) shift: 1.84 2.32 ...... Frame ( 31) shift: 1.82 2.30 ...... Frame ( 32) shift: 1.80 2.28 ...... Frame ( 33) shift: 1.80 2.27 ...... Frame ( 34) shift: 1.81 2.28 ...... Frame ( 35) shift: 1.83 2.30 ...... Frame ( 36) shift: 1.82 2.29 ...... Frame ( 37) shift: 1.81 2.26 ...... Frame ( 38) shift: 1.79 2.24 ...... Frame ( 39) shift: 1.78 2.22 ...... Frame ( 40) shift: 1.76 2.19 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.227292 Iteration 2 Error: 0.267995 Iteration 3 Error: 0.046983 Align patch 2 23 left Iteration 1 Error: 1.142942 Iteration 2 Error: 0.233715 Iteration 3 Error: 0.053428 Iteration 4 Error: 0.019467 Align patch 3 22 left Iteration 1 Error: 0.698489 Iteration 2 Error: 0.151639 Iteration 3 Error: 0.025681 Align patch 4 21 left Iteration 1 Error: 1.052367 Iteration 2 Error: 0.217237 Iteration 3 Error: 0.059718 Iteration 4 Error: 0.018097 Align patch 5 20 left Iteration 1 Error: 0.807275 Iteration 2 Error: 0.102388 Iteration 3 Error: 0.031766 Align patch 6 19 left Iteration 1 Error: 0.670927 Iteration 2 Error: 0.151327 Iteration 3 Error: 0.043353 Align patch 7 18 left Iteration 1 Error: 0.675919 Iteration 2 Error: 0.083942 Iteration 3 Error: 0.026032 Align patch 8 17 left Iteration 1 Error: 0.684623 Iteration 2 Error: 0.097188 Iteration 3 Error: 0.033364 Align patch 9 16 left Iteration 1 Error: 0.923404 Iteration 2 Error: 0.202187 Iteration 3 Error: 0.077620 Iteration 4 Error: 0.027015 Align patch 10 15 left Iteration 1 Error: 0.713116 Iteration 2 Error: 0.098487 Iteration 3 Error: 0.031235 Align patch 11 14 left Iteration 1 Error: 1.058355 Iteration 2 Error: 0.116727 Iteration 3 Error: 0.028711 Align patch 12 13 left Iteration 1 Error: 0.665902 Iteration 2 Error: 0.168750 Iteration 3 Error: 0.037947 Align patch 13 12 left Iteration 1 Error: 0.588606 Iteration 2 Error: 0.105434 Iteration 3 Error: 0.034057 Align patch 14 11 left Iteration 1 Error: 0.643838 Iteration 2 Error: 0.193953 Iteration 3 Error: 0.047024 Align patch 15 10 left Iteration 1 Error: 0.656454 Iteration 2 Error: 0.128256 Iteration 3 Error: 0.022535 Align patch 16 9 left Iteration 1 Error: 0.802460 Iteration 2 Error: 0.119125 Iteration 3 Error: 0.021530 Align patch 17 8 left Iteration 1 Error: 0.744029 Iteration 2 Error: 0.107370 Iteration 3 Error: 0.026384 Align patch 18 7 left Iteration 1 Error: 0.569084 Iteration 2 Error: 0.078609 Iteration 3 Error: 0.027556 Align patch 19 6 left Iteration 1 Error: 0.635201 Iteration 2 Error: 0.098411 Iteration 3 Error: 0.030947 Align patch 20 5 left Iteration 1 Error: 0.748295 Iteration 2 Error: 0.176761 Iteration 3 Error: 0.037647 Align patch 21 4 left Iteration 1 Error: 0.906695 Iteration 2 Error: 0.122319 Iteration 3 Error: 0.021694 Align patch 22 3 left Iteration 1 Error: 1.098978 Iteration 2 Error: 0.111655 Iteration 3 Error: 0.029463 Align patch 23 2 left Iteration 1 Error: 0.960003 Iteration 2 Error: 0.143879 Iteration 3 Error: 0.058215 Iteration 4 Error: 0.011521 Align patch 24 1 left Iteration 1 Error: 0.756190 Iteration 2 Error: 0.154207 Iteration 3 Error: 0.051459 Iteration 4 Error: 0.017767 Align patch 25 0 left Iteration 1 Error: 0.634891 Iteration 2 Error: 0.175150 Iteration 3 Error: 0.053820 Iteration 4 Error: 0.018330 3D Fitting completed. Patch alignment time: 12.66(sec) Local motion has been corrected. Process thread exits. Computational time: 27.220881 sec Total time: 35.119751 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00029hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00029hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.469549s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00029hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.215536s ........................................ >>>>>>TIME<<<<<< FFT: 1.160376s Defocus_U Defocus_V Angle CCC 18062.50 17445.31 89.27 0.034530 Final Values Defocus_U Defocus_V Angle CCC 18060.96 17431.27 89.27 0.056639 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00030hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00030hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.998e-02 CC threshold: 0.734 Mean Std: 41.45 6.85 Num Hot pixels: 206 Hot pixel threshold: 82.57 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.200393 Iteration 2 Error: 0.262094 Iteration 3 Error: 0.070783 Iteration 4 Error: 0.029831 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.12 -0.18 ...... Frame ( 3) shift: -0.24 -0.37 ...... Frame ( 4) shift: -0.36 -0.55 ...... Frame ( 5) shift: -0.48 -0.73 ...... Frame ( 6) shift: -0.49 -0.78 ...... Frame ( 7) shift: -0.40 -0.70 ...... Frame ( 8) shift: -0.30 -0.62 ...... Frame ( 9) shift: -0.18 -0.56 ...... Frame ( 10) shift: -0.06 -0.52 ...... Frame ( 11) shift: 0.07 -0.48 ...... Frame ( 12) shift: 0.16 -0.43 ...... Frame ( 13) shift: 0.21 -0.36 ...... Frame ( 14) shift: 0.25 -0.29 ...... Frame ( 15) shift: 0.32 -0.23 ...... Frame ( 16) shift: 0.40 -0.19 ...... Frame ( 17) shift: 0.49 -0.15 ...... Frame ( 18) shift: 0.60 -0.13 ...... Frame ( 19) shift: 0.72 -0.11 ...... Frame ( 20) shift: 0.85 -0.09 ...... Frame ( 21) shift: 0.92 -0.05 ...... Frame ( 22) shift: 0.92 0.02 ...... Frame ( 23) shift: 0.92 0.09 ...... Frame ( 24) shift: 0.96 0.15 ...... Frame ( 25) shift: 1.02 0.18 ...... Frame ( 26) shift: 1.08 0.22 ...... Frame ( 27) shift: 1.16 0.26 ...... Frame ( 28) shift: 1.26 0.29 ...... Frame ( 29) shift: 1.35 0.32 ...... Frame ( 30) shift: 1.45 0.34 ...... Frame ( 31) shift: 1.55 0.35 ...... Frame ( 32) shift: 1.65 0.36 ...... Frame ( 33) shift: 1.70 0.36 ...... Frame ( 34) shift: 1.68 0.34 ...... Frame ( 35) shift: 1.66 0.32 ...... Frame ( 36) shift: 1.67 0.33 ...... Frame ( 37) shift: 1.70 0.37 ...... Frame ( 38) shift: 1.72 0.41 ...... Frame ( 39) shift: 1.75 0.45 ...... Frame ( 40) shift: 1.78 0.49 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.438344 Iteration 2 Error: 0.399419 Iteration 3 Error: 0.125749 Iteration 4 Error: 0.052032 Iteration 5 Error: 0.021552 Align patch 2 23 left Iteration 1 Error: 2.197972 Iteration 2 Error: 0.377834 Iteration 3 Error: 0.138323 Iteration 4 Error: 0.047545 Align patch 3 22 left Iteration 1 Error: 1.067346 Iteration 2 Error: 0.214401 Iteration 3 Error: 0.047101 Align patch 4 21 left Iteration 1 Error: 1.169517 Iteration 2 Error: 0.150763 Iteration 3 Error: 0.040327 Align patch 5 20 left Iteration 1 Error: 1.125132 Iteration 2 Error: 0.328030 Iteration 3 Error: 0.123054 Iteration 4 Error: 0.047607 Align patch 6 19 left Iteration 1 Error: 0.805134 Iteration 2 Error: 0.224632 Iteration 3 Error: 0.086948 Iteration 4 Error: 0.028401 Align patch 7 18 left Iteration 1 Error: 0.812434 Iteration 2 Error: 0.294503 Iteration 3 Error: 0.068068 Iteration 4 Error: 0.031590 Align patch 8 17 left Iteration 1 Error: 0.878266 Iteration 2 Error: 0.222437 Iteration 3 Error: 0.059482 Iteration 4 Error: 0.033804 Align patch 9 16 left Iteration 1 Error: 1.146776 Iteration 2 Error: 0.176989 Iteration 3 Error: 0.044999 Align patch 10 15 left Iteration 1 Error: 0.569610 Iteration 2 Error: 0.122746 Iteration 3 Error: 0.054685 Iteration 4 Error: 0.035141 Align patch 11 14 left Iteration 1 Error: 0.776278 Iteration 2 Error: 0.174445 Iteration 3 Error: 0.065622 Iteration 4 Error: 0.031560 Align patch 12 13 left Iteration 1 Error: 0.820526 Iteration 2 Error: 0.154222 Iteration 3 Error: 0.055295 Iteration 4 Error: 0.025762 Align patch 13 12 left Iteration 1 Error: 0.639363 Iteration 2 Error: 0.101361 Iteration 3 Error: 0.036496 Align patch 14 11 left Iteration 1 Error: 1.012492 Iteration 2 Error: 0.193146 Iteration 3 Error: 0.075633 Iteration 4 Error: 0.025507 Align patch 15 10 left Iteration 1 Error: 0.843071 Iteration 2 Error: 0.187363 Iteration 3 Error: 0.053779 Iteration 4 Error: 0.022051 Align patch 16 9 left Iteration 1 Error: 0.940152 Iteration 2 Error: 0.211905 Iteration 3 Error: 0.086150 Iteration 4 Error: 0.025270 Align patch 17 8 left Iteration 1 Error: 0.673152 Iteration 2 Error: 0.111393 Iteration 3 Error: 0.030008 Align patch 18 7 left Iteration 1 Error: 0.777519 Iteration 2 Error: 0.225216 Iteration 3 Error: 0.047488 Align patch 19 6 left Iteration 1 Error: 1.182885 Iteration 2 Error: 0.247696 Iteration 3 Error: 0.068369 Iteration 4 Error: 0.012940 Align patch 20 5 left Iteration 1 Error: 0.891276 Iteration 2 Error: 0.151982 Iteration 3 Error: 0.044567 Align patch 21 4 left Iteration 1 Error: 0.797068 Iteration 2 Error: 0.177130 Iteration 3 Error: 0.030679 Align patch 22 3 left Iteration 1 Error: 1.067491 Iteration 2 Error: 0.142272 Iteration 3 Error: 0.039349 Align patch 23 2 left Iteration 1 Error: 0.999997 Iteration 2 Error: 0.253866 Iteration 3 Error: 0.064088 Iteration 4 Error: 0.026226 Align patch 24 1 left Iteration 1 Error: 1.086892 Iteration 2 Error: 0.205363 Iteration 3 Error: 0.063073 Iteration 4 Error: 0.013361 Align patch 25 0 left Iteration 1 Error: 1.251851 Iteration 2 Error: 0.158118 Iteration 3 Error: 0.034077 3D Fitting completed. Patch alignment time: 13.48(sec) Local motion has been corrected. Process thread exits. Computational time: 26.714211 sec Total time: 34.499641 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00030hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00030hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.646241s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00030hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.934012s ........................................ >>>>>>TIME<<<<<< FFT: 0.953026s Defocus_U Defocus_V Angle CCC 13957.03 14742.19 15.19 0.044549 Final Values Defocus_U Defocus_V Angle CCC 13958.60 14753.13 14.25 0.069912 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00030hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00030hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.993e-02 CC threshold: 0.734 Mean Std: 42.11 6.90 Num Hot pixels: 199 Hot pixel threshold: 83.54 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.299872 Iteration 2 Error: 0.285796 Iteration 3 Error: 0.066408 Iteration 4 Error: 0.020089 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.01 -0.24 ...... Frame ( 3) shift: 0.03 -0.48 ...... Frame ( 4) shift: 0.04 -0.71 ...... Frame ( 5) shift: 0.05 -0.95 ...... Frame ( 6) shift: 0.11 -1.01 ...... Frame ( 7) shift: 0.23 -0.90 ...... Frame ( 8) shift: 0.34 -0.79 ...... Frame ( 9) shift: 0.43 -0.71 ...... Frame ( 10) shift: 0.50 -0.68 ...... Frame ( 11) shift: 0.57 -0.64 ...... Frame ( 12) shift: 0.65 -0.54 ...... Frame ( 13) shift: 0.76 -0.36 ...... Frame ( 14) shift: 0.86 -0.18 ...... Frame ( 15) shift: 0.93 -0.09 ...... Frame ( 16) shift: 0.97 -0.10 ...... Frame ( 17) shift: 1.01 -0.11 ...... Frame ( 18) shift: 1.03 -0.11 ...... Frame ( 19) shift: 1.03 -0.10 ...... Frame ( 20) shift: 1.04 -0.10 ...... Frame ( 21) shift: 1.11 -0.08 ...... Frame ( 22) shift: 1.25 -0.03 ...... Frame ( 23) shift: 1.39 0.01 ...... Frame ( 24) shift: 1.50 0.08 ...... Frame ( 25) shift: 1.58 0.19 ...... Frame ( 26) shift: 1.66 0.29 ...... Frame ( 27) shift: 1.74 0.28 ...... Frame ( 28) shift: 1.81 0.18 ...... Frame ( 29) shift: 1.88 0.07 ...... Frame ( 30) shift: 2.01 0.03 ...... Frame ( 31) shift: 2.21 0.04 ...... Frame ( 32) shift: 2.41 0.05 ...... Frame ( 33) shift: 2.49 0.09 ...... Frame ( 34) shift: 2.43 0.14 ...... Frame ( 35) shift: 2.37 0.20 ...... Frame ( 36) shift: 2.38 0.23 ...... Frame ( 37) shift: 2.47 0.23 ...... Frame ( 38) shift: 2.55 0.23 ...... Frame ( 39) shift: 2.64 0.23 ...... Frame ( 40) shift: 2.73 0.24 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.877462 Iteration 2 Error: 0.170156 Iteration 3 Error: 0.054781 Iteration 4 Error: 0.016109 Align patch 2 23 left Iteration 1 Error: 1.393446 Iteration 2 Error: 0.195140 Iteration 3 Error: 0.068175 Iteration 4 Error: 0.019717 Align patch 3 22 left Iteration 1 Error: 0.971354 Iteration 2 Error: 0.113399 Iteration 3 Error: 0.036139 Align patch 4 21 left Iteration 1 Error: 0.780990 Iteration 2 Error: 0.226630 Iteration 3 Error: 0.057028 Iteration 4 Error: 0.024711 Align patch 5 20 left Iteration 1 Error: 1.661098 Iteration 2 Error: 0.235059 Iteration 3 Error: 0.042174 Align patch 6 19 left Iteration 1 Error: 1.128962 Iteration 2 Error: 0.175454 Iteration 3 Error: 0.062459 Iteration 4 Error: 0.015636 Align patch 7 18 left Iteration 1 Error: 0.621927 Iteration 2 Error: 0.109209 Iteration 3 Error: 0.047600 Align patch 8 17 left Iteration 1 Error: 0.763873 Iteration 2 Error: 0.171760 Iteration 3 Error: 0.059810 Iteration 4 Error: 0.032210 Align patch 9 16 left Iteration 1 Error: 0.917945 Iteration 2 Error: 0.245000 Iteration 3 Error: 0.062736 Iteration 4 Error: 0.022033 Align patch 10 15 left Iteration 1 Error: 0.825666 Iteration 2 Error: 0.269181 Iteration 3 Error: 0.092953 Iteration 4 Error: 0.027285 Align patch 11 14 left Iteration 1 Error: 0.580218 Iteration 2 Error: 0.171646 Iteration 3 Error: 0.048846 Align patch 12 13 left Iteration 1 Error: 0.709517 Iteration 2 Error: 0.205367 Iteration 3 Error: 0.076748 Iteration 4 Error: 0.020843 Align patch 13 12 left Iteration 1 Error: 0.748815 Iteration 2 Error: 0.128995 Iteration 3 Error: 0.037882 Align patch 14 11 left Iteration 1 Error: 0.769119 Iteration 2 Error: 0.136829 Iteration 3 Error: 0.040893 Align patch 15 10 left Iteration 1 Error: 1.428465 Iteration 2 Error: 0.204757 Iteration 3 Error: 0.058792 Iteration 4 Error: 0.029183 Align patch 16 9 left Iteration 1 Error: 0.897787 Iteration 2 Error: 0.328021 Iteration 3 Error: 0.092864 Iteration 4 Error: 0.041857 Align patch 17 8 left Iteration 1 Error: 1.318371 Iteration 2 Error: 0.267198 Iteration 3 Error: 0.067887 Iteration 4 Error: 0.027418 Align patch 18 7 left Iteration 1 Error: 1.261504 Iteration 2 Error: 0.273753 Iteration 3 Error: 0.140123 Iteration 4 Error: 0.048982 Align patch 19 6 left Iteration 1 Error: 0.586856 Iteration 2 Error: 0.098024 Iteration 3 Error: 0.032641 Align patch 20 5 left Iteration 1 Error: 0.880661 Iteration 2 Error: 0.236809 Iteration 3 Error: 0.063256 Iteration 4 Error: 0.020375 Align patch 21 4 left Iteration 1 Error: 0.981162 Iteration 2 Error: 0.167810 Iteration 3 Error: 0.051217 Iteration 4 Error: 0.017315 Align patch 22 3 left Iteration 1 Error: 0.559243 Iteration 2 Error: 0.083989 Iteration 3 Error: 0.037922 Align patch 23 2 left Iteration 1 Error: 1.522138 Iteration 2 Error: 0.231387 Iteration 3 Error: 0.067459 Iteration 4 Error: 0.028319 Align patch 24 1 left Iteration 1 Error: 0.973879 Iteration 2 Error: 0.242413 Iteration 3 Error: 0.073031 Iteration 4 Error: 0.024681 Align patch 25 0 left Iteration 1 Error: 0.762101 Iteration 2 Error: 0.172022 Iteration 3 Error: 0.059810 Iteration 4 Error: 0.021924 3D Fitting completed. Patch alignment time: 13.78(sec) Local motion has been corrected. Process thread exits. Computational time: 28.998800 sec Total time: 37.324432 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00030hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00030hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.454344s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00030hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.326025s ........................................ >>>>>>TIME<<<<<< FFT: 1.250781s Defocus_U Defocus_V Angle CCC 14929.69 15773.44 9.39 0.047270 Final Values Defocus_U Defocus_V Angle CCC 14920.31 15785.95 9.39 0.077635 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00030hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00030hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.992e-02 CC threshold: 0.734 Mean Std: 41.43 6.84 Num Hot pixels: 199 Hot pixel threshold: 82.50 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.664936 Iteration 2 Error: 0.487777 Iteration 3 Error: 0.134954 Iteration 4 Error: 0.056373 Iteration 5 Error: 0.029978 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.00 -0.21 ...... Frame ( 3) shift: 0.00 -0.42 ...... Frame ( 4) shift: 0.00 -0.64 ...... Frame ( 5) shift: 0.00 -0.85 ...... Frame ( 6) shift: 0.07 -0.91 ...... Frame ( 7) shift: 0.20 -0.82 ...... Frame ( 8) shift: 0.32 -0.74 ...... Frame ( 9) shift: 0.47 -0.66 ...... Frame ( 10) shift: 0.63 -0.61 ...... Frame ( 11) shift: 0.79 -0.55 ...... Frame ( 12) shift: 0.94 -0.44 ...... Frame ( 13) shift: 1.08 -0.28 ...... Frame ( 14) shift: 1.21 -0.12 ...... Frame ( 15) shift: 1.30 0.01 ...... Frame ( 16) shift: 1.33 0.10 ...... Frame ( 17) shift: 1.37 0.19 ...... Frame ( 18) shift: 1.46 0.25 ...... Frame ( 19) shift: 1.62 0.27 ...... Frame ( 20) shift: 1.78 0.29 ...... Frame ( 21) shift: 1.89 0.32 ...... Frame ( 22) shift: 1.96 0.38 ...... Frame ( 23) shift: 2.03 0.44 ...... Frame ( 24) shift: 2.10 0.54 ...... Frame ( 25) shift: 2.19 0.66 ...... Frame ( 26) shift: 2.27 0.79 ...... Frame ( 27) shift: 2.35 0.93 ...... Frame ( 28) shift: 2.43 1.08 ...... Frame ( 29) shift: 2.51 1.24 ...... Frame ( 30) shift: 2.57 1.29 ...... Frame ( 31) shift: 2.63 1.26 ...... Frame ( 32) shift: 2.68 1.22 ...... Frame ( 33) shift: 2.74 1.25 ...... Frame ( 34) shift: 2.81 1.35 ...... Frame ( 35) shift: 2.87 1.44 ...... Frame ( 36) shift: 2.92 1.51 ...... Frame ( 37) shift: 2.96 1.55 ...... Frame ( 38) shift: 3.00 1.59 ...... Frame ( 39) shift: 3.04 1.63 ...... Frame ( 40) shift: 3.08 1.67 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.822701 Iteration 2 Error: 0.256214 Iteration 3 Error: 0.090911 Iteration 4 Error: 0.064316 Iteration 5 Error: 0.019621 Align patch 2 23 left Iteration 1 Error: 0.756479 Iteration 2 Error: 0.091038 Iteration 3 Error: 0.029163 Align patch 3 22 left Iteration 1 Error: 0.948662 Iteration 2 Error: 0.181664 Iteration 3 Error: 0.082746 Iteration 4 Error: 0.035775 Align patch 4 21 left Iteration 1 Error: 2.154403 Iteration 2 Error: 0.345332 Iteration 3 Error: 0.144664 Iteration 4 Error: 0.065085 Iteration 5 Error: 0.022660 Align patch 5 20 left Iteration 1 Error: 0.873711 Iteration 2 Error: 0.221866 Iteration 3 Error: 0.077040 Iteration 4 Error: 0.031631 Align patch 6 19 left Iteration 1 Error: 1.111681 Iteration 2 Error: 0.229059 Iteration 3 Error: 0.066239 Iteration 4 Error: 0.019225 Align patch 7 18 left Iteration 1 Error: 1.183188 Iteration 2 Error: 0.209291 Iteration 3 Error: 0.045185 Align patch 8 17 left Iteration 1 Error: 0.674351 Iteration 2 Error: 0.104888 Iteration 3 Error: 0.037247 Align patch 9 16 left Iteration 1 Error: 0.604899 Iteration 2 Error: 0.108352 Iteration 3 Error: 0.036329 Align patch 10 15 left Iteration 1 Error: 1.482504 Iteration 2 Error: 0.207326 Iteration 3 Error: 0.070000 Iteration 4 Error: 0.032227 Align patch 11 14 left Iteration 1 Error: 0.506613 Iteration 2 Error: 0.115769 Iteration 3 Error: 0.041081 Align patch 12 13 left Iteration 1 Error: 0.831902 Iteration 2 Error: 0.197708 Iteration 3 Error: 0.073406 Iteration 4 Error: 0.034351 Align patch 13 12 left Iteration 1 Error: 0.806829 Iteration 2 Error: 0.196346 Iteration 3 Error: 0.074589 Iteration 4 Error: 0.033421 Align patch 14 11 left Iteration 1 Error: 0.827627 Iteration 2 Error: 0.465445 Iteration 3 Error: 0.297333 Iteration 4 Error: 0.149599 Iteration 5 Error: 0.077897 Align patch 14 11 left Iteration 1 Error: 0.897102 Iteration 2 Error: 0.179229 Iteration 3 Error: 0.035175 Align patch 15 10 left Iteration 1 Error: 0.701803 Iteration 2 Error: 0.104818 Iteration 3 Error: 0.039848 Align patch 16 9 left Iteration 1 Error: 0.912824 Iteration 2 Error: 0.227010 Iteration 3 Error: 0.057831 Iteration 4 Error: 0.024661 Align patch 17 8 left Iteration 1 Error: 0.681568 Iteration 2 Error: 0.189510 Iteration 3 Error: 0.091311 Iteration 4 Error: 0.033266 Align patch 18 7 left Iteration 1 Error: 1.041186 Iteration 2 Error: 0.317308 Iteration 3 Error: 0.110042 Iteration 4 Error: 0.035304 Align patch 19 6 left Iteration 1 Error: 0.906055 Iteration 2 Error: 0.156207 Iteration 3 Error: 0.052299 Iteration 4 Error: 0.025483 Align patch 20 5 left Iteration 1 Error: 0.619495 Iteration 2 Error: 0.093216 Iteration 3 Error: 0.027517 Align patch 21 4 left Iteration 1 Error: 1.096026 Iteration 2 Error: 0.175904 Iteration 3 Error: 0.043786 Align patch 22 3 left Iteration 1 Error: 1.043991 Iteration 2 Error: 0.159245 Iteration 3 Error: 0.043670 Align patch 23 2 left Iteration 1 Error: 0.702906 Iteration 2 Error: 0.110321 Iteration 3 Error: 0.029222 Align patch 24 1 left Iteration 1 Error: 1.187639 Iteration 2 Error: 0.187806 Iteration 3 Error: 0.035726 Align patch 25 0 left Iteration 1 Error: 1.160951 Iteration 2 Error: 0.293189 Iteration 3 Error: 0.074088 Iteration 4 Error: 0.043349 3D Fitting completed. Patch alignment time: 14.52(sec) Local motion has been corrected. Process thread exits. Computational time: 30.673531 sec Total time: 38.673279 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00030hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00030hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.651117s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00030hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.027168s ........................................ >>>>>>TIME<<<<<< FFT: 0.949636s Defocus_U Defocus_V Angle CCC 16722.65 17492.21 2.19 0.038755 Final Values Defocus_U Defocus_V Angle CCC 16716.40 17485.96 2.19 0.067334 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00031hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00031hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.991e-02 CC threshold: 0.734 Mean Std: 41.18 6.81 Num Hot pixels: 212 Hot pixel threshold: 82.05 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.577902 Iteration 2 Error: 0.433135 Iteration 3 Error: 0.129061 Iteration 4 Error: 0.040418 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.18 0.02 ...... Frame ( 3) shift: 0.35 0.04 ...... Frame ( 4) shift: 0.53 0.06 ...... Frame ( 5) shift: 0.70 0.08 ...... Frame ( 6) shift: 0.83 0.11 ...... Frame ( 7) shift: 0.90 0.15 ...... Frame ( 8) shift: 0.98 0.20 ...... Frame ( 9) shift: 1.00 0.28 ...... Frame ( 10) shift: 0.98 0.40 ...... Frame ( 11) shift: 0.96 0.53 ...... Frame ( 12) shift: 0.97 0.63 ...... Frame ( 13) shift: 1.02 0.72 ...... Frame ( 14) shift: 1.08 0.81 ...... Frame ( 15) shift: 1.14 0.89 ...... Frame ( 16) shift: 1.21 0.96 ...... Frame ( 17) shift: 1.27 1.03 ...... Frame ( 18) shift: 1.36 1.11 ...... Frame ( 19) shift: 1.47 1.20 ...... Frame ( 20) shift: 1.57 1.28 ...... Frame ( 21) shift: 1.65 1.38 ...... Frame ( 22) shift: 1.69 1.49 ...... Frame ( 23) shift: 1.74 1.61 ...... Frame ( 24) shift: 1.79 1.71 ...... Frame ( 25) shift: 1.84 1.81 ...... Frame ( 26) shift: 1.89 1.90 ...... Frame ( 27) shift: 1.93 1.96 ...... Frame ( 28) shift: 1.97 1.99 ...... Frame ( 29) shift: 2.00 2.01 ...... Frame ( 30) shift: 2.08 2.07 ...... Frame ( 31) shift: 2.20 2.18 ...... Frame ( 32) shift: 2.31 2.28 ...... Frame ( 33) shift: 2.39 2.34 ...... Frame ( 34) shift: 2.43 2.37 ...... Frame ( 35) shift: 2.47 2.39 ...... Frame ( 36) shift: 2.52 2.40 ...... Frame ( 37) shift: 2.57 2.41 ...... Frame ( 38) shift: 2.63 2.41 ...... Frame ( 39) shift: 2.68 2.42 ...... Frame ( 40) shift: 2.73 2.42 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.823295 Iteration 2 Error: 0.227395 Iteration 3 Error: 0.063066 Iteration 4 Error: 0.021247 Align patch 2 23 left Iteration 1 Error: 0.743528 Iteration 2 Error: 0.203726 Iteration 3 Error: 0.063780 Iteration 4 Error: 0.017121 Align patch 3 22 left Iteration 1 Error: 0.883705 Iteration 2 Error: 0.156471 Iteration 3 Error: 0.028241 Align patch 4 21 left Iteration 1 Error: 0.719652 Iteration 2 Error: 0.139382 Iteration 3 Error: 0.032365 Align patch 5 20 left Iteration 1 Error: 1.265219 Iteration 2 Error: 0.141767 Iteration 3 Error: 0.053216 Iteration 4 Error: 0.021426 Align patch 6 19 left Iteration 1 Error: 0.922352 Iteration 2 Error: 0.226913 Iteration 3 Error: 0.084436 Iteration 4 Error: 0.028041 Align patch 7 18 left Iteration 1 Error: 1.219533 Iteration 2 Error: 0.219072 Iteration 3 Error: 0.073882 Iteration 4 Error: 0.030298 Align patch 8 17 left Iteration 1 Error: 0.750671 Iteration 2 Error: 0.142001 Iteration 3 Error: 0.041874 Align patch 9 16 left Iteration 1 Error: 0.809247 Iteration 2 Error: 0.200847 Iteration 3 Error: 0.064956 Iteration 4 Error: 0.043551 Align patch 10 15 left Iteration 1 Error: 1.052652 Iteration 2 Error: 0.371763 Iteration 3 Error: 0.100699 Iteration 4 Error: 0.043186 Align patch 11 14 left Iteration 1 Error: 0.951211 Iteration 2 Error: 0.239548 Iteration 3 Error: 0.078714 Iteration 4 Error: 0.058337 Iteration 5 Error: 0.022412 Align patch 12 13 left Iteration 1 Error: 1.153967 Iteration 2 Error: 0.211829 Iteration 3 Error: 0.067436 Iteration 4 Error: 0.018940 Align patch 13 12 left Iteration 1 Error: 0.843160 Iteration 2 Error: 0.073111 Iteration 3 Error: 0.015701 Align patch 14 11 left Iteration 1 Error: 0.763496 Iteration 2 Error: 0.313191 Iteration 3 Error: 0.098701 Iteration 4 Error: 0.042660 Align patch 15 10 left Iteration 1 Error: 0.988222 Iteration 2 Error: 0.216727 Iteration 3 Error: 0.069290 Iteration 4 Error: 0.036732 Align patch 16 9 left Iteration 1 Error: 0.797869 Iteration 2 Error: 0.268807 Iteration 3 Error: 0.056470 Iteration 4 Error: 0.025989 Align patch 17 8 left Iteration 1 Error: 1.062631 Iteration 2 Error: 0.204647 Iteration 3 Error: 0.070509 Iteration 4 Error: 0.020106 Align patch 18 7 left Iteration 1 Error: 0.898853 Iteration 2 Error: 0.168623 Iteration 3 Error: 0.032253 Align patch 19 6 left Iteration 1 Error: 0.909110 Iteration 2 Error: 0.177873 Iteration 3 Error: 0.049028 Align patch 20 5 left Iteration 1 Error: 0.639995 Iteration 2 Error: 0.108736 Iteration 3 Error: 0.026872 Align patch 21 4 left Iteration 1 Error: 0.768563 Iteration 2 Error: 0.084743 Iteration 3 Error: 0.017206 Align patch 22 3 left Iteration 1 Error: 0.932700 Iteration 2 Error: 0.148522 Iteration 3 Error: 0.042837 Align patch 23 2 left Iteration 1 Error: 0.987473 Iteration 2 Error: 0.160475 Iteration 3 Error: 0.057489 Iteration 4 Error: 0.021501 Align patch 24 1 left Iteration 1 Error: 1.074927 Iteration 2 Error: 0.262041 Iteration 3 Error: 0.116176 Iteration 4 Error: 0.040762 Align patch 25 0 left Iteration 1 Error: 1.097957 Iteration 2 Error: 0.146668 Iteration 3 Error: 0.035682 3D Fitting completed. Patch alignment time: 12.54(sec) Local motion has been corrected. Process thread exits. Computational time: 24.950607 sec Total time: 31.666574 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00031hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00031hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.865477s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00031hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.754120s ........................................ >>>>>>TIME<<<<<< FFT: 0.927482s Defocus_U Defocus_V Angle CCC 12613.28 13347.66 10.81 0.044766 Final Values Defocus_U Defocus_V Angle CCC 12610.15 13353.91 11.44 0.076141 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00031hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00031hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.995e-02 CC threshold: 0.734 Mean Std: 40.79 6.80 Num Hot pixels: 202 Hot pixel threshold: 81.57 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.298502 Iteration 2 Error: 0.215971 Iteration 3 Error: 0.056835 Iteration 4 Error: 0.015147 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.16 0.09 ...... Frame ( 3) shift: 0.31 0.17 ...... Frame ( 4) shift: 0.47 0.26 ...... Frame ( 5) shift: 0.62 0.35 ...... Frame ( 6) shift: 0.72 0.36 ...... Frame ( 7) shift: 0.76 0.29 ...... Frame ( 8) shift: 0.81 0.23 ...... Frame ( 9) shift: 0.87 0.24 ...... Frame ( 10) shift: 0.95 0.31 ...... Frame ( 11) shift: 1.04 0.39 ...... Frame ( 12) shift: 1.08 0.49 ...... Frame ( 13) shift: 1.08 0.61 ...... Frame ( 14) shift: 1.07 0.73 ...... Frame ( 15) shift: 1.09 0.80 ...... Frame ( 16) shift: 1.13 0.82 ...... Frame ( 17) shift: 1.16 0.84 ...... Frame ( 18) shift: 1.21 0.90 ...... Frame ( 19) shift: 1.26 1.00 ...... Frame ( 20) shift: 1.31 1.10 ...... Frame ( 21) shift: 1.39 1.18 ...... Frame ( 22) shift: 1.50 1.25 ...... Frame ( 23) shift: 1.60 1.31 ...... Frame ( 24) shift: 1.69 1.36 ...... Frame ( 25) shift: 1.77 1.41 ...... Frame ( 26) shift: 1.84 1.45 ...... Frame ( 27) shift: 1.86 1.48 ...... Frame ( 28) shift: 1.82 1.51 ...... Frame ( 29) shift: 1.79 1.54 ...... Frame ( 30) shift: 1.80 1.57 ...... Frame ( 31) shift: 1.86 1.61 ...... Frame ( 32) shift: 1.92 1.66 ...... Frame ( 33) shift: 1.96 1.70 ...... Frame ( 34) shift: 1.98 1.75 ...... Frame ( 35) shift: 2.00 1.80 ...... Frame ( 36) shift: 2.06 1.85 ...... Frame ( 37) shift: 2.15 1.90 ...... Frame ( 38) shift: 2.23 1.95 ...... Frame ( 39) shift: 2.32 1.99 ...... Frame ( 40) shift: 2.41 2.04 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.275981 Iteration 2 Error: 0.163979 Iteration 3 Error: 0.033000 Align patch 2 23 left Iteration 1 Error: 0.851971 Iteration 2 Error: 0.126076 Iteration 3 Error: 0.034548 Align patch 3 22 left Iteration 1 Error: 0.923248 Iteration 2 Error: 0.192479 Iteration 3 Error: 0.048764 Align patch 4 21 left Iteration 1 Error: 0.908677 Iteration 2 Error: 0.183100 Iteration 3 Error: 0.052443 Iteration 4 Error: 0.024106 Align patch 5 20 left Iteration 1 Error: 0.554733 Iteration 2 Error: 0.114664 Iteration 3 Error: 0.027610 Align patch 6 19 left Iteration 1 Error: 0.633660 Iteration 2 Error: 0.136646 Iteration 3 Error: 0.035904 Align patch 7 18 left Iteration 1 Error: 0.904810 Iteration 2 Error: 0.157059 Iteration 3 Error: 0.034657 Align patch 8 17 left Iteration 1 Error: 0.806359 Iteration 2 Error: 0.178347 Iteration 3 Error: 0.061515 Iteration 4 Error: 0.022536 Align patch 9 16 left Iteration 1 Error: 0.790206 Iteration 2 Error: 0.183681 Iteration 3 Error: 0.042543 Align patch 10 15 left Iteration 1 Error: 0.881738 Iteration 2 Error: 0.170002 Iteration 3 Error: 0.049068 Align patch 11 14 left Iteration 1 Error: 0.927631 Iteration 2 Error: 0.157787 Iteration 3 Error: 0.039715 Align patch 12 13 left Iteration 1 Error: 0.859529 Iteration 2 Error: 0.168117 Iteration 3 Error: 0.047488 Align patch 13 12 left Iteration 1 Error: 0.898448 Iteration 2 Error: 0.209533 Iteration 3 Error: 0.057893 Iteration 4 Error: 0.025569 Align patch 14 11 left Iteration 1 Error: 0.920910 Iteration 2 Error: 0.095747 Iteration 3 Error: 0.033275 Align patch 15 10 left Iteration 1 Error: 0.927203 Iteration 2 Error: 0.165983 Iteration 3 Error: 0.047051 Align patch 16 9 left Iteration 1 Error: 0.791967 Iteration 2 Error: 0.094148 Iteration 3 Error: 0.015861 Align patch 17 8 left Iteration 1 Error: 0.539233 Iteration 2 Error: 0.120631 Iteration 3 Error: 0.043902 Align patch 18 7 left Iteration 1 Error: 0.737998 Iteration 2 Error: 0.107050 Iteration 3 Error: 0.030335 Align patch 19 6 left Iteration 1 Error: 0.716713 Iteration 2 Error: 0.100013 Iteration 3 Error: 0.018060 Align patch 20 5 left Iteration 1 Error: 0.661871 Iteration 2 Error: 0.141998 Iteration 3 Error: 0.021284 Align patch 21 4 left Iteration 1 Error: 0.931694 Iteration 2 Error: 0.139088 Iteration 3 Error: 0.033250 Align patch 22 3 left Iteration 1 Error: 1.012085 Iteration 2 Error: 0.212879 Iteration 3 Error: 0.050361 Iteration 4 Error: 0.022650 Align patch 23 2 left Iteration 1 Error: 0.680081 Iteration 2 Error: 0.163413 Iteration 3 Error: 0.035034 Align patch 24 1 left Iteration 1 Error: 0.654170 Iteration 2 Error: 0.104902 Iteration 3 Error: 0.020836 Align patch 25 0 left Iteration 1 Error: 0.845679 Iteration 2 Error: 0.141912 Iteration 3 Error: 0.025774 3D Fitting completed. Patch alignment time: 11.64(sec) Local motion has been corrected. Process thread exits. Computational time: 26.751249 sec Total time: 34.928997 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00031hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00031hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.867157s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00031hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.875492s ........................................ >>>>>>TIME<<<<<< FFT: 0.996087s Defocus_U Defocus_V Angle CCC 15527.34 16417.97 9.34 0.047088 Final Values Defocus_U Defocus_V Angle CCC 15524.21 16427.35 9.34 0.075766 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00031hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00031hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 41.18 6.83 Num Hot pixels: 197 Hot pixel threshold: 82.17 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.527133 Iteration 2 Error: 0.333710 Iteration 3 Error: 0.065233 Iteration 4 Error: 0.018834 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.17 -0.10 ...... Frame ( 3) shift: 0.35 -0.19 ...... Frame ( 4) shift: 0.52 -0.29 ...... Frame ( 5) shift: 0.69 -0.38 ...... Frame ( 6) shift: 0.85 -0.39 ...... Frame ( 7) shift: 0.98 -0.30 ...... Frame ( 8) shift: 1.12 -0.22 ...... Frame ( 9) shift: 1.20 -0.16 ...... Frame ( 10) shift: 1.21 -0.13 ...... Frame ( 11) shift: 1.23 -0.11 ...... Frame ( 12) shift: 1.25 -0.00 ...... Frame ( 13) shift: 1.26 0.18 ...... Frame ( 14) shift: 1.28 0.37 ...... Frame ( 15) shift: 1.26 0.52 ...... Frame ( 16) shift: 1.20 0.64 ...... Frame ( 17) shift: 1.15 0.76 ...... Frame ( 18) shift: 1.16 0.90 ...... Frame ( 19) shift: 1.23 1.04 ...... Frame ( 20) shift: 1.31 1.18 ...... Frame ( 21) shift: 1.39 1.29 ...... Frame ( 22) shift: 1.46 1.35 ...... Frame ( 23) shift: 1.54 1.42 ...... Frame ( 24) shift: 1.57 1.50 ...... Frame ( 25) shift: 1.57 1.61 ...... Frame ( 26) shift: 1.56 1.72 ...... Frame ( 27) shift: 1.58 1.82 ...... Frame ( 28) shift: 1.62 1.92 ...... Frame ( 29) shift: 1.66 2.02 ...... Frame ( 30) shift: 1.71 2.06 ...... Frame ( 31) shift: 1.78 2.04 ...... Frame ( 32) shift: 1.85 2.02 ...... Frame ( 33) shift: 1.92 2.04 ...... Frame ( 34) shift: 1.98 2.11 ...... Frame ( 35) shift: 2.04 2.17 ...... Frame ( 36) shift: 2.12 2.21 ...... Frame ( 37) shift: 2.23 2.23 ...... Frame ( 38) shift: 2.33 2.24 ...... Frame ( 39) shift: 2.43 2.26 ...... Frame ( 40) shift: 2.54 2.27 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.806895 Iteration 2 Error: 0.231118 Iteration 3 Error: 0.066353 Iteration 4 Error: 0.020288 Align patch 2 23 left Iteration 1 Error: 0.697397 Iteration 2 Error: 0.096439 Iteration 3 Error: 0.016929 Align patch 3 22 left Iteration 1 Error: 1.262665 Iteration 2 Error: 0.181417 Iteration 3 Error: 0.065576 Iteration 4 Error: 0.022289 Align patch 4 21 left Iteration 1 Error: 0.574407 Iteration 2 Error: 0.144661 Iteration 3 Error: 0.042718 Align patch 5 20 left Iteration 1 Error: 0.805064 Iteration 2 Error: 0.189065 Iteration 3 Error: 0.064198 Iteration 4 Error: 0.023498 Align patch 6 19 left Iteration 1 Error: 0.768030 Iteration 2 Error: 0.125000 Iteration 3 Error: 0.049310 Align patch 7 18 left Iteration 1 Error: 0.806524 Iteration 2 Error: 0.083816 Iteration 3 Error: 0.023785 Align patch 8 17 left Iteration 1 Error: 0.895147 Iteration 2 Error: 0.172979 Iteration 3 Error: 0.051313 Iteration 4 Error: 0.025812 Align patch 9 16 left Iteration 1 Error: 1.150651 Iteration 2 Error: 0.124705 Iteration 3 Error: 0.036199 Align patch 10 15 left Iteration 1 Error: 1.048587 Iteration 2 Error: 0.123648 Iteration 3 Error: 0.039385 Align patch 11 14 left Iteration 1 Error: 0.700307 Iteration 2 Error: 0.179578 Iteration 3 Error: 0.044591 Align patch 12 13 left Iteration 1 Error: 0.588066 Iteration 2 Error: 0.142501 Iteration 3 Error: 0.037545 Align patch 13 12 left Iteration 1 Error: 0.792222 Iteration 2 Error: 0.177578 Iteration 3 Error: 0.061078 Iteration 4 Error: 0.019283 Align patch 14 11 left Iteration 1 Error: 0.802882 Iteration 2 Error: 0.137854 Iteration 3 Error: 0.030216 Align patch 15 10 left Iteration 1 Error: 0.847386 Iteration 2 Error: 0.086594 Iteration 3 Error: 0.021281 Align patch 16 9 left Iteration 1 Error: 0.837561 Iteration 2 Error: 0.071235 Iteration 3 Error: 0.017739 Align patch 17 8 left Iteration 1 Error: 0.672735 Iteration 2 Error: 0.134894 Iteration 3 Error: 0.034781 Align patch 18 7 left Iteration 1 Error: 0.639019 Iteration 2 Error: 0.100873 Iteration 3 Error: 0.020125 Align patch 19 6 left Iteration 1 Error: 0.720703 Iteration 2 Error: 0.127051 Iteration 3 Error: 0.029368 Align patch 20 5 left Iteration 1 Error: 0.666606 Iteration 2 Error: 0.104582 Iteration 3 Error: 0.031833 Align patch 21 4 left Iteration 1 Error: 1.042974 Iteration 2 Error: 0.143236 Iteration 3 Error: 0.029168 Align patch 22 3 left Iteration 1 Error: 0.684700 Iteration 2 Error: 0.086236 Iteration 3 Error: 0.037391 Align patch 23 2 left Iteration 1 Error: 0.459360 Iteration 2 Error: 0.038856 Align patch 24 1 left Iteration 1 Error: 0.826671 Iteration 2 Error: 0.178140 Iteration 3 Error: 0.059192 Iteration 4 Error: 0.018919 Align patch 25 0 left Iteration 1 Error: 1.047709 Iteration 2 Error: 0.121738 Iteration 3 Error: 0.031225 3D Fitting completed. Patch alignment time: 11.85(sec) Local motion has been corrected. Process thread exits. Computational time: 25.014139 sec Total time: 32.498306 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00031hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00031hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.108667s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00031hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.707927s ........................................ >>>>>>TIME<<<<<< FFT: 1.022866s Defocus_U Defocus_V Angle CCC 13367.19 14085.94 1.76 0.057656 Final Values Defocus_U Defocus_V Angle CCC 13368.75 14084.38 1.45 0.092981 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00031hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00031hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.991e-02 CC threshold: 0.734 Mean Std: 40.67 6.82 Num Hot pixels: 198 Hot pixel threshold: 81.58 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.085937 Iteration 2 Error: 0.236515 Iteration 3 Error: 0.063618 Iteration 4 Error: 0.014881 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.14 -0.02 ...... Frame ( 3) shift: 0.27 -0.04 ...... Frame ( 4) shift: 0.41 -0.06 ...... Frame ( 5) shift: 0.55 -0.08 ...... Frame ( 6) shift: 0.65 -0.10 ...... Frame ( 7) shift: 0.72 -0.11 ...... Frame ( 8) shift: 0.79 -0.12 ...... Frame ( 9) shift: 0.82 -0.02 ...... Frame ( 10) shift: 0.81 0.19 ...... Frame ( 11) shift: 0.81 0.41 ...... Frame ( 12) shift: 0.81 0.53 ...... Frame ( 13) shift: 0.81 0.57 ...... Frame ( 14) shift: 0.81 0.61 ...... Frame ( 15) shift: 0.81 0.70 ...... Frame ( 16) shift: 0.81 0.83 ...... Frame ( 17) shift: 0.81 0.96 ...... Frame ( 18) shift: 0.81 1.04 ...... Frame ( 19) shift: 0.81 1.08 ...... Frame ( 20) shift: 0.81 1.13 ...... Frame ( 21) shift: 0.82 1.18 ...... Frame ( 22) shift: 0.85 1.26 ...... Frame ( 23) shift: 0.88 1.33 ...... Frame ( 24) shift: 0.92 1.42 ...... Frame ( 25) shift: 0.95 1.51 ...... Frame ( 26) shift: 0.99 1.60 ...... Frame ( 27) shift: 1.02 1.67 ...... Frame ( 28) shift: 1.05 1.71 ...... Frame ( 29) shift: 1.08 1.75 ...... Frame ( 30) shift: 1.12 1.82 ...... Frame ( 31) shift: 1.15 1.91 ...... Frame ( 32) shift: 1.19 2.00 ...... Frame ( 33) shift: 1.21 2.04 ...... Frame ( 34) shift: 1.22 2.03 ...... Frame ( 35) shift: 1.23 2.02 ...... Frame ( 36) shift: 1.24 2.03 ...... Frame ( 37) shift: 1.26 2.07 ...... Frame ( 38) shift: 1.28 2.11 ...... Frame ( 39) shift: 1.30 2.15 ...... Frame ( 40) shift: 1.32 2.18 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.110077 Iteration 2 Error: 0.182776 Iteration 3 Error: 0.038088 Align patch 2 23 left Iteration 1 Error: 1.068462 Iteration 2 Error: 0.126795 Iteration 3 Error: 0.035902 Align patch 3 22 left Iteration 1 Error: 0.591428 Iteration 2 Error: 0.121377 Iteration 3 Error: 0.045260 Align patch 4 21 left Iteration 1 Error: 0.973850 Iteration 2 Error: 0.197903 Iteration 3 Error: 0.070642 Iteration 4 Error: 0.033198 Align patch 5 20 left Iteration 1 Error: 0.716307 Iteration 2 Error: 0.191546 Iteration 3 Error: 0.060820 Iteration 4 Error: 0.017685 Align patch 6 19 left Iteration 1 Error: 0.751257 Iteration 2 Error: 0.118901 Iteration 3 Error: 0.030595 Align patch 7 18 left Iteration 1 Error: 0.937154 Iteration 2 Error: 0.137833 Iteration 3 Error: 0.031237 Align patch 8 17 left Iteration 1 Error: 0.581202 Iteration 2 Error: 0.086435 Iteration 3 Error: 0.013539 Align patch 9 16 left Iteration 1 Error: 0.782088 Iteration 2 Error: 0.113344 Iteration 3 Error: 0.026905 Align patch 10 15 left Iteration 1 Error: 0.876199 Iteration 2 Error: 0.204515 Iteration 3 Error: 0.046021 Align patch 11 14 left Iteration 1 Error: 0.845792 Iteration 2 Error: 0.156317 Iteration 3 Error: 0.043294 Align patch 12 13 left Iteration 1 Error: 0.726604 Iteration 2 Error: 0.107189 Iteration 3 Error: 0.022297 Align patch 13 12 left Iteration 1 Error: 4.249190 Iteration 2 Error: 0.740084 Iteration 3 Error: 0.455840 Iteration 4 Error: 0.189882 Iteration 5 Error: 0.125818 Align patch 13 12 left Iteration 1 Error: 2.534459 Iteration 2 Error: 0.465770 Iteration 3 Error: 0.144680 Iteration 4 Error: 0.044463 Align patch 14 11 left Iteration 1 Error: 1.160429 Iteration 2 Error: 0.228644 Iteration 3 Error: 0.067643 Iteration 4 Error: 0.030055 Align patch 15 10 left Iteration 1 Error: 0.757607 Iteration 2 Error: 0.171622 Iteration 3 Error: 0.044821 Align patch 16 9 left Iteration 1 Error: 0.697671 Iteration 2 Error: 0.203620 Iteration 3 Error: 0.047169 Align patch 17 8 left Iteration 1 Error: 0.647354 Iteration 2 Error: 0.084756 Iteration 3 Error: 0.024375 Align patch 18 7 left Iteration 1 Error: 1.293205 Iteration 2 Error: 0.309190 Iteration 3 Error: 0.076651 Iteration 4 Error: 0.032172 Align patch 19 6 left Iteration 1 Error: 0.580444 Iteration 2 Error: 0.078043 Iteration 3 Error: 0.018800 Align patch 20 5 left Iteration 1 Error: 0.691435 Iteration 2 Error: 0.149649 Iteration 3 Error: 0.041700 Align patch 21 4 left Iteration 1 Error: 0.645761 Iteration 2 Error: 0.078787 Iteration 3 Error: 0.020116 Align patch 22 3 left Iteration 1 Error: 1.062852 Iteration 2 Error: 0.141271 Iteration 3 Error: 0.031711 Align patch 23 2 left Iteration 1 Error: 0.590119 Iteration 2 Error: 0.113332 Iteration 3 Error: 0.031860 Align patch 24 1 left Iteration 1 Error: 0.750754 Iteration 2 Error: 0.192166 Iteration 3 Error: 0.039043 Align patch 25 0 left Iteration 1 Error: 0.808140 Iteration 2 Error: 0.109251 Iteration 3 Error: 0.033174 3D Fitting completed. Patch alignment time: 12.79(sec) Local motion has been corrected. Process thread exits. Computational time: 24.124428 sec Total time: 31.033516 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00031hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00031hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.681719s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00031hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.505644s ........................................ >>>>>>TIME<<<<<< FFT: 1.013866s Defocus_U Defocus_V Angle CCC 13482.43 12677.74 87.59 0.036571 Final Values Defocus_U Defocus_V Angle CCC 13483.97 12669.95 89.16 0.057806 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00032hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00032hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.994e-02 CC threshold: 0.734 Mean Std: 36.33 6.58 Num Hot pixels: 174 Hot pixel threshold: 75.80 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.026598 Iteration 2 Error: 0.121889 Iteration 3 Error: 0.025943 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.34 -0.36 ...... Frame ( 3) shift: -0.68 -0.71 ...... Frame ( 4) shift: -1.03 -1.07 ...... Frame ( 5) shift: -1.37 -1.42 ...... Frame ( 6) shift: -1.52 -1.54 ...... Frame ( 7) shift: -1.50 -1.43 ...... Frame ( 8) shift: -1.47 -1.31 ...... Frame ( 9) shift: -1.41 -1.20 ...... Frame ( 10) shift: -1.32 -1.09 ...... Frame ( 11) shift: -1.24 -0.98 ...... Frame ( 12) shift: -1.17 -0.91 ...... Frame ( 13) shift: -1.11 -0.88 ...... Frame ( 14) shift: -1.05 -0.86 ...... Frame ( 15) shift: -1.00 -0.85 ...... Frame ( 16) shift: -0.98 -0.86 ...... Frame ( 17) shift: -0.95 -0.87 ...... Frame ( 18) shift: -0.92 -0.85 ...... Frame ( 19) shift: -0.88 -0.78 ...... Frame ( 20) shift: -0.85 -0.71 ...... Frame ( 21) shift: -0.80 -0.64 ...... Frame ( 22) shift: -0.72 -0.58 ...... Frame ( 23) shift: -0.65 -0.51 ...... Frame ( 24) shift: -0.62 -0.52 ...... Frame ( 25) shift: -0.64 -0.60 ...... Frame ( 26) shift: -0.66 -0.68 ...... Frame ( 27) shift: -0.66 -0.72 ...... Frame ( 28) shift: -0.62 -0.71 ...... Frame ( 29) shift: -0.59 -0.71 ...... Frame ( 30) shift: -0.53 -0.70 ...... Frame ( 31) shift: -0.44 -0.69 ...... Frame ( 32) shift: -0.34 -0.68 ...... Frame ( 33) shift: -0.25 -0.66 ...... Frame ( 34) shift: -0.17 -0.63 ...... Frame ( 35) shift: -0.08 -0.61 ...... Frame ( 36) shift: -0.05 -0.59 ...... Frame ( 37) shift: -0.06 -0.59 ...... Frame ( 38) shift: -0.08 -0.58 ...... Frame ( 39) shift: -0.10 -0.58 ...... Frame ( 40) shift: -0.11 -0.58 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.090099 Iteration 2 Error: 0.178897 Iteration 3 Error: 0.071583 Iteration 4 Error: 0.023496 Align patch 2 23 left Iteration 1 Error: 1.899998 Iteration 2 Error: 0.322109 Iteration 3 Error: 0.077693 Iteration 4 Error: 0.036722 Align patch 3 22 left Iteration 1 Error: 1.165690 Iteration 2 Error: 0.226002 Iteration 3 Error: 0.056979 Iteration 4 Error: 0.016186 Align patch 4 21 left Iteration 1 Error: 0.695440 Iteration 2 Error: 0.281364 Iteration 3 Error: 0.112904 Iteration 4 Error: 0.036144 Align patch 5 20 left Iteration 1 Error: 0.675682 Iteration 2 Error: 0.132032 Iteration 3 Error: 0.065961 Iteration 4 Error: 0.050757 Iteration 5 Error: 0.017929 Align patch 6 19 left Iteration 1 Error: 0.487967 Iteration 2 Error: 0.104164 Iteration 3 Error: 0.020987 Align patch 7 18 left Iteration 1 Error: 1.336898 Iteration 2 Error: 0.193389 Iteration 3 Error: 0.048655 Align patch 8 17 left Iteration 1 Error: 1.184305 Iteration 2 Error: 0.194302 Iteration 3 Error: 0.065683 Iteration 4 Error: 0.020724 Align patch 9 16 left Iteration 1 Error: 0.731669 Iteration 2 Error: 0.180600 Iteration 3 Error: 0.035981 Align patch 10 15 left Iteration 1 Error: 1.605623 Iteration 2 Error: 0.272543 Iteration 3 Error: 0.080623 Iteration 4 Error: 0.028625 Align patch 11 14 left Iteration 1 Error: 1.298339 Iteration 2 Error: 0.263503 Iteration 3 Error: 0.090721 Iteration 4 Error: 0.053233 Iteration 5 Error: 0.021549 Align patch 12 13 left Iteration 1 Error: 0.781410 Iteration 2 Error: 0.122719 Iteration 3 Error: 0.035954 Align patch 13 12 left Iteration 1 Error: 0.735674 Iteration 2 Error: 0.218775 Iteration 3 Error: 0.068874 Iteration 4 Error: 0.022871 Align patch 14 11 left Iteration 1 Error: 0.580318 Iteration 2 Error: 0.103316 Iteration 3 Error: 0.043618 Align patch 15 10 left Iteration 1 Error: 0.894278 Iteration 2 Error: 0.122050 Iteration 3 Error: 0.023047 Align patch 16 9 left Iteration 1 Error: 0.981637 Iteration 2 Error: 0.175713 Iteration 3 Error: 0.045838 Align patch 17 8 left Iteration 1 Error: 0.675823 Iteration 2 Error: 0.253430 Iteration 3 Error: 0.066522 Iteration 4 Error: 0.033042 Align patch 18 7 left Iteration 1 Error: 0.885379 Iteration 2 Error: 0.125644 Iteration 3 Error: 0.035508 Align patch 19 6 left Iteration 1 Error: 1.011597 Iteration 2 Error: 0.208641 Iteration 3 Error: 0.061426 Iteration 4 Error: 0.022482 Align patch 20 5 left Iteration 1 Error: 0.832862 Iteration 2 Error: 0.110620 Iteration 3 Error: 0.033363 Align patch 21 4 left Iteration 1 Error: 0.716971 Iteration 2 Error: 0.120299 Iteration 3 Error: 0.025982 Align patch 22 3 left Iteration 1 Error: 1.042192 Iteration 2 Error: 0.268222 Iteration 3 Error: 0.092029 Iteration 4 Error: 0.023849 Align patch 23 2 left Iteration 1 Error: 1.242986 Iteration 2 Error: 0.153728 Iteration 3 Error: 0.048549 Align patch 24 1 left Iteration 1 Error: 0.959454 Iteration 2 Error: 0.129542 Iteration 3 Error: 0.030541 Align patch 25 0 left Iteration 1 Error: 1.274853 Iteration 2 Error: 0.137389 Iteration 3 Error: 0.030873 3D Fitting completed. Patch alignment time: 12.65(sec) Local motion has been corrected. Process thread exits. Computational time: 25.886358 sec Total time: 33.714817 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00032hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00032hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.461207s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00032hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.966184s ........................................ >>>>>>TIME<<<<<< FFT: 1.167468s Defocus_U Defocus_V Angle CCC 12250.03 13082.12 9.87 0.029180 Final Values Defocus_U Defocus_V Angle CCC 12218.78 13210.32 4.34 0.042160 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00032hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00032hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.993e-02 CC threshold: 0.734 Mean Std: 40.89 6.79 Num Hot pixels: 216 Hot pixel threshold: 81.66 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.988361 Iteration 2 Error: 0.444391 Iteration 3 Error: 0.160252 Iteration 4 Error: 0.066488 Iteration 5 Error: 0.022442 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.04 -0.14 ...... Frame ( 3) shift: 0.07 -0.27 ...... Frame ( 4) shift: 0.11 -0.41 ...... Frame ( 5) shift: 0.14 -0.55 ...... Frame ( 6) shift: 0.19 -0.55 ...... Frame ( 7) shift: 0.24 -0.43 ...... Frame ( 8) shift: 0.30 -0.30 ...... Frame ( 9) shift: 0.43 -0.17 ...... Frame ( 10) shift: 0.64 -0.03 ...... Frame ( 11) shift: 0.85 0.11 ...... Frame ( 12) shift: 1.02 0.26 ...... Frame ( 13) shift: 1.15 0.43 ...... Frame ( 14) shift: 1.28 0.60 ...... Frame ( 15) shift: 1.42 0.73 ...... Frame ( 16) shift: 1.55 0.83 ...... Frame ( 17) shift: 1.69 0.92 ...... Frame ( 18) shift: 1.78 1.01 ...... Frame ( 19) shift: 1.83 1.09 ...... Frame ( 20) shift: 1.88 1.16 ...... Frame ( 21) shift: 1.96 1.25 ...... Frame ( 22) shift: 2.08 1.35 ...... Frame ( 23) shift: 2.19 1.44 ...... Frame ( 24) shift: 2.31 1.54 ...... Frame ( 25) shift: 2.43 1.63 ...... Frame ( 26) shift: 2.56 1.72 ...... Frame ( 27) shift: 2.66 1.80 ...... Frame ( 28) shift: 2.75 1.87 ...... Frame ( 29) shift: 2.83 1.95 ...... Frame ( 30) shift: 2.96 1.99 ...... Frame ( 31) shift: 3.12 2.00 ...... Frame ( 32) shift: 3.28 2.01 ...... Frame ( 33) shift: 3.39 2.04 ...... Frame ( 34) shift: 3.45 2.09 ...... Frame ( 35) shift: 3.51 2.14 ...... Frame ( 36) shift: 3.57 2.18 ...... Frame ( 37) shift: 3.65 2.21 ...... Frame ( 38) shift: 3.72 2.24 ...... Frame ( 39) shift: 3.79 2.27 ...... Frame ( 40) shift: 3.87 2.30 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.566795 Iteration 2 Error: 0.241889 Iteration 3 Error: 0.054582 Iteration 4 Error: 0.017133 Align patch 2 23 left Iteration 1 Error: 0.745613 Iteration 2 Error: 0.136984 Iteration 3 Error: 0.050090 Iteration 4 Error: 0.031579 Align patch 3 22 left Iteration 1 Error: 0.618334 Iteration 2 Error: 0.177120 Iteration 3 Error: 0.041553 Align patch 4 21 left Iteration 1 Error: 0.616073 Iteration 2 Error: 0.144003 Iteration 3 Error: 0.039685 Align patch 5 20 left Iteration 1 Error: 0.713809 Iteration 2 Error: 0.223684 Iteration 3 Error: 0.053869 Iteration 4 Error: 0.014655 Align patch 6 19 left Iteration 1 Error: 1.398308 Iteration 2 Error: 0.200324 Iteration 3 Error: 0.048030 Align patch 7 18 left Iteration 1 Error: 0.819025 Iteration 2 Error: 0.084197 Iteration 3 Error: 0.032199 Align patch 8 17 left Iteration 1 Error: 0.600261 Iteration 2 Error: 0.161706 Iteration 3 Error: 0.061004 Iteration 4 Error: 0.039144 Align patch 9 16 left Iteration 1 Error: 0.689324 Iteration 2 Error: 0.241038 Iteration 3 Error: 0.085342 Iteration 4 Error: 0.031939 Align patch 10 15 left Iteration 1 Error: 0.740687 Iteration 2 Error: 0.167206 Iteration 3 Error: 0.054305 Iteration 4 Error: 0.019335 Align patch 11 14 left Iteration 1 Error: 1.107477 Iteration 2 Error: 0.178723 Iteration 3 Error: 0.037437 Align patch 12 13 left Iteration 1 Error: 1.118541 Iteration 2 Error: 0.188012 Iteration 3 Error: 0.075172 Iteration 4 Error: 0.035012 Align patch 13 12 left Iteration 1 Error: 0.840543 Iteration 2 Error: 0.191523 Iteration 3 Error: 0.102142 Iteration 4 Error: 0.037717 Align patch 14 11 left Iteration 1 Error: 0.638538 Iteration 2 Error: 0.119626 Iteration 3 Error: 0.032032 Align patch 15 10 left Iteration 1 Error: 1.043357 Iteration 2 Error: 0.210512 Iteration 3 Error: 0.090944 Iteration 4 Error: 0.034187 Align patch 16 9 left Iteration 1 Error: 0.798015 Iteration 2 Error: 0.140130 Iteration 3 Error: 0.034406 Align patch 17 8 left Iteration 1 Error: 0.849541 Iteration 2 Error: 0.137083 Iteration 3 Error: 0.052948 Iteration 4 Error: 0.022033 Align patch 18 7 left Iteration 1 Error: 0.727418 Iteration 2 Error: 0.249868 Iteration 3 Error: 0.106429 Iteration 4 Error: 0.038170 Align patch 19 6 left Iteration 1 Error: 0.734776 Iteration 2 Error: 0.109473 Iteration 3 Error: 0.038147 Align patch 20 5 left Iteration 1 Error: 0.760981 Iteration 2 Error: 0.177447 Iteration 3 Error: 0.071192 Iteration 4 Error: 0.025194 Align patch 21 4 left Iteration 1 Error: 0.551472 Iteration 2 Error: 0.114141 Iteration 3 Error: 0.026296 Align patch 22 3 left Iteration 1 Error: 1.064576 Iteration 2 Error: 0.156723 Iteration 3 Error: 0.017893 Align patch 23 2 left Iteration 1 Error: 1.051366 Iteration 2 Error: 0.206207 Iteration 3 Error: 0.053545 Iteration 4 Error: 0.036727 Align patch 24 1 left Iteration 1 Error: 0.767332 Iteration 2 Error: 0.117279 Iteration 3 Error: 0.048390 Align patch 25 0 left Iteration 1 Error: 1.414520 Iteration 2 Error: 0.261222 Iteration 3 Error: 0.059465 Iteration 4 Error: 0.036631 3D Fitting completed. Patch alignment time: 14.28(sec) Local motion has been corrected. Process thread exits. Computational time: 29.810987 sec Total time: 37.561146 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00032hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00032hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.570571s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00032hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.203302s ........................................ >>>>>>TIME<<<<<< FFT: 1.140588s Defocus_U Defocus_V Angle CCC 13289.08 14000.01 2.51 0.054829 Final Values Defocus_U Defocus_V Angle CCC 13284.39 14004.70 2.19 0.086528 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00033hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00033hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.992e-02 CC threshold: 0.734 Mean Std: 41.55 6.85 Num Hot pixels: 209 Hot pixel threshold: 82.67 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.528059 Iteration 2 Error: 0.322475 Iteration 3 Error: 0.095845 Iteration 4 Error: 0.027832 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.13 -0.25 ...... Frame ( 3) shift: 0.27 -0.49 ...... Frame ( 4) shift: 0.40 -0.74 ...... Frame ( 5) shift: 0.54 -0.99 ...... Frame ( 6) shift: 0.61 -1.05 ...... Frame ( 7) shift: 0.60 -0.94 ...... Frame ( 8) shift: 0.60 -0.82 ...... Frame ( 9) shift: 0.63 -0.68 ...... Frame ( 10) shift: 0.70 -0.51 ...... Frame ( 11) shift: 0.77 -0.34 ...... Frame ( 12) shift: 0.83 -0.20 ...... Frame ( 13) shift: 0.89 -0.11 ...... Frame ( 14) shift: 0.96 -0.01 ...... Frame ( 15) shift: 1.00 0.10 ...... Frame ( 16) shift: 1.01 0.23 ...... Frame ( 17) shift: 1.02 0.35 ...... Frame ( 18) shift: 1.03 0.49 ...... Frame ( 19) shift: 1.03 0.65 ...... Frame ( 20) shift: 1.03 0.80 ...... Frame ( 21) shift: 1.05 0.93 ...... Frame ( 22) shift: 1.09 1.03 ...... Frame ( 23) shift: 1.14 1.13 ...... Frame ( 24) shift: 1.19 1.25 ...... Frame ( 25) shift: 1.26 1.37 ...... Frame ( 26) shift: 1.32 1.49 ...... Frame ( 27) shift: 1.36 1.59 ...... Frame ( 28) shift: 1.39 1.67 ...... Frame ( 29) shift: 1.41 1.74 ...... Frame ( 30) shift: 1.43 1.79 ...... Frame ( 31) shift: 1.46 1.81 ...... Frame ( 32) shift: 1.49 1.83 ...... Frame ( 33) shift: 1.52 1.87 ...... Frame ( 34) shift: 1.55 1.95 ...... Frame ( 35) shift: 1.58 2.02 ...... Frame ( 36) shift: 1.65 2.05 ...... Frame ( 37) shift: 1.75 2.05 ...... Frame ( 38) shift: 1.85 2.04 ...... Frame ( 39) shift: 1.95 2.03 ...... Frame ( 40) shift: 2.05 2.03 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.129923 Iteration 2 Error: 0.186377 Iteration 3 Error: 0.047773 Align patch 2 23 left Iteration 1 Error: 1.040207 Iteration 2 Error: 0.210341 Iteration 3 Error: 0.051206 Iteration 4 Error: 0.025901 Align patch 3 22 left Iteration 1 Error: 0.729965 Iteration 2 Error: 0.208346 Iteration 3 Error: 0.043661 Align patch 4 21 left Iteration 1 Error: 1.192920 Iteration 2 Error: 0.171571 Iteration 3 Error: 0.056945 Iteration 4 Error: 0.032395 Align patch 5 20 left Iteration 1 Error: 0.758097 Iteration 2 Error: 0.122175 Iteration 3 Error: 0.052703 Iteration 4 Error: 0.027228 Align patch 6 19 left Iteration 1 Error: 1.599997 Iteration 2 Error: 0.362355 Iteration 3 Error: 0.071902 Iteration 4 Error: 0.038493 Align patch 7 18 left Iteration 1 Error: 1.033365 Iteration 2 Error: 0.180252 Iteration 3 Error: 0.055768 Iteration 4 Error: 0.020637 Align patch 8 17 left Iteration 1 Error: 1.348654 Iteration 2 Error: 0.338340 Iteration 3 Error: 0.146007 Iteration 4 Error: 0.062899 Iteration 5 Error: 0.035114 Align patch 9 16 left Iteration 1 Error: 1.412365 Iteration 2 Error: 0.190191 Iteration 3 Error: 0.064292 Iteration 4 Error: 0.020879 Align patch 10 15 left Iteration 1 Error: 0.926810 Iteration 2 Error: 0.117755 Iteration 3 Error: 0.036298 Align patch 11 14 left Iteration 1 Error: 0.960539 Iteration 2 Error: 0.276146 Iteration 3 Error: 0.088212 Iteration 4 Error: 0.066338 Iteration 5 Error: 0.025499 Align patch 12 13 left Iteration 1 Error: 0.623148 Iteration 2 Error: 0.123702 Iteration 3 Error: 0.040394 Align patch 13 12 left Iteration 1 Error: 0.787585 Iteration 2 Error: 0.146913 Iteration 3 Error: 0.031293 Align patch 14 11 left Iteration 1 Error: 1.084870 Iteration 2 Error: 0.120980 Iteration 3 Error: 0.049124 Align patch 15 10 left Iteration 1 Error: 0.930544 Iteration 2 Error: 0.097060 Iteration 3 Error: 0.021810 Align patch 16 9 left Iteration 1 Error: 0.847436 Iteration 2 Error: 0.152570 Iteration 3 Error: 0.041080 Align patch 17 8 left Iteration 1 Error: 0.753226 Iteration 2 Error: 0.201514 Iteration 3 Error: 0.061199 Iteration 4 Error: 0.021019 Align patch 18 7 left Iteration 1 Error: 0.935307 Iteration 2 Error: 0.105504 Iteration 3 Error: 0.042339 Align patch 19 6 left Iteration 1 Error: 0.565737 Iteration 2 Error: 0.186711 Iteration 3 Error: 0.047615 Align patch 20 5 left Iteration 1 Error: 1.223039 Iteration 2 Error: 0.223444 Iteration 3 Error: 0.050400 Iteration 4 Error: 0.020447 Align patch 21 4 left Iteration 1 Error: 0.947179 Iteration 2 Error: 0.226499 Iteration 3 Error: 0.064805 Iteration 4 Error: 0.024634 Align patch 22 3 left Iteration 1 Error: 0.753004 Iteration 2 Error: 0.150661 Iteration 3 Error: 0.037023 Align patch 23 2 left Iteration 1 Error: 1.041443 Iteration 2 Error: 0.221569 Iteration 3 Error: 0.051572 Iteration 4 Error: 0.018717 Align patch 24 1 left Iteration 1 Error: 0.788476 Iteration 2 Error: 0.166677 Iteration 3 Error: 0.045176 Align patch 25 0 left Iteration 1 Error: 0.778088 Iteration 2 Error: 0.168257 Iteration 3 Error: 0.047212 3D Fitting completed. Patch alignment time: 14.01(sec) Local motion has been corrected. Process thread exits. Computational time: 26.860537 sec Total time: 34.690186 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00033hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00033hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.599386s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00033hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.596177s ........................................ >>>>>>TIME<<<<<< FFT: 0.944610s Defocus_U Defocus_V Angle CCC 14283.21 15044.92 11.12 0.054259 Final Values Defocus_U Defocus_V Angle CCC 14278.53 15040.23 11.12 0.087852 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00033hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00033hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.991e-02 CC threshold: 0.734 Mean Std: 41.25 6.83 Num Hot pixels: 200 Hot pixel threshold: 82.20 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.303207 Iteration 2 Error: 0.246663 Iteration 3 Error: 0.060093 Iteration 4 Error: 0.022021 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.17 -0.24 ...... Frame ( 3) shift: 0.35 -0.48 ...... Frame ( 4) shift: 0.52 -0.72 ...... Frame ( 5) shift: 0.70 -0.96 ...... Frame ( 6) shift: 0.83 -1.07 ...... Frame ( 7) shift: 0.92 -1.03 ...... Frame ( 8) shift: 1.02 -0.99 ...... Frame ( 9) shift: 1.06 -0.89 ...... Frame ( 10) shift: 1.06 -0.72 ...... Frame ( 11) shift: 1.06 -0.55 ...... Frame ( 12) shift: 1.11 -0.40 ...... Frame ( 13) shift: 1.22 -0.28 ...... Frame ( 14) shift: 1.33 -0.15 ...... Frame ( 15) shift: 1.40 -0.01 ...... Frame ( 16) shift: 1.45 0.16 ...... Frame ( 17) shift: 1.50 0.32 ...... Frame ( 18) shift: 1.51 0.43 ...... Frame ( 19) shift: 1.48 0.48 ...... Frame ( 20) shift: 1.44 0.52 ...... Frame ( 21) shift: 1.46 0.58 ...... Frame ( 22) shift: 1.54 0.65 ...... Frame ( 23) shift: 1.61 0.71 ...... Frame ( 24) shift: 1.64 0.78 ...... Frame ( 25) shift: 1.63 0.85 ...... Frame ( 26) shift: 1.62 0.92 ...... Frame ( 27) shift: 1.62 0.97 ...... Frame ( 28) shift: 1.63 1.00 ...... Frame ( 29) shift: 1.65 1.03 ...... Frame ( 30) shift: 1.66 1.06 ...... Frame ( 31) shift: 1.67 1.09 ...... Frame ( 32) shift: 1.69 1.11 ...... Frame ( 33) shift: 1.74 1.16 ...... Frame ( 34) shift: 1.83 1.21 ...... Frame ( 35) shift: 1.92 1.27 ...... Frame ( 36) shift: 1.98 1.32 ...... Frame ( 37) shift: 2.00 1.38 ...... Frame ( 38) shift: 2.02 1.43 ...... Frame ( 39) shift: 2.04 1.48 ...... Frame ( 40) shift: 2.06 1.54 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.678122 Iteration 2 Error: 0.283089 Iteration 3 Error: 0.072212 Iteration 4 Error: 0.032521 Align patch 2 23 left Iteration 1 Error: 1.270057 Iteration 2 Error: 0.225414 Iteration 3 Error: 0.086142 Iteration 4 Error: 0.032507 Align patch 3 22 left Iteration 1 Error: 0.737149 Iteration 2 Error: 0.130572 Iteration 3 Error: 0.037767 Align patch 4 21 left Iteration 1 Error: 0.806100 Iteration 2 Error: 0.112305 Iteration 3 Error: 0.031612 Align patch 5 20 left Iteration 1 Error: 1.042725 Iteration 2 Error: 0.173018 Iteration 3 Error: 0.041086 Align patch 6 19 left Iteration 1 Error: 0.932102 Iteration 2 Error: 0.146948 Iteration 3 Error: 0.032847 Align patch 7 18 left Iteration 1 Error: 1.091058 Iteration 2 Error: 0.165347 Iteration 3 Error: 0.043977 Align patch 8 17 left Iteration 1 Error: 0.956436 Iteration 2 Error: 0.097633 Iteration 3 Error: 0.034538 Align patch 9 16 left Iteration 1 Error: 0.670988 Iteration 2 Error: 0.159626 Iteration 3 Error: 0.044231 Align patch 10 15 left Iteration 1 Error: 0.771042 Iteration 2 Error: 0.157904 Iteration 3 Error: 0.061216 Iteration 4 Error: 0.022949 Align patch 11 14 left Iteration 1 Error: 0.692446 Iteration 2 Error: 0.136632 Iteration 3 Error: 0.045079 Align patch 12 13 left Iteration 1 Error: 0.917728 Iteration 2 Error: 0.320481 Iteration 3 Error: 0.111147 Iteration 4 Error: 0.038646 Align patch 13 12 left Iteration 1 Error: 0.798088 Iteration 2 Error: 0.132520 Iteration 3 Error: 0.023898 Align patch 14 11 left Iteration 1 Error: 0.662123 Iteration 2 Error: 0.167825 Iteration 3 Error: 0.051765 Iteration 4 Error: 0.025669 Align patch 15 10 left Iteration 1 Error: 0.588569 Iteration 2 Error: 0.122490 Iteration 3 Error: 0.036313 Align patch 16 9 left Iteration 1 Error: 0.647265 Iteration 2 Error: 0.126132 Iteration 3 Error: 0.020981 Align patch 17 8 left Iteration 1 Error: 0.849505 Iteration 2 Error: 0.172889 Iteration 3 Error: 0.042891 Align patch 18 7 left Iteration 1 Error: 0.853851 Iteration 2 Error: 0.160200 Iteration 3 Error: 0.042913 Align patch 19 6 left Iteration 1 Error: 0.891017 Iteration 2 Error: 0.112979 Iteration 3 Error: 0.031668 Align patch 20 5 left Iteration 1 Error: 0.689164 Iteration 2 Error: 0.144392 Iteration 3 Error: 0.030465 Align patch 21 4 left Iteration 1 Error: 0.711565 Iteration 2 Error: 0.206792 Iteration 3 Error: 0.041123 Align patch 22 3 left Iteration 1 Error: 1.108808 Iteration 2 Error: 0.120341 Iteration 3 Error: 0.027166 Align patch 23 2 left Iteration 1 Error: 0.952388 Iteration 2 Error: 0.162490 Iteration 3 Error: 0.040976 Align patch 24 1 left Iteration 1 Error: 0.542833 Iteration 2 Error: 0.083910 Iteration 3 Error: 0.018463 Align patch 25 0 left Iteration 1 Error: 0.491671 Iteration 2 Error: 0.101067 Iteration 3 Error: 0.042197 3D Fitting completed. Patch alignment time: 12.64(sec) Local motion has been corrected. Process thread exits. Computational time: 26.796877 sec Total time: 34.328537 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00033hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00033hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.704139s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00033hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.006446s ........................................ >>>>>>TIME<<<<<< FFT: 0.937644s Defocus_U Defocus_V Angle CCC 12785.16 13562.50 5.58 0.042518 Final Values Defocus_U Defocus_V Angle CCC 12788.28 13559.38 6.21 0.071017 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00033hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00033hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.994e-02 CC threshold: 0.734 Mean Std: 41.38 6.83 Num Hot pixels: 202 Hot pixel threshold: 82.37 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.408047 Iteration 2 Error: 0.208632 Iteration 3 Error: 0.055852 Iteration 4 Error: 0.008685 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.02 -0.20 ...... Frame ( 3) shift: 0.04 -0.39 ...... Frame ( 4) shift: 0.06 -0.59 ...... Frame ( 5) shift: 0.08 -0.78 ...... Frame ( 6) shift: 0.14 -0.80 ...... Frame ( 7) shift: 0.23 -0.64 ...... Frame ( 8) shift: 0.32 -0.48 ...... Frame ( 9) shift: 0.32 -0.33 ...... Frame ( 10) shift: 0.23 -0.17 ...... Frame ( 11) shift: 0.14 -0.02 ...... Frame ( 12) shift: 0.10 0.08 ...... Frame ( 13) shift: 0.10 0.13 ...... Frame ( 14) shift: 0.11 0.17 ...... Frame ( 15) shift: 0.14 0.27 ...... Frame ( 16) shift: 0.17 0.43 ...... Frame ( 17) shift: 0.21 0.58 ...... Frame ( 18) shift: 0.23 0.72 ...... Frame ( 19) shift: 0.21 0.85 ...... Frame ( 20) shift: 0.20 0.97 ...... Frame ( 21) shift: 0.19 1.03 ...... Frame ( 22) shift: 0.18 1.04 ...... Frame ( 23) shift: 0.17 1.05 ...... Frame ( 24) shift: 0.16 1.09 ...... Frame ( 25) shift: 0.15 1.18 ...... Frame ( 26) shift: 0.14 1.27 ...... Frame ( 27) shift: 0.15 1.33 ...... Frame ( 28) shift: 0.17 1.34 ...... Frame ( 29) shift: 0.19 1.36 ...... Frame ( 30) shift: 0.21 1.42 ...... Frame ( 31) shift: 0.24 1.52 ...... Frame ( 32) shift: 0.27 1.63 ...... Frame ( 33) shift: 0.31 1.68 ...... Frame ( 34) shift: 0.36 1.67 ...... Frame ( 35) shift: 0.42 1.67 ...... Frame ( 36) shift: 0.44 1.70 ...... Frame ( 37) shift: 0.44 1.75 ...... Frame ( 38) shift: 0.43 1.81 ...... Frame ( 39) shift: 0.43 1.87 ...... Frame ( 40) shift: 0.42 1.92 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.906487 Iteration 2 Error: 0.115851 Iteration 3 Error: 0.026740 Align patch 2 23 left Iteration 1 Error: 0.877839 Iteration 2 Error: 0.093253 Iteration 3 Error: 0.025547 Align patch 3 22 left Iteration 1 Error: 0.805413 Iteration 2 Error: 0.277603 Iteration 3 Error: 0.076289 Iteration 4 Error: 0.027173 Align patch 4 21 left Iteration 1 Error: 0.703254 Iteration 2 Error: 0.108931 Iteration 3 Error: 0.019890 Align patch 5 20 left Iteration 1 Error: 0.764411 Iteration 2 Error: 0.196042 Iteration 3 Error: 0.042678 Align patch 6 19 left Iteration 1 Error: 1.105894 Iteration 2 Error: 0.167144 Iteration 3 Error: 0.064115 Iteration 4 Error: 0.028006 Align patch 7 18 left Iteration 1 Error: 1.116234 Iteration 2 Error: 0.108765 Iteration 3 Error: 0.025734 Align patch 8 17 left Iteration 1 Error: 0.912323 Iteration 2 Error: 0.150717 Iteration 3 Error: 0.054143 Iteration 4 Error: 0.026652 Align patch 9 16 left Iteration 1 Error: 0.889221 Iteration 2 Error: 0.100983 Iteration 3 Error: 0.035306 Align patch 10 15 left Iteration 1 Error: 0.928675 Iteration 2 Error: 0.211484 Iteration 3 Error: 0.051711 Iteration 4 Error: 0.028650 Align patch 11 14 left Iteration 1 Error: 1.041459 Iteration 2 Error: 0.258300 Iteration 3 Error: 0.050338 Iteration 4 Error: 0.031250 Align patch 12 13 left Iteration 1 Error: 0.774799 Iteration 2 Error: 0.155337 Iteration 3 Error: 0.040811 Align patch 13 12 left Iteration 1 Error: 0.731818 Iteration 2 Error: 0.158057 Iteration 3 Error: 0.075875 Iteration 4 Error: 0.021163 Align patch 14 11 left Iteration 1 Error: 0.600022 Iteration 2 Error: 0.107662 Iteration 3 Error: 0.024071 Align patch 15 10 left Iteration 1 Error: 0.572284 Iteration 2 Error: 0.122912 Iteration 3 Error: 0.032041 Align patch 16 9 left Iteration 1 Error: 0.890081 Iteration 2 Error: 0.178655 Iteration 3 Error: 0.059772 Iteration 4 Error: 0.019176 Align patch 17 8 left Iteration 1 Error: 1.021848 Iteration 2 Error: 0.173263 Iteration 3 Error: 0.042930 Align patch 18 7 left Iteration 1 Error: 0.931358 Iteration 2 Error: 0.185965 Iteration 3 Error: 0.040436 Align patch 19 6 left Iteration 1 Error: 0.974605 Iteration 2 Error: 0.182830 Iteration 3 Error: 0.067888 Iteration 4 Error: 0.017182 Align patch 20 5 left Iteration 1 Error: 0.811133 Iteration 2 Error: 0.156080 Iteration 3 Error: 0.039614 Align patch 21 4 left Iteration 1 Error: 0.740737 Iteration 2 Error: 0.154410 Iteration 3 Error: 0.034693 Align patch 22 3 left Iteration 1 Error: 0.806039 Iteration 2 Error: 0.155653 Iteration 3 Error: 0.058716 Iteration 4 Error: 0.020415 Align patch 23 2 left Iteration 1 Error: 0.834839 Iteration 2 Error: 0.151042 Iteration 3 Error: 0.033922 Align patch 24 1 left Iteration 1 Error: 0.791952 Iteration 2 Error: 0.162270 Iteration 3 Error: 0.044245 Align patch 25 0 left Iteration 1 Error: 0.840977 Iteration 2 Error: 0.158140 Iteration 3 Error: 0.042433 3D Fitting completed. Patch alignment time: 12.93(sec) Local motion has been corrected. Process thread exits. Computational time: 27.744001 sec Total time: 35.433781 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00033hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00033hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.542712s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00033hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 4.646867s ........................................ >>>>>>TIME<<<<<< FFT: 1.069699s Defocus_U Defocus_V Angle CCC 14369.18 14990.27 2.17 0.050521 Final Values Defocus_U Defocus_V Angle CCC 14395.75 14991.84 4.37 0.081765 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00033hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00033hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.734 Mean Std: 40.98 6.81 Num Hot pixels: 213 Hot pixel threshold: 81.87 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.845684 Iteration 2 Error: 0.093889 Iteration 3 Error: 0.017990 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.17 -0.27 ...... Frame ( 3) shift: 0.34 -0.54 ...... Frame ( 4) shift: 0.52 -0.81 ...... Frame ( 5) shift: 0.69 -1.08 ...... Frame ( 6) shift: 0.76 -1.19 ...... Frame ( 7) shift: 0.72 -1.15 ...... Frame ( 8) shift: 0.68 -1.11 ...... Frame ( 9) shift: 0.66 -1.02 ...... Frame ( 10) shift: 0.65 -0.90 ...... Frame ( 11) shift: 0.64 -0.77 ...... Frame ( 12) shift: 0.64 -0.66 ...... Frame ( 13) shift: 0.65 -0.56 ...... Frame ( 14) shift: 0.66 -0.47 ...... Frame ( 15) shift: 0.65 -0.41 ...... Frame ( 16) shift: 0.60 -0.39 ...... Frame ( 17) shift: 0.55 -0.36 ...... Frame ( 18) shift: 0.57 -0.31 ...... Frame ( 19) shift: 0.66 -0.23 ...... Frame ( 20) shift: 0.75 -0.15 ...... Frame ( 21) shift: 0.77 -0.10 ...... Frame ( 22) shift: 0.73 -0.06 ...... Frame ( 23) shift: 0.69 -0.03 ...... Frame ( 24) shift: 0.65 -0.02 ...... Frame ( 25) shift: 0.63 -0.02 ...... Frame ( 26) shift: 0.61 -0.02 ...... Frame ( 27) shift: 0.60 -0.02 ...... Frame ( 28) shift: 0.58 -0.03 ...... Frame ( 29) shift: 0.57 -0.03 ...... Frame ( 30) shift: 0.60 -0.03 ...... Frame ( 31) shift: 0.66 -0.01 ...... Frame ( 32) shift: 0.73 0.01 ...... Frame ( 33) shift: 0.73 0.04 ...... Frame ( 34) shift: 0.67 0.09 ...... Frame ( 35) shift: 0.62 0.13 ...... Frame ( 36) shift: 0.61 0.16 ...... Frame ( 37) shift: 0.67 0.17 ...... Frame ( 38) shift: 0.72 0.17 ...... Frame ( 39) shift: 0.78 0.18 ...... Frame ( 40) shift: 0.83 0.19 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.128931 Iteration 2 Error: 0.168119 Iteration 3 Error: 0.018367 Align patch 2 23 left Iteration 1 Error: 0.599784 Iteration 2 Error: 0.186834 Iteration 3 Error: 0.051291 Iteration 4 Error: 0.021699 Align patch 3 22 left Iteration 1 Error: 0.831064 Iteration 2 Error: 0.190215 Iteration 3 Error: 0.049190 Align patch 4 21 left Iteration 1 Error: 0.843171 Iteration 2 Error: 0.116869 Iteration 3 Error: 0.028318 Align patch 5 20 left Iteration 1 Error: 1.051727 Iteration 2 Error: 0.128428 Iteration 3 Error: 0.023705 Align patch 6 19 left Iteration 1 Error: 0.627325 Iteration 2 Error: 0.099570 Iteration 3 Error: 0.016899 Align patch 7 18 left Iteration 1 Error: 0.901393 Iteration 2 Error: 0.116812 Iteration 3 Error: 0.034673 Align patch 8 17 left Iteration 1 Error: 0.897941 Iteration 2 Error: 0.136683 Iteration 3 Error: 0.034913 Align patch 9 16 left Iteration 1 Error: 0.857763 Iteration 2 Error: 0.123032 Iteration 3 Error: 0.037483 Align patch 10 15 left Iteration 1 Error: 0.755156 Iteration 2 Error: 0.135020 Iteration 3 Error: 0.031934 Align patch 11 14 left Iteration 1 Error: 0.889879 Iteration 2 Error: 0.172750 Iteration 3 Error: 0.029937 Align patch 12 13 left Iteration 1 Error: 0.699669 Iteration 2 Error: 0.106934 Iteration 3 Error: 0.032423 Align patch 13 12 left Iteration 1 Error: 0.692348 Iteration 2 Error: 0.110639 Iteration 3 Error: 0.027237 Align patch 14 11 left Iteration 1 Error: 0.651826 Iteration 2 Error: 0.119517 Iteration 3 Error: 0.026734 Align patch 15 10 left Iteration 1 Error: 0.876898 Iteration 2 Error: 0.099059 Iteration 3 Error: 0.018812 Align patch 16 9 left Iteration 1 Error: 0.720279 Iteration 2 Error: 0.126582 Iteration 3 Error: 0.035543 Align patch 17 8 left Iteration 1 Error: 0.665585 Iteration 2 Error: 0.069607 Iteration 3 Error: 0.018260 Align patch 18 7 left Iteration 1 Error: 0.737554 Iteration 2 Error: 0.096007 Iteration 3 Error: 0.022058 Align patch 19 6 left Iteration 1 Error: 0.694768 Iteration 2 Error: 0.130124 Iteration 3 Error: 0.025657 Align patch 20 5 left Iteration 1 Error: 0.624844 Iteration 2 Error: 0.133063 Iteration 3 Error: 0.034039 Align patch 21 4 left Iteration 1 Error: 1.142071 Iteration 2 Error: 0.180247 Iteration 3 Error: 0.040123 Align patch 22 3 left Iteration 1 Error: 1.050723 Iteration 2 Error: 0.158883 Iteration 3 Error: 0.027572 Align patch 23 2 left Iteration 1 Error: 0.732304 Iteration 2 Error: 0.147211 Iteration 3 Error: 0.020383 Align patch 24 1 left Iteration 1 Error: 0.712032 Iteration 2 Error: 0.068587 Iteration 3 Error: 0.019834 Align patch 25 0 left Iteration 1 Error: 0.887231 Iteration 2 Error: 0.182271 Iteration 3 Error: 0.047047 3D Fitting completed. Patch alignment time: 11.12(sec) Local motion has been corrected. Process thread exits. Computational time: 24.319397 sec Total time: 33.581268 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00033hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00033hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.571052s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00033hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.952605s ........................................ >>>>>>TIME<<<<<< FFT: 0.943938s Defocus_U Defocus_V Angle CCC 17536.55 18412.67 1.01 0.033890 Final Values Defocus_U Defocus_V Angle CCC 17564.70 18418.94 1.95 0.056228 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00034hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00034hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.988e-02 CC threshold: 0.734 Mean Std: 37.89 6.60 Num Hot pixels: 182 Hot pixel threshold: 77.49 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.385411 Iteration 2 Error: 0.312594 Iteration 3 Error: 0.104085 Iteration 4 Error: 0.037701 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.12 -0.28 ...... Frame ( 3) shift: 0.24 -0.56 ...... Frame ( 4) shift: 0.37 -0.83 ...... Frame ( 5) shift: 0.49 -1.11 ...... Frame ( 6) shift: 0.62 -1.23 ...... Frame ( 7) shift: 0.77 -1.18 ...... Frame ( 8) shift: 0.91 -1.13 ...... Frame ( 9) shift: 0.99 -1.04 ...... Frame ( 10) shift: 0.99 -0.91 ...... Frame ( 11) shift: 0.99 -0.77 ...... Frame ( 12) shift: 1.05 -0.68 ...... Frame ( 13) shift: 1.17 -0.61 ...... Frame ( 14) shift: 1.28 -0.55 ...... Frame ( 15) shift: 1.40 -0.50 ...... Frame ( 16) shift: 1.52 -0.48 ...... Frame ( 17) shift: 1.65 -0.45 ...... Frame ( 18) shift: 1.76 -0.42 ...... Frame ( 19) shift: 1.87 -0.37 ...... Frame ( 20) shift: 1.98 -0.33 ...... Frame ( 21) shift: 2.04 -0.28 ...... Frame ( 22) shift: 2.05 -0.24 ...... Frame ( 23) shift: 2.07 -0.20 ...... Frame ( 24) shift: 2.10 -0.16 ...... Frame ( 25) shift: 2.14 -0.10 ...... Frame ( 26) shift: 2.18 -0.05 ...... Frame ( 27) shift: 2.25 0.02 ...... Frame ( 28) shift: 2.36 0.12 ...... Frame ( 29) shift: 2.47 0.21 ...... Frame ( 30) shift: 2.54 0.28 ...... Frame ( 31) shift: 2.58 0.32 ...... Frame ( 32) shift: 2.61 0.37 ...... Frame ( 33) shift: 2.68 0.39 ...... Frame ( 34) shift: 2.79 0.41 ...... Frame ( 35) shift: 2.90 0.42 ...... Frame ( 36) shift: 2.96 0.42 ...... Frame ( 37) shift: 2.98 0.42 ...... Frame ( 38) shift: 3.00 0.42 ...... Frame ( 39) shift: 3.01 0.42 ...... Frame ( 40) shift: 3.03 0.42 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.694197 Iteration 2 Error: 0.186753 Iteration 3 Error: 0.091355 Iteration 4 Error: 0.035795 Align patch 2 23 left Iteration 1 Error: 0.840857 Iteration 2 Error: 0.217307 Iteration 3 Error: 0.069696 Iteration 4 Error: 0.019004 Align patch 3 22 left Iteration 1 Error: 0.997553 Iteration 2 Error: 0.154254 Iteration 3 Error: 0.050120 Iteration 4 Error: 0.015930 Align patch 4 21 left Iteration 1 Error: 0.956880 Iteration 2 Error: 0.128800 Iteration 3 Error: 0.041574 Align patch 5 20 left Iteration 1 Error: 1.213940 Iteration 2 Error: 0.249231 Iteration 3 Error: 0.072134 Iteration 4 Error: 0.019159 Align patch 6 19 left Iteration 1 Error: 0.541580 Iteration 2 Error: 0.118871 Iteration 3 Error: 0.030056 Align patch 7 18 left Iteration 1 Error: 1.074814 Iteration 2 Error: 0.236791 Iteration 3 Error: 0.087882 Iteration 4 Error: 0.026328 Align patch 8 17 left Iteration 1 Error: 1.093686 Iteration 2 Error: 0.213407 Iteration 3 Error: 0.038892 Align patch 9 16 left Iteration 1 Error: 0.733558 Iteration 2 Error: 0.138322 Iteration 3 Error: 0.034706 Align patch 10 15 left Iteration 1 Error: 0.980199 Iteration 2 Error: 0.183756 Iteration 3 Error: 0.029641 Align patch 11 14 left Iteration 1 Error: 0.990748 Iteration 2 Error: 0.179048 Iteration 3 Error: 0.055362 Iteration 4 Error: 0.029170 Align patch 12 13 left Iteration 1 Error: 1.098752 Iteration 2 Error: 0.278928 Iteration 3 Error: 0.102975 Iteration 4 Error: 0.050422 Iteration 5 Error: 0.029392 Align patch 13 12 left Iteration 1 Error: 1.056522 Iteration 2 Error: 0.231424 Iteration 3 Error: 0.048442 Align patch 14 11 left Iteration 1 Error: 0.952609 Iteration 2 Error: 0.275612 Iteration 3 Error: 0.085203 Iteration 4 Error: 0.045519 Align patch 15 10 left Iteration 1 Error: 0.794967 Iteration 2 Error: 0.176293 Iteration 3 Error: 0.050839 Iteration 4 Error: 0.024977 Align patch 16 9 left Iteration 1 Error: 1.487604 Iteration 2 Error: 0.236226 Iteration 3 Error: 0.064339 Iteration 4 Error: 0.021699 Align patch 17 8 left Iteration 1 Error: 0.762025 Iteration 2 Error: 0.191675 Iteration 3 Error: 0.050920 Iteration 4 Error: 0.020032 Align patch 18 7 left Iteration 1 Error: 0.916750 Iteration 2 Error: 0.187292 Iteration 3 Error: 0.047460 Align patch 19 6 left Iteration 1 Error: 0.813747 Iteration 2 Error: 0.337827 Iteration 3 Error: 0.095770 Iteration 4 Error: 0.039674 Align patch 20 5 left Iteration 1 Error: 0.788729 Iteration 2 Error: 0.204921 Iteration 3 Error: 0.090040 Iteration 4 Error: 0.022235 Align patch 21 4 left Iteration 1 Error: 0.834067 Iteration 2 Error: 0.131263 Iteration 3 Error: 0.044144 Align patch 22 3 left Iteration 1 Error: 1.021207 Iteration 2 Error: 0.324071 Iteration 3 Error: 0.111778 Iteration 4 Error: 0.043153 Align patch 23 2 left Iteration 1 Error: 0.691461 Iteration 2 Error: 0.133252 Iteration 3 Error: 0.056363 Iteration 4 Error: 0.010261 Align patch 24 1 left Iteration 1 Error: 0.760794 Iteration 2 Error: 0.194904 Iteration 3 Error: 0.064779 Iteration 4 Error: 0.022146 Align patch 25 0 left Iteration 1 Error: 0.693033 Iteration 2 Error: 0.246106 Iteration 3 Error: 0.043894 3D Fitting completed. Patch alignment time: 13.85(sec) Local motion has been corrected. Process thread exits. Computational time: 28.466360 sec Total time: 35.711578 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00034hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00034hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.479589s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00034hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.440883s ........................................ >>>>>>TIME<<<<<< FFT: 0.985121s Defocus_U Defocus_V Angle CCC 12533.20 13466.80 9.00 0.031570 Final Values Defocus_U Defocus_V Angle CCC 12536.50 13360.78 8.06 0.046276 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00034hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00034hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.996e-02 CC threshold: 0.734 Mean Std: 40.42 6.76 Num Hot pixels: 210 Hot pixel threshold: 80.95 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.672766 Iteration 2 Error: 0.398478 Iteration 3 Error: 0.119379 Iteration 4 Error: 0.051003 Iteration 5 Error: 0.018151 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.00 -0.09 ...... Frame ( 3) shift: 0.01 -0.18 ...... Frame ( 4) shift: 0.01 -0.27 ...... Frame ( 5) shift: 0.01 -0.36 ...... Frame ( 6) shift: 0.06 -0.35 ...... Frame ( 7) shift: 0.15 -0.25 ...... Frame ( 8) shift: 0.24 -0.15 ...... Frame ( 9) shift: 0.32 -0.02 ...... Frame ( 10) shift: 0.39 0.14 ...... Frame ( 11) shift: 0.47 0.30 ...... Frame ( 12) shift: 0.52 0.47 ...... Frame ( 13) shift: 0.53 0.65 ...... Frame ( 14) shift: 0.55 0.82 ...... Frame ( 15) shift: 0.62 0.98 ...... Frame ( 16) shift: 0.73 1.11 ...... Frame ( 17) shift: 0.85 1.24 ...... Frame ( 18) shift: 0.93 1.37 ...... Frame ( 19) shift: 0.98 1.48 ...... Frame ( 20) shift: 1.02 1.60 ...... Frame ( 21) shift: 1.08 1.70 ...... Frame ( 22) shift: 1.13 1.78 ...... Frame ( 23) shift: 1.19 1.86 ...... Frame ( 24) shift: 1.23 1.97 ...... Frame ( 25) shift: 1.25 2.11 ...... Frame ( 26) shift: 1.27 2.25 ...... Frame ( 27) shift: 1.28 2.36 ...... Frame ( 28) shift: 1.29 2.43 ...... Frame ( 29) shift: 1.29 2.51 ...... Frame ( 30) shift: 1.33 2.59 ...... Frame ( 31) shift: 1.40 2.67 ...... Frame ( 32) shift: 1.47 2.75 ...... Frame ( 33) shift: 1.53 2.85 ...... Frame ( 34) shift: 1.59 2.95 ...... Frame ( 35) shift: 1.64 3.06 ...... Frame ( 36) shift: 1.70 3.15 ...... Frame ( 37) shift: 1.76 3.21 ...... Frame ( 38) shift: 1.82 3.27 ...... Frame ( 39) shift: 1.88 3.33 ...... Frame ( 40) shift: 1.94 3.39 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.032029 Iteration 2 Error: 0.173395 Iteration 3 Error: 0.051904 Iteration 4 Error: 0.031564 Align patch 2 23 left Iteration 1 Error: 0.758742 Iteration 2 Error: 0.116423 Iteration 3 Error: 0.033205 Align patch 3 22 left Iteration 1 Error: 0.912592 Iteration 2 Error: 0.148771 Iteration 3 Error: 0.049418 Align patch 4 21 left Iteration 1 Error: 1.028345 Iteration 2 Error: 0.222392 Iteration 3 Error: 0.072191 Iteration 4 Error: 0.029341 Align patch 5 20 left Iteration 1 Error: 0.869628 Iteration 2 Error: 0.117883 Iteration 3 Error: 0.033073 Align patch 6 19 left Iteration 1 Error: 0.831774 Iteration 2 Error: 0.172399 Iteration 3 Error: 0.053021 Iteration 4 Error: 0.025752 Align patch 7 18 left Iteration 1 Error: 1.009902 Iteration 2 Error: 0.139761 Iteration 3 Error: 0.046544 Align patch 8 17 left Iteration 1 Error: 0.982844 Iteration 2 Error: 0.147569 Iteration 3 Error: 0.033484 Align patch 9 16 left Iteration 1 Error: 0.872256 Iteration 2 Error: 0.112827 Iteration 3 Error: 0.030930 Align patch 10 15 left Iteration 1 Error: 0.704787 Iteration 2 Error: 0.190572 Iteration 3 Error: 0.059497 Iteration 4 Error: 0.019113 Align patch 11 14 left Iteration 1 Error: 0.709282 Iteration 2 Error: 0.156866 Iteration 3 Error: 0.031646 Align patch 12 13 left Iteration 1 Error: 1.043682 Iteration 2 Error: 0.135594 Iteration 3 Error: 0.036205 Align patch 13 12 left Iteration 1 Error: 0.763147 Iteration 2 Error: 0.142417 Iteration 3 Error: 0.056478 Iteration 4 Error: 0.020568 Align patch 14 11 left Iteration 1 Error: 0.801249 Iteration 2 Error: 0.208593 Iteration 3 Error: 0.063138 Iteration 4 Error: 0.037011 Align patch 15 10 left Iteration 1 Error: 0.590508 Iteration 2 Error: 0.112937 Iteration 3 Error: 0.024285 Align patch 16 9 left Iteration 1 Error: 0.795583 Iteration 2 Error: 0.195840 Iteration 3 Error: 0.091039 Iteration 4 Error: 0.024901 Align patch 17 8 left Iteration 1 Error: 1.011494 Iteration 2 Error: 0.121615 Iteration 3 Error: 0.028138 Align patch 18 7 left Iteration 1 Error: 0.854165 Iteration 2 Error: 0.146305 Iteration 3 Error: 0.040845 Align patch 19 6 left Iteration 1 Error: 1.340702 Iteration 2 Error: 0.180991 Iteration 3 Error: 0.035953 Align patch 20 5 left Iteration 1 Error: 0.950027 Iteration 2 Error: 0.275741 Iteration 3 Error: 0.049891 Align patch 21 4 left Iteration 1 Error: 0.559136 Iteration 2 Error: 0.179025 Iteration 3 Error: 0.049188 Align patch 22 3 left Iteration 1 Error: 0.641530 Iteration 2 Error: 0.112475 Iteration 3 Error: 0.032245 Align patch 23 2 left Iteration 1 Error: 0.594485 Iteration 2 Error: 0.084269 Iteration 3 Error: 0.017284 Align patch 24 1 left Iteration 1 Error: 0.733152 Iteration 2 Error: 0.284856 Iteration 3 Error: 0.089148 Iteration 4 Error: 0.039754 Align patch 25 0 left Iteration 1 Error: 1.359152 Iteration 2 Error: 0.295043 Iteration 3 Error: 0.083519 Iteration 4 Error: 0.041418 3D Fitting completed. Patch alignment time: 13.20(sec) Local motion has been corrected. Process thread exits. Computational time: 27.619062 sec Total time: 36.790314 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00034hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00034hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.669974s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00034hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.281315s ........................................ >>>>>>TIME<<<<<< FFT: 1.263620s Defocus_U Defocus_V Angle CCC 12818.36 13443.36 9.34 0.049473 Final Values Defocus_U Defocus_V Angle CCC 12813.67 13451.18 9.34 0.080992 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00034hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00034hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 37.76 6.68 Num Hot pixels: 171 Hot pixel threshold: 77.83 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.543498 Iteration 2 Error: 0.230551 Iteration 3 Error: 0.047724 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.05 -0.16 ...... Frame ( 3) shift: -0.09 -0.32 ...... Frame ( 4) shift: -0.14 -0.48 ...... Frame ( 5) shift: -0.18 -0.65 ...... Frame ( 6) shift: -0.25 -0.63 ...... Frame ( 7) shift: -0.34 -0.42 ...... Frame ( 8) shift: -0.43 -0.22 ...... Frame ( 9) shift: -0.54 -0.06 ...... Frame ( 10) shift: -0.66 0.07 ...... Frame ( 11) shift: -0.78 0.19 ...... Frame ( 12) shift: -0.86 0.35 ...... Frame ( 13) shift: -0.91 0.54 ...... Frame ( 14) shift: -0.96 0.74 ...... Frame ( 15) shift: -1.01 0.90 ...... Frame ( 16) shift: -1.05 1.03 ...... Frame ( 17) shift: -1.09 1.15 ...... Frame ( 18) shift: -1.05 1.29 ...... Frame ( 19) shift: -0.95 1.43 ...... Frame ( 20) shift: -0.84 1.57 ...... Frame ( 21) shift: -0.76 1.66 ...... Frame ( 22) shift: -0.72 1.69 ...... Frame ( 23) shift: -0.67 1.73 ...... Frame ( 24) shift: -0.60 1.76 ...... Frame ( 25) shift: -0.51 1.78 ...... Frame ( 26) shift: -0.41 1.81 ...... Frame ( 27) shift: -0.31 1.82 ...... Frame ( 28) shift: -0.18 1.80 ...... Frame ( 29) shift: -0.05 1.79 ...... Frame ( 30) shift: 0.09 1.74 ...... Frame ( 31) shift: 0.24 1.67 ...... Frame ( 32) shift: 0.39 1.60 ...... Frame ( 33) shift: 0.50 1.51 ...... Frame ( 34) shift: 0.58 1.40 ...... Frame ( 35) shift: 0.65 1.30 ...... Frame ( 36) shift: 0.77 1.21 ...... Frame ( 37) shift: 0.93 1.15 ...... Frame ( 38) shift: 1.10 1.09 ...... Frame ( 39) shift: 1.26 1.03 ...... Frame ( 40) shift: 1.42 0.97 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.060979 Iteration 2 Error: 0.155156 Iteration 3 Error: 0.047853 Align patch 2 23 left Iteration 1 Error: 0.869322 Iteration 2 Error: 0.178329 Iteration 3 Error: 0.046662 Align patch 3 22 left Iteration 1 Error: 0.921123 Iteration 2 Error: 0.137946 Iteration 3 Error: 0.052177 Iteration 4 Error: 0.011917 Align patch 4 21 left Iteration 1 Error: 0.652907 Iteration 2 Error: 0.161617 Iteration 3 Error: 0.032514 Align patch 5 20 left Iteration 1 Error: 1.212819 Iteration 2 Error: 0.237205 Iteration 3 Error: 0.061812 Iteration 4 Error: 0.024479 Align patch 6 19 left Iteration 1 Error: 1.182376 Iteration 2 Error: 0.165864 Iteration 3 Error: 0.049008 Align patch 7 18 left Iteration 1 Error: 0.891888 Iteration 2 Error: 0.111539 Iteration 3 Error: 0.023998 Align patch 8 17 left Iteration 1 Error: 0.964047 Iteration 2 Error: 0.281975 Iteration 3 Error: 0.064963 Iteration 4 Error: 0.022241 Align patch 9 16 left Iteration 1 Error: 0.651190 Iteration 2 Error: 0.170371 Iteration 3 Error: 0.035271 Align patch 10 15 left Iteration 1 Error: 0.865689 Iteration 2 Error: 0.188510 Iteration 3 Error: 0.049412 Align patch 11 14 left Iteration 1 Error: 1.100222 Iteration 2 Error: 0.273298 Iteration 3 Error: 0.075460 Iteration 4 Error: 0.032479 Align patch 12 13 left Iteration 1 Error: 1.138164 Iteration 2 Error: 0.236396 Iteration 3 Error: 0.057296 Iteration 4 Error: 0.013966 Align patch 13 12 left Iteration 1 Error: 0.821972 Iteration 2 Error: 0.185117 Iteration 3 Error: 0.044798 Align patch 14 11 left Iteration 1 Error: 1.218903 Iteration 2 Error: 0.150909 Iteration 3 Error: 0.066402 Iteration 4 Error: 0.018160 Align patch 15 10 left Iteration 1 Error: 1.053947 Iteration 2 Error: 0.227113 Iteration 3 Error: 0.042464 Align patch 16 9 left Iteration 1 Error: 0.949705 Iteration 2 Error: 0.286114 Iteration 3 Error: 0.075038 Iteration 4 Error: 0.040957 Align patch 17 8 left Iteration 1 Error: 0.668782 Iteration 2 Error: 0.120001 Iteration 3 Error: 0.039365 Align patch 18 7 left Iteration 1 Error: 1.147864 Iteration 2 Error: 0.221909 Iteration 3 Error: 0.036877 Align patch 19 6 left Iteration 1 Error: 1.019614 Iteration 2 Error: 0.148315 Iteration 3 Error: 0.024018 Align patch 20 5 left Iteration 1 Error: 1.054539 Iteration 2 Error: 0.164973 Iteration 3 Error: 0.052929 Iteration 4 Error: 0.009801 Align patch 21 4 left Iteration 1 Error: 2.973344 Iteration 2 Error: 0.468670 Iteration 3 Error: 0.083063 Iteration 4 Error: 0.020036 Align patch 22 3 left Iteration 1 Error: 0.893945 Iteration 2 Error: 0.270778 Iteration 3 Error: 0.075689 Iteration 4 Error: 0.037968 Align patch 23 2 left Iteration 1 Error: 1.195353 Iteration 2 Error: 0.201700 Iteration 3 Error: 0.033916 Align patch 24 1 left Iteration 1 Error: 1.494929 Iteration 2 Error: 0.304984 Iteration 3 Error: 0.066650 Iteration 4 Error: 0.022932 Align patch 25 0 left Iteration 1 Error: 1.562866 Iteration 2 Error: 0.308737 Iteration 3 Error: 0.082232 Iteration 4 Error: 0.044966 3D Fitting completed. Patch alignment time: 13.66(sec) Local motion has been corrected. Process thread exits. Computational time: 31.355894 sec Total time: 38.366943 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00034hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00034hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.837359s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00034hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.106763s ........................................ >>>>>>TIME<<<<<< FFT: 1.052064s Defocus_U Defocus_V Angle CCC 17271.49 16451.17 84.60 0.038199 Final Values Defocus_U Defocus_V Angle CCC 17201.29 16409.18 87.23 0.056207 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00035hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00035hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.989e-02 CC threshold: 0.734 Mean Std: 39.08 6.62 Num Hot pixels: 191 Hot pixel threshold: 78.81 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.647611 Iteration 2 Error: 0.626938 Iteration 3 Error: 0.204614 Iteration 4 Error: 0.085716 Iteration 5 Error: 0.043110 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.09 0.17 ...... Frame ( 3) shift: 0.18 0.34 ...... Frame ( 4) shift: 0.27 0.51 ...... Frame ( 5) shift: 0.36 0.68 ...... Frame ( 6) shift: 0.43 0.80 ...... Frame ( 7) shift: 0.49 0.87 ...... Frame ( 8) shift: 0.55 0.95 ...... Frame ( 9) shift: 0.64 1.03 ...... Frame ( 10) shift: 0.78 1.12 ...... Frame ( 11) shift: 0.92 1.20 ...... Frame ( 12) shift: 1.10 1.31 ...... Frame ( 13) shift: 1.31 1.45 ...... Frame ( 14) shift: 1.53 1.58 ...... Frame ( 15) shift: 1.78 1.77 ...... Frame ( 16) shift: 2.08 2.02 ...... Frame ( 17) shift: 2.37 2.26 ...... Frame ( 18) shift: 2.60 2.42 ...... Frame ( 19) shift: 2.78 2.50 ...... Frame ( 20) shift: 2.95 2.58 ...... Frame ( 21) shift: 3.09 2.68 ...... Frame ( 22) shift: 3.19 2.82 ...... Frame ( 23) shift: 3.30 2.95 ...... Frame ( 24) shift: 3.38 3.02 ...... Frame ( 25) shift: 3.45 3.02 ...... Frame ( 26) shift: 3.51 3.02 ...... Frame ( 27) shift: 3.57 2.99 ...... Frame ( 28) shift: 3.62 2.94 ...... Frame ( 29) shift: 3.68 2.89 ...... Frame ( 30) shift: 3.72 2.85 ...... Frame ( 31) shift: 3.74 2.80 ...... Frame ( 32) shift: 3.76 2.75 ...... Frame ( 33) shift: 3.84 2.75 ...... Frame ( 34) shift: 3.97 2.81 ...... Frame ( 35) shift: 4.10 2.86 ...... Frame ( 36) shift: 4.33 3.00 ...... Frame ( 37) shift: 4.64 3.21 ...... Frame ( 38) shift: 4.96 3.42 ...... Frame ( 39) shift: 5.27 3.64 ...... Frame ( 40) shift: 5.59 3.85 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.866409 Iteration 2 Error: 0.193624 Iteration 3 Error: 0.062685 Iteration 4 Error: 0.033960 Align patch 2 23 left Iteration 1 Error: 0.656158 Iteration 2 Error: 0.185407 Iteration 3 Error: 0.075453 Iteration 4 Error: 0.026567 Align patch 3 22 left Iteration 1 Error: 0.715657 Iteration 2 Error: 0.149168 Iteration 3 Error: 0.086945 Iteration 4 Error: 0.038632 Align patch 4 21 left Iteration 1 Error: 1.058972 Iteration 2 Error: 0.196376 Iteration 3 Error: 0.070587 Iteration 4 Error: 0.027133 Align patch 5 20 left Iteration 1 Error: 1.730040 Iteration 2 Error: 0.255382 Iteration 3 Error: 0.067292 Iteration 4 Error: 0.019016 Align patch 6 19 left Iteration 1 Error: 0.992525 Iteration 2 Error: 0.231811 Iteration 3 Error: 0.099053 Iteration 4 Error: 0.049868 Align patch 7 18 left Iteration 1 Error: 0.762806 Iteration 2 Error: 0.169811 Iteration 3 Error: 0.050923 Iteration 4 Error: 0.012475 Align patch 8 17 left Iteration 1 Error: 0.747434 Iteration 2 Error: 0.195262 Iteration 3 Error: 0.080699 Iteration 4 Error: 0.048588 Align patch 9 16 left Iteration 1 Error: 0.941560 Iteration 2 Error: 0.360425 Iteration 3 Error: 0.110852 Iteration 4 Error: 0.048347 Align patch 10 15 left Iteration 1 Error: 1.250589 Iteration 2 Error: 0.182887 Iteration 3 Error: 0.043903 Align patch 11 14 left Iteration 1 Error: 0.681688 Iteration 2 Error: 0.140208 Iteration 3 Error: 0.070261 Iteration 4 Error: 0.026520 Align patch 12 13 left Iteration 1 Error: 0.609873 Iteration 2 Error: 0.077010 Iteration 3 Error: 0.023184 Align patch 13 12 left Iteration 1 Error: 1.666034 Iteration 2 Error: 0.148873 Iteration 3 Error: 0.030543 Align patch 14 11 left Iteration 1 Error: 0.823341 Iteration 2 Error: 0.139343 Iteration 3 Error: 0.052788 Iteration 4 Error: 0.019148 Align patch 15 10 left Iteration 1 Error: 0.805068 Iteration 2 Error: 0.142442 Iteration 3 Error: 0.057173 Iteration 4 Error: 0.023114 Align patch 16 9 left Iteration 1 Error: 1.143065 Iteration 2 Error: 0.171631 Iteration 3 Error: 0.062855 Iteration 4 Error: 0.016171 Align patch 17 8 left Iteration 1 Error: 1.369550 Iteration 2 Error: 0.122687 Iteration 3 Error: 0.040009 Align patch 18 7 left Iteration 1 Error: 0.936049 Iteration 2 Error: 0.270787 Iteration 3 Error: 0.132647 Iteration 4 Error: 0.040885 Align patch 19 6 left Iteration 1 Error: 0.914843 Iteration 2 Error: 0.216470 Iteration 3 Error: 0.069210 Iteration 4 Error: 0.033106 Align patch 20 5 left Iteration 1 Error: 2.230628 Iteration 2 Error: 0.370872 Iteration 3 Error: 0.066496 Iteration 4 Error: 0.021815 Align patch 21 4 left Iteration 1 Error: 1.329290 Iteration 2 Error: 0.203960 Iteration 3 Error: 0.083495 Iteration 4 Error: 0.030982 Align patch 22 3 left Iteration 1 Error: 0.969218 Iteration 2 Error: 0.176033 Iteration 3 Error: 0.073495 Iteration 4 Error: 0.033001 Align patch 23 2 left Iteration 1 Error: 0.919752 Iteration 2 Error: 0.220425 Iteration 3 Error: 0.042813 Align patch 24 1 left Iteration 1 Error: 0.985964 Iteration 2 Error: 0.303324 Iteration 3 Error: 0.108117 Iteration 4 Error: 0.045641 Align patch 25 0 left Iteration 1 Error: 1.129000 Iteration 2 Error: 0.255969 Iteration 3 Error: 0.132255 Iteration 4 Error: 0.102273 Iteration 5 Error: 0.067899 Align patch 25 0 left Iteration 1 Error: 1.165950 Iteration 2 Error: 0.155844 Iteration 3 Error: 0.054038 Iteration 4 Error: 0.015522 3D Fitting completed. Patch alignment time: 13.74(sec) Local motion has been corrected. Process thread exits. Computational time: 36.848133 sec Total time: 43.874130 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00035hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00035hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.121069s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00035hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.682534s ........................................ >>>>>>TIME<<<<<< FFT: 1.024927s Defocus_U Defocus_V Angle CCC 15839.87 16566.44 9.03 0.037388 Final Values Defocus_U Defocus_V Angle CCC 15833.63 16585.20 9.03 0.057466 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00035hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00035hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.989e-02 CC threshold: 0.734 Mean Std: 38.14 6.55 Num Hot pixels: 183 Hot pixel threshold: 77.46 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.909517 Iteration 2 Error: 0.396841 Iteration 3 Error: 0.108623 Iteration 4 Error: 0.037802 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.02 -0.08 ...... Frame ( 3) shift: -0.04 -0.17 ...... Frame ( 4) shift: -0.06 -0.25 ...... Frame ( 5) shift: -0.08 -0.33 ...... Frame ( 6) shift: -0.03 -0.32 ...... Frame ( 7) shift: 0.10 -0.21 ...... Frame ( 8) shift: 0.22 -0.10 ...... Frame ( 9) shift: 0.35 0.02 ...... Frame ( 10) shift: 0.48 0.16 ...... Frame ( 11) shift: 0.61 0.30 ...... Frame ( 12) shift: 0.75 0.45 ...... Frame ( 13) shift: 0.89 0.60 ...... Frame ( 14) shift: 1.03 0.75 ...... Frame ( 15) shift: 1.19 0.88 ...... Frame ( 16) shift: 1.38 1.01 ...... Frame ( 17) shift: 1.56 1.14 ...... Frame ( 18) shift: 1.70 1.25 ...... Frame ( 19) shift: 1.79 1.34 ...... Frame ( 20) shift: 1.89 1.43 ...... Frame ( 21) shift: 1.95 1.47 ...... Frame ( 22) shift: 1.98 1.46 ...... Frame ( 23) shift: 2.01 1.46 ...... Frame ( 24) shift: 2.04 1.49 ...... Frame ( 25) shift: 2.08 1.56 ...... Frame ( 26) shift: 2.12 1.63 ...... Frame ( 27) shift: 2.19 1.70 ...... Frame ( 28) shift: 2.30 1.77 ...... Frame ( 29) shift: 2.41 1.84 ...... Frame ( 30) shift: 2.52 1.88 ...... Frame ( 31) shift: 2.63 1.89 ...... Frame ( 32) shift: 2.74 1.91 ...... Frame ( 33) shift: 2.77 1.92 ...... Frame ( 34) shift: 2.73 1.92 ...... Frame ( 35) shift: 2.68 1.92 ...... Frame ( 36) shift: 2.68 1.93 ...... Frame ( 37) shift: 2.72 1.96 ...... Frame ( 38) shift: 2.76 1.99 ...... Frame ( 39) shift: 2.81 2.01 ...... Frame ( 40) shift: 2.85 2.04 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.765706 Iteration 2 Error: 0.162862 Iteration 3 Error: 0.065606 Iteration 4 Error: 0.028851 Align patch 2 23 left Iteration 1 Error: 1.111249 Iteration 2 Error: 0.256572 Iteration 3 Error: 0.108375 Iteration 4 Error: 0.056106 Iteration 5 Error: 0.022779 Align patch 3 22 left Iteration 1 Error: 0.756943 Iteration 2 Error: 0.132137 Iteration 3 Error: 0.034878 Align patch 4 21 left Iteration 1 Error: 0.927363 Iteration 2 Error: 0.153293 Iteration 3 Error: 0.059683 Iteration 4 Error: 0.024246 Align patch 5 20 left Iteration 1 Error: 1.134208 Iteration 2 Error: 0.167615 Iteration 3 Error: 0.061137 Iteration 4 Error: 0.018454 Align patch 6 19 left Iteration 1 Error: 0.881653 Iteration 2 Error: 0.109938 Iteration 3 Error: 0.025653 Align patch 7 18 left Iteration 1 Error: 1.002899 Iteration 2 Error: 0.168510 Iteration 3 Error: 0.037229 Align patch 8 17 left Iteration 1 Error: 0.867885 Iteration 2 Error: 0.237536 Iteration 3 Error: 0.039908 Align patch 9 16 left Iteration 1 Error: 1.263889 Iteration 2 Error: 0.184706 Iteration 3 Error: 0.083831 Iteration 4 Error: 0.036381 Align patch 10 15 left Iteration 1 Error: 0.960210 Iteration 2 Error: 0.155223 Iteration 3 Error: 0.046110 Align patch 11 14 left Iteration 1 Error: 0.755627 Iteration 2 Error: 0.137958 Iteration 3 Error: 0.045356 Align patch 12 13 left Iteration 1 Error: 1.025674 Iteration 2 Error: 0.183734 Iteration 3 Error: 0.051630 Iteration 4 Error: 0.024819 Align patch 13 12 left Iteration 1 Error: 0.836753 Iteration 2 Error: 0.266747 Iteration 3 Error: 0.104500 Iteration 4 Error: 0.031200 Align patch 14 11 left Iteration 1 Error: 0.811024 Iteration 2 Error: 0.191742 Iteration 3 Error: 0.064303 Iteration 4 Error: 0.021572 Align patch 15 10 left Iteration 1 Error: 0.801208 Iteration 2 Error: 0.136541 Iteration 3 Error: 0.036577 Align patch 16 9 left Iteration 1 Error: 0.741762 Iteration 2 Error: 0.117876 Iteration 3 Error: 0.034538 Align patch 17 8 left Iteration 1 Error: 0.824382 Iteration 2 Error: 0.120133 Iteration 3 Error: 0.044264 Align patch 18 7 left Iteration 1 Error: 0.746899 Iteration 2 Error: 0.134567 Iteration 3 Error: 0.033743 Align patch 19 6 left Iteration 1 Error: 1.252475 Iteration 2 Error: 0.186705 Iteration 3 Error: 0.064030 Iteration 4 Error: 0.022487 Align patch 20 5 left Iteration 1 Error: 0.999687 Iteration 2 Error: 0.126599 Iteration 3 Error: 0.032694 Align patch 21 4 left Iteration 1 Error: 0.655524 Iteration 2 Error: 0.141066 Iteration 3 Error: 0.034896 Align patch 22 3 left Iteration 1 Error: 0.897659 Iteration 2 Error: 0.190771 Iteration 3 Error: 0.049857 Align patch 23 2 left Iteration 1 Error: 0.693991 Iteration 2 Error: 0.196511 Iteration 3 Error: 0.088297 Iteration 4 Error: 0.040991 Align patch 24 1 left Iteration 1 Error: 1.186536 Iteration 2 Error: 0.162153 Iteration 3 Error: 0.036555 Align patch 25 0 left Iteration 1 Error: 1.194773 Iteration 2 Error: 0.147571 Iteration 3 Error: 0.049120 3D Fitting completed. Patch alignment time: 13.03(sec) Local motion has been corrected. Process thread exits. Computational time: 27.178822 sec Total time: 35.190617 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00035hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00035hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.812309s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00035hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.099196s ........................................ >>>>>>TIME<<<<<< FFT: 1.127486s Defocus_U Defocus_V Angle CCC 16037.11 17021.53 8.17 0.032562 Final Values Defocus_U Defocus_V Angle CCC 16019.93 17048.14 8.80 0.046119 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00035hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00035hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.997e-02 CC threshold: 0.734 Mean Std: 39.11 6.64 Num Hot pixels: 190 Hot pixel threshold: 78.95 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.453139 Iteration 2 Error: 0.223119 Iteration 3 Error: 0.059762 Iteration 4 Error: 0.019366 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.04 0.10 ...... Frame ( 3) shift: 0.08 0.20 ...... Frame ( 4) shift: 0.11 0.30 ...... Frame ( 5) shift: 0.15 0.40 ...... Frame ( 6) shift: 0.19 0.47 ...... Frame ( 7) shift: 0.24 0.51 ...... Frame ( 8) shift: 0.28 0.55 ...... Frame ( 9) shift: 0.34 0.63 ...... Frame ( 10) shift: 0.41 0.75 ...... Frame ( 11) shift: 0.48 0.88 ...... Frame ( 12) shift: 0.58 0.97 ...... Frame ( 13) shift: 0.72 1.02 ...... Frame ( 14) shift: 0.86 1.08 ...... Frame ( 15) shift: 0.95 1.16 ...... Frame ( 16) shift: 0.99 1.26 ...... Frame ( 17) shift: 1.03 1.37 ...... Frame ( 18) shift: 1.05 1.44 ...... Frame ( 19) shift: 1.03 1.48 ...... Frame ( 20) shift: 1.01 1.52 ...... Frame ( 21) shift: 1.02 1.53 ...... Frame ( 22) shift: 1.06 1.52 ...... Frame ( 23) shift: 1.10 1.51 ...... Frame ( 24) shift: 1.20 1.54 ...... Frame ( 25) shift: 1.38 1.62 ...... Frame ( 26) shift: 1.56 1.71 ...... Frame ( 27) shift: 1.67 1.77 ...... Frame ( 28) shift: 1.71 1.81 ...... Frame ( 29) shift: 1.75 1.84 ...... Frame ( 30) shift: 1.79 1.84 ...... Frame ( 31) shift: 1.82 1.80 ...... Frame ( 32) shift: 1.85 1.75 ...... Frame ( 33) shift: 1.90 1.76 ...... Frame ( 34) shift: 1.96 1.83 ...... Frame ( 35) shift: 2.02 1.90 ...... Frame ( 36) shift: 2.04 1.98 ...... Frame ( 37) shift: 2.04 2.07 ...... Frame ( 38) shift: 2.03 2.16 ...... Frame ( 39) shift: 2.03 2.25 ...... Frame ( 40) shift: 2.02 2.34 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.795116 Iteration 2 Error: 0.194281 Iteration 3 Error: 0.045366 Align patch 2 23 left Iteration 1 Error: 1.327092 Iteration 2 Error: 0.205608 Iteration 3 Error: 0.049102 Align patch 3 22 left Iteration 1 Error: 0.894473 Iteration 2 Error: 0.220108 Iteration 3 Error: 0.050474 Iteration 4 Error: 0.014239 Align patch 4 21 left Iteration 1 Error: 1.006612 Iteration 2 Error: 0.092455 Iteration 3 Error: 0.021064 Align patch 5 20 left Iteration 1 Error: 0.776247 Iteration 2 Error: 0.208955 Iteration 3 Error: 0.071999 Iteration 4 Error: 0.023207 Align patch 6 19 left Iteration 1 Error: 0.909784 Iteration 2 Error: 0.141848 Iteration 3 Error: 0.034797 Align patch 7 18 left Iteration 1 Error: 0.482328 Iteration 2 Error: 0.117501 Iteration 3 Error: 0.025703 Align patch 8 17 left Iteration 1 Error: 1.088940 Iteration 2 Error: 0.188027 Iteration 3 Error: 0.060190 Iteration 4 Error: 0.020469 Align patch 9 16 left Iteration 1 Error: 0.725893 Iteration 2 Error: 0.124726 Iteration 3 Error: 0.025945 Align patch 10 15 left Iteration 1 Error: 1.005980 Iteration 2 Error: 0.205523 Iteration 3 Error: 0.036309 Align patch 11 14 left Iteration 1 Error: 0.916514 Iteration 2 Error: 0.126769 Iteration 3 Error: 0.039505 Align patch 12 13 left Iteration 1 Error: 0.716912 Iteration 2 Error: 0.166426 Iteration 3 Error: 0.073278 Iteration 4 Error: 0.021734 Align patch 13 12 left Iteration 1 Error: 0.866533 Iteration 2 Error: 0.277095 Iteration 3 Error: 0.065761 Iteration 4 Error: 0.025778 Align patch 14 11 left Iteration 1 Error: 0.741290 Iteration 2 Error: 0.101051 Iteration 3 Error: 0.027226 Align patch 15 10 left Iteration 1 Error: 1.030082 Iteration 2 Error: 0.182140 Iteration 3 Error: 0.032627 Align patch 16 9 left Iteration 1 Error: 0.772936 Iteration 2 Error: 0.138871 Iteration 3 Error: 0.039276 Align patch 17 8 left Iteration 1 Error: 0.984345 Iteration 2 Error: 0.132601 Iteration 3 Error: 0.044367 Align patch 18 7 left Iteration 1 Error: 0.626276 Iteration 2 Error: 0.061920 Iteration 3 Error: 0.012913 Align patch 19 6 left Iteration 1 Error: 0.833816 Iteration 2 Error: 0.190640 Iteration 3 Error: 0.059826 Iteration 4 Error: 0.011965 Align patch 20 5 left Iteration 1 Error: 0.810575 Iteration 2 Error: 0.105193 Iteration 3 Error: 0.021888 Align patch 21 4 left Iteration 1 Error: 0.854672 Iteration 2 Error: 0.162452 Iteration 3 Error: 0.053438 Iteration 4 Error: 0.017476 Align patch 22 3 left Iteration 1 Error: 0.805246 Iteration 2 Error: 0.133049 Iteration 3 Error: 0.025607 Align patch 23 2 left Iteration 1 Error: 0.702671 Iteration 2 Error: 0.216672 Iteration 3 Error: 0.067407 Iteration 4 Error: 0.032172 Align patch 24 1 left Iteration 1 Error: 0.955074 Iteration 2 Error: 0.146029 Iteration 3 Error: 0.045592 Align patch 25 0 left Iteration 1 Error: 0.783797 Iteration 2 Error: 0.096540 Iteration 3 Error: 0.018333 3D Fitting completed. Patch alignment time: 11.70(sec) Local motion has been corrected. Process thread exits. Computational time: 27.159203 sec Total time: 34.475262 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00035hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00035hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.598437s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00035hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.348945s ........................................ >>>>>>TIME<<<<<< FFT: 1.070577s Defocus_U Defocus_V Angle CCC 16148.44 16742.19 3.47 0.038447 Final Values Defocus_U Defocus_V Angle CCC 16134.37 16756.26 3.16 0.057643 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00035hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00035hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.991e-02 CC threshold: 0.734 Mean Std: 39.11 6.65 Num Hot pixels: 183 Hot pixel threshold: 79.03 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.614540 Iteration 2 Error: 0.276783 Iteration 3 Error: 0.083417 Iteration 4 Error: 0.022274 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.02 0.08 ...... Frame ( 3) shift: -0.04 0.17 ...... Frame ( 4) shift: -0.06 0.25 ...... Frame ( 5) shift: -0.08 0.34 ...... Frame ( 6) shift: -0.05 0.47 ...... Frame ( 7) shift: 0.02 0.65 ...... Frame ( 8) shift: 0.09 0.83 ...... Frame ( 9) shift: 0.16 0.93 ...... Frame ( 10) shift: 0.22 0.95 ...... Frame ( 11) shift: 0.28 0.97 ...... Frame ( 12) shift: 0.33 1.04 ...... Frame ( 13) shift: 0.36 1.15 ...... Frame ( 14) shift: 0.39 1.25 ...... Frame ( 15) shift: 0.49 1.37 ...... Frame ( 16) shift: 0.68 1.50 ...... Frame ( 17) shift: 0.86 1.62 ...... Frame ( 18) shift: 0.99 1.68 ...... Frame ( 19) shift: 1.08 1.68 ...... Frame ( 20) shift: 1.17 1.67 ...... Frame ( 21) shift: 1.23 1.65 ...... Frame ( 22) shift: 1.27 1.62 ...... Frame ( 23) shift: 1.31 1.59 ...... Frame ( 24) shift: 1.41 1.61 ...... Frame ( 25) shift: 1.56 1.69 ...... Frame ( 26) shift: 1.71 1.77 ...... Frame ( 27) shift: 1.83 1.83 ...... Frame ( 28) shift: 1.93 1.87 ...... Frame ( 29) shift: 2.02 1.91 ...... Frame ( 30) shift: 2.03 1.93 ...... Frame ( 31) shift: 1.97 1.93 ...... Frame ( 32) shift: 1.90 1.94 ...... Frame ( 33) shift: 1.87 2.00 ...... Frame ( 34) shift: 1.88 2.11 ...... Frame ( 35) shift: 1.89 2.22 ...... Frame ( 36) shift: 1.92 2.30 ...... Frame ( 37) shift: 1.98 2.36 ...... Frame ( 38) shift: 2.04 2.42 ...... Frame ( 39) shift: 2.09 2.47 ...... Frame ( 40) shift: 2.15 2.53 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.724289 Iteration 2 Error: 0.171906 Iteration 3 Error: 0.051197 Iteration 4 Error: 0.020561 Align patch 2 23 left Iteration 1 Error: 1.003144 Iteration 2 Error: 0.220413 Iteration 3 Error: 0.042848 Align patch 3 22 left Iteration 1 Error: 0.827393 Iteration 2 Error: 0.157695 Iteration 3 Error: 0.043492 Align patch 4 21 left Iteration 1 Error: 0.848770 Iteration 2 Error: 0.185415 Iteration 3 Error: 0.053117 Iteration 4 Error: 0.008228 Align patch 5 20 left Iteration 1 Error: 1.098631 Iteration 2 Error: 0.123149 Iteration 3 Error: 0.034780 Align patch 6 19 left Iteration 1 Error: 1.140128 Iteration 2 Error: 0.161682 Iteration 3 Error: 0.044220 Align patch 7 18 left Iteration 1 Error: 0.732451 Iteration 2 Error: 0.115380 Iteration 3 Error: 0.033405 Align patch 8 17 left Iteration 1 Error: 0.788787 Iteration 2 Error: 0.123036 Iteration 3 Error: 0.040546 Align patch 9 16 left Iteration 1 Error: 0.948952 Iteration 2 Error: 0.206225 Iteration 3 Error: 0.052176 Iteration 4 Error: 0.021332 Align patch 10 15 left Iteration 1 Error: 0.589358 Iteration 2 Error: 0.139756 Iteration 3 Error: 0.035296 Align patch 11 14 left Iteration 1 Error: 0.783996 Iteration 2 Error: 0.135963 Iteration 3 Error: 0.043306 Align patch 12 13 left Iteration 1 Error: 0.989915 Iteration 2 Error: 0.174713 Iteration 3 Error: 0.030514 Align patch 13 12 left Iteration 1 Error: 0.668486 Iteration 2 Error: 0.176386 Iteration 3 Error: 0.026877 Align patch 14 11 left Iteration 1 Error: 0.754936 Iteration 2 Error: 0.130493 Iteration 3 Error: 0.037890 Align patch 15 10 left Iteration 1 Error: 0.742744 Iteration 2 Error: 0.128815 Iteration 3 Error: 0.045314 Align patch 16 9 left Iteration 1 Error: 0.619404 Iteration 2 Error: 0.141030 Iteration 3 Error: 0.043677 Align patch 17 8 left Iteration 1 Error: 0.881399 Iteration 2 Error: 0.132064 Iteration 3 Error: 0.042835 Align patch 18 7 left Iteration 1 Error: 0.839187 Iteration 2 Error: 0.186560 Iteration 3 Error: 0.055401 Iteration 4 Error: 0.014837 Align patch 19 6 left Iteration 1 Error: 0.644283 Iteration 2 Error: 0.100675 Iteration 3 Error: 0.033419 Align patch 20 5 left Iteration 1 Error: 1.111182 Iteration 2 Error: 0.134034 Iteration 3 Error: 0.022460 Align patch 21 4 left Iteration 1 Error: 1.023014 Iteration 2 Error: 0.170300 Iteration 3 Error: 0.095870 Iteration 4 Error: 0.027484 Align patch 22 3 left Iteration 1 Error: 0.688229 Iteration 2 Error: 0.150461 Iteration 3 Error: 0.045023 Align patch 23 2 left Iteration 1 Error: 0.860272 Iteration 2 Error: 0.194943 Iteration 3 Error: 0.043145 Align patch 24 1 left Iteration 1 Error: 1.163704 Iteration 2 Error: 0.215650 Iteration 3 Error: 0.057103 Iteration 4 Error: 0.019933 Align patch 25 0 left Iteration 1 Error: 0.837574 Iteration 2 Error: 0.128522 Iteration 3 Error: 0.030778 3D Fitting completed. Patch alignment time: 11.75(sec) Local motion has been corrected. Process thread exits. Computational time: 25.161880 sec Total time: 33.795185 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00035hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00035hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.590024s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00035hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.487737s ........................................ >>>>>>TIME<<<<<< FFT: 0.870819s Defocus_U Defocus_V Angle CCC 14787.11 13888.67 87.74 0.039094 Final Values Defocus_U Defocus_V Angle CCC 14762.10 13888.68 87.74 0.057102 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00036hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00036hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.995e-02 CC threshold: 0.734 Mean Std: 41.18 6.84 Num Hot pixels: 210 Hot pixel threshold: 82.20 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.555720 Iteration 2 Error: 0.464470 Iteration 3 Error: 0.150775 Iteration 4 Error: 0.068782 Iteration 5 Error: 0.029232 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.03 -0.16 ...... Frame ( 3) shift: -0.07 -0.32 ...... Frame ( 4) shift: -0.10 -0.48 ...... Frame ( 5) shift: -0.14 -0.64 ...... Frame ( 6) shift: -0.10 -0.67 ...... Frame ( 7) shift: 0.02 -0.58 ...... Frame ( 8) shift: 0.14 -0.48 ...... Frame ( 9) shift: 0.23 -0.38 ...... Frame ( 10) shift: 0.29 -0.27 ...... Frame ( 11) shift: 0.36 -0.17 ...... Frame ( 12) shift: 0.44 -0.08 ...... Frame ( 13) shift: 0.52 -0.03 ...... Frame ( 14) shift: 0.61 0.02 ...... Frame ( 15) shift: 0.71 0.15 ...... Frame ( 16) shift: 0.82 0.36 ...... Frame ( 17) shift: 0.93 0.57 ...... Frame ( 18) shift: 1.01 0.70 ...... Frame ( 19) shift: 1.07 0.74 ...... Frame ( 20) shift: 1.12 0.78 ...... Frame ( 21) shift: 1.17 0.83 ...... Frame ( 22) shift: 1.20 0.89 ...... Frame ( 23) shift: 1.23 0.95 ...... Frame ( 24) shift: 1.28 1.03 ...... Frame ( 25) shift: 1.33 1.12 ...... Frame ( 26) shift: 1.39 1.22 ...... Frame ( 27) shift: 1.45 1.31 ...... Frame ( 28) shift: 1.53 1.40 ...... Frame ( 29) shift: 1.60 1.49 ...... Frame ( 30) shift: 1.64 1.59 ...... Frame ( 31) shift: 1.65 1.70 ...... Frame ( 32) shift: 1.66 1.82 ...... Frame ( 33) shift: 1.75 1.88 ...... Frame ( 34) shift: 1.92 1.89 ...... Frame ( 35) shift: 2.08 1.91 ...... Frame ( 36) shift: 2.19 1.93 ...... Frame ( 37) shift: 2.24 1.96 ...... Frame ( 38) shift: 2.29 1.99 ...... Frame ( 39) shift: 2.35 2.02 ...... Frame ( 40) shift: 2.40 2.06 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.132163 Iteration 2 Error: 0.215850 Iteration 3 Error: 0.051658 Iteration 4 Error: 0.017360 Align patch 2 23 left Iteration 1 Error: 1.123533 Iteration 2 Error: 0.174300 Iteration 3 Error: 0.061386 Iteration 4 Error: 0.021222 Align patch 3 22 left Iteration 1 Error: 0.884832 Iteration 2 Error: 0.134732 Iteration 3 Error: 0.043202 Align patch 4 21 left Iteration 1 Error: 1.051043 Iteration 2 Error: 0.289440 Iteration 3 Error: 0.137071 Iteration 4 Error: 0.042229 Align patch 5 20 left Iteration 1 Error: 0.681701 Iteration 2 Error: 0.125013 Iteration 3 Error: 0.037663 Align patch 6 19 left Iteration 1 Error: 0.829709 Iteration 2 Error: 0.284719 Iteration 3 Error: 0.107478 Iteration 4 Error: 0.043475 Align patch 7 18 left Iteration 1 Error: 0.697141 Iteration 2 Error: 0.116893 Iteration 3 Error: 0.038176 Align patch 8 17 left Iteration 1 Error: 0.719150 Iteration 2 Error: 0.168711 Iteration 3 Error: 0.061605 Iteration 4 Error: 0.031292 Align patch 9 16 left Iteration 1 Error: 0.929336 Iteration 2 Error: 0.158466 Iteration 3 Error: 0.038551 Align patch 10 15 left Iteration 1 Error: 0.881047 Iteration 2 Error: 0.200805 Iteration 3 Error: 0.084254 Iteration 4 Error: 0.051865 Iteration 5 Error: 0.035751 Align patch 11 14 left Iteration 1 Error: 0.897166 Iteration 2 Error: 0.162736 Iteration 3 Error: 0.064674 Iteration 4 Error: 0.029082 Align patch 12 13 left Iteration 1 Error: 0.751298 Iteration 2 Error: 0.173196 Iteration 3 Error: 0.056744 Iteration 4 Error: 0.037530 Align patch 13 12 left Iteration 1 Error: 1.654829 Iteration 2 Error: 0.394048 Iteration 3 Error: 0.163302 Iteration 4 Error: 0.062842 Iteration 5 Error: 0.030938 Align patch 14 11 left Iteration 1 Error: 0.925592 Iteration 2 Error: 0.162005 Iteration 3 Error: 0.074445 Iteration 4 Error: 0.051454 Iteration 5 Error: 0.023600 Align patch 15 10 left Iteration 1 Error: 0.668821 Iteration 2 Error: 0.215727 Iteration 3 Error: 0.061967 Iteration 4 Error: 0.029432 Align patch 16 9 left Iteration 1 Error: 0.988265 Iteration 2 Error: 0.177957 Iteration 3 Error: 0.065605 Iteration 4 Error: 0.028492 Align patch 17 8 left Iteration 1 Error: 0.926050 Iteration 2 Error: 0.171981 Iteration 3 Error: 0.043404 Align patch 18 7 left Iteration 1 Error: 0.978829 Iteration 2 Error: 0.188975 Iteration 3 Error: 0.037313 Align patch 19 6 left Iteration 1 Error: 1.103213 Iteration 2 Error: 0.166745 Iteration 3 Error: 0.046641 Align patch 20 5 left Iteration 1 Error: 1.025100 Iteration 2 Error: 0.179601 Iteration 3 Error: 0.065660 Iteration 4 Error: 0.014279 Align patch 21 4 left Iteration 1 Error: 0.753895 Iteration 2 Error: 0.234528 Iteration 3 Error: 0.062638 Iteration 4 Error: 0.016499 Align patch 22 3 left Iteration 1 Error: 0.813942 Iteration 2 Error: 0.154899 Iteration 3 Error: 0.058911 Iteration 4 Error: 0.018159 Align patch 23 2 left Iteration 1 Error: 0.980373 Iteration 2 Error: 0.109084 Iteration 3 Error: 0.045876 Align patch 24 1 left Iteration 1 Error: 0.793192 Iteration 2 Error: 0.188369 Iteration 3 Error: 0.099446 Iteration 4 Error: 0.038039 Align patch 25 0 left Iteration 1 Error: 1.107576 Iteration 2 Error: 0.201533 Iteration 3 Error: 0.093743 Iteration 4 Error: 0.045780 3D Fitting completed. Patch alignment time: 12.99(sec) Local motion has been corrected. Process thread exits. Computational time: 28.138006 sec Total time: 35.434013 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00036hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00036hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.821341s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00036hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.772397s ........................................ >>>>>>TIME<<<<<< FFT: 1.046019s Defocus_U Defocus_V Angle CCC 11609.38 12417.97 11.40 0.041659 Final Values Defocus_U Defocus_V Angle CCC 11620.32 12413.29 11.08 0.071218 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00036hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00036hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.993e-02 CC threshold: 0.734 Mean Std: 41.04 6.81 Num Hot pixels: 206 Hot pixel threshold: 81.90 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.800992 Iteration 2 Error: 0.357376 Iteration 3 Error: 0.101674 Iteration 4 Error: 0.037318 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.03 -0.18 ...... Frame ( 3) shift: -0.06 -0.37 ...... Frame ( 4) shift: -0.09 -0.55 ...... Frame ( 5) shift: -0.12 -0.74 ...... Frame ( 6) shift: -0.09 -0.73 ...... Frame ( 7) shift: -0.02 -0.54 ...... Frame ( 8) shift: 0.06 -0.35 ...... Frame ( 9) shift: 0.14 -0.19 ...... Frame ( 10) shift: 0.21 -0.05 ...... Frame ( 11) shift: 0.29 0.09 ...... Frame ( 12) shift: 0.36 0.25 ...... Frame ( 13) shift: 0.43 0.44 ...... Frame ( 14) shift: 0.50 0.63 ...... Frame ( 15) shift: 0.55 0.81 ...... Frame ( 16) shift: 0.60 1.00 ...... Frame ( 17) shift: 0.64 1.18 ...... Frame ( 18) shift: 0.68 1.30 ...... Frame ( 19) shift: 0.71 1.36 ...... Frame ( 20) shift: 0.74 1.42 ...... Frame ( 21) shift: 0.79 1.47 ...... Frame ( 22) shift: 0.87 1.52 ...... Frame ( 23) shift: 0.94 1.58 ...... Frame ( 24) shift: 0.98 1.60 ...... Frame ( 25) shift: 0.98 1.61 ...... Frame ( 26) shift: 0.99 1.61 ...... Frame ( 27) shift: 1.02 1.67 ...... Frame ( 28) shift: 1.09 1.78 ...... Frame ( 29) shift: 1.15 1.89 ...... Frame ( 30) shift: 1.22 1.97 ...... Frame ( 31) shift: 1.30 2.01 ...... Frame ( 32) shift: 1.37 2.05 ...... Frame ( 33) shift: 1.37 2.12 ...... Frame ( 34) shift: 1.29 2.23 ...... Frame ( 35) shift: 1.20 2.35 ...... Frame ( 36) shift: 1.20 2.42 ...... Frame ( 37) shift: 1.29 2.44 ...... Frame ( 38) shift: 1.38 2.47 ...... Frame ( 39) shift: 1.47 2.50 ...... Frame ( 40) shift: 1.56 2.53 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.195438 Iteration 2 Error: 0.190214 Iteration 3 Error: 0.044713 Align patch 2 23 left Iteration 1 Error: 0.840374 Iteration 2 Error: 0.181106 Iteration 3 Error: 0.042709 Align patch 3 22 left Iteration 1 Error: 1.176047 Iteration 2 Error: 0.182341 Iteration 3 Error: 0.041978 Align patch 4 21 left Iteration 1 Error: 1.185248 Iteration 2 Error: 0.155735 Iteration 3 Error: 0.047296 Align patch 5 20 left Iteration 1 Error: 0.710504 Iteration 2 Error: 0.116340 Iteration 3 Error: 0.041103 Align patch 6 19 left Iteration 1 Error: 1.114344 Iteration 2 Error: 0.151661 Iteration 3 Error: 0.064938 Iteration 4 Error: 0.016851 Align patch 7 18 left Iteration 1 Error: 0.910658 Iteration 2 Error: 0.237672 Iteration 3 Error: 0.068551 Iteration 4 Error: 0.035923 Align patch 8 17 left Iteration 1 Error: 1.161652 Iteration 2 Error: 0.266680 Iteration 3 Error: 0.091755 Iteration 4 Error: 0.031457 Align patch 9 16 left Iteration 1 Error: 0.923186 Iteration 2 Error: 0.279278 Iteration 3 Error: 0.084950 Iteration 4 Error: 0.045467 Align patch 10 15 left Iteration 1 Error: 0.784571 Iteration 2 Error: 0.150270 Iteration 3 Error: 0.068648 Iteration 4 Error: 0.019089 Align patch 11 14 left Iteration 1 Error: 0.821855 Iteration 2 Error: 0.153489 Iteration 3 Error: 0.037348 Align patch 12 13 left Iteration 1 Error: 0.684574 Iteration 2 Error: 0.123032 Iteration 3 Error: 0.044469 Align patch 13 12 left Iteration 1 Error: 1.093680 Iteration 2 Error: 0.298408 Iteration 3 Error: 0.082059 Iteration 4 Error: 0.028114 Align patch 14 11 left Iteration 1 Error: 0.888068 Iteration 2 Error: 0.134063 Iteration 3 Error: 0.032284 Align patch 15 10 left Iteration 1 Error: 0.619882 Iteration 2 Error: 0.156538 Iteration 3 Error: 0.050795 Iteration 4 Error: 0.030644 Align patch 16 9 left Iteration 1 Error: 1.029370 Iteration 2 Error: 0.125576 Iteration 3 Error: 0.036791 Align patch 17 8 left Iteration 1 Error: 1.146661 Iteration 2 Error: 0.172448 Iteration 3 Error: 0.029882 Align patch 18 7 left Iteration 1 Error: 0.712606 Iteration 2 Error: 0.155087 Iteration 3 Error: 0.042224 Align patch 19 6 left Iteration 1 Error: 1.013769 Iteration 2 Error: 0.147768 Iteration 3 Error: 0.059891 Iteration 4 Error: 0.029143 Align patch 20 5 left Iteration 1 Error: 0.736942 Iteration 2 Error: 0.124723 Iteration 3 Error: 0.044380 Align patch 21 4 left Iteration 1 Error: 0.785053 Iteration 2 Error: 0.095985 Iteration 3 Error: 0.025112 Align patch 22 3 left Iteration 1 Error: 0.824922 Iteration 2 Error: 0.243782 Iteration 3 Error: 0.041828 Align patch 23 2 left Iteration 1 Error: 0.689308 Iteration 2 Error: 0.157399 Iteration 3 Error: 0.038688 Align patch 24 1 left Iteration 1 Error: 0.782102 Iteration 2 Error: 0.108276 Iteration 3 Error: 0.027912 Align patch 25 0 left Iteration 1 Error: 0.829085 Iteration 2 Error: 0.205056 Iteration 3 Error: 0.045836 3D Fitting completed. Patch alignment time: 11.91(sec) Local motion has been corrected. Process thread exits. Computational time: 22.473169 sec Total time: 28.523363 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00036hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00036hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.453896s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00036hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.365442s ........................................ >>>>>>TIME<<<<<< FFT: 1.008934s Defocus_U Defocus_V Angle CCC 14953.12 15765.62 8.20 0.047422 Final Values Defocus_U Defocus_V Angle CCC 14970.31 15767.19 8.52 0.076544 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00036hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00036hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 40.37 6.77 Num Hot pixels: 220 Hot pixel threshold: 80.99 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.403940 Iteration 2 Error: 0.318101 Iteration 3 Error: 0.069704 Iteration 4 Error: 0.018020 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.08 -0.14 ...... Frame ( 3) shift: -0.17 -0.28 ...... Frame ( 4) shift: -0.25 -0.42 ...... Frame ( 5) shift: -0.33 -0.56 ...... Frame ( 6) shift: -0.37 -0.61 ...... Frame ( 7) shift: -0.36 -0.55 ...... Frame ( 8) shift: -0.36 -0.50 ...... Frame ( 9) shift: -0.33 -0.42 ...... Frame ( 10) shift: -0.30 -0.33 ...... Frame ( 11) shift: -0.26 -0.24 ...... Frame ( 12) shift: -0.19 -0.09 ...... Frame ( 13) shift: -0.07 0.10 ...... Frame ( 14) shift: 0.04 0.30 ...... Frame ( 15) shift: 0.14 0.44 ...... Frame ( 16) shift: 0.21 0.54 ...... Frame ( 17) shift: 0.29 0.64 ...... Frame ( 18) shift: 0.34 0.75 ...... Frame ( 19) shift: 0.37 0.88 ...... Frame ( 20) shift: 0.40 1.01 ...... Frame ( 21) shift: 0.47 1.14 ...... Frame ( 22) shift: 0.57 1.27 ...... Frame ( 23) shift: 0.68 1.40 ...... Frame ( 24) shift: 0.72 1.47 ...... Frame ( 25) shift: 0.71 1.48 ...... Frame ( 26) shift: 0.70 1.48 ...... Frame ( 27) shift: 0.73 1.52 ...... Frame ( 28) shift: 0.78 1.59 ...... Frame ( 29) shift: 0.83 1.66 ...... Frame ( 30) shift: 0.88 1.75 ...... Frame ( 31) shift: 0.92 1.86 ...... Frame ( 32) shift: 0.95 1.96 ...... Frame ( 33) shift: 0.99 2.03 ...... Frame ( 34) shift: 1.02 2.07 ...... Frame ( 35) shift: 1.04 2.10 ...... Frame ( 36) shift: 1.06 2.14 ...... Frame ( 37) shift: 1.07 2.18 ...... Frame ( 38) shift: 1.07 2.23 ...... Frame ( 39) shift: 1.08 2.27 ...... Frame ( 40) shift: 1.08 2.31 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.091741 Iteration 2 Error: 0.133287 Iteration 3 Error: 0.044568 Align patch 2 23 left Iteration 1 Error: 1.082993 Iteration 2 Error: 0.111790 Iteration 3 Error: 0.025097 Align patch 3 22 left Iteration 1 Error: 0.948045 Iteration 2 Error: 0.113461 Iteration 3 Error: 0.033550 Align patch 4 21 left Iteration 1 Error: 0.857209 Iteration 2 Error: 0.153879 Iteration 3 Error: 0.033096 Align patch 5 20 left Iteration 1 Error: 0.948987 Iteration 2 Error: 0.114088 Iteration 3 Error: 0.021452 Align patch 6 19 left Iteration 1 Error: 0.927309 Iteration 2 Error: 0.121332 Iteration 3 Error: 0.023830 Align patch 7 18 left Iteration 1 Error: 0.849935 Iteration 2 Error: 0.115297 Iteration 3 Error: 0.024015 Align patch 8 17 left Iteration 1 Error: 0.707260 Iteration 2 Error: 0.129085 Iteration 3 Error: 0.027760 Align patch 9 16 left Iteration 1 Error: 0.651156 Iteration 2 Error: 0.110711 Iteration 3 Error: 0.026228 Align patch 10 15 left Iteration 1 Error: 0.724071 Iteration 2 Error: 0.097311 Iteration 3 Error: 0.016093 Align patch 11 14 left Iteration 1 Error: 0.698774 Iteration 2 Error: 0.107975 Iteration 3 Error: 0.022180 Align patch 12 13 left Iteration 1 Error: 0.610378 Iteration 2 Error: 0.197223 Iteration 3 Error: 0.044381 Align patch 13 12 left Iteration 1 Error: 0.800188 Iteration 2 Error: 0.089177 Iteration 3 Error: 0.016715 Align patch 14 11 left Iteration 1 Error: 0.568315 Iteration 2 Error: 0.116081 Iteration 3 Error: 0.041726 Align patch 15 10 left Iteration 1 Error: 0.809084 Iteration 2 Error: 0.084568 Iteration 3 Error: 0.027778 Align patch 16 9 left Iteration 1 Error: 0.389128 Iteration 2 Error: 0.092550 Iteration 3 Error: 0.023143 Align patch 17 8 left Iteration 1 Error: 0.633835 Iteration 2 Error: 0.126340 Iteration 3 Error: 0.044899 Align patch 18 7 left Iteration 1 Error: 0.622524 Iteration 2 Error: 0.091983 Iteration 3 Error: 0.027711 Align patch 19 6 left Iteration 1 Error: 0.756580 Iteration 2 Error: 0.205263 Iteration 3 Error: 0.043135 Align patch 20 5 left Iteration 1 Error: 0.527069 Iteration 2 Error: 0.078342 Iteration 3 Error: 0.022288 Align patch 21 4 left Iteration 1 Error: 1.041694 Iteration 2 Error: 0.139141 Iteration 3 Error: 0.038079 Align patch 22 3 left Iteration 1 Error: 0.873969 Iteration 2 Error: 0.121445 Iteration 3 Error: 0.025255 Align patch 23 2 left Iteration 1 Error: 0.442012 Iteration 2 Error: 0.121954 Iteration 3 Error: 0.036370 Align patch 24 1 left Iteration 1 Error: 0.538749 Iteration 2 Error: 0.066967 Iteration 3 Error: 0.031328 Align patch 25 0 left Iteration 1 Error: 0.676529 Iteration 2 Error: 0.100393 Iteration 3 Error: 0.027545 3D Fitting completed. Patch alignment time: 11.45(sec) Local motion has been corrected. Process thread exits. Computational time: 24.002962 sec Total time: 32.104450 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00036hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00036hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.616798s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00036hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.582872s ........................................ >>>>>>TIME<<<<<< FFT: 1.054277s Defocus_U Defocus_V Angle CCC 15457.03 15996.09 2.29 0.056171 Final Values Defocus_U Defocus_V Angle CCC 15453.91 15989.84 1.97 0.089203 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00036hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00036hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 40.00 6.73 Num Hot pixels: 214 Hot pixel threshold: 80.36 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.299179 Iteration 2 Error: 0.303959 Iteration 3 Error: 0.072173 Iteration 4 Error: 0.023920 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.04 -0.14 ...... Frame ( 3) shift: -0.08 -0.28 ...... Frame ( 4) shift: -0.12 -0.42 ...... Frame ( 5) shift: -0.16 -0.57 ...... Frame ( 6) shift: -0.17 -0.64 ...... Frame ( 7) shift: -0.17 -0.63 ...... Frame ( 8) shift: -0.17 -0.63 ...... Frame ( 9) shift: -0.16 -0.56 ...... Frame ( 10) shift: -0.15 -0.42 ...... Frame ( 11) shift: -0.13 -0.28 ...... Frame ( 12) shift: -0.09 -0.16 ...... Frame ( 13) shift: -0.00 -0.07 ...... Frame ( 14) shift: 0.08 0.02 ...... Frame ( 15) shift: 0.17 0.14 ...... Frame ( 16) shift: 0.27 0.28 ...... Frame ( 17) shift: 0.37 0.42 ...... Frame ( 18) shift: 0.43 0.52 ...... Frame ( 19) shift: 0.45 0.57 ...... Frame ( 20) shift: 0.47 0.62 ...... Frame ( 21) shift: 0.51 0.70 ...... Frame ( 22) shift: 0.59 0.81 ...... Frame ( 23) shift: 0.66 0.92 ...... Frame ( 24) shift: 0.74 1.02 ...... Frame ( 25) shift: 0.82 1.12 ...... Frame ( 26) shift: 0.90 1.22 ...... Frame ( 27) shift: 0.95 1.28 ...... Frame ( 28) shift: 0.99 1.31 ...... Frame ( 29) shift: 1.02 1.34 ...... Frame ( 30) shift: 1.07 1.37 ...... Frame ( 31) shift: 1.15 1.39 ...... Frame ( 32) shift: 1.23 1.42 ...... Frame ( 33) shift: 1.31 1.48 ...... Frame ( 34) shift: 1.39 1.55 ...... Frame ( 35) shift: 1.47 1.63 ...... Frame ( 36) shift: 1.55 1.63 ...... Frame ( 37) shift: 1.62 1.57 ...... Frame ( 38) shift: 1.69 1.50 ...... Frame ( 39) shift: 1.76 1.44 ...... Frame ( 40) shift: 1.83 1.38 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.083915 Iteration 2 Error: 0.165270 Iteration 3 Error: 0.060936 Iteration 4 Error: 0.022427 Align patch 2 23 left Iteration 1 Error: 0.941593 Iteration 2 Error: 0.165137 Iteration 3 Error: 0.048807 Align patch 3 22 left Iteration 1 Error: 0.738319 Iteration 2 Error: 0.117445 Iteration 3 Error: 0.024392 Align patch 4 21 left Iteration 1 Error: 0.998515 Iteration 2 Error: 0.167737 Iteration 3 Error: 0.055763 Iteration 4 Error: 0.012197 Align patch 5 20 left Iteration 1 Error: 1.119966 Iteration 2 Error: 0.128105 Iteration 3 Error: 0.039938 Align patch 6 19 left Iteration 1 Error: 0.938892 Iteration 2 Error: 0.108522 Iteration 3 Error: 0.019101 Align patch 7 18 left Iteration 1 Error: 0.889104 Iteration 2 Error: 0.152339 Iteration 3 Error: 0.047542 Align patch 8 17 left Iteration 1 Error: 0.623381 Iteration 2 Error: 0.238348 Iteration 3 Error: 0.068189 Iteration 4 Error: 0.031693 Align patch 9 16 left Iteration 1 Error: 0.656409 Iteration 2 Error: 0.102456 Iteration 3 Error: 0.038578 Align patch 10 15 left Iteration 1 Error: 1.151646 Iteration 2 Error: 0.110344 Iteration 3 Error: 0.025940 Align patch 11 14 left Iteration 1 Error: 0.655224 Iteration 2 Error: 0.145860 Iteration 3 Error: 0.034981 Align patch 12 13 left Iteration 1 Error: 0.684772 Iteration 2 Error: 0.148674 Iteration 3 Error: 0.047254 Align patch 13 12 left Iteration 1 Error: 0.536602 Iteration 2 Error: 0.086845 Iteration 3 Error: 0.015681 Align patch 14 11 left Iteration 1 Error: 0.706766 Iteration 2 Error: 0.108432 Iteration 3 Error: 0.029933 Align patch 15 10 left Iteration 1 Error: 0.621338 Iteration 2 Error: 0.205011 Iteration 3 Error: 0.076752 Iteration 4 Error: 0.028893 Align patch 16 9 left Iteration 1 Error: 0.598894 Iteration 2 Error: 0.072477 Iteration 3 Error: 0.012226 Align patch 17 8 left Iteration 1 Error: 1.026654 Iteration 2 Error: 0.114538 Iteration 3 Error: 0.037911 Align patch 18 7 left Iteration 1 Error: 0.700651 Iteration 2 Error: 0.123490 Iteration 3 Error: 0.034702 Align patch 19 6 left Iteration 1 Error: 0.672644 Iteration 2 Error: 0.194908 Iteration 3 Error: 0.030163 Align patch 20 5 left Iteration 1 Error: 0.751670 Iteration 2 Error: 0.119939 Iteration 3 Error: 0.019220 Align patch 21 4 left Iteration 1 Error: 0.922892 Iteration 2 Error: 0.157537 Iteration 3 Error: 0.026988 Align patch 22 3 left Iteration 1 Error: 1.149591 Iteration 2 Error: 0.142519 Iteration 3 Error: 0.042943 Align patch 23 2 left Iteration 1 Error: 0.978597 Iteration 2 Error: 0.098798 Iteration 3 Error: 0.017232 Align patch 24 1 left Iteration 1 Error: 0.931324 Iteration 2 Error: 0.141438 Iteration 3 Error: 0.059876 Iteration 4 Error: 0.017255 Align patch 25 0 left Iteration 1 Error: 0.923889 Iteration 2 Error: 0.306692 Iteration 3 Error: 0.103442 Iteration 4 Error: 0.038447 3D Fitting completed. Patch alignment time: 12.23(sec) Local motion has been corrected. Process thread exits. Computational time: 25.734379 sec Total time: 32.802078 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00036hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00036hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.777316s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00036hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 4.270349s ........................................ >>>>>>TIME<<<<<< FFT: 1.128172s Defocus_U Defocus_V Angle CCC 15654.30 16357.42 3.10 0.040512 Final Values Defocus_U Defocus_V Angle CCC 15652.73 16352.73 2.79 0.064412 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00037hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00037hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.998e-02 CC threshold: 0.734 Mean Std: 39.55 6.68 Num Hot pixels: 207 Hot pixel threshold: 79.60 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.976743 Iteration 2 Error: 0.356048 Iteration 3 Error: 0.098964 Iteration 4 Error: 0.035632 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.14 0.11 ...... Frame ( 3) shift: 0.29 0.22 ...... Frame ( 4) shift: 0.43 0.34 ...... Frame ( 5) shift: 0.58 0.45 ...... Frame ( 6) shift: 0.69 0.55 ...... Frame ( 7) shift: 0.78 0.65 ...... Frame ( 8) shift: 0.87 0.75 ...... Frame ( 9) shift: 0.95 0.85 ...... Frame ( 10) shift: 1.03 0.94 ...... Frame ( 11) shift: 1.11 1.04 ...... Frame ( 12) shift: 1.20 1.13 ...... Frame ( 13) shift: 1.28 1.22 ...... Frame ( 14) shift: 1.36 1.31 ...... Frame ( 15) shift: 1.43 1.40 ...... Frame ( 16) shift: 1.51 1.49 ...... Frame ( 17) shift: 1.58 1.58 ...... Frame ( 18) shift: 1.63 1.69 ...... Frame ( 19) shift: 1.68 1.81 ...... Frame ( 20) shift: 1.72 1.94 ...... Frame ( 21) shift: 1.78 2.04 ...... Frame ( 22) shift: 1.84 2.12 ...... Frame ( 23) shift: 1.90 2.19 ...... Frame ( 24) shift: 1.99 2.30 ...... Frame ( 25) shift: 2.11 2.43 ...... Frame ( 26) shift: 2.24 2.56 ...... Frame ( 27) shift: 2.30 2.64 ...... Frame ( 28) shift: 2.30 2.68 ...... Frame ( 29) shift: 2.31 2.72 ...... Frame ( 30) shift: 2.35 2.75 ...... Frame ( 31) shift: 2.42 2.77 ...... Frame ( 32) shift: 2.50 2.79 ...... Frame ( 33) shift: 2.58 2.81 ...... Frame ( 34) shift: 2.66 2.83 ...... Frame ( 35) shift: 2.74 2.85 ...... Frame ( 36) shift: 2.76 2.86 ...... Frame ( 37) shift: 2.74 2.87 ...... Frame ( 38) shift: 2.71 2.87 ...... Frame ( 39) shift: 2.69 2.88 ...... Frame ( 40) shift: 2.67 2.89 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.740120 Iteration 2 Error: 0.191078 Iteration 3 Error: 0.037100 Align patch 2 23 left Iteration 1 Error: 0.896146 Iteration 2 Error: 0.186360 Iteration 3 Error: 0.042021 Align patch 3 22 left Iteration 1 Error: 0.871025 Iteration 2 Error: 0.125624 Iteration 3 Error: 0.033804 Align patch 4 21 left Iteration 1 Error: 0.844479 Iteration 2 Error: 0.088825 Iteration 3 Error: 0.020494 Align patch 5 20 left Iteration 1 Error: 0.645595 Iteration 2 Error: 0.124508 Iteration 3 Error: 0.030538 Align patch 6 19 left Iteration 1 Error: 0.591137 Iteration 2 Error: 0.167202 Iteration 3 Error: 0.032954 Align patch 7 18 left Iteration 1 Error: 0.699619 Iteration 2 Error: 0.107833 Iteration 3 Error: 0.030763 Align patch 8 17 left Iteration 1 Error: 0.672208 Iteration 2 Error: 0.087002 Iteration 3 Error: 0.029707 Align patch 9 16 left Iteration 1 Error: 0.867173 Iteration 2 Error: 0.159363 Iteration 3 Error: 0.039838 Align patch 10 15 left Iteration 1 Error: 0.790917 Iteration 2 Error: 0.162990 Iteration 3 Error: 0.035738 Align patch 11 14 left Iteration 1 Error: 0.428546 Iteration 2 Error: 0.098657 Iteration 3 Error: 0.031292 Align patch 12 13 left Iteration 1 Error: 0.851763 Iteration 2 Error: 0.127001 Iteration 3 Error: 0.037080 Align patch 13 12 left Iteration 1 Error: 0.993089 Iteration 2 Error: 0.167591 Iteration 3 Error: 0.038524 Align patch 14 11 left Iteration 1 Error: 0.636639 Iteration 2 Error: 0.136147 Iteration 3 Error: 0.048817 Align patch 15 10 left Iteration 1 Error: 1.398985 Iteration 2 Error: 0.196728 Iteration 3 Error: 0.049300 Align patch 16 9 left Iteration 1 Error: 0.648825 Iteration 2 Error: 0.159425 Iteration 3 Error: 0.041840 Align patch 17 8 left Iteration 1 Error: 0.705363 Iteration 2 Error: 0.099228 Iteration 3 Error: 0.024813 Align patch 18 7 left Iteration 1 Error: 0.749085 Iteration 2 Error: 0.115466 Iteration 3 Error: 0.022312 Align patch 19 6 left Iteration 1 Error: 0.678636 Iteration 2 Error: 0.138886 Iteration 3 Error: 0.047484 Align patch 20 5 left Iteration 1 Error: 0.978663 Iteration 2 Error: 0.139257 Iteration 3 Error: 0.038468 Align patch 21 4 left Iteration 1 Error: 0.885127 Iteration 2 Error: 0.157785 Iteration 3 Error: 0.048471 Align patch 22 3 left Iteration 1 Error: 0.650342 Iteration 2 Error: 0.073801 Iteration 3 Error: 0.021575 Align patch 23 2 left Iteration 1 Error: 0.559515 Iteration 2 Error: 0.139928 Iteration 3 Error: 0.027350 Align patch 24 1 left Iteration 1 Error: 0.893087 Iteration 2 Error: 0.123951 Iteration 3 Error: 0.047727 Align patch 25 0 left Iteration 1 Error: 0.794709 Iteration 2 Error: 0.125836 Iteration 3 Error: 0.045121 3D Fitting completed. Patch alignment time: 11.14(sec) Local motion has been corrected. Process thread exits. Computational time: 24.378841 sec Total time: 31.597195 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00037hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00037hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.456636s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00037hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.853919s ........................................ >>>>>>TIME<<<<<< FFT: 1.038232s Defocus_U Defocus_V Angle CCC 12175.76 13109.42 13.00 0.046820 Final Values Defocus_U Defocus_V Angle CCC 12180.45 13107.86 12.06 0.074202 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00037hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00037hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.992e-02 CC threshold: 0.734 Mean Std: 39.64 6.69 Num Hot pixels: 190 Hot pixel threshold: 79.80 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.700368 Iteration 2 Error: 0.426689 Iteration 3 Error: 0.101411 Iteration 4 Error: 0.043081 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.07 -0.00 ...... Frame ( 3) shift: 0.13 -0.01 ...... Frame ( 4) shift: 0.20 -0.01 ...... Frame ( 5) shift: 0.27 -0.01 ...... Frame ( 6) shift: 0.39 -0.00 ...... Frame ( 7) shift: 0.56 0.03 ...... Frame ( 8) shift: 0.74 0.06 ...... Frame ( 9) shift: 0.88 0.13 ...... Frame ( 10) shift: 0.98 0.26 ...... Frame ( 11) shift: 1.08 0.38 ...... Frame ( 12) shift: 1.19 0.44 ...... Frame ( 13) shift: 1.30 0.45 ...... Frame ( 14) shift: 1.41 0.45 ...... Frame ( 15) shift: 1.50 0.55 ...... Frame ( 16) shift: 1.58 0.72 ...... Frame ( 17) shift: 1.66 0.90 ...... Frame ( 18) shift: 1.75 1.02 ...... Frame ( 19) shift: 1.83 1.08 ...... Frame ( 20) shift: 1.92 1.14 ...... Frame ( 21) shift: 2.01 1.19 ...... Frame ( 22) shift: 2.12 1.24 ...... Frame ( 23) shift: 2.22 1.28 ...... Frame ( 24) shift: 2.29 1.36 ...... Frame ( 25) shift: 2.33 1.48 ...... Frame ( 26) shift: 2.36 1.60 ...... Frame ( 27) shift: 2.41 1.70 ...... Frame ( 28) shift: 2.47 1.77 ...... Frame ( 29) shift: 2.53 1.84 ...... Frame ( 30) shift: 2.62 1.90 ...... Frame ( 31) shift: 2.73 1.93 ...... Frame ( 32) shift: 2.85 1.96 ...... Frame ( 33) shift: 2.91 2.00 ...... Frame ( 34) shift: 2.92 2.03 ...... Frame ( 35) shift: 2.94 2.06 ...... Frame ( 36) shift: 2.98 2.10 ...... Frame ( 37) shift: 3.05 2.13 ...... Frame ( 38) shift: 3.12 2.16 ...... Frame ( 39) shift: 3.19 2.20 ...... Frame ( 40) shift: 3.26 2.23 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.769424 Iteration 2 Error: 0.185163 Iteration 3 Error: 0.053931 Iteration 4 Error: 0.024131 Align patch 2 23 left Iteration 1 Error: 1.230419 Iteration 2 Error: 0.129302 Iteration 3 Error: 0.048415 Align patch 3 22 left Iteration 1 Error: 0.855501 Iteration 2 Error: 0.213153 Iteration 3 Error: 0.053125 Iteration 4 Error: 0.026639 Align patch 4 21 left Iteration 1 Error: 0.893871 Iteration 2 Error: 0.191327 Iteration 3 Error: 0.062291 Iteration 4 Error: 0.030656 Align patch 5 20 left Iteration 1 Error: 0.520465 Iteration 2 Error: 0.102551 Iteration 3 Error: 0.031404 Align patch 6 19 left Iteration 1 Error: 1.146552 Iteration 2 Error: 0.185003 Iteration 3 Error: 0.058648 Iteration 4 Error: 0.025050 Align patch 7 18 left Iteration 1 Error: 0.807237 Iteration 2 Error: 0.132731 Iteration 3 Error: 0.034525 Align patch 8 17 left Iteration 1 Error: 0.642474 Iteration 2 Error: 0.118181 Iteration 3 Error: 0.039910 Align patch 9 16 left Iteration 1 Error: 0.951888 Iteration 2 Error: 0.148822 Iteration 3 Error: 0.047929 Align patch 10 15 left Iteration 1 Error: 0.915377 Iteration 2 Error: 0.158921 Iteration 3 Error: 0.054065 Iteration 4 Error: 0.016773 Align patch 11 14 left Iteration 1 Error: 0.709089 Iteration 2 Error: 0.089975 Iteration 3 Error: 0.044680 Align patch 12 13 left Iteration 1 Error: 0.630871 Iteration 2 Error: 0.085274 Iteration 3 Error: 0.023506 Align patch 13 12 left Iteration 1 Error: 1.564130 Iteration 2 Error: 0.224611 Iteration 3 Error: 0.022418 Align patch 14 11 left Iteration 1 Error: 0.893987 Iteration 2 Error: 0.125584 Iteration 3 Error: 0.024474 Align patch 15 10 left Iteration 1 Error: 1.113809 Iteration 2 Error: 0.137879 Iteration 3 Error: 0.038469 Align patch 16 9 left Iteration 1 Error: 0.731174 Iteration 2 Error: 0.121904 Iteration 3 Error: 0.025212 Align patch 17 8 left Iteration 1 Error: 0.948921 Iteration 2 Error: 0.220999 Iteration 3 Error: 0.043946 Align patch 18 7 left Iteration 1 Error: 0.632325 Iteration 2 Error: 0.152683 Iteration 3 Error: 0.041151 Align patch 19 6 left Iteration 1 Error: 0.580877 Iteration 2 Error: 0.085115 Iteration 3 Error: 0.026848 Align patch 20 5 left Iteration 1 Error: 1.028231 Iteration 2 Error: 0.216284 Iteration 3 Error: 0.071068 Iteration 4 Error: 0.027347 Align patch 21 4 left Iteration 1 Error: 1.048209 Iteration 2 Error: 0.218900 Iteration 3 Error: 0.074745 Iteration 4 Error: 0.040064 Align patch 22 3 left Iteration 1 Error: 1.209874 Iteration 2 Error: 0.227993 Iteration 3 Error: 0.094480 Iteration 4 Error: 0.040053 Align patch 23 2 left Iteration 1 Error: 1.133489 Iteration 2 Error: 0.175392 Iteration 3 Error: 0.052032 Iteration 4 Error: 0.019929 Align patch 24 1 left Iteration 1 Error: 0.978175 Iteration 2 Error: 0.172240 Iteration 3 Error: 0.080978 Iteration 4 Error: 0.013663 Align patch 25 0 left Iteration 1 Error: 0.938805 Iteration 2 Error: 0.264871 Iteration 3 Error: 0.069353 Iteration 4 Error: 0.025822 3D Fitting completed. Patch alignment time: 12.12(sec) Local motion has been corrected. Process thread exits. Computational time: 24.516195 sec Total time: 31.536776 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00037hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00037hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.646479s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00037hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.634929s ........................................ >>>>>>TIME<<<<<< FFT: 0.979628s Defocus_U Defocus_V Angle CCC 14462.89 15216.80 10.35 0.044889 Final Values Defocus_U Defocus_V Angle CCC 14447.26 15232.43 11.29 0.067756 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00037hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00037hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.991e-02 CC threshold: 0.734 Mean Std: 39.99 6.71 Num Hot pixels: 202 Hot pixel threshold: 80.28 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.462787 Iteration 2 Error: 0.235656 Iteration 3 Error: 0.066506 Iteration 4 Error: 0.023916 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.10 -0.19 ...... Frame ( 3) shift: 0.20 -0.39 ...... Frame ( 4) shift: 0.30 -0.58 ...... Frame ( 5) shift: 0.40 -0.78 ...... Frame ( 6) shift: 0.46 -0.78 ...... Frame ( 7) shift: 0.48 -0.59 ...... Frame ( 8) shift: 0.51 -0.40 ...... Frame ( 9) shift: 0.56 -0.25 ...... Frame ( 10) shift: 0.64 -0.14 ...... Frame ( 11) shift: 0.72 -0.03 ...... Frame ( 12) shift: 0.77 0.08 ...... Frame ( 13) shift: 0.79 0.20 ...... Frame ( 14) shift: 0.81 0.31 ...... Frame ( 15) shift: 0.84 0.40 ...... Frame ( 16) shift: 0.88 0.47 ...... Frame ( 17) shift: 0.92 0.55 ...... Frame ( 18) shift: 0.95 0.64 ...... Frame ( 19) shift: 0.97 0.75 ...... Frame ( 20) shift: 0.99 0.87 ...... Frame ( 21) shift: 1.07 0.96 ...... Frame ( 22) shift: 1.22 1.04 ...... Frame ( 23) shift: 1.37 1.12 ...... Frame ( 24) shift: 1.43 1.18 ...... Frame ( 25) shift: 1.40 1.23 ...... Frame ( 26) shift: 1.37 1.27 ...... Frame ( 27) shift: 1.33 1.33 ...... Frame ( 28) shift: 1.28 1.40 ...... Frame ( 29) shift: 1.23 1.47 ...... Frame ( 30) shift: 1.23 1.54 ...... Frame ( 31) shift: 1.27 1.62 ...... Frame ( 32) shift: 1.30 1.69 ...... Frame ( 33) shift: 1.35 1.72 ...... Frame ( 34) shift: 1.41 1.69 ...... Frame ( 35) shift: 1.47 1.67 ...... Frame ( 36) shift: 1.53 1.69 ...... Frame ( 37) shift: 1.59 1.74 ...... Frame ( 38) shift: 1.66 1.79 ...... Frame ( 39) shift: 1.72 1.85 ...... Frame ( 40) shift: 1.78 1.90 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.681095 Iteration 2 Error: 0.193776 Iteration 3 Error: 0.050386 Iteration 4 Error: 0.029173 Align patch 2 23 left Iteration 1 Error: 0.750562 Iteration 2 Error: 0.230617 Iteration 3 Error: 0.088228 Iteration 4 Error: 0.037132 Align patch 3 22 left Iteration 1 Error: 0.794067 Iteration 2 Error: 0.280745 Iteration 3 Error: 0.107963 Iteration 4 Error: 0.059989 Iteration 5 Error: 0.026466 Align patch 4 21 left Iteration 1 Error: 1.301957 Iteration 2 Error: 0.197533 Iteration 3 Error: 0.062341 Iteration 4 Error: 0.021531 Align patch 5 20 left Iteration 1 Error: 0.883593 Iteration 2 Error: 0.163750 Iteration 3 Error: 0.055304 Iteration 4 Error: 0.025750 Align patch 6 19 left Iteration 1 Error: 0.629165 Iteration 2 Error: 0.111916 Iteration 3 Error: 0.022686 Align patch 7 18 left Iteration 1 Error: 0.747104 Iteration 2 Error: 0.176151 Iteration 3 Error: 0.038849 Align patch 8 17 left Iteration 1 Error: 0.982231 Iteration 2 Error: 0.128064 Iteration 3 Error: 0.040524 Align patch 9 16 left Iteration 1 Error: 0.856588 Iteration 2 Error: 0.247369 Iteration 3 Error: 0.066578 Iteration 4 Error: 0.027782 Align patch 10 15 left Iteration 1 Error: 0.727848 Iteration 2 Error: 0.195914 Iteration 3 Error: 0.055179 Iteration 4 Error: 0.016164 Align patch 11 14 left Iteration 1 Error: 0.892136 Iteration 2 Error: 0.108186 Iteration 3 Error: 0.036297 Align patch 12 13 left Iteration 1 Error: 0.730061 Iteration 2 Error: 0.225520 Iteration 3 Error: 0.105333 Iteration 4 Error: 0.048893 Align patch 13 12 left Iteration 1 Error: 0.765670 Iteration 2 Error: 0.125427 Iteration 3 Error: 0.033877 Align patch 14 11 left Iteration 1 Error: 0.935174 Iteration 2 Error: 0.235671 Iteration 3 Error: 0.057704 Iteration 4 Error: 0.017118 Align patch 15 10 left Iteration 1 Error: 0.494522 Iteration 2 Error: 0.089799 Iteration 3 Error: 0.021468 Align patch 16 9 left Iteration 1 Error: 1.260036 Iteration 2 Error: 0.132890 Iteration 3 Error: 0.017327 Align patch 17 8 left Iteration 1 Error: 0.964314 Iteration 2 Error: 0.103087 Iteration 3 Error: 0.027666 Align patch 18 7 left Iteration 1 Error: 0.765445 Iteration 2 Error: 0.136818 Iteration 3 Error: 0.046611 Align patch 19 6 left Iteration 1 Error: 0.638049 Iteration 2 Error: 0.097324 Iteration 3 Error: 0.024710 Align patch 20 5 left Iteration 1 Error: 0.966281 Iteration 2 Error: 0.287887 Iteration 3 Error: 0.067014 Iteration 4 Error: 0.026306 Align patch 21 4 left Iteration 1 Error: 0.785905 Iteration 2 Error: 0.121310 Iteration 3 Error: 0.027866 Align patch 22 3 left Iteration 1 Error: 0.785670 Iteration 2 Error: 0.128105 Iteration 3 Error: 0.031696 Align patch 23 2 left Iteration 1 Error: 0.861792 Iteration 2 Error: 0.167697 Iteration 3 Error: 0.042429 Align patch 24 1 left Iteration 1 Error: 0.995761 Iteration 2 Error: 0.138261 Iteration 3 Error: 0.029780 Align patch 25 0 left Iteration 1 Error: 0.803763 Iteration 2 Error: 0.161712 Iteration 3 Error: 0.031139 3D Fitting completed. Patch alignment time: 12.39(sec) Local motion has been corrected. Process thread exits. Computational time: 28.490173 sec Total time: 35.531933 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00037hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00037hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.017741s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00037hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 4.662295s ........................................ >>>>>>TIME<<<<<< FFT: 1.144369s Defocus_U Defocus_V Angle CCC 16187.47 16761.74 1.67 0.040646 Final Values Defocus_U Defocus_V Angle CCC 16187.48 16768.00 1.67 0.066202 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00037hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00037hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 9.998e-02 CC threshold: 0.734 Mean Std: 39.40 6.67 Num Hot pixels: 180 Hot pixel threshold: 79.45 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.935346 Iteration 2 Error: 0.137237 Iteration 3 Error: 0.031726 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.02 -0.05 ...... Frame ( 3) shift: -0.04 -0.10 ...... Frame ( 4) shift: -0.06 -0.14 ...... Frame ( 5) shift: -0.08 -0.19 ...... Frame ( 6) shift: -0.08 -0.16 ...... Frame ( 7) shift: -0.04 -0.04 ...... Frame ( 8) shift: 0.00 0.07 ...... Frame ( 9) shift: 0.03 0.16 ...... Frame ( 10) shift: 0.06 0.21 ...... Frame ( 11) shift: 0.09 0.27 ...... Frame ( 12) shift: 0.09 0.33 ...... Frame ( 13) shift: 0.07 0.39 ...... Frame ( 14) shift: 0.05 0.45 ...... Frame ( 15) shift: 0.09 0.51 ...... Frame ( 16) shift: 0.18 0.57 ...... Frame ( 17) shift: 0.27 0.63 ...... Frame ( 18) shift: 0.37 0.71 ...... Frame ( 19) shift: 0.48 0.82 ...... Frame ( 20) shift: 0.58 0.92 ...... Frame ( 21) shift: 0.63 1.01 ...... Frame ( 22) shift: 0.61 1.08 ...... Frame ( 23) shift: 0.60 1.15 ...... Frame ( 24) shift: 0.60 1.16 ...... Frame ( 25) shift: 0.61 1.10 ...... Frame ( 26) shift: 0.63 1.05 ...... Frame ( 27) shift: 0.62 1.04 ...... Frame ( 28) shift: 0.59 1.07 ...... Frame ( 29) shift: 0.56 1.10 ...... Frame ( 30) shift: 0.61 1.12 ...... Frame ( 31) shift: 0.74 1.12 ...... Frame ( 32) shift: 0.86 1.13 ...... Frame ( 33) shift: 0.91 1.15 ...... Frame ( 34) shift: 0.89 1.17 ...... Frame ( 35) shift: 0.87 1.20 ...... Frame ( 36) shift: 0.87 1.24 ...... Frame ( 37) shift: 0.88 1.29 ...... Frame ( 38) shift: 0.89 1.35 ...... Frame ( 39) shift: 0.89 1.40 ...... Frame ( 40) shift: 0.90 1.45 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.922833 Iteration 2 Error: 0.172650 Iteration 3 Error: 0.040340 Align patch 2 23 left Iteration 1 Error: 0.726638 Iteration 2 Error: 0.117840 Iteration 3 Error: 0.028438 Align patch 3 22 left Iteration 1 Error: 1.174373 Iteration 2 Error: 0.225566 Iteration 3 Error: 0.054152 Iteration 4 Error: 0.022593 Align patch 4 21 left Iteration 1 Error: 1.256845 Iteration 2 Error: 0.259949 Iteration 3 Error: 0.071664 Iteration 4 Error: 0.029908 Align patch 5 20 left Iteration 1 Error: 0.982943 Iteration 2 Error: 0.221868 Iteration 3 Error: 0.046968 Align patch 6 19 left Iteration 1 Error: 0.632916 Iteration 2 Error: 0.103331 Iteration 3 Error: 0.042418 Align patch 7 18 left Iteration 1 Error: 0.719380 Iteration 2 Error: 0.092051 Iteration 3 Error: 0.016738 Align patch 8 17 left Iteration 1 Error: 0.903249 Iteration 2 Error: 0.087179 Iteration 3 Error: 0.024561 Align patch 9 16 left Iteration 1 Error: 0.958485 Iteration 2 Error: 0.193904 Iteration 3 Error: 0.050982 Iteration 4 Error: 0.019013 Align patch 10 15 left Iteration 1 Error: 0.662261 Iteration 2 Error: 0.131698 Iteration 3 Error: 0.028165 Align patch 11 14 left Iteration 1 Error: 0.744896 Iteration 2 Error: 0.172506 Iteration 3 Error: 0.042429 Align patch 12 13 left Iteration 1 Error: 0.865659 Iteration 2 Error: 0.129850 Iteration 3 Error: 0.024245 Align patch 13 12 left Iteration 1 Error: 0.604205 Iteration 2 Error: 0.120437 Iteration 3 Error: 0.031337 Align patch 14 11 left Iteration 1 Error: 0.616561 Iteration 2 Error: 0.097062 Iteration 3 Error: 0.022893 Align patch 15 10 left Iteration 1 Error: 0.768632 Iteration 2 Error: 0.082712 Iteration 3 Error: 0.019159 Align patch 16 9 left Iteration 1 Error: 0.826735 Iteration 2 Error: 0.107662 Iteration 3 Error: 0.025465 Align patch 17 8 left Iteration 1 Error: 0.762299 Iteration 2 Error: 0.158262 Iteration 3 Error: 0.044303 Align patch 18 7 left Iteration 1 Error: 0.971406 Iteration 2 Error: 0.125351 Iteration 3 Error: 0.030591 Align patch 19 6 left Iteration 1 Error: 0.820381 Iteration 2 Error: 0.130843 Iteration 3 Error: 0.033927 Align patch 20 5 left Iteration 1 Error: 0.788990 Iteration 2 Error: 0.166915 Iteration 3 Error: 0.038985 Align patch 21 4 left Iteration 1 Error: 1.068863 Iteration 2 Error: 0.139173 Iteration 3 Error: 0.040767 Align patch 22 3 left Iteration 1 Error: 0.554744 Iteration 2 Error: 0.124435 Iteration 3 Error: 0.054545 Iteration 4 Error: 0.017070 Align patch 23 2 left Iteration 1 Error: 0.683583 Iteration 2 Error: 0.105773 Iteration 3 Error: 0.022205 Align patch 24 1 left Iteration 1 Error: 1.054173 Iteration 2 Error: 0.168950 Iteration 3 Error: 0.044672 Align patch 25 0 left Iteration 1 Error: 0.950028 Iteration 2 Error: 0.113231 Iteration 3 Error: 0.022743 3D Fitting completed. Patch alignment time: 11.21(sec) Local motion has been corrected. Process thread exits. Computational time: 25.361900 sec Total time: 32.623264 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00037hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00037hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.655210s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00037hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.744647s ........................................ >>>>>>TIME<<<<<< FFT: 0.933641s Defocus_U Defocus_V Angle CCC 13580.08 14322.27 1.58 0.041551 Final Values Defocus_U Defocus_V Angle CCC 13580.08 14322.27 1.58 0.064637 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00038hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00038hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.988e-02 CC threshold: 0.734 Mean Std: 40.21 6.72 Num Hot pixels: 202 Hot pixel threshold: 80.53 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.205330 Iteration 2 Error: 0.699614 Iteration 3 Error: 0.236958 Iteration 4 Error: 0.118048 Iteration 5 Error: 0.058417 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.15 -0.15 ...... Frame ( 3) shift: 0.29 -0.30 ...... Frame ( 4) shift: 0.44 -0.45 ...... Frame ( 5) shift: 0.58 -0.60 ...... Frame ( 6) shift: 0.73 -0.64 ...... Frame ( 7) shift: 0.89 -0.56 ...... Frame ( 8) shift: 1.05 -0.49 ...... Frame ( 9) shift: 1.14 -0.37 ...... Frame ( 10) shift: 1.18 -0.21 ...... Frame ( 11) shift: 1.22 -0.05 ...... Frame ( 12) shift: 1.34 0.06 ...... Frame ( 13) shift: 1.53 0.14 ...... Frame ( 14) shift: 1.73 0.21 ...... Frame ( 15) shift: 1.90 0.28 ...... Frame ( 16) shift: 2.05 0.35 ...... Frame ( 17) shift: 2.19 0.41 ...... Frame ( 18) shift: 2.33 0.53 ...... Frame ( 19) shift: 2.46 0.70 ...... Frame ( 20) shift: 2.60 0.86 ...... Frame ( 21) shift: 2.70 0.99 ...... Frame ( 22) shift: 2.77 1.08 ...... Frame ( 23) shift: 2.84 1.17 ...... Frame ( 24) shift: 2.93 1.26 ...... Frame ( 25) shift: 3.04 1.37 ...... Frame ( 26) shift: 3.16 1.47 ...... Frame ( 27) shift: 3.26 1.59 ...... Frame ( 28) shift: 3.34 1.73 ...... Frame ( 29) shift: 3.43 1.87 ...... Frame ( 30) shift: 3.49 1.95 ...... Frame ( 31) shift: 3.54 1.99 ...... Frame ( 32) shift: 3.59 2.02 ...... Frame ( 33) shift: 3.69 2.07 ...... Frame ( 34) shift: 3.85 2.14 ...... Frame ( 35) shift: 4.00 2.21 ...... Frame ( 36) shift: 4.13 2.30 ...... Frame ( 37) shift: 4.23 2.39 ...... Frame ( 38) shift: 4.34 2.48 ...... Frame ( 39) shift: 4.44 2.58 ...... Frame ( 40) shift: 4.54 2.67 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.361646 Iteration 2 Error: 0.352453 Iteration 3 Error: 0.157842 Iteration 4 Error: 0.056603 Iteration 5 Error: 0.028981 Align patch 2 23 left Iteration 1 Error: 1.541090 Iteration 2 Error: 0.257936 Iteration 3 Error: 0.091569 Iteration 4 Error: 0.048847 Align patch 3 22 left Iteration 1 Error: 0.841457 Iteration 2 Error: 0.260650 Iteration 3 Error: 0.089899 Iteration 4 Error: 0.041308 Align patch 4 21 left Iteration 1 Error: 0.859561 Iteration 2 Error: 0.119487 Iteration 3 Error: 0.041214 Align patch 5 20 left Iteration 1 Error: 0.800563 Iteration 2 Error: 0.247205 Iteration 3 Error: 0.110693 Iteration 4 Error: 0.068293 Iteration 5 Error: 0.030182 Align patch 6 19 left Iteration 1 Error: 0.729599 Iteration 2 Error: 0.108836 Iteration 3 Error: 0.045347 Align patch 7 18 left Iteration 1 Error: 0.623200 Iteration 2 Error: 0.155748 Iteration 3 Error: 0.049752 Align patch 8 17 left Iteration 1 Error: 0.867744 Iteration 2 Error: 0.216028 Iteration 3 Error: 0.096599 Iteration 4 Error: 0.037239 Align patch 9 16 left Iteration 1 Error: 1.201473 Iteration 2 Error: 0.248082 Iteration 3 Error: 0.099496 Iteration 4 Error: 0.069294 Iteration 5 Error: 0.035476 Align patch 10 15 left Iteration 1 Error: 0.809260 Iteration 2 Error: 0.322695 Iteration 3 Error: 0.132451 Iteration 4 Error: 0.060217 Iteration 5 Error: 0.032706 Align patch 11 14 left Iteration 1 Error: 1.135167 Iteration 2 Error: 0.291513 Iteration 3 Error: 0.106839 Iteration 4 Error: 0.054352 Iteration 5 Error: 0.023818 Align patch 12 13 left Iteration 1 Error: 0.751123 Iteration 2 Error: 0.260887 Iteration 3 Error: 0.086522 Iteration 4 Error: 0.041016 Align patch 13 12 left Iteration 1 Error: 0.956375 Iteration 2 Error: 0.258065 Iteration 3 Error: 0.091868 Iteration 4 Error: 0.041205 Align patch 14 11 left Iteration 1 Error: 1.368853 Iteration 2 Error: 0.262392 Iteration 3 Error: 0.077666 Iteration 4 Error: 0.040992 Align patch 15 10 left Iteration 1 Error: 0.839149 Iteration 2 Error: 0.173933 Iteration 3 Error: 0.049280 Align patch 16 9 left Iteration 1 Error: 0.562899 Iteration 2 Error: 0.107905 Iteration 3 Error: 0.076138 Iteration 4 Error: 0.023271 Align patch 17 8 left Iteration 1 Error: 0.840383 Iteration 2 Error: 0.268617 Iteration 3 Error: 0.055731 Iteration 4 Error: 0.036771 Align patch 18 7 left Iteration 1 Error: 1.113031 Iteration 2 Error: 0.380911 Iteration 3 Error: 0.190613 Iteration 4 Error: 0.112880 Iteration 5 Error: 0.064719 Align patch 18 7 left Iteration 1 Error: 0.738901 Iteration 2 Error: 0.110558 Iteration 3 Error: 0.036710 Align patch 19 6 left Iteration 1 Error: 1.618369 Iteration 2 Error: 0.271342 Iteration 3 Error: 0.037646 Align patch 20 5 left Iteration 1 Error: 1.295699 Iteration 2 Error: 0.221805 Iteration 3 Error: 0.080238 Iteration 4 Error: 0.040546 Align patch 21 4 left Iteration 1 Error: 0.655554 Iteration 2 Error: 0.171902 Iteration 3 Error: 0.054229 Iteration 4 Error: 0.014556 Align patch 22 3 left Iteration 1 Error: 0.926259 Iteration 2 Error: 0.399133 Iteration 3 Error: 0.146000 Iteration 4 Error: 0.053577 Iteration 5 Error: 0.021986 Align patch 23 2 left Iteration 1 Error: 1.466272 Iteration 2 Error: 0.183363 Iteration 3 Error: 0.058004 Iteration 4 Error: 0.028977 Align patch 24 1 left Iteration 1 Error: 0.729583 Iteration 2 Error: 0.227111 Iteration 3 Error: 0.069684 Iteration 4 Error: 0.033044 Align patch 25 0 left Iteration 1 Error: 0.846778 Iteration 2 Error: 0.224216 Iteration 3 Error: 0.066095 Iteration 4 Error: 0.033684 3D Fitting completed. Patch alignment time: 13.03(sec) Local motion has been corrected. Process thread exits. Computational time: 27.787222 sec Total time: 36.950481 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00038hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00038hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.772971s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00038hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.614915s ........................................ >>>>>>TIME<<<<<< FFT: 0.939989s Defocus_U Defocus_V Angle CCC 12082.03 12851.56 13.34 0.044533 Final Values Defocus_U Defocus_V Angle CCC 12086.69 12871.93 13.66 0.073183 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00038hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00038hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.992e-02 CC threshold: 0.734 Mean Std: 40.00 6.72 Num Hot pixels: 210 Hot pixel threshold: 80.34 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.163699 Iteration 2 Error: 0.398368 Iteration 3 Error: 0.104462 Iteration 4 Error: 0.038182 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.11 -0.13 ...... Frame ( 3) shift: -0.21 -0.26 ...... Frame ( 4) shift: -0.32 -0.39 ...... Frame ( 5) shift: -0.43 -0.52 ...... Frame ( 6) shift: -0.43 -0.49 ...... Frame ( 7) shift: -0.33 -0.31 ...... Frame ( 8) shift: -0.22 -0.13 ...... Frame ( 9) shift: -0.07 0.03 ...... Frame ( 10) shift: 0.14 0.16 ...... Frame ( 11) shift: 0.35 0.29 ...... Frame ( 12) shift: 0.51 0.42 ...... Frame ( 13) shift: 0.64 0.55 ...... Frame ( 14) shift: 0.77 0.68 ...... Frame ( 15) shift: 0.88 0.81 ...... Frame ( 16) shift: 0.97 0.94 ...... Frame ( 17) shift: 1.07 1.06 ...... Frame ( 18) shift: 1.14 1.19 ...... Frame ( 19) shift: 1.17 1.31 ...... Frame ( 20) shift: 1.21 1.44 ...... Frame ( 21) shift: 1.31 1.53 ...... Frame ( 22) shift: 1.47 1.58 ...... Frame ( 23) shift: 1.63 1.63 ...... Frame ( 24) shift: 1.73 1.70 ...... Frame ( 25) shift: 1.78 1.81 ...... Frame ( 26) shift: 1.83 1.91 ...... Frame ( 27) shift: 1.90 2.00 ...... Frame ( 28) shift: 1.97 2.06 ...... Frame ( 29) shift: 2.04 2.12 ...... Frame ( 30) shift: 2.10 2.18 ...... Frame ( 31) shift: 2.14 2.26 ...... Frame ( 32) shift: 2.19 2.33 ...... Frame ( 33) shift: 2.24 2.37 ...... Frame ( 34) shift: 2.28 2.39 ...... Frame ( 35) shift: 2.33 2.40 ...... Frame ( 36) shift: 2.36 2.44 ...... Frame ( 37) shift: 2.39 2.49 ...... Frame ( 38) shift: 2.42 2.55 ...... Frame ( 39) shift: 2.44 2.60 ...... Frame ( 40) shift: 2.47 2.66 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.660319 Iteration 2 Error: 0.141225 Iteration 3 Error: 0.042812 Align patch 2 23 left Iteration 1 Error: 0.794421 Iteration 2 Error: 0.205037 Iteration 3 Error: 0.093302 Iteration 4 Error: 0.031239 Align patch 3 22 left Iteration 1 Error: 1.071740 Iteration 2 Error: 0.170208 Iteration 3 Error: 0.041509 Align patch 4 21 left Iteration 1 Error: 0.903530 Iteration 2 Error: 0.204221 Iteration 3 Error: 0.037484 Align patch 5 20 left Iteration 1 Error: 0.649128 Iteration 2 Error: 0.165262 Iteration 3 Error: 0.055261 Iteration 4 Error: 0.018709 Align patch 6 19 left Iteration 1 Error: 0.756074 Iteration 2 Error: 0.151163 Iteration 3 Error: 0.051988 Iteration 4 Error: 0.019607 Align patch 7 18 left Iteration 1 Error: 1.063188 Iteration 2 Error: 0.265108 Iteration 3 Error: 0.092741 Iteration 4 Error: 0.046360 Align patch 8 17 left Iteration 1 Error: 0.732607 Iteration 2 Error: 0.133308 Iteration 3 Error: 0.032014 Align patch 9 16 left Iteration 1 Error: 0.773575 Iteration 2 Error: 0.241191 Iteration 3 Error: 0.074029 Iteration 4 Error: 0.032085 Align patch 10 15 left Iteration 1 Error: 0.752184 Iteration 2 Error: 0.140019 Iteration 3 Error: 0.026585 Align patch 11 14 left Iteration 1 Error: 0.695036 Iteration 2 Error: 0.136547 Iteration 3 Error: 0.037120 Align patch 12 13 left Iteration 1 Error: 0.734799 Iteration 2 Error: 0.190428 Iteration 3 Error: 0.056433 Iteration 4 Error: 0.025710 Align patch 13 12 left Iteration 1 Error: 0.597745 Iteration 2 Error: 0.217681 Iteration 3 Error: 0.083985 Iteration 4 Error: 0.036312 Align patch 14 11 left Iteration 1 Error: 0.532674 Iteration 2 Error: 0.081743 Iteration 3 Error: 0.018740 Align patch 15 10 left Iteration 1 Error: 0.728914 Iteration 2 Error: 0.125309 Iteration 3 Error: 0.036422 Align patch 16 9 left Iteration 1 Error: 1.224467 Iteration 2 Error: 0.244807 Iteration 3 Error: 0.097800 Iteration 4 Error: 0.035691 Align patch 17 8 left Iteration 1 Error: 0.692728 Iteration 2 Error: 0.296203 Iteration 3 Error: 0.137200 Iteration 4 Error: 0.059537 Iteration 5 Error: 0.037052 Align patch 18 7 left Iteration 1 Error: 0.650658 Iteration 2 Error: 0.129170 Iteration 3 Error: 0.049256 Align patch 19 6 left Iteration 1 Error: 0.773442 Iteration 2 Error: 0.198480 Iteration 3 Error: 0.094472 Iteration 4 Error: 0.047020 Align patch 20 5 left Iteration 1 Error: 0.983785 Iteration 2 Error: 0.248860 Iteration 3 Error: 0.099762 Iteration 4 Error: 0.045980 Align patch 21 4 left Iteration 1 Error: 0.746408 Iteration 2 Error: 0.406778 Iteration 3 Error: 0.082967 Iteration 4 Error: 0.043858 Align patch 22 3 left Iteration 1 Error: 1.274604 Iteration 2 Error: 0.319292 Iteration 3 Error: 0.093041 Iteration 4 Error: 0.047564 Align patch 23 2 left Iteration 1 Error: 1.103388 Iteration 2 Error: 0.223267 Iteration 3 Error: 0.084435 Iteration 4 Error: 0.031880 Align patch 24 1 left Iteration 1 Error: 1.651867 Iteration 2 Error: 0.197310 Iteration 3 Error: 0.049864 Align patch 25 0 left Iteration 1 Error: 1.682775 Iteration 2 Error: 0.312617 Iteration 3 Error: 0.069642 Iteration 4 Error: 0.024073 3D Fitting completed. Patch alignment time: 12.77(sec) Local motion has been corrected. Process thread exits. Computational time: 26.870823 sec Total time: 33.674217 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00038hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00038hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.491324s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00038hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.608476s ........................................ >>>>>>TIME<<<<<< FFT: 1.133532s Defocus_U Defocus_V Angle CCC 15207.04 15980.48 5.39 0.044936 Final Values Defocus_U Defocus_V Angle CCC 15203.92 15980.48 5.08 0.068150 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00038hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00038hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.994e-02 CC threshold: 0.734 Mean Std: 41.57 6.85 Num Hot pixels: 210 Hot pixel threshold: 82.66 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.045403 Iteration 2 Error: 0.190392 Iteration 3 Error: 0.054028 Iteration 4 Error: 0.016501 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.09 -0.20 ...... Frame ( 3) shift: -0.18 -0.39 ...... Frame ( 4) shift: -0.27 -0.59 ...... Frame ( 5) shift: -0.36 -0.78 ...... Frame ( 6) shift: -0.37 -0.86 ...... Frame ( 7) shift: -0.32 -0.80 ...... Frame ( 8) shift: -0.26 -0.74 ...... Frame ( 9) shift: -0.20 -0.69 ...... Frame ( 10) shift: -0.14 -0.63 ...... Frame ( 11) shift: -0.08 -0.58 ...... Frame ( 12) shift: -0.02 -0.47 ...... Frame ( 13) shift: 0.06 -0.29 ...... Frame ( 14) shift: 0.13 -0.12 ...... Frame ( 15) shift: 0.18 -0.01 ...... Frame ( 16) shift: 0.21 0.03 ...... Frame ( 17) shift: 0.24 0.07 ...... Frame ( 18) shift: 0.25 0.16 ...... Frame ( 19) shift: 0.25 0.28 ...... Frame ( 20) shift: 0.25 0.41 ...... Frame ( 21) shift: 0.26 0.48 ...... Frame ( 22) shift: 0.30 0.51 ...... Frame ( 23) shift: 0.33 0.53 ...... Frame ( 24) shift: 0.39 0.59 ...... Frame ( 25) shift: 0.48 0.68 ...... Frame ( 26) shift: 0.57 0.78 ...... Frame ( 27) shift: 0.60 0.80 ...... Frame ( 28) shift: 0.57 0.77 ...... Frame ( 29) shift: 0.54 0.73 ...... Frame ( 30) shift: 0.54 0.75 ...... Frame ( 31) shift: 0.57 0.84 ...... Frame ( 32) shift: 0.60 0.93 ...... Frame ( 33) shift: 0.63 0.98 ...... Frame ( 34) shift: 0.65 0.99 ...... Frame ( 35) shift: 0.67 1.01 ...... Frame ( 36) shift: 0.74 1.03 ...... Frame ( 37) shift: 0.87 1.05 ...... Frame ( 38) shift: 1.01 1.07 ...... Frame ( 39) shift: 1.14 1.09 ...... Frame ( 40) shift: 1.27 1.10 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.473841 Iteration 2 Error: 0.093478 Iteration 3 Error: 0.026047 Align patch 2 23 left Iteration 1 Error: 0.637347 Iteration 2 Error: 0.075567 Iteration 3 Error: 0.026161 Align patch 3 22 left Iteration 1 Error: 0.505705 Iteration 2 Error: 0.108992 Iteration 3 Error: 0.034676 Align patch 4 21 left Iteration 1 Error: 0.914134 Iteration 2 Error: 0.150791 Iteration 3 Error: 0.039087 Align patch 5 20 left Iteration 1 Error: 0.596915 Iteration 2 Error: 0.138737 Iteration 3 Error: 0.055301 Iteration 4 Error: 0.016731 Align patch 6 19 left Iteration 1 Error: 0.648040 Iteration 2 Error: 0.097192 Iteration 3 Error: 0.027401 Align patch 7 18 left Iteration 1 Error: 0.743635 Iteration 2 Error: 0.125642 Iteration 3 Error: 0.040712 Align patch 8 17 left Iteration 1 Error: 0.695454 Iteration 2 Error: 0.106549 Iteration 3 Error: 0.030652 Align patch 9 16 left Iteration 1 Error: 1.086123 Iteration 2 Error: 0.155609 Iteration 3 Error: 0.065212 Iteration 4 Error: 0.021464 Align patch 10 15 left Iteration 1 Error: 0.976074 Iteration 2 Error: 0.101124 Iteration 3 Error: 0.028316 Align patch 11 14 left Iteration 1 Error: 1.353352 Iteration 2 Error: 0.183302 Iteration 3 Error: 0.054295 Iteration 4 Error: 0.021059 Align patch 12 13 left Iteration 1 Error: 0.626429 Iteration 2 Error: 0.149266 Iteration 3 Error: 0.069914 Iteration 4 Error: 0.042879 Align patch 13 12 left Iteration 1 Error: 0.664872 Iteration 2 Error: 0.123618 Iteration 3 Error: 0.045516 Align patch 14 11 left Iteration 1 Error: 0.653696 Iteration 2 Error: 0.107818 Iteration 3 Error: 0.024738 Align patch 15 10 left Iteration 1 Error: 0.708540 Iteration 2 Error: 0.098211 Iteration 3 Error: 0.027495 Align patch 16 9 left Iteration 1 Error: 0.840222 Iteration 2 Error: 0.104355 Iteration 3 Error: 0.024682 Align patch 17 8 left Iteration 1 Error: 0.718821 Iteration 2 Error: 0.109548 Iteration 3 Error: 0.037727 Align patch 18 7 left Iteration 1 Error: 0.832386 Iteration 2 Error: 0.330178 Iteration 3 Error: 0.061663 Iteration 4 Error: 0.044061 Align patch 19 6 left Iteration 1 Error: 0.608883 Iteration 2 Error: 0.133893 Iteration 3 Error: 0.027137 Align patch 20 5 left Iteration 1 Error: 0.853954 Iteration 2 Error: 0.116419 Iteration 3 Error: 0.042628 Align patch 21 4 left Iteration 1 Error: 0.674508 Iteration 2 Error: 0.142150 Iteration 3 Error: 0.038891 Align patch 22 3 left Iteration 1 Error: 0.770571 Iteration 2 Error: 0.125389 Iteration 3 Error: 0.026297 Align patch 23 2 left Iteration 1 Error: 0.901535 Iteration 2 Error: 0.230805 Iteration 3 Error: 0.041444 Align patch 24 1 left Iteration 1 Error: 0.583065 Iteration 2 Error: 0.123180 Iteration 3 Error: 0.044394 Align patch 25 0 left Iteration 1 Error: 0.807039 Iteration 2 Error: 0.194744 Iteration 3 Error: 0.064669 Iteration 4 Error: 0.021058 3D Fitting completed. Patch alignment time: 12.19(sec) Local motion has been corrected. Process thread exits. Computational time: 27.378704 sec Total time: 35.144024 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00038hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00038hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.597257s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00038hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.714114s ........................................ >>>>>>TIME<<<<<< FFT: 0.985037s Defocus_U Defocus_V Angle CCC 13828.14 14453.14 3.48 0.050433 Final Values Defocus_U Defocus_V Angle CCC 13832.83 14445.33 2.86 0.079684 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00038hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00038hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.350e-01 1.005e-01 CC threshold: 0.738 Mean Std: 39.07 6.79 Num Hot pixels: 196 Hot pixel threshold: 79.78 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.816106 Iteration 2 Error: 0.274238 Iteration 3 Error: 0.042670 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.01 -0.21 ...... Frame ( 3) shift: 0.02 -0.41 ...... Frame ( 4) shift: 0.03 -0.62 ...... Frame ( 5) shift: 0.04 -0.82 ...... Frame ( 6) shift: 0.10 -0.89 ...... Frame ( 7) shift: 0.20 -0.80 ...... Frame ( 8) shift: 0.31 -0.72 ...... Frame ( 9) shift: 0.42 -0.64 ...... Frame ( 10) shift: 0.54 -0.56 ...... Frame ( 11) shift: 0.66 -0.48 ...... Frame ( 12) shift: 0.76 -0.39 ...... Frame ( 13) shift: 0.84 -0.31 ...... Frame ( 14) shift: 0.92 -0.22 ...... Frame ( 15) shift: 0.99 -0.15 ...... Frame ( 16) shift: 1.05 -0.09 ...... Frame ( 17) shift: 1.11 -0.03 ...... Frame ( 18) shift: 1.19 0.04 ...... Frame ( 19) shift: 1.30 0.12 ...... Frame ( 20) shift: 1.40 0.20 ...... Frame ( 21) shift: 1.47 0.28 ...... Frame ( 22) shift: 1.49 0.36 ...... Frame ( 23) shift: 1.52 0.44 ...... Frame ( 24) shift: 1.57 0.49 ...... Frame ( 25) shift: 1.64 0.52 ...... Frame ( 26) shift: 1.70 0.55 ...... Frame ( 27) shift: 1.79 0.56 ...... Frame ( 28) shift: 1.90 0.55 ...... Frame ( 29) shift: 2.01 0.54 ...... Frame ( 30) shift: 2.08 0.57 ...... Frame ( 31) shift: 2.11 0.62 ...... Frame ( 32) shift: 2.13 0.68 ...... Frame ( 33) shift: 2.19 0.72 ...... Frame ( 34) shift: 2.30 0.76 ...... Frame ( 35) shift: 2.40 0.79 ...... Frame ( 36) shift: 2.47 0.81 ...... Frame ( 37) shift: 2.52 0.81 ...... Frame ( 38) shift: 2.57 0.81 ...... Frame ( 39) shift: 2.62 0.81 ...... Frame ( 40) shift: 2.67 0.81 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.752379 Iteration 2 Error: 0.233481 Iteration 3 Error: 0.073679 Iteration 4 Error: 0.026183 Align patch 2 23 left Iteration 1 Error: 0.645681 Iteration 2 Error: 0.147017 Iteration 3 Error: 0.048449 Align patch 3 22 left Iteration 1 Error: 0.559632 Iteration 2 Error: 0.110499 Iteration 3 Error: 0.021825 Align patch 4 21 left Iteration 1 Error: 0.802303 Iteration 2 Error: 0.222319 Iteration 3 Error: 0.064460 Iteration 4 Error: 0.026433 Align patch 5 20 left Iteration 1 Error: 0.868932 Iteration 2 Error: 0.187407 Iteration 3 Error: 0.055401 Iteration 4 Error: 0.022893 Align patch 6 19 left Iteration 1 Error: 0.347953 Iteration 2 Error: 0.127364 Iteration 3 Error: 0.050800 Iteration 4 Error: 0.023004 Align patch 7 18 left Iteration 1 Error: 0.413424 Iteration 2 Error: 0.091557 Iteration 3 Error: 0.024384 Align patch 8 17 left Iteration 1 Error: 0.621372 Iteration 2 Error: 0.088933 Iteration 3 Error: 0.028015 Align patch 9 16 left Iteration 1 Error: 0.663886 Iteration 2 Error: 0.201735 Iteration 3 Error: 0.059382 Iteration 4 Error: 0.020636 Align patch 10 15 left Iteration 1 Error: 0.850814 Iteration 2 Error: 0.200281 Iteration 3 Error: 0.050732 Iteration 4 Error: 0.018644 Align patch 11 14 left Iteration 1 Error: 0.857184 Iteration 2 Error: 0.129409 Iteration 3 Error: 0.023295 Align patch 12 13 left Iteration 1 Error: 0.429101 Iteration 2 Error: 0.101624 Iteration 3 Error: 0.025918 Align patch 13 12 left Iteration 1 Error: 0.423572 Iteration 2 Error: 0.075077 Iteration 3 Error: 0.015725 Align patch 14 11 left Iteration 1 Error: 0.948741 Iteration 2 Error: 0.126176 Iteration 3 Error: 0.031258 Align patch 15 10 left Iteration 1 Error: 1.167800 Iteration 2 Error: 0.249499 Iteration 3 Error: 0.050936 Iteration 4 Error: 0.013321 Align patch 16 9 left Iteration 1 Error: 1.084378 Iteration 2 Error: 0.177911 Iteration 3 Error: 0.041295 Align patch 17 8 left Iteration 1 Error: 1.027158 Iteration 2 Error: 0.185480 Iteration 3 Error: 0.039994 Align patch 18 7 left Iteration 1 Error: 0.663146 Iteration 2 Error: 0.187062 Iteration 3 Error: 0.053855 Iteration 4 Error: 0.014081 Align patch 19 6 left Iteration 1 Error: 0.609497 Iteration 2 Error: 0.095569 Iteration 3 Error: 0.017633 Align patch 20 5 left Iteration 1 Error: 2.144670 Iteration 2 Error: 0.243916 Iteration 3 Error: 0.058456 Iteration 4 Error: 0.029954 Align patch 21 4 left Iteration 1 Error: 0.667943 Iteration 2 Error: 0.210384 Iteration 3 Error: 0.062224 Iteration 4 Error: 0.015721 Align patch 22 3 left Iteration 1 Error: 0.564674 Iteration 2 Error: 0.089342 Iteration 3 Error: 0.019903 Align patch 23 2 left Iteration 1 Error: 1.137071 Iteration 2 Error: 0.277297 Iteration 3 Error: 0.072787 Iteration 4 Error: 0.023954 Align patch 24 1 left Iteration 1 Error: 0.639228 Iteration 2 Error: 0.103070 Iteration 3 Error: 0.035733 Align patch 25 0 left Iteration 1 Error: 1.099257 Iteration 2 Error: 0.244533 Iteration 3 Error: 0.039696 3D Fitting completed. Patch alignment time: 11.97(sec) Local motion has been corrected. Process thread exits. Computational time: 26.014074 sec Total time: 32.881905 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00038hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00038hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.480526s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00038hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.762407s ........................................ >>>>>>TIME<<<<<< FFT: 0.927098s Defocus_U Defocus_V Angle CCC 17285.18 18062.54 0.62 0.063521 Final Values Defocus_U Defocus_V Angle CCC 17283.62 18064.10 0.31 0.105748 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00039hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00039hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.993e-02 CC threshold: 0.734 Mean Std: 40.29 6.73 Num Hot pixels: 204 Hot pixel threshold: 80.69 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.081548 Iteration 2 Error: 0.365292 Iteration 3 Error: 0.125930 Iteration 4 Error: 0.040274 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.18 -0.19 ...... Frame ( 3) shift: 0.36 -0.37 ...... Frame ( 4) shift: 0.54 -0.56 ...... Frame ( 5) shift: 0.72 -0.75 ...... Frame ( 6) shift: 0.91 -0.77 ...... Frame ( 7) shift: 1.11 -0.62 ...... Frame ( 8) shift: 1.31 -0.48 ...... Frame ( 9) shift: 1.42 -0.29 ...... Frame ( 10) shift: 1.47 -0.05 ...... Frame ( 11) shift: 1.51 0.19 ...... Frame ( 12) shift: 1.56 0.36 ...... Frame ( 13) shift: 1.62 0.47 ...... Frame ( 14) shift: 1.68 0.57 ...... Frame ( 15) shift: 1.76 0.71 ...... Frame ( 16) shift: 1.84 0.87 ...... Frame ( 17) shift: 1.93 1.04 ...... Frame ( 18) shift: 1.97 1.15 ...... Frame ( 19) shift: 1.95 1.22 ...... Frame ( 20) shift: 1.94 1.28 ...... Frame ( 21) shift: 1.99 1.36 ...... Frame ( 22) shift: 2.11 1.46 ...... Frame ( 23) shift: 2.23 1.55 ...... Frame ( 24) shift: 2.34 1.65 ...... Frame ( 25) shift: 2.46 1.76 ...... Frame ( 26) shift: 2.58 1.87 ...... Frame ( 27) shift: 2.62 2.01 ...... Frame ( 28) shift: 2.59 2.18 ...... Frame ( 29) shift: 2.55 2.34 ...... Frame ( 30) shift: 2.60 2.47 ...... Frame ( 31) shift: 2.74 2.57 ...... Frame ( 32) shift: 2.87 2.66 ...... Frame ( 33) shift: 3.03 2.77 ...... Frame ( 34) shift: 3.20 2.90 ...... Frame ( 35) shift: 3.38 3.03 ...... Frame ( 36) shift: 3.46 3.11 ...... Frame ( 37) shift: 3.43 3.14 ...... Frame ( 38) shift: 3.40 3.18 ...... Frame ( 39) shift: 3.37 3.21 ...... Frame ( 40) shift: 3.34 3.25 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.785529 Iteration 2 Error: 0.185945 Iteration 3 Error: 0.034941 Align patch 2 23 left Iteration 1 Error: 0.784091 Iteration 2 Error: 0.243868 Iteration 3 Error: 0.063316 Iteration 4 Error: 0.026467 Align patch 3 22 left Iteration 1 Error: 0.835835 Iteration 2 Error: 0.109601 Iteration 3 Error: 0.032884 Align patch 4 21 left Iteration 1 Error: 0.827761 Iteration 2 Error: 0.120363 Iteration 3 Error: 0.041249 Align patch 5 20 left Iteration 1 Error: 0.885187 Iteration 2 Error: 0.280791 Iteration 3 Error: 0.113633 Iteration 4 Error: 0.032898 Align patch 6 19 left Iteration 1 Error: 0.634451 Iteration 2 Error: 0.111950 Iteration 3 Error: 0.037520 Align patch 7 18 left Iteration 1 Error: 1.046488 Iteration 2 Error: 0.193057 Iteration 3 Error: 0.067572 Iteration 4 Error: 0.036505 Align patch 8 17 left Iteration 1 Error: 0.742906 Iteration 2 Error: 0.119472 Iteration 3 Error: 0.023851 Align patch 9 16 left Iteration 1 Error: 0.602165 Iteration 2 Error: 0.145618 Iteration 3 Error: 0.035988 Align patch 10 15 left Iteration 1 Error: 0.444309 Iteration 2 Error: 0.092906 Iteration 3 Error: 0.039229 Align patch 11 14 left Iteration 1 Error: 0.827743 Iteration 2 Error: 0.220268 Iteration 3 Error: 0.060645 Iteration 4 Error: 0.026319 Align patch 12 13 left Iteration 1 Error: 0.840618 Iteration 2 Error: 0.247545 Iteration 3 Error: 0.110362 Iteration 4 Error: 0.053834 Iteration 5 Error: 0.022352 Align patch 13 12 left Iteration 1 Error: 0.680637 Iteration 2 Error: 0.108908 Iteration 3 Error: 0.027157 Align patch 14 11 left Iteration 1 Error: 0.677973 Iteration 2 Error: 0.109098 Iteration 3 Error: 0.037961 Align patch 15 10 left Iteration 1 Error: 0.997119 Iteration 2 Error: 0.257898 Iteration 3 Error: 0.053821 Iteration 4 Error: 0.025369 Align patch 16 9 left Iteration 1 Error: 0.865448 Iteration 2 Error: 0.195315 Iteration 3 Error: 0.043494 Align patch 17 8 left Iteration 1 Error: 0.809759 Iteration 2 Error: 0.132599 Iteration 3 Error: 0.037137 Align patch 18 7 left Iteration 1 Error: 0.634262 Iteration 2 Error: 0.101720 Iteration 3 Error: 0.053973 Iteration 4 Error: 0.016944 Align patch 19 6 left Iteration 1 Error: 0.727092 Iteration 2 Error: 0.120179 Iteration 3 Error: 0.038324 Align patch 20 5 left Iteration 1 Error: 0.688285 Iteration 2 Error: 0.116527 Iteration 3 Error: 0.045424 Align patch 21 4 left Iteration 1 Error: 0.739008 Iteration 2 Error: 0.132414 Iteration 3 Error: 0.026814 Align patch 22 3 left Iteration 1 Error: 0.631187 Iteration 2 Error: 0.168416 Iteration 3 Error: 0.045563 Align patch 23 2 left Iteration 1 Error: 0.963552 Iteration 2 Error: 0.272917 Iteration 3 Error: 0.108669 Iteration 4 Error: 0.026593 Align patch 24 1 left Iteration 1 Error: 0.779288 Iteration 2 Error: 0.139543 Iteration 3 Error: 0.027123 Align patch 25 0 left Iteration 1 Error: 0.954179 Iteration 2 Error: 0.129987 Iteration 3 Error: 0.028278 3D Fitting completed. Patch alignment time: 12.06(sec) Local motion has been corrected. Process thread exits. Computational time: 30.179880 sec Total time: 37.330036 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00039hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00039hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.936072s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00039hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.570503s ........................................ >>>>>>TIME<<<<<< FFT: 1.025068s Defocus_U Defocus_V Angle CCC 14902.33 15644.54 7.52 0.050866 Final Values Defocus_U Defocus_V Angle CCC 14877.33 15644.55 8.78 0.081246 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00039hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00039hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.994e-02 CC threshold: 0.734 Mean Std: 39.96 6.71 Num Hot pixels: 203 Hot pixel threshold: 80.20 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.291335 Iteration 2 Error: 0.256710 Iteration 3 Error: 0.061986 Iteration 4 Error: 0.018413 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.15 -0.28 ...... Frame ( 3) shift: 0.30 -0.56 ...... Frame ( 4) shift: 0.45 -0.85 ...... Frame ( 5) shift: 0.60 -1.13 ...... Frame ( 6) shift: 0.70 -1.25 ...... Frame ( 7) shift: 0.76 -1.22 ...... Frame ( 8) shift: 0.82 -1.19 ...... Frame ( 9) shift: 0.83 -1.10 ...... Frame ( 10) shift: 0.80 -0.97 ...... Frame ( 11) shift: 0.78 -0.84 ...... Frame ( 12) shift: 0.75 -0.72 ...... Frame ( 13) shift: 0.72 -0.63 ...... Frame ( 14) shift: 0.69 -0.54 ...... Frame ( 15) shift: 0.69 -0.43 ...... Frame ( 16) shift: 0.70 -0.32 ...... Frame ( 17) shift: 0.72 -0.21 ...... Frame ( 18) shift: 0.72 -0.09 ...... Frame ( 19) shift: 0.71 0.04 ...... Frame ( 20) shift: 0.70 0.17 ...... Frame ( 21) shift: 0.68 0.29 ...... Frame ( 22) shift: 0.67 0.40 ...... Frame ( 23) shift: 0.66 0.51 ...... Frame ( 24) shift: 0.71 0.59 ...... Frame ( 25) shift: 0.81 0.65 ...... Frame ( 26) shift: 0.92 0.71 ...... Frame ( 27) shift: 0.98 0.75 ...... Frame ( 28) shift: 0.99 0.76 ...... Frame ( 29) shift: 1.00 0.78 ...... Frame ( 30) shift: 1.00 0.82 ...... Frame ( 31) shift: 0.99 0.89 ...... Frame ( 32) shift: 0.98 0.95 ...... Frame ( 33) shift: 1.03 0.99 ...... Frame ( 34) shift: 1.15 1.01 ...... Frame ( 35) shift: 1.27 1.03 ...... Frame ( 36) shift: 1.35 1.09 ...... Frame ( 37) shift: 1.40 1.19 ...... Frame ( 38) shift: 1.44 1.30 ...... Frame ( 39) shift: 1.48 1.40 ...... Frame ( 40) shift: 1.52 1.50 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.237468 Iteration 2 Error: 0.182116 Iteration 3 Error: 0.075947 Iteration 4 Error: 0.017366 Align patch 2 23 left Iteration 1 Error: 0.623474 Iteration 2 Error: 0.131484 Iteration 3 Error: 0.025062 Align patch 3 22 left Iteration 1 Error: 0.614827 Iteration 2 Error: 0.103300 Iteration 3 Error: 0.028220 Align patch 4 21 left Iteration 1 Error: 0.959232 Iteration 2 Error: 0.220638 Iteration 3 Error: 0.058000 Iteration 4 Error: 0.015683 Align patch 5 20 left Iteration 1 Error: 0.593998 Iteration 2 Error: 0.117594 Iteration 3 Error: 0.018116 Align patch 6 19 left Iteration 1 Error: 0.841700 Iteration 2 Error: 0.216168 Iteration 3 Error: 0.087108 Iteration 4 Error: 0.030679 Align patch 7 18 left Iteration 1 Error: 0.700575 Iteration 2 Error: 0.125889 Iteration 3 Error: 0.031349 Align patch 8 17 left Iteration 1 Error: 0.705113 Iteration 2 Error: 0.188659 Iteration 3 Error: 0.033829 Align patch 9 16 left Iteration 1 Error: 0.935084 Iteration 2 Error: 0.207680 Iteration 3 Error: 0.051182 Iteration 4 Error: 0.016679 Align patch 10 15 left Iteration 1 Error: 0.745156 Iteration 2 Error: 0.119319 Iteration 3 Error: 0.036671 Align patch 11 14 left Iteration 1 Error: 0.559560 Iteration 2 Error: 0.200394 Iteration 3 Error: 0.040516 Align patch 12 13 left Iteration 1 Error: 0.555796 Iteration 2 Error: 0.084924 Iteration 3 Error: 0.025008 Align patch 13 12 left Iteration 1 Error: 0.847115 Iteration 2 Error: 0.160235 Iteration 3 Error: 0.045768 Align patch 14 11 left Iteration 1 Error: 0.723958 Iteration 2 Error: 0.083058 Iteration 3 Error: 0.021474 Align patch 15 10 left Iteration 1 Error: 0.674570 Iteration 2 Error: 0.122730 Iteration 3 Error: 0.020342 Align patch 16 9 left Iteration 1 Error: 0.458330 Iteration 2 Error: 0.089564 Iteration 3 Error: 0.021848 Align patch 17 8 left Iteration 1 Error: 0.795860 Iteration 2 Error: 0.168053 Iteration 3 Error: 0.038680 Align patch 18 7 left Iteration 1 Error: 0.507241 Iteration 2 Error: 0.144094 Iteration 3 Error: 0.039934 Align patch 19 6 left Iteration 1 Error: 0.761905 Iteration 2 Error: 0.241529 Iteration 3 Error: 0.105847 Iteration 4 Error: 0.042934 Align patch 20 5 left Iteration 1 Error: 0.896979 Iteration 2 Error: 0.211653 Iteration 3 Error: 0.067791 Iteration 4 Error: 0.023423 Align patch 21 4 left Iteration 1 Error: 0.663845 Iteration 2 Error: 0.166022 Iteration 3 Error: 0.036384 Align patch 22 3 left Iteration 1 Error: 0.760019 Iteration 2 Error: 0.108102 Iteration 3 Error: 0.050314 Iteration 4 Error: 0.010886 Align patch 23 2 left Iteration 1 Error: 0.629449 Iteration 2 Error: 0.184590 Iteration 3 Error: 0.039337 Align patch 24 1 left Iteration 1 Error: 0.580943 Iteration 2 Error: 0.081487 Iteration 3 Error: 0.017110 Align patch 25 0 left Iteration 1 Error: 1.070947 Iteration 2 Error: 0.193997 Iteration 3 Error: 0.043297 3D Fitting completed. Patch alignment time: 11.67(sec) Local motion has been corrected. Process thread exits. Computational time: 26.215656 sec Total time: 32.947796 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00039hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00039hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.899947s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00039hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.957946s ........................................ >>>>>>TIME<<<<<< FFT: 1.015994s Defocus_U Defocus_V Angle CCC 14703.13 15500.01 6.70 0.046951 Final Values Defocus_U Defocus_V Angle CCC 14690.63 15512.51 6.39 0.072074 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00039hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00039hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.996e-02 CC threshold: 0.734 Mean Std: 39.66 6.68 Num Hot pixels: 195 Hot pixel threshold: 79.76 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.457665 Iteration 2 Error: 0.306995 Iteration 3 Error: 0.074663 Iteration 4 Error: 0.025202 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.04 -0.22 ...... Frame ( 3) shift: 0.08 -0.44 ...... Frame ( 4) shift: 0.11 -0.66 ...... Frame ( 5) shift: 0.15 -0.89 ...... Frame ( 6) shift: 0.16 -0.97 ...... Frame ( 7) shift: 0.14 -0.92 ...... Frame ( 8) shift: 0.12 -0.86 ...... Frame ( 9) shift: 0.13 -0.77 ...... Frame ( 10) shift: 0.17 -0.65 ...... Frame ( 11) shift: 0.21 -0.53 ...... Frame ( 12) shift: 0.24 -0.37 ...... Frame ( 13) shift: 0.28 -0.19 ...... Frame ( 14) shift: 0.31 -0.00 ...... Frame ( 15) shift: 0.32 0.13 ...... Frame ( 16) shift: 0.31 0.21 ...... Frame ( 17) shift: 0.31 0.29 ...... Frame ( 18) shift: 0.31 0.41 ...... Frame ( 19) shift: 0.31 0.58 ...... Frame ( 20) shift: 0.31 0.75 ...... Frame ( 21) shift: 0.33 0.90 ...... Frame ( 22) shift: 0.38 1.03 ...... Frame ( 23) shift: 0.42 1.16 ...... Frame ( 24) shift: 0.48 1.27 ...... Frame ( 25) shift: 0.57 1.36 ...... Frame ( 26) shift: 0.65 1.45 ...... Frame ( 27) shift: 0.68 1.53 ...... Frame ( 28) shift: 0.67 1.58 ...... Frame ( 29) shift: 0.66 1.64 ...... Frame ( 30) shift: 0.66 1.70 ...... Frame ( 31) shift: 0.67 1.77 ...... Frame ( 32) shift: 0.68 1.84 ...... Frame ( 33) shift: 0.71 1.90 ...... Frame ( 34) shift: 0.77 1.97 ...... Frame ( 35) shift: 0.83 2.03 ...... Frame ( 36) shift: 0.84 2.08 ...... Frame ( 37) shift: 0.79 2.12 ...... Frame ( 38) shift: 0.74 2.15 ...... Frame ( 39) shift: 0.69 2.19 ...... Frame ( 40) shift: 0.64 2.22 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.340211 Iteration 2 Error: 0.160484 Iteration 3 Error: 0.037756 Align patch 2 23 left Iteration 1 Error: 0.792566 Iteration 2 Error: 0.168301 Iteration 3 Error: 0.057352 Iteration 4 Error: 0.021030 Align patch 3 22 left Iteration 1 Error: 0.576321 Iteration 2 Error: 0.074785 Iteration 3 Error: 0.021500 Align patch 4 21 left Iteration 1 Error: 0.512307 Iteration 2 Error: 0.101876 Iteration 3 Error: 0.020125 Align patch 5 20 left Iteration 1 Error: 0.696534 Iteration 2 Error: 0.106075 Iteration 3 Error: 0.035222 Align patch 6 19 left Iteration 1 Error: 0.786767 Iteration 2 Error: 0.107099 Iteration 3 Error: 0.028789 Align patch 7 18 left Iteration 1 Error: 1.030507 Iteration 2 Error: 0.175893 Iteration 3 Error: 0.082595 Iteration 4 Error: 0.033774 Align patch 8 17 left Iteration 1 Error: 0.865646 Iteration 2 Error: 0.199374 Iteration 3 Error: 0.066115 Iteration 4 Error: 0.025570 Align patch 9 16 left Iteration 1 Error: 1.046715 Iteration 2 Error: 0.255100 Iteration 3 Error: 0.073495 Iteration 4 Error: 0.028708 Align patch 10 15 left Iteration 1 Error: 0.618048 Iteration 2 Error: 0.086162 Iteration 3 Error: 0.024844 Align patch 11 14 left Iteration 1 Error: 0.448303 Iteration 2 Error: 0.101758 Iteration 3 Error: 0.030802 Align patch 12 13 left Iteration 1 Error: 1.230124 Iteration 2 Error: 0.160971 Iteration 3 Error: 0.061812 Iteration 4 Error: 0.021551 Align patch 13 12 left Iteration 1 Error: 1.054868 Iteration 2 Error: 0.280591 Iteration 3 Error: 0.101953 Iteration 4 Error: 0.034437 Align patch 14 11 left Iteration 1 Error: 0.897156 Iteration 2 Error: 0.151527 Iteration 3 Error: 0.037961 Align patch 15 10 left Iteration 1 Error: 0.833472 Iteration 2 Error: 0.142652 Iteration 3 Error: 0.042818 Align patch 16 9 left Iteration 1 Error: 0.647090 Iteration 2 Error: 0.182501 Iteration 3 Error: 0.038871 Align patch 17 8 left Iteration 1 Error: 0.685719 Iteration 2 Error: 0.105147 Iteration 3 Error: 0.040720 Align patch 18 7 left Iteration 1 Error: 0.770912 Iteration 2 Error: 0.089973 Iteration 3 Error: 0.022421 Align patch 19 6 left Iteration 1 Error: 1.205368 Iteration 2 Error: 0.190954 Iteration 3 Error: 0.036343 Align patch 20 5 left Iteration 1 Error: 1.158781 Iteration 2 Error: 0.172263 Iteration 3 Error: 0.042826 Align patch 21 4 left Iteration 1 Error: 1.136280 Iteration 2 Error: 0.140900 Iteration 3 Error: 0.030186 Align patch 22 3 left Iteration 1 Error: 0.582172 Iteration 2 Error: 0.190432 Iteration 3 Error: 0.058383 Iteration 4 Error: 0.023709 Align patch 23 2 left Iteration 1 Error: 0.919135 Iteration 2 Error: 0.295026 Iteration 3 Error: 0.079596 Iteration 4 Error: 0.042703 Align patch 24 1 left Iteration 1 Error: 0.985409 Iteration 2 Error: 0.130652 Iteration 3 Error: 0.033535 Align patch 25 0 left Iteration 1 Error: 0.547391 Iteration 2 Error: 0.089048 Iteration 3 Error: 0.023466 3D Fitting completed. Patch alignment time: 12.14(sec) Local motion has been corrected. Process thread exits. Computational time: 22.728012 sec Total time: 28.694078 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00039hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00039hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.434396s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00039hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.959548s ........................................ >>>>>>TIME<<<<<< FFT: 0.891019s Defocus_U Defocus_V Angle CCC 17085.88 17761.80 3.63 0.035974 Final Values Defocus_U Defocus_V Angle CCC 17112.43 17732.12 5.53 0.059692 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00039hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00039hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.002e-01 CC threshold: 0.736 Mean Std: 36.95 6.49 Num Hot pixels: 200 Hot pixel threshold: 75.90 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.050080 Iteration 2 Error: 0.219941 Iteration 3 Error: 0.054298 Iteration 4 Error: 0.015053 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.11 -0.33 ...... Frame ( 3) shift: 0.23 -0.67 ...... Frame ( 4) shift: 0.34 -1.00 ...... Frame ( 5) shift: 0.45 -1.34 ...... Frame ( 6) shift: 0.55 -1.51 ...... Frame ( 7) shift: 0.64 -1.53 ...... Frame ( 8) shift: 0.73 -1.56 ...... Frame ( 9) shift: 0.82 -1.54 ...... Frame ( 10) shift: 0.91 -1.49 ...... Frame ( 11) shift: 1.01 -1.44 ...... Frame ( 12) shift: 1.01 -1.36 ...... Frame ( 13) shift: 0.93 -1.26 ...... Frame ( 14) shift: 0.85 -1.15 ...... Frame ( 15) shift: 0.86 -1.06 ...... Frame ( 16) shift: 0.94 -0.97 ...... Frame ( 17) shift: 1.03 -0.88 ...... Frame ( 18) shift: 1.11 -0.76 ...... Frame ( 19) shift: 1.17 -0.62 ...... Frame ( 20) shift: 1.23 -0.49 ...... Frame ( 21) shift: 1.29 -0.38 ...... Frame ( 22) shift: 1.34 -0.30 ...... Frame ( 23) shift: 1.39 -0.22 ...... Frame ( 24) shift: 1.44 -0.13 ...... Frame ( 25) shift: 1.49 -0.04 ...... Frame ( 26) shift: 1.53 0.06 ...... Frame ( 27) shift: 1.56 0.15 ...... Frame ( 28) shift: 1.57 0.24 ...... Frame ( 29) shift: 1.58 0.33 ...... Frame ( 30) shift: 1.60 0.42 ...... Frame ( 31) shift: 1.63 0.52 ...... Frame ( 32) shift: 1.66 0.61 ...... Frame ( 33) shift: 1.70 0.66 ...... Frame ( 34) shift: 1.77 0.66 ...... Frame ( 35) shift: 1.83 0.65 ...... Frame ( 36) shift: 1.83 0.64 ...... Frame ( 37) shift: 1.79 0.62 ...... Frame ( 38) shift: 1.74 0.59 ...... Frame ( 39) shift: 1.69 0.57 ...... Frame ( 40) shift: 1.64 0.55 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.624849 Iteration 2 Error: 0.118252 Iteration 3 Error: 0.017335 Align patch 2 23 left Iteration 1 Error: 0.705751 Iteration 2 Error: 0.085855 Iteration 3 Error: 0.017079 Align patch 3 22 left Iteration 1 Error: 0.743304 Iteration 2 Error: 0.093212 Iteration 3 Error: 0.022504 Align patch 4 21 left Iteration 1 Error: 0.654341 Iteration 2 Error: 0.095293 Iteration 3 Error: 0.024908 Align patch 5 20 left Iteration 1 Error: 0.682468 Iteration 2 Error: 0.204015 Iteration 3 Error: 0.046797 Align patch 6 19 left Iteration 1 Error: 0.808878 Iteration 2 Error: 0.150178 Iteration 3 Error: 0.026996 Align patch 7 18 left Iteration 1 Error: 1.042170 Iteration 2 Error: 0.116033 Iteration 3 Error: 0.027847 Align patch 8 17 left Iteration 1 Error: 0.606192 Iteration 2 Error: 0.112699 Iteration 3 Error: 0.021893 Align patch 9 16 left Iteration 1 Error: 0.965461 Iteration 2 Error: 0.134298 Iteration 3 Error: 0.031760 Align patch 10 15 left Iteration 1 Error: 0.833178 Iteration 2 Error: 0.112382 Iteration 3 Error: 0.021692 Align patch 11 14 left Iteration 1 Error: 0.701440 Iteration 2 Error: 0.053520 Iteration 3 Error: 0.009644 Align patch 12 13 left Iteration 1 Error: 0.492387 Iteration 2 Error: 0.120681 Iteration 3 Error: 0.021940 Align patch 13 12 left Iteration 1 Error: 0.723581 Iteration 2 Error: 0.128569 Iteration 3 Error: 0.027883 Align patch 14 11 left Iteration 1 Error: 0.462630 Iteration 2 Error: 0.056325 Iteration 3 Error: 0.019197 Align patch 15 10 left Iteration 1 Error: 0.445598 Iteration 2 Error: 0.091979 Iteration 3 Error: 0.021096 Align patch 16 9 left Iteration 1 Error: 0.763637 Iteration 2 Error: 0.117166 Iteration 3 Error: 0.039703 Align patch 17 8 left Iteration 1 Error: 0.867035 Iteration 2 Error: 0.126868 Iteration 3 Error: 0.044395 Align patch 18 7 left Iteration 1 Error: 0.762026 Iteration 2 Error: 0.094871 Iteration 3 Error: 0.018822 Align patch 19 6 left Iteration 1 Error: 0.788180 Iteration 2 Error: 0.084685 Iteration 3 Error: 0.018791 Align patch 20 5 left Iteration 1 Error: 0.620491 Iteration 2 Error: 0.106744 Iteration 3 Error: 0.030336 Align patch 21 4 left Iteration 1 Error: 0.803999 Iteration 2 Error: 0.101285 Iteration 3 Error: 0.020924 Align patch 22 3 left Iteration 1 Error: 0.863795 Iteration 2 Error: 0.102241 Iteration 3 Error: 0.024582 Align patch 23 2 left Iteration 1 Error: 0.511775 Iteration 2 Error: 0.067014 Iteration 3 Error: 0.016491 Align patch 24 1 left Iteration 1 Error: 0.618834 Iteration 2 Error: 0.085574 Iteration 3 Error: 0.014092 Align patch 25 0 left Iteration 1 Error: 0.612203 Iteration 2 Error: 0.082534 Iteration 3 Error: 0.027987 3D Fitting completed. Patch alignment time: 10.94(sec) Local motion has been corrected. Process thread exits. Computational time: 20.687220 sec Total time: 28.042362 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00039hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00039hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.508160s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00039hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.359692s ........................................ >>>>>>TIME<<<<<< FFT: 0.939949s Defocus_U Defocus_V Angle CCC 13167.97 13890.62 1.34 0.058546 Final Values Defocus_U Defocus_V Angle CCC 13185.16 13854.69 1.66 0.084760 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00040hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00040hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.992e-02 CC threshold: 0.734 Mean Std: 40.65 6.77 Num Hot pixels: 186 Hot pixel threshold: 81.24 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.750165 Iteration 2 Error: 0.454722 Iteration 3 Error: 0.105440 Iteration 4 Error: 0.042048 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.02 -0.01 ...... Frame ( 3) shift: 0.04 -0.02 ...... Frame ( 4) shift: 0.06 -0.03 ...... Frame ( 5) shift: 0.08 -0.04 ...... Frame ( 6) shift: 0.12 -0.03 ...... Frame ( 7) shift: 0.18 -0.01 ...... Frame ( 8) shift: 0.23 0.01 ...... Frame ( 9) shift: 0.28 0.10 ...... Frame ( 10) shift: 0.32 0.28 ...... Frame ( 11) shift: 0.37 0.46 ...... Frame ( 12) shift: 0.42 0.60 ...... Frame ( 13) shift: 0.49 0.72 ...... Frame ( 14) shift: 0.56 0.84 ...... Frame ( 15) shift: 0.66 0.96 ...... Frame ( 16) shift: 0.80 1.09 ...... Frame ( 17) shift: 0.94 1.22 ...... Frame ( 18) shift: 1.04 1.33 ...... Frame ( 19) shift: 1.10 1.41 ...... Frame ( 20) shift: 1.16 1.48 ...... Frame ( 21) shift: 1.23 1.60 ...... Frame ( 22) shift: 1.31 1.76 ...... Frame ( 23) shift: 1.39 1.92 ...... Frame ( 24) shift: 1.45 2.01 ...... Frame ( 25) shift: 1.50 2.04 ...... Frame ( 26) shift: 1.54 2.08 ...... Frame ( 27) shift: 1.60 2.14 ...... Frame ( 28) shift: 1.67 2.23 ...... Frame ( 29) shift: 1.74 2.32 ...... Frame ( 30) shift: 1.82 2.41 ...... Frame ( 31) shift: 1.92 2.51 ...... Frame ( 32) shift: 2.02 2.61 ...... Frame ( 33) shift: 2.07 2.65 ...... Frame ( 34) shift: 2.08 2.65 ...... Frame ( 35) shift: 2.08 2.64 ...... Frame ( 36) shift: 2.11 2.69 ...... Frame ( 37) shift: 2.17 2.80 ...... Frame ( 38) shift: 2.24 2.92 ...... Frame ( 39) shift: 2.30 3.03 ...... Frame ( 40) shift: 2.36 3.14 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.951851 Iteration 2 Error: 0.132000 Iteration 3 Error: 0.025107 Align patch 2 23 left Iteration 1 Error: 1.212694 Iteration 2 Error: 0.248861 Iteration 3 Error: 0.072081 Iteration 4 Error: 0.031336 Align patch 3 22 left Iteration 1 Error: 0.768383 Iteration 2 Error: 0.192510 Iteration 3 Error: 0.073075 Iteration 4 Error: 0.035610 Align patch 4 21 left Iteration 1 Error: 0.737041 Iteration 2 Error: 0.098255 Iteration 3 Error: 0.034451 Align patch 5 20 left Iteration 1 Error: 0.777732 Iteration 2 Error: 0.261179 Iteration 3 Error: 0.062299 Iteration 4 Error: 0.037396 Align patch 6 19 left Iteration 1 Error: 0.861571 Iteration 2 Error: 0.260191 Iteration 3 Error: 0.069484 Iteration 4 Error: 0.034447 Align patch 7 18 left Iteration 1 Error: 0.626806 Iteration 2 Error: 0.089982 Iteration 3 Error: 0.020778 Align patch 8 17 left Iteration 1 Error: 0.696462 Iteration 2 Error: 0.179496 Iteration 3 Error: 0.102270 Iteration 4 Error: 0.044710 Align patch 9 16 left Iteration 1 Error: 0.782218 Iteration 2 Error: 0.200948 Iteration 3 Error: 0.065907 Iteration 4 Error: 0.039999 Align patch 10 15 left Iteration 1 Error: 1.036788 Iteration 2 Error: 0.233391 Iteration 3 Error: 0.083785 Iteration 4 Error: 0.032292 Align patch 11 14 left Iteration 1 Error: 0.712547 Iteration 2 Error: 0.152490 Iteration 3 Error: 0.057272 Iteration 4 Error: 0.013024 Align patch 12 13 left Iteration 1 Error: 0.980659 Iteration 2 Error: 0.392191 Iteration 3 Error: 0.088836 Iteration 4 Error: 0.051241 Iteration 5 Error: 0.022704 Align patch 13 12 left Iteration 1 Error: 0.795879 Iteration 2 Error: 0.180442 Iteration 3 Error: 0.053029 Iteration 4 Error: 0.016910 Align patch 14 11 left Iteration 1 Error: 0.709401 Iteration 2 Error: 0.164914 Iteration 3 Error: 0.037426 Align patch 15 10 left Iteration 1 Error: 0.829843 Iteration 2 Error: 0.154454 Iteration 3 Error: 0.051264 Iteration 4 Error: 0.011350 Align patch 16 9 left Iteration 1 Error: 0.701202 Iteration 2 Error: 0.163426 Iteration 3 Error: 0.043057 Align patch 17 8 left Iteration 1 Error: 0.620214 Iteration 2 Error: 0.133554 Iteration 3 Error: 0.039086 Align patch 18 7 left Iteration 1 Error: 0.679901 Iteration 2 Error: 0.190441 Iteration 3 Error: 0.057558 Iteration 4 Error: 0.027036 Align patch 19 6 left Iteration 1 Error: 0.686624 Iteration 2 Error: 0.132211 Iteration 3 Error: 0.044905 Align patch 20 5 left Iteration 1 Error: 1.004198 Iteration 2 Error: 0.174519 Iteration 3 Error: 0.041131 Align patch 21 4 left Iteration 1 Error: 0.725265 Iteration 2 Error: 0.179910 Iteration 3 Error: 0.036798 Align patch 22 3 left Iteration 1 Error: 0.768107 Iteration 2 Error: 0.093398 Iteration 3 Error: 0.025417 Align patch 23 2 left Iteration 1 Error: 0.938414 Iteration 2 Error: 0.201735 Iteration 3 Error: 0.041633 Align patch 24 1 left Iteration 1 Error: 0.944894 Iteration 2 Error: 0.186314 Iteration 3 Error: 0.068471 Iteration 4 Error: 0.018392 Align patch 25 0 left Iteration 1 Error: 1.101185 Iteration 2 Error: 0.291209 Iteration 3 Error: 0.062837 Iteration 4 Error: 0.022134 3D Fitting completed. Patch alignment time: 12.06(sec) Local motion has been corrected. Process thread exits. Computational time: 25.041534 sec Total time: 32.782467 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00040hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00040hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.593455s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00040hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.931382s ........................................ >>>>>>TIME<<<<<< FFT: 0.917822s Defocus_U Defocus_V Angle CCC 15970.70 16759.77 7.58 0.041145 Final Values Defocus_U Defocus_V Angle CCC 15970.74 16731.70 7.58 0.065451 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00040hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00040hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.994e-02 CC threshold: 0.734 Mean Std: 40.26 6.73 Num Hot pixels: 221 Hot pixel threshold: 80.62 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.011391 Iteration 2 Error: 0.518935 Iteration 3 Error: 0.219487 Iteration 4 Error: 0.094871 Iteration 5 Error: 0.044980 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.07 -0.12 ...... Frame ( 3) shift: 0.13 -0.25 ...... Frame ( 4) shift: 0.20 -0.37 ...... Frame ( 5) shift: 0.27 -0.50 ...... Frame ( 6) shift: 0.37 -0.52 ...... Frame ( 7) shift: 0.51 -0.44 ...... Frame ( 8) shift: 0.64 -0.36 ...... Frame ( 9) shift: 0.76 -0.28 ...... Frame ( 10) shift: 0.85 -0.19 ...... Frame ( 11) shift: 0.94 -0.11 ...... Frame ( 12) shift: 1.08 0.05 ...... Frame ( 13) shift: 1.28 0.28 ...... Frame ( 14) shift: 1.48 0.51 ...... Frame ( 15) shift: 1.60 0.72 ...... Frame ( 16) shift: 1.63 0.91 ...... Frame ( 17) shift: 1.67 1.11 ...... Frame ( 18) shift: 1.81 1.32 ...... Frame ( 19) shift: 2.04 1.55 ...... Frame ( 20) shift: 2.27 1.78 ...... Frame ( 21) shift: 2.44 1.93 ...... Frame ( 22) shift: 2.53 2.00 ...... Frame ( 23) shift: 2.62 2.07 ...... Frame ( 24) shift: 2.74 2.09 ...... Frame ( 25) shift: 2.88 2.06 ...... Frame ( 26) shift: 3.03 2.02 ...... Frame ( 27) shift: 3.15 2.01 ...... Frame ( 28) shift: 3.24 2.03 ...... Frame ( 29) shift: 3.34 2.05 ...... Frame ( 30) shift: 3.45 2.08 ...... Frame ( 31) shift: 3.58 2.12 ...... Frame ( 32) shift: 3.71 2.16 ...... Frame ( 33) shift: 3.81 2.21 ...... Frame ( 34) shift: 3.87 2.26 ...... Frame ( 35) shift: 3.93 2.31 ...... Frame ( 36) shift: 3.99 2.37 ...... Frame ( 37) shift: 4.07 2.44 ...... Frame ( 38) shift: 4.14 2.51 ...... Frame ( 39) shift: 4.22 2.57 ...... Frame ( 40) shift: 4.29 2.64 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.170951 Iteration 2 Error: 0.427493 Iteration 3 Error: 0.143499 Iteration 4 Error: 0.103550 Iteration 5 Error: 0.050815 Align patch 1 24 left Iteration 1 Error: 1.050374 Iteration 2 Error: 0.199603 Iteration 3 Error: 0.051437 Iteration 4 Error: 0.023338 Align patch 2 23 left Iteration 1 Error: 1.773645 Iteration 2 Error: 0.485102 Iteration 3 Error: 0.182467 Iteration 4 Error: 0.072439 Iteration 5 Error: 0.032528 Align patch 3 22 left Iteration 1 Error: 0.846338 Iteration 2 Error: 0.303059 Iteration 3 Error: 0.080234 Iteration 4 Error: 0.048167 Align patch 4 21 left Iteration 1 Error: 0.651349 Iteration 2 Error: 0.200003 Iteration 3 Error: 0.068644 Iteration 4 Error: 0.031439 Align patch 5 20 left Iteration 1 Error: 0.608909 Iteration 2 Error: 0.209585 Iteration 3 Error: 0.050648 Iteration 4 Error: 0.018831 Align patch 6 19 left Iteration 1 Error: 1.047489 Iteration 2 Error: 0.204049 Iteration 3 Error: 0.067599 Iteration 4 Error: 0.038021 Align patch 7 18 left Iteration 1 Error: 0.869927 Iteration 2 Error: 0.370031 Iteration 3 Error: 0.133942 Iteration 4 Error: 0.076581 Iteration 5 Error: 0.031049 Align patch 8 17 left Iteration 1 Error: 0.906415 Iteration 2 Error: 0.154780 Iteration 3 Error: 0.088574 Iteration 4 Error: 0.063433 Iteration 5 Error: 0.026787 Align patch 9 16 left Iteration 1 Error: 0.543051 Iteration 2 Error: 0.104398 Iteration 3 Error: 0.030234 Align patch 10 15 left Iteration 1 Error: 0.974025 Iteration 2 Error: 0.300316 Iteration 3 Error: 0.091051 Iteration 4 Error: 0.046745 Align patch 11 14 left Iteration 1 Error: 0.882508 Iteration 2 Error: 0.231784 Iteration 3 Error: 0.049742 Align patch 12 13 left Iteration 1 Error: 1.432663 Iteration 2 Error: 0.350755 Iteration 3 Error: 0.113650 Iteration 4 Error: 0.056549 Iteration 5 Error: 0.030986 Align patch 13 12 left Iteration 1 Error: 0.912276 Iteration 2 Error: 0.151817 Iteration 3 Error: 0.078120 Iteration 4 Error: 0.027355 Align patch 14 11 left Iteration 1 Error: 0.994838 Iteration 2 Error: 0.265677 Iteration 3 Error: 0.089078 Iteration 4 Error: 0.036921 Align patch 15 10 left Iteration 1 Error: 0.630304 Iteration 2 Error: 0.145082 Iteration 3 Error: 0.029956 Align patch 16 9 left Iteration 1 Error: 0.866996 Iteration 2 Error: 0.207911 Iteration 3 Error: 0.086325 Iteration 4 Error: 0.029592 Align patch 17 8 left Iteration 1 Error: 1.032585 Iteration 2 Error: 0.220940 Iteration 3 Error: 0.064015 Iteration 4 Error: 0.026688 Align patch 18 7 left Iteration 1 Error: 1.158936 Iteration 2 Error: 0.232905 Iteration 3 Error: 0.094114 Iteration 4 Error: 0.046594 Align patch 19 6 left Iteration 1 Error: 0.642697 Iteration 2 Error: 0.135119 Iteration 3 Error: 0.060743 Iteration 4 Error: 0.027595 Align patch 20 5 left Iteration 1 Error: 0.860649 Iteration 2 Error: 0.197867 Iteration 3 Error: 0.050865 Iteration 4 Error: 0.020239 Align patch 21 4 left Iteration 1 Error: 0.816562 Iteration 2 Error: 0.209023 Iteration 3 Error: 0.074097 Iteration 4 Error: 0.020189 Align patch 22 3 left Iteration 1 Error: 1.241479 Iteration 2 Error: 0.479116 Iteration 3 Error: 0.100025 Iteration 4 Error: 0.046231 Align patch 23 2 left Iteration 1 Error: 0.682509 Iteration 2 Error: 0.143196 Iteration 3 Error: 0.041564 Align patch 24 1 left Iteration 1 Error: 1.309691 Iteration 2 Error: 0.362329 Iteration 3 Error: 0.113403 Iteration 4 Error: 0.041278 Align patch 25 0 left Iteration 1 Error: 1.255618 Iteration 2 Error: 0.461359 Iteration 3 Error: 0.163357 Iteration 4 Error: 0.104458 Iteration 5 Error: 0.058287 Align patch 25 0 left Iteration 1 Error: 0.515086 Iteration 2 Error: 0.061910 Iteration 3 Error: 0.014949 3D Fitting completed. Patch alignment time: 14.98(sec) Local motion has been corrected. Process thread exits. Computational time: 29.327282 sec Total time: 37.550552 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00040hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00040hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.622424s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00040hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.941319s ........................................ >>>>>>TIME<<<<<< FFT: 0.946244s Defocus_U Defocus_V Angle CCC 14166.03 14962.90 10.63 0.051224 Final Values Defocus_U Defocus_V Angle CCC 14183.22 14955.09 10.32 0.078890 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00040hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00040hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.990e-02 CC threshold: 0.734 Mean Std: 39.59 6.68 Num Hot pixels: 186 Hot pixel threshold: 79.64 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.212605 Iteration 2 Error: 0.557780 Iteration 3 Error: 0.209417 Iteration 4 Error: 0.100115 Iteration 5 Error: 0.049290 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.04 -0.08 ...... Frame ( 3) shift: 0.08 -0.16 ...... Frame ( 4) shift: 0.12 -0.24 ...... Frame ( 5) shift: 0.16 -0.32 ...... Frame ( 6) shift: 0.17 -0.32 ...... Frame ( 7) shift: 0.17 -0.24 ...... Frame ( 8) shift: 0.16 -0.16 ...... Frame ( 9) shift: 0.23 -0.07 ...... Frame ( 10) shift: 0.38 0.03 ...... Frame ( 11) shift: 0.54 0.13 ...... Frame ( 12) shift: 0.70 0.30 ...... Frame ( 13) shift: 0.88 0.55 ...... Frame ( 14) shift: 1.05 0.80 ...... Frame ( 15) shift: 1.20 1.00 ...... Frame ( 16) shift: 1.32 1.15 ...... Frame ( 17) shift: 1.45 1.30 ...... Frame ( 18) shift: 1.56 1.47 ...... Frame ( 19) shift: 1.66 1.67 ...... Frame ( 20) shift: 1.76 1.87 ...... Frame ( 21) shift: 1.81 2.05 ...... Frame ( 22) shift: 1.82 2.21 ...... Frame ( 23) shift: 1.82 2.38 ...... Frame ( 24) shift: 1.90 2.51 ...... Frame ( 25) shift: 2.06 2.61 ...... Frame ( 26) shift: 2.22 2.70 ...... Frame ( 27) shift: 2.30 2.86 ...... Frame ( 28) shift: 2.30 3.07 ...... Frame ( 29) shift: 2.30 3.28 ...... Frame ( 30) shift: 2.37 3.41 ...... Frame ( 31) shift: 2.50 3.47 ...... Frame ( 32) shift: 2.63 3.53 ...... Frame ( 33) shift: 2.68 3.57 ...... Frame ( 34) shift: 2.64 3.61 ...... Frame ( 35) shift: 2.60 3.65 ...... Frame ( 36) shift: 2.65 3.74 ...... Frame ( 37) shift: 2.78 3.86 ...... Frame ( 38) shift: 2.91 3.99 ...... Frame ( 39) shift: 3.04 4.12 ...... Frame ( 40) shift: 3.17 4.24 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.731292 Iteration 2 Error: 0.220291 Iteration 3 Error: 0.090065 Iteration 4 Error: 0.047505 Align patch 2 23 left Iteration 1 Error: 0.802357 Iteration 2 Error: 0.253534 Iteration 3 Error: 0.072770 Iteration 4 Error: 0.023931 Align patch 3 22 left Iteration 1 Error: 0.767163 Iteration 2 Error: 0.153032 Iteration 3 Error: 0.050485 Iteration 4 Error: 0.022321 Align patch 4 21 left Iteration 1 Error: 1.110702 Iteration 2 Error: 0.260818 Iteration 3 Error: 0.061782 Iteration 4 Error: 0.035881 Align patch 5 20 left Iteration 1 Error: 0.829265 Iteration 2 Error: 0.217368 Iteration 3 Error: 0.087320 Iteration 4 Error: 0.034016 Align patch 6 19 left Iteration 1 Error: 1.030660 Iteration 2 Error: 0.186803 Iteration 3 Error: 0.059909 Iteration 4 Error: 0.024025 Align patch 7 18 left Iteration 1 Error: 0.655557 Iteration 2 Error: 0.134312 Iteration 3 Error: 0.028734 Align patch 8 17 left Iteration 1 Error: 0.712615 Iteration 2 Error: 0.205456 Iteration 3 Error: 0.104163 Iteration 4 Error: 0.032737 Align patch 9 16 left Iteration 1 Error: 1.336333 Iteration 2 Error: 0.222634 Iteration 3 Error: 0.080053 Iteration 4 Error: 0.041309 Align patch 10 15 left Iteration 1 Error: 1.129465 Iteration 2 Error: 0.177520 Iteration 3 Error: 0.062001 Iteration 4 Error: 0.025894 Align patch 11 14 left Iteration 1 Error: 1.169552 Iteration 2 Error: 0.189351 Iteration 3 Error: 0.075419 Iteration 4 Error: 0.048122 Align patch 12 13 left Iteration 1 Error: 1.380701 Iteration 2 Error: 0.337575 Iteration 3 Error: 0.097913 Iteration 4 Error: 0.050438 Iteration 5 Error: 0.018339 Align patch 13 12 left Iteration 1 Error: 0.640792 Iteration 2 Error: 0.117677 Iteration 3 Error: 0.046085 Align patch 14 11 left Iteration 1 Error: 0.897031 Iteration 2 Error: 0.227268 Iteration 3 Error: 0.082173 Iteration 4 Error: 0.032149 Align patch 15 10 left Iteration 1 Error: 0.720830 Iteration 2 Error: 0.415758 Iteration 3 Error: 0.219469 Iteration 4 Error: 0.130466 Iteration 5 Error: 0.070503 Align patch 15 10 left Iteration 1 Error: 0.902378 Iteration 2 Error: 0.129908 Iteration 3 Error: 0.034108 Align patch 16 9 left Iteration 1 Error: 1.176899 Iteration 2 Error: 0.326800 Iteration 3 Error: 0.078410 Iteration 4 Error: 0.027563 Align patch 17 8 left Iteration 1 Error: 0.810654 Iteration 2 Error: 0.186492 Iteration 3 Error: 0.048303 Align patch 18 7 left Iteration 1 Error: 0.854012 Iteration 2 Error: 0.268230 Iteration 3 Error: 0.144745 Iteration 4 Error: 0.053701 Iteration 5 Error: 0.026332 Align patch 19 6 left Iteration 1 Error: 0.813788 Iteration 2 Error: 0.142436 Iteration 3 Error: 0.053212 Iteration 4 Error: 0.032346 Align patch 20 5 left Iteration 1 Error: 0.863817 Iteration 2 Error: 0.172970 Iteration 3 Error: 0.064802 Iteration 4 Error: 0.030846 Align patch 21 4 left Iteration 1 Error: 1.082038 Iteration 2 Error: 0.233226 Iteration 3 Error: 0.062274 Iteration 4 Error: 0.023724 Align patch 22 3 left Iteration 1 Error: 0.822062 Iteration 2 Error: 0.262532 Iteration 3 Error: 0.074129 Iteration 4 Error: 0.017578 Align patch 23 2 left Iteration 1 Error: 0.947740 Iteration 2 Error: 0.214794 Iteration 3 Error: 0.073739 Iteration 4 Error: 0.018198 Align patch 24 1 left Iteration 1 Error: 1.041089 Iteration 2 Error: 0.267354 Iteration 3 Error: 0.117374 Iteration 4 Error: 0.045164 Align patch 25 0 left Iteration 1 Error: 1.176733 Iteration 2 Error: 0.340675 Iteration 3 Error: 0.108922 Iteration 4 Error: 0.049921 3D Fitting completed. Patch alignment time: 13.30(sec) Local motion has been corrected. Process thread exits. Computational time: 25.808779 sec Total time: 32.718102 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00040hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00040hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.508097s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00040hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.095508s ........................................ >>>>>>TIME<<<<<< FFT: 0.962987s Defocus_U Defocus_V Angle CCC 15271.49 15818.37 2.64 0.046692 Final Values Defocus_U Defocus_V Angle CCC 15271.49 15808.99 0.46 0.072217 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00040hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00040hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.995e-02 CC threshold: 0.734 Mean Std: 38.58 6.58 Num Hot pixels: 197 Hot pixel threshold: 78.08 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.839210 Iteration 2 Error: 0.323538 Iteration 3 Error: 0.106198 Iteration 4 Error: 0.043095 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.10 0.05 ...... Frame ( 3) shift: 0.21 0.10 ...... Frame ( 4) shift: 0.31 0.15 ...... Frame ( 5) shift: 0.42 0.20 ...... Frame ( 6) shift: 0.49 0.29 ...... Frame ( 7) shift: 0.55 0.41 ...... Frame ( 8) shift: 0.60 0.53 ...... Frame ( 9) shift: 0.66 0.66 ...... Frame ( 10) shift: 0.73 0.80 ...... Frame ( 11) shift: 0.81 0.94 ...... Frame ( 12) shift: 0.88 1.10 ...... Frame ( 13) shift: 0.94 1.27 ...... Frame ( 14) shift: 1.01 1.44 ...... Frame ( 15) shift: 1.04 1.57 ...... Frame ( 16) shift: 1.04 1.66 ...... Frame ( 17) shift: 1.04 1.74 ...... Frame ( 18) shift: 1.10 1.86 ...... Frame ( 19) shift: 1.21 2.01 ...... Frame ( 20) shift: 1.32 2.16 ...... Frame ( 21) shift: 1.41 2.25 ...... Frame ( 22) shift: 1.46 2.27 ...... Frame ( 23) shift: 1.52 2.29 ...... Frame ( 24) shift: 1.58 2.35 ...... Frame ( 25) shift: 1.65 2.46 ...... Frame ( 26) shift: 1.73 2.56 ...... Frame ( 27) shift: 1.78 2.62 ...... Frame ( 28) shift: 1.80 2.65 ...... Frame ( 29) shift: 1.83 2.68 ...... Frame ( 30) shift: 1.87 2.69 ...... Frame ( 31) shift: 1.92 2.68 ...... Frame ( 32) shift: 1.98 2.67 ...... Frame ( 33) shift: 2.02 2.69 ...... Frame ( 34) shift: 2.06 2.74 ...... Frame ( 35) shift: 2.10 2.78 ...... Frame ( 36) shift: 2.14 2.79 ...... Frame ( 37) shift: 2.18 2.76 ...... Frame ( 38) shift: 2.21 2.73 ...... Frame ( 39) shift: 2.25 2.70 ...... Frame ( 40) shift: 2.28 2.67 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.840055 Iteration 2 Error: 0.157638 Iteration 3 Error: 0.063997 Iteration 4 Error: 0.025025 Align patch 2 23 left Iteration 1 Error: 1.249551 Iteration 2 Error: 0.289894 Iteration 3 Error: 0.098936 Iteration 4 Error: 0.022708 Align patch 3 22 left Iteration 1 Error: 0.937921 Iteration 2 Error: 0.138575 Iteration 3 Error: 0.024488 Align patch 4 21 left Iteration 1 Error: 0.729854 Iteration 2 Error: 0.106051 Iteration 3 Error: 0.030637 Align patch 5 20 left Iteration 1 Error: 1.054436 Iteration 2 Error: 0.147030 Iteration 3 Error: 0.051599 Iteration 4 Error: 0.015570 Align patch 6 19 left Iteration 1 Error: 0.894904 Iteration 2 Error: 0.146551 Iteration 3 Error: 0.020791 Align patch 7 18 left Iteration 1 Error: 0.454362 Iteration 2 Error: 0.207386 Iteration 3 Error: 0.057788 Iteration 4 Error: 0.023197 Align patch 8 17 left Iteration 1 Error: 0.718455 Iteration 2 Error: 0.217835 Iteration 3 Error: 0.098539 Iteration 4 Error: 0.043561 Align patch 9 16 left Iteration 1 Error: 0.677103 Iteration 2 Error: 0.226671 Iteration 3 Error: 0.074005 Iteration 4 Error: 0.026466 Align patch 10 15 left Iteration 1 Error: 1.081935 Iteration 2 Error: 0.186942 Iteration 3 Error: 0.041814 Align patch 11 14 left Iteration 1 Error: 0.802950 Iteration 2 Error: 0.116573 Iteration 3 Error: 0.049494 Align patch 12 13 left Iteration 1 Error: 0.846370 Iteration 2 Error: 0.199561 Iteration 3 Error: 0.034369 Align patch 13 12 left Iteration 1 Error: 1.021859 Iteration 2 Error: 0.172401 Iteration 3 Error: 0.031587 Align patch 14 11 left Iteration 1 Error: 0.769483 Iteration 2 Error: 0.196633 Iteration 3 Error: 0.054721 Iteration 4 Error: 0.028446 Align patch 15 10 left Iteration 1 Error: 0.792132 Iteration 2 Error: 0.174638 Iteration 3 Error: 0.043826 Align patch 16 9 left Iteration 1 Error: 1.532374 Iteration 2 Error: 0.428199 Iteration 3 Error: 0.130569 Iteration 4 Error: 0.053656 Iteration 5 Error: 0.031391 Align patch 17 8 left Iteration 1 Error: 0.792599 Iteration 2 Error: 0.193787 Iteration 3 Error: 0.060445 Iteration 4 Error: 0.026306 Align patch 18 7 left Iteration 1 Error: 0.719532 Iteration 2 Error: 0.137145 Iteration 3 Error: 0.036685 Align patch 19 6 left Iteration 1 Error: 0.944889 Iteration 2 Error: 0.122887 Iteration 3 Error: 0.038026 Align patch 20 5 left Iteration 1 Error: 0.818432 Iteration 2 Error: 0.101491 Iteration 3 Error: 0.026193 Align patch 21 4 left Iteration 1 Error: 0.797195 Iteration 2 Error: 0.123533 Iteration 3 Error: 0.036159 Align patch 22 3 left Iteration 1 Error: 0.735230 Iteration 2 Error: 0.160095 Iteration 3 Error: 0.045897 Align patch 23 2 left Iteration 1 Error: 1.200656 Iteration 2 Error: 0.138301 Iteration 3 Error: 0.026170 Align patch 24 1 left Iteration 1 Error: 0.562142 Iteration 2 Error: 0.196093 Iteration 3 Error: 0.066435 Iteration 4 Error: 0.023434 Align patch 25 0 left Iteration 1 Error: 1.253690 Iteration 2 Error: 0.509021 Iteration 3 Error: 0.075528 Iteration 4 Error: 0.058281 Iteration 5 Error: 0.024261 3D Fitting completed. Patch alignment time: 12.10(sec) Local motion has been corrected. Process thread exits. Computational time: 25.241224 sec Total time: 32.122265 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00040hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00040hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.440128s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00040hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.762855s ........................................ >>>>>>TIME<<<<<< FFT: 0.971464s Defocus_U Defocus_V Angle CCC 13662.11 14404.30 1.91 0.038518 Final Values Defocus_U Defocus_V Angle CCC 14330.89 13698.01 89.73 0.056353 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00041hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00041hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.994e-02 CC threshold: 0.734 Mean Std: 37.94 6.54 Num Hot pixels: 232 Hot pixel threshold: 77.16 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.031276 Iteration 2 Error: 0.514916 Iteration 3 Error: 0.172667 Iteration 4 Error: 0.072510 Iteration 5 Error: 0.030696 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.05 -0.07 ...... Frame ( 3) shift: 0.11 -0.15 ...... Frame ( 4) shift: 0.16 -0.22 ...... Frame ( 5) shift: 0.22 -0.30 ...... Frame ( 6) shift: 0.31 -0.26 ...... Frame ( 7) shift: 0.44 -0.11 ...... Frame ( 8) shift: 0.57 0.05 ...... Frame ( 9) shift: 0.71 0.19 ...... Frame ( 10) shift: 0.86 0.34 ...... Frame ( 11) shift: 1.02 0.48 ...... Frame ( 12) shift: 1.16 0.62 ...... Frame ( 13) shift: 1.28 0.78 ...... Frame ( 14) shift: 1.40 0.94 ...... Frame ( 15) shift: 1.49 1.10 ...... Frame ( 16) shift: 1.55 1.26 ...... Frame ( 17) shift: 1.61 1.42 ...... Frame ( 18) shift: 1.73 1.53 ...... Frame ( 19) shift: 1.90 1.60 ...... Frame ( 20) shift: 2.07 1.66 ...... Frame ( 21) shift: 2.21 1.77 ...... Frame ( 22) shift: 2.33 1.91 ...... Frame ( 23) shift: 2.45 2.05 ...... Frame ( 24) shift: 2.56 2.16 ...... Frame ( 25) shift: 2.65 2.24 ...... Frame ( 26) shift: 2.75 2.32 ...... Frame ( 27) shift: 2.84 2.38 ...... Frame ( 28) shift: 2.93 2.43 ...... Frame ( 29) shift: 3.02 2.48 ...... Frame ( 30) shift: 3.12 2.55 ...... Frame ( 31) shift: 3.22 2.64 ...... Frame ( 32) shift: 3.33 2.73 ...... Frame ( 33) shift: 3.40 2.79 ...... Frame ( 34) shift: 3.43 2.82 ...... Frame ( 35) shift: 3.47 2.84 ...... Frame ( 36) shift: 3.52 2.85 ...... Frame ( 37) shift: 3.59 2.84 ...... Frame ( 38) shift: 3.65 2.83 ...... Frame ( 39) shift: 3.72 2.82 ...... Frame ( 40) shift: 3.79 2.81 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.189861 Iteration 2 Error: 0.353165 Iteration 3 Error: 0.106336 Iteration 4 Error: 0.046441 Align patch 2 23 left Iteration 1 Error: 0.862998 Iteration 2 Error: 0.255986 Iteration 3 Error: 0.096477 Iteration 4 Error: 0.043384 Align patch 3 22 left Iteration 1 Error: 1.020791 Iteration 2 Error: 0.194972 Iteration 3 Error: 0.073202 Iteration 4 Error: 0.035436 Align patch 4 21 left Iteration 1 Error: 0.635632 Iteration 2 Error: 0.181760 Iteration 3 Error: 0.088343 Iteration 4 Error: 0.038957 Align patch 5 20 left Iteration 1 Error: 0.982719 Iteration 2 Error: 0.157364 Iteration 3 Error: 0.047281 Align patch 6 19 left Iteration 1 Error: 1.018822 Iteration 2 Error: 0.187190 Iteration 3 Error: 0.063114 Iteration 4 Error: 0.024010 Align patch 7 18 left Iteration 1 Error: 0.965612 Iteration 2 Error: 0.296835 Iteration 3 Error: 0.104391 Iteration 4 Error: 0.043329 Align patch 8 17 left Iteration 1 Error: 0.806042 Iteration 2 Error: 0.219704 Iteration 3 Error: 0.073546 Iteration 4 Error: 0.049588 Align patch 9 16 left Iteration 1 Error: 0.785176 Iteration 2 Error: 0.167901 Iteration 3 Error: 0.048168 Align patch 10 15 left Iteration 1 Error: 1.041750 Iteration 2 Error: 0.341723 Iteration 3 Error: 0.181637 Iteration 4 Error: 0.059005 Iteration 5 Error: 0.036247 Align patch 11 14 left Iteration 1 Error: 0.943368 Iteration 2 Error: 0.512201 Iteration 3 Error: 0.319243 Iteration 4 Error: 0.170684 Iteration 5 Error: 0.099011 Align patch 11 14 left Iteration 1 Error: 0.804197 Iteration 2 Error: 0.161527 Iteration 3 Error: 0.033450 Align patch 12 13 left Iteration 1 Error: 1.092963 Iteration 2 Error: 0.296077 Iteration 3 Error: 0.107499 Iteration 4 Error: 0.048405 Align patch 13 12 left Iteration 1 Error: 0.845572 Iteration 2 Error: 0.168060 Iteration 3 Error: 0.049628 Align patch 14 11 left Iteration 1 Error: 0.769125 Iteration 2 Error: 0.250933 Iteration 3 Error: 0.082025 Iteration 4 Error: 0.044419 Align patch 15 10 left Iteration 1 Error: 0.887145 Iteration 2 Error: 0.152524 Iteration 3 Error: 0.042559 Align patch 16 9 left Iteration 1 Error: 0.633356 Iteration 2 Error: 0.113750 Iteration 3 Error: 0.036110 Align patch 17 8 left Iteration 1 Error: 0.756711 Iteration 2 Error: 0.183957 Iteration 3 Error: 0.067490 Iteration 4 Error: 0.016909 Align patch 18 7 left Iteration 1 Error: 1.754516 Iteration 2 Error: 0.379501 Iteration 3 Error: 0.061084 Iteration 4 Error: 0.035456 Align patch 19 6 left Iteration 1 Error: 0.853877 Iteration 2 Error: 0.110653 Iteration 3 Error: 0.034968 Align patch 20 5 left Iteration 1 Error: 0.811246 Iteration 2 Error: 0.228934 Iteration 3 Error: 0.061579 Iteration 4 Error: 0.017795 Align patch 21 4 left Iteration 1 Error: 0.957528 Iteration 2 Error: 0.203921 Iteration 3 Error: 0.048160 Align patch 22 3 left Iteration 1 Error: 0.800120 Iteration 2 Error: 0.145310 Iteration 3 Error: 0.037886 Align patch 23 2 left Iteration 1 Error: 0.600966 Iteration 2 Error: 0.195426 Iteration 3 Error: 0.069931 Iteration 4 Error: 0.041063 Align patch 24 1 left Iteration 1 Error: 0.932635 Iteration 2 Error: 0.264940 Iteration 3 Error: 0.060599 Iteration 4 Error: 0.031151 Align patch 25 0 left Iteration 1 Error: 0.779942 Iteration 2 Error: 0.119881 Iteration 3 Error: 0.062802 Iteration 4 Error: 0.019375 3D Fitting completed. Patch alignment time: 21.87(sec) Local motion has been corrected. Process thread exits. Computational time: 37.963612 sec Total time: 46.638004 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00041hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00041hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.596229s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00041hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.004349s ........................................ >>>>>>TIME<<<<<< FFT: 1.328304s Defocus_U Defocus_V Angle CCC 15117.16 15769.56 10.67 0.035795 Final Values Defocus_U Defocus_V Angle CCC 15112.48 15764.87 10.67 0.050563 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00041hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00041hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.993e-02 CC threshold: 0.734 Mean Std: 37.09 6.45 Num Hot pixels: 212 Hot pixel threshold: 75.82 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.493510 Iteration 2 Error: 0.364304 Iteration 3 Error: 0.091654 Iteration 4 Error: 0.032217 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.01 -0.12 ...... Frame ( 3) shift: -0.02 -0.24 ...... Frame ( 4) shift: -0.04 -0.37 ...... Frame ( 5) shift: -0.05 -0.49 ...... Frame ( 6) shift: -0.06 -0.53 ...... Frame ( 7) shift: -0.08 -0.48 ...... Frame ( 8) shift: -0.09 -0.44 ...... Frame ( 9) shift: -0.03 -0.38 ...... Frame ( 10) shift: 0.12 -0.29 ...... Frame ( 11) shift: 0.27 -0.20 ...... Frame ( 12) shift: 0.36 -0.10 ...... Frame ( 13) shift: 0.40 -0.00 ...... Frame ( 14) shift: 0.44 0.10 ...... Frame ( 15) shift: 0.49 0.19 ...... Frame ( 16) shift: 0.56 0.28 ...... Frame ( 17) shift: 0.63 0.37 ...... Frame ( 18) shift: 0.66 0.46 ...... Frame ( 19) shift: 0.66 0.53 ...... Frame ( 20) shift: 0.65 0.60 ...... Frame ( 21) shift: 0.65 0.69 ...... Frame ( 22) shift: 0.65 0.80 ...... Frame ( 23) shift: 0.66 0.90 ...... Frame ( 24) shift: 0.69 0.97 ...... Frame ( 25) shift: 0.74 1.02 ...... Frame ( 26) shift: 0.79 1.06 ...... Frame ( 27) shift: 0.84 1.09 ...... Frame ( 28) shift: 0.90 1.09 ...... Frame ( 29) shift: 0.95 1.10 ...... Frame ( 30) shift: 1.02 1.15 ...... Frame ( 31) shift: 1.12 1.24 ...... Frame ( 32) shift: 1.21 1.33 ...... Frame ( 33) shift: 1.32 1.42 ...... Frame ( 34) shift: 1.45 1.51 ...... Frame ( 35) shift: 1.57 1.60 ...... Frame ( 36) shift: 1.66 1.66 ...... Frame ( 37) shift: 1.72 1.70 ...... Frame ( 38) shift: 1.77 1.73 ...... Frame ( 39) shift: 1.82 1.77 ...... Frame ( 40) shift: 1.88 1.80 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.154298 Iteration 2 Error: 0.114741 Iteration 3 Error: 0.031718 Align patch 2 23 left Iteration 1 Error: 0.999769 Iteration 2 Error: 0.160462 Iteration 3 Error: 0.034430 Align patch 3 22 left Iteration 1 Error: 1.288728 Iteration 2 Error: 0.189457 Iteration 3 Error: 0.029059 Align patch 4 21 left Iteration 1 Error: 0.938863 Iteration 2 Error: 0.189841 Iteration 3 Error: 0.066931 Iteration 4 Error: 0.022251 Align patch 5 20 left Iteration 1 Error: 1.149174 Iteration 2 Error: 0.268998 Iteration 3 Error: 0.091233 Iteration 4 Error: 0.034402 Align patch 6 19 left Iteration 1 Error: 1.020076 Iteration 2 Error: 0.185956 Iteration 3 Error: 0.033676 Align patch 7 18 left Iteration 1 Error: 0.599410 Iteration 2 Error: 0.094963 Iteration 3 Error: 0.031223 Align patch 8 17 left Iteration 1 Error: 0.734504 Iteration 2 Error: 0.120257 Iteration 3 Error: 0.024421 Align patch 9 16 left Iteration 1 Error: 0.788954 Iteration 2 Error: 0.121249 Iteration 3 Error: 0.049195 Align patch 10 15 left Iteration 1 Error: 0.761511 Iteration 2 Error: 0.188114 Iteration 3 Error: 0.030078 Align patch 11 14 left Iteration 1 Error: 0.783645 Iteration 2 Error: 0.186928 Iteration 3 Error: 0.033491 Align patch 12 13 left Iteration 1 Error: 1.287714 Iteration 2 Error: 0.205536 Iteration 3 Error: 0.068233 Iteration 4 Error: 0.028365 Align patch 13 12 left Iteration 1 Error: 0.652599 Iteration 2 Error: 0.152235 Iteration 3 Error: 0.067900 Iteration 4 Error: 0.035597 Align patch 14 11 left Iteration 1 Error: 0.667628 Iteration 2 Error: 0.149544 Iteration 3 Error: 0.062363 Iteration 4 Error: 0.030430 Align patch 15 10 left Iteration 1 Error: 0.628124 Iteration 2 Error: 0.095645 Iteration 3 Error: 0.025248 Align patch 16 9 left Iteration 1 Error: 0.788767 Iteration 2 Error: 0.171735 Iteration 3 Error: 0.040923 Align patch 17 8 left Iteration 1 Error: 0.964844 Iteration 2 Error: 0.385497 Iteration 3 Error: 0.187446 Iteration 4 Error: 0.092033 Iteration 5 Error: 0.050161 Align patch 17 8 left Iteration 1 Error: 0.932508 Iteration 2 Error: 0.145338 Iteration 3 Error: 0.041286 Align patch 18 7 left Iteration 1 Error: 0.695986 Iteration 2 Error: 0.165730 Iteration 3 Error: 0.055623 Iteration 4 Error: 0.041274 Align patch 19 6 left Iteration 1 Error: 0.658780 Iteration 2 Error: 0.128476 Iteration 3 Error: 0.035396 Align patch 20 5 left Iteration 1 Error: 0.823042 Iteration 2 Error: 0.121114 Iteration 3 Error: 0.032084 Align patch 21 4 left Iteration 1 Error: 0.923843 Iteration 2 Error: 0.129192 Iteration 3 Error: 0.025528 Align patch 22 3 left Iteration 1 Error: 0.955412 Iteration 2 Error: 0.360670 Iteration 3 Error: 0.105000 Iteration 4 Error: 0.051862 Iteration 5 Error: 0.020635 Align patch 23 2 left Iteration 1 Error: 0.898059 Iteration 2 Error: 0.454476 Iteration 3 Error: 0.302041 Iteration 4 Error: 0.304143 Iteration 5 Error: 0.177925 Align patch 23 2 left Iteration 1 Error: 0.872453 Iteration 2 Error: 0.148938 Iteration 3 Error: 0.039336 Align patch 24 1 left Iteration 1 Error: 0.704499 Iteration 2 Error: 0.109792 Iteration 3 Error: 0.034316 Align patch 25 0 left Iteration 1 Error: 0.990400 Iteration 2 Error: 0.167790 Iteration 3 Error: 0.112864 Iteration 4 Error: 0.045323 3D Fitting completed. Patch alignment time: 19.98(sec) Local motion has been corrected. Process thread exits. Computational time: 34.572121 sec Total time: 42.436829 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00041hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00041hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.115850s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00041hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.438957s ........................................ >>>>>>TIME<<<<<< FFT: 1.604353s Defocus_U Defocus_V Angle CCC 13689.48 14607.52 12.05 0.033975 Final Values Defocus_U Defocus_V Angle CCC 13602.00 14629.42 11.74 0.047916 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00041hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00041hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.994e-02 CC threshold: 0.734 Mean Std: 38.29 6.58 Num Hot pixels: 214 Hot pixel threshold: 77.76 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.115660 Iteration 2 Error: 0.244527 Iteration 3 Error: 0.082128 Iteration 4 Error: 0.024560 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.01 -0.02 ...... Frame ( 3) shift: -0.01 -0.05 ...... Frame ( 4) shift: -0.02 -0.07 ...... Frame ( 5) shift: -0.03 -0.09 ...... Frame ( 6) shift: 0.01 -0.06 ...... Frame ( 7) shift: 0.09 0.03 ...... Frame ( 8) shift: 0.17 0.11 ...... Frame ( 9) shift: 0.18 0.17 ...... Frame ( 10) shift: 0.14 0.19 ...... Frame ( 11) shift: 0.11 0.21 ...... Frame ( 12) shift: 0.11 0.30 ...... Frame ( 13) shift: 0.16 0.44 ...... Frame ( 14) shift: 0.21 0.59 ...... Frame ( 15) shift: 0.27 0.69 ...... Frame ( 16) shift: 0.34 0.74 ...... Frame ( 17) shift: 0.41 0.80 ...... Frame ( 18) shift: 0.48 0.89 ...... Frame ( 19) shift: 0.55 1.02 ...... Frame ( 20) shift: 0.62 1.14 ...... Frame ( 21) shift: 0.71 1.21 ...... Frame ( 22) shift: 0.83 1.22 ...... Frame ( 23) shift: 0.94 1.24 ...... Frame ( 24) shift: 0.99 1.26 ...... Frame ( 25) shift: 0.97 1.29 ...... Frame ( 26) shift: 0.96 1.32 ...... Frame ( 27) shift: 0.98 1.38 ...... Frame ( 28) shift: 1.04 1.45 ...... Frame ( 29) shift: 1.10 1.53 ...... Frame ( 30) shift: 1.15 1.57 ...... Frame ( 31) shift: 1.17 1.57 ...... Frame ( 32) shift: 1.20 1.56 ...... Frame ( 33) shift: 1.26 1.60 ...... Frame ( 34) shift: 1.35 1.69 ...... Frame ( 35) shift: 1.44 1.77 ...... Frame ( 36) shift: 1.51 1.83 ...... Frame ( 37) shift: 1.54 1.87 ...... Frame ( 38) shift: 1.57 1.92 ...... Frame ( 39) shift: 1.61 1.96 ...... Frame ( 40) shift: 1.64 2.01 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.219840 Iteration 2 Error: 0.127096 Iteration 3 Error: 0.043145 Align patch 2 23 left Iteration 1 Error: 0.929453 Iteration 2 Error: 0.174885 Iteration 3 Error: 0.049162 Align patch 3 22 left Iteration 1 Error: 0.909309 Iteration 2 Error: 0.201971 Iteration 3 Error: 0.066010 Iteration 4 Error: 0.019132 Align patch 4 21 left Iteration 1 Error: 0.941093 Iteration 2 Error: 0.207601 Iteration 3 Error: 0.077543 Iteration 4 Error: 0.035319 Align patch 5 20 left Iteration 1 Error: 0.868978 Iteration 2 Error: 0.158376 Iteration 3 Error: 0.052532 Iteration 4 Error: 0.020564 Align patch 6 19 left Iteration 1 Error: 1.193344 Iteration 2 Error: 0.246059 Iteration 3 Error: 0.117067 Iteration 4 Error: 0.038288 Align patch 7 18 left Iteration 1 Error: 0.777442 Iteration 2 Error: 0.297048 Iteration 3 Error: 0.141258 Iteration 4 Error: 0.047315 Align patch 8 17 left Iteration 1 Error: 1.091066 Iteration 2 Error: 0.143465 Iteration 3 Error: 0.044919 Align patch 9 16 left Iteration 1 Error: 0.903130 Iteration 2 Error: 0.147712 Iteration 3 Error: 0.032261 Align patch 10 15 left Iteration 1 Error: 0.832074 Iteration 2 Error: 0.092391 Iteration 3 Error: 0.044670 Align patch 11 14 left Iteration 1 Error: 0.807961 Iteration 2 Error: 0.214515 Iteration 3 Error: 0.069550 Iteration 4 Error: 0.024836 Align patch 12 13 left Iteration 1 Error: 0.736696 Iteration 2 Error: 0.189703 Iteration 3 Error: 0.046175 Align patch 13 12 left Iteration 1 Error: 0.905963 Iteration 2 Error: 0.158498 Iteration 3 Error: 0.045719 Align patch 14 11 left Iteration 1 Error: 0.853711 Iteration 2 Error: 0.178039 Iteration 3 Error: 0.034565 Align patch 15 10 left Iteration 1 Error: 1.253481 Iteration 2 Error: 0.196658 Iteration 3 Error: 0.057509 Iteration 4 Error: 0.010975 Align patch 16 9 left Iteration 1 Error: 0.715742 Iteration 2 Error: 0.102082 Iteration 3 Error: 0.037154 Align patch 17 8 left Iteration 1 Error: 0.614456 Iteration 2 Error: 0.094339 Iteration 3 Error: 0.034180 Align patch 18 7 left Iteration 1 Error: 0.974818 Iteration 2 Error: 0.143968 Iteration 3 Error: 0.036916 Align patch 19 6 left Iteration 1 Error: 0.965993 Iteration 2 Error: 0.188448 Iteration 3 Error: 0.046860 Align patch 20 5 left Iteration 1 Error: 1.232754 Iteration 2 Error: 0.321095 Iteration 3 Error: 0.095113 Iteration 4 Error: 0.037683 Align patch 21 4 left Iteration 1 Error: 1.184269 Iteration 2 Error: 0.231441 Iteration 3 Error: 0.051117 Iteration 4 Error: 0.018379 Align patch 22 3 left Iteration 1 Error: 0.974321 Iteration 2 Error: 0.268725 Iteration 3 Error: 0.076995 Iteration 4 Error: 0.027695 Align patch 23 2 left Iteration 1 Error: 1.331217 Iteration 2 Error: 0.117769 Iteration 3 Error: 0.024457 Align patch 24 1 left Iteration 1 Error: 0.846842 Iteration 2 Error: 0.254902 Iteration 3 Error: 0.137207 Iteration 4 Error: 0.070644 Iteration 5 Error: 0.037366 Align patch 25 0 left Iteration 1 Error: 1.318108 Iteration 2 Error: 0.325584 Iteration 3 Error: 0.089280 Iteration 4 Error: 0.033324 3D Fitting completed. Patch alignment time: 19.81(sec) Local motion has been corrected. Process thread exits. Computational time: 36.189182 sec Total time: 45.823326 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00041hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00041hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.616172s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00041hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.519324s ........................................ >>>>>>TIME<<<<<< FFT: 1.494570s Defocus_U Defocus_V Angle CCC 15345.67 15791.05 2.40 0.037876 Final Values Defocus_U Defocus_V Angle CCC 15347.23 15789.49 1.78 0.054134 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00041hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00041hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.992e-02 CC threshold: 0.734 Mean Std: 37.44 6.49 Num Hot pixels: 225 Hot pixel threshold: 76.36 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.098553 Iteration 2 Error: 0.265053 Iteration 3 Error: 0.071602 Iteration 4 Error: 0.027087 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.11 0.04 ...... Frame ( 3) shift: -0.22 0.08 ...... Frame ( 4) shift: -0.34 0.12 ...... Frame ( 5) shift: -0.45 0.17 ...... Frame ( 6) shift: -0.45 0.22 ...... Frame ( 7) shift: -0.36 0.28 ...... Frame ( 8) shift: -0.26 0.35 ...... Frame ( 9) shift: -0.22 0.41 ...... Frame ( 10) shift: -0.24 0.47 ...... Frame ( 11) shift: -0.27 0.53 ...... Frame ( 12) shift: -0.20 0.60 ...... Frame ( 13) shift: -0.03 0.70 ...... Frame ( 14) shift: 0.14 0.79 ...... Frame ( 15) shift: 0.29 0.90 ...... Frame ( 16) shift: 0.42 1.02 ...... Frame ( 17) shift: 0.56 1.14 ...... Frame ( 18) shift: 0.63 1.28 ...... Frame ( 19) shift: 0.64 1.44 ...... Frame ( 20) shift: 0.65 1.59 ...... Frame ( 21) shift: 0.63 1.68 ...... Frame ( 22) shift: 0.57 1.70 ...... Frame ( 23) shift: 0.51 1.73 ...... Frame ( 24) shift: 0.51 1.75 ...... Frame ( 25) shift: 0.58 1.77 ...... Frame ( 26) shift: 0.64 1.78 ...... Frame ( 27) shift: 0.68 1.84 ...... Frame ( 28) shift: 0.70 1.93 ...... Frame ( 29) shift: 0.72 2.01 ...... Frame ( 30) shift: 0.76 2.07 ...... Frame ( 31) shift: 0.82 2.10 ...... Frame ( 32) shift: 0.88 2.13 ...... Frame ( 33) shift: 0.89 2.17 ...... Frame ( 34) shift: 0.85 2.24 ...... Frame ( 35) shift: 0.82 2.31 ...... Frame ( 36) shift: 0.84 2.31 ...... Frame ( 37) shift: 0.93 2.27 ...... Frame ( 38) shift: 1.02 2.22 ...... Frame ( 39) shift: 1.11 2.17 ...... Frame ( 40) shift: 1.20 2.12 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.779303 Iteration 2 Error: 0.248452 Iteration 3 Error: 0.092106 Iteration 4 Error: 0.037285 Align patch 2 23 left Iteration 1 Error: 0.856596 Iteration 2 Error: 0.205858 Iteration 3 Error: 0.097711 Iteration 4 Error: 0.034708 Align patch 3 22 left Iteration 1 Error: 0.788318 Iteration 2 Error: 0.201367 Iteration 3 Error: 0.043130 Align patch 4 21 left Iteration 1 Error: 0.599250 Iteration 2 Error: 0.154374 Iteration 3 Error: 0.035233 Align patch 5 20 left Iteration 1 Error: 0.824851 Iteration 2 Error: 0.167909 Iteration 3 Error: 0.053848 Iteration 4 Error: 0.015515 Align patch 6 19 left Iteration 1 Error: 0.817362 Iteration 2 Error: 0.229523 Iteration 3 Error: 0.077241 Iteration 4 Error: 0.020686 Align patch 7 18 left Iteration 1 Error: 0.958430 Iteration 2 Error: 0.308921 Iteration 3 Error: 0.094475 Iteration 4 Error: 0.033969 Align patch 8 17 left Iteration 1 Error: 0.564415 Iteration 2 Error: 0.095394 Iteration 3 Error: 0.030277 Align patch 9 16 left Iteration 1 Error: 0.887162 Iteration 2 Error: 0.137359 Iteration 3 Error: 0.033840 Align patch 10 15 left Iteration 1 Error: 0.725154 Iteration 2 Error: 0.157039 Iteration 3 Error: 0.043182 Align patch 11 14 left Iteration 1 Error: 1.296880 Iteration 2 Error: 0.372646 Iteration 3 Error: 0.071578 Iteration 4 Error: 0.034267 Align patch 12 13 left Iteration 1 Error: 0.872621 Iteration 2 Error: 0.294077 Iteration 3 Error: 0.154927 Iteration 4 Error: 0.045428 Align patch 13 12 left Iteration 1 Error: 0.800439 Iteration 2 Error: 0.215783 Iteration 3 Error: 0.072665 Iteration 4 Error: 0.027014 Align patch 14 11 left Iteration 1 Error: 0.773374 Iteration 2 Error: 0.142512 Iteration 3 Error: 0.036850 Align patch 15 10 left Iteration 1 Error: 0.812507 Iteration 2 Error: 0.106543 Iteration 3 Error: 0.029093 Align patch 16 9 left Iteration 1 Error: 1.160528 Iteration 2 Error: 0.303068 Iteration 3 Error: 0.089551 Iteration 4 Error: 0.022162 Align patch 17 8 left Iteration 1 Error: 0.797669 Iteration 2 Error: 0.137168 Iteration 3 Error: 0.045486 Align patch 18 7 left Iteration 1 Error: 0.813770 Iteration 2 Error: 0.190437 Iteration 3 Error: 0.060704 Iteration 4 Error: 0.027963 Align patch 19 6 left Iteration 1 Error: 0.796903 Iteration 2 Error: 0.128575 Iteration 3 Error: 0.029189 Align patch 20 5 left Iteration 1 Error: 0.771467 Iteration 2 Error: 0.204961 Iteration 3 Error: 0.051040 Iteration 4 Error: 0.023862 Align patch 21 4 left Iteration 1 Error: 0.834545 Iteration 2 Error: 0.160044 Iteration 3 Error: 0.048819 Align patch 22 3 left Iteration 1 Error: 1.019242 Iteration 2 Error: 0.159678 Iteration 3 Error: 0.043718 Align patch 23 2 left Iteration 1 Error: 0.958152 Iteration 2 Error: 0.300468 Iteration 3 Error: 0.055001 Iteration 4 Error: 0.015706 Align patch 24 1 left Iteration 1 Error: 1.079824 Iteration 2 Error: 0.152072 Iteration 3 Error: 0.033845 Align patch 25 0 left Iteration 1 Error: 0.604382 Iteration 2 Error: 0.169645 Iteration 3 Error: 0.032826 3D Fitting completed. Patch alignment time: 18.84(sec) Local motion has been corrected. Process thread exits. Computational time: 30.968426 sec Total time: 38.838058 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00041hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00041hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.507627s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00041hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.372243s ........................................ >>>>>>TIME<<<<<< FFT: 1.376767s Defocus_U Defocus_V Angle CCC 18105.47 17222.66 87.68 0.025874 Final Values Defocus_U Defocus_V Angle CCC 18124.22 17188.29 87.68 0.039111 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00042hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00042hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.366e-01 1.015e-01 CC threshold: 0.745 Mean Std: 14.76 12.21 Num Hot pixels: 32 Hot pixel threshold: 88.04 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.443277 Iteration 2 Error: 0.195958 Iteration 3 Error: 0.042645 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.12 -0.20 ...... Frame ( 3) shift: -0.25 -0.41 ...... Frame ( 4) shift: -0.37 -0.61 ...... Frame ( 5) shift: -0.49 -0.82 ...... Frame ( 6) shift: -0.53 -0.92 ...... Frame ( 7) shift: -0.48 -0.92 ...... Frame ( 8) shift: -0.43 -0.91 ...... Frame ( 9) shift: -0.40 -0.87 ...... Frame ( 10) shift: -0.39 -0.78 ...... Frame ( 11) shift: -0.39 -0.69 ...... Frame ( 12) shift: -0.34 -0.58 ...... Frame ( 13) shift: -0.25 -0.45 ...... Frame ( 14) shift: -0.16 -0.32 ...... Frame ( 15) shift: -0.10 -0.21 ...... Frame ( 16) shift: -0.08 -0.12 ...... Frame ( 17) shift: -0.06 -0.03 ...... Frame ( 18) shift: -0.00 0.06 ...... Frame ( 19) shift: 0.08 0.15 ...... Frame ( 20) shift: 0.16 0.24 ...... Frame ( 21) shift: 0.22 0.32 ...... Frame ( 22) shift: 0.25 0.38 ...... Frame ( 23) shift: 0.28 0.45 ...... Frame ( 24) shift: 0.29 0.50 ...... Frame ( 25) shift: 0.27 0.56 ...... Frame ( 26) shift: 0.25 0.61 ...... Frame ( 27) shift: 0.25 0.67 ...... Frame ( 28) shift: 0.26 0.75 ...... Frame ( 29) shift: 0.27 0.82 ...... Frame ( 30) shift: 0.29 0.89 ...... Frame ( 31) shift: 0.32 0.95 ...... Frame ( 32) shift: 0.35 1.01 ...... Frame ( 33) shift: 0.37 1.07 ...... Frame ( 34) shift: 0.38 1.11 ...... Frame ( 35) shift: 0.38 1.15 ...... Frame ( 36) shift: 0.40 1.23 ...... Frame ( 37) shift: 0.42 1.33 ...... Frame ( 38) shift: 0.45 1.43 ...... Frame ( 39) shift: 0.47 1.53 ...... Frame ( 40) shift: 0.50 1.62 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.841901 Iteration 2 Error: 0.221317 Iteration 3 Error: 0.050366 Iteration 4 Error: 0.019860 Align patch 2 23 left Iteration 1 Error: 0.586784 Iteration 2 Error: 0.088259 Iteration 3 Error: 0.027272 Align patch 3 22 left Iteration 1 Error: 0.484889 Iteration 2 Error: 0.244045 Iteration 3 Error: 0.127393 Iteration 4 Error: 0.064329 Iteration 5 Error: 0.033750 Align patch 4 21 left Iteration 1 Error: 0.478045 Iteration 2 Error: 0.163301 Iteration 3 Error: 0.054258 Iteration 4 Error: 0.018610 Align patch 5 20 left Iteration 1 Error: 1.127485 Iteration 2 Error: 0.081612 Iteration 3 Error: 0.009296 Align patch 6 19 left Iteration 1 Error: 0.722908 Iteration 2 Error: 0.148733 Iteration 3 Error: 0.029240 Align patch 7 18 left Iteration 1 Error: 0.503586 Iteration 2 Error: 0.189625 Iteration 3 Error: 0.057358 Iteration 4 Error: 0.021840 Align patch 8 17 left Iteration 1 Error: 0.704334 Iteration 2 Error: 0.237052 Iteration 3 Error: 0.075500 Iteration 4 Error: 0.030216 Align patch 9 16 left Iteration 1 Error: 0.846154 Iteration 2 Error: 0.070795 Iteration 3 Error: 0.005502 Align patch 10 15 left Iteration 1 Error: 1.265004 Iteration 2 Error: 0.056903 Iteration 3 Error: 0.004851 Align patch 11 14 left Iteration 1 Error: 0.599912 Iteration 2 Error: 0.097727 Iteration 3 Error: 0.015698 Align patch 12 13 left Iteration 1 Error: 0.393361 Iteration 2 Error: 0.063611 Iteration 3 Error: 0.013370 Align patch 13 12 left Iteration 1 Error: 0.509895 Iteration 2 Error: 0.045611 Align patch 14 11 left Iteration 1 Error: 0.725943 Iteration 2 Error: 0.094342 Iteration 3 Error: 0.012565 Align patch 15 10 left Iteration 1 Error: 1.245157 Iteration 2 Error: 0.072866 Iteration 3 Error: 0.005445 Align patch 16 9 left Iteration 1 Error: 1.058841 Iteration 2 Error: 0.056322 Iteration 3 Error: 0.004326 Align patch 17 8 left Iteration 1 Error: 0.995787 Iteration 2 Error: 0.090440 Iteration 3 Error: 0.010813 Align patch 18 7 left Iteration 1 Error: 0.783406 Iteration 2 Error: 0.081322 Iteration 3 Error: 0.012514 Align patch 19 6 left Iteration 1 Error: 1.394539 Iteration 2 Error: 0.077849 Iteration 3 Error: 0.010659 Align patch 20 5 left Iteration 1 Error: 1.727409 Iteration 2 Error: 0.067201 Iteration 3 Error: 0.005986 Align patch 21 4 left Iteration 1 Error: 0.310898 Iteration 2 Error: 0.017995 Align patch 22 3 left Iteration 1 Error: 1.002065 Iteration 2 Error: 0.050362 Iteration 3 Error: 0.005860 Align patch 23 2 left Iteration 1 Error: 1.014378 Iteration 2 Error: 0.065404 Iteration 3 Error: 0.004930 Align patch 24 1 left Iteration 1 Error: 0.672524 Iteration 2 Error: 0.070521 Iteration 3 Error: 0.006201 Align patch 25 0 left Iteration 1 Error: 1.073354 Iteration 2 Error: 0.249844 Iteration 3 Error: 0.061653 Iteration 4 Error: 0.015250 3D Fitting completed. Patch alignment time: 18.87(sec) Local motion has been corrected. Process thread exits. Computational time: 34.105553 sec Total time: 42.413795 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00042hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00042hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 3.047123s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00042hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.166662s ........................................ >>>>>>TIME<<<<<< FFT: 1.204332s Defocus_U Defocus_V Angle CCC 12335.96 13117.21 15.60 0.003177 Final Values Defocus_U Defocus_V Angle CCC 12282.88 13095.39 13.73 0.020461 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00042hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00042hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.365e-01 1.014e-01 CC threshold: 0.745 Mean Std: 13.77 12.32 Num Hot pixels: 26 Hot pixel threshold: 87.67 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.070403 Iteration 2 Error: 0.213942 Iteration 3 Error: 0.041653 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.12 -0.24 ...... Frame ( 3) shift: -0.23 -0.48 ...... Frame ( 4) shift: -0.35 -0.71 ...... Frame ( 5) shift: -0.47 -0.95 ...... Frame ( 6) shift: -0.50 -1.05 ...... Frame ( 7) shift: -0.45 -1.01 ...... Frame ( 8) shift: -0.41 -0.98 ...... Frame ( 9) shift: -0.37 -0.91 ...... Frame ( 10) shift: -0.34 -0.80 ...... Frame ( 11) shift: -0.31 -0.70 ...... Frame ( 12) shift: -0.31 -0.60 ...... Frame ( 13) shift: -0.33 -0.51 ...... Frame ( 14) shift: -0.35 -0.42 ...... Frame ( 15) shift: -0.36 -0.33 ...... Frame ( 16) shift: -0.35 -0.24 ...... Frame ( 17) shift: -0.35 -0.14 ...... Frame ( 18) shift: -0.34 -0.07 ...... Frame ( 19) shift: -0.32 -0.03 ...... Frame ( 20) shift: -0.30 0.02 ...... Frame ( 21) shift: -0.28 0.06 ...... Frame ( 22) shift: -0.26 0.08 ...... Frame ( 23) shift: -0.24 0.11 ...... Frame ( 24) shift: -0.23 0.13 ...... Frame ( 25) shift: -0.23 0.15 ...... Frame ( 26) shift: -0.23 0.17 ...... Frame ( 27) shift: -0.24 0.20 ...... Frame ( 28) shift: -0.26 0.24 ...... Frame ( 29) shift: -0.29 0.29 ...... Frame ( 30) shift: -0.28 0.31 ...... Frame ( 31) shift: -0.26 0.31 ...... Frame ( 32) shift: -0.24 0.31 ...... Frame ( 33) shift: -0.19 0.34 ...... Frame ( 34) shift: -0.12 0.39 ...... Frame ( 35) shift: -0.06 0.43 ...... Frame ( 36) shift: -0.02 0.47 ...... Frame ( 37) shift: -0.02 0.50 ...... Frame ( 38) shift: -0.01 0.53 ...... Frame ( 39) shift: -0.01 0.56 ...... Frame ( 40) shift: -0.00 0.59 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.618787 Iteration 2 Error: 0.194512 Iteration 3 Error: 0.042395 Align patch 2 23 left Iteration 1 Error: 1.090139 Iteration 2 Error: 0.132826 Iteration 3 Error: 0.042401 Align patch 3 22 left Iteration 1 Error: 0.839648 Iteration 2 Error: 0.278527 Iteration 3 Error: 0.087884 Iteration 4 Error: 0.029020 Align patch 4 21 left Iteration 1 Error: 0.370550 Iteration 2 Error: 0.086136 Iteration 3 Error: 0.019763 Align patch 5 20 left Iteration 1 Error: 1.174648 Iteration 2 Error: 0.046335 Align patch 6 19 left Iteration 1 Error: 0.583627 Iteration 2 Error: 0.111180 Iteration 3 Error: 0.016801 Align patch 7 18 left Iteration 1 Error: 0.796285 Iteration 2 Error: 0.154820 Iteration 3 Error: 0.040032 Align patch 8 17 left Iteration 1 Error: 0.987567 Iteration 2 Error: 0.429507 Iteration 3 Error: 0.127149 Iteration 4 Error: 0.052541 Iteration 5 Error: 0.021728 Align patch 9 16 left Iteration 1 Error: 0.794156 Iteration 2 Error: 0.145172 Iteration 3 Error: 0.027533 Align patch 10 15 left Iteration 1 Error: 1.695329 Iteration 2 Error: 0.074798 Iteration 3 Error: 0.008616 Align patch 11 14 left Iteration 1 Error: 0.506914 Iteration 2 Error: 0.155885 Iteration 3 Error: 0.033792 Align patch 12 13 left Iteration 1 Error: 0.352185 Iteration 2 Error: 0.077904 Iteration 3 Error: 0.018003 Align patch 13 12 left Iteration 1 Error: 1.446214 Iteration 2 Error: 0.366012 Iteration 3 Error: 0.110756 Iteration 4 Error: 0.045306 Align patch 14 11 left Iteration 1 Error: 0.898301 Iteration 2 Error: 0.158713 Iteration 3 Error: 0.022666 Align patch 15 10 left Iteration 1 Error: 0.705089 Iteration 2 Error: 0.061164 Iteration 3 Error: 0.006310 Align patch 16 9 left Iteration 1 Error: 0.901675 Iteration 2 Error: 0.104749 Iteration 3 Error: 0.009384 Align patch 17 8 left Iteration 1 Error: 0.701657 Iteration 2 Error: 0.052539 Iteration 3 Error: 0.005134 Align patch 18 7 left Iteration 1 Error: 1.585029 Iteration 2 Error: 0.120445 Iteration 3 Error: 0.014195 Align patch 19 6 left Iteration 1 Error: 0.785007 Iteration 2 Error: 0.066730 Iteration 3 Error: 0.015646 Align patch 20 5 left Iteration 1 Error: 2.049557 Iteration 2 Error: 0.070690 Iteration 3 Error: 0.006513 Align patch 21 4 left Iteration 1 Error: 0.307924 Iteration 2 Error: 0.021545 Align patch 22 3 left Iteration 1 Error: 1.982758 Iteration 2 Error: 0.213568 Iteration 3 Error: 0.045692 Align patch 23 2 left Iteration 1 Error: 1.873573 Iteration 2 Error: 0.225898 Iteration 3 Error: 0.027962 Align patch 24 1 left Iteration 1 Error: 1.558957 Iteration 2 Error: 0.099796 Iteration 3 Error: 0.009879 Align patch 25 0 left Iteration 1 Error: 0.950375 Iteration 2 Error: 0.060741 Iteration 3 Error: 0.003711 3D Fitting completed. Patch alignment time: 16.92(sec) Local motion has been corrected. Process thread exits. Computational time: 32.993507 sec Total time: 41.606232 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00042hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00042hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.287520s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00042hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.886824s ........................................ >>>>>>TIME<<<<<< FFT: 1.540107s Defocus_U Defocus_V Angle CCC 16466.73 17220.77 7.59 0.003265 Final Values Defocus_U Defocus_V Angle CCC 16415.13 17188.02 3.89 0.018390 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00042hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00042hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.360e-01 1.011e-01 CC threshold: 0.743 Mean Std: 14.43 13.00 Num Hot pixels: 24 Hot pixel threshold: 92.44 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.268155 Iteration 2 Error: 0.178138 Iteration 3 Error: 0.040257 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.16 -0.22 ...... Frame ( 3) shift: -0.33 -0.43 ...... Frame ( 4) shift: -0.49 -0.65 ...... Frame ( 5) shift: -0.65 -0.87 ...... Frame ( 6) shift: -0.74 -0.97 ...... Frame ( 7) shift: -0.75 -0.96 ...... Frame ( 8) shift: -0.76 -0.94 ...... Frame ( 9) shift: -0.76 -0.89 ...... Frame ( 10) shift: -0.73 -0.80 ...... Frame ( 11) shift: -0.69 -0.71 ...... Frame ( 12) shift: -0.62 -0.61 ...... Frame ( 13) shift: -0.49 -0.50 ...... Frame ( 14) shift: -0.37 -0.39 ...... Frame ( 15) shift: -0.30 -0.30 ...... Frame ( 16) shift: -0.29 -0.24 ...... Frame ( 17) shift: -0.28 -0.17 ...... Frame ( 18) shift: -0.28 -0.11 ...... Frame ( 19) shift: -0.30 -0.05 ...... Frame ( 20) shift: -0.33 0.01 ...... Frame ( 21) shift: -0.32 0.08 ...... Frame ( 22) shift: -0.29 0.15 ...... Frame ( 23) shift: -0.26 0.23 ...... Frame ( 24) shift: -0.25 0.29 ...... Frame ( 25) shift: -0.26 0.34 ...... Frame ( 26) shift: -0.27 0.39 ...... Frame ( 27) shift: -0.27 0.44 ...... Frame ( 28) shift: -0.25 0.51 ...... Frame ( 29) shift: -0.24 0.57 ...... Frame ( 30) shift: -0.21 0.64 ...... Frame ( 31) shift: -0.17 0.71 ...... Frame ( 32) shift: -0.12 0.79 ...... Frame ( 33) shift: -0.07 0.88 ...... Frame ( 34) shift: -0.02 0.99 ...... Frame ( 35) shift: 0.03 1.10 ...... Frame ( 36) shift: 0.07 1.17 ...... Frame ( 37) shift: 0.08 1.19 ...... Frame ( 38) shift: 0.10 1.21 ...... Frame ( 39) shift: 0.11 1.23 ...... Frame ( 40) shift: 0.13 1.25 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.773120 Iteration 2 Error: 0.103579 Iteration 3 Error: 0.024874 Align patch 2 23 left Iteration 1 Error: 0.818669 Iteration 2 Error: 0.071652 Iteration 3 Error: 0.017612 Align patch 3 22 left Iteration 1 Error: 0.425565 Iteration 2 Error: 0.143414 Iteration 3 Error: 0.044981 Align patch 4 21 left Iteration 1 Error: 0.610537 Iteration 2 Error: 0.246580 Iteration 3 Error: 0.077847 Iteration 4 Error: 0.033320 Align patch 5 20 left Iteration 1 Error: 45.789539 Iteration 2 Error: 47.768890 Iteration 3 Error: 38.068153 Iteration 4 Error: 21.029472 Iteration 5 Error: 19.774656 Align patch 5 20 left Iteration 1 Error: 0.612802 Iteration 2 Error: 0.144013 Iteration 3 Error: 0.059193 Iteration 4 Error: 0.015355 Align patch 6 19 left Iteration 1 Error: 0.830679 Iteration 2 Error: 0.169831 Iteration 3 Error: 0.042040 Align patch 7 18 left Iteration 1 Error: 0.538191 Iteration 2 Error: 0.161020 Iteration 3 Error: 0.046257 Align patch 8 17 left Iteration 1 Error: 0.492093 Iteration 2 Error: 0.160464 Iteration 3 Error: 0.051347 Iteration 4 Error: 0.019344 Align patch 9 16 left Iteration 1 Error: 0.576290 Iteration 2 Error: 0.111043 Iteration 3 Error: 0.021308 Align patch 10 15 left Iteration 1 Error: 40.341427 Iteration 2 Error: 35.953934 Iteration 3 Error: 41.335850 Iteration 4 Error: 0.609155 Iteration 5 Error: 0.268920 Align patch 10 15 left Iteration 1 Error: 2.489460 Iteration 2 Error: 0.315068 Iteration 3 Error: 0.036235 Align patch 11 14 left Iteration 1 Error: 0.533570 Iteration 2 Error: 0.122958 Iteration 3 Error: 0.027403 Align patch 12 13 left Iteration 1 Error: 0.561847 Iteration 2 Error: 0.128298 Iteration 3 Error: 0.038312 Align patch 13 12 left Iteration 1 Error: 50.823299 Iteration 2 Error: 50.823299 Iteration 3 Error: 43.594296 Iteration 4 Error: 46.671051 Iteration 5 Error: 32.293552 Align patch 13 12 left Iteration 1 Error: 0.909118 Iteration 2 Error: 0.260128 Iteration 3 Error: 0.063662 Iteration 4 Error: 0.020514 Align patch 14 11 left Iteration 1 Error: 1.393248 Iteration 2 Error: 0.180292 Iteration 3 Error: 0.040972 Align patch 15 10 left Iteration 1 Error: 36.049469 Iteration 2 Error: 42.810020 Iteration 3 Error: 32.429142 Iteration 4 Error: 3.965426 Iteration 5 Error: 2.208004 Align patch 15 10 left Iteration 1 Error: 2.641282 Iteration 2 Error: 0.433068 Iteration 3 Error: 0.081492 Iteration 4 Error: 0.018246 Align patch 16 9 left Iteration 1 Error: 0.835090 Iteration 2 Error: 0.106275 Iteration 3 Error: 0.021513 Align patch 17 8 left Iteration 1 Error: 0.798093 Iteration 2 Error: 0.062285 Iteration 3 Error: 0.006068 Align patch 18 7 left Iteration 1 Error: 1.832918 Iteration 2 Error: 0.121201 Iteration 3 Error: 0.007622 Align patch 19 6 left Iteration 1 Error: 1.759252 Iteration 2 Error: 0.086825 Iteration 3 Error: 0.007721 Align patch 20 5 left Iteration 1 Error: 1.355528 Iteration 2 Error: 0.221945 Iteration 3 Error: 0.034935 Align patch 21 4 left Iteration 1 Error: 1.121532 Iteration 2 Error: 0.140486 Iteration 3 Error: 0.020307 Align patch 22 3 left Iteration 1 Error: 0.763527 Iteration 2 Error: 0.093972 Iteration 3 Error: 0.021368 Align patch 23 2 left Iteration 1 Error: 1.838167 Iteration 2 Error: 0.276576 Iteration 3 Error: 0.037535 Align patch 24 1 left Iteration 1 Error: 1.476966 Iteration 2 Error: 0.108155 Iteration 3 Error: 0.015941 Align patch 25 0 left Iteration 1 Error: 1.123288 Iteration 2 Error: 0.090114 Iteration 3 Error: 0.010000 3D Fitting completed. Patch alignment time: 22.70(sec) Local motion has been corrected. Process thread exits. Computational time: 32.938042 sec Total time: 40.200203 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00042hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00042hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.543438s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00042hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.458554s ........................................ >>>>>>TIME<<<<<< FFT: 0.970021s Defocus_U Defocus_V Angle CCC 14605.47 15007.81 4.29 0.004751 Final Values Defocus_U Defocus_V Angle CCC 14600.77 15006.26 6.50 0.019851 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00002sq_v01_00042hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00002sq_v01_00042hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.362e-01 1.012e-01 CC threshold: 0.744 Mean Std: 16.00 12.80 Num Hot pixels: 22 Hot pixel threshold: 92.78 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.123622 Iteration 2 Error: 0.179446 Iteration 3 Error: 0.029315 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.12 -0.29 ...... Frame ( 3) shift: -0.24 -0.57 ...... Frame ( 4) shift: -0.36 -0.86 ...... Frame ( 5) shift: -0.48 -1.14 ...... Frame ( 6) shift: -0.55 -1.29 ...... Frame ( 7) shift: -0.57 -1.29 ...... Frame ( 8) shift: -0.59 -1.29 ...... Frame ( 9) shift: -0.59 -1.25 ...... Frame ( 10) shift: -0.56 -1.16 ...... Frame ( 11) shift: -0.53 -1.07 ...... Frame ( 12) shift: -0.49 -0.98 ...... Frame ( 13) shift: -0.43 -0.87 ...... Frame ( 14) shift: -0.37 -0.77 ...... Frame ( 15) shift: -0.35 -0.68 ...... Frame ( 16) shift: -0.36 -0.60 ...... Frame ( 17) shift: -0.37 -0.53 ...... Frame ( 18) shift: -0.35 -0.44 ...... Frame ( 19) shift: -0.30 -0.32 ...... Frame ( 20) shift: -0.24 -0.21 ...... Frame ( 21) shift: -0.23 -0.13 ...... Frame ( 22) shift: -0.24 -0.07 ...... Frame ( 23) shift: -0.25 -0.01 ...... Frame ( 24) shift: -0.23 0.03 ...... Frame ( 25) shift: -0.18 0.05 ...... Frame ( 26) shift: -0.13 0.07 ...... Frame ( 27) shift: -0.12 0.08 ...... Frame ( 28) shift: -0.14 0.09 ...... Frame ( 29) shift: -0.17 0.10 ...... Frame ( 30) shift: -0.16 0.12 ...... Frame ( 31) shift: -0.14 0.17 ...... Frame ( 32) shift: -0.11 0.22 ...... Frame ( 33) shift: -0.07 0.24 ...... Frame ( 34) shift: -0.02 0.25 ...... Frame ( 35) shift: 0.04 0.25 ...... Frame ( 36) shift: 0.10 0.29 ...... Frame ( 37) shift: 0.16 0.37 ...... Frame ( 38) shift: 0.22 0.45 ...... Frame ( 39) shift: 0.27 0.53 ...... Frame ( 40) shift: 0.33 0.62 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.993912 Iteration 2 Error: 0.136973 Iteration 3 Error: 0.043851 Align patch 2 23 left Iteration 1 Error: 0.676502 Iteration 2 Error: 0.076781 Iteration 3 Error: 0.024685 Align patch 3 22 left Iteration 1 Error: 0.368617 Iteration 2 Error: 0.045763 Align patch 4 21 left Iteration 1 Error: 0.380816 Iteration 2 Error: 0.116393 Iteration 3 Error: 0.040743 Align patch 5 20 left Iteration 1 Error: 0.624303 Iteration 2 Error: 0.204053 Iteration 3 Error: 0.071925 Iteration 4 Error: 0.024157 Align patch 6 19 left Iteration 1 Error: 0.812767 Iteration 2 Error: 0.131401 Iteration 3 Error: 0.026237 Align patch 7 18 left Iteration 1 Error: 0.403590 Iteration 2 Error: 0.154966 Iteration 3 Error: 0.055532 Iteration 4 Error: 0.023236 Align patch 8 17 left Iteration 1 Error: 0.501240 Iteration 2 Error: 0.073258 Iteration 3 Error: 0.015149 Align patch 9 16 left Iteration 1 Error: 0.689549 Iteration 2 Error: 0.046288 Align patch 10 15 left Iteration 1 Error: 1.310232 Iteration 2 Error: 0.213241 Iteration 3 Error: 0.035866 Align patch 11 14 left Iteration 1 Error: 1.050915 Iteration 2 Error: 0.290022 Iteration 3 Error: 0.062509 Iteration 4 Error: 0.019707 Align patch 12 13 left Iteration 1 Error: 0.685790 Iteration 2 Error: 0.202297 Iteration 3 Error: 0.042651 Align patch 13 12 left Iteration 1 Error: 0.748717 Iteration 2 Error: 0.082754 Iteration 3 Error: 0.008684 Align patch 14 11 left Iteration 1 Error: 2.628970 Iteration 2 Error: 0.704010 Iteration 3 Error: 0.406305 Iteration 4 Error: 0.224353 Iteration 5 Error: 0.125361 Align patch 14 11 left Iteration 1 Error: 1.731354 Iteration 2 Error: 0.259729 Iteration 3 Error: 0.042664 Align patch 15 10 left Iteration 1 Error: 3.098794 Iteration 2 Error: 0.647258 Iteration 3 Error: 0.445476 Iteration 4 Error: 0.304101 Iteration 5 Error: 0.218390 Align patch 15 10 left Iteration 1 Error: 2.177109 Iteration 2 Error: 0.383581 Iteration 3 Error: 0.082674 Iteration 4 Error: 0.019382 Align patch 16 9 left Iteration 1 Error: 2.497729 Iteration 2 Error: 0.224271 Iteration 3 Error: 0.076520 Iteration 4 Error: 0.033791 Align patch 17 8 left Iteration 1 Error: 36.170998 Iteration 2 Error: 43.928024 Iteration 3 Error: 12.362638 Iteration 4 Error: 0.202858 Iteration 5 Error: 0.041835 Align patch 18 7 left Iteration 1 Error: 50.823299 Iteration 2 Error: 50.917587 Iteration 3 Error: 50.823299 Iteration 4 Error: 43.848923 Iteration 5 Error: 40.576340 Align patch 18 7 left Iteration 1 Error: 58.056244 Iteration 2 Error: 57.988083 Iteration 3 Error: 81.317276 Iteration 4 Error: 57.464306 Iteration 5 Error: 66.372864 Align patch 19 6 left Iteration 1 Error: 0.654044 Iteration 2 Error: 0.049824 Align patch 20 5 left Iteration 1 Error: 0.731039 Iteration 2 Error: 0.072845 Iteration 3 Error: 0.007810 Align patch 21 4 left Iteration 1 Error: 1.920350 Iteration 2 Error: 0.192587 Iteration 3 Error: 0.022690 Align patch 22 3 left Iteration 1 Error: 1.126708 Iteration 2 Error: 0.204286 Iteration 3 Error: 0.023308 Align patch 23 2 left Iteration 1 Error: 1.287963 Iteration 2 Error: 0.233398 Iteration 3 Error: 0.026572 Align patch 24 1 left Iteration 1 Error: 0.701245 Iteration 2 Error: 0.070701 Iteration 3 Error: 0.007224 Align patch 25 0 left Iteration 1 Error: 0.615846 Iteration 2 Error: 0.106464 Iteration 3 Error: 0.013279 3D Fitting completed. Patch alignment time: 18.90(sec) Local motion has been corrected. Process thread exits. Computational time: 30.690859 sec Total time: 40.338974 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00002sq_v01_00042hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00002sq_v01_00042hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.619173s Reading file: gc_18feb27f_CTD_00011gr_00002sq_v01_00042hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.674249s ........................................ >>>>>>TIME<<<<<< FFT: 1.533081s Defocus_U Defocus_V Angle CCC 17837.89 16978.52 89.87 0.001490 Final Values Defocus_U Defocus_V Angle CCC 17791.00 16978.53 88.31 0.014446 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00003sq_v01_00004hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00003sq_v01_00004hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.989e-02 CC threshold: 0.734 Mean Std: 32.30 6.15 Num Hot pixels: 168 Hot pixel threshold: 69.18 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.113816 Iteration 2 Error: 0.217532 Iteration 3 Error: 0.067018 Iteration 4 Error: 0.027112 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.11 -0.18 ...... Frame ( 3) shift: 0.22 -0.36 ...... Frame ( 4) shift: 0.34 -0.54 ...... Frame ( 5) shift: 0.45 -0.72 ...... Frame ( 6) shift: 0.56 -0.76 ...... Frame ( 7) shift: 0.68 -0.66 ...... Frame ( 8) shift: 0.80 -0.57 ...... Frame ( 9) shift: 0.90 -0.50 ...... Frame ( 10) shift: 0.99 -0.47 ...... Frame ( 11) shift: 1.08 -0.44 ...... Frame ( 12) shift: 1.15 -0.44 ...... Frame ( 13) shift: 1.20 -0.46 ...... Frame ( 14) shift: 1.26 -0.48 ...... Frame ( 15) shift: 1.29 -0.46 ...... Frame ( 16) shift: 1.31 -0.39 ...... Frame ( 17) shift: 1.32 -0.32 ...... Frame ( 18) shift: 1.33 -0.29 ...... Frame ( 19) shift: 1.33 -0.30 ...... Frame ( 20) shift: 1.33 -0.32 ...... Frame ( 21) shift: 1.39 -0.26 ...... Frame ( 22) shift: 1.52 -0.13 ...... Frame ( 23) shift: 1.64 -0.01 ...... Frame ( 24) shift: 1.70 0.08 ...... Frame ( 25) shift: 1.69 0.14 ...... Frame ( 26) shift: 1.67 0.20 ...... Frame ( 27) shift: 1.67 0.24 ...... Frame ( 28) shift: 1.66 0.27 ...... Frame ( 29) shift: 1.66 0.30 ...... Frame ( 30) shift: 1.69 0.37 ...... Frame ( 31) shift: 1.77 0.49 ...... Frame ( 32) shift: 1.85 0.61 ...... Frame ( 33) shift: 1.89 0.69 ...... Frame ( 34) shift: 1.89 0.73 ...... Frame ( 35) shift: 1.90 0.77 ...... Frame ( 36) shift: 1.94 0.81 ...... Frame ( 37) shift: 2.04 0.84 ...... Frame ( 38) shift: 2.13 0.88 ...... Frame ( 39) shift: 2.22 0.92 ...... Frame ( 40) shift: 2.31 0.96 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.752873 Iteration 2 Error: 0.165998 Iteration 3 Error: 0.054116 Iteration 4 Error: 0.016906 Align patch 2 23 left Iteration 1 Error: 0.964633 Iteration 2 Error: 0.184212 Iteration 3 Error: 0.044567 Align patch 3 22 left Iteration 1 Error: 0.975498 Iteration 2 Error: 0.145015 Iteration 3 Error: 0.061375 Iteration 4 Error: 0.015371 Align patch 4 21 left Iteration 1 Error: 0.876285 Iteration 2 Error: 0.315541 Iteration 3 Error: 0.129304 Iteration 4 Error: 0.035847 Align patch 5 20 left Iteration 1 Error: 0.866371 Iteration 2 Error: 0.383826 Iteration 3 Error: 0.163038 Iteration 4 Error: 0.072758 Iteration 5 Error: 0.041243 Align patch 6 19 left Iteration 1 Error: 0.638931 Iteration 2 Error: 0.190522 Iteration 3 Error: 0.054960 Iteration 4 Error: 0.020483 Align patch 7 18 left Iteration 1 Error: 0.813443 Iteration 2 Error: 0.124468 Iteration 3 Error: 0.029601 Align patch 8 17 left Iteration 1 Error: 0.731637 Iteration 2 Error: 0.226144 Iteration 3 Error: 0.053156 Iteration 4 Error: 0.014967 Align patch 9 16 left Iteration 1 Error: 1.544086 Iteration 2 Error: 0.403598 Iteration 3 Error: 0.189127 Iteration 4 Error: 0.060746 Iteration 5 Error: 0.037301 Align patch 10 15 left Iteration 1 Error: 0.890682 Iteration 2 Error: 0.243824 Iteration 3 Error: 0.096876 Iteration 4 Error: 0.022897 Align patch 11 14 left Iteration 1 Error: 0.979931 Iteration 2 Error: 0.121546 Iteration 3 Error: 0.033138 Align patch 12 13 left Iteration 1 Error: 0.942443 Iteration 2 Error: 0.202406 Iteration 3 Error: 0.078655 Iteration 4 Error: 0.017154 Align patch 13 12 left Iteration 1 Error: 0.630469 Iteration 2 Error: 0.085968 Iteration 3 Error: 0.032560 Align patch 14 11 left Iteration 1 Error: 0.805958 Iteration 2 Error: 0.240310 Iteration 3 Error: 0.103661 Iteration 4 Error: 0.031620 Align patch 15 10 left Iteration 1 Error: 1.115410 Iteration 2 Error: 0.222238 Iteration 3 Error: 0.070798 Iteration 4 Error: 0.030410 Align patch 16 9 left Iteration 1 Error: 1.169263 Iteration 2 Error: 0.236313 Iteration 3 Error: 0.064770 Iteration 4 Error: 0.028467 Align patch 17 8 left Iteration 1 Error: 1.014829 Iteration 2 Error: 0.261681 Iteration 3 Error: 0.078879 Iteration 4 Error: 0.018259 Align patch 18 7 left Iteration 1 Error: 0.994331 Iteration 2 Error: 0.230291 Iteration 3 Error: 0.057687 Iteration 4 Error: 0.020408 Align patch 19 6 left Iteration 1 Error: 1.057966 Iteration 2 Error: 0.283469 Iteration 3 Error: 0.054339 Iteration 4 Error: 0.017256 Align patch 20 5 left Iteration 1 Error: 0.994634 Iteration 2 Error: 0.208804 Iteration 3 Error: 0.067927 Iteration 4 Error: 0.034783 Align patch 21 4 left Iteration 1 Error: 1.031232 Iteration 2 Error: 0.454240 Iteration 3 Error: 0.103240 Iteration 4 Error: 0.066348 Iteration 5 Error: 0.022136 Align patch 22 3 left Iteration 1 Error: 0.762852 Iteration 2 Error: 0.230201 Iteration 3 Error: 0.078802 Iteration 4 Error: 0.028399 Align patch 23 2 left Iteration 1 Error: 0.883279 Iteration 2 Error: 0.226781 Iteration 3 Error: 0.049500 Align patch 24 1 left Iteration 1 Error: 1.461867 Iteration 2 Error: 0.364333 Iteration 3 Error: 0.105188 Iteration 4 Error: 0.036630 Align patch 25 0 left Iteration 1 Error: 1.239754 Iteration 2 Error: 0.299178 Iteration 3 Error: 0.077274 Iteration 4 Error: 0.026897 3D Fitting completed. Patch alignment time: 16.84(sec) Local motion has been corrected. Process thread exits. Computational time: 31.280445 sec Total time: 41.520031 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00003sq_v01_00004hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00003sq_v01_00004hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.577120s Reading file: gc_18feb27f_CTD_00011gr_00003sq_v01_00004hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.455149s ........................................ >>>>>>TIME<<<<<< FFT: 1.414156s Defocus_U Defocus_V Angle CCC 13406.35 15129.08 8.01 0.022733 Final Values Defocus_U Defocus_V Angle CCC 13364.13 15143.23 5.54 0.027812 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00003sq_v01_00004hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00003sq_v01_00004hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.994e-02 CC threshold: 0.734 Mean Std: 36.04 6.39 Num Hot pixels: 188 Hot pixel threshold: 74.38 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.324578 Iteration 2 Error: 0.269953 Iteration 3 Error: 0.066056 Iteration 4 Error: 0.021091 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.10 -0.08 ...... Frame ( 3) shift: 0.21 -0.16 ...... Frame ( 4) shift: 0.31 -0.25 ...... Frame ( 5) shift: 0.41 -0.33 ...... Frame ( 6) shift: 0.50 -0.30 ...... Frame ( 7) shift: 0.57 -0.17 ...... Frame ( 8) shift: 0.64 -0.03 ...... Frame ( 9) shift: 0.73 0.06 ...... Frame ( 10) shift: 0.83 0.12 ...... Frame ( 11) shift: 0.93 0.17 ...... Frame ( 12) shift: 1.00 0.25 ...... Frame ( 13) shift: 1.05 0.36 ...... Frame ( 14) shift: 1.09 0.47 ...... Frame ( 15) shift: 1.14 0.52 ...... Frame ( 16) shift: 1.19 0.51 ...... Frame ( 17) shift: 1.24 0.50 ...... Frame ( 18) shift: 1.29 0.52 ...... Frame ( 19) shift: 1.34 0.55 ...... Frame ( 20) shift: 1.39 0.59 ...... Frame ( 21) shift: 1.41 0.63 ...... Frame ( 22) shift: 1.40 0.69 ...... Frame ( 23) shift: 1.40 0.75 ...... Frame ( 24) shift: 1.44 0.82 ...... Frame ( 25) shift: 1.53 0.89 ...... Frame ( 26) shift: 1.63 0.96 ...... Frame ( 27) shift: 1.69 1.04 ...... Frame ( 28) shift: 1.72 1.11 ...... Frame ( 29) shift: 1.76 1.18 ...... Frame ( 30) shift: 1.80 1.25 ...... Frame ( 31) shift: 1.86 1.30 ...... Frame ( 32) shift: 1.92 1.35 ...... Frame ( 33) shift: 1.97 1.45 ...... Frame ( 34) shift: 2.00 1.58 ...... Frame ( 35) shift: 2.04 1.71 ...... Frame ( 36) shift: 2.08 1.80 ...... Frame ( 37) shift: 2.11 1.84 ...... Frame ( 38) shift: 2.14 1.88 ...... Frame ( 39) shift: 2.17 1.92 ...... Frame ( 40) shift: 2.20 1.96 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.836620 Iteration 2 Error: 0.239938 Iteration 3 Error: 0.072122 Iteration 4 Error: 0.019358 Align patch 2 23 left Iteration 1 Error: 1.641987 Iteration 2 Error: 0.216709 Iteration 3 Error: 0.046967 Align patch 3 22 left Iteration 1 Error: 1.279591 Iteration 2 Error: 0.296134 Iteration 3 Error: 0.073815 Iteration 4 Error: 0.026951 Align patch 4 21 left Iteration 1 Error: 0.866497 Iteration 2 Error: 0.171808 Iteration 3 Error: 0.054957 Iteration 4 Error: 0.022450 Align patch 5 20 left Iteration 1 Error: 0.818041 Iteration 2 Error: 0.107734 Iteration 3 Error: 0.026940 Align patch 6 19 left Iteration 1 Error: 0.978078 Iteration 2 Error: 0.238333 Iteration 3 Error: 0.059607 Iteration 4 Error: 0.018536 Align patch 7 18 left Iteration 1 Error: 1.054961 Iteration 2 Error: 0.163830 Iteration 3 Error: 0.054647 Iteration 4 Error: 0.022450 Align patch 8 17 left Iteration 1 Error: 0.781889 Iteration 2 Error: 0.121862 Iteration 3 Error: 0.036772 Align patch 9 16 left Iteration 1 Error: 0.642064 Iteration 2 Error: 0.116604 Iteration 3 Error: 0.035367 Align patch 10 15 left Iteration 1 Error: 0.924310 Iteration 2 Error: 0.112426 Iteration 3 Error: 0.016467 Align patch 11 14 left Iteration 1 Error: 0.953331 Iteration 2 Error: 0.129968 Iteration 3 Error: 0.019641 Align patch 12 13 left Iteration 1 Error: 0.672235 Iteration 2 Error: 0.114987 Iteration 3 Error: 0.035065 Align patch 13 12 left Iteration 1 Error: 0.690164 Iteration 2 Error: 0.148671 Iteration 3 Error: 0.050236 Iteration 4 Error: 0.021998 Align patch 14 11 left Iteration 1 Error: 1.052783 Iteration 2 Error: 0.233592 Iteration 3 Error: 0.060794 Iteration 4 Error: 0.014755 Align patch 15 10 left Iteration 1 Error: 0.756067 Iteration 2 Error: 0.134930 Iteration 3 Error: 0.042416 Align patch 16 9 left Iteration 1 Error: 1.097300 Iteration 2 Error: 0.238348 Iteration 3 Error: 0.082755 Iteration 4 Error: 0.029414 Align patch 17 8 left Iteration 1 Error: 0.742898 Iteration 2 Error: 0.146031 Iteration 3 Error: 0.063900 Iteration 4 Error: 0.019235 Align patch 18 7 left Iteration 1 Error: 0.685694 Iteration 2 Error: 0.139669 Iteration 3 Error: 0.040853 Align patch 19 6 left Iteration 1 Error: 1.139916 Iteration 2 Error: 0.141799 Iteration 3 Error: 0.046441 Align patch 20 5 left Iteration 1 Error: 0.629438 Iteration 2 Error: 0.119229 Iteration 3 Error: 0.033280 Align patch 21 4 left Iteration 1 Error: 1.214391 Iteration 2 Error: 0.165585 Iteration 3 Error: 0.046953 Align patch 22 3 left Iteration 1 Error: 0.862299 Iteration 2 Error: 0.128768 Iteration 3 Error: 0.028677 Align patch 23 2 left Iteration 1 Error: 0.844149 Iteration 2 Error: 0.176762 Iteration 3 Error: 0.055945 Iteration 4 Error: 0.018307 Align patch 24 1 left Iteration 1 Error: 1.136604 Iteration 2 Error: 0.133517 Iteration 3 Error: 0.037366 Align patch 25 0 left Iteration 1 Error: 0.893663 Iteration 2 Error: 0.207713 Iteration 3 Error: 0.051152 Iteration 4 Error: 0.023715 3D Fitting completed. Patch alignment time: 18.89(sec) Local motion has been corrected. Process thread exits. Computational time: 35.197254 sec Total time: 43.282429 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00003sq_v01_00004hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00003sq_v01_00004hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.577801s Reading file: gc_18feb27f_CTD_00011gr_00003sq_v01_00004hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.722063s ........................................ >>>>>>TIME<<<<<< FFT: 1.801467s Defocus_U Defocus_V Angle CCC 14447.26 14787.15 17.02 0.033816 Final Values Defocus_U Defocus_V Angle CCC 14553.51 14696.67 33.80 0.045355 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00003sq_v01_00004hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00003sq_v01_00004hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.996e-02 CC threshold: 0.734 Mean Std: 36.17 6.37 Num Hot pixels: 218 Hot pixel threshold: 74.41 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.757506 Iteration 2 Error: 0.114002 Iteration 3 Error: 0.030518 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.10 -0.15 ...... Frame ( 3) shift: 0.19 -0.29 ...... Frame ( 4) shift: 0.29 -0.44 ...... Frame ( 5) shift: 0.38 -0.59 ...... Frame ( 6) shift: 0.43 -0.64 ...... Frame ( 7) shift: 0.42 -0.61 ...... Frame ( 8) shift: 0.42 -0.57 ...... Frame ( 9) shift: 0.45 -0.55 ...... Frame ( 10) shift: 0.52 -0.53 ...... Frame ( 11) shift: 0.59 -0.51 ...... Frame ( 12) shift: 0.62 -0.47 ...... Frame ( 13) shift: 0.60 -0.40 ...... Frame ( 14) shift: 0.59 -0.33 ...... Frame ( 15) shift: 0.60 -0.27 ...... Frame ( 16) shift: 0.62 -0.21 ...... Frame ( 17) shift: 0.65 -0.16 ...... Frame ( 18) shift: 0.65 -0.14 ...... Frame ( 19) shift: 0.62 -0.15 ...... Frame ( 20) shift: 0.60 -0.16 ...... Frame ( 21) shift: 0.62 -0.15 ...... Frame ( 22) shift: 0.70 -0.13 ...... Frame ( 23) shift: 0.78 -0.10 ...... Frame ( 24) shift: 0.83 -0.10 ...... Frame ( 25) shift: 0.85 -0.13 ...... Frame ( 26) shift: 0.88 -0.16 ...... Frame ( 27) shift: 0.89 -0.19 ...... Frame ( 28) shift: 0.89 -0.20 ...... Frame ( 29) shift: 0.89 -0.22 ...... Frame ( 30) shift: 0.94 -0.21 ...... Frame ( 31) shift: 1.03 -0.18 ...... Frame ( 32) shift: 1.13 -0.16 ...... Frame ( 33) shift: 1.19 -0.08 ...... Frame ( 34) shift: 1.22 0.04 ...... Frame ( 35) shift: 1.24 0.16 ...... Frame ( 36) shift: 1.26 0.25 ...... Frame ( 37) shift: 1.26 0.32 ...... Frame ( 38) shift: 1.27 0.38 ...... Frame ( 39) shift: 1.27 0.45 ...... Frame ( 40) shift: 1.28 0.51 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.245910 Iteration 2 Error: 0.210730 Iteration 3 Error: 0.049553 Align patch 2 23 left Iteration 1 Error: 0.634064 Iteration 2 Error: 0.125167 Iteration 3 Error: 0.052670 Iteration 4 Error: 0.017205 Align patch 3 22 left Iteration 1 Error: 0.698090 Iteration 2 Error: 0.156536 Iteration 3 Error: 0.037431 Align patch 4 21 left Iteration 1 Error: 0.954416 Iteration 2 Error: 0.159784 Iteration 3 Error: 0.048569 Align patch 5 20 left Iteration 1 Error: 1.362984 Iteration 2 Error: 0.147454 Iteration 3 Error: 0.025702 Align patch 6 19 left Iteration 1 Error: 0.963330 Iteration 2 Error: 0.188036 Iteration 3 Error: 0.056002 Iteration 4 Error: 0.014428 Align patch 7 18 left Iteration 1 Error: 0.790359 Iteration 2 Error: 0.181450 Iteration 3 Error: 0.038156 Align patch 8 17 left Iteration 1 Error: 0.825809 Iteration 2 Error: 0.126576 Iteration 3 Error: 0.028306 Align patch 9 16 left Iteration 1 Error: 0.857237 Iteration 2 Error: 0.085899 Iteration 3 Error: 0.025396 Align patch 10 15 left Iteration 1 Error: 1.149671 Iteration 2 Error: 0.187518 Iteration 3 Error: 0.040483 Align patch 11 14 left Iteration 1 Error: 0.799051 Iteration 2 Error: 0.102126 Iteration 3 Error: 0.017550 Align patch 12 13 left Iteration 1 Error: 0.784060 Iteration 2 Error: 0.122919 Iteration 3 Error: 0.041367 Align patch 13 12 left Iteration 1 Error: 1.088259 Iteration 2 Error: 0.185034 Iteration 3 Error: 0.023111 Align patch 14 11 left Iteration 1 Error: 1.012308 Iteration 2 Error: 0.174945 Iteration 3 Error: 0.051501 Iteration 4 Error: 0.011280 Align patch 15 10 left Iteration 1 Error: 0.894922 Iteration 2 Error: 0.110051 Iteration 3 Error: 0.033288 Align patch 16 9 left Iteration 1 Error: 0.723536 Iteration 2 Error: 0.094845 Iteration 3 Error: 0.026973 Align patch 17 8 left Iteration 1 Error: 0.964910 Iteration 2 Error: 0.169963 Iteration 3 Error: 0.034867 Align patch 18 7 left Iteration 1 Error: 0.876478 Iteration 2 Error: 0.239053 Iteration 3 Error: 0.114424 Iteration 4 Error: 0.049857 Align patch 19 6 left Iteration 1 Error: 0.734554 Iteration 2 Error: 0.123358 Iteration 3 Error: 0.021832 Align patch 20 5 left Iteration 1 Error: 0.706295 Iteration 2 Error: 0.129845 Iteration 3 Error: 0.038194 Align patch 21 4 left Iteration 1 Error: 0.732374 Iteration 2 Error: 0.114912 Iteration 3 Error: 0.022472 Align patch 22 3 left Iteration 1 Error: 0.903540 Iteration 2 Error: 0.145061 Iteration 3 Error: 0.027692 Align patch 23 2 left Iteration 1 Error: 0.979931 Iteration 2 Error: 0.197544 Iteration 3 Error: 0.062692 Iteration 4 Error: 0.020966 Align patch 24 1 left Iteration 1 Error: 0.718862 Iteration 2 Error: 0.141479 Iteration 3 Error: 0.035952 Align patch 25 0 left Iteration 1 Error: 0.817498 Iteration 2 Error: 0.155060 Iteration 3 Error: 0.038161 3D Fitting completed. Patch alignment time: 15.24(sec) Local motion has been corrected. Process thread exits. Computational time: 29.006338 sec Total time: 36.258633 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00003sq_v01_00004hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00003sq_v01_00004hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.796207s Reading file: gc_18feb27f_CTD_00011gr_00003sq_v01_00004hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.527414s ........................................ >>>>>>TIME<<<<<< FFT: 1.188190s Defocus_U Defocus_V Angle CCC 13373.10 13771.62 13.23 0.026095 Final Values Defocus_U Defocus_V Angle CCC 13255.86 13685.84 2.40 0.033844 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00003sq_v01_00004hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00003sq_v01_00004hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.994e-02 CC threshold: 0.734 Mean Std: 36.82 6.46 Num Hot pixels: 206 Hot pixel threshold: 75.59 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.438356 Iteration 2 Error: 0.248307 Iteration 3 Error: 0.060649 Iteration 4 Error: 0.018864 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.15 -0.10 ...... Frame ( 3) shift: 0.30 -0.19 ...... Frame ( 4) shift: 0.45 -0.29 ...... Frame ( 5) shift: 0.59 -0.39 ...... Frame ( 6) shift: 0.73 -0.40 ...... Frame ( 7) shift: 0.84 -0.32 ...... Frame ( 8) shift: 0.95 -0.25 ...... Frame ( 9) shift: 1.03 -0.13 ...... Frame ( 10) shift: 1.06 0.03 ...... Frame ( 11) shift: 1.10 0.19 ...... Frame ( 12) shift: 1.17 0.32 ...... Frame ( 13) shift: 1.28 0.42 ...... Frame ( 14) shift: 1.39 0.52 ...... Frame ( 15) shift: 1.47 0.62 ...... Frame ( 16) shift: 1.54 0.72 ...... Frame ( 17) shift: 1.60 0.83 ...... Frame ( 18) shift: 1.69 0.90 ...... Frame ( 19) shift: 1.80 0.94 ...... Frame ( 20) shift: 1.92 0.98 ...... Frame ( 21) shift: 1.99 1.01 ...... Frame ( 22) shift: 2.00 1.05 ...... Frame ( 23) shift: 2.02 1.08 ...... Frame ( 24) shift: 2.02 1.14 ...... Frame ( 25) shift: 2.02 1.22 ...... Frame ( 26) shift: 2.02 1.31 ...... Frame ( 27) shift: 2.00 1.40 ...... Frame ( 28) shift: 1.96 1.51 ...... Frame ( 29) shift: 1.93 1.61 ...... Frame ( 30) shift: 1.91 1.68 ...... Frame ( 31) shift: 1.91 1.69 ...... Frame ( 32) shift: 1.91 1.71 ...... Frame ( 33) shift: 1.91 1.72 ...... Frame ( 34) shift: 1.92 1.73 ...... Frame ( 35) shift: 1.93 1.74 ...... Frame ( 36) shift: 1.95 1.76 ...... Frame ( 37) shift: 1.98 1.80 ...... Frame ( 38) shift: 2.01 1.83 ...... Frame ( 39) shift: 2.04 1.87 ...... Frame ( 40) shift: 2.08 1.90 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.860435 Iteration 2 Error: 0.208378 Iteration 3 Error: 0.044032 Align patch 2 23 left Iteration 1 Error: 0.897456 Iteration 2 Error: 0.166004 Iteration 3 Error: 0.057747 Iteration 4 Error: 0.024273 Align patch 3 22 left Iteration 1 Error: 0.910415 Iteration 2 Error: 0.302056 Iteration 3 Error: 0.110929 Iteration 4 Error: 0.043113 Align patch 4 21 left Iteration 1 Error: 0.658228 Iteration 2 Error: 0.126185 Iteration 3 Error: 0.038753 Align patch 5 20 left Iteration 1 Error: 0.908375 Iteration 2 Error: 0.115585 Iteration 3 Error: 0.017644 Align patch 6 19 left Iteration 1 Error: 0.636150 Iteration 2 Error: 0.135790 Iteration 3 Error: 0.053258 Iteration 4 Error: 0.017054 Align patch 7 18 left Iteration 1 Error: 0.931691 Iteration 2 Error: 0.185106 Iteration 3 Error: 0.051299 Iteration 4 Error: 0.019394 Align patch 8 17 left Iteration 1 Error: 0.875607 Iteration 2 Error: 0.192201 Iteration 3 Error: 0.058294 Iteration 4 Error: 0.022852 Align patch 9 16 left Iteration 1 Error: 0.849120 Iteration 2 Error: 0.131270 Iteration 3 Error: 0.040803 Align patch 10 15 left Iteration 1 Error: 0.647102 Iteration 2 Error: 0.134586 Iteration 3 Error: 0.040963 Align patch 11 14 left Iteration 1 Error: 0.909667 Iteration 2 Error: 0.239120 Iteration 3 Error: 0.077812 Iteration 4 Error: 0.038798 Align patch 12 13 left Iteration 1 Error: 0.604533 Iteration 2 Error: 0.152302 Iteration 3 Error: 0.059443 Iteration 4 Error: 0.018265 Align patch 13 12 left Iteration 1 Error: 0.812874 Iteration 2 Error: 0.188616 Iteration 3 Error: 0.060955 Iteration 4 Error: 0.014518 Align patch 14 11 left Iteration 1 Error: 0.868112 Iteration 2 Error: 0.160700 Iteration 3 Error: 0.050034 Iteration 4 Error: 0.013278 Align patch 15 10 left Iteration 1 Error: 0.818652 Iteration 2 Error: 0.146110 Iteration 3 Error: 0.062780 Iteration 4 Error: 0.027347 Align patch 16 9 left Iteration 1 Error: 0.839311 Iteration 2 Error: 0.132293 Iteration 3 Error: 0.032847 Align patch 17 8 left Iteration 1 Error: 0.770169 Iteration 2 Error: 0.101790 Iteration 3 Error: 0.033613 Align patch 18 7 left Iteration 1 Error: 0.655185 Iteration 2 Error: 0.152864 Iteration 3 Error: 0.037395 Align patch 19 6 left Iteration 1 Error: 0.714354 Iteration 2 Error: 0.108587 Iteration 3 Error: 0.020186 Align patch 20 5 left Iteration 1 Error: 0.746559 Iteration 2 Error: 0.224129 Iteration 3 Error: 0.075330 Iteration 4 Error: 0.024203 Align patch 21 4 left Iteration 1 Error: 0.963472 Iteration 2 Error: 0.264718 Iteration 3 Error: 0.104629 Iteration 4 Error: 0.034539 Align patch 22 3 left Iteration 1 Error: 1.140321 Iteration 2 Error: 0.203710 Iteration 3 Error: 0.043444 Align patch 23 2 left Iteration 1 Error: 0.715778 Iteration 2 Error: 0.187564 Iteration 3 Error: 0.030947 Align patch 24 1 left Iteration 1 Error: 0.981391 Iteration 2 Error: 0.178777 Iteration 3 Error: 0.029492 Align patch 25 0 left Iteration 1 Error: 0.898953 Iteration 2 Error: 0.239833 Iteration 3 Error: 0.074308 Iteration 4 Error: 0.033561 3D Fitting completed. Patch alignment time: 16.98(sec) Local motion has been corrected. Process thread exits. Computational time: 33.264626 sec Total time: 42.539341 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00003sq_v01_00004hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00003sq_v01_00004hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.603562s Reading file: gc_18feb27f_CTD_00011gr_00003sq_v01_00004hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.223631s ........................................ >>>>>>TIME<<<<<< FFT: 1.134090s Defocus_U Defocus_V Angle CCC 25500.01 24632.82 88.20 0.031083 Final Values Defocus_U Defocus_V Angle CCC 24581.26 25473.46 2.59 0.043028 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00003sq_v01_00005hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00003sq_v01_00005hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.998e-02 CC threshold: 0.734 Mean Std: 35.17 6.30 Num Hot pixels: 197 Hot pixel threshold: 72.96 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.454733 Iteration 2 Error: 0.297458 Iteration 3 Error: 0.072350 Iteration 4 Error: 0.027222 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.16 -0.09 ...... Frame ( 3) shift: 0.32 -0.17 ...... Frame ( 4) shift: 0.48 -0.26 ...... Frame ( 5) shift: 0.64 -0.35 ...... Frame ( 6) shift: 0.74 -0.38 ...... Frame ( 7) shift: 0.78 -0.35 ...... Frame ( 8) shift: 0.81 -0.33 ...... Frame ( 9) shift: 0.90 -0.26 ...... Frame ( 10) shift: 1.03 -0.14 ...... Frame ( 11) shift: 1.17 -0.02 ...... Frame ( 12) shift: 1.26 0.06 ...... Frame ( 13) shift: 1.31 0.09 ...... Frame ( 14) shift: 1.36 0.13 ...... Frame ( 15) shift: 1.42 0.22 ...... Frame ( 16) shift: 1.48 0.34 ...... Frame ( 17) shift: 1.55 0.47 ...... Frame ( 18) shift: 1.59 0.57 ...... Frame ( 19) shift: 1.60 0.63 ...... Frame ( 20) shift: 1.61 0.70 ...... Frame ( 21) shift: 1.66 0.78 ...... Frame ( 22) shift: 1.74 0.87 ...... Frame ( 23) shift: 1.82 0.96 ...... Frame ( 24) shift: 1.90 1.04 ...... Frame ( 25) shift: 1.98 1.11 ...... Frame ( 26) shift: 2.07 1.17 ...... Frame ( 27) shift: 2.16 1.20 ...... Frame ( 28) shift: 2.26 1.20 ...... Frame ( 29) shift: 2.35 1.20 ...... Frame ( 30) shift: 2.44 1.24 ...... Frame ( 31) shift: 2.52 1.32 ...... Frame ( 32) shift: 2.60 1.41 ...... Frame ( 33) shift: 2.68 1.45 ...... Frame ( 34) shift: 2.75 1.46 ...... Frame ( 35) shift: 2.82 1.47 ...... Frame ( 36) shift: 2.87 1.50 ...... Frame ( 37) shift: 2.89 1.54 ...... Frame ( 38) shift: 2.90 1.57 ...... Frame ( 39) shift: 2.92 1.61 ...... Frame ( 40) shift: 2.93 1.65 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.759669 Iteration 2 Error: 0.152926 Iteration 3 Error: 0.048897 Align patch 2 23 left Iteration 1 Error: 1.094934 Iteration 2 Error: 0.173879 Iteration 3 Error: 0.039521 Align patch 3 22 left Iteration 1 Error: 0.668667 Iteration 2 Error: 0.251069 Iteration 3 Error: 0.081091 Iteration 4 Error: 0.026490 Align patch 4 21 left Iteration 1 Error: 0.921702 Iteration 2 Error: 0.131537 Iteration 3 Error: 0.039817 Align patch 5 20 left Iteration 1 Error: 0.725717 Iteration 2 Error: 0.146717 Iteration 3 Error: 0.040645 Align patch 6 19 left Iteration 1 Error: 0.896894 Iteration 2 Error: 0.175782 Iteration 3 Error: 0.041908 Align patch 7 18 left Iteration 1 Error: 0.761219 Iteration 2 Error: 0.235959 Iteration 3 Error: 0.050949 Iteration 4 Error: 0.015191 Align patch 8 17 left Iteration 1 Error: 0.451070 Iteration 2 Error: 0.092174 Iteration 3 Error: 0.026274 Align patch 9 16 left Iteration 1 Error: 0.641064 Iteration 2 Error: 0.092525 Iteration 3 Error: 0.025241 Align patch 10 15 left Iteration 1 Error: 0.697794 Iteration 2 Error: 0.121508 Iteration 3 Error: 0.029794 Align patch 11 14 left Iteration 1 Error: 0.931092 Iteration 2 Error: 0.273464 Iteration 3 Error: 0.106921 Iteration 4 Error: 0.053682 Iteration 5 Error: 0.030672 Align patch 12 13 left Iteration 1 Error: 1.297870 Iteration 2 Error: 0.252060 Iteration 3 Error: 0.076111 Iteration 4 Error: 0.037201 Align patch 13 12 left Iteration 1 Error: 0.939466 Iteration 2 Error: 0.239647 Iteration 3 Error: 0.041384 Align patch 14 11 left Iteration 1 Error: 1.021990 Iteration 2 Error: 0.236304 Iteration 3 Error: 0.057737 Iteration 4 Error: 0.022888 Align patch 15 10 left Iteration 1 Error: 0.756999 Iteration 2 Error: 0.176157 Iteration 3 Error: 0.063073 Iteration 4 Error: 0.025140 Align patch 16 9 left Iteration 1 Error: 0.949699 Iteration 2 Error: 0.225839 Iteration 3 Error: 0.038459 Align patch 17 8 left Iteration 1 Error: 1.717601 Iteration 2 Error: 0.321312 Iteration 3 Error: 0.158104 Iteration 4 Error: 0.076208 Iteration 5 Error: 0.053927 Align patch 17 8 left Iteration 1 Error: 0.851695 Iteration 2 Error: 0.093695 Iteration 3 Error: 0.026113 Align patch 18 7 left Iteration 1 Error: 1.022642 Iteration 2 Error: 0.176340 Iteration 3 Error: 0.049392 Align patch 19 6 left Iteration 1 Error: 0.815815 Iteration 2 Error: 0.146866 Iteration 3 Error: 0.043446 Align patch 20 5 left Iteration 1 Error: 0.720636 Iteration 2 Error: 0.120951 Iteration 3 Error: 0.030612 Align patch 21 4 left Iteration 1 Error: 0.829678 Iteration 2 Error: 0.151591 Iteration 3 Error: 0.042308 Align patch 22 3 left Iteration 1 Error: 0.819260 Iteration 2 Error: 0.141822 Iteration 3 Error: 0.032463 Align patch 23 2 left Iteration 1 Error: 0.811334 Iteration 2 Error: 0.193571 Iteration 3 Error: 0.084809 Iteration 4 Error: 0.027715 Align patch 24 1 left Iteration 1 Error: 0.865630 Iteration 2 Error: 0.111082 Iteration 3 Error: 0.050024 Iteration 4 Error: 0.018566 Align patch 25 0 left Iteration 1 Error: 0.762210 Iteration 2 Error: 0.163189 Iteration 3 Error: 0.046085 3D Fitting completed. Patch alignment time: 18.29(sec) Local motion has been corrected. Process thread exits. Computational time: 34.116432 sec Total time: 42.887974 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00003sq_v01_00005hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00003sq_v01_00005hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 3.281642s Reading file: gc_18feb27f_CTD_00011gr_00003sq_v01_00005hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.652774s ........................................ >>>>>>TIME<<<<<< FFT: 1.342237s Defocus_U Defocus_V Angle CCC 23070.33 23937.51 5.54 0.025499 Final Values Defocus_U Defocus_V Angle CCC 23032.78 23709.51 7.25 0.035600 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00003sq_v01_00005hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00003sq_v01_00005hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.994e-02 CC threshold: 0.734 Mean Std: 36.60 6.40 Num Hot pixels: 184 Hot pixel threshold: 75.02 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.927602 Iteration 2 Error: 0.407029 Iteration 3 Error: 0.105580 Iteration 4 Error: 0.030853 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.00 -0.28 ...... Frame ( 3) shift: 0.01 -0.56 ...... Frame ( 4) shift: 0.01 -0.85 ...... Frame ( 5) shift: 0.02 -1.13 ...... Frame ( 6) shift: 0.06 -1.27 ...... Frame ( 7) shift: 0.15 -1.26 ...... Frame ( 8) shift: 0.24 -1.25 ...... Frame ( 9) shift: 0.35 -1.23 ...... Frame ( 10) shift: 0.48 -1.20 ...... Frame ( 11) shift: 0.62 -1.17 ...... Frame ( 12) shift: 0.70 -1.09 ...... Frame ( 13) shift: 0.73 -0.94 ...... Frame ( 14) shift: 0.76 -0.80 ...... Frame ( 15) shift: 0.85 -0.68 ...... Frame ( 16) shift: 1.01 -0.60 ...... Frame ( 17) shift: 1.17 -0.53 ...... Frame ( 18) shift: 1.31 -0.42 ...... Frame ( 19) shift: 1.41 -0.30 ...... Frame ( 20) shift: 1.51 -0.17 ...... Frame ( 21) shift: 1.59 -0.05 ...... Frame ( 22) shift: 1.66 0.07 ...... Frame ( 23) shift: 1.73 0.19 ...... Frame ( 24) shift: 1.80 0.22 ...... Frame ( 25) shift: 1.88 0.17 ...... Frame ( 26) shift: 1.96 0.12 ...... Frame ( 27) shift: 2.05 0.20 ...... Frame ( 28) shift: 2.15 0.43 ...... Frame ( 29) shift: 2.26 0.66 ...... Frame ( 30) shift: 2.32 0.80 ...... Frame ( 31) shift: 2.36 0.86 ...... Frame ( 32) shift: 2.39 0.92 ...... Frame ( 33) shift: 2.44 0.97 ...... Frame ( 34) shift: 2.50 0.99 ...... Frame ( 35) shift: 2.56 1.01 ...... Frame ( 36) shift: 2.67 1.03 ...... Frame ( 37) shift: 2.82 1.04 ...... Frame ( 38) shift: 2.96 1.06 ...... Frame ( 39) shift: 3.11 1.07 ...... Frame ( 40) shift: 3.26 1.09 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.791988 Iteration 2 Error: 0.316508 Iteration 3 Error: 0.107728 Iteration 4 Error: 0.045694 Align patch 2 23 left Iteration 1 Error: 1.540585 Iteration 2 Error: 0.626408 Iteration 3 Error: 0.273418 Iteration 4 Error: 0.230248 Iteration 5 Error: 0.120558 Align patch 2 23 left Iteration 1 Error: 1.554318 Iteration 2 Error: 0.138901 Iteration 3 Error: 0.019017 Align patch 3 22 left Iteration 1 Error: 1.135146 Iteration 2 Error: 0.407714 Iteration 3 Error: 0.143347 Iteration 4 Error: 0.055019 Iteration 5 Error: 0.019864 Align patch 4 21 left Iteration 1 Error: 1.281707 Iteration 2 Error: 0.275575 Iteration 3 Error: 0.137427 Iteration 4 Error: 0.065468 Iteration 5 Error: 0.027372 Align patch 5 20 left Iteration 1 Error: 1.535354 Iteration 2 Error: 0.286137 Iteration 3 Error: 0.127700 Iteration 4 Error: 0.057873 Iteration 5 Error: 0.033813 Align patch 6 19 left Iteration 1 Error: 1.497245 Iteration 2 Error: 0.321723 Iteration 3 Error: 0.098684 Iteration 4 Error: 0.025874 Align patch 7 18 left Iteration 1 Error: 1.444895 Iteration 2 Error: 0.267022 Iteration 3 Error: 0.055502 Iteration 4 Error: 0.019093 Align patch 8 17 left Iteration 1 Error: 1.286461 Iteration 2 Error: 0.297904 Iteration 3 Error: 0.082720 Iteration 4 Error: 0.031361 Align patch 9 16 left Iteration 1 Error: 0.930331 Iteration 2 Error: 0.167746 Iteration 3 Error: 0.052168 Iteration 4 Error: 0.020296 Align patch 10 15 left Iteration 1 Error: 0.789996 Iteration 2 Error: 0.155781 Iteration 3 Error: 0.038886 Align patch 11 14 left Iteration 1 Error: 0.868554 Iteration 2 Error: 0.314237 Iteration 3 Error: 0.094317 Iteration 4 Error: 0.033270 Align patch 12 13 left Iteration 1 Error: 1.587389 Iteration 2 Error: 0.231551 Iteration 3 Error: 0.090586 Iteration 4 Error: 0.025530 Align patch 13 12 left Iteration 1 Error: 1.053973 Iteration 2 Error: 0.196515 Iteration 3 Error: 0.037293 Align patch 14 11 left Iteration 1 Error: 1.356362 Iteration 2 Error: 0.269048 Iteration 3 Error: 0.089172 Iteration 4 Error: 0.033765 Align patch 15 10 left Iteration 1 Error: 1.290881 Iteration 2 Error: 0.292117 Iteration 3 Error: 0.078461 Iteration 4 Error: 0.024665 Align patch 16 9 left Iteration 1 Error: 1.086123 Iteration 2 Error: 0.112195 Iteration 3 Error: 0.034585 Align patch 17 8 left Iteration 1 Error: 0.907410 Iteration 2 Error: 0.181106 Iteration 3 Error: 0.052015 Iteration 4 Error: 0.027019 Align patch 18 7 left Iteration 1 Error: 1.030243 Iteration 2 Error: 0.166087 Iteration 3 Error: 0.040731 Align patch 19 6 left Iteration 1 Error: 1.082505 Iteration 2 Error: 0.187830 Iteration 3 Error: 0.038607 Align patch 20 5 left Iteration 1 Error: 0.820432 Iteration 2 Error: 0.174838 Iteration 3 Error: 0.060102 Iteration 4 Error: 0.024535 Align patch 21 4 left Iteration 1 Error: 0.806298 Iteration 2 Error: 0.180470 Iteration 3 Error: 0.080490 Iteration 4 Error: 0.025227 Align patch 22 3 left Iteration 1 Error: 1.069171 Iteration 2 Error: 0.235873 Iteration 3 Error: 0.069999 Iteration 4 Error: 0.028616 Align patch 23 2 left Iteration 1 Error: 0.483355 Iteration 2 Error: 0.109229 Iteration 3 Error: 0.029243 Align patch 24 1 left Iteration 1 Error: 0.818706 Iteration 2 Error: 0.245508 Iteration 3 Error: 0.101352 Iteration 4 Error: 0.028471 Align patch 25 0 left Iteration 1 Error: 1.098216 Iteration 2 Error: 0.198940 Iteration 3 Error: 0.083001 Iteration 4 Error: 0.039633 3D Fitting completed. Patch alignment time: 21.79(sec) Local motion has been corrected. Process thread exits. Computational time: 40.280319 sec Total time: 49.918144 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00003sq_v01_00005hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00003sq_v01_00005hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.939290s Reading file: gc_18feb27f_CTD_00011gr_00003sq_v01_00005hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.721935s ........................................ >>>>>>TIME<<<<<< FFT: 1.529480s Defocus_U Defocus_V Angle CCC 25431.64 26322.27 11.87 0.030041 Final Values Defocus_U Defocus_V Angle CCC 25386.33 26389.50 13.44 0.041087 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00003sq_v01_00005hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00003sq_v01_00005hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.992e-02 CC threshold: 0.734 Mean Std: 36.67 6.42 Num Hot pixels: 233 Hot pixel threshold: 75.21 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.798337 Iteration 2 Error: 0.142725 Iteration 3 Error: 0.040548 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.05 -0.04 ...... Frame ( 3) shift: 0.10 -0.09 ...... Frame ( 4) shift: 0.15 -0.13 ...... Frame ( 5) shift: 0.20 -0.18 ...... Frame ( 6) shift: 0.21 -0.17 ...... Frame ( 7) shift: 0.19 -0.12 ...... Frame ( 8) shift: 0.17 -0.07 ...... Frame ( 9) shift: 0.18 -0.01 ...... Frame ( 10) shift: 0.21 0.05 ...... Frame ( 11) shift: 0.25 0.11 ...... Frame ( 12) shift: 0.33 0.18 ...... Frame ( 13) shift: 0.44 0.24 ...... Frame ( 14) shift: 0.56 0.31 ...... Frame ( 15) shift: 0.62 0.39 ...... Frame ( 16) shift: 0.62 0.50 ...... Frame ( 17) shift: 0.63 0.61 ...... Frame ( 18) shift: 0.66 0.71 ...... Frame ( 19) shift: 0.73 0.79 ...... Frame ( 20) shift: 0.80 0.87 ...... Frame ( 21) shift: 0.84 0.92 ...... Frame ( 22) shift: 0.87 0.92 ...... Frame ( 23) shift: 0.89 0.92 ...... Frame ( 24) shift: 0.89 0.97 ...... Frame ( 25) shift: 0.84 1.06 ...... Frame ( 26) shift: 0.79 1.14 ...... Frame ( 27) shift: 0.80 1.17 ...... Frame ( 28) shift: 0.85 1.15 ...... Frame ( 29) shift: 0.90 1.12 ...... Frame ( 30) shift: 0.91 1.13 ...... Frame ( 31) shift: 0.86 1.19 ...... Frame ( 32) shift: 0.81 1.24 ...... Frame ( 33) shift: 0.85 1.25 ...... Frame ( 34) shift: 0.97 1.20 ...... Frame ( 35) shift: 1.10 1.16 ...... Frame ( 36) shift: 1.14 1.16 ...... Frame ( 37) shift: 1.11 1.22 ...... Frame ( 38) shift: 1.08 1.27 ...... Frame ( 39) shift: 1.05 1.32 ...... Frame ( 40) shift: 1.02 1.37 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.805809 Iteration 2 Error: 0.182316 Iteration 3 Error: 0.042085 Align patch 2 23 left Iteration 1 Error: 0.868273 Iteration 2 Error: 0.229236 Iteration 3 Error: 0.077733 Iteration 4 Error: 0.039507 Align patch 3 22 left Iteration 1 Error: 1.146980 Iteration 2 Error: 0.339020 Iteration 3 Error: 0.082760 Iteration 4 Error: 0.039828 Align patch 4 21 left Iteration 1 Error: 0.803741 Iteration 2 Error: 0.123154 Iteration 3 Error: 0.028729 Align patch 5 20 left Iteration 1 Error: 1.070214 Iteration 2 Error: 0.113929 Iteration 3 Error: 0.018133 Align patch 6 19 left Iteration 1 Error: 0.594216 Iteration 2 Error: 0.144767 Iteration 3 Error: 0.027654 Align patch 7 18 left Iteration 1 Error: 0.886648 Iteration 2 Error: 0.149412 Iteration 3 Error: 0.041129 Align patch 8 17 left Iteration 1 Error: 1.437216 Iteration 2 Error: 0.219164 Iteration 3 Error: 0.067104 Iteration 4 Error: 0.017175 Align patch 9 16 left Iteration 1 Error: 0.623764 Iteration 2 Error: 0.143020 Iteration 3 Error: 0.022532 Align patch 10 15 left Iteration 1 Error: 1.025423 Iteration 2 Error: 0.260963 Iteration 3 Error: 0.042862 Align patch 11 14 left Iteration 1 Error: 0.941367 Iteration 2 Error: 0.230611 Iteration 3 Error: 0.046144 Align patch 12 13 left Iteration 1 Error: 0.854324 Iteration 2 Error: 0.137158 Iteration 3 Error: 0.034788 Align patch 13 12 left Iteration 1 Error: 0.614726 Iteration 2 Error: 0.107210 Iteration 3 Error: 0.040265 Align patch 14 11 left Iteration 1 Error: 1.259629 Iteration 2 Error: 0.285384 Iteration 3 Error: 0.097735 Iteration 4 Error: 0.030968 Align patch 15 10 left Iteration 1 Error: 0.814164 Iteration 2 Error: 0.225239 Iteration 3 Error: 0.055570 Iteration 4 Error: 0.020152 Align patch 16 9 left Iteration 1 Error: 0.784701 Iteration 2 Error: 0.179800 Iteration 3 Error: 0.069222 Iteration 4 Error: 0.025744 Align patch 17 8 left Iteration 1 Error: 0.514666 Iteration 2 Error: 0.150045 Iteration 3 Error: 0.049847 Align patch 18 7 left Iteration 1 Error: 0.615259 Iteration 2 Error: 0.118153 Iteration 3 Error: 0.052390 Iteration 4 Error: 0.023100 Align patch 19 6 left Iteration 1 Error: 0.796283 Iteration 2 Error: 0.127995 Iteration 3 Error: 0.046472 Align patch 20 5 left Iteration 1 Error: 0.786896 Iteration 2 Error: 0.153041 Iteration 3 Error: 0.021864 Align patch 21 4 left Iteration 1 Error: 0.659048 Iteration 2 Error: 0.092969 Iteration 3 Error: 0.029747 Align patch 22 3 left Iteration 1 Error: 0.556664 Iteration 2 Error: 0.129280 Iteration 3 Error: 0.056463 Iteration 4 Error: 0.018211 Align patch 23 2 left Iteration 1 Error: 1.166121 Iteration 2 Error: 0.227865 Iteration 3 Error: 0.055073 Iteration 4 Error: 0.014432 Align patch 24 1 left Iteration 1 Error: 1.214993 Iteration 2 Error: 0.207693 Iteration 3 Error: 0.044217 Align patch 25 0 left Iteration 1 Error: 1.014790 Iteration 2 Error: 0.157299 Iteration 3 Error: 0.036372 3D Fitting completed. Patch alignment time: 19.86(sec) Local motion has been corrected. Process thread exits. Computational time: 37.364876 sec Total time: 47.746548 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00003sq_v01_00005hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00003sq_v01_00005hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.563571s Reading file: gc_18feb27f_CTD_00011gr_00003sq_v01_00005hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.256828s ........................................ >>>>>>TIME<<<<<< FFT: 1.367427s Defocus_U Defocus_V Angle CCC 26056.62 26654.44 1.43 0.030686 Final Values Defocus_U Defocus_V Angle CCC 26041.05 26470.21 2.41 0.041032 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00003sq_v01_00005hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00003sq_v01_00005hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.997e-02 CC threshold: 0.734 Mean Std: 37.42 6.50 Num Hot pixels: 221 Hot pixel threshold: 76.44 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.010461 Iteration 2 Error: 0.161730 Iteration 3 Error: 0.023735 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.11 -0.14 ...... Frame ( 3) shift: -0.22 -0.29 ...... Frame ( 4) shift: -0.33 -0.43 ...... Frame ( 5) shift: -0.43 -0.58 ...... Frame ( 6) shift: -0.46 -0.62 ...... Frame ( 7) shift: -0.39 -0.57 ...... Frame ( 8) shift: -0.33 -0.52 ...... Frame ( 9) shift: -0.27 -0.42 ...... Frame ( 10) shift: -0.21 -0.28 ...... Frame ( 11) shift: -0.14 -0.15 ...... Frame ( 12) shift: -0.13 -0.08 ...... Frame ( 13) shift: -0.18 -0.09 ...... Frame ( 14) shift: -0.22 -0.10 ...... Frame ( 15) shift: -0.22 -0.03 ...... Frame ( 16) shift: -0.19 0.11 ...... Frame ( 17) shift: -0.16 0.24 ...... Frame ( 18) shift: -0.15 0.29 ...... Frame ( 19) shift: -0.16 0.26 ...... Frame ( 20) shift: -0.18 0.23 ...... Frame ( 21) shift: -0.19 0.26 ...... Frame ( 22) shift: -0.20 0.35 ...... Frame ( 23) shift: -0.20 0.45 ...... Frame ( 24) shift: -0.19 0.51 ...... Frame ( 25) shift: -0.15 0.54 ...... Frame ( 26) shift: -0.11 0.57 ...... Frame ( 27) shift: -0.07 0.61 ...... Frame ( 28) shift: -0.02 0.67 ...... Frame ( 29) shift: 0.02 0.73 ...... Frame ( 30) shift: 0.05 0.78 ...... Frame ( 31) shift: 0.07 0.82 ...... Frame ( 32) shift: 0.08 0.86 ...... Frame ( 33) shift: 0.08 0.90 ...... Frame ( 34) shift: 0.07 0.94 ...... Frame ( 35) shift: 0.05 0.99 ...... Frame ( 36) shift: 0.06 1.05 ...... Frame ( 37) shift: 0.10 1.13 ...... Frame ( 38) shift: 0.15 1.22 ...... Frame ( 39) shift: 0.19 1.30 ...... Frame ( 40) shift: 0.23 1.39 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.968942 Iteration 2 Error: 0.156473 Iteration 3 Error: 0.043747 Align patch 2 23 left Iteration 1 Error: 0.868724 Iteration 2 Error: 0.151695 Iteration 3 Error: 0.028169 Align patch 3 22 left Iteration 1 Error: 0.957788 Iteration 2 Error: 0.158395 Iteration 3 Error: 0.038328 Align patch 4 21 left Iteration 1 Error: 0.890394 Iteration 2 Error: 0.115868 Iteration 3 Error: 0.029280 Align patch 5 20 left Iteration 1 Error: 0.969666 Iteration 2 Error: 0.179612 Iteration 3 Error: 0.055214 Iteration 4 Error: 0.019781 Align patch 6 19 left Iteration 1 Error: 0.821743 Iteration 2 Error: 0.176625 Iteration 3 Error: 0.044283 Align patch 7 18 left Iteration 1 Error: 0.700959 Iteration 2 Error: 0.156578 Iteration 3 Error: 0.049350 Align patch 8 17 left Iteration 1 Error: 0.827396 Iteration 2 Error: 0.159728 Iteration 3 Error: 0.049647 Align patch 9 16 left Iteration 1 Error: 1.322278 Iteration 2 Error: 0.200158 Iteration 3 Error: 0.071427 Iteration 4 Error: 0.020495 Align patch 10 15 left Iteration 1 Error: 0.929226 Iteration 2 Error: 0.196102 Iteration 3 Error: 0.050907 Iteration 4 Error: 0.013863 Align patch 11 14 left Iteration 1 Error: 1.718106 Iteration 2 Error: 0.192080 Iteration 3 Error: 0.040627 Align patch 12 13 left Iteration 1 Error: 0.915990 Iteration 2 Error: 0.110070 Iteration 3 Error: 0.025457 Align patch 13 12 left Iteration 1 Error: 0.913538 Iteration 2 Error: 0.206048 Iteration 3 Error: 0.039383 Align patch 14 11 left Iteration 1 Error: 0.565322 Iteration 2 Error: 0.130943 Iteration 3 Error: 0.019137 Align patch 15 10 left Iteration 1 Error: 0.605531 Iteration 2 Error: 0.137182 Iteration 3 Error: 0.029310 Align patch 16 9 left Iteration 1 Error: 0.886520 Iteration 2 Error: 0.097611 Iteration 3 Error: 0.025905 Align patch 17 8 left Iteration 1 Error: 0.920076 Iteration 2 Error: 0.166025 Iteration 3 Error: 0.027275 Align patch 18 7 left Iteration 1 Error: 0.532842 Iteration 2 Error: 0.073199 Iteration 3 Error: 0.018776 Align patch 19 6 left Iteration 1 Error: 0.648767 Iteration 2 Error: 0.137312 Iteration 3 Error: 0.041653 Align patch 20 5 left Iteration 1 Error: 0.720384 Iteration 2 Error: 0.142459 Iteration 3 Error: 0.037851 Align patch 21 4 left Iteration 1 Error: 0.584243 Iteration 2 Error: 0.140687 Iteration 3 Error: 0.038132 Align patch 22 3 left Iteration 1 Error: 0.528299 Iteration 2 Error: 0.075534 Iteration 3 Error: 0.017356 Align patch 23 2 left Iteration 1 Error: 0.651582 Iteration 2 Error: 0.110441 Iteration 3 Error: 0.033547 Align patch 24 1 left Iteration 1 Error: 0.791765 Iteration 2 Error: 0.116424 Iteration 3 Error: 0.017657 Align patch 25 0 left Iteration 1 Error: 0.935469 Iteration 2 Error: 0.083651 Iteration 3 Error: 0.017756 3D Fitting completed. Patch alignment time: 18.48(sec) Local motion has been corrected. Process thread exits. Computational time: 39.343792 sec Total time: 47.863350 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00003sq_v01_00005hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00003sq_v01_00005hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.596294s Reading file: gc_18feb27f_CTD_00011gr_00003sq_v01_00005hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.998365s ........................................ >>>>>>TIME<<<<<< FFT: 1.295721s Defocus_U Defocus_V Angle CCC 28927.73 28892.58 36.71 0.022496 Final Values Defocus_U Defocus_V Angle CCC 29367.61 28688.63 77.43 0.036474 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00003sq_v01_00006hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00003sq_v01_00006hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.996e-02 CC threshold: 0.734 Mean Std: 36.47 6.42 Num Hot pixels: 210 Hot pixel threshold: 75.01 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.981522 Iteration 2 Error: 0.157507 Iteration 3 Error: 0.038177 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.04 -0.23 ...... Frame ( 3) shift: -0.09 -0.46 ...... Frame ( 4) shift: -0.13 -0.69 ...... Frame ( 5) shift: -0.17 -0.92 ...... Frame ( 6) shift: -0.19 -1.01 ...... Frame ( 7) shift: -0.19 -0.97 ...... Frame ( 8) shift: -0.19 -0.93 ...... Frame ( 9) shift: -0.18 -0.87 ...... Frame ( 10) shift: -0.16 -0.80 ...... Frame ( 11) shift: -0.14 -0.73 ...... Frame ( 12) shift: -0.13 -0.64 ...... Frame ( 13) shift: -0.14 -0.55 ...... Frame ( 14) shift: -0.15 -0.45 ...... Frame ( 15) shift: -0.14 -0.38 ...... Frame ( 16) shift: -0.11 -0.33 ...... Frame ( 17) shift: -0.09 -0.29 ...... Frame ( 18) shift: -0.04 -0.24 ...... Frame ( 19) shift: 0.01 -0.17 ...... Frame ( 20) shift: 0.07 -0.11 ...... Frame ( 21) shift: 0.15 -0.03 ...... Frame ( 22) shift: 0.26 0.06 ...... Frame ( 23) shift: 0.36 0.15 ...... Frame ( 24) shift: 0.39 0.18 ...... Frame ( 25) shift: 0.35 0.15 ...... Frame ( 26) shift: 0.31 0.11 ...... Frame ( 27) shift: 0.32 0.11 ...... Frame ( 28) shift: 0.38 0.15 ...... Frame ( 29) shift: 0.45 0.18 ...... Frame ( 30) shift: 0.49 0.22 ...... Frame ( 31) shift: 0.50 0.28 ...... Frame ( 32) shift: 0.52 0.33 ...... Frame ( 33) shift: 0.52 0.39 ...... Frame ( 34) shift: 0.51 0.47 ...... Frame ( 35) shift: 0.50 0.54 ...... Frame ( 36) shift: 0.47 0.62 ...... Frame ( 37) shift: 0.44 0.72 ...... Frame ( 38) shift: 0.40 0.82 ...... Frame ( 39) shift: 0.37 0.92 ...... Frame ( 40) shift: 0.34 1.01 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.737273 Iteration 2 Error: 0.109179 Iteration 3 Error: 0.029620 Align patch 2 23 left Iteration 1 Error: 0.748200 Iteration 2 Error: 0.095398 Iteration 3 Error: 0.030845 Align patch 3 22 left Iteration 1 Error: 0.763874 Iteration 2 Error: 0.154081 Iteration 3 Error: 0.037980 Align patch 4 21 left Iteration 1 Error: 0.832569 Iteration 2 Error: 0.164134 Iteration 3 Error: 0.044255 Align patch 5 20 left Iteration 1 Error: 0.991720 Iteration 2 Error: 0.279298 Iteration 3 Error: 0.109059 Iteration 4 Error: 0.021391 Align patch 6 19 left Iteration 1 Error: 0.871357 Iteration 2 Error: 0.243373 Iteration 3 Error: 0.064330 Iteration 4 Error: 0.021753 Align patch 7 18 left Iteration 1 Error: 0.482096 Iteration 2 Error: 0.083835 Iteration 3 Error: 0.025506 Align patch 8 17 left Iteration 1 Error: 0.469258 Iteration 2 Error: 0.089793 Iteration 3 Error: 0.014251 Align patch 9 16 left Iteration 1 Error: 0.788268 Iteration 2 Error: 0.127386 Iteration 3 Error: 0.034914 Align patch 10 15 left Iteration 1 Error: 0.878250 Iteration 2 Error: 0.183605 Iteration 3 Error: 0.039024 Align patch 11 14 left Iteration 1 Error: 0.962166 Iteration 2 Error: 0.257408 Iteration 3 Error: 0.100797 Iteration 4 Error: 0.046121 Align patch 12 13 left Iteration 1 Error: 0.644269 Iteration 2 Error: 0.137556 Iteration 3 Error: 0.054108 Iteration 4 Error: 0.018968 Align patch 13 12 left Iteration 1 Error: 0.753610 Iteration 2 Error: 0.111228 Iteration 3 Error: 0.020070 Align patch 14 11 left Iteration 1 Error: 0.937502 Iteration 2 Error: 0.139394 Iteration 3 Error: 0.046234 Align patch 15 10 left Iteration 1 Error: 1.266283 Iteration 2 Error: 0.153047 Iteration 3 Error: 0.039754 Align patch 16 9 left Iteration 1 Error: 0.666798 Iteration 2 Error: 0.127536 Iteration 3 Error: 0.023271 Align patch 17 8 left Iteration 1 Error: 1.102290 Iteration 2 Error: 0.127169 Iteration 3 Error: 0.030479 Align patch 18 7 left Iteration 1 Error: 0.742616 Iteration 2 Error: 0.145182 Iteration 3 Error: 0.044157 Align patch 19 6 left Iteration 1 Error: 0.869004 Iteration 2 Error: 0.160238 Iteration 3 Error: 0.043316 Align patch 20 5 left Iteration 1 Error: 0.872768 Iteration 2 Error: 0.100792 Iteration 3 Error: 0.029784 Align patch 21 4 left Iteration 1 Error: 0.844734 Iteration 2 Error: 0.232045 Iteration 3 Error: 0.060517 Iteration 4 Error: 0.022564 Align patch 22 3 left Iteration 1 Error: 0.785402 Iteration 2 Error: 0.124589 Iteration 3 Error: 0.021138 Align patch 23 2 left Iteration 1 Error: 0.769252 Iteration 2 Error: 0.140302 Iteration 3 Error: 0.036739 Align patch 24 1 left Iteration 1 Error: 0.702116 Iteration 2 Error: 0.120649 Iteration 3 Error: 0.038171 Align patch 25 0 left Iteration 1 Error: 0.983068 Iteration 2 Error: 0.207784 Iteration 3 Error: 0.071199 Iteration 4 Error: 0.023278 3D Fitting completed. Patch alignment time: 18.26(sec) Local motion has been corrected. Process thread exits. Computational time: 32.512371 sec Total time: 42.958702 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00003sq_v01_00006hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00003sq_v01_00006hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.633348s Reading file: gc_18feb27f_CTD_00011gr_00003sq_v01_00006hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.761005s ........................................ >>>>>>TIME<<<<<< FFT: 1.414898s Defocus_U Defocus_V Angle CCC 24988.31 25960.97 9.28 0.030389 Final Values Defocus_U Defocus_V Angle CCC 24911.81 25856.37 9.29 0.039055 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00003sq_v01_00006hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00003sq_v01_00006hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.996e-02 CC threshold: 0.734 Mean Std: 37.19 6.47 Num Hot pixels: 197 Hot pixel threshold: 76.03 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.212976 Iteration 2 Error: 0.246033 Iteration 3 Error: 0.051778 Iteration 4 Error: 0.017467 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.16 -0.48 ...... Frame ( 3) shift: -0.33 -0.96 ...... Frame ( 4) shift: -0.49 -1.43 ...... Frame ( 5) shift: -0.66 -1.91 ...... Frame ( 6) shift: -0.71 -2.15 ...... Frame ( 7) shift: -0.64 -2.14 ...... Frame ( 8) shift: -0.57 -2.13 ...... Frame ( 9) shift: -0.51 -2.06 ...... Frame ( 10) shift: -0.46 -1.93 ...... Frame ( 11) shift: -0.41 -1.80 ...... Frame ( 12) shift: -0.35 -1.68 ...... Frame ( 13) shift: -0.28 -1.56 ...... Frame ( 14) shift: -0.20 -1.45 ...... Frame ( 15) shift: -0.19 -1.36 ...... Frame ( 16) shift: -0.23 -1.30 ...... Frame ( 17) shift: -0.27 -1.24 ...... Frame ( 18) shift: -0.26 -1.17 ...... Frame ( 19) shift: -0.21 -1.09 ...... Frame ( 20) shift: -0.15 -1.02 ...... Frame ( 21) shift: -0.06 -0.97 ...... Frame ( 22) shift: 0.05 -0.96 ...... Frame ( 23) shift: 0.16 -0.95 ...... Frame ( 24) shift: 0.20 -0.90 ...... Frame ( 25) shift: 0.18 -0.83 ...... Frame ( 26) shift: 0.15 -0.75 ...... Frame ( 27) shift: 0.12 -0.65 ...... Frame ( 28) shift: 0.09 -0.54 ...... Frame ( 29) shift: 0.06 -0.43 ...... Frame ( 30) shift: 0.05 -0.32 ...... Frame ( 31) shift: 0.08 -0.23 ...... Frame ( 32) shift: 0.10 -0.13 ...... Frame ( 33) shift: 0.15 -0.07 ...... Frame ( 34) shift: 0.23 -0.05 ...... Frame ( 35) shift: 0.31 -0.02 ...... Frame ( 36) shift: 0.35 -0.00 ...... Frame ( 37) shift: 0.35 0.01 ...... Frame ( 38) shift: 0.36 0.02 ...... Frame ( 39) shift: 0.36 0.04 ...... Frame ( 40) shift: 0.36 0.05 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.174326 Iteration 2 Error: 0.187013 Iteration 3 Error: 0.047062 Align patch 2 23 left Iteration 1 Error: 0.531539 Iteration 2 Error: 0.113715 Iteration 3 Error: 0.034156 Align patch 3 22 left Iteration 1 Error: 1.067719 Iteration 2 Error: 0.257177 Iteration 3 Error: 0.088614 Iteration 4 Error: 0.035553 Align patch 4 21 left Iteration 1 Error: 0.645379 Iteration 2 Error: 0.119294 Iteration 3 Error: 0.052094 Iteration 4 Error: 0.009302 Align patch 5 20 left Iteration 1 Error: 1.078920 Iteration 2 Error: 0.159095 Iteration 3 Error: 0.049272 Align patch 6 19 left Iteration 1 Error: 0.959051 Iteration 2 Error: 0.136791 Iteration 3 Error: 0.054173 Iteration 4 Error: 0.021278 Align patch 7 18 left Iteration 1 Error: 0.675931 Iteration 2 Error: 0.110203 Iteration 3 Error: 0.026413 Align patch 8 17 left Iteration 1 Error: 0.599765 Iteration 2 Error: 0.112159 Iteration 3 Error: 0.040766 Align patch 9 16 left Iteration 1 Error: 0.958276 Iteration 2 Error: 0.151721 Iteration 3 Error: 0.032004 Align patch 10 15 left Iteration 1 Error: 1.250015 Iteration 2 Error: 0.173357 Iteration 3 Error: 0.070617 Iteration 4 Error: 0.028106 Align patch 11 14 left Iteration 1 Error: 0.989710 Iteration 2 Error: 0.185590 Iteration 3 Error: 0.059201 Iteration 4 Error: 0.018948 Align patch 12 13 left Iteration 1 Error: 0.751687 Iteration 2 Error: 0.139284 Iteration 3 Error: 0.060371 Iteration 4 Error: 0.017847 Align patch 13 12 left Iteration 1 Error: 0.658126 Iteration 2 Error: 0.094183 Iteration 3 Error: 0.021716 Align patch 14 11 left Iteration 1 Error: 0.786167 Iteration 2 Error: 0.099539 Iteration 3 Error: 0.023761 Align patch 15 10 left Iteration 1 Error: 0.958420 Iteration 2 Error: 0.100215 Iteration 3 Error: 0.018716 Align patch 16 9 left Iteration 1 Error: 0.750084 Iteration 2 Error: 0.094126 Iteration 3 Error: 0.029345 Align patch 17 8 left Iteration 1 Error: 0.868006 Iteration 2 Error: 0.129507 Iteration 3 Error: 0.066999 Iteration 4 Error: 0.039482 Align patch 18 7 left Iteration 1 Error: 1.045506 Iteration 2 Error: 0.115899 Iteration 3 Error: 0.033873 Align patch 19 6 left Iteration 1 Error: 0.810080 Iteration 2 Error: 0.195985 Iteration 3 Error: 0.074450 Iteration 4 Error: 0.030282 Align patch 20 5 left Iteration 1 Error: 1.057793 Iteration 2 Error: 0.132646 Iteration 3 Error: 0.030605 Align patch 21 4 left Iteration 1 Error: 0.649056 Iteration 2 Error: 0.137600 Iteration 3 Error: 0.042962 Align patch 22 3 left Iteration 1 Error: 0.780012 Iteration 2 Error: 0.118079 Iteration 3 Error: 0.035140 Align patch 23 2 left Iteration 1 Error: 1.140615 Iteration 2 Error: 0.143394 Iteration 3 Error: 0.034851 Align patch 24 1 left Iteration 1 Error: 0.797317 Iteration 2 Error: 0.137753 Iteration 3 Error: 0.042822 Align patch 25 0 left Iteration 1 Error: 1.032745 Iteration 2 Error: 0.107471 Iteration 3 Error: 0.031935 3D Fitting completed. Patch alignment time: 19.29(sec) Local motion has been corrected. Process thread exits. Computational time: 31.973906 sec Total time: 39.336540 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00003sq_v01_00006hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00003sq_v01_00006hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.548981s Reading file: gc_18feb27f_CTD_00011gr_00003sq_v01_00006hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.915795s ........................................ >>>>>>TIME<<<<<< FFT: 1.349973s Defocus_U Defocus_V Angle CCC 25736.33 26517.62 6.64 0.030303 Final Values Defocus_U Defocus_V Angle CCC 25728.47 26559.88 6.96 0.041876 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00003sq_v01_00006hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00003sq_v01_00006hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.996e-02 CC threshold: 0.734 Mean Std: 37.24 6.47 Num Hot pixels: 204 Hot pixel threshold: 76.09 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.300218 Iteration 2 Error: 0.223089 Iteration 3 Error: 0.072807 Iteration 4 Error: 0.022527 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.10 -0.27 ...... Frame ( 3) shift: -0.20 -0.54 ...... Frame ( 4) shift: -0.30 -0.81 ...... Frame ( 5) shift: -0.40 -1.09 ...... Frame ( 6) shift: -0.44 -1.22 ...... Frame ( 7) shift: -0.42 -1.20 ...... Frame ( 8) shift: -0.40 -1.19 ...... Frame ( 9) shift: -0.39 -1.10 ...... Frame ( 10) shift: -0.38 -0.94 ...... Frame ( 11) shift: -0.36 -0.78 ...... Frame ( 12) shift: -0.29 -0.64 ...... Frame ( 13) shift: -0.15 -0.52 ...... Frame ( 14) shift: -0.00 -0.40 ...... Frame ( 15) shift: 0.08 -0.29 ...... Frame ( 16) shift: 0.11 -0.18 ...... Frame ( 17) shift: 0.14 -0.06 ...... Frame ( 18) shift: 0.17 0.03 ...... Frame ( 19) shift: 0.22 0.11 ...... Frame ( 20) shift: 0.26 0.19 ...... Frame ( 21) shift: 0.31 0.26 ...... Frame ( 22) shift: 0.36 0.34 ...... Frame ( 23) shift: 0.42 0.41 ...... Frame ( 24) shift: 0.45 0.49 ...... Frame ( 25) shift: 0.47 0.59 ...... Frame ( 26) shift: 0.48 0.68 ...... Frame ( 27) shift: 0.57 0.76 ...... Frame ( 28) shift: 0.74 0.83 ...... Frame ( 29) shift: 0.92 0.89 ...... Frame ( 30) shift: 0.97 0.95 ...... Frame ( 31) shift: 0.91 1.00 ...... Frame ( 32) shift: 0.84 1.05 ...... Frame ( 33) shift: 0.80 1.10 ...... Frame ( 34) shift: 0.77 1.14 ...... Frame ( 35) shift: 0.75 1.19 ...... Frame ( 36) shift: 0.73 1.22 ...... Frame ( 37) shift: 0.71 1.25 ...... Frame ( 38) shift: 0.70 1.28 ...... Frame ( 39) shift: 0.69 1.30 ...... Frame ( 40) shift: 0.67 1.33 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.992580 Iteration 2 Error: 0.216678 Iteration 3 Error: 0.055262 Iteration 4 Error: 0.024730 Align patch 2 23 left Iteration 1 Error: 0.744826 Iteration 2 Error: 0.216975 Iteration 3 Error: 0.069426 Iteration 4 Error: 0.031336 Align patch 3 22 left Iteration 1 Error: 0.713724 Iteration 2 Error: 0.192819 Iteration 3 Error: 0.057773 Iteration 4 Error: 0.018387 Align patch 4 21 left Iteration 1 Error: 0.774093 Iteration 2 Error: 0.173350 Iteration 3 Error: 0.041540 Align patch 5 20 left Iteration 1 Error: 1.294649 Iteration 2 Error: 0.148116 Iteration 3 Error: 0.041211 Align patch 6 19 left Iteration 1 Error: 0.900526 Iteration 2 Error: 0.199944 Iteration 3 Error: 0.049426 Align patch 7 18 left Iteration 1 Error: 1.276016 Iteration 2 Error: 0.120293 Iteration 3 Error: 0.039378 Align patch 8 17 left Iteration 1 Error: 0.964235 Iteration 2 Error: 0.269911 Iteration 3 Error: 0.060044 Iteration 4 Error: 0.021191 Align patch 9 16 left Iteration 1 Error: 0.746997 Iteration 2 Error: 0.107086 Iteration 3 Error: 0.018131 Align patch 10 15 left Iteration 1 Error: 0.736932 Iteration 2 Error: 0.098118 Iteration 3 Error: 0.014906 Align patch 11 14 left Iteration 1 Error: 0.833733 Iteration 2 Error: 0.134819 Iteration 3 Error: 0.037251 Align patch 12 13 left Iteration 1 Error: 0.590790 Iteration 2 Error: 0.081040 Iteration 3 Error: 0.039482 Align patch 13 12 left Iteration 1 Error: 0.861337 Iteration 2 Error: 0.119711 Iteration 3 Error: 0.023665 Align patch 14 11 left Iteration 1 Error: 0.547167 Iteration 2 Error: 0.104676 Iteration 3 Error: 0.028449 Align patch 15 10 left Iteration 1 Error: 0.622950 Iteration 2 Error: 0.106456 Iteration 3 Error: 0.039628 Align patch 16 9 left Iteration 1 Error: 0.905309 Iteration 2 Error: 0.210463 Iteration 3 Error: 0.067995 Iteration 4 Error: 0.022549 Align patch 17 8 left Iteration 1 Error: 0.841977 Iteration 2 Error: 0.183215 Iteration 3 Error: 0.055857 Iteration 4 Error: 0.019268 Align patch 18 7 left Iteration 1 Error: 1.005718 Iteration 2 Error: 0.171806 Iteration 3 Error: 0.051419 Iteration 4 Error: 0.021927 Align patch 19 6 left Iteration 1 Error: 0.624785 Iteration 2 Error: 0.119454 Iteration 3 Error: 0.043025 Align patch 20 5 left Iteration 1 Error: 0.469640 Iteration 2 Error: 0.098032 Iteration 3 Error: 0.028848 Align patch 21 4 left Iteration 1 Error: 0.768832 Iteration 2 Error: 0.145011 Iteration 3 Error: 0.037137 Align patch 22 3 left Iteration 1 Error: 0.937409 Iteration 2 Error: 0.188658 Iteration 3 Error: 0.063739 Iteration 4 Error: 0.021249 Align patch 23 2 left Iteration 1 Error: 1.016526 Iteration 2 Error: 0.173558 Iteration 3 Error: 0.047518 Align patch 24 1 left Iteration 1 Error: 1.298657 Iteration 2 Error: 0.272983 Iteration 3 Error: 0.079706 Iteration 4 Error: 0.028521 Align patch 25 0 left Iteration 1 Error: 1.108972 Iteration 2 Error: 0.283962 Iteration 3 Error: 0.081156 Iteration 4 Error: 0.030900 3D Fitting completed. Patch alignment time: 20.98(sec) Local motion has been corrected. Process thread exits. Computational time: 37.242802 sec Total time: 44.881001 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00003sq_v01_00006hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00003sq_v01_00006hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.834116s Reading file: gc_18feb27f_CTD_00011gr_00003sq_v01_00006hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.711854s ........................................ >>>>>>TIME<<<<<< FFT: 1.198322s Defocus_U Defocus_V Angle CCC 24039.15 23335.97 85.80 0.033013 Final Values Defocus_U Defocus_V Angle CCC 24039.13 23161.10 82.76 0.046061 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00003sq_v01_00006hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00003sq_v01_00006hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 1.000e-01 CC threshold: 0.735 Mean Std: 37.05 6.48 Num Hot pixels: 195 Hot pixel threshold: 75.93 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.940174 Iteration 2 Error: 0.136489 Iteration 3 Error: 0.016786 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.20 -0.37 ...... Frame ( 3) shift: -0.39 -0.75 ...... Frame ( 4) shift: -0.59 -1.12 ...... Frame ( 5) shift: -0.79 -1.50 ...... Frame ( 6) shift: -0.90 -1.69 ...... Frame ( 7) shift: -0.94 -1.69 ...... Frame ( 8) shift: -0.97 -1.70 ...... Frame ( 9) shift: -0.97 -1.64 ...... Frame ( 10) shift: -0.93 -1.51 ...... Frame ( 11) shift: -0.89 -1.39 ...... Frame ( 12) shift: -0.83 -1.31 ...... Frame ( 13) shift: -0.75 -1.27 ...... Frame ( 14) shift: -0.66 -1.24 ...... Frame ( 15) shift: -0.62 -1.20 ...... Frame ( 16) shift: -0.63 -1.15 ...... Frame ( 17) shift: -0.64 -1.10 ...... Frame ( 18) shift: -0.63 -1.02 ...... Frame ( 19) shift: -0.60 -0.91 ...... Frame ( 20) shift: -0.57 -0.80 ...... Frame ( 21) shift: -0.50 -0.73 ...... Frame ( 22) shift: -0.39 -0.69 ...... Frame ( 23) shift: -0.29 -0.65 ...... Frame ( 24) shift: -0.23 -0.62 ...... Frame ( 25) shift: -0.23 -0.60 ...... Frame ( 26) shift: -0.22 -0.58 ...... Frame ( 27) shift: -0.20 -0.56 ...... Frame ( 28) shift: -0.14 -0.55 ...... Frame ( 29) shift: -0.09 -0.54 ...... Frame ( 30) shift: -0.05 -0.51 ...... Frame ( 31) shift: -0.02 -0.48 ...... Frame ( 32) shift: 0.02 -0.44 ...... Frame ( 33) shift: 0.03 -0.40 ...... Frame ( 34) shift: 0.02 -0.35 ...... Frame ( 35) shift: 0.01 -0.30 ...... Frame ( 36) shift: 0.02 -0.28 ...... Frame ( 37) shift: 0.06 -0.29 ...... Frame ( 38) shift: 0.09 -0.30 ...... Frame ( 39) shift: 0.13 -0.31 ...... Frame ( 40) shift: 0.16 -0.32 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.777021 Iteration 2 Error: 0.143930 Iteration 3 Error: 0.021057 Align patch 2 23 left Iteration 1 Error: 0.883437 Iteration 2 Error: 0.156709 Iteration 3 Error: 0.044148 Align patch 3 22 left Iteration 1 Error: 0.998476 Iteration 2 Error: 0.127801 Iteration 3 Error: 0.021006 Align patch 4 21 left Iteration 1 Error: 1.101755 Iteration 2 Error: 0.133874 Iteration 3 Error: 0.023691 Align patch 5 20 left Iteration 1 Error: 0.746328 Iteration 2 Error: 0.097433 Iteration 3 Error: 0.027857 Align patch 6 19 left Iteration 1 Error: 0.962340 Iteration 2 Error: 0.203761 Iteration 3 Error: 0.035684 Align patch 7 18 left Iteration 1 Error: 0.819560 Iteration 2 Error: 0.094418 Iteration 3 Error: 0.025898 Align patch 8 17 left Iteration 1 Error: 0.834275 Iteration 2 Error: 0.093177 Iteration 3 Error: 0.018049 Align patch 9 16 left Iteration 1 Error: 0.905390 Iteration 2 Error: 0.181974 Iteration 3 Error: 0.049775 Align patch 10 15 left Iteration 1 Error: 0.849417 Iteration 2 Error: 0.124712 Iteration 3 Error: 0.037027 Align patch 11 14 left Iteration 1 Error: 0.493928 Iteration 2 Error: 0.072417 Iteration 3 Error: 0.018808 Align patch 12 13 left Iteration 1 Error: 0.588306 Iteration 2 Error: 0.111665 Iteration 3 Error: 0.021525 Align patch 13 12 left Iteration 1 Error: 0.641471 Iteration 2 Error: 0.183492 Iteration 3 Error: 0.054380 Iteration 4 Error: 0.013249 Align patch 14 11 left Iteration 1 Error: 0.735301 Iteration 2 Error: 0.118229 Iteration 3 Error: 0.021813 Align patch 15 10 left Iteration 1 Error: 0.536169 Iteration 2 Error: 0.161194 Iteration 3 Error: 0.027198 Align patch 16 9 left Iteration 1 Error: 0.778198 Iteration 2 Error: 0.078727 Iteration 3 Error: 0.014834 Align patch 17 8 left Iteration 1 Error: 0.860390 Iteration 2 Error: 0.112039 Iteration 3 Error: 0.036178 Align patch 18 7 left Iteration 1 Error: 0.838834 Iteration 2 Error: 0.119775 Iteration 3 Error: 0.017234 Align patch 19 6 left Iteration 1 Error: 0.463554 Iteration 2 Error: 0.073131 Iteration 3 Error: 0.016012 Align patch 20 5 left Iteration 1 Error: 0.507453 Iteration 2 Error: 0.089334 Iteration 3 Error: 0.022301 Align patch 21 4 left Iteration 1 Error: 0.936092 Iteration 2 Error: 0.219486 Iteration 3 Error: 0.077776 Iteration 4 Error: 0.026497 Align patch 22 3 left Iteration 1 Error: 0.560499 Iteration 2 Error: 0.098939 Iteration 3 Error: 0.021868 Align patch 23 2 left Iteration 1 Error: 0.594506 Iteration 2 Error: 0.077832 Iteration 3 Error: 0.015329 Align patch 24 1 left Iteration 1 Error: 0.768044 Iteration 2 Error: 0.149182 Iteration 3 Error: 0.030810 Align patch 25 0 left Iteration 1 Error: 0.787134 Iteration 2 Error: 0.084284 Iteration 3 Error: 0.017890 3D Fitting completed. Patch alignment time: 18.20(sec) Local motion has been corrected. Process thread exits. Computational time: 39.730534 sec Total time: 49.304630 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00003sq_v01_00006hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00003sq_v01_00006hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.760678s Reading file: gc_18feb27f_CTD_00011gr_00003sq_v01_00006hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.099901s ........................................ >>>>>>TIME<<<<<< FFT: 1.255377s Defocus_U Defocus_V Angle CCC 26209.01 25314.46 85.03 0.033267 Final Values Defocus_U Defocus_V Angle CCC 26216.82 25278.53 85.35 0.046157 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00003sq_v01_00007hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00003sq_v01_00007hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.991e-02 CC threshold: 0.734 Mean Std: 36.77 6.43 Num Hot pixels: 198 Hot pixel threshold: 75.37 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.925558 Iteration 2 Error: 0.240124 Iteration 3 Error: 0.054757 Iteration 4 Error: 0.018284 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.04 -0.26 ...... Frame ( 3) shift: 0.09 -0.51 ...... Frame ( 4) shift: 0.13 -0.77 ...... Frame ( 5) shift: 0.17 -1.02 ...... Frame ( 6) shift: 0.22 -1.14 ...... Frame ( 7) shift: 0.25 -1.13 ...... Frame ( 8) shift: 0.29 -1.11 ...... Frame ( 9) shift: 0.32 -1.05 ...... Frame ( 10) shift: 0.33 -0.95 ...... Frame ( 11) shift: 0.35 -0.85 ...... Frame ( 12) shift: 0.38 -0.78 ...... Frame ( 13) shift: 0.44 -0.73 ...... Frame ( 14) shift: 0.50 -0.68 ...... Frame ( 15) shift: 0.53 -0.60 ...... Frame ( 16) shift: 0.53 -0.50 ...... Frame ( 17) shift: 0.53 -0.40 ...... Frame ( 18) shift: 0.54 -0.33 ...... Frame ( 19) shift: 0.57 -0.29 ...... Frame ( 20) shift: 0.60 -0.24 ...... Frame ( 21) shift: 0.62 -0.19 ...... Frame ( 22) shift: 0.62 -0.13 ...... Frame ( 23) shift: 0.62 -0.07 ...... Frame ( 24) shift: 0.68 0.03 ...... Frame ( 25) shift: 0.79 0.17 ...... Frame ( 26) shift: 0.90 0.31 ...... Frame ( 27) shift: 0.95 0.35 ...... Frame ( 28) shift: 0.93 0.29 ...... Frame ( 29) shift: 0.91 0.24 ...... Frame ( 30) shift: 0.93 0.25 ...... Frame ( 31) shift: 0.99 0.34 ...... Frame ( 32) shift: 1.04 0.43 ...... Frame ( 33) shift: 1.10 0.48 ...... Frame ( 34) shift: 1.17 0.51 ...... Frame ( 35) shift: 1.24 0.53 ...... Frame ( 36) shift: 1.25 0.57 ...... Frame ( 37) shift: 1.21 0.63 ...... Frame ( 38) shift: 1.16 0.69 ...... Frame ( 39) shift: 1.11 0.74 ...... Frame ( 40) shift: 1.07 0.80 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.842972 Iteration 2 Error: 0.156859 Iteration 3 Error: 0.056573 Iteration 4 Error: 0.016053 Align patch 2 23 left Iteration 1 Error: 0.939894 Iteration 2 Error: 0.333952 Iteration 3 Error: 0.097246 Iteration 4 Error: 0.057962 Iteration 5 Error: 0.037396 Align patch 3 22 left Iteration 1 Error: 0.773995 Iteration 2 Error: 0.113843 Iteration 3 Error: 0.025390 Align patch 4 21 left Iteration 1 Error: 0.573256 Iteration 2 Error: 0.112165 Iteration 3 Error: 0.033224 Align patch 5 20 left Iteration 1 Error: 0.907056 Iteration 2 Error: 0.203358 Iteration 3 Error: 0.040393 Align patch 6 19 left Iteration 1 Error: 1.024040 Iteration 2 Error: 0.173687 Iteration 3 Error: 0.033098 Align patch 7 18 left Iteration 1 Error: 1.067771 Iteration 2 Error: 0.283265 Iteration 3 Error: 0.101817 Iteration 4 Error: 0.039153 Align patch 8 17 left Iteration 1 Error: 0.986198 Iteration 2 Error: 0.252942 Iteration 3 Error: 0.048804 Align patch 9 16 left Iteration 1 Error: 1.062612 Iteration 2 Error: 0.177767 Iteration 3 Error: 0.075625 Iteration 4 Error: 0.021981 Align patch 10 15 left Iteration 1 Error: 0.822241 Iteration 2 Error: 0.111678 Iteration 3 Error: 0.028652 Align patch 11 14 left Iteration 1 Error: 0.882631 Iteration 2 Error: 0.217531 Iteration 3 Error: 0.066078 Iteration 4 Error: 0.024121 Align patch 12 13 left Iteration 1 Error: 0.927441 Iteration 2 Error: 0.184667 Iteration 3 Error: 0.052825 Iteration 4 Error: 0.021087 Align patch 13 12 left Iteration 1 Error: 0.849345 Iteration 2 Error: 0.152307 Iteration 3 Error: 0.040955 Align patch 14 11 left Iteration 1 Error: 0.887276 Iteration 2 Error: 0.213946 Iteration 3 Error: 0.071376 Iteration 4 Error: 0.026230 Align patch 15 10 left Iteration 1 Error: 1.194262 Iteration 2 Error: 0.142838 Iteration 3 Error: 0.041879 Align patch 16 9 left Iteration 1 Error: 0.726709 Iteration 2 Error: 0.120795 Iteration 3 Error: 0.034342 Align patch 17 8 left Iteration 1 Error: 0.600278 Iteration 2 Error: 0.088976 Iteration 3 Error: 0.027868 Align patch 18 7 left Iteration 1 Error: 0.791808 Iteration 2 Error: 0.115140 Iteration 3 Error: 0.035368 Align patch 19 6 left Iteration 1 Error: 0.695904 Iteration 2 Error: 0.178612 Iteration 3 Error: 0.033720 Align patch 20 5 left Iteration 1 Error: 0.777774 Iteration 2 Error: 0.178777 Iteration 3 Error: 0.054992 Iteration 4 Error: 0.015646 Align patch 21 4 left Iteration 1 Error: 0.962380 Iteration 2 Error: 0.159987 Iteration 3 Error: 0.049223 Align patch 22 3 left Iteration 1 Error: 0.660842 Iteration 2 Error: 0.165551 Iteration 3 Error: 0.047632 Align patch 23 2 left Iteration 1 Error: 0.675407 Iteration 2 Error: 0.166532 Iteration 3 Error: 0.029777 Align patch 24 1 left Iteration 1 Error: 0.544791 Iteration 2 Error: 0.166819 Iteration 3 Error: 0.081251 Iteration 4 Error: 0.045947 Align patch 25 0 left Iteration 1 Error: 0.676619 Iteration 2 Error: 0.101442 Iteration 3 Error: 0.033069 3D Fitting completed. Patch alignment time: 17.86(sec) Local motion has been corrected. Process thread exits. Computational time: 33.130875 sec Total time: 40.968739 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00003sq_v01_00007hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00003sq_v01_00007hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.079427s Reading file: gc_18feb27f_CTD_00011gr_00003sq_v01_00007hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.677393s ........................................ >>>>>>TIME<<<<<< FFT: 1.114009s Defocus_U Defocus_V Angle CCC 25287.11 25908.21 6.88 0.029869 Final Values Defocus_U Defocus_V Angle CCC 25294.94 25803.55 11.28 0.039395 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00003sq_v01_00007hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00003sq_v01_00007hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.992e-02 CC threshold: 0.734 Mean Std: 36.61 6.42 Num Hot pixels: 192 Hot pixel threshold: 75.13 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.060974 Iteration 2 Error: 0.210390 Iteration 3 Error: 0.036642 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.14 -0.45 ...... Frame ( 3) shift: 0.27 -0.89 ...... Frame ( 4) shift: 0.41 -1.34 ...... Frame ( 5) shift: 0.55 -1.78 ...... Frame ( 6) shift: 0.65 -2.01 ...... Frame ( 7) shift: 0.71 -2.02 ...... Frame ( 8) shift: 0.77 -2.03 ...... Frame ( 9) shift: 0.81 -1.98 ...... Frame ( 10) shift: 0.82 -1.88 ...... Frame ( 11) shift: 0.82 -1.77 ...... Frame ( 12) shift: 0.87 -1.64 ...... Frame ( 13) shift: 0.95 -1.50 ...... Frame ( 14) shift: 1.04 -1.35 ...... Frame ( 15) shift: 1.07 -1.24 ...... Frame ( 16) shift: 1.05 -1.17 ...... Frame ( 17) shift: 1.03 -1.10 ...... Frame ( 18) shift: 1.06 -1.05 ...... Frame ( 19) shift: 1.13 -1.01 ...... Frame ( 20) shift: 1.19 -0.97 ...... Frame ( 21) shift: 1.24 -0.90 ...... Frame ( 22) shift: 1.27 -0.81 ...... Frame ( 23) shift: 1.30 -0.72 ...... Frame ( 24) shift: 1.33 -0.67 ...... Frame ( 25) shift: 1.34 -0.65 ...... Frame ( 26) shift: 1.35 -0.63 ...... Frame ( 27) shift: 1.37 -0.58 ...... Frame ( 28) shift: 1.40 -0.50 ...... Frame ( 29) shift: 1.44 -0.43 ...... Frame ( 30) shift: 1.46 -0.38 ...... Frame ( 31) shift: 1.48 -0.36 ...... Frame ( 32) shift: 1.49 -0.34 ...... Frame ( 33) shift: 1.51 -0.36 ...... Frame ( 34) shift: 1.52 -0.41 ...... Frame ( 35) shift: 1.53 -0.47 ...... Frame ( 36) shift: 1.55 -0.46 ...... Frame ( 37) shift: 1.56 -0.38 ...... Frame ( 38) shift: 1.58 -0.31 ...... Frame ( 39) shift: 1.59 -0.24 ...... Frame ( 40) shift: 1.61 -0.17 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.318486 Iteration 2 Error: 0.161436 Iteration 3 Error: 0.038615 Align patch 2 23 left Iteration 1 Error: 1.070925 Iteration 2 Error: 0.278549 Iteration 3 Error: 0.072052 Iteration 4 Error: 0.026441 Align patch 3 22 left Iteration 1 Error: 1.198194 Iteration 2 Error: 0.221855 Iteration 3 Error: 0.044019 Align patch 4 21 left Iteration 1 Error: 0.746780 Iteration 2 Error: 0.266309 Iteration 3 Error: 0.042355 Align patch 5 20 left Iteration 1 Error: 0.694237 Iteration 2 Error: 0.225299 Iteration 3 Error: 0.055675 Iteration 4 Error: 0.035101 Align patch 6 19 left Iteration 1 Error: 1.159357 Iteration 2 Error: 0.210578 Iteration 3 Error: 0.059002 Iteration 4 Error: 0.021740 Align patch 7 18 left Iteration 1 Error: 0.693104 Iteration 2 Error: 0.100623 Iteration 3 Error: 0.019399 Align patch 8 17 left Iteration 1 Error: 0.874646 Iteration 2 Error: 0.208120 Iteration 3 Error: 0.043358 Align patch 9 16 left Iteration 1 Error: 0.669297 Iteration 2 Error: 0.179440 Iteration 3 Error: 0.057005 Iteration 4 Error: 0.023475 Align patch 10 15 left Iteration 1 Error: 0.738180 Iteration 2 Error: 0.161645 Iteration 3 Error: 0.067150 Iteration 4 Error: 0.026659 Align patch 11 14 left Iteration 1 Error: 0.972259 Iteration 2 Error: 0.159648 Iteration 3 Error: 0.032309 Align patch 12 13 left Iteration 1 Error: 1.048451 Iteration 2 Error: 0.178302 Iteration 3 Error: 0.042403 Align patch 13 12 left Iteration 1 Error: 0.673326 Iteration 2 Error: 0.138140 Iteration 3 Error: 0.051271 Iteration 4 Error: 0.016698 Align patch 14 11 left Iteration 1 Error: 1.040941 Iteration 2 Error: 0.167564 Iteration 3 Error: 0.037855 Align patch 15 10 left Iteration 1 Error: 1.017948 Iteration 2 Error: 0.167355 Iteration 3 Error: 0.041868 Align patch 16 9 left Iteration 1 Error: 0.740977 Iteration 2 Error: 0.110128 Iteration 3 Error: 0.028576 Align patch 17 8 left Iteration 1 Error: 0.755677 Iteration 2 Error: 0.116670 Iteration 3 Error: 0.026480 Align patch 18 7 left Iteration 1 Error: 1.260956 Iteration 2 Error: 0.269204 Iteration 3 Error: 0.064373 Iteration 4 Error: 0.032455 Align patch 19 6 left Iteration 1 Error: 0.777488 Iteration 2 Error: 0.117240 Iteration 3 Error: 0.024576 Align patch 20 5 left Iteration 1 Error: 0.929527 Iteration 2 Error: 0.219438 Iteration 3 Error: 0.059506 Iteration 4 Error: 0.025754 Align patch 21 4 left Iteration 1 Error: 0.789572 Iteration 2 Error: 0.179042 Iteration 3 Error: 0.043160 Align patch 22 3 left Iteration 1 Error: 0.689448 Iteration 2 Error: 0.162727 Iteration 3 Error: 0.056924 Iteration 4 Error: 0.023163 Align patch 23 2 left Iteration 1 Error: 0.822268 Iteration 2 Error: 0.101847 Iteration 3 Error: 0.019419 Align patch 24 1 left Iteration 1 Error: 0.972655 Iteration 2 Error: 0.222015 Iteration 3 Error: 0.049526 Align patch 25 0 left Iteration 1 Error: 0.919549 Iteration 2 Error: 0.166175 Iteration 3 Error: 0.068859 Iteration 4 Error: 0.027198 3D Fitting completed. Patch alignment time: 18.13(sec) Local motion has been corrected. Process thread exits. Computational time: 32.517467 sec Total time: 40.773697 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00003sq_v01_00007hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00003sq_v01_00007hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.601769s Reading file: gc_18feb27f_CTD_00011gr_00003sq_v01_00007hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.364046s ........................................ >>>>>>TIME<<<<<< FFT: 1.457155s Defocus_U Defocus_V Angle CCC 23984.38 24882.81 8.51 0.028743 Final Values Defocus_U Defocus_V Angle CCC 23920.29 24843.78 12.91 0.040365 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00003sq_v01_00007hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00003sq_v01_00007hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 37.24 6.48 Num Hot pixels: 190 Hot pixel threshold: 76.14 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.824641 Iteration 2 Error: 0.163476 Iteration 3 Error: 0.026625 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.08 -0.44 ...... Frame ( 3) shift: -0.16 -0.89 ...... Frame ( 4) shift: -0.24 -1.33 ...... Frame ( 5) shift: -0.32 -1.77 ...... Frame ( 6) shift: -0.34 -2.01 ...... Frame ( 7) shift: -0.30 -2.06 ...... Frame ( 8) shift: -0.25 -2.10 ...... Frame ( 9) shift: -0.27 -2.12 ...... Frame ( 10) shift: -0.35 -2.13 ...... Frame ( 11) shift: -0.42 -2.13 ...... Frame ( 12) shift: -0.44 -2.14 ...... Frame ( 13) shift: -0.41 -2.15 ...... Frame ( 14) shift: -0.37 -2.16 ...... Frame ( 15) shift: -0.32 -2.08 ...... Frame ( 16) shift: -0.25 -1.93 ...... Frame ( 17) shift: -0.19 -1.77 ...... Frame ( 18) shift: -0.15 -1.66 ...... Frame ( 19) shift: -0.14 -1.59 ...... Frame ( 20) shift: -0.13 -1.52 ...... Frame ( 21) shift: -0.15 -1.46 ...... Frame ( 22) shift: -0.19 -1.40 ...... Frame ( 23) shift: -0.22 -1.34 ...... Frame ( 24) shift: -0.21 -1.25 ...... Frame ( 25) shift: -0.15 -1.12 ...... Frame ( 26) shift: -0.09 -0.99 ...... Frame ( 27) shift: -0.07 -0.89 ...... Frame ( 28) shift: -0.08 -0.82 ...... Frame ( 29) shift: -0.08 -0.75 ...... Frame ( 30) shift: -0.09 -0.72 ...... Frame ( 31) shift: -0.10 -0.75 ...... Frame ( 32) shift: -0.10 -0.77 ...... Frame ( 33) shift: -0.12 -0.76 ...... Frame ( 34) shift: -0.16 -0.72 ...... Frame ( 35) shift: -0.20 -0.68 ...... Frame ( 36) shift: -0.20 -0.63 ...... Frame ( 37) shift: -0.18 -0.59 ...... Frame ( 38) shift: -0.15 -0.54 ...... Frame ( 39) shift: -0.13 -0.49 ...... Frame ( 40) shift: -0.10 -0.45 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.868804 Iteration 2 Error: 0.097455 Iteration 3 Error: 0.028287 Align patch 2 23 left Iteration 1 Error: 1.330337 Iteration 2 Error: 0.172193 Iteration 3 Error: 0.036490 Align patch 3 22 left Iteration 1 Error: 1.125552 Iteration 2 Error: 0.219560 Iteration 3 Error: 0.024161 Align patch 4 21 left Iteration 1 Error: 0.629087 Iteration 2 Error: 0.116430 Iteration 3 Error: 0.023903 Align patch 5 20 left Iteration 1 Error: 0.944571 Iteration 2 Error: 0.237404 Iteration 3 Error: 0.060541 Iteration 4 Error: 0.021386 Align patch 6 19 left Iteration 1 Error: 0.762276 Iteration 2 Error: 0.113764 Iteration 3 Error: 0.016046 Align patch 7 18 left Iteration 1 Error: 0.840952 Iteration 2 Error: 0.113146 Iteration 3 Error: 0.024005 Align patch 8 17 left Iteration 1 Error: 0.631646 Iteration 2 Error: 0.112734 Iteration 3 Error: 0.018492 Align patch 9 16 left Iteration 1 Error: 0.844907 Iteration 2 Error: 0.100404 Iteration 3 Error: 0.035078 Align patch 10 15 left Iteration 1 Error: 0.729962 Iteration 2 Error: 0.129633 Iteration 3 Error: 0.037130 Align patch 11 14 left Iteration 1 Error: 1.200181 Iteration 2 Error: 0.202907 Iteration 3 Error: 0.058198 Iteration 4 Error: 0.015260 Align patch 12 13 left Iteration 1 Error: 0.822631 Iteration 2 Error: 0.130523 Iteration 3 Error: 0.037592 Align patch 13 12 left Iteration 1 Error: 0.527397 Iteration 2 Error: 0.115047 Iteration 3 Error: 0.032381 Align patch 14 11 left Iteration 1 Error: 0.806342 Iteration 2 Error: 0.225823 Iteration 3 Error: 0.057964 Iteration 4 Error: 0.012519 Align patch 15 10 left Iteration 1 Error: 0.680932 Iteration 2 Error: 0.079210 Iteration 3 Error: 0.016533 Align patch 16 9 left Iteration 1 Error: 1.290073 Iteration 2 Error: 0.146698 Iteration 3 Error: 0.024126 Align patch 17 8 left Iteration 1 Error: 0.909704 Iteration 2 Error: 0.133711 Iteration 3 Error: 0.024568 Align patch 18 7 left Iteration 1 Error: 0.782161 Iteration 2 Error: 0.148881 Iteration 3 Error: 0.058541 Iteration 4 Error: 0.017490 Align patch 19 6 left Iteration 1 Error: 0.637859 Iteration 2 Error: 0.090012 Iteration 3 Error: 0.026045 Align patch 20 5 left Iteration 1 Error: 0.768580 Iteration 2 Error: 0.081942 Iteration 3 Error: 0.019974 Align patch 21 4 left Iteration 1 Error: 0.741438 Iteration 2 Error: 0.116467 Iteration 3 Error: 0.033222 Align patch 22 3 left Iteration 1 Error: 0.824656 Iteration 2 Error: 0.140320 Iteration 3 Error: 0.032292 Align patch 23 2 left Iteration 1 Error: 1.023935 Iteration 2 Error: 0.109834 Iteration 3 Error: 0.026455 Align patch 24 1 left Iteration 1 Error: 0.735888 Iteration 2 Error: 0.122459 Iteration 3 Error: 0.036477 Align patch 25 0 left Iteration 1 Error: 0.966499 Iteration 2 Error: 0.194894 Iteration 3 Error: 0.042905 3D Fitting completed. Patch alignment time: 16.11(sec) Local motion has been corrected. Process thread exits. Computational time: 30.482080 sec Total time: 38.455696 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00003sq_v01_00007hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00003sq_v01_00007hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.462318s Reading file: gc_18feb27f_CTD_00011gr_00003sq_v01_00007hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.564152s ........................................ >>>>>>TIME<<<<<< FFT: 1.197423s Defocus_U Defocus_V Angle CCC 28385.76 27817.39 86.76 0.032398 Final Values Defocus_U Defocus_V Angle CCC 28445.11 27767.43 86.47 0.048314 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00003sq_v01_00007hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00003sq_v01_00007hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 1.000e-01 CC threshold: 0.734 Mean Std: 37.56 6.52 Num Hot pixels: 204 Hot pixel threshold: 76.68 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.059012 Iteration 2 Error: 0.150087 Iteration 3 Error: 0.021699 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.01 -0.53 ...... Frame ( 3) shift: 0.02 -1.06 ...... Frame ( 4) shift: 0.03 -1.59 ...... Frame ( 5) shift: 0.04 -2.13 ...... Frame ( 6) shift: 0.08 -2.38 ...... Frame ( 7) shift: 0.14 -2.36 ...... Frame ( 8) shift: 0.21 -2.34 ...... Frame ( 9) shift: 0.25 -2.30 ...... Frame ( 10) shift: 0.27 -2.24 ...... Frame ( 11) shift: 0.28 -2.19 ...... Frame ( 12) shift: 0.26 -2.17 ...... Frame ( 13) shift: 0.20 -2.17 ...... Frame ( 14) shift: 0.14 -2.17 ...... Frame ( 15) shift: 0.10 -2.16 ...... Frame ( 16) shift: 0.08 -2.14 ...... Frame ( 17) shift: 0.07 -2.12 ...... Frame ( 18) shift: 0.05 -2.07 ...... Frame ( 19) shift: 0.03 -2.01 ...... Frame ( 20) shift: 0.01 -1.94 ...... Frame ( 21) shift: -0.03 -1.87 ...... Frame ( 22) shift: -0.09 -1.79 ...... Frame ( 23) shift: -0.15 -1.72 ...... Frame ( 24) shift: -0.17 -1.66 ...... Frame ( 25) shift: -0.15 -1.63 ...... Frame ( 26) shift: -0.13 -1.59 ...... Frame ( 27) shift: -0.12 -1.57 ...... Frame ( 28) shift: -0.12 -1.55 ...... Frame ( 29) shift: -0.12 -1.54 ...... Frame ( 30) shift: -0.08 -1.48 ...... Frame ( 31) shift: -0.01 -1.36 ...... Frame ( 32) shift: 0.06 -1.25 ...... Frame ( 33) shift: 0.09 -1.18 ...... Frame ( 34) shift: 0.09 -1.15 ...... Frame ( 35) shift: 0.09 -1.12 ...... Frame ( 36) shift: 0.10 -1.09 ...... Frame ( 37) shift: 0.14 -1.05 ...... Frame ( 38) shift: 0.17 -1.02 ...... Frame ( 39) shift: 0.21 -0.98 ...... Frame ( 40) shift: 0.24 -0.94 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.068388 Iteration 2 Error: 0.087672 Iteration 3 Error: 0.022335 Align patch 2 23 left Iteration 1 Error: 0.919535 Iteration 2 Error: 0.143456 Iteration 3 Error: 0.028708 Align patch 3 22 left Iteration 1 Error: 1.147185 Iteration 2 Error: 0.290332 Iteration 3 Error: 0.102038 Iteration 4 Error: 0.042274 Align patch 4 21 left Iteration 1 Error: 1.342828 Iteration 2 Error: 0.131596 Iteration 3 Error: 0.026307 Align patch 5 20 left Iteration 1 Error: 0.906065 Iteration 2 Error: 0.192327 Iteration 3 Error: 0.058636 Iteration 4 Error: 0.019039 Align patch 6 19 left Iteration 1 Error: 0.520925 Iteration 2 Error: 0.081007 Iteration 3 Error: 0.017648 Align patch 7 18 left Iteration 1 Error: 0.775493 Iteration 2 Error: 0.094025 Iteration 3 Error: 0.025060 Align patch 8 17 left Iteration 1 Error: 1.566315 Iteration 2 Error: 0.579416 Iteration 3 Error: 0.219120 Iteration 4 Error: 0.137524 Iteration 5 Error: 0.072924 Align patch 8 17 left Iteration 1 Error: 0.882379 Iteration 2 Error: 0.091992 Iteration 3 Error: 0.017043 Align patch 9 16 left Iteration 1 Error: 1.018541 Iteration 2 Error: 0.098824 Iteration 3 Error: 0.028700 Align patch 10 15 left Iteration 1 Error: 0.806893 Iteration 2 Error: 0.098669 Iteration 3 Error: 0.027852 Align patch 11 14 left Iteration 1 Error: 0.880537 Iteration 2 Error: 0.139259 Iteration 3 Error: 0.030000 Align patch 12 13 left Iteration 1 Error: 1.082667 Iteration 2 Error: 0.306160 Iteration 3 Error: 0.055328 Iteration 4 Error: 0.020692 Align patch 13 12 left Iteration 1 Error: 0.920807 Iteration 2 Error: 0.136721 Iteration 3 Error: 0.026463 Align patch 14 11 left Iteration 1 Error: 1.044098 Iteration 2 Error: 0.090593 Iteration 3 Error: 0.012734 Align patch 15 10 left Iteration 1 Error: 1.264799 Iteration 2 Error: 0.125340 Iteration 3 Error: 0.036853 Align patch 16 9 left Iteration 1 Error: 0.719287 Iteration 2 Error: 0.090575 Iteration 3 Error: 0.017606 Align patch 17 8 left Iteration 1 Error: 0.669725 Iteration 2 Error: 0.065150 Iteration 3 Error: 0.019187 Align patch 18 7 left Iteration 1 Error: 0.918131 Iteration 2 Error: 0.156804 Iteration 3 Error: 0.029189 Align patch 19 6 left Iteration 1 Error: 0.825968 Iteration 2 Error: 0.221981 Iteration 3 Error: 0.073311 Iteration 4 Error: 0.027581 Align patch 20 5 left Iteration 1 Error: 0.875749 Iteration 2 Error: 0.179580 Iteration 3 Error: 0.037732 Align patch 21 4 left Iteration 1 Error: 1.357490 Iteration 2 Error: 0.181744 Iteration 3 Error: 0.048112 Align patch 22 3 left Iteration 1 Error: 1.083254 Iteration 2 Error: 0.113545 Iteration 3 Error: 0.028623 Align patch 23 2 left Iteration 1 Error: 0.850821 Iteration 2 Error: 0.253993 Iteration 3 Error: 0.063597 Iteration 4 Error: 0.026482 Align patch 24 1 left Iteration 1 Error: 0.715901 Iteration 2 Error: 0.120729 Iteration 3 Error: 0.032433 Align patch 25 0 left Iteration 1 Error: 0.889788 Iteration 2 Error: 0.197295 Iteration 3 Error: 0.028494 3D Fitting completed. Patch alignment time: 13.65(sec) Local motion has been corrected. Process thread exits. Computational time: 25.953007 sec Total time: 35.995853 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00003sq_v01_00007hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00003sq_v01_00007hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.669938s Reading file: gc_18feb27f_CTD_00011gr_00003sq_v01_00007hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.310289s ........................................ >>>>>>TIME<<<<<< FFT: 1.076458s Defocus_U Defocus_V Angle CCC 29144.57 28492.15 78.51 0.027150 Final Values Defocus_U Defocus_V Angle CCC 29150.82 28485.90 76.96 0.040387 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00003sq_v01_00008hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00003sq_v01_00008hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.994e-02 CC threshold: 0.734 Mean Std: 37.17 6.47 Num Hot pixels: 200 Hot pixel threshold: 76.00 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.933797 Iteration 2 Error: 0.271450 Iteration 3 Error: 0.066287 Iteration 4 Error: 0.022113 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.16 -0.47 ...... Frame ( 3) shift: 0.33 -0.95 ...... Frame ( 4) shift: 0.49 -1.42 ...... Frame ( 5) shift: 0.65 -1.90 ...... Frame ( 6) shift: 0.74 -2.02 ...... Frame ( 7) shift: 0.74 -1.79 ...... Frame ( 8) shift: 0.74 -1.56 ...... Frame ( 9) shift: 0.75 -1.35 ...... Frame ( 10) shift: 0.76 -1.16 ...... Frame ( 11) shift: 0.77 -0.96 ...... Frame ( 12) shift: 0.82 -0.80 ...... Frame ( 13) shift: 0.90 -0.68 ...... Frame ( 14) shift: 0.99 -0.55 ...... Frame ( 15) shift: 1.03 -0.43 ...... Frame ( 16) shift: 1.04 -0.34 ...... Frame ( 17) shift: 1.05 -0.24 ...... Frame ( 18) shift: 1.07 -0.14 ...... Frame ( 19) shift: 1.10 -0.03 ...... Frame ( 20) shift: 1.12 0.07 ...... Frame ( 21) shift: 1.10 0.14 ...... Frame ( 22) shift: 1.03 0.19 ...... Frame ( 23) shift: 0.96 0.24 ...... Frame ( 24) shift: 0.95 0.34 ...... Frame ( 25) shift: 0.98 0.51 ...... Frame ( 26) shift: 1.02 0.68 ...... Frame ( 27) shift: 1.06 0.80 ...... Frame ( 28) shift: 1.10 0.87 ...... Frame ( 29) shift: 1.14 0.93 ...... Frame ( 30) shift: 1.20 0.99 ...... Frame ( 31) shift: 1.26 1.05 ...... Frame ( 32) shift: 1.33 1.10 ...... Frame ( 33) shift: 1.34 1.17 ...... Frame ( 34) shift: 1.29 1.25 ...... Frame ( 35) shift: 1.23 1.33 ...... Frame ( 36) shift: 1.22 1.37 ...... Frame ( 37) shift: 1.25 1.37 ...... Frame ( 38) shift: 1.27 1.36 ...... Frame ( 39) shift: 1.30 1.36 ...... Frame ( 40) shift: 1.32 1.36 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.997118 Iteration 2 Error: 0.239367 Iteration 3 Error: 0.052717 Iteration 4 Error: 0.022264 Align patch 2 23 left Iteration 1 Error: 1.365470 Iteration 2 Error: 0.304843 Iteration 3 Error: 0.088212 Iteration 4 Error: 0.040117 Align patch 3 22 left Iteration 1 Error: 0.832931 Iteration 2 Error: 0.224334 Iteration 3 Error: 0.050214 Iteration 4 Error: 0.023797 Align patch 4 21 left Iteration 1 Error: 1.001163 Iteration 2 Error: 0.261447 Iteration 3 Error: 0.095806 Iteration 4 Error: 0.063738 Iteration 5 Error: 0.024591 Align patch 5 20 left Iteration 1 Error: 1.060489 Iteration 2 Error: 0.265776 Iteration 3 Error: 0.093614 Iteration 4 Error: 0.050488 Iteration 5 Error: 0.026291 Align patch 6 19 left Iteration 1 Error: 0.930273 Iteration 2 Error: 0.206769 Iteration 3 Error: 0.044081 Align patch 7 18 left Iteration 1 Error: 1.010822 Iteration 2 Error: 0.138452 Iteration 3 Error: 0.053942 Iteration 4 Error: 0.033582 Align patch 8 17 left Iteration 1 Error: 1.035680 Iteration 2 Error: 0.130407 Iteration 3 Error: 0.047081 Align patch 9 16 left Iteration 1 Error: 0.854025 Iteration 2 Error: 0.173695 Iteration 3 Error: 0.050588 Iteration 4 Error: 0.017874 Align patch 10 15 left Iteration 1 Error: 0.919104 Iteration 2 Error: 0.190475 Iteration 3 Error: 0.035773 Align patch 11 14 left Iteration 1 Error: 1.175420 Iteration 2 Error: 0.185345 Iteration 3 Error: 0.062595 Iteration 4 Error: 0.020418 Align patch 12 13 left Iteration 1 Error: 0.780385 Iteration 2 Error: 0.112809 Iteration 3 Error: 0.027236 Align patch 13 12 left Iteration 1 Error: 0.749940 Iteration 2 Error: 0.135004 Iteration 3 Error: 0.036027 Align patch 14 11 left Iteration 1 Error: 0.916004 Iteration 2 Error: 0.161766 Iteration 3 Error: 0.034793 Align patch 15 10 left Iteration 1 Error: 0.935810 Iteration 2 Error: 0.196699 Iteration 3 Error: 0.041704 Align patch 16 9 left Iteration 1 Error: 1.134943 Iteration 2 Error: 0.101468 Iteration 3 Error: 0.019956 Align patch 17 8 left Iteration 1 Error: 0.757095 Iteration 2 Error: 0.144829 Iteration 3 Error: 0.040807 Align patch 18 7 left Iteration 1 Error: 0.714833 Iteration 2 Error: 0.125909 Iteration 3 Error: 0.039257 Align patch 19 6 left Iteration 1 Error: 0.871092 Iteration 2 Error: 0.096149 Iteration 3 Error: 0.017758 Align patch 20 5 left Iteration 1 Error: 0.941996 Iteration 2 Error: 0.217917 Iteration 3 Error: 0.056358 Iteration 4 Error: 0.016047 Align patch 21 4 left Iteration 1 Error: 0.860536 Iteration 2 Error: 0.240523 Iteration 3 Error: 0.076684 Iteration 4 Error: 0.026251 Align patch 22 3 left Iteration 1 Error: 1.093027 Iteration 2 Error: 0.216620 Iteration 3 Error: 0.031981 Align patch 23 2 left Iteration 1 Error: 0.636783 Iteration 2 Error: 0.166293 Iteration 3 Error: 0.052052 Iteration 4 Error: 0.014784 Align patch 24 1 left Iteration 1 Error: 0.898240 Iteration 2 Error: 0.148962 Iteration 3 Error: 0.031505 Align patch 25 0 left Iteration 1 Error: 1.046537 Iteration 2 Error: 0.215164 Iteration 3 Error: 0.044843 3D Fitting completed. Patch alignment time: 13.37(sec) Local motion has been corrected. Process thread exits. Computational time: 22.715534 sec Total time: 29.407869 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00003sq_v01_00008hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00003sq_v01_00008hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.656521s Reading file: gc_18feb27f_CTD_00011gr_00003sq_v01_00008hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.126995s ........................................ >>>>>>TIME<<<<<< FFT: 1.009549s Defocus_U Defocus_V Angle CCC 23720.76 24552.81 0.13 0.032625 Final Values Defocus_U Defocus_V Angle CCC 24577.83 23683.23 83.39 0.046297 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00003sq_v01_00008hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00003sq_v01_00008hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.996e-02 CC threshold: 0.734 Mean Std: 37.51 6.51 Num Hot pixels: 208 Hot pixel threshold: 76.59 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.489625 Iteration 2 Error: 0.205780 Iteration 3 Error: 0.044418 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.16 -0.40 ...... Frame ( 3) shift: 0.33 -0.80 ...... Frame ( 4) shift: 0.49 -1.20 ...... Frame ( 5) shift: 0.65 -1.61 ...... Frame ( 6) shift: 0.74 -1.76 ...... Frame ( 7) shift: 0.76 -1.67 ...... Frame ( 8) shift: 0.78 -1.57 ...... Frame ( 9) shift: 0.81 -1.46 ...... Frame ( 10) shift: 0.85 -1.32 ...... Frame ( 11) shift: 0.90 -1.19 ...... Frame ( 12) shift: 0.91 -1.06 ...... Frame ( 13) shift: 0.90 -0.92 ...... Frame ( 14) shift: 0.89 -0.79 ...... Frame ( 15) shift: 0.89 -0.68 ...... Frame ( 16) shift: 0.90 -0.60 ...... Frame ( 17) shift: 0.92 -0.52 ...... Frame ( 18) shift: 0.88 -0.43 ...... Frame ( 19) shift: 0.81 -0.32 ...... Frame ( 20) shift: 0.73 -0.20 ...... Frame ( 21) shift: 0.73 -0.08 ...... Frame ( 22) shift: 0.81 0.04 ...... Frame ( 23) shift: 0.88 0.17 ...... Frame ( 24) shift: 0.93 0.28 ...... Frame ( 25) shift: 0.93 0.37 ...... Frame ( 26) shift: 0.94 0.47 ...... Frame ( 27) shift: 0.97 0.54 ...... Frame ( 28) shift: 1.02 0.59 ...... Frame ( 29) shift: 1.07 0.64 ...... Frame ( 30) shift: 1.10 0.68 ...... Frame ( 31) shift: 1.11 0.70 ...... Frame ( 32) shift: 1.12 0.73 ...... Frame ( 33) shift: 1.13 0.74 ...... Frame ( 34) shift: 1.14 0.75 ...... Frame ( 35) shift: 1.14 0.75 ...... Frame ( 36) shift: 1.15 0.80 ...... Frame ( 37) shift: 1.16 0.89 ...... Frame ( 38) shift: 1.17 0.98 ...... Frame ( 39) shift: 1.19 1.07 ...... Frame ( 40) shift: 1.20 1.16 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.394616 Iteration 2 Error: 0.202137 Iteration 3 Error: 0.039324 Align patch 2 23 left Iteration 1 Error: 1.028858 Iteration 2 Error: 0.143575 Iteration 3 Error: 0.032554 Align patch 3 22 left Iteration 1 Error: 0.792440 Iteration 2 Error: 0.204107 Iteration 3 Error: 0.058342 Iteration 4 Error: 0.016712 Align patch 4 21 left Iteration 1 Error: 0.975694 Iteration 2 Error: 0.141843 Iteration 3 Error: 0.031787 Align patch 5 20 left Iteration 1 Error: 1.050250 Iteration 2 Error: 0.173622 Iteration 3 Error: 0.038769 Align patch 6 19 left Iteration 1 Error: 0.714994 Iteration 2 Error: 0.146632 Iteration 3 Error: 0.039094 Align patch 7 18 left Iteration 1 Error: 0.776846 Iteration 2 Error: 0.278116 Iteration 3 Error: 0.055926 Iteration 4 Error: 0.018339 Align patch 8 17 left Iteration 1 Error: 1.026217 Iteration 2 Error: 0.129929 Iteration 3 Error: 0.034423 Align patch 9 16 left Iteration 1 Error: 0.908070 Iteration 2 Error: 0.257221 Iteration 3 Error: 0.066032 Iteration 4 Error: 0.018711 Align patch 10 15 left Iteration 1 Error: 0.831861 Iteration 2 Error: 0.112906 Iteration 3 Error: 0.034674 Align patch 11 14 left Iteration 1 Error: 0.924518 Iteration 2 Error: 0.138895 Iteration 3 Error: 0.037913 Align patch 12 13 left Iteration 1 Error: 0.876839 Iteration 2 Error: 0.114199 Iteration 3 Error: 0.026614 Align patch 13 12 left Iteration 1 Error: 0.715395 Iteration 2 Error: 0.101211 Iteration 3 Error: 0.033760 Align patch 14 11 left Iteration 1 Error: 0.984747 Iteration 2 Error: 0.183716 Iteration 3 Error: 0.026063 Align patch 15 10 left Iteration 1 Error: 0.584487 Iteration 2 Error: 0.093041 Iteration 3 Error: 0.022244 Align patch 16 9 left Iteration 1 Error: 0.625004 Iteration 2 Error: 0.082397 Iteration 3 Error: 0.017459 Align patch 17 8 left Iteration 1 Error: 0.765955 Iteration 2 Error: 0.162660 Iteration 3 Error: 0.024343 Align patch 18 7 left Iteration 1 Error: 0.882317 Iteration 2 Error: 0.106737 Iteration 3 Error: 0.021885 Align patch 19 6 left Iteration 1 Error: 0.925879 Iteration 2 Error: 0.110695 Iteration 3 Error: 0.026628 Align patch 20 5 left Iteration 1 Error: 0.757910 Iteration 2 Error: 0.150569 Iteration 3 Error: 0.028986 Align patch 21 4 left Iteration 1 Error: 0.714448 Iteration 2 Error: 0.137487 Iteration 3 Error: 0.028416 Align patch 22 3 left Iteration 1 Error: 0.623823 Iteration 2 Error: 0.097521 Iteration 3 Error: 0.024675 Align patch 23 2 left Iteration 1 Error: 0.711581 Iteration 2 Error: 0.161916 Iteration 3 Error: 0.043837 Align patch 24 1 left Iteration 1 Error: 1.024261 Iteration 2 Error: 0.121369 Iteration 3 Error: 0.025496 Align patch 25 0 left Iteration 1 Error: 1.113419 Iteration 2 Error: 0.247803 Iteration 3 Error: 0.037837 3D Fitting completed. Patch alignment time: 11.10(sec) Local motion has been corrected. Process thread exits. Computational time: 19.309032 sec Total time: 27.936687 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00003sq_v01_00008hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00003sq_v01_00008hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.568486s Reading file: gc_18feb27f_CTD_00011gr_00003sq_v01_00008hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.367895s ........................................ >>>>>>TIME<<<<<< FFT: 0.842461s Defocus_U Defocus_V Angle CCC 27568.35 28541.04 2.27 0.036457 Final Values Defocus_U Defocus_V Angle CCC 27521.44 28537.96 0.72 0.053029 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00003sq_v01_00008hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00003sq_v01_00008hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 36.94 6.48 Num Hot pixels: 197 Hot pixel threshold: 75.82 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.548029 Iteration 2 Error: 0.219290 Iteration 3 Error: 0.050071 Iteration 4 Error: 0.015238 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.23 -0.66 ...... Frame ( 3) shift: 0.45 -1.32 ...... Frame ( 4) shift: 0.68 -1.98 ...... Frame ( 5) shift: 0.91 -2.63 ...... Frame ( 6) shift: 1.05 -2.96 ...... Frame ( 7) shift: 1.11 -2.94 ...... Frame ( 8) shift: 1.16 -2.92 ...... Frame ( 9) shift: 1.24 -2.84 ...... Frame ( 10) shift: 1.33 -2.70 ...... Frame ( 11) shift: 1.42 -2.55 ...... Frame ( 12) shift: 1.47 -2.45 ...... Frame ( 13) shift: 1.46 -2.41 ...... Frame ( 14) shift: 1.45 -2.36 ...... Frame ( 15) shift: 1.48 -2.31 ...... Frame ( 16) shift: 1.54 -2.27 ...... Frame ( 17) shift: 1.61 -2.23 ...... Frame ( 18) shift: 1.71 -2.09 ...... Frame ( 19) shift: 1.84 -1.83 ...... Frame ( 20) shift: 1.97 -1.58 ...... Frame ( 21) shift: 2.10 -1.39 ...... Frame ( 22) shift: 2.23 -1.26 ...... Frame ( 23) shift: 2.36 -1.13 ...... Frame ( 24) shift: 2.41 -1.00 ...... Frame ( 25) shift: 2.39 -0.89 ...... Frame ( 26) shift: 2.37 -0.77 ...... Frame ( 27) shift: 2.32 -0.72 ...... Frame ( 28) shift: 2.24 -0.73 ...... Frame ( 29) shift: 2.15 -0.75 ...... Frame ( 30) shift: 2.14 -0.72 ...... Frame ( 31) shift: 2.18 -0.64 ...... Frame ( 32) shift: 2.23 -0.57 ...... Frame ( 33) shift: 2.24 -0.52 ...... Frame ( 34) shift: 2.21 -0.48 ...... Frame ( 35) shift: 2.19 -0.44 ...... Frame ( 36) shift: 2.17 -0.44 ...... Frame ( 37) shift: 2.16 -0.45 ...... Frame ( 38) shift: 2.15 -0.47 ...... Frame ( 39) shift: 2.13 -0.49 ...... Frame ( 40) shift: 2.12 -0.50 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.066758 Iteration 2 Error: 0.166189 Iteration 3 Error: 0.032907 Align patch 2 23 left Iteration 1 Error: 0.617095 Iteration 2 Error: 0.091817 Iteration 3 Error: 0.015837 Align patch 3 22 left Iteration 1 Error: 0.971427 Iteration 2 Error: 0.118417 Iteration 3 Error: 0.024082 Align patch 4 21 left Iteration 1 Error: 1.021651 Iteration 2 Error: 0.134802 Iteration 3 Error: 0.018282 Align patch 5 20 left Iteration 1 Error: 0.854192 Iteration 2 Error: 0.120601 Iteration 3 Error: 0.039943 Align patch 6 19 left Iteration 1 Error: 0.893105 Iteration 2 Error: 0.171300 Iteration 3 Error: 0.035863 Align patch 7 18 left Iteration 1 Error: 0.633214 Iteration 2 Error: 0.095674 Iteration 3 Error: 0.019284 Align patch 8 17 left Iteration 1 Error: 1.242553 Iteration 2 Error: 0.121075 Iteration 3 Error: 0.026771 Align patch 9 16 left Iteration 1 Error: 0.810956 Iteration 2 Error: 0.107821 Iteration 3 Error: 0.024118 Align patch 10 15 left Iteration 1 Error: 0.725883 Iteration 2 Error: 0.144325 Iteration 3 Error: 0.038388 Align patch 11 14 left Iteration 1 Error: 0.819563 Iteration 2 Error: 0.142099 Iteration 3 Error: 0.029587 Align patch 12 13 left Iteration 1 Error: 0.707207 Iteration 2 Error: 0.142906 Iteration 3 Error: 0.048907 Align patch 13 12 left Iteration 1 Error: 1.096774 Iteration 2 Error: 0.148348 Iteration 3 Error: 0.037780 Align patch 14 11 left Iteration 1 Error: 0.591556 Iteration 2 Error: 0.078757 Iteration 3 Error: 0.021105 Align patch 15 10 left Iteration 1 Error: 0.401039 Iteration 2 Error: 0.065042 Iteration 3 Error: 0.010174 Align patch 16 9 left Iteration 1 Error: 0.902999 Iteration 2 Error: 0.161373 Iteration 3 Error: 0.026777 Align patch 17 8 left Iteration 1 Error: 1.017920 Iteration 2 Error: 0.163587 Iteration 3 Error: 0.039021 Align patch 18 7 left Iteration 1 Error: 0.810975 Iteration 2 Error: 0.124460 Iteration 3 Error: 0.036724 Align patch 19 6 left Iteration 1 Error: 1.139516 Iteration 2 Error: 0.118309 Iteration 3 Error: 0.026117 Align patch 20 5 left Iteration 1 Error: 0.659302 Iteration 2 Error: 0.103910 Iteration 3 Error: 0.020631 Align patch 21 4 left Iteration 1 Error: 0.724936 Iteration 2 Error: 0.097610 Iteration 3 Error: 0.025971 Align patch 22 3 left Iteration 1 Error: 0.888783 Iteration 2 Error: 0.172792 Iteration 3 Error: 0.045514 Align patch 23 2 left Iteration 1 Error: 0.839873 Iteration 2 Error: 0.131596 Iteration 3 Error: 0.039733 Align patch 24 1 left Iteration 1 Error: 0.880680 Iteration 2 Error: 0.156288 Iteration 3 Error: 0.037234 Align patch 25 0 left Iteration 1 Error: 0.635914 Iteration 2 Error: 0.111977 Iteration 3 Error: 0.017866 3D Fitting completed. Patch alignment time: 10.94(sec) Local motion has been corrected. Process thread exits. Computational time: 20.406343 sec Total time: 28.277758 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00003sq_v01_00008hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00003sq_v01_00008hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.540503s Reading file: gc_18feb27f_CTD_00011gr_00003sq_v01_00008hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.700284s ........................................ >>>>>>TIME<<<<<< FFT: 0.952549s Defocus_U Defocus_V Angle CCC 25324.23 24515.64 83.98 0.039347 Final Values Defocus_U Defocus_V Angle CCC 25325.82 24501.60 83.67 0.055482 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00011gr_00003sq_v01_00008hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00011gr_00003sq_v01_00008hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 37.88 6.56 Num Hot pixels: 212 Hot pixel threshold: 77.21 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.175506 Iteration 2 Error: 0.150926 Iteration 3 Error: 0.022518 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.11 -0.61 ...... Frame ( 3) shift: 0.21 -1.23 ...... Frame ( 4) shift: 0.32 -1.84 ...... Frame ( 5) shift: 0.42 -2.45 ...... Frame ( 6) shift: 0.48 -2.78 ...... Frame ( 7) shift: 0.50 -2.81 ...... Frame ( 8) shift: 0.51 -2.84 ...... Frame ( 9) shift: 0.51 -2.79 ...... Frame ( 10) shift: 0.50 -2.66 ...... Frame ( 11) shift: 0.49 -2.52 ...... Frame ( 12) shift: 0.51 -2.40 ...... Frame ( 13) shift: 0.56 -2.28 ...... Frame ( 14) shift: 0.61 -2.17 ...... Frame ( 15) shift: 0.65 -2.05 ...... Frame ( 16) shift: 0.68 -1.93 ...... Frame ( 17) shift: 0.71 -1.81 ...... Frame ( 18) shift: 0.73 -1.71 ...... Frame ( 19) shift: 0.73 -1.64 ...... Frame ( 20) shift: 0.73 -1.56 ...... Frame ( 21) shift: 0.74 -1.51 ...... Frame ( 22) shift: 0.76 -1.48 ...... Frame ( 23) shift: 0.77 -1.45 ...... Frame ( 24) shift: 0.75 -1.42 ...... Frame ( 25) shift: 0.70 -1.39 ...... Frame ( 26) shift: 0.65 -1.36 ...... Frame ( 27) shift: 0.64 -1.30 ...... Frame ( 28) shift: 0.67 -1.20 ...... Frame ( 29) shift: 0.71 -1.10 ...... Frame ( 30) shift: 0.77 -1.02 ...... Frame ( 31) shift: 0.86 -0.98 ...... Frame ( 32) shift: 0.95 -0.93 ...... Frame ( 33) shift: 1.01 -0.91 ...... Frame ( 34) shift: 1.03 -0.91 ...... Frame ( 35) shift: 1.05 -0.91 ...... Frame ( 36) shift: 1.05 -0.89 ...... Frame ( 37) shift: 1.03 -0.85 ...... Frame ( 38) shift: 1.01 -0.80 ...... Frame ( 39) shift: 0.99 -0.75 ...... Frame ( 40) shift: 0.97 -0.70 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.035286 Iteration 2 Error: 0.169855 Iteration 3 Error: 0.038146 Align patch 2 23 left Iteration 1 Error: 1.210753 Iteration 2 Error: 0.137748 Iteration 3 Error: 0.031880 Align patch 3 22 left Iteration 1 Error: 0.950832 Iteration 2 Error: 0.101157 Iteration 3 Error: 0.018047 Align patch 4 21 left Iteration 1 Error: 1.120252 Iteration 2 Error: 0.078507 Iteration 3 Error: 0.014445 Align patch 5 20 left Iteration 1 Error: 0.984816 Iteration 2 Error: 0.178900 Iteration 3 Error: 0.042204 Align patch 6 19 left Iteration 1 Error: 0.821067 Iteration 2 Error: 0.060161 Iteration 3 Error: 0.017482 Align patch 7 18 left Iteration 1 Error: 0.501908 Iteration 2 Error: 0.101891 Iteration 3 Error: 0.016725 Align patch 8 17 left Iteration 1 Error: 0.653578 Iteration 2 Error: 0.104870 Iteration 3 Error: 0.025928 Align patch 9 16 left Iteration 1 Error: 1.286168 Iteration 2 Error: 0.206108 Iteration 3 Error: 0.048754 Align patch 10 15 left Iteration 1 Error: 0.905321 Iteration 2 Error: 0.147151 Iteration 3 Error: 0.045514 Align patch 11 14 left Iteration 1 Error: 0.803750 Iteration 2 Error: 0.072384 Iteration 3 Error: 0.018190 Align patch 12 13 left Iteration 1 Error: 0.739756 Iteration 2 Error: 0.137843 Iteration 3 Error: 0.027980 Align patch 13 12 left Iteration 1 Error: 0.940507 Iteration 2 Error: 0.098322 Iteration 3 Error: 0.023750 Align patch 14 11 left Iteration 1 Error: 0.758201 Iteration 2 Error: 0.134808 Iteration 3 Error: 0.026552 Align patch 15 10 left Iteration 1 Error: 0.684104 Iteration 2 Error: 0.093102 Iteration 3 Error: 0.016464 Align patch 16 9 left Iteration 1 Error: 0.683994 Iteration 2 Error: 0.068350 Iteration 3 Error: 0.011356 Align patch 17 8 left Iteration 1 Error: 0.631821 Iteration 2 Error: 0.106760 Iteration 3 Error: 0.022345 Align patch 18 7 left Iteration 1 Error: 0.662304 Iteration 2 Error: 0.095548 Iteration 3 Error: 0.024332 Align patch 19 6 left Iteration 1 Error: 0.804494 Iteration 2 Error: 0.091899 Iteration 3 Error: 0.020209 Align patch 20 5 left Iteration 1 Error: 0.739283 Iteration 2 Error: 0.176367 Iteration 3 Error: 0.039095 Align patch 21 4 left Iteration 1 Error: 0.701434 Iteration 2 Error: 0.133248 Iteration 3 Error: 0.031557 Align patch 22 3 left Iteration 1 Error: 0.530075 Iteration 2 Error: 0.077561 Iteration 3 Error: 0.024624 Align patch 23 2 left Iteration 1 Error: 0.457644 Iteration 2 Error: 0.071235 Iteration 3 Error: 0.014654 Align patch 24 1 left Iteration 1 Error: 0.693562 Iteration 2 Error: 0.152241 Iteration 3 Error: 0.034295 Align patch 25 0 left Iteration 1 Error: 0.673514 Iteration 2 Error: 0.084337 Iteration 3 Error: 0.016711 3D Fitting completed. Patch alignment time: 10.87(sec) Local motion has been corrected. Process thread exits. Computational time: 20.718342 sec Total time: 28.850700 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00011gr_00003sq_v01_00008hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00011gr_00003sq_v01_00008hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.778899s Reading file: gc_18feb27f_CTD_00011gr_00003sq_v01_00008hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.422866s ........................................ >>>>>>TIME<<<<<< FFT: 0.922066s Defocus_U Defocus_V Angle CCC 28136.78 27304.70 87.33 0.037019 Final Values Defocus_U Defocus_V Angle CCC 28141.47 27275.10 87.33 0.053838 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00023gr_00001sq_v02_00002hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00023gr_00001sq_v02_00002hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.366e-01 1.014e-01 CC threshold: 0.745 Mean Std: 10.16 5.56 Num Hot pixels: 95 Hot pixel threshold: 43.55 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.263968 Iteration 2 Error: 0.120292 Iteration 3 Error: 0.009625 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.01 0.13 ...... Frame ( 3) shift: -0.02 0.26 ...... Frame ( 4) shift: -0.03 0.40 ...... Frame ( 5) shift: -0.05 0.53 ...... Frame ( 6) shift: -0.02 0.66 ...... Frame ( 7) shift: 0.06 0.79 ...... Frame ( 8) shift: 0.13 0.92 ...... Frame ( 9) shift: 0.25 1.06 ...... Frame ( 10) shift: 0.43 1.21 ...... Frame ( 11) shift: 0.60 1.37 ...... Frame ( 12) shift: 0.77 1.49 ...... Frame ( 13) shift: 0.93 1.60 ...... Frame ( 14) shift: 1.10 1.71 ...... Frame ( 15) shift: 1.21 1.79 ...... Frame ( 16) shift: 1.27 1.86 ...... Frame ( 17) shift: 1.33 1.93 ...... Frame ( 18) shift: 1.41 1.98 ...... Frame ( 19) shift: 1.50 2.01 ...... Frame ( 20) shift: 1.60 2.04 ...... Frame ( 21) shift: 1.65 2.07 ...... Frame ( 22) shift: 1.67 2.10 ...... Frame ( 23) shift: 1.69 2.13 ...... Frame ( 24) shift: 1.69 2.17 ...... Frame ( 25) shift: 1.66 2.23 ...... Frame ( 26) shift: 1.64 2.29 ...... Frame ( 27) shift: 1.62 2.35 ...... Frame ( 28) shift: 1.62 2.43 ...... Frame ( 29) shift: 1.61 2.50 ...... Frame ( 30) shift: 1.61 2.59 ...... Frame ( 31) shift: 1.62 2.70 ...... Frame ( 32) shift: 1.64 2.81 ...... Frame ( 33) shift: 1.64 2.89 ...... Frame ( 34) shift: 1.64 2.96 ...... Frame ( 35) shift: 1.64 3.03 ...... Frame ( 36) shift: 1.65 3.11 ...... Frame ( 37) shift: 1.67 3.22 ...... Frame ( 38) shift: 1.69 3.32 ...... Frame ( 39) shift: 1.70 3.42 ...... Frame ( 40) shift: 1.72 3.53 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.489069 Iteration 2 Error: 0.023662 Align patch 2 23 left Iteration 1 Error: 0.483203 Iteration 2 Error: 0.026418 Align patch 3 22 left Iteration 1 Error: 0.447711 Iteration 2 Error: 0.028505 Align patch 4 21 left Iteration 1 Error: 0.468864 Iteration 2 Error: 0.102424 Iteration 3 Error: 0.033750 Align patch 5 20 left Iteration 1 Error: 0.299524 Iteration 2 Error: 0.034838 Align patch 6 19 left Iteration 1 Error: 0.373737 Iteration 2 Error: 0.018840 Align patch 7 18 left Iteration 1 Error: 0.424975 Iteration 2 Error: 0.031800 Align patch 8 17 left Iteration 1 Error: 0.394665 Iteration 2 Error: 0.025916 Align patch 9 16 left Iteration 1 Error: 0.326817 Iteration 2 Error: 0.036835 Align patch 10 15 left Iteration 1 Error: 0.424664 Iteration 2 Error: 0.017231 Align patch 11 14 left Iteration 1 Error: 0.473471 Iteration 2 Error: 0.031886 Align patch 12 13 left Iteration 1 Error: 1.433735 Iteration 2 Error: 0.063383 Iteration 3 Error: 0.007166 Align patch 13 12 left Iteration 1 Error: 0.268133 Iteration 2 Error: 0.018120 Align patch 14 11 left Iteration 1 Error: 0.383517 Iteration 2 Error: 0.034069 Align patch 15 10 left Iteration 1 Error: 0.570452 Iteration 2 Error: 0.022599 Align patch 16 9 left Iteration 1 Error: 0.906860 Iteration 2 Error: 0.028247 Align patch 17 8 left Iteration 1 Error: 2.394942 Iteration 2 Error: 0.528514 Iteration 3 Error: 0.148826 Iteration 4 Error: 0.051262 Iteration 5 Error: 0.020261 Align patch 18 7 left Iteration 1 Error: 0.643067 Iteration 2 Error: 0.062073 Iteration 3 Error: 0.012943 Align patch 19 6 left Iteration 1 Error: 0.670403 Iteration 2 Error: 0.046427 Align patch 20 5 left Iteration 1 Error: 1.284087 Iteration 2 Error: 0.059523 Iteration 3 Error: 0.007400 Align patch 21 4 left Iteration 1 Error: 1.018420 Iteration 2 Error: 0.109555 Iteration 3 Error: 0.009142 Align patch 22 3 left Iteration 1 Error: 1.772511 Iteration 2 Error: 0.313958 Iteration 3 Error: 0.110997 Iteration 4 Error: 0.033256 Align patch 23 2 left Iteration 1 Error: 1.185644 Iteration 2 Error: 0.169590 Iteration 3 Error: 0.036198 Align patch 24 1 left Iteration 1 Error: 0.416685 Iteration 2 Error: 0.071597 Iteration 3 Error: 0.016258 Align patch 25 0 left Iteration 1 Error: 0.528984 Iteration 2 Error: 0.042508 3D Fitting completed. Patch alignment time: 17.30(sec) Local motion has been corrected. Process thread exits. Computational time: 32.891544 sec Total time: 43.554081 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00023gr_00001sq_v02_00002hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00023gr_00001sq_v02_00002hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 3.025684s Reading file: gc_18feb27f_CTD_00023gr_00001sq_v02_00002hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.678974s ........................................ >>>>>>TIME<<<<<< FFT: 1.383644s Defocus_U Defocus_V Angle CCC 15894.52 16789.08 9.19 0.019683 Final Values Defocus_U Defocus_V Angle CCC 15813.23 16795.37 9.19 0.047612 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00023gr_00001sq_v02_00002hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00023gr_00001sq_v02_00002hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.364e-01 1.013e-01 CC threshold: 0.745 Mean Std: 9.45 5.13 Num Hot pixels: 389 Hot pixel threshold: 40.24 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.719694 Iteration 2 Error: 0.179139 Iteration 3 Error: 0.010202 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.04 0.14 ...... Frame ( 3) shift: 0.08 0.28 ...... Frame ( 4) shift: 0.11 0.41 ...... Frame ( 5) shift: 0.15 0.55 ...... Frame ( 6) shift: 0.22 0.68 ...... Frame ( 7) shift: 0.33 0.81 ...... Frame ( 8) shift: 0.44 0.94 ...... Frame ( 9) shift: 0.58 1.04 ...... Frame ( 10) shift: 0.74 1.10 ...... Frame ( 11) shift: 0.90 1.16 ...... Frame ( 12) shift: 1.05 1.21 ...... Frame ( 13) shift: 1.17 1.24 ...... Frame ( 14) shift: 1.29 1.28 ...... Frame ( 15) shift: 1.44 1.33 ...... Frame ( 16) shift: 1.62 1.40 ...... Frame ( 17) shift: 1.81 1.47 ...... Frame ( 18) shift: 1.95 1.58 ...... Frame ( 19) shift: 2.07 1.72 ...... Frame ( 20) shift: 2.19 1.86 ...... Frame ( 21) shift: 2.30 1.99 ...... Frame ( 22) shift: 2.42 2.11 ...... Frame ( 23) shift: 2.53 2.24 ...... Frame ( 24) shift: 2.61 2.34 ...... Frame ( 25) shift: 2.65 2.42 ...... Frame ( 26) shift: 2.69 2.49 ...... Frame ( 27) shift: 2.71 2.57 ...... Frame ( 28) shift: 2.71 2.66 ...... Frame ( 29) shift: 2.70 2.74 ...... Frame ( 30) shift: 2.71 2.83 ...... Frame ( 31) shift: 2.73 2.92 ...... Frame ( 32) shift: 2.76 3.02 ...... Frame ( 33) shift: 2.85 3.12 ...... Frame ( 34) shift: 3.01 3.23 ...... Frame ( 35) shift: 3.17 3.33 ...... Frame ( 36) shift: 3.31 3.45 ...... Frame ( 37) shift: 3.42 3.57 ...... Frame ( 38) shift: 3.53 3.70 ...... Frame ( 39) shift: 3.65 3.82 ...... Frame ( 40) shift: 3.76 3.95 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.795028 Iteration 2 Error: 0.014519 Align patch 2 23 left Iteration 1 Error: 0.230920 Iteration 2 Error: 0.022507 Align patch 3 22 left Iteration 1 Error: 0.479681 Iteration 2 Error: 0.053514 Iteration 3 Error: 0.007213 Align patch 4 21 left Iteration 1 Error: 0.567034 Iteration 2 Error: 0.031918 Align patch 5 20 left Iteration 1 Error: 0.355232 Iteration 2 Error: 0.010868 Align patch 6 19 left Iteration 1 Error: 0.470049 Iteration 2 Error: 0.039410 Align patch 7 18 left Iteration 1 Error: 0.739583 Iteration 2 Error: 0.022930 Align patch 8 17 left Iteration 1 Error: 0.320347 Iteration 2 Error: 0.037257 Align patch 9 16 left Iteration 1 Error: 0.553600 Iteration 2 Error: 0.033416 Align patch 10 15 left Iteration 1 Error: 0.539898 Iteration 2 Error: 0.096947 Iteration 3 Error: 0.024797 Align patch 11 14 left Iteration 1 Error: 2.228143 Iteration 2 Error: 0.215333 Iteration 3 Error: 0.029374 Align patch 12 13 left Iteration 1 Error: 1.976872 Iteration 2 Error: 0.123224 Iteration 3 Error: 0.017776 Align patch 13 12 left Iteration 1 Error: 1.108472 Iteration 2 Error: 0.043878 Align patch 14 11 left Iteration 1 Error: 0.880317 Iteration 2 Error: 0.115452 Iteration 3 Error: 0.011448 Align patch 15 10 left Iteration 1 Error: 1.943717 Iteration 2 Error: 0.193747 Iteration 3 Error: 0.030705 Align patch 16 9 left Iteration 1 Error: 0.337458 Iteration 2 Error: 0.018344 Align patch 17 8 left Iteration 1 Error: 0.263282 Iteration 2 Error: 0.030934 Align patch 18 7 left Iteration 1 Error: 1.606172 Iteration 2 Error: 0.175240 Iteration 3 Error: 0.025747 Align patch 19 6 left Iteration 1 Error: 2.685633 Iteration 2 Error: 0.346835 Iteration 3 Error: 0.104007 Iteration 4 Error: 0.026939 Align patch 20 5 left Iteration 1 Error: 1.114127 Iteration 2 Error: 0.066258 Iteration 3 Error: 0.007044 Align patch 21 4 left Iteration 1 Error: 0.395497 Iteration 2 Error: 0.048851 Align patch 22 3 left Iteration 1 Error: 0.286712 Iteration 2 Error: 0.022812 Align patch 23 2 left Iteration 1 Error: 0.450981 Iteration 2 Error: 0.062296 Iteration 3 Error: 0.005947 Align patch 24 1 left Iteration 1 Error: 0.383126 Iteration 2 Error: 0.074335 Iteration 3 Error: 0.016252 Align patch 25 0 left Iteration 1 Error: 1.105608 Iteration 2 Error: 0.106666 Iteration 3 Error: 0.014732 3D Fitting completed. Patch alignment time: 16.42(sec) Local motion has been corrected. Process thread exits. Computational time: 32.580963 sec Total time: 43.812115 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00023gr_00001sq_v02_00002hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00023gr_00001sq_v02_00002hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.616548s Reading file: gc_18feb27f_CTD_00023gr_00001sq_v02_00002hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 4.466797s ........................................ >>>>>>TIME<<<<<< FFT: 1.475725s Defocus_U Defocus_V Angle CCC 13804.69 14730.47 11.40 0.017348 Final Values Defocus_U Defocus_V Angle CCC 13781.21 14713.32 11.09 0.050300 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00023gr_00001sq_v02_00002hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00023gr_00001sq_v02_00002hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.359e-01 1.010e-01 CC threshold: 0.742 Mean Std: 11.21 5.65 Num Hot pixels: 64 Hot pixel threshold: 45.09 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 3.000329 Iteration 2 Error: 0.102017 Iteration 3 Error: 0.015145 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.02 0.05 ...... Frame ( 3) shift: -0.05 0.11 ...... Frame ( 4) shift: -0.07 0.16 ...... Frame ( 5) shift: -0.09 0.21 ...... Frame ( 6) shift: 0.01 0.28 ...... Frame ( 7) shift: 0.23 0.37 ...... Frame ( 8) shift: 0.46 0.47 ...... Frame ( 9) shift: 0.71 0.55 ...... Frame ( 10) shift: 0.99 0.63 ...... Frame ( 11) shift: 1.27 0.71 ...... Frame ( 12) shift: 1.49 0.75 ...... Frame ( 13) shift: 1.64 0.75 ...... Frame ( 14) shift: 1.78 0.75 ...... Frame ( 15) shift: 1.94 0.79 ...... Frame ( 16) shift: 2.10 0.88 ...... Frame ( 17) shift: 2.26 0.97 ...... Frame ( 18) shift: 2.43 1.07 ...... Frame ( 19) shift: 2.62 1.17 ...... Frame ( 20) shift: 2.81 1.26 ...... Frame ( 21) shift: 2.98 1.37 ...... Frame ( 22) shift: 3.13 1.48 ...... Frame ( 23) shift: 3.29 1.59 ...... Frame ( 24) shift: 3.41 1.68 ...... Frame ( 25) shift: 3.50 1.76 ...... Frame ( 26) shift: 3.59 1.83 ...... Frame ( 27) shift: 3.67 1.93 ...... Frame ( 28) shift: 3.75 2.05 ...... Frame ( 29) shift: 3.82 2.17 ...... Frame ( 30) shift: 3.91 2.25 ...... Frame ( 31) shift: 4.02 2.29 ...... Frame ( 32) shift: 4.12 2.33 ...... Frame ( 33) shift: 4.24 2.40 ...... Frame ( 34) shift: 4.38 2.49 ...... Frame ( 35) shift: 4.51 2.58 ...... Frame ( 36) shift: 4.56 2.60 ...... Frame ( 37) shift: 4.54 2.56 ...... Frame ( 38) shift: 4.52 2.53 ...... Frame ( 39) shift: 4.50 2.49 ...... Frame ( 40) shift: 4.47 2.45 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.060151 Iteration 2 Error: 0.073426 Iteration 3 Error: 0.006558 Align patch 2 23 left Iteration 1 Error: 0.498363 Iteration 2 Error: 0.037056 Align patch 3 22 left Iteration 1 Error: 0.300699 Iteration 2 Error: 0.023842 Align patch 4 21 left Iteration 1 Error: 0.551018 Iteration 2 Error: 0.062917 Iteration 3 Error: 0.009445 Align patch 5 20 left Iteration 1 Error: 0.571258 Iteration 2 Error: 0.041972 Align patch 6 19 left Iteration 1 Error: 0.529579 Iteration 2 Error: 0.026831 Align patch 7 18 left Iteration 1 Error: 0.519477 Iteration 2 Error: 0.024760 Align patch 8 17 left Iteration 1 Error: 0.972785 Iteration 2 Error: 0.028063 Align patch 9 16 left Iteration 1 Error: 0.914570 Iteration 2 Error: 0.040683 Align patch 10 15 left Iteration 1 Error: 1.176303 Iteration 2 Error: 0.079564 Iteration 3 Error: 0.005567 Align patch 11 14 left Iteration 1 Error: 1.006871 Iteration 2 Error: 0.075939 Iteration 3 Error: 0.008075 Align patch 12 13 left Iteration 1 Error: 1.841161 Iteration 2 Error: 0.279240 Iteration 3 Error: 0.068928 Iteration 4 Error: 0.021209 Align patch 13 12 left Iteration 1 Error: 0.598982 Iteration 2 Error: 0.046987 Align patch 14 11 left Iteration 1 Error: 0.678003 Iteration 2 Error: 0.053382 Iteration 3 Error: 0.005611 Align patch 15 10 left Iteration 1 Error: 0.590235 Iteration 2 Error: 0.050630 Iteration 3 Error: 0.007650 Align patch 16 9 left Iteration 1 Error: 35.985020 Iteration 2 Error: 31.977793 Iteration 3 Error: 26.097467 Iteration 4 Error: 7.237936 Iteration 5 Error: 3.595748 Align patch 16 9 left Iteration 1 Error: 6.760836 Iteration 2 Error: 2.479894 Iteration 3 Error: 1.969496 Iteration 4 Error: 2.318735 Iteration 5 Error: 2.073799 Align patch 17 8 left Iteration 1 Error: 4.705726 Iteration 2 Error: 0.730427 Iteration 3 Error: 0.448778 Iteration 4 Error: 0.275090 Iteration 5 Error: 0.217156 Align patch 17 8 left Iteration 1 Error: 2.557801 Iteration 2 Error: 0.165814 Iteration 3 Error: 0.022147 Align patch 18 7 left Iteration 1 Error: 2.273640 Iteration 2 Error: 0.088361 Iteration 3 Error: 0.006127 Align patch 19 6 left Iteration 1 Error: 0.614460 Iteration 2 Error: 0.031113 Align patch 20 5 left Iteration 1 Error: 0.593237 Iteration 2 Error: 0.042360 Align patch 21 4 left Iteration 1 Error: 1.245662 Iteration 2 Error: 0.358826 Iteration 3 Error: 0.130950 Iteration 4 Error: 0.052207 Iteration 5 Error: 0.019836 Align patch 22 3 left Iteration 1 Error: 0.864066 Iteration 2 Error: 0.046187 Align patch 23 2 left Iteration 1 Error: 0.634566 Iteration 2 Error: 0.053365 Iteration 3 Error: 0.003823 Align patch 24 1 left Iteration 1 Error: 0.396711 Iteration 2 Error: 0.044008 Align patch 25 0 left Iteration 1 Error: 0.676790 Iteration 2 Error: 0.121848 Iteration 3 Error: 0.015442 3D Fitting completed. Patch alignment time: 20.43(sec) Local motion has been corrected. Process thread exits. Computational time: 39.256783 sec Total time: 52.366627 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00023gr_00001sq_v02_00002hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00023gr_00001sq_v02_00002hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 3.653869s Reading file: gc_18feb27f_CTD_00023gr_00001sq_v02_00002hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.327775s ........................................ >>>>>>TIME<<<<<< FFT: 1.545010s Defocus_U Defocus_V Angle CCC 14099.58 14580.11 2.44 0.062975 Final Values Defocus_U Defocus_V Angle CCC 14071.45 14573.87 2.13 0.111696 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00023gr_00001sq_v02_00002hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00023gr_00001sq_v02_00002hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.364e-01 1.013e-01 CC threshold: 0.744 Mean Std: 10.07 5.37 Num Hot pixels: 173 Hot pixel threshold: 42.29 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.771052 Iteration 2 Error: 0.183449 Iteration 3 Error: 0.018032 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.03 0.06 ...... Frame ( 3) shift: 0.06 0.13 ...... Frame ( 4) shift: 0.09 0.19 ...... Frame ( 5) shift: 0.13 0.26 ...... Frame ( 6) shift: 0.18 0.30 ...... Frame ( 7) shift: 0.24 0.33 ...... Frame ( 8) shift: 0.31 0.36 ...... Frame ( 9) shift: 0.40 0.39 ...... Frame ( 10) shift: 0.52 0.43 ...... Frame ( 11) shift: 0.64 0.47 ...... Frame ( 12) shift: 0.77 0.51 ...... Frame ( 13) shift: 0.90 0.55 ...... Frame ( 14) shift: 1.04 0.59 ...... Frame ( 15) shift: 1.16 0.64 ...... Frame ( 16) shift: 1.27 0.69 ...... Frame ( 17) shift: 1.38 0.74 ...... Frame ( 18) shift: 1.47 0.79 ...... Frame ( 19) shift: 1.55 0.85 ...... Frame ( 20) shift: 1.64 0.91 ...... Frame ( 21) shift: 1.73 1.00 ...... Frame ( 22) shift: 1.83 1.12 ...... Frame ( 23) shift: 1.93 1.24 ...... Frame ( 24) shift: 2.03 1.36 ...... Frame ( 25) shift: 2.14 1.47 ...... Frame ( 26) shift: 2.24 1.59 ...... Frame ( 27) shift: 2.34 1.69 ...... Frame ( 28) shift: 2.42 1.78 ...... Frame ( 29) shift: 2.50 1.87 ...... Frame ( 30) shift: 2.59 1.97 ...... Frame ( 31) shift: 2.69 2.10 ...... Frame ( 32) shift: 2.79 2.23 ...... Frame ( 33) shift: 2.98 2.36 ...... Frame ( 34) shift: 3.27 2.49 ...... Frame ( 35) shift: 3.56 2.62 ...... Frame ( 36) shift: 3.76 2.66 ...... Frame ( 37) shift: 3.89 2.61 ...... Frame ( 38) shift: 4.01 2.57 ...... Frame ( 39) shift: 4.14 2.52 ...... Frame ( 40) shift: 4.26 2.47 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.856689 Iteration 2 Error: 0.034213 Align patch 2 23 left Iteration 1 Error: 0.430533 Iteration 2 Error: 0.018955 Align patch 3 22 left Iteration 1 Error: 0.387127 Iteration 2 Error: 0.024591 Align patch 4 21 left Iteration 1 Error: 1.241758 Iteration 2 Error: 0.082585 Iteration 3 Error: 0.012294 Align patch 5 20 left Iteration 1 Error: 0.470497 Iteration 2 Error: 0.040941 Align patch 6 19 left Iteration 1 Error: 0.341240 Iteration 2 Error: 0.036705 Align patch 7 18 left Iteration 1 Error: 0.277554 Iteration 2 Error: 0.016321 Align patch 8 17 left Iteration 1 Error: 0.385618 Iteration 2 Error: 0.015376 Align patch 9 16 left Iteration 1 Error: 0.271503 Iteration 2 Error: 0.019300 Align patch 10 15 left Iteration 1 Error: 0.607935 Iteration 2 Error: 0.042682 Align patch 11 14 left Iteration 1 Error: 36.155552 Iteration 2 Error: 30.160221 Iteration 3 Error: 21.026615 Iteration 4 Error: 5.341548 Iteration 5 Error: 2.219993 Align patch 11 14 left Iteration 1 Error: 5.264159 Iteration 2 Error: 0.795555 Iteration 3 Error: 0.259437 Iteration 4 Error: 0.088398 Iteration 5 Error: 0.029834 Align patch 12 13 left Iteration 1 Error: 1.720697 Iteration 2 Error: 0.195579 Iteration 3 Error: 0.030393 Align patch 13 12 left Iteration 1 Error: 0.223383 Iteration 2 Error: 0.025826 Align patch 14 11 left Iteration 1 Error: 0.345783 Iteration 2 Error: 0.066913 Iteration 3 Error: 0.014009 Align patch 15 10 left Iteration 1 Error: 0.236374 Iteration 2 Error: 0.016396 Align patch 16 9 left Iteration 1 Error: 0.878514 Iteration 2 Error: 0.059871 Iteration 3 Error: 0.008015 Align patch 17 8 left Iteration 1 Error: 1.293150 Iteration 2 Error: 0.104492 Iteration 3 Error: 0.018714 Align patch 18 7 left Iteration 1 Error: 0.261704 Iteration 2 Error: 0.035969 Align patch 19 6 left Iteration 1 Error: 0.412471 Iteration 2 Error: 0.034139 Align patch 20 5 left Iteration 1 Error: 0.216311 Iteration 2 Error: 0.020946 Align patch 21 4 left Iteration 1 Error: 0.802359 Iteration 2 Error: 0.149401 Iteration 3 Error: 0.027893 Align patch 22 3 left Iteration 1 Error: 1.366818 Iteration 2 Error: 0.266287 Iteration 3 Error: 0.065488 Iteration 4 Error: 0.014406 Align patch 23 2 left Iteration 1 Error: 0.324345 Iteration 2 Error: 0.031315 Align patch 24 1 left Iteration 1 Error: 0.507721 Iteration 2 Error: 0.121953 Iteration 3 Error: 0.026758 Align patch 25 0 left Iteration 1 Error: 1.230784 Iteration 2 Error: 0.192325 Iteration 3 Error: 0.052061 Iteration 4 Error: 0.016045 3D Fitting completed. Patch alignment time: 18.21(sec) Local motion has been corrected. Process thread exits. Computational time: 35.009804 sec Total time: 45.528782 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00023gr_00001sq_v02_00002hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00023gr_00001sq_v02_00002hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.948397s Reading file: gc_18feb27f_CTD_00023gr_00001sq_v02_00002hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.527415s ........................................ >>>>>>TIME<<<<<< FFT: 1.397896s Defocus_U Defocus_V Angle CCC 11992.19 12839.84 1.69 0.045136 Final Values Defocus_U Defocus_V Angle CCC 11992.19 12827.34 2.00 0.090948 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00023gr_00001sq_v02_00003hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00023gr_00001sq_v02_00003hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.341e-01 9.982e-02 CC threshold: 0.733 Mean Std: 49.18 7.50 Num Hot pixels: 74 Hot pixel threshold: 94.18 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.121441 Iteration 2 Error: 0.226566 Iteration 3 Error: 0.062092 Iteration 4 Error: 0.026635 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.03 -0.05 ...... Frame ( 3) shift: 0.05 -0.10 ...... Frame ( 4) shift: 0.08 -0.15 ...... Frame ( 5) shift: 0.11 -0.21 ...... Frame ( 6) shift: 0.12 -0.18 ...... Frame ( 7) shift: 0.13 -0.07 ...... Frame ( 8) shift: 0.14 0.04 ...... Frame ( 9) shift: 0.16 0.14 ...... Frame ( 10) shift: 0.20 0.23 ...... Frame ( 11) shift: 0.24 0.31 ...... Frame ( 12) shift: 0.32 0.40 ...... Frame ( 13) shift: 0.43 0.49 ...... Frame ( 14) shift: 0.55 0.58 ...... Frame ( 15) shift: 0.65 0.67 ...... Frame ( 16) shift: 0.75 0.75 ...... Frame ( 17) shift: 0.85 0.84 ...... Frame ( 18) shift: 0.93 0.88 ...... Frame ( 19) shift: 1.00 0.88 ...... Frame ( 20) shift: 1.07 0.88 ...... Frame ( 21) shift: 1.08 0.88 ...... Frame ( 22) shift: 1.03 0.89 ...... Frame ( 23) shift: 0.99 0.90 ...... Frame ( 24) shift: 1.01 0.91 ...... Frame ( 25) shift: 1.11 0.92 ...... Frame ( 26) shift: 1.20 0.92 ...... Frame ( 27) shift: 1.26 0.96 ...... Frame ( 28) shift: 1.29 1.04 ...... Frame ( 29) shift: 1.32 1.11 ...... Frame ( 30) shift: 1.41 1.13 ...... Frame ( 31) shift: 1.55 1.09 ...... Frame ( 32) shift: 1.69 1.05 ...... Frame ( 33) shift: 1.84 1.06 ...... Frame ( 34) shift: 2.00 1.11 ...... Frame ( 35) shift: 2.16 1.17 ...... Frame ( 36) shift: 2.20 1.22 ...... Frame ( 37) shift: 2.11 1.28 ...... Frame ( 38) shift: 2.02 1.34 ...... Frame ( 39) shift: 1.93 1.40 ...... Frame ( 40) shift: 1.84 1.46 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.818748 Iteration 2 Error: 0.453361 Iteration 3 Error: 0.079429 Iteration 4 Error: 0.018338 Align patch 2 23 left Iteration 1 Error: 1.854483 Iteration 2 Error: 0.630235 Iteration 3 Error: 0.237714 Iteration 4 Error: 0.100180 Iteration 5 Error: 0.032382 Align patch 3 22 left Iteration 1 Error: 1.427004 Iteration 2 Error: 0.221521 Iteration 3 Error: 0.070547 Iteration 4 Error: 0.018351 Align patch 4 21 left Iteration 1 Error: 1.536300 Iteration 2 Error: 0.314575 Iteration 3 Error: 0.071221 Iteration 4 Error: 0.028121 Align patch 5 20 left Iteration 1 Error: 1.608783 Iteration 2 Error: 0.272119 Iteration 3 Error: 0.093668 Iteration 4 Error: 0.026729 Align patch 6 19 left Iteration 1 Error: 1.815050 Iteration 2 Error: 0.312678 Iteration 3 Error: 0.050785 Iteration 4 Error: 0.019259 Align patch 7 18 left Iteration 1 Error: 1.182542 Iteration 2 Error: 0.359716 Iteration 3 Error: 0.145039 Iteration 4 Error: 0.077890 Iteration 5 Error: 0.037963 Align patch 8 17 left Iteration 1 Error: 1.137331 Iteration 2 Error: 0.217721 Iteration 3 Error: 0.065825 Iteration 4 Error: 0.023826 Align patch 9 16 left Iteration 1 Error: 0.962081 Iteration 2 Error: 0.333650 Iteration 3 Error: 0.167259 Iteration 4 Error: 0.073311 Iteration 5 Error: 0.030054 Align patch 10 15 left Iteration 1 Error: 1.209477 Iteration 2 Error: 0.453610 Iteration 3 Error: 0.119797 Iteration 4 Error: 0.076053 Iteration 5 Error: 0.026666 Align patch 11 14 left Iteration 1 Error: 1.816598 Iteration 2 Error: 0.290111 Iteration 3 Error: 0.128437 Iteration 4 Error: 0.043136 Align patch 12 13 left Iteration 1 Error: 1.078076 Iteration 2 Error: 0.198904 Iteration 3 Error: 0.069194 Iteration 4 Error: 0.020708 Align patch 13 12 left Iteration 1 Error: 0.960929 Iteration 2 Error: 0.288740 Iteration 3 Error: 0.068943 Iteration 4 Error: 0.022271 Align patch 14 11 left Iteration 1 Error: 1.479432 Iteration 2 Error: 0.280843 Iteration 3 Error: 0.112515 Iteration 4 Error: 0.053267 Iteration 5 Error: 0.026563 Align patch 15 10 left Iteration 1 Error: 1.379838 Iteration 2 Error: 0.198710 Iteration 3 Error: 0.038111 Align patch 16 9 left Iteration 1 Error: 1.728287 Iteration 2 Error: 0.319923 Iteration 3 Error: 0.152746 Iteration 4 Error: 0.046985 Align patch 17 8 left Iteration 1 Error: 1.667041 Iteration 2 Error: 0.295725 Iteration 3 Error: 0.193854 Iteration 4 Error: 0.096396 Iteration 5 Error: 0.064296 Align patch 17 8 left Iteration 1 Error: 2.102525 Iteration 2 Error: 0.233250 Iteration 3 Error: 0.064207 Iteration 4 Error: 0.030219 Align patch 18 7 left Iteration 1 Error: 0.933648 Iteration 2 Error: 0.191857 Iteration 3 Error: 0.042094 Align patch 19 6 left Iteration 1 Error: 1.321052 Iteration 2 Error: 0.161625 Iteration 3 Error: 0.058048 Iteration 4 Error: 0.018819 Align patch 20 5 left Iteration 1 Error: 0.983909 Iteration 2 Error: 0.156427 Iteration 3 Error: 0.044043 Align patch 21 4 left Iteration 1 Error: 1.015387 Iteration 2 Error: 0.211264 Iteration 3 Error: 0.085455 Iteration 4 Error: 0.039351 Align patch 22 3 left Iteration 1 Error: 1.589328 Iteration 2 Error: 0.309390 Iteration 3 Error: 0.119254 Iteration 4 Error: 0.068828 Iteration 5 Error: 0.019810 Align patch 23 2 left Iteration 1 Error: 1.174248 Iteration 2 Error: 0.314410 Iteration 3 Error: 0.111942 Iteration 4 Error: 0.055101 Iteration 5 Error: 0.027881 Align patch 24 1 left Iteration 1 Error: 0.741625 Iteration 2 Error: 0.088257 Iteration 3 Error: 0.019118 Align patch 25 0 left Iteration 1 Error: 1.159359 Iteration 2 Error: 0.106139 Iteration 3 Error: 0.038261 3D Fitting completed. Patch alignment time: 21.92(sec) Local motion has been corrected. Process thread exits. Computational time: 39.347668 sec Total time: 47.545052 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00023gr_00001sq_v02_00003hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00023gr_00001sq_v02_00003hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.677971s Reading file: gc_18feb27f_CTD_00023gr_00001sq_v02_00003hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 4.346642s ........................................ >>>>>>TIME<<<<<< FFT: 1.585616s Defocus_U Defocus_V Angle CCC 15687.51 16417.97 11.66 0.049221 Final Values Defocus_U Defocus_V Angle CCC 15676.57 16438.29 11.35 0.089484 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00023gr_00001sq_v02_00003hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00023gr_00001sq_v02_00003hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.341e-01 9.979e-02 CC threshold: 0.733 Mean Std: 49.36 7.53 Num Hot pixels: 98 Hot pixel threshold: 94.53 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.566301 Iteration 2 Error: 0.296025 Iteration 3 Error: 0.098326 Iteration 4 Error: 0.045154 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.04 -0.09 ...... Frame ( 3) shift: 0.08 -0.18 ...... Frame ( 4) shift: 0.12 -0.27 ...... Frame ( 5) shift: 0.16 -0.36 ...... Frame ( 6) shift: 0.22 -0.40 ...... Frame ( 7) shift: 0.29 -0.37 ...... Frame ( 8) shift: 0.36 -0.35 ...... Frame ( 9) shift: 0.40 -0.32 ...... Frame ( 10) shift: 0.42 -0.31 ...... Frame ( 11) shift: 0.44 -0.29 ...... Frame ( 12) shift: 0.52 -0.27 ...... Frame ( 13) shift: 0.67 -0.26 ...... Frame ( 14) shift: 0.82 -0.25 ...... Frame ( 15) shift: 0.92 -0.22 ...... Frame ( 16) shift: 0.98 -0.16 ...... Frame ( 17) shift: 1.03 -0.10 ...... Frame ( 18) shift: 1.04 -0.02 ...... Frame ( 19) shift: 1.01 0.09 ...... Frame ( 20) shift: 0.99 0.20 ...... Frame ( 21) shift: 0.99 0.28 ...... Frame ( 22) shift: 1.01 0.32 ...... Frame ( 23) shift: 1.03 0.37 ...... Frame ( 24) shift: 1.08 0.46 ...... Frame ( 25) shift: 1.17 0.60 ...... Frame ( 26) shift: 1.25 0.73 ...... Frame ( 27) shift: 1.30 0.84 ...... Frame ( 28) shift: 1.32 0.92 ...... Frame ( 29) shift: 1.34 0.99 ...... Frame ( 30) shift: 1.32 1.09 ...... Frame ( 31) shift: 1.25 1.21 ...... Frame ( 32) shift: 1.18 1.34 ...... Frame ( 33) shift: 1.16 1.41 ...... Frame ( 34) shift: 1.19 1.45 ...... Frame ( 35) shift: 1.22 1.48 ...... Frame ( 36) shift: 1.30 1.58 ...... Frame ( 37) shift: 1.42 1.76 ...... Frame ( 38) shift: 1.54 1.94 ...... Frame ( 39) shift: 1.66 2.11 ...... Frame ( 40) shift: 1.78 2.29 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.534823 Iteration 2 Error: 0.193107 Iteration 3 Error: 0.058586 Iteration 4 Error: 0.031119 Align patch 2 23 left Iteration 1 Error: 1.015105 Iteration 2 Error: 0.304699 Iteration 3 Error: 0.062811 Iteration 4 Error: 0.031082 Align patch 3 22 left Iteration 1 Error: 0.883846 Iteration 2 Error: 0.185302 Iteration 3 Error: 0.043674 Align patch 4 21 left Iteration 1 Error: 1.256550 Iteration 2 Error: 0.266862 Iteration 3 Error: 0.127643 Iteration 4 Error: 0.061773 Iteration 5 Error: 0.042051 Align patch 5 20 left Iteration 1 Error: 2.546991 Iteration 2 Error: 0.262392 Iteration 3 Error: 0.077494 Iteration 4 Error: 0.013718 Align patch 6 19 left Iteration 1 Error: 0.965033 Iteration 2 Error: 0.322062 Iteration 3 Error: 0.143132 Iteration 4 Error: 0.077051 Iteration 5 Error: 0.056267 Align patch 6 19 left Iteration 1 Error: 1.574124 Iteration 2 Error: 0.319569 Iteration 3 Error: 0.071370 Iteration 4 Error: 0.053826 Iteration 5 Error: 0.027664 Align patch 7 18 left Iteration 1 Error: 1.588116 Iteration 2 Error: 0.213000 Iteration 3 Error: 0.057129 Iteration 4 Error: 0.032664 Align patch 8 17 left Iteration 1 Error: 1.587742 Iteration 2 Error: 0.262130 Iteration 3 Error: 0.091545 Iteration 4 Error: 0.029447 Align patch 9 16 left Iteration 1 Error: 2.002628 Iteration 2 Error: 0.270395 Iteration 3 Error: 0.075534 Iteration 4 Error: 0.030886 Align patch 10 15 left Iteration 1 Error: 2.047244 Iteration 2 Error: 0.321926 Iteration 3 Error: 0.100996 Iteration 4 Error: 0.048207 Align patch 11 14 left Iteration 1 Error: 0.948838 Iteration 2 Error: 0.439741 Iteration 3 Error: 0.172328 Iteration 4 Error: 0.055433 Iteration 5 Error: 0.063646 Align patch 11 14 left Iteration 1 Error: 1.690091 Iteration 2 Error: 0.287071 Iteration 3 Error: 0.077584 Iteration 4 Error: 0.029358 Align patch 12 13 left Iteration 1 Error: 1.056557 Iteration 2 Error: 0.235348 Iteration 3 Error: 0.124810 Iteration 4 Error: 0.059443 Iteration 5 Error: 0.036600 Align patch 13 12 left Iteration 1 Error: 1.049337 Iteration 2 Error: 0.298009 Iteration 3 Error: 0.105160 Iteration 4 Error: 0.030283 Align patch 14 11 left Iteration 1 Error: 1.364320 Iteration 2 Error: 0.455014 Iteration 3 Error: 0.184532 Iteration 4 Error: 0.066661 Iteration 5 Error: 0.043849 Align patch 15 10 left Iteration 1 Error: 0.956149 Iteration 2 Error: 0.219663 Iteration 3 Error: 0.065585 Iteration 4 Error: 0.017105 Align patch 16 9 left Iteration 1 Error: 1.085459 Iteration 2 Error: 0.469403 Iteration 3 Error: 0.123092 Iteration 4 Error: 0.029647 Align patch 17 8 left Iteration 1 Error: 1.386383 Iteration 2 Error: 0.340393 Iteration 3 Error: 0.090907 Iteration 4 Error: 0.055400 Iteration 5 Error: 0.032006 Align patch 18 7 left Iteration 1 Error: 2.032820 Iteration 2 Error: 0.330806 Iteration 3 Error: 0.089561 Iteration 4 Error: 0.043163 Align patch 19 6 left Iteration 1 Error: 1.923475 Iteration 2 Error: 0.520928 Iteration 3 Error: 0.461998 Iteration 4 Error: 0.134872 Iteration 5 Error: 0.158403 Align patch 19 6 left Iteration 1 Error: 1.705710 Iteration 2 Error: 0.319396 Iteration 3 Error: 0.077866 Iteration 4 Error: 0.037645 Align patch 20 5 left Iteration 1 Error: 1.983840 Iteration 2 Error: 0.231654 Iteration 3 Error: 0.115519 Iteration 4 Error: 0.048393 Align patch 21 4 left Iteration 1 Error: 1.519526 Iteration 2 Error: 0.335060 Iteration 3 Error: 0.101321 Iteration 4 Error: 0.028568 Align patch 22 3 left Iteration 1 Error: 1.146972 Iteration 2 Error: 0.215036 Iteration 3 Error: 0.056097 Iteration 4 Error: 0.023624 Align patch 23 2 left Iteration 1 Error: 2.063364 Iteration 2 Error: 0.403334 Iteration 3 Error: 0.070448 Iteration 4 Error: 0.058620 Iteration 5 Error: 0.026395 Align patch 24 1 left Iteration 1 Error: 1.033668 Iteration 2 Error: 0.172073 Iteration 3 Error: 0.033430 Align patch 25 0 left Iteration 1 Error: 1.050301 Iteration 2 Error: 0.149864 Iteration 3 Error: 0.037472 3D Fitting completed. Patch alignment time: 24.82(sec) Local motion has been corrected. Process thread exits. Computational time: 45.505585 sec Total time: 53.930115 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00023gr_00001sq_v02_00003hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00023gr_00001sq_v02_00003hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.621893s Reading file: gc_18feb27f_CTD_00023gr_00001sq_v02_00003hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.432439s ........................................ >>>>>>TIME<<<<<< FFT: 1.441405s Defocus_U Defocus_V Angle CCC 15781.29 16785.20 9.69 0.046578 Final Values Defocus_U Defocus_V Angle CCC 15779.72 16783.64 9.07 0.084483 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00023gr_00001sq_v02_00003hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00023gr_00001sq_v02_00003hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.341e-01 9.980e-02 CC threshold: 0.733 Mean Std: 49.61 7.48 Num Hot pixels: 85 Hot pixel threshold: 94.47 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.327395 Iteration 2 Error: 0.232420 Iteration 3 Error: 0.065965 Iteration 4 Error: 0.023105 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.08 -0.03 ...... Frame ( 3) shift: 0.16 -0.06 ...... Frame ( 4) shift: 0.25 -0.09 ...... Frame ( 5) shift: 0.33 -0.12 ...... Frame ( 6) shift: 0.41 -0.09 ...... Frame ( 7) shift: 0.48 0.02 ...... Frame ( 8) shift: 0.55 0.12 ...... Frame ( 9) shift: 0.62 0.20 ...... Frame ( 10) shift: 0.67 0.27 ...... Frame ( 11) shift: 0.72 0.34 ...... Frame ( 12) shift: 0.73 0.39 ...... Frame ( 13) shift: 0.70 0.42 ...... Frame ( 14) shift: 0.68 0.45 ...... Frame ( 15) shift: 0.64 0.50 ...... Frame ( 16) shift: 0.59 0.56 ...... Frame ( 17) shift: 0.54 0.63 ...... Frame ( 18) shift: 0.60 0.68 ...... Frame ( 19) shift: 0.78 0.74 ...... Frame ( 20) shift: 0.96 0.79 ...... Frame ( 21) shift: 1.05 0.87 ...... Frame ( 22) shift: 1.04 0.97 ...... Frame ( 23) shift: 1.04 1.08 ...... Frame ( 24) shift: 1.01 1.15 ...... Frame ( 25) shift: 0.95 1.18 ...... Frame ( 26) shift: 0.89 1.22 ...... Frame ( 27) shift: 0.89 1.27 ...... Frame ( 28) shift: 0.95 1.33 ...... Frame ( 29) shift: 1.01 1.39 ...... Frame ( 30) shift: 1.08 1.46 ...... Frame ( 31) shift: 1.18 1.52 ...... Frame ( 32) shift: 1.28 1.59 ...... Frame ( 33) shift: 1.30 1.68 ...... Frame ( 34) shift: 1.25 1.79 ...... Frame ( 35) shift: 1.20 1.89 ...... Frame ( 36) shift: 1.18 2.00 ...... Frame ( 37) shift: 1.21 2.10 ...... Frame ( 38) shift: 1.23 2.19 ...... Frame ( 39) shift: 1.26 2.29 ...... Frame ( 40) shift: 1.28 2.39 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.562306 Iteration 2 Error: 0.255240 Iteration 3 Error: 0.208997 Iteration 4 Error: 0.109469 Iteration 5 Error: 0.089966 Align patch 1 24 left Iteration 1 Error: 3.292058 Iteration 2 Error: 0.303840 Iteration 3 Error: 0.086342 Iteration 4 Error: 0.040821 Align patch 2 23 left Iteration 1 Error: 3.548088 Iteration 2 Error: 0.396777 Iteration 3 Error: 0.109356 Iteration 4 Error: 0.041258 Align patch 3 22 left Iteration 1 Error: 1.430824 Iteration 2 Error: 0.282778 Iteration 3 Error: 0.076935 Iteration 4 Error: 0.023087 Align patch 4 21 left Iteration 1 Error: 1.253401 Iteration 2 Error: 0.327040 Iteration 3 Error: 0.096823 Iteration 4 Error: 0.040933 Align patch 5 20 left Iteration 1 Error: 0.999918 Iteration 2 Error: 0.161723 Iteration 3 Error: 0.060365 Iteration 4 Error: 0.045449 Align patch 6 19 left Iteration 1 Error: 1.071025 Iteration 2 Error: 0.240383 Iteration 3 Error: 0.058533 Iteration 4 Error: 0.026866 Align patch 7 18 left Iteration 1 Error: 0.919821 Iteration 2 Error: 0.258070 Iteration 3 Error: 0.072523 Iteration 4 Error: 0.018258 Align patch 8 17 left Iteration 1 Error: 4.767865 Iteration 2 Error: 0.791808 Iteration 3 Error: 0.528223 Iteration 4 Error: 0.203548 Iteration 5 Error: 0.134144 Align patch 8 17 left Iteration 1 Error: 2.366721 Iteration 2 Error: 0.301010 Iteration 3 Error: 0.065563 Iteration 4 Error: 0.022556 Align patch 9 16 left Iteration 1 Error: 0.938258 Iteration 2 Error: 0.379555 Iteration 3 Error: 0.129229 Iteration 4 Error: 0.041518 Align patch 10 15 left Iteration 1 Error: 1.470872 Iteration 2 Error: 0.181686 Iteration 3 Error: 0.080970 Iteration 4 Error: 0.019433 Align patch 11 14 left Iteration 1 Error: 1.235982 Iteration 2 Error: 0.172508 Iteration 3 Error: 0.072862 Iteration 4 Error: 0.026535 Align patch 12 13 left Iteration 1 Error: 1.754944 Iteration 2 Error: 0.491297 Iteration 3 Error: 0.227886 Iteration 4 Error: 0.084975 Iteration 5 Error: 0.037927 Align patch 13 12 left Iteration 1 Error: 1.174929 Iteration 2 Error: 0.262910 Iteration 3 Error: 0.076427 Iteration 4 Error: 0.019382 Align patch 14 11 left Iteration 1 Error: 1.234207 Iteration 2 Error: 0.227892 Iteration 3 Error: 0.073569 Iteration 4 Error: 0.026615 Align patch 15 10 left Iteration 1 Error: 0.748321 Iteration 2 Error: 0.190322 Iteration 3 Error: 0.049772 Align patch 16 9 left Iteration 1 Error: 1.879812 Iteration 2 Error: 0.346622 Iteration 3 Error: 0.102823 Iteration 4 Error: 0.044098 Align patch 17 8 left Iteration 1 Error: 2.019356 Iteration 2 Error: 0.461446 Iteration 3 Error: 0.301696 Iteration 4 Error: 0.085011 Iteration 5 Error: 0.045843 Align patch 18 7 left Iteration 1 Error: 1.520137 Iteration 2 Error: 0.263499 Iteration 3 Error: 0.069631 Iteration 4 Error: 0.020403 Align patch 19 6 left Iteration 1 Error: 1.063448 Iteration 2 Error: 0.323769 Iteration 3 Error: 0.130715 Iteration 4 Error: 0.054994 Iteration 5 Error: 0.024921 Align patch 20 5 left Iteration 1 Error: 1.272167 Iteration 2 Error: 0.209754 Iteration 3 Error: 0.074661 Iteration 4 Error: 0.031220 Align patch 21 4 left Iteration 1 Error: 1.303297 Iteration 2 Error: 0.235401 Iteration 3 Error: 0.055729 Iteration 4 Error: 0.023202 Align patch 22 3 left Iteration 1 Error: 1.137747 Iteration 2 Error: 0.315269 Iteration 3 Error: 0.091390 Iteration 4 Error: 0.037944 Align patch 23 2 left Iteration 1 Error: 1.408910 Iteration 2 Error: 0.329429 Iteration 3 Error: 0.069136 Iteration 4 Error: 0.029806 Align patch 24 1 left Iteration 1 Error: 1.012592 Iteration 2 Error: 0.147784 Iteration 3 Error: 0.074743 Iteration 4 Error: 0.028990 Align patch 25 0 left Iteration 1 Error: 1.539417 Iteration 2 Error: 0.140993 Iteration 3 Error: 0.033395 3D Fitting completed. Patch alignment time: 19.74(sec) Local motion has been corrected. Process thread exits. Computational time: 33.033440 sec Total time: 49.163277 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00023gr_00001sq_v02_00003hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00023gr_00001sq_v02_00003hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.537995s Reading file: gc_18feb27f_CTD_00023gr_00001sq_v02_00003hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.263382s ........................................ >>>>>>TIME<<<<<< FFT: 1.364177s Defocus_U Defocus_V Angle CCC 15869.18 16541.06 0.06 0.045450 Final Values Defocus_U Defocus_V Angle CCC 15876.95 16539.55 0.69 0.083080 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00023gr_00001sq_v02_00003hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00023gr_00001sq_v02_00003hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.338e-01 9.957e-02 CC threshold: 0.731 Mean Std: 49.97 7.47 Num Hot pixels: 98 Hot pixel threshold: 94.79 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.641927 Iteration 2 Error: 0.091848 Iteration 3 Error: 0.039016 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.14 0.07 ...... Frame ( 3) shift: 0.28 0.14 ...... Frame ( 4) shift: 0.42 0.21 ...... Frame ( 5) shift: 0.55 0.28 ...... Frame ( 6) shift: 0.65 0.29 ...... Frame ( 7) shift: 0.71 0.25 ...... Frame ( 8) shift: 0.76 0.21 ...... Frame ( 9) shift: 0.81 0.19 ...... Frame ( 10) shift: 0.85 0.19 ...... Frame ( 11) shift: 0.89 0.19 ...... Frame ( 12) shift: 0.91 0.21 ...... Frame ( 13) shift: 0.91 0.26 ...... Frame ( 14) shift: 0.92 0.30 ...... Frame ( 15) shift: 0.92 0.34 ...... Frame ( 16) shift: 0.90 0.37 ...... Frame ( 17) shift: 0.89 0.40 ...... Frame ( 18) shift: 0.91 0.42 ...... Frame ( 19) shift: 0.97 0.43 ...... Frame ( 20) shift: 1.03 0.44 ...... Frame ( 21) shift: 1.04 0.40 ...... Frame ( 22) shift: 0.99 0.30 ...... Frame ( 23) shift: 0.95 0.21 ...... Frame ( 24) shift: 0.97 0.20 ...... Frame ( 25) shift: 1.07 0.28 ...... Frame ( 26) shift: 1.16 0.36 ...... Frame ( 27) shift: 1.15 0.42 ...... Frame ( 28) shift: 1.05 0.45 ...... Frame ( 29) shift: 0.94 0.48 ...... Frame ( 30) shift: 0.89 0.50 ...... Frame ( 31) shift: 0.88 0.52 ...... Frame ( 32) shift: 0.88 0.54 ...... Frame ( 33) shift: 0.91 0.50 ...... Frame ( 34) shift: 0.98 0.42 ...... Frame ( 35) shift: 1.05 0.33 ...... Frame ( 36) shift: 1.00 0.29 ...... Frame ( 37) shift: 0.83 0.29 ...... Frame ( 38) shift: 0.66 0.30 ...... Frame ( 39) shift: 0.49 0.30 ...... Frame ( 40) shift: 0.33 0.30 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 19.211386 Iteration 2 Error: 12.453415 Iteration 3 Error: 11.597555 Iteration 4 Error: 4.664051 Iteration 5 Error: 2.430390 Align patch 1 24 left Iteration 1 Error: 3.339622 Iteration 2 Error: 1.487011 Iteration 3 Error: 0.750486 Iteration 4 Error: 0.493083 Iteration 5 Error: 0.638526 Align patch 2 23 left Iteration 1 Error: 7.140763 Iteration 2 Error: 20.649601 Iteration 3 Error: 20.703928 Iteration 4 Error: 23.017479 Iteration 5 Error: 22.991356 Align patch 2 23 left Iteration 1 Error: 3.155966 Iteration 2 Error: 0.636179 Iteration 3 Error: 0.927220 Iteration 4 Error: 0.657798 Iteration 5 Error: 0.340528 Align patch 3 22 left Iteration 1 Error: 33.844021 Iteration 2 Error: 35.148907 Iteration 3 Error: 39.030102 Iteration 4 Error: 43.701118 Iteration 5 Error: 43.963989 Align patch 3 22 left Iteration 1 Error: 18.090553 Iteration 2 Error: 13.194221 Iteration 3 Error: 1.110927 Iteration 4 Error: 0.670125 Iteration 5 Error: 0.293246 Align patch 4 21 left Iteration 1 Error: 35.197803 Iteration 2 Error: 36.213943 Iteration 3 Error: 1.117827 Iteration 4 Error: 0.497528 Iteration 5 Error: 0.266802 Align patch 4 21 left Iteration 1 Error: 2.980469 Iteration 2 Error: 1.060300 Iteration 3 Error: 0.554134 Iteration 4 Error: 0.529126 Iteration 5 Error: 0.255791 Align patch 5 20 left Iteration 1 Error: 18.627964 Iteration 2 Error: 1.396820 Iteration 3 Error: 40.408291 Iteration 4 Error: 22.005184 Iteration 5 Error: 0.608225 Align patch 5 20 left Iteration 1 Error: 3.124020 Iteration 2 Error: 0.565050 Iteration 3 Error: 0.197778 Iteration 4 Error: 0.113021 Iteration 5 Error: 0.122343 Align patch 6 19 left Iteration 1 Error: 16.484760 Iteration 2 Error: 5.278889 Iteration 3 Error: 2.047301 Iteration 4 Error: 0.992243 Iteration 5 Error: 0.518223 Align patch 6 19 left Iteration 1 Error: 3.372547 Iteration 2 Error: 1.892149 Iteration 3 Error: 0.917173 Iteration 4 Error: 0.567142 Iteration 5 Error: 0.349917 Align patch 7 18 left Iteration 1 Error: 47.505322 Iteration 2 Error: 47.736275 Iteration 3 Error: 46.868519 Iteration 4 Error: 46.967335 Iteration 5 Error: 45.953838 Align patch 7 18 left Iteration 1 Error: 3.142087 Iteration 2 Error: 0.475467 Iteration 3 Error: 0.323796 Iteration 4 Error: 0.163164 Iteration 5 Error: 0.151530 Align patch 8 17 left Iteration 1 Error: 44.514294 Iteration 2 Error: 47.361526 Iteration 3 Error: 51.527527 Iteration 4 Error: 51.855034 Iteration 5 Error: 51.590923 Align patch 8 17 left Iteration 1 Error: 43.222256 Iteration 2 Error: 47.841801 Iteration 3 Error: 47.954643 Iteration 4 Error: 47.718887 Iteration 5 Error: 48.269466 Align patch 9 16 left Iteration 1 Error: 37.033646 Iteration 2 Error: 44.319042 Iteration 3 Error: 43.087841 Iteration 4 Error: 42.115593 Iteration 5 Error: 40.947475 Align patch 9 16 left Iteration 1 Error: 46.463310 Iteration 2 Error: 2.116673 Iteration 3 Error: 19.251854 Iteration 4 Error: 1.455030 Iteration 5 Error: 0.422401 Align patch 10 15 left Iteration 1 Error: 45.625523 Iteration 2 Error: 27.726557 Iteration 3 Error: 20.564934 Iteration 4 Error: 21.610662 Iteration 5 Error: 21.434364 Align patch 10 15 left Iteration 1 Error: 4.095950 Iteration 2 Error: 1.645203 Iteration 3 Error: 0.487758 Iteration 4 Error: 0.203167 Iteration 5 Error: 0.214581 Align patch 11 14 left Iteration 1 Error: 22.424753 Iteration 2 Error: 17.326910 Iteration 3 Error: 31.996384 Iteration 4 Error: 28.831572 Iteration 5 Error: 2.080366 Align patch 11 14 left Iteration 1 Error: 6.402015 Iteration 2 Error: 18.199829 Iteration 3 Error: 3.054899 Iteration 4 Error: 1.556563 Iteration 5 Error: 0.719858 Align patch 12 13 left Iteration 1 Error: 27.764784 Iteration 2 Error: 20.084150 Iteration 3 Error: 28.497318 Iteration 4 Error: 17.084080 Iteration 5 Error: 38.224072 Align patch 12 13 left Iteration 1 Error: 25.714119 Iteration 2 Error: 1.168951 Iteration 3 Error: 0.942934 Iteration 4 Error: 0.719079 Iteration 5 Error: 0.348061 Align patch 13 12 left Iteration 1 Error: 34.562679 Iteration 2 Error: 35.209373 Iteration 3 Error: 35.625416 Iteration 4 Error: 35.581238 Iteration 5 Error: 34.403992 Align patch 13 12 left Iteration 1 Error: 71.020996 Iteration 2 Error: 74.872940 Iteration 3 Error: 77.374252 Iteration 4 Error: 77.410477 Iteration 5 Error: 63.465446 Align patch 14 11 left Iteration 1 Error: 33.330288 Iteration 2 Error: 44.864136 Iteration 3 Error: 43.631672 Iteration 4 Error: 44.173679 Iteration 5 Error: 45.002605 Align patch 14 11 left Iteration 1 Error: 71.612328 Iteration 2 Error: 68.013916 Iteration 3 Error: 68.055580 Iteration 4 Error: 68.871552 Iteration 5 Error: 69.044441 Align patch 15 10 left Iteration 1 Error: 34.172470 Iteration 2 Error: 34.298382 Iteration 3 Error: 34.321342 Iteration 4 Error: 34.601238 Iteration 5 Error: 34.623451 Align patch 15 10 left Iteration 1 Error: 37.649578 Iteration 2 Error: 2.092562 Iteration 3 Error: 0.669993 Iteration 4 Error: 0.472985 Iteration 5 Error: 0.239713 Align patch 16 9 left Iteration 1 Error: 16.982395 Iteration 2 Error: 26.496929 Iteration 3 Error: 7.706708 Iteration 4 Error: 2.797677 Iteration 5 Error: 2.613711 Align patch 16 9 left Iteration 1 Error: 8.689154 Iteration 2 Error: 12.765262 Iteration 3 Error: 18.267279 Iteration 4 Error: 21.379330 Iteration 5 Error: 26.453493 Align patch 17 8 left Iteration 1 Error: 30.966728 Iteration 2 Error: 29.798309 Iteration 3 Error: 30.086069 Iteration 4 Error: 30.104155 Iteration 5 Error: 30.648840 Align patch 17 8 left Iteration 1 Error: 10.992131 Iteration 2 Error: 17.663246 Iteration 3 Error: 1.389392 Iteration 4 Error: 0.785771 Iteration 5 Error: 0.658515 Align patch 18 7 left Iteration 1 Error: 41.433910 Iteration 2 Error: 39.640747 Iteration 3 Error: 40.132324 Iteration 4 Error: 39.518303 Iteration 5 Error: 38.253765 Align patch 18 7 left Iteration 1 Error: 16.616463 Iteration 2 Error: 16.826973 Iteration 3 Error: 17.655426 Iteration 4 Error: 11.279840 Iteration 5 Error: 0.881255 Align patch 19 6 left Iteration 1 Error: 35.796463 Iteration 2 Error: 36.948372 Iteration 3 Error: 37.129612 Iteration 4 Error: 37.275589 Iteration 5 Error: 37.587593 Align patch 19 6 left Iteration 1 Error: 42.761265 Iteration 2 Error: 40.498020 Iteration 3 Error: 42.232567 Iteration 4 Error: 37.701000 Iteration 5 Error: 1.507235 Align patch 20 5 left Iteration 1 Error: 38.804165 Iteration 2 Error: 39.552891 Iteration 3 Error: 40.300976 Iteration 4 Error: 40.403008 Iteration 5 Error: 40.416512 Align patch 20 5 left Iteration 1 Error: 41.537575 Iteration 2 Error: 2.067948 Iteration 3 Error: 0.654072 Iteration 4 Error: 0.662266 Iteration 5 Error: 0.750394 Align patch 21 4 left Iteration 1 Error: 8.670342 Iteration 2 Error: 14.294195 Iteration 3 Error: 15.129518 Iteration 4 Error: 1.205255 Iteration 5 Error: 0.287340 Align patch 21 4 left Iteration 1 Error: 7.350905 Iteration 2 Error: 11.922171 Iteration 3 Error: 14.699895 Iteration 4 Error: 2.312989 Iteration 5 Error: 0.396161 Align patch 22 3 left Iteration 1 Error: 20.510771 Iteration 2 Error: 16.365469 Iteration 3 Error: 20.756849 Iteration 4 Error: 12.351124 Iteration 5 Error: 1.021484 Align patch 22 3 left Iteration 1 Error: 12.104582 Iteration 2 Error: 14.947343 Iteration 3 Error: 24.490770 Iteration 4 Error: 4.021755 Iteration 5 Error: 4.318218 Align patch 23 2 left Iteration 1 Error: 29.931866 Iteration 2 Error: 31.202850 Iteration 3 Error: 31.791504 Iteration 4 Error: 32.376854 Iteration 5 Error: 32.840939 Align patch 23 2 left Iteration 1 Error: 28.287506 Iteration 2 Error: 28.885294 Iteration 3 Error: 29.430981 Iteration 4 Error: 29.465599 Iteration 5 Error: 30.376890 Align patch 24 1 left Iteration 1 Error: 14.959555 Iteration 2 Error: 13.223395 Iteration 3 Error: 13.724455 Iteration 4 Error: 13.666875 Iteration 5 Error: 13.709067 Align patch 24 1 left Iteration 1 Error: 47.139832 Iteration 2 Error: 1.440138 Iteration 3 Error: 0.659505 Iteration 4 Error: 0.428775 Iteration 5 Error: 0.397051 Align patch 25 0 left Iteration 1 Error: 2.375232 Iteration 2 Error: 1.068473 Iteration 3 Error: 0.736954 Iteration 4 Error: 0.416055 Iteration 5 Error: 0.301539 Align patch 25 0 left Iteration 1 Error: 2.350161 Iteration 2 Error: 0.724822 Iteration 3 Error: 0.287518 Iteration 4 Error: 0.248314 Iteration 5 Error: 0.233277 3D Fitting completed. Patch alignment time: 42.83(sec) Local motion has been corrected. Process thread exits. Computational time: 54.800602 sec Total time: 64.294662 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00023gr_00001sq_v02_00003hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00023gr_00001sq_v02_00003hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.763149s Reading file: gc_18feb27f_CTD_00023gr_00001sq_v02_00003hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.119220s ........................................ >>>>>>TIME<<<<<< FFT: 1.055553s Defocus_U Defocus_V Angle CCC 15115.20 15830.11 30.82 0.026493 Final Values Defocus_U Defocus_V Angle CCC 15130.89 15755.33 35.57 0.052890 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00023gr_00001sq_v02_00004hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00023gr_00001sq_v02_00004hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.341e-01 9.979e-02 CC threshold: 0.733 Mean Std: 49.55 7.50 Num Hot pixels: 93 Hot pixel threshold: 94.53 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.476153 Iteration 2 Error: 0.364007 Iteration 3 Error: 0.141654 Iteration 4 Error: 0.052077 Iteration 5 Error: 0.029298 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.02 -0.05 ...... Frame ( 3) shift: 0.04 -0.10 ...... Frame ( 4) shift: 0.06 -0.15 ...... Frame ( 5) shift: 0.07 -0.20 ...... Frame ( 6) shift: 0.12 -0.18 ...... Frame ( 7) shift: 0.20 -0.10 ...... Frame ( 8) shift: 0.28 -0.02 ...... Frame ( 9) shift: 0.41 0.04 ...... Frame ( 10) shift: 0.60 0.07 ...... Frame ( 11) shift: 0.79 0.10 ...... Frame ( 12) shift: 0.90 0.11 ...... Frame ( 13) shift: 0.94 0.11 ...... Frame ( 14) shift: 0.99 0.12 ...... Frame ( 15) shift: 1.09 0.16 ...... Frame ( 16) shift: 1.26 0.25 ...... Frame ( 17) shift: 1.43 0.34 ...... Frame ( 18) shift: 1.55 0.38 ...... Frame ( 19) shift: 1.63 0.37 ...... Frame ( 20) shift: 1.70 0.36 ...... Frame ( 21) shift: 1.81 0.36 ...... Frame ( 22) shift: 1.94 0.37 ...... Frame ( 23) shift: 2.07 0.39 ...... Frame ( 24) shift: 2.19 0.43 ...... Frame ( 25) shift: 2.29 0.50 ...... Frame ( 26) shift: 2.38 0.57 ...... Frame ( 27) shift: 2.48 0.64 ...... Frame ( 28) shift: 2.58 0.72 ...... Frame ( 29) shift: 2.67 0.80 ...... Frame ( 30) shift: 2.74 0.82 ...... Frame ( 31) shift: 2.80 0.78 ...... Frame ( 32) shift: 2.85 0.74 ...... Frame ( 33) shift: 2.93 0.75 ...... Frame ( 34) shift: 3.05 0.80 ...... Frame ( 35) shift: 3.17 0.85 ...... Frame ( 36) shift: 3.25 0.91 ...... Frame ( 37) shift: 3.30 0.98 ...... Frame ( 38) shift: 3.35 1.05 ...... Frame ( 39) shift: 3.40 1.12 ...... Frame ( 40) shift: 3.45 1.19 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.438793 Iteration 2 Error: 0.327357 Iteration 3 Error: 0.181673 Iteration 4 Error: 0.074300 Iteration 5 Error: 0.064097 Align patch 1 24 left Iteration 1 Error: 3.252531 Iteration 2 Error: 0.387124 Iteration 3 Error: 0.046503 Align patch 2 23 left Iteration 1 Error: 1.299137 Iteration 2 Error: 0.382984 Iteration 3 Error: 0.110448 Iteration 4 Error: 0.040139 Align patch 3 22 left Iteration 1 Error: 2.714359 Iteration 2 Error: 0.493358 Iteration 3 Error: 0.126418 Iteration 4 Error: 0.068254 Iteration 5 Error: 0.026964 Align patch 4 21 left Iteration 1 Error: 2.225451 Iteration 2 Error: 0.495011 Iteration 3 Error: 0.164223 Iteration 4 Error: 0.056400 Iteration 5 Error: 0.020650 Align patch 5 20 left Iteration 1 Error: 1.935076 Iteration 2 Error: 0.382420 Iteration 3 Error: 0.098477 Iteration 4 Error: 0.039174 Align patch 6 19 left Iteration 1 Error: 0.877466 Iteration 2 Error: 0.361070 Iteration 3 Error: 0.176607 Iteration 4 Error: 0.119292 Iteration 5 Error: 0.087470 Align patch 6 19 left Iteration 1 Error: 2.935545 Iteration 2 Error: 0.319854 Iteration 3 Error: 0.053442 Iteration 4 Error: 0.031350 Align patch 7 18 left Iteration 1 Error: 1.279294 Iteration 2 Error: 0.306402 Iteration 3 Error: 0.191667 Iteration 4 Error: 0.110955 Iteration 5 Error: 0.067528 Align patch 7 18 left Iteration 1 Error: 2.573455 Iteration 2 Error: 0.371816 Iteration 3 Error: 0.059302 Iteration 4 Error: 0.030845 Align patch 8 17 left Iteration 1 Error: 2.378056 Iteration 2 Error: 0.166621 Iteration 3 Error: 0.074216 Iteration 4 Error: 0.027765 Align patch 9 16 left Iteration 1 Error: 1.924624 Iteration 2 Error: 0.822435 Iteration 3 Error: 0.335293 Iteration 4 Error: 0.180170 Iteration 5 Error: 0.063590 Align patch 9 16 left Iteration 1 Error: 1.993488 Iteration 2 Error: 0.253653 Iteration 3 Error: 0.059881 Iteration 4 Error: 0.021532 Align patch 10 15 left Iteration 1 Error: 1.342561 Iteration 2 Error: 0.741864 Iteration 3 Error: 0.242785 Iteration 4 Error: 0.107809 Iteration 5 Error: 0.056471 Align patch 10 15 left Iteration 1 Error: 2.032547 Iteration 2 Error: 0.205918 Iteration 3 Error: 0.028973 Align patch 11 14 left Iteration 1 Error: 4.877700 Iteration 2 Error: 0.863215 Iteration 3 Error: 0.387465 Iteration 4 Error: 0.190893 Iteration 5 Error: 0.083523 Align patch 11 14 left Iteration 1 Error: 3.226943 Iteration 2 Error: 0.251426 Iteration 3 Error: 0.049362 Align patch 12 13 left Iteration 1 Error: 1.754902 Iteration 2 Error: 0.817461 Iteration 3 Error: 0.272385 Iteration 4 Error: 0.224892 Iteration 5 Error: 0.157756 Align patch 12 13 left Iteration 1 Error: 2.308937 Iteration 2 Error: 0.246447 Iteration 3 Error: 0.051889 Iteration 4 Error: 0.020136 Align patch 13 12 left Iteration 1 Error: 1.437629 Iteration 2 Error: 0.329083 Iteration 3 Error: 0.170853 Iteration 4 Error: 0.052935 Iteration 5 Error: 0.076286 Align patch 13 12 left Iteration 1 Error: 1.341498 Iteration 2 Error: 0.257760 Iteration 3 Error: 0.086640 Iteration 4 Error: 0.032873 Align patch 14 11 left Iteration 1 Error: 1.149645 Iteration 2 Error: 0.519204 Iteration 3 Error: 0.413902 Iteration 4 Error: 0.162751 Iteration 5 Error: 0.132065 Align patch 14 11 left Iteration 1 Error: 1.142345 Iteration 2 Error: 0.169078 Iteration 3 Error: 0.057512 Iteration 4 Error: 0.029894 Align patch 15 10 left Iteration 1 Error: 1.062732 Iteration 2 Error: 0.359621 Iteration 3 Error: 0.109071 Iteration 4 Error: 0.110380 Iteration 5 Error: 0.047172 Align patch 16 9 left Iteration 1 Error: 1.887387 Iteration 2 Error: 0.208749 Iteration 3 Error: 0.071580 Iteration 4 Error: 0.028075 Align patch 17 8 left Iteration 1 Error: 3.387814 Iteration 2 Error: 0.726738 Iteration 3 Error: 0.232058 Iteration 4 Error: 0.106740 Iteration 5 Error: 0.044523 Align patch 18 7 left Iteration 1 Error: 1.839189 Iteration 2 Error: 0.638579 Iteration 3 Error: 0.240652 Iteration 4 Error: 0.121050 Iteration 5 Error: 0.063396 Align patch 18 7 left Iteration 1 Error: 1.649130 Iteration 2 Error: 0.290683 Iteration 3 Error: 0.084780 Iteration 4 Error: 0.032020 Align patch 19 6 left Iteration 1 Error: 1.357736 Iteration 2 Error: 0.330096 Iteration 3 Error: 0.101380 Iteration 4 Error: 0.052425 Iteration 5 Error: 0.027117 Align patch 20 5 left Iteration 1 Error: 1.480082 Iteration 2 Error: 0.260955 Iteration 3 Error: 0.057284 Iteration 4 Error: 0.029128 Align patch 21 4 left Iteration 1 Error: 0.846441 Iteration 2 Error: 0.134536 Iteration 3 Error: 0.053785 Iteration 4 Error: 0.021347 Align patch 22 3 left Iteration 1 Error: 0.929805 Iteration 2 Error: 0.183647 Iteration 3 Error: 0.071479 Iteration 4 Error: 0.031568 Align patch 23 2 left Iteration 1 Error: 0.919719 Iteration 2 Error: 0.301886 Iteration 3 Error: 0.082823 Iteration 4 Error: 0.033841 Align patch 24 1 left Iteration 1 Error: 1.433844 Iteration 2 Error: 0.270841 Iteration 3 Error: 0.217042 Iteration 4 Error: 0.062790 Iteration 5 Error: 0.049353 Align patch 25 0 left Iteration 1 Error: 1.197015 Iteration 2 Error: 0.485603 Iteration 3 Error: 0.139564 Iteration 4 Error: 0.089136 Iteration 5 Error: 0.041264 3D Fitting completed. Patch alignment time: 30.90(sec) Local motion has been corrected. Process thread exits. Computational time: 48.547474 sec Total time: 60.855453 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00023gr_00001sq_v02_00004hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00023gr_00001sq_v02_00004hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.622962s Reading file: gc_18feb27f_CTD_00023gr_00001sq_v02_00004hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.959471s ........................................ >>>>>>TIME<<<<<< FFT: 1.332134s Defocus_U Defocus_V Angle CCC 25367.24 26004.01 6.23 0.043233 Final Values Defocus_U Defocus_V Angle CCC 25387.56 25977.46 8.73 0.075521 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00023gr_00001sq_v02_00004hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00023gr_00001sq_v02_00004hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.336e-01 9.946e-02 CC threshold: 0.730 Mean Std: 51.62 7.50 Num Hot pixels: 82 Hot pixel threshold: 96.64 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.416065 Iteration 2 Error: 0.064588 Iteration 3 Error: 0.020361 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.02 0.06 ...... Frame ( 3) shift: -0.05 0.11 ...... Frame ( 4) shift: -0.07 0.17 ...... Frame ( 5) shift: -0.09 0.22 ...... Frame ( 6) shift: -0.09 0.25 ...... Frame ( 7) shift: -0.06 0.25 ...... Frame ( 8) shift: -0.03 0.25 ...... Frame ( 9) shift: -0.09 0.27 ...... Frame ( 10) shift: -0.22 0.31 ...... Frame ( 11) shift: -0.36 0.35 ...... Frame ( 12) shift: -0.40 0.38 ...... Frame ( 13) shift: -0.35 0.38 ...... Frame ( 14) shift: -0.29 0.39 ...... Frame ( 15) shift: -0.29 0.32 ...... Frame ( 16) shift: -0.33 0.18 ...... Frame ( 17) shift: -0.37 0.04 ...... Frame ( 18) shift: -0.33 0.07 ...... Frame ( 19) shift: -0.19 0.27 ...... Frame ( 20) shift: -0.06 0.47 ...... Frame ( 21) shift: 0.00 0.52 ...... Frame ( 22) shift: 0.00 0.43 ...... Frame ( 23) shift: -0.00 0.33 ...... Frame ( 24) shift: -0.01 0.26 ...... Frame ( 25) shift: -0.04 0.22 ...... Frame ( 26) shift: -0.07 0.17 ...... Frame ( 27) shift: -0.10 0.19 ...... Frame ( 28) shift: -0.15 0.27 ...... Frame ( 29) shift: -0.20 0.35 ...... Frame ( 30) shift: -0.18 0.39 ...... Frame ( 31) shift: -0.08 0.39 ...... Frame ( 32) shift: 0.02 0.39 ...... Frame ( 33) shift: 0.05 0.33 ...... Frame ( 34) shift: 0.02 0.20 ...... Frame ( 35) shift: -0.01 0.07 ...... Frame ( 36) shift: -0.01 0.05 ...... Frame ( 37) shift: 0.02 0.14 ...... Frame ( 38) shift: 0.05 0.23 ...... Frame ( 39) shift: 0.08 0.32 ...... Frame ( 40) shift: 0.11 0.41 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 45.946587 Iteration 2 Error: 42.774380 Iteration 3 Error: 41.929443 Iteration 4 Error: 41.931175 Iteration 5 Error: 41.087120 Align patch 1 24 left Iteration 1 Error: 57.388008 Iteration 2 Error: 63.872555 Iteration 3 Error: 82.656815 Iteration 4 Error: 80.279381 Iteration 5 Error: 80.474548 Align patch 2 23 left Iteration 1 Error: 38.493946 Iteration 2 Error: 38.683277 Iteration 3 Error: 37.961922 Iteration 4 Error: 43.392834 Iteration 5 Error: 46.640621 Align patch 2 23 left Iteration 1 Error: 63.667046 Iteration 2 Error: 59.783447 Iteration 3 Error: 60.640884 Iteration 4 Error: 60.863617 Iteration 5 Error: 60.904865 Align patch 3 22 left Iteration 1 Error: 41.571678 Iteration 2 Error: 37.883698 Iteration 3 Error: 40.886448 Iteration 4 Error: 42.276390 Iteration 5 Error: 41.497982 Align patch 3 22 left Iteration 1 Error: 62.457985 Iteration 2 Error: 62.062317 Iteration 3 Error: 62.541767 Iteration 4 Error: 62.331406 Iteration 5 Error: 62.680481 Align patch 4 21 left Iteration 1 Error: 49.350113 Iteration 2 Error: 48.658688 Iteration 3 Error: 48.274483 Iteration 4 Error: 48.359150 Iteration 5 Error: 47.977211 Align patch 4 21 left Iteration 1 Error: 61.809998 Iteration 2 Error: 69.664963 Iteration 3 Error: 64.007072 Iteration 4 Error: 64.647232 Iteration 5 Error: 63.339756 Align patch 5 20 left Iteration 1 Error: 37.235748 Iteration 2 Error: 36.265419 Iteration 3 Error: 36.841541 Iteration 4 Error: 29.604391 Iteration 5 Error: 37.333996 Align patch 5 20 left Iteration 1 Error: 80.586502 Iteration 2 Error: 77.823769 Iteration 3 Error: 78.138260 Iteration 4 Error: 71.956345 Iteration 5 Error: 71.517212 Align patch 6 19 left Iteration 1 Error: 31.229382 Iteration 2 Error: 39.438538 Iteration 3 Error: 30.056566 Iteration 4 Error: 31.243830 Iteration 5 Error: 31.234861 Align patch 6 19 left Iteration 1 Error: 58.106522 Iteration 2 Error: 59.722240 Iteration 3 Error: 59.465065 Iteration 4 Error: 59.333385 Iteration 5 Error: 59.720169 Align patch 7 18 left Iteration 1 Error: 45.745487 Iteration 2 Error: 26.524818 Iteration 3 Error: 26.806639 Iteration 4 Error: 38.085667 Iteration 5 Error: 38.120758 Align patch 7 18 left Iteration 1 Error: 63.563843 Iteration 2 Error: 72.786461 Iteration 3 Error: 62.414322 Iteration 4 Error: 62.112175 Iteration 5 Error: 62.526402 Align patch 8 17 left Iteration 1 Error: 49.153538 Iteration 2 Error: 48.278469 Iteration 3 Error: 47.713337 Iteration 4 Error: 47.871147 Iteration 5 Error: 48.117008 Align patch 8 17 left Iteration 1 Error: 69.652634 Iteration 2 Error: 69.329041 Iteration 3 Error: 68.801369 Iteration 4 Error: 70.081909 Iteration 5 Error: 70.104431 Align patch 9 16 left Iteration 1 Error: 42.935776 Iteration 2 Error: 41.983585 Iteration 3 Error: 41.418488 Iteration 4 Error: 40.889450 Iteration 5 Error: 39.993603 Align patch 9 16 left Iteration 1 Error: 66.950523 Iteration 2 Error: 67.500687 Iteration 3 Error: 75.792015 Iteration 4 Error: 76.765808 Iteration 5 Error: 77.654968 Align patch 10 15 left Iteration 1 Error: 37.155411 Iteration 2 Error: 36.413422 Iteration 3 Error: 39.887798 Iteration 4 Error: 40.740063 Iteration 5 Error: 40.864864 Align patch 10 15 left Iteration 1 Error: 64.095123 Iteration 2 Error: 63.655830 Iteration 3 Error: 62.954647 Iteration 4 Error: 63.258663 Iteration 5 Error: 62.455685 Align patch 11 14 left Iteration 1 Error: 41.214340 Iteration 2 Error: 44.928802 Iteration 3 Error: 46.084980 Iteration 4 Error: 45.963783 Iteration 5 Error: 46.240620 Align patch 11 14 left Iteration 1 Error: 69.237457 Iteration 2 Error: 68.978706 Iteration 3 Error: 71.018745 Iteration 4 Error: 69.910828 Iteration 5 Error: 67.633347 Align patch 12 13 left Iteration 1 Error: 43.358334 Iteration 2 Error: 45.521706 Iteration 3 Error: 50.420738 Iteration 4 Error: 51.101452 Iteration 5 Error: 51.741215 Align patch 12 13 left Iteration 1 Error: 67.358994 Iteration 2 Error: 66.996399 Iteration 3 Error: 60.220795 Iteration 4 Error: 60.747765 Iteration 5 Error: 61.258770 Align patch 13 12 left Iteration 1 Error: 26.352690 Iteration 2 Error: 44.749744 Iteration 3 Error: 32.035217 Iteration 4 Error: 33.344948 Iteration 5 Error: 33.381001 Align patch 13 12 left Iteration 1 Error: 68.973785 Iteration 2 Error: 69.686096 Iteration 3 Error: 72.181198 Iteration 4 Error: 54.617153 Iteration 5 Error: 54.378597 Align patch 14 11 left Iteration 1 Error: 42.342495 Iteration 2 Error: 35.287174 Iteration 3 Error: 35.867229 Iteration 4 Error: 34.880371 Iteration 5 Error: 34.733459 Align patch 14 11 left Iteration 1 Error: 75.099731 Iteration 2 Error: 76.534485 Iteration 3 Error: 73.674126 Iteration 4 Error: 73.299271 Iteration 5 Error: 73.060059 Align patch 15 10 left Iteration 1 Error: 33.328655 Iteration 2 Error: 33.788399 Iteration 3 Error: 34.018753 Iteration 4 Error: 33.760170 Iteration 5 Error: 34.203922 Align patch 15 10 left Iteration 1 Error: 79.289032 Iteration 2 Error: 78.602356 Iteration 3 Error: 78.421440 Iteration 4 Error: 78.951241 Iteration 5 Error: 79.629799 Align patch 16 9 left Iteration 1 Error: 36.584450 Iteration 2 Error: 36.373932 Iteration 3 Error: 36.030979 Iteration 4 Error: 36.224483 Iteration 5 Error: 40.605450 Align patch 16 9 left Iteration 1 Error: 62.040741 Iteration 2 Error: 61.795982 Iteration 3 Error: 63.559555 Iteration 4 Error: 63.505943 Iteration 5 Error: 62.224442 Align patch 17 8 left Iteration 1 Error: 37.755535 Iteration 2 Error: 43.290302 Iteration 3 Error: 42.586693 Iteration 4 Error: 41.765675 Iteration 5 Error: 41.955578 Align patch 17 8 left Iteration 1 Error: 42.960289 Iteration 2 Error: 63.599545 Iteration 3 Error: 63.183655 Iteration 4 Error: 63.380726 Iteration 5 Error: 63.343124 Align patch 18 7 left Iteration 1 Error: 22.258183 Iteration 2 Error: 30.389536 Iteration 3 Error: 37.160217 Iteration 4 Error: 13.536174 Iteration 5 Error: 13.815450 Align patch 18 7 left Iteration 1 Error: 46.904804 Iteration 2 Error: 4.547857 Iteration 3 Error: 1.891589 Iteration 4 Error: 1.136305 Iteration 5 Error: 0.439540 Align patch 19 6 left Iteration 1 Error: 45.616413 Iteration 2 Error: 45.693390 Iteration 3 Error: 45.162399 Iteration 4 Error: 45.552029 Iteration 5 Error: 45.349575 Align patch 19 6 left Iteration 1 Error: 72.985893 Iteration 2 Error: 71.739052 Iteration 3 Error: 66.056862 Iteration 4 Error: 66.158493 Iteration 5 Error: 66.791412 Align patch 20 5 left Iteration 1 Error: 35.499130 Iteration 2 Error: 37.136547 Iteration 3 Error: 37.191669 Iteration 4 Error: 41.167152 Iteration 5 Error: 40.136917 Align patch 20 5 left Iteration 1 Error: 72.646088 Iteration 2 Error: 74.463943 Iteration 3 Error: 74.386047 Iteration 4 Error: 73.696533 Iteration 5 Error: 65.610260 Align patch 21 4 left Iteration 1 Error: 41.501793 Iteration 2 Error: 42.616661 Iteration 3 Error: 42.041565 Iteration 4 Error: 42.064381 Iteration 5 Error: 42.039360 Align patch 21 4 left Iteration 1 Error: 73.293640 Iteration 2 Error: 64.633888 Iteration 3 Error: 65.054077 Iteration 4 Error: 58.872375 Iteration 5 Error: 51.832096 Align patch 22 3 left Iteration 1 Error: 39.432858 Iteration 2 Error: 46.003757 Iteration 3 Error: 45.858818 Iteration 4 Error: 46.398991 Iteration 5 Error: 46.451233 Align patch 22 3 left Iteration 1 Error: 57.516499 Iteration 2 Error: 57.075127 Iteration 3 Error: 58.454212 Iteration 4 Error: 60.146358 Iteration 5 Error: 60.649532 Align patch 23 2 left Iteration 1 Error: 40.858974 Iteration 2 Error: 37.255936 Iteration 3 Error: 37.509838 Iteration 4 Error: 36.477211 Iteration 5 Error: 36.611835 Align patch 23 2 left Iteration 1 Error: 54.113888 Iteration 2 Error: 52.547527 Iteration 3 Error: 52.311344 Iteration 4 Error: 51.169125 Iteration 5 Error: 49.994537 Align patch 24 1 left Iteration 1 Error: 45.954502 Iteration 2 Error: 46.804028 Iteration 3 Error: 46.079384 Iteration 4 Error: 46.261406 Iteration 5 Error: 46.246128 Align patch 24 1 left Iteration 1 Error: 75.149673 Iteration 2 Error: 39.624657 Iteration 3 Error: 53.751797 Iteration 4 Error: 54.295368 Iteration 5 Error: 54.658291 Align patch 25 0 left Iteration 1 Error: 40.136757 Iteration 2 Error: 34.695072 Iteration 3 Error: 42.336449 Iteration 4 Error: 33.100319 Iteration 5 Error: 31.810497 Align patch 25 0 left Iteration 1 Error: 76.364670 Iteration 2 Error: 56.648262 Iteration 3 Error: 66.806297 Iteration 4 Error: 65.597763 Iteration 5 Error: 57.664688 3D Fitting completed. Patch alignment time: 51.72(sec) Local motion has been corrected. Process thread exits. Computational time: 67.964401 sec Total time: 84.147598 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00023gr_00001sq_v02_00004hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00023gr_00001sq_v02_00004hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.644108s Reading file: gc_18feb27f_CTD_00023gr_00001sq_v02_00004hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.518261s ........................................ >>>>>>TIME<<<<<< FFT: 1.485003s Defocus_U Defocus_V Angle CCC 27320.32 27796.89 18.75 0.024249 Final Values Defocus_U Defocus_V Angle CCC 27359.33 27761.02 11.27 0.047910 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00023gr_00001sq_v02_00004hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00023gr_00001sq_v02_00004hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.337e-01 9.948e-02 CC threshold: 0.731 Mean Std: 51.64 7.51 Num Hot pixels: 98 Hot pixel threshold: 96.69 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.503660 Iteration 2 Error: 0.059228 Iteration 3 Error: 0.040336 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.17 -0.09 ...... Frame ( 3) shift: -0.34 -0.18 ...... Frame ( 4) shift: -0.52 -0.27 ...... Frame ( 5) shift: -0.69 -0.37 ...... Frame ( 6) shift: -0.75 -0.34 ...... Frame ( 7) shift: -0.70 -0.20 ...... Frame ( 8) shift: -0.66 -0.07 ...... Frame ( 9) shift: -0.59 -0.03 ...... Frame ( 10) shift: -0.51 -0.09 ...... Frame ( 11) shift: -0.43 -0.15 ...... Frame ( 12) shift: -0.39 -0.21 ...... Frame ( 13) shift: -0.37 -0.29 ...... Frame ( 14) shift: -0.36 -0.36 ...... Frame ( 15) shift: -0.38 -0.36 ...... Frame ( 16) shift: -0.42 -0.29 ...... Frame ( 17) shift: -0.47 -0.22 ...... Frame ( 18) shift: -0.46 -0.18 ...... Frame ( 19) shift: -0.41 -0.19 ...... Frame ( 20) shift: -0.35 -0.20 ...... Frame ( 21) shift: -0.32 -0.14 ...... Frame ( 22) shift: -0.31 -0.02 ...... Frame ( 23) shift: -0.30 0.10 ...... Frame ( 24) shift: -0.30 0.08 ...... Frame ( 25) shift: -0.29 -0.08 ...... Frame ( 26) shift: -0.28 -0.24 ...... Frame ( 27) shift: -0.27 -0.26 ...... Frame ( 28) shift: -0.26 -0.13 ...... Frame ( 29) shift: -0.25 0.00 ...... Frame ( 30) shift: -0.21 0.03 ...... Frame ( 31) shift: -0.15 -0.04 ...... Frame ( 32) shift: -0.08 -0.12 ...... Frame ( 33) shift: -0.08 -0.14 ...... Frame ( 34) shift: -0.15 -0.12 ...... Frame ( 35) shift: -0.21 -0.09 ...... Frame ( 36) shift: -0.23 -0.08 ...... Frame ( 37) shift: -0.20 -0.07 ...... Frame ( 38) shift: -0.17 -0.05 ...... Frame ( 39) shift: -0.14 -0.04 ...... Frame ( 40) shift: -0.11 -0.03 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 41.413250 Iteration 2 Error: 39.676933 Iteration 3 Error: 39.712479 Iteration 4 Error: 39.511612 Iteration 5 Error: 39.734840 Align patch 1 24 left Iteration 1 Error: 58.724594 Iteration 2 Error: 58.658581 Iteration 3 Error: 74.952492 Iteration 4 Error: 75.410988 Iteration 5 Error: 75.251572 Align patch 2 23 left Iteration 1 Error: 38.284592 Iteration 2 Error: 37.756042 Iteration 3 Error: 37.657501 Iteration 4 Error: 37.846527 Iteration 5 Error: 37.980713 Align patch 2 23 left Iteration 1 Error: 68.501228 Iteration 2 Error: 57.408440 Iteration 3 Error: 56.477928 Iteration 4 Error: 56.062210 Iteration 5 Error: 62.359772 Align patch 3 22 left Iteration 1 Error: 48.814114 Iteration 2 Error: 47.458820 Iteration 3 Error: 37.216202 Iteration 4 Error: 37.576134 Iteration 5 Error: 37.750389 Align patch 3 22 left Iteration 1 Error: 58.301037 Iteration 2 Error: 75.121864 Iteration 3 Error: 76.787193 Iteration 4 Error: 76.847862 Iteration 5 Error: 41.880352 Align patch 4 21 left Iteration 1 Error: 39.478611 Iteration 2 Error: 40.529366 Iteration 3 Error: 40.411110 Iteration 4 Error: 35.756001 Iteration 5 Error: 24.477373 Align patch 4 21 left Iteration 1 Error: 57.213306 Iteration 2 Error: 60.924252 Iteration 3 Error: 60.957680 Iteration 4 Error: 60.926937 Iteration 5 Error: 60.836903 Align patch 5 20 left Iteration 1 Error: 48.654537 Iteration 2 Error: 40.626507 Iteration 3 Error: 40.917152 Iteration 4 Error: 41.136776 Iteration 5 Error: 28.653967 Align patch 5 20 left Iteration 1 Error: 62.962307 Iteration 2 Error: 63.448475 Iteration 3 Error: 20.431534 Iteration 4 Error: 45.343548 Iteration 5 Error: 45.373001 Align patch 6 19 left Iteration 1 Error: 43.834850 Iteration 2 Error: 37.373619 Iteration 3 Error: 37.776333 Iteration 4 Error: 38.395054 Iteration 5 Error: 38.417992 Align patch 6 19 left Iteration 1 Error: 46.817379 Iteration 2 Error: 66.839493 Iteration 3 Error: 78.669777 Iteration 4 Error: 67.904282 Iteration 5 Error: 68.277161 Align patch 7 18 left Iteration 1 Error: 49.934265 Iteration 2 Error: 34.934959 Iteration 3 Error: 34.924843 Iteration 4 Error: 34.709759 Iteration 5 Error: 34.815113 Align patch 7 18 left Iteration 1 Error: 44.542728 Iteration 2 Error: 52.825241 Iteration 3 Error: 59.824745 Iteration 4 Error: 59.901279 Iteration 5 Error: 59.031540 Align patch 8 17 left Iteration 1 Error: 45.368412 Iteration 2 Error: 42.983936 Iteration 3 Error: 40.852196 Iteration 4 Error: 40.894268 Iteration 5 Error: 50.389286 Align patch 8 17 left Iteration 1 Error: 79.325157 Iteration 2 Error: 64.813637 Iteration 3 Error: 64.942703 Iteration 4 Error: 65.578712 Iteration 5 Error: 65.515923 Align patch 9 16 left Iteration 1 Error: 50.658001 Iteration 2 Error: 37.804661 Iteration 3 Error: 37.097649 Iteration 4 Error: 37.963020 Iteration 5 Error: 37.633514 Align patch 9 16 left Iteration 1 Error: 58.688240 Iteration 2 Error: 63.743813 Iteration 3 Error: 72.480453 Iteration 4 Error: 72.156158 Iteration 5 Error: 72.947540 Align patch 10 15 left Iteration 1 Error: 31.057467 Iteration 2 Error: 26.543684 Iteration 3 Error: 26.102968 Iteration 4 Error: 26.148464 Iteration 5 Error: 26.042147 Align patch 10 15 left Iteration 1 Error: 72.531693 Iteration 2 Error: 72.149719 Iteration 3 Error: 58.677353 Iteration 4 Error: 59.660084 Iteration 5 Error: 60.142467 Align patch 11 14 left Iteration 1 Error: 35.440601 Iteration 2 Error: 37.462574 Iteration 3 Error: 37.380524 Iteration 4 Error: 37.065639 Iteration 5 Error: 36.428246 Align patch 11 14 left Iteration 1 Error: 75.626602 Iteration 2 Error: 54.735428 Iteration 3 Error: 68.323082 Iteration 4 Error: 58.922207 Iteration 5 Error: 55.769581 Align patch 12 13 left Iteration 1 Error: 43.243294 Iteration 2 Error: 36.651478 Iteration 3 Error: 36.833862 Iteration 4 Error: 36.271030 Iteration 5 Error: 36.322258 Align patch 12 13 left Iteration 1 Error: 46.288883 Iteration 2 Error: 51.116673 Iteration 3 Error: 40.118813 Iteration 4 Error: 39.852341 Iteration 5 Error: 40.479053 Align patch 13 12 left Iteration 1 Error: 47.046089 Iteration 2 Error: 46.773758 Iteration 3 Error: 45.680943 Iteration 4 Error: 45.750916 Iteration 5 Error: 45.715363 Align patch 13 12 left Iteration 1 Error: 61.666069 Iteration 2 Error: 53.378784 Iteration 3 Error: 59.952732 Iteration 4 Error: 59.709759 Iteration 5 Error: 63.009121 Align patch 14 11 left Iteration 1 Error: 46.180183 Iteration 2 Error: 46.511284 Iteration 3 Error: 47.523933 Iteration 4 Error: 46.966015 Iteration 5 Error: 47.309555 Align patch 14 11 left Iteration 1 Error: 67.392838 Iteration 2 Error: 68.142746 Iteration 3 Error: 71.548645 Iteration 4 Error: 69.521210 Iteration 5 Error: 69.610924 Align patch 15 10 left Iteration 1 Error: 40.993107 Iteration 2 Error: 42.212372 Iteration 3 Error: 41.878735 Iteration 4 Error: 43.089199 Iteration 5 Error: 43.386902 Align patch 15 10 left Iteration 1 Error: 75.741516 Iteration 2 Error: 77.768761 Iteration 3 Error: 77.289909 Iteration 4 Error: 77.580742 Iteration 5 Error: 78.239487 Align patch 16 9 left Iteration 1 Error: 35.727238 Iteration 2 Error: 36.078678 Iteration 3 Error: 35.804283 Iteration 4 Error: 38.138920 Iteration 5 Error: 38.158302 Align patch 16 9 left Iteration 1 Error: 57.905163 Iteration 2 Error: 58.986153 Iteration 3 Error: 58.487671 Iteration 4 Error: 60.715298 Iteration 5 Error: 60.667183 Align patch 17 8 left Iteration 1 Error: 45.986790 Iteration 2 Error: 24.502346 Iteration 3 Error: 24.382973 Iteration 4 Error: 37.935638 Iteration 5 Error: 38.000645 Align patch 17 8 left Iteration 1 Error: 58.902821 Iteration 2 Error: 81.824600 Iteration 3 Error: 82.376320 Iteration 4 Error: 80.650124 Iteration 5 Error: 80.033585 Align patch 18 7 left Iteration 1 Error: 41.568237 Iteration 2 Error: 41.766479 Iteration 3 Error: 44.410492 Iteration 4 Error: 43.335407 Iteration 5 Error: 44.291885 Align patch 18 7 left Iteration 1 Error: 66.119980 Iteration 2 Error: 66.717079 Iteration 3 Error: 66.293350 Iteration 4 Error: 66.493553 Iteration 5 Error: 65.880898 Align patch 19 6 left Iteration 1 Error: 36.103424 Iteration 2 Error: 43.695774 Iteration 3 Error: 43.131439 Iteration 4 Error: 42.754864 Iteration 5 Error: 42.440105 Align patch 19 6 left Iteration 1 Error: 72.590858 Iteration 2 Error: 72.694954 Iteration 3 Error: 72.360229 Iteration 4 Error: 72.374046 Iteration 5 Error: 57.853325 Align patch 20 5 left Iteration 1 Error: 33.920002 Iteration 2 Error: 38.450500 Iteration 3 Error: 38.377716 Iteration 4 Error: 38.603596 Iteration 5 Error: 38.371033 Align patch 20 5 left Iteration 1 Error: 61.986626 Iteration 2 Error: 76.040573 Iteration 3 Error: 75.786896 Iteration 4 Error: 75.367264 Iteration 5 Error: 75.556534 Align patch 21 4 left Iteration 1 Error: 39.341850 Iteration 2 Error: 41.017132 Iteration 3 Error: 41.560986 Iteration 4 Error: 41.406288 Iteration 5 Error: 42.666267 Align patch 21 4 left Iteration 1 Error: 54.283138 Iteration 2 Error: 49.281052 Iteration 3 Error: 48.663830 Iteration 4 Error: 54.898727 Iteration 5 Error: 57.523384 Align patch 22 3 left Iteration 1 Error: 39.642490 Iteration 2 Error: 39.484806 Iteration 3 Error: 39.620014 Iteration 4 Error: 40.392914 Iteration 5 Error: 38.821575 Align patch 22 3 left Iteration 1 Error: 66.862457 Iteration 2 Error: 63.771091 Iteration 3 Error: 74.037849 Iteration 4 Error: 73.908562 Iteration 5 Error: 72.794014 Align patch 23 2 left Iteration 1 Error: 38.204727 Iteration 2 Error: 37.725426 Iteration 3 Error: 37.732101 Iteration 4 Error: 37.766182 Iteration 5 Error: 38.084118 Align patch 23 2 left Iteration 1 Error: 62.063393 Iteration 2 Error: 61.924049 Iteration 3 Error: 63.677883 Iteration 4 Error: 80.698494 Iteration 5 Error: 79.206398 Align patch 24 1 left Iteration 1 Error: 22.269650 Iteration 2 Error: 0.509987 Iteration 3 Error: 0.205156 Iteration 4 Error: 0.077120 Iteration 5 Error: 0.032990 Align patch 25 0 left Iteration 1 Error: 37.177597 Iteration 2 Error: 36.407536 Iteration 3 Error: 35.339821 Iteration 4 Error: 35.384327 Iteration 5 Error: 35.299034 Align patch 25 0 left Iteration 1 Error: 78.360336 Iteration 2 Error: 67.015121 Iteration 3 Error: 71.252724 Iteration 4 Error: 75.848099 Iteration 5 Error: 76.644836 3D Fitting completed. Patch alignment time: 51.26(sec) Local motion has been corrected. Process thread exits. Computational time: 68.476974 sec Total time: 84.384895 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00023gr_00001sq_v02_00004hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00023gr_00001sq_v02_00004hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.621776s Reading file: gc_18feb27f_CTD_00023gr_00001sq_v02_00004hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.343961s ........................................ >>>>>>TIME<<<<<< FFT: 1.395853s Defocus_U Defocus_V Angle CCC 79481.21 79763.07 80.08 0.025894 Final Values Defocus_U Defocus_V Angle CCC 79484.34 79753.70 79.14 0.051137 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_00023gr_00001sq_v02_00004hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_00023gr_00001sq_v02_00004hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.336e-01 9.946e-02 CC threshold: 0.730 Mean Std: 51.64 7.51 Num Hot pixels: 102 Hot pixel threshold: 96.68 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.463329 Iteration 2 Error: 0.054102 Iteration 3 Error: 0.019908 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.03 0.01 ...... Frame ( 3) shift: -0.05 0.03 ...... Frame ( 4) shift: -0.08 0.04 ...... Frame ( 5) shift: -0.11 0.05 ...... Frame ( 6) shift: -0.14 -0.01 ...... Frame ( 7) shift: -0.16 -0.15 ...... Frame ( 8) shift: -0.19 -0.29 ...... Frame ( 9) shift: -0.18 -0.30 ...... Frame ( 10) shift: -0.13 -0.17 ...... Frame ( 11) shift: -0.08 -0.05 ...... Frame ( 12) shift: -0.11 -0.02 ...... Frame ( 13) shift: -0.21 -0.09 ...... Frame ( 14) shift: -0.32 -0.16 ...... Frame ( 15) shift: -0.36 -0.17 ...... Frame ( 16) shift: -0.34 -0.12 ...... Frame ( 17) shift: -0.32 -0.07 ...... Frame ( 18) shift: -0.28 -0.04 ...... Frame ( 19) shift: -0.21 -0.03 ...... Frame ( 20) shift: -0.14 -0.03 ...... Frame ( 21) shift: -0.09 -0.02 ...... Frame ( 22) shift: -0.07 -0.02 ...... Frame ( 23) shift: -0.05 -0.02 ...... Frame ( 24) shift: -0.12 0.02 ...... Frame ( 25) shift: -0.30 0.11 ...... Frame ( 26) shift: -0.48 0.19 ...... Frame ( 27) shift: -0.49 0.15 ...... Frame ( 28) shift: -0.34 -0.02 ...... Frame ( 29) shift: -0.19 -0.19 ...... Frame ( 30) shift: -0.10 -0.24 ...... Frame ( 31) shift: -0.06 -0.17 ...... Frame ( 32) shift: -0.02 -0.11 ...... Frame ( 33) shift: -0.04 -0.06 ...... Frame ( 34) shift: -0.10 -0.03 ...... Frame ( 35) shift: -0.17 -0.01 ...... Frame ( 36) shift: -0.21 -0.02 ...... Frame ( 37) shift: -0.23 -0.08 ...... Frame ( 38) shift: -0.25 -0.13 ...... Frame ( 39) shift: -0.26 -0.18 ...... Frame ( 40) shift: -0.28 -0.24 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 43.777397 Iteration 2 Error: 28.409969 Iteration 3 Error: 41.305012 Iteration 4 Error: 42.085114 Iteration 5 Error: 42.077343 Align patch 1 24 left Iteration 1 Error: 60.045456 Iteration 2 Error: 62.077705 Iteration 3 Error: 61.302502 Iteration 4 Error: 61.901340 Iteration 5 Error: 61.907192 Align patch 2 23 left Iteration 1 Error: 33.923405 Iteration 2 Error: 29.971560 Iteration 3 Error: 0.774905 Iteration 4 Error: 0.520005 Iteration 5 Error: 0.489792 Align patch 2 23 left Iteration 1 Error: 66.360657 Iteration 2 Error: 66.354019 Iteration 3 Error: 65.985634 Iteration 4 Error: 65.908089 Iteration 5 Error: 66.835815 Align patch 3 22 left Iteration 1 Error: 42.768375 Iteration 2 Error: 44.192078 Iteration 3 Error: 46.246342 Iteration 4 Error: 45.070103 Iteration 5 Error: 44.409866 Align patch 3 22 left Iteration 1 Error: 68.146843 Iteration 2 Error: 62.492233 Iteration 3 Error: 65.163742 Iteration 4 Error: 79.838310 Iteration 5 Error: 79.013374 Align patch 4 21 left Iteration 1 Error: 27.276386 Iteration 2 Error: 39.230530 Iteration 3 Error: 40.224987 Iteration 4 Error: 41.375706 Iteration 5 Error: 29.659344 Align patch 4 21 left Iteration 1 Error: 30.527180 Iteration 2 Error: 73.713615 Iteration 3 Error: 63.223087 Iteration 4 Error: 60.864502 Iteration 5 Error: 65.494255 Align patch 5 20 left Iteration 1 Error: 35.763084 Iteration 2 Error: 42.482750 Iteration 3 Error: 34.131092 Iteration 4 Error: 34.174862 Iteration 5 Error: 34.201450 Align patch 5 20 left Iteration 1 Error: 59.305401 Iteration 2 Error: 54.811535 Iteration 3 Error: 55.010349 Iteration 4 Error: 54.918186 Iteration 5 Error: 54.803318 Align patch 6 19 left Iteration 1 Error: 41.963985 Iteration 2 Error: 42.337063 Iteration 3 Error: 44.169327 Iteration 4 Error: 47.276314 Iteration 5 Error: 48.745750 Align patch 6 19 left Iteration 1 Error: 56.977379 Iteration 2 Error: 59.065086 Iteration 3 Error: 53.554070 Iteration 4 Error: 50.541718 Iteration 5 Error: 51.285530 Align patch 7 18 left Iteration 1 Error: 35.583477 Iteration 2 Error: 40.437309 Iteration 3 Error: 40.164028 Iteration 4 Error: 40.486729 Iteration 5 Error: 44.080490 Align patch 7 18 left Iteration 1 Error: 61.100082 Iteration 2 Error: 68.693848 Iteration 3 Error: 67.376869 Iteration 4 Error: 31.364695 Iteration 5 Error: 30.802124 Align patch 8 17 left Iteration 1 Error: 35.887657 Iteration 2 Error: 37.411716 Iteration 3 Error: 37.436958 Iteration 4 Error: 41.318478 Iteration 5 Error: 41.163498 Align patch 8 17 left Iteration 1 Error: 69.277817 Iteration 2 Error: 62.230900 Iteration 3 Error: 66.582024 Iteration 4 Error: 51.569885 Iteration 5 Error: 31.984461 Align patch 9 16 left Iteration 1 Error: 46.573116 Iteration 2 Error: 49.776924 Iteration 3 Error: 49.549263 Iteration 4 Error: 48.965961 Iteration 5 Error: 48.808487 Align patch 9 16 left Iteration 1 Error: 59.654560 Iteration 2 Error: 54.314022 Iteration 3 Error: 54.991829 Iteration 4 Error: 56.396519 Iteration 5 Error: 63.731335 Align patch 10 15 left Iteration 1 Error: 40.611752 Iteration 2 Error: 44.803051 Iteration 3 Error: 48.921551 Iteration 4 Error: 40.853596 Iteration 5 Error: 40.876408 Align patch 10 15 left Iteration 1 Error: 59.479015 Iteration 2 Error: 69.062111 Iteration 3 Error: 69.816681 Iteration 4 Error: 68.793877 Iteration 5 Error: 51.575325 Align patch 11 14 left Iteration 1 Error: 43.573967 Iteration 2 Error: 33.635860 Iteration 3 Error: 34.086597 Iteration 4 Error: 34.656307 Iteration 5 Error: 35.069115 Align patch 11 14 left Iteration 1 Error: 76.849564 Iteration 2 Error: 76.209465 Iteration 3 Error: 75.141945 Iteration 4 Error: 74.333000 Iteration 5 Error: 72.375465 Align patch 12 13 left Iteration 1 Error: 40.018456 Iteration 2 Error: 44.847343 Iteration 3 Error: 45.038776 Iteration 4 Error: 44.988403 Iteration 5 Error: 45.428875 Align patch 12 13 left Iteration 1 Error: 76.839615 Iteration 2 Error: 76.745636 Iteration 3 Error: 72.288429 Iteration 4 Error: 72.136414 Iteration 5 Error: 72.200439 Align patch 13 12 left Iteration 1 Error: 36.561131 Iteration 2 Error: 25.649473 Iteration 3 Error: 26.394394 Iteration 4 Error: 26.346680 Iteration 5 Error: 36.179714 Align patch 13 12 left Iteration 1 Error: 70.763763 Iteration 2 Error: 73.291290 Iteration 3 Error: 74.100433 Iteration 4 Error: 77.666931 Iteration 5 Error: 77.960709 Align patch 14 11 left Iteration 1 Error: 50.140045 Iteration 2 Error: 50.069889 Iteration 3 Error: 50.118996 Iteration 4 Error: 46.694706 Iteration 5 Error: 46.672802 Align patch 14 11 left Iteration 1 Error: 62.854755 Iteration 2 Error: 62.861031 Iteration 3 Error: 64.768776 Iteration 4 Error: 63.743443 Iteration 5 Error: 64.733376 Align patch 15 10 left Iteration 1 Error: 45.785706 Iteration 2 Error: 46.024593 Iteration 3 Error: 46.964001 Iteration 4 Error: 47.173805 Iteration 5 Error: 46.739296 Align patch 15 10 left Iteration 1 Error: 63.192059 Iteration 2 Error: 74.166275 Iteration 3 Error: 60.506680 Iteration 4 Error: 64.245819 Iteration 5 Error: 64.408028 Align patch 16 9 left Iteration 1 Error: 46.513668 Iteration 2 Error: 39.889626 Iteration 3 Error: 39.703465 Iteration 4 Error: 42.908043 Iteration 5 Error: 42.929344 Align patch 16 9 left Iteration 1 Error: 81.691101 Iteration 2 Error: 59.438171 Iteration 3 Error: 60.551830 Iteration 4 Error: 60.574890 Iteration 5 Error: 60.278290 Align patch 17 8 left Iteration 1 Error: 35.849594 Iteration 2 Error: 41.549236 Iteration 3 Error: 42.456722 Iteration 4 Error: 42.960472 Iteration 5 Error: 43.961403 Align patch 17 8 left Iteration 1 Error: 74.739601 Iteration 2 Error: 75.387924 Iteration 3 Error: 73.563873 Iteration 4 Error: 73.654106 Iteration 5 Error: 73.776268 Align patch 18 7 left Iteration 1 Error: 37.407440 Iteration 2 Error: 37.056694 Iteration 3 Error: 37.744793 Iteration 4 Error: 38.270470 Iteration 5 Error: 38.483574 Align patch 18 7 left Iteration 1 Error: 53.077877 Iteration 2 Error: 53.646935 Iteration 3 Error: 69.382538 Iteration 4 Error: 72.956001 Iteration 5 Error: 72.443993 Align patch 19 6 left Iteration 1 Error: 39.657223 Iteration 2 Error: 31.738758 Iteration 3 Error: 33.293877 Iteration 4 Error: 33.386955 Iteration 5 Error: 33.677662 Align patch 19 6 left Iteration 1 Error: 63.834583 Iteration 2 Error: 68.542244 Iteration 3 Error: 67.384895 Iteration 4 Error: 72.680504 Iteration 5 Error: 72.325302 Align patch 20 5 left Iteration 1 Error: 38.440002 Iteration 2 Error: 44.855713 Iteration 3 Error: 44.764481 Iteration 4 Error: 45.627777 Iteration 5 Error: 45.674347 Align patch 20 5 left Iteration 1 Error: 52.524048 Iteration 2 Error: 46.081398 Iteration 3 Error: 44.633286 Iteration 4 Error: 32.511177 Iteration 5 Error: 1.883527 Align patch 21 4 left Iteration 1 Error: 43.600353 Iteration 2 Error: 33.293297 Iteration 3 Error: 30.269197 Iteration 4 Error: 27.826553 Iteration 5 Error: 28.240829 Align patch 21 4 left Iteration 1 Error: 68.828941 Iteration 2 Error: 75.339897 Iteration 3 Error: 76.043571 Iteration 4 Error: 75.850159 Iteration 5 Error: 75.626770 Align patch 22 3 left Iteration 1 Error: 35.598686 Iteration 2 Error: 39.408546 Iteration 3 Error: 40.057491 Iteration 4 Error: 40.930302 Iteration 5 Error: 40.951138 Align patch 22 3 left Iteration 1 Error: 65.823036 Iteration 2 Error: 65.372200 Iteration 3 Error: 66.143814 Iteration 4 Error: 65.580246 Iteration 5 Error: 64.604706 Align patch 23 2 left Iteration 1 Error: 45.465691 Iteration 2 Error: 37.963528 Iteration 3 Error: 37.233288 Iteration 4 Error: 44.920109 Iteration 5 Error: 44.978645 Align patch 23 2 left Iteration 1 Error: 58.128605 Iteration 2 Error: 68.493195 Iteration 3 Error: 58.916039 Iteration 4 Error: 52.553478 Iteration 5 Error: 50.418903 Align patch 24 1 left Iteration 1 Error: 45.065990 Iteration 2 Error: 43.985245 Iteration 3 Error: 44.017456 Iteration 4 Error: 43.866741 Iteration 5 Error: 43.425655 Align patch 24 1 left Iteration 1 Error: 61.684803 Iteration 2 Error: 59.194977 Iteration 3 Error: 58.855537 Iteration 4 Error: 59.819992 Iteration 5 Error: 58.654121 Align patch 25 0 left Iteration 1 Error: 41.904598 Iteration 2 Error: 44.680271 Iteration 3 Error: 45.007851 Iteration 4 Error: 44.304169 Iteration 5 Error: 44.164070 Align patch 25 0 left Iteration 1 Error: 60.929893 Iteration 2 Error: 62.490036 Iteration 3 Error: 60.683441 Iteration 4 Error: 59.205364 Iteration 5 Error: 64.284996 3D Fitting completed. Patch alignment time: 51.25(sec) Local motion has been corrected. Process thread exits. Computational time: 67.356567 sec Total time: 78.135155 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_00023gr_00001sq_v02_00004hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_00023gr_00001sq_v02_00004hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.673805s Reading file: gc_18feb27f_CTD_00023gr_00001sq_v02_00004hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 5.484241s ........................................ >>>>>>TIME<<<<<< FFT: 1.530046s Defocus_U Defocus_V Angle CCC 13216.93 12392.98 1.90 0.026729 Final Values Defocus_U Defocus_V Angle CCC 13173.14 12502.43 8.56 0.051702 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00001sq_v01_00002hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00002hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.004e-01 CC threshold: 0.737 Mean Std: 40.63 7.06 Num Hot pixels: 202 Hot pixel threshold: 82.98 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.235136 Iteration 2 Error: 0.127286 Iteration 3 Error: 0.018669 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.03 -0.33 ...... Frame ( 3) shift: -0.06 -0.66 ...... Frame ( 4) shift: -0.08 -0.99 ...... Frame ( 5) shift: -0.11 -1.32 ...... Frame ( 6) shift: -0.08 -1.46 ...... Frame ( 7) shift: 0.02 -1.43 ...... Frame ( 8) shift: 0.13 -1.39 ...... Frame ( 9) shift: 0.20 -1.32 ...... Frame ( 10) shift: 0.26 -1.23 ...... Frame ( 11) shift: 0.32 -1.14 ...... Frame ( 12) shift: 0.37 -1.04 ...... Frame ( 13) shift: 0.42 -0.94 ...... Frame ( 14) shift: 0.46 -0.85 ...... Frame ( 15) shift: 0.51 -0.79 ...... Frame ( 16) shift: 0.55 -0.77 ...... Frame ( 17) shift: 0.60 -0.75 ...... Frame ( 18) shift: 0.67 -0.71 ...... Frame ( 19) shift: 0.76 -0.63 ...... Frame ( 20) shift: 0.85 -0.55 ...... Frame ( 21) shift: 0.87 -0.47 ...... Frame ( 22) shift: 0.81 -0.40 ...... Frame ( 23) shift: 0.75 -0.33 ...... Frame ( 24) shift: 0.75 -0.25 ...... Frame ( 25) shift: 0.82 -0.15 ...... Frame ( 26) shift: 0.89 -0.05 ...... Frame ( 27) shift: 0.93 0.01 ...... Frame ( 28) shift: 0.93 0.04 ...... Frame ( 29) shift: 0.94 0.07 ...... Frame ( 30) shift: 0.97 0.12 ...... Frame ( 31) shift: 1.04 0.20 ...... Frame ( 32) shift: 1.10 0.29 ...... Frame ( 33) shift: 1.16 0.34 ...... Frame ( 34) shift: 1.20 0.38 ...... Frame ( 35) shift: 1.24 0.42 ...... Frame ( 36) shift: 1.29 0.41 ...... Frame ( 37) shift: 1.34 0.37 ...... Frame ( 38) shift: 1.39 0.32 ...... Frame ( 39) shift: 1.44 0.28 ...... Frame ( 40) shift: 1.49 0.23 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.646836 Iteration 2 Error: 0.164781 Iteration 3 Error: 0.029159 Align patch 2 23 left Iteration 1 Error: 1.443664 Iteration 2 Error: 0.188206 Iteration 3 Error: 0.049983 Align patch 3 22 left Iteration 1 Error: 0.940949 Iteration 2 Error: 0.151384 Iteration 3 Error: 0.042312 Align patch 4 21 left Iteration 1 Error: 1.196742 Iteration 2 Error: 0.226871 Iteration 3 Error: 0.035089 Align patch 5 20 left Iteration 1 Error: 1.164131 Iteration 2 Error: 0.170636 Iteration 3 Error: 0.023519 Align patch 6 19 left Iteration 1 Error: 0.948429 Iteration 2 Error: 0.067841 Iteration 3 Error: 0.009679 Align patch 7 18 left Iteration 1 Error: 0.610260 Iteration 2 Error: 0.076245 Iteration 3 Error: 0.016987 Align patch 8 17 left Iteration 1 Error: 0.705734 Iteration 2 Error: 0.075530 Iteration 3 Error: 0.015542 Align patch 9 16 left Iteration 1 Error: 0.894024 Iteration 2 Error: 0.109782 Iteration 3 Error: 0.021385 Align patch 10 15 left Iteration 1 Error: 0.748582 Iteration 2 Error: 0.112592 Iteration 3 Error: 0.023707 Align patch 11 14 left Iteration 1 Error: 0.550060 Iteration 2 Error: 0.046039 Align patch 12 13 left Iteration 1 Error: 0.707138 Iteration 2 Error: 0.068385 Iteration 3 Error: 0.012764 Align patch 13 12 left Iteration 1 Error: 0.504506 Iteration 2 Error: 0.076619 Iteration 3 Error: 0.013325 Align patch 14 11 left Iteration 1 Error: 0.539735 Iteration 2 Error: 0.065523 Iteration 3 Error: 0.010725 Align patch 15 10 left Iteration 1 Error: 0.591118 Iteration 2 Error: 0.070741 Iteration 3 Error: 0.009716 Align patch 16 9 left Iteration 1 Error: 0.666432 Iteration 2 Error: 0.071876 Iteration 3 Error: 0.009090 Align patch 17 8 left Iteration 1 Error: 0.557534 Iteration 2 Error: 0.049165 Align patch 18 7 left Iteration 1 Error: 0.523660 Iteration 2 Error: 0.053236 Iteration 3 Error: 0.009655 Align patch 19 6 left Iteration 1 Error: 0.478313 Iteration 2 Error: 0.050369 Iteration 3 Error: 0.011209 Align patch 20 5 left Iteration 1 Error: 0.540264 Iteration 2 Error: 0.072729 Iteration 3 Error: 0.014707 Align patch 21 4 left Iteration 1 Error: 0.435330 Iteration 2 Error: 0.065839 Iteration 3 Error: 0.010923 Align patch 22 3 left Iteration 1 Error: 0.538684 Iteration 2 Error: 0.073507 Iteration 3 Error: 0.007510 Align patch 23 2 left Iteration 1 Error: 0.579047 Iteration 2 Error: 0.042504 Align patch 24 1 left Iteration 1 Error: 0.561264 Iteration 2 Error: 0.066885 Iteration 3 Error: 0.011362 Align patch 25 0 left Iteration 1 Error: 0.328831 Iteration 2 Error: 0.032178 3D Fitting completed. Patch alignment time: 18.10(sec) Local motion has been corrected. Process thread exits. Computational time: 32.516624 sec Total time: 43.504436 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00002hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00002hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.560299s Reading file: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00002hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.809915s ........................................ >>>>>>TIME<<<<<< FFT: 1.420034s Defocus_U Defocus_V Angle CCC 29423.83 28669.93 82.01 0.055949 Final Values Defocus_U Defocus_V Angle CCC 29414.46 28685.55 82.01 0.086937 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00001sq_v01_00002hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00002hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 41.85 7.04 Num Hot pixels: 199 Hot pixel threshold: 84.10 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.472784 Iteration 2 Error: 0.415654 Iteration 3 Error: 0.103296 Iteration 4 Error: 0.029702 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.06 -0.26 ...... Frame ( 3) shift: 0.13 -0.51 ...... Frame ( 4) shift: 0.19 -0.77 ...... Frame ( 5) shift: 0.26 -1.03 ...... Frame ( 6) shift: 0.42 -1.12 ...... Frame ( 7) shift: 0.68 -1.06 ...... Frame ( 8) shift: 0.95 -0.99 ...... Frame ( 9) shift: 1.16 -0.89 ...... Frame ( 10) shift: 1.32 -0.76 ...... Frame ( 11) shift: 1.48 -0.62 ...... Frame ( 12) shift: 1.64 -0.45 ...... Frame ( 13) shift: 1.79 -0.25 ...... Frame ( 14) shift: 1.94 -0.05 ...... Frame ( 15) shift: 2.08 0.15 ...... Frame ( 16) shift: 2.20 0.35 ...... Frame ( 17) shift: 2.33 0.55 ...... Frame ( 18) shift: 2.47 0.66 ...... Frame ( 19) shift: 2.64 0.68 ...... Frame ( 20) shift: 2.81 0.71 ...... Frame ( 21) shift: 2.96 0.78 ...... Frame ( 22) shift: 3.07 0.90 ...... Frame ( 23) shift: 3.18 1.02 ...... Frame ( 24) shift: 3.29 1.13 ...... Frame ( 25) shift: 3.38 1.23 ...... Frame ( 26) shift: 3.48 1.33 ...... Frame ( 27) shift: 3.54 1.43 ...... Frame ( 28) shift: 3.57 1.54 ...... Frame ( 29) shift: 3.60 1.64 ...... Frame ( 30) shift: 3.66 1.76 ...... Frame ( 31) shift: 3.76 1.91 ...... Frame ( 32) shift: 3.86 2.05 ...... Frame ( 33) shift: 3.96 2.15 ...... Frame ( 34) shift: 4.05 2.20 ...... Frame ( 35) shift: 4.14 2.25 ...... Frame ( 36) shift: 4.17 2.32 ...... Frame ( 37) shift: 4.14 2.41 ...... Frame ( 38) shift: 4.10 2.49 ...... Frame ( 39) shift: 4.07 2.57 ...... Frame ( 40) shift: 4.03 2.66 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.705941 Iteration 2 Error: 0.316577 Iteration 3 Error: 0.080982 Iteration 4 Error: 0.020464 Align patch 2 23 left Iteration 1 Error: 2.472872 Iteration 2 Error: 0.263173 Iteration 3 Error: 0.035259 Align patch 3 22 left Iteration 1 Error: 2.670531 Iteration 2 Error: 0.424188 Iteration 3 Error: 0.072822 Iteration 4 Error: 0.031313 Align patch 4 21 left Iteration 1 Error: 1.781520 Iteration 2 Error: 0.246934 Iteration 3 Error: 0.085281 Iteration 4 Error: 0.021265 Align patch 5 20 left Iteration 1 Error: 1.704753 Iteration 2 Error: 0.232391 Iteration 3 Error: 0.046116 Align patch 6 19 left Iteration 1 Error: 1.367920 Iteration 2 Error: 0.354537 Iteration 3 Error: 0.065789 Iteration 4 Error: 0.026864 Align patch 7 18 left Iteration 1 Error: 1.460304 Iteration 2 Error: 0.156203 Iteration 3 Error: 0.032728 Align patch 8 17 left Iteration 1 Error: 1.355071 Iteration 2 Error: 0.224086 Iteration 3 Error: 0.041859 Align patch 9 16 left Iteration 1 Error: 1.444763 Iteration 2 Error: 0.173968 Iteration 3 Error: 0.042306 Align patch 10 15 left Iteration 1 Error: 1.085344 Iteration 2 Error: 0.124112 Iteration 3 Error: 0.022099 Align patch 11 14 left Iteration 1 Error: 0.638713 Iteration 2 Error: 0.097033 Iteration 3 Error: 0.026974 Align patch 12 13 left Iteration 1 Error: 0.623597 Iteration 2 Error: 0.085938 Iteration 3 Error: 0.030388 Align patch 13 12 left Iteration 1 Error: 0.668996 Iteration 2 Error: 0.129675 Iteration 3 Error: 0.030379 Align patch 14 11 left Iteration 1 Error: 0.520592 Iteration 2 Error: 0.112311 Iteration 3 Error: 0.031072 Align patch 15 10 left Iteration 1 Error: 0.938105 Iteration 2 Error: 0.104007 Iteration 3 Error: 0.020032 Align patch 16 9 left Iteration 1 Error: 0.713969 Iteration 2 Error: 0.213945 Iteration 3 Error: 0.073905 Iteration 4 Error: 0.022543 Align patch 17 8 left Iteration 1 Error: 0.834656 Iteration 2 Error: 0.213291 Iteration 3 Error: 0.066053 Iteration 4 Error: 0.021531 Align patch 18 7 left Iteration 1 Error: 1.296418 Iteration 2 Error: 0.133139 Iteration 3 Error: 0.022577 Align patch 19 6 left Iteration 1 Error: 1.695305 Iteration 2 Error: 0.266158 Iteration 3 Error: 0.044203 Align patch 20 5 left Iteration 1 Error: 1.384078 Iteration 2 Error: 0.291722 Iteration 3 Error: 0.056254 Iteration 4 Error: 0.017883 Align patch 21 4 left Iteration 1 Error: 1.428242 Iteration 2 Error: 0.210283 Iteration 3 Error: 0.037272 Align patch 22 3 left Iteration 1 Error: 1.561752 Iteration 2 Error: 0.260888 Iteration 3 Error: 0.057681 Iteration 4 Error: 0.018041 Align patch 23 2 left Iteration 1 Error: 1.842374 Iteration 2 Error: 0.224123 Iteration 3 Error: 0.045517 Align patch 24 1 left Iteration 1 Error: 1.659563 Iteration 2 Error: 0.232805 Iteration 3 Error: 0.038097 Align patch 25 0 left Iteration 1 Error: 1.984904 Iteration 2 Error: 0.327688 Iteration 3 Error: 0.036032 3D Fitting completed. Patch alignment time: 15.26(sec) Local motion has been corrected. Process thread exits. Computational time: 27.661100 sec Total time: 37.495705 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00002hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00002hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.912098s Reading file: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00002hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.887823s ........................................ >>>>>>TIME<<<<<< FFT: 1.042587s Defocus_U Defocus_V Angle CCC 25232.45 26130.89 9.44 0.068258 Final Values Defocus_U Defocus_V Angle CCC 25243.42 26129.36 9.13 0.107769 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00001sq_v01_00002hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00002hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 43.16 7.11 Num Hot pixels: 214 Hot pixel threshold: 85.80 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.639541 Iteration 2 Error: 0.250680 Iteration 3 Error: 0.061335 Iteration 4 Error: 0.015374 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.32 -0.02 ...... Frame ( 3) shift: 0.65 -0.05 ...... Frame ( 4) shift: 0.97 -0.07 ...... Frame ( 5) shift: 1.30 -0.10 ...... Frame ( 6) shift: 1.54 -0.07 ...... Frame ( 7) shift: 1.70 -0.01 ...... Frame ( 8) shift: 1.86 0.06 ...... Frame ( 9) shift: 2.02 0.17 ...... Frame ( 10) shift: 2.20 0.32 ...... Frame ( 11) shift: 2.38 0.47 ...... Frame ( 12) shift: 2.54 0.64 ...... Frame ( 13) shift: 2.67 0.81 ...... Frame ( 14) shift: 2.80 0.99 ...... Frame ( 15) shift: 2.91 1.13 ...... Frame ( 16) shift: 2.98 1.23 ...... Frame ( 17) shift: 3.06 1.33 ...... Frame ( 18) shift: 3.13 1.42 ...... Frame ( 19) shift: 3.20 1.51 ...... Frame ( 20) shift: 3.27 1.59 ...... Frame ( 21) shift: 3.34 1.65 ...... Frame ( 22) shift: 3.40 1.70 ...... Frame ( 23) shift: 3.46 1.74 ...... Frame ( 24) shift: 3.51 1.80 ...... Frame ( 25) shift: 3.56 1.89 ...... Frame ( 26) shift: 3.61 1.99 ...... Frame ( 27) shift: 3.61 2.05 ...... Frame ( 28) shift: 3.58 2.08 ...... Frame ( 29) shift: 3.55 2.10 ...... Frame ( 30) shift: 3.54 2.13 ...... Frame ( 31) shift: 3.57 2.14 ...... Frame ( 32) shift: 3.60 2.15 ...... Frame ( 33) shift: 3.64 2.18 ...... Frame ( 34) shift: 3.70 2.23 ...... Frame ( 35) shift: 3.77 2.28 ...... Frame ( 36) shift: 3.84 2.31 ...... Frame ( 37) shift: 3.94 2.32 ...... Frame ( 38) shift: 4.03 2.33 ...... Frame ( 39) shift: 4.12 2.34 ...... Frame ( 40) shift: 4.21 2.35 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.234587 Iteration 2 Error: 0.267048 Iteration 3 Error: 0.095314 Iteration 4 Error: 0.026982 Align patch 2 23 left Iteration 1 Error: 2.070534 Iteration 2 Error: 0.269494 Iteration 3 Error: 0.057416 Iteration 4 Error: 0.019722 Align patch 3 22 left Iteration 1 Error: 1.385631 Iteration 2 Error: 0.180352 Iteration 3 Error: 0.082683 Iteration 4 Error: 0.031528 Align patch 4 21 left Iteration 1 Error: 1.934726 Iteration 2 Error: 0.139979 Iteration 3 Error: 0.033689 Align patch 5 20 left Iteration 1 Error: 2.099682 Iteration 2 Error: 0.156075 Iteration 3 Error: 0.048503 Align patch 6 19 left Iteration 1 Error: 1.313440 Iteration 2 Error: 0.125036 Iteration 3 Error: 0.037375 Align patch 7 18 left Iteration 1 Error: 0.599918 Iteration 2 Error: 0.105081 Iteration 3 Error: 0.029159 Align patch 8 17 left Iteration 1 Error: 0.669702 Iteration 2 Error: 0.153262 Iteration 3 Error: 0.046498 Align patch 9 16 left Iteration 1 Error: 0.751497 Iteration 2 Error: 0.115541 Iteration 3 Error: 0.046300 Align patch 10 15 left Iteration 1 Error: 0.558817 Iteration 2 Error: 0.107421 Iteration 3 Error: 0.032676 Align patch 11 14 left Iteration 1 Error: 0.377660 Iteration 2 Error: 0.072876 Iteration 3 Error: 0.017174 Align patch 12 13 left Iteration 1 Error: 0.644383 Iteration 2 Error: 0.068861 Iteration 3 Error: 0.020801 Align patch 13 12 left Iteration 1 Error: 0.560589 Iteration 2 Error: 0.102633 Iteration 3 Error: 0.017440 Align patch 14 11 left Iteration 1 Error: 0.512096 Iteration 2 Error: 0.076401 Iteration 3 Error: 0.016367 Align patch 15 10 left Iteration 1 Error: 0.645675 Iteration 2 Error: 0.100790 Iteration 3 Error: 0.023644 Align patch 16 9 left Iteration 1 Error: 1.432295 Iteration 2 Error: 0.084056 Iteration 3 Error: 0.012232 Align patch 17 8 left Iteration 1 Error: 0.918632 Iteration 2 Error: 0.068318 Iteration 3 Error: 0.011406 Align patch 18 7 left Iteration 1 Error: 0.722115 Iteration 2 Error: 0.083776 Iteration 3 Error: 0.026015 Align patch 19 6 left Iteration 1 Error: 0.685877 Iteration 2 Error: 0.096644 Iteration 3 Error: 0.026896 Align patch 20 5 left Iteration 1 Error: 1.295892 Iteration 2 Error: 0.145845 Iteration 3 Error: 0.041970 Align patch 21 4 left Iteration 1 Error: 1.059842 Iteration 2 Error: 0.092846 Iteration 3 Error: 0.016307 Align patch 22 3 left Iteration 1 Error: 1.259383 Iteration 2 Error: 0.108201 Iteration 3 Error: 0.016558 Align patch 23 2 left Iteration 1 Error: 0.924573 Iteration 2 Error: 0.089071 Iteration 3 Error: 0.020572 Align patch 24 1 left Iteration 1 Error: 1.401898 Iteration 2 Error: 0.203329 Iteration 3 Error: 0.030490 Align patch 25 0 left Iteration 1 Error: 2.027857 Iteration 2 Error: 0.155754 Iteration 3 Error: 0.035077 3D Fitting completed. Patch alignment time: 19.68(sec) Local motion has been corrected. Process thread exits. Computational time: 36.344448 sec Total time: 46.904091 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00002hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00002hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.489675s Reading file: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00002hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.114319s ........................................ >>>>>>TIME<<<<<< FFT: 1.327566s Defocus_U Defocus_V Angle CCC 27710.94 27085.94 86.67 0.059019 Final Values Defocus_U Defocus_V Angle CCC 27695.31 27089.07 86.67 0.094611 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00001sq_v01_00002hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00002hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.350e-01 1.004e-01 CC threshold: 0.738 Mean Std: 39.80 8.06 Num Hot pixels: 131 Hot pixel threshold: 88.16 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.918322 Iteration 2 Error: 0.129780 Iteration 3 Error: 0.024861 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.15 -0.30 ...... Frame ( 3) shift: -0.31 -0.60 ...... Frame ( 4) shift: -0.46 -0.90 ...... Frame ( 5) shift: -0.61 -1.20 ...... Frame ( 6) shift: -0.71 -1.34 ...... Frame ( 7) shift: -0.75 -1.32 ...... Frame ( 8) shift: -0.79 -1.30 ...... Frame ( 9) shift: -0.78 -1.26 ...... Frame ( 10) shift: -0.73 -1.21 ...... Frame ( 11) shift: -0.68 -1.15 ...... Frame ( 12) shift: -0.66 -1.09 ...... Frame ( 13) shift: -0.67 -1.02 ...... Frame ( 14) shift: -0.68 -0.96 ...... Frame ( 15) shift: -0.68 -0.88 ...... Frame ( 16) shift: -0.66 -0.79 ...... Frame ( 17) shift: -0.64 -0.70 ...... Frame ( 18) shift: -0.61 -0.60 ...... Frame ( 19) shift: -0.57 -0.49 ...... Frame ( 20) shift: -0.52 -0.39 ...... Frame ( 21) shift: -0.49 -0.32 ...... Frame ( 22) shift: -0.48 -0.30 ...... Frame ( 23) shift: -0.47 -0.27 ...... Frame ( 24) shift: -0.48 -0.23 ...... Frame ( 25) shift: -0.50 -0.17 ...... Frame ( 26) shift: -0.52 -0.12 ...... Frame ( 27) shift: -0.51 -0.10 ...... Frame ( 28) shift: -0.47 -0.13 ...... Frame ( 29) shift: -0.43 -0.15 ...... Frame ( 30) shift: -0.41 -0.12 ...... Frame ( 31) shift: -0.39 -0.03 ...... Frame ( 32) shift: -0.38 0.06 ...... Frame ( 33) shift: -0.35 0.12 ...... Frame ( 34) shift: -0.30 0.16 ...... Frame ( 35) shift: -0.26 0.19 ...... Frame ( 36) shift: -0.23 0.22 ...... Frame ( 37) shift: -0.21 0.24 ...... Frame ( 38) shift: -0.20 0.26 ...... Frame ( 39) shift: -0.19 0.28 ...... Frame ( 40) shift: -0.18 0.30 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.332754 Iteration 2 Error: 0.392319 Iteration 3 Error: 0.111550 Iteration 4 Error: 0.033973 Align patch 2 23 left Iteration 1 Error: 1.472831 Iteration 2 Error: 0.267898 Iteration 3 Error: 0.065037 Iteration 4 Error: 0.018563 Align patch 3 22 left Iteration 1 Error: 0.923787 Iteration 2 Error: 0.114333 Iteration 3 Error: 0.031324 Align patch 4 21 left Iteration 1 Error: 0.876998 Iteration 2 Error: 0.136790 Iteration 3 Error: 0.018471 Align patch 5 20 left Iteration 1 Error: 0.589833 Iteration 2 Error: 0.050230 Iteration 3 Error: 0.007765 Align patch 6 19 left Iteration 1 Error: 1.067820 Iteration 2 Error: 0.141100 Iteration 3 Error: 0.033865 Align patch 7 18 left Iteration 1 Error: 1.089327 Iteration 2 Error: 0.195962 Iteration 3 Error: 0.048361 Align patch 8 17 left Iteration 1 Error: 1.057114 Iteration 2 Error: 0.156900 Iteration 3 Error: 0.039753 Align patch 9 16 left Iteration 1 Error: 0.540113 Iteration 2 Error: 0.064023 Iteration 3 Error: 0.014064 Align patch 10 15 left Iteration 1 Error: 0.615035 Iteration 2 Error: 0.053958 Iteration 3 Error: 0.011845 Align patch 11 14 left Iteration 1 Error: 0.598698 Iteration 2 Error: 0.085154 Iteration 3 Error: 0.016952 Align patch 12 13 left Iteration 1 Error: 0.729812 Iteration 2 Error: 0.115772 Iteration 3 Error: 0.035864 Align patch 13 12 left Iteration 1 Error: 0.791462 Iteration 2 Error: 0.148634 Iteration 3 Error: 0.021662 Align patch 14 11 left Iteration 1 Error: 0.262821 Iteration 2 Error: 0.031735 Align patch 15 10 left Iteration 1 Error: 0.372938 Iteration 2 Error: 0.047919 Align patch 16 9 left Iteration 1 Error: 0.530251 Iteration 2 Error: 0.058631 Iteration 3 Error: 0.012887 Align patch 17 8 left Iteration 1 Error: 0.624846 Iteration 2 Error: 0.068754 Iteration 3 Error: 0.012926 Align patch 18 7 left Iteration 1 Error: 0.497390 Iteration 2 Error: 0.058147 Iteration 3 Error: 0.011189 Align patch 19 6 left Iteration 1 Error: 0.304431 Iteration 2 Error: 0.032932 Align patch 20 5 left Iteration 1 Error: 0.258496 Iteration 2 Error: 0.095713 Iteration 3 Error: 0.035520 Align patch 21 4 left Iteration 1 Error: 1.027366 Iteration 2 Error: 0.083271 Iteration 3 Error: 0.016830 Align patch 22 3 left Iteration 1 Error: 0.867289 Iteration 2 Error: 0.096298 Iteration 3 Error: 0.018111 Align patch 23 2 left Iteration 1 Error: 0.395709 Iteration 2 Error: 0.034384 Align patch 24 1 left Iteration 1 Error: 0.451782 Iteration 2 Error: 0.058521 Iteration 3 Error: 0.010285 Align patch 25 0 left Iteration 1 Error: 0.381798 Iteration 2 Error: 0.085898 Iteration 3 Error: 0.036376 3D Fitting completed. Patch alignment time: 19.78(sec) Local motion has been corrected. Process thread exits. Computational time: 35.876949 sec Total time: 47.329384 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00002hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00002hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.579672s Reading file: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00002hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.935682s ........................................ >>>>>>TIME<<<<<< FFT: 1.460644s Defocus_U Defocus_V Angle CCC 26589.84 27523.44 4.09 0.050833 Final Values Defocus_U Defocus_V Angle CCC 26588.28 27546.88 4.09 0.080304 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00001sq_v01_00003hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00003hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 24.29 5.33 Num Hot pixels: 159 Hot pixel threshold: 56.27 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 8.865114 Iteration 2 Error: 0.973393 Iteration 3 Error: 0.277870 Iteration 4 Error: 0.081866 Iteration 5 Error: 0.024513 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.92 -0.86 ...... Frame ( 3) shift: 1.84 -1.71 ...... Frame ( 4) shift: 2.75 -2.57 ...... Frame ( 5) shift: 3.67 -3.42 ...... Frame ( 6) shift: 4.44 -4.09 ...... Frame ( 7) shift: 5.06 -4.57 ...... Frame ( 8) shift: 5.69 -5.04 ...... Frame ( 9) shift: 6.19 -5.39 ...... Frame ( 10) shift: 6.56 -5.61 ...... Frame ( 11) shift: 6.94 -5.82 ...... Frame ( 12) shift: 7.28 -6.00 ...... Frame ( 13) shift: 7.58 -6.15 ...... Frame ( 14) shift: 7.88 -6.29 ...... Frame ( 15) shift: 8.12 -6.44 ...... Frame ( 16) shift: 8.30 -6.57 ...... Frame ( 17) shift: 8.48 -6.71 ...... Frame ( 18) shift: 8.65 -6.84 ...... Frame ( 19) shift: 8.80 -6.95 ...... Frame ( 20) shift: 8.96 -7.06 ...... Frame ( 21) shift: 9.11 -7.18 ...... Frame ( 22) shift: 9.27 -7.32 ...... Frame ( 23) shift: 9.42 -7.45 ...... Frame ( 24) shift: 9.57 -7.55 ...... Frame ( 25) shift: 9.72 -7.61 ...... Frame ( 26) shift: 9.86 -7.67 ...... Frame ( 27) shift: 9.94 -7.75 ...... Frame ( 28) shift: 9.96 -7.85 ...... Frame ( 29) shift: 9.98 -7.95 ...... Frame ( 30) shift: 10.07 -8.02 ...... Frame ( 31) shift: 10.22 -8.06 ...... Frame ( 32) shift: 10.38 -8.10 ...... Frame ( 33) shift: 10.52 -8.15 ...... Frame ( 34) shift: 10.63 -8.21 ...... Frame ( 35) shift: 10.75 -8.27 ...... Frame ( 36) shift: 10.83 -8.36 ...... Frame ( 37) shift: 10.88 -8.49 ...... Frame ( 38) shift: 10.92 -8.62 ...... Frame ( 39) shift: 10.97 -8.75 ...... Frame ( 40) shift: 11.01 -8.88 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.444322 Iteration 2 Error: 0.394940 Iteration 3 Error: 0.090905 Iteration 4 Error: 0.039388 Align patch 2 23 left Iteration 1 Error: 2.352960 Iteration 2 Error: 0.358412 Iteration 3 Error: 0.094366 Iteration 4 Error: 0.035531 Align patch 3 22 left Iteration 1 Error: 2.170654 Iteration 2 Error: 0.255781 Iteration 3 Error: 0.093067 Iteration 4 Error: 0.020279 Align patch 4 21 left Iteration 1 Error: 2.677488 Iteration 2 Error: 0.410168 Iteration 3 Error: 0.205035 Iteration 4 Error: 0.122777 Iteration 5 Error: 0.065581 Align patch 4 21 left Iteration 1 Error: 2.732057 Iteration 2 Error: 0.208954 Iteration 3 Error: 0.028447 Align patch 5 20 left Iteration 1 Error: 4.262641 Iteration 2 Error: 0.778992 Iteration 3 Error: 0.420923 Iteration 4 Error: 0.160819 Iteration 5 Error: 0.076847 Align patch 5 20 left Iteration 1 Error: 3.113804 Iteration 2 Error: 0.209147 Iteration 3 Error: 0.030505 Align patch 6 19 left Iteration 1 Error: 1.306070 Iteration 2 Error: 0.354378 Iteration 3 Error: 0.154256 Iteration 4 Error: 0.065647 Iteration 5 Error: 0.034742 Align patch 7 18 left Iteration 1 Error: 0.812452 Iteration 2 Error: 0.192136 Iteration 3 Error: 0.069588 Iteration 4 Error: 0.027695 Align patch 8 17 left Iteration 1 Error: 0.961390 Iteration 2 Error: 0.223471 Iteration 3 Error: 0.051380 Iteration 4 Error: 0.017612 Align patch 9 16 left Iteration 1 Error: 1.490504 Iteration 2 Error: 0.279415 Iteration 3 Error: 0.137334 Iteration 4 Error: 0.043202 Align patch 10 15 left Iteration 1 Error: 2.433411 Iteration 2 Error: 0.320328 Iteration 3 Error: 0.103441 Iteration 4 Error: 0.036655 Align patch 11 14 left Iteration 1 Error: 0.945816 Iteration 2 Error: 0.528696 Iteration 3 Error: 0.260418 Iteration 4 Error: 0.192781 Iteration 5 Error: 0.102431 Align patch 11 14 left Iteration 1 Error: 1.243397 Iteration 2 Error: 0.136771 Iteration 3 Error: 0.028191 Align patch 12 13 left Iteration 1 Error: 2.051719 Iteration 2 Error: 0.467824 Iteration 3 Error: 0.129122 Iteration 4 Error: 0.078442 Iteration 5 Error: 0.027586 Align patch 13 12 left Iteration 1 Error: 1.250548 Iteration 2 Error: 0.556576 Iteration 3 Error: 0.320172 Iteration 4 Error: 0.159275 Iteration 5 Error: 0.098670 Align patch 13 12 left Iteration 1 Error: 0.989933 Iteration 2 Error: 0.117839 Iteration 3 Error: 0.024227 Align patch 14 11 left Iteration 1 Error: 1.794449 Iteration 2 Error: 0.221924 Iteration 3 Error: 0.073759 Iteration 4 Error: 0.018563 Align patch 15 10 left Iteration 1 Error: 1.629150 Iteration 2 Error: 0.539571 Iteration 3 Error: 0.161172 Iteration 4 Error: 0.049796 Align patch 16 9 left Iteration 1 Error: 2.560424 Iteration 2 Error: 1.023550 Iteration 3 Error: 0.319445 Iteration 4 Error: 0.166859 Iteration 5 Error: 0.068097 Align patch 16 9 left Iteration 1 Error: 2.640284 Iteration 2 Error: 0.269899 Iteration 3 Error: 0.035578 Align patch 17 8 left Iteration 1 Error: 2.936517 Iteration 2 Error: 0.558575 Iteration 3 Error: 0.197772 Iteration 4 Error: 0.092621 Iteration 5 Error: 0.067655 Align patch 17 8 left Iteration 1 Error: 2.508924 Iteration 2 Error: 0.207133 Iteration 3 Error: 0.037963 Align patch 18 7 left Iteration 1 Error: 1.379057 Iteration 2 Error: 0.356951 Iteration 3 Error: 0.137136 Iteration 4 Error: 0.060901 Iteration 5 Error: 0.029822 Align patch 19 6 left Iteration 1 Error: 1.284068 Iteration 2 Error: 0.351214 Iteration 3 Error: 0.091546 Iteration 4 Error: 0.059197 Iteration 5 Error: 0.024453 Align patch 20 5 left Iteration 1 Error: 1.617177 Iteration 2 Error: 0.445104 Iteration 3 Error: 0.103731 Iteration 4 Error: 0.052349 Iteration 5 Error: 0.020986 Align patch 21 4 left Iteration 1 Error: 3.185684 Iteration 2 Error: 0.600356 Iteration 3 Error: 0.196518 Iteration 4 Error: 0.091957 Iteration 5 Error: 0.038060 Align patch 22 3 left Iteration 1 Error: 2.371422 Iteration 2 Error: 0.418441 Iteration 3 Error: 0.125360 Iteration 4 Error: 0.069206 Iteration 5 Error: 0.021460 Align patch 23 2 left Iteration 1 Error: 1.974784 Iteration 2 Error: 0.519326 Iteration 3 Error: 0.229780 Iteration 4 Error: 0.092974 Iteration 5 Error: 0.052002 Align patch 23 2 left Iteration 1 Error: 2.164477 Iteration 2 Error: 0.155009 Iteration 3 Error: 0.023252 Align patch 24 1 left Iteration 1 Error: 1.833473 Iteration 2 Error: 0.265269 Iteration 3 Error: 0.068276 Iteration 4 Error: 0.031415 Align patch 25 0 left Iteration 1 Error: 1.116104 Iteration 2 Error: 0.222220 Iteration 3 Error: 0.097175 Iteration 4 Error: 0.047821 3D Fitting completed. Patch alignment time: 27.52(sec) Local motion has been corrected. Process thread exits. Computational time: 42.640976 sec Total time: 53.912743 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00003hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00003hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.865697s Reading file: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00003hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.617815s ........................................ >>>>>>TIME<<<<<< FFT: 1.396385s Defocus_U Defocus_V Angle CCC 26291.01 27248.06 23.66 0.015524 Final Values Defocus_U Defocus_V Angle CCC 26242.59 27249.80 23.03 0.010501 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00001sq_v01_00003hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00003hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.001e-01 CC threshold: 0.735 Mean Std: 35.04 6.36 Num Hot pixels: 171 Hot pixel threshold: 73.22 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.277040 Iteration 2 Error: 0.021104 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.06 -0.06 ...... Frame ( 3) shift: 0.11 -0.13 ...... Frame ( 4) shift: 0.17 -0.19 ...... Frame ( 5) shift: 0.23 -0.26 ...... Frame ( 6) shift: 0.21 -0.32 ...... Frame ( 7) shift: 0.12 -0.37 ...... Frame ( 8) shift: 0.03 -0.42 ...... Frame ( 9) shift: -0.02 -0.46 ...... Frame ( 10) shift: -0.03 -0.47 ...... Frame ( 11) shift: -0.03 -0.48 ...... Frame ( 12) shift: -0.04 -0.46 ...... Frame ( 13) shift: -0.03 -0.43 ...... Frame ( 14) shift: -0.02 -0.39 ...... Frame ( 15) shift: -0.04 -0.34 ...... Frame ( 16) shift: -0.09 -0.27 ...... Frame ( 17) shift: -0.14 -0.20 ...... Frame ( 18) shift: -0.14 -0.20 ...... Frame ( 19) shift: -0.10 -0.26 ...... Frame ( 20) shift: -0.06 -0.32 ...... Frame ( 21) shift: -0.07 -0.34 ...... Frame ( 22) shift: -0.12 -0.33 ...... Frame ( 23) shift: -0.17 -0.32 ...... Frame ( 24) shift: -0.18 -0.31 ...... Frame ( 25) shift: -0.13 -0.30 ...... Frame ( 26) shift: -0.09 -0.29 ...... Frame ( 27) shift: -0.08 -0.31 ...... Frame ( 28) shift: -0.11 -0.36 ...... Frame ( 29) shift: -0.14 -0.41 ...... Frame ( 30) shift: -0.15 -0.41 ...... Frame ( 31) shift: -0.12 -0.36 ...... Frame ( 32) shift: -0.10 -0.31 ...... Frame ( 33) shift: -0.06 -0.27 ...... Frame ( 34) shift: -0.02 -0.24 ...... Frame ( 35) shift: 0.03 -0.21 ...... Frame ( 36) shift: 0.06 -0.20 ...... Frame ( 37) shift: 0.08 -0.21 ...... Frame ( 38) shift: 0.09 -0.22 ...... Frame ( 39) shift: 0.10 -0.24 ...... Frame ( 40) shift: 0.12 -0.25 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.956614 Iteration 2 Error: 0.117757 Iteration 3 Error: 0.018052 Align patch 2 23 left Iteration 1 Error: 0.872963 Iteration 2 Error: 0.142955 Iteration 3 Error: 0.022736 Align patch 3 22 left Iteration 1 Error: 0.881655 Iteration 2 Error: 0.198052 Iteration 3 Error: 0.042677 Align patch 4 21 left Iteration 1 Error: 0.798525 Iteration 2 Error: 0.182408 Iteration 3 Error: 0.068789 Iteration 4 Error: 0.019216 Align patch 5 20 left Iteration 1 Error: 0.799039 Iteration 2 Error: 0.123621 Iteration 3 Error: 0.020098 Align patch 6 19 left Iteration 1 Error: 1.022792 Iteration 2 Error: 0.127297 Iteration 3 Error: 0.034445 Align patch 7 18 left Iteration 1 Error: 0.747348 Iteration 2 Error: 0.122413 Iteration 3 Error: 0.031001 Align patch 8 17 left Iteration 1 Error: 0.983275 Iteration 2 Error: 0.149665 Iteration 3 Error: 0.025049 Align patch 9 16 left Iteration 1 Error: 0.847690 Iteration 2 Error: 0.110753 Iteration 3 Error: 0.018607 Align patch 10 15 left Iteration 1 Error: 0.807304 Iteration 2 Error: 0.125481 Iteration 3 Error: 0.026408 Align patch 11 14 left Iteration 1 Error: 0.816868 Iteration 2 Error: 0.196871 Iteration 3 Error: 0.044727 Align patch 12 13 left Iteration 1 Error: 0.776141 Iteration 2 Error: 0.124039 Iteration 3 Error: 0.022359 Align patch 13 12 left Iteration 1 Error: 0.767404 Iteration 2 Error: 0.115139 Iteration 3 Error: 0.029525 Align patch 14 11 left Iteration 1 Error: 0.876020 Iteration 2 Error: 0.127606 Iteration 3 Error: 0.031120 Align patch 15 10 left Iteration 1 Error: 0.891270 Iteration 2 Error: 0.104606 Iteration 3 Error: 0.026356 Align patch 16 9 left Iteration 1 Error: 0.785646 Iteration 2 Error: 0.175925 Iteration 3 Error: 0.046046 Align patch 17 8 left Iteration 1 Error: 0.533105 Iteration 2 Error: 0.100042 Iteration 3 Error: 0.024350 Align patch 18 7 left Iteration 1 Error: 0.629037 Iteration 2 Error: 0.121148 Iteration 3 Error: 0.023811 Align patch 19 6 left Iteration 1 Error: 0.825280 Iteration 2 Error: 0.159073 Iteration 3 Error: 0.037226 Align patch 20 5 left Iteration 1 Error: 0.676676 Iteration 2 Error: 0.138137 Iteration 3 Error: 0.027153 Align patch 21 4 left Iteration 1 Error: 0.760929 Iteration 2 Error: 0.103134 Iteration 3 Error: 0.028274 Align patch 22 3 left Iteration 1 Error: 0.804402 Iteration 2 Error: 0.146067 Iteration 3 Error: 0.052841 Iteration 4 Error: 0.014219 Align patch 23 2 left Iteration 1 Error: 0.698780 Iteration 2 Error: 0.143167 Iteration 3 Error: 0.044463 Align patch 24 1 left Iteration 1 Error: 1.298669 Iteration 2 Error: 0.220884 Iteration 3 Error: 0.047295 Align patch 25 0 left Iteration 1 Error: 0.671979 Iteration 2 Error: 0.116964 Iteration 3 Error: 0.033438 3D Fitting completed. Patch alignment time: 19.16(sec) Local motion has been corrected. Process thread exits. Computational time: 33.801861 sec Total time: 42.470707 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00003hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00003hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.634656s Reading file: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00003hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.066586s ........................................ >>>>>>TIME<<<<<< FFT: 1.422854s Defocus_U Defocus_V Angle CCC 28345.73 27208.97 72.21 0.018519 Final Values Defocus_U Defocus_V Angle CCC 28397.29 27160.53 70.65 0.023726 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00001sq_v01_00003hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00003hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.734 Mean Std: 38.91 6.66 Num Hot pixels: 202 Hot pixel threshold: 78.90 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.456521 Iteration 2 Error: 0.063555 Iteration 3 Error: 0.014148 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.02 -0.16 ...... Frame ( 3) shift: 0.05 -0.31 ...... Frame ( 4) shift: 0.07 -0.47 ...... Frame ( 5) shift: 0.10 -0.63 ...... Frame ( 6) shift: 0.08 -0.74 ...... Frame ( 7) shift: 0.03 -0.80 ...... Frame ( 8) shift: -0.03 -0.86 ...... Frame ( 9) shift: -0.06 -0.89 ...... Frame ( 10) shift: -0.07 -0.87 ...... Frame ( 11) shift: -0.07 -0.86 ...... Frame ( 12) shift: -0.04 -0.81 ...... Frame ( 13) shift: 0.04 -0.72 ...... Frame ( 14) shift: 0.11 -0.63 ...... Frame ( 15) shift: 0.12 -0.58 ...... Frame ( 16) shift: 0.06 -0.56 ...... Frame ( 17) shift: -0.01 -0.54 ...... Frame ( 18) shift: -0.00 -0.55 ...... Frame ( 19) shift: 0.07 -0.58 ...... Frame ( 20) shift: 0.15 -0.61 ...... Frame ( 21) shift: 0.25 -0.62 ...... Frame ( 22) shift: 0.36 -0.61 ...... Frame ( 23) shift: 0.48 -0.60 ...... Frame ( 24) shift: 0.52 -0.56 ...... Frame ( 25) shift: 0.48 -0.51 ...... Frame ( 26) shift: 0.45 -0.45 ...... Frame ( 27) shift: 0.43 -0.40 ...... Frame ( 28) shift: 0.43 -0.35 ...... Frame ( 29) shift: 0.42 -0.31 ...... Frame ( 30) shift: 0.40 -0.29 ...... Frame ( 31) shift: 0.37 -0.30 ...... Frame ( 32) shift: 0.33 -0.31 ...... Frame ( 33) shift: 0.31 -0.32 ...... Frame ( 34) shift: 0.31 -0.31 ...... Frame ( 35) shift: 0.31 -0.31 ...... Frame ( 36) shift: 0.33 -0.30 ...... Frame ( 37) shift: 0.38 -0.28 ...... Frame ( 38) shift: 0.43 -0.26 ...... Frame ( 39) shift: 0.48 -0.24 ...... Frame ( 40) shift: 0.53 -0.22 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.892265 Iteration 2 Error: 0.154393 Iteration 3 Error: 0.041704 Align patch 2 23 left Iteration 1 Error: 0.897229 Iteration 2 Error: 0.085370 Iteration 3 Error: 0.021662 Align patch 3 22 left Iteration 1 Error: 0.675868 Iteration 2 Error: 0.118198 Iteration 3 Error: 0.029369 Align patch 4 21 left Iteration 1 Error: 0.716879 Iteration 2 Error: 0.105973 Iteration 3 Error: 0.020068 Align patch 5 20 left Iteration 1 Error: 0.785863 Iteration 2 Error: 0.123429 Iteration 3 Error: 0.022009 Align patch 6 19 left Iteration 1 Error: 0.953435 Iteration 2 Error: 0.112768 Iteration 3 Error: 0.021745 Align patch 7 18 left Iteration 1 Error: 1.200691 Iteration 2 Error: 0.128456 Iteration 3 Error: 0.035038 Align patch 8 17 left Iteration 1 Error: 0.760224 Iteration 2 Error: 0.126347 Iteration 3 Error: 0.031530 Align patch 9 16 left Iteration 1 Error: 0.791971 Iteration 2 Error: 0.126800 Iteration 3 Error: 0.023991 Align patch 10 15 left Iteration 1 Error: 0.875343 Iteration 2 Error: 0.133560 Iteration 3 Error: 0.038477 Align patch 11 14 left Iteration 1 Error: 0.848715 Iteration 2 Error: 0.179718 Iteration 3 Error: 0.061487 Iteration 4 Error: 0.022210 Align patch 12 13 left Iteration 1 Error: 1.154752 Iteration 2 Error: 0.116053 Iteration 3 Error: 0.045514 Align patch 13 12 left Iteration 1 Error: 0.985166 Iteration 2 Error: 0.117877 Iteration 3 Error: 0.024850 Align patch 14 11 left Iteration 1 Error: 0.720221 Iteration 2 Error: 0.108471 Iteration 3 Error: 0.015883 Align patch 15 10 left Iteration 1 Error: 1.103736 Iteration 2 Error: 0.118202 Iteration 3 Error: 0.020249 Align patch 16 9 left Iteration 1 Error: 0.685719 Iteration 2 Error: 0.157345 Iteration 3 Error: 0.057859 Iteration 4 Error: 0.020654 Align patch 17 8 left Iteration 1 Error: 0.529365 Iteration 2 Error: 0.065882 Iteration 3 Error: 0.014359 Align patch 18 7 left Iteration 1 Error: 0.706183 Iteration 2 Error: 0.156363 Iteration 3 Error: 0.047707 Align patch 19 6 left Iteration 1 Error: 0.709277 Iteration 2 Error: 0.115138 Iteration 3 Error: 0.019415 Align patch 20 5 left Iteration 1 Error: 1.176658 Iteration 2 Error: 0.169908 Iteration 3 Error: 0.037848 Align patch 21 4 left Iteration 1 Error: 1.462659 Iteration 2 Error: 0.173275 Iteration 3 Error: 0.040119 Align patch 22 3 left Iteration 1 Error: 0.798897 Iteration 2 Error: 0.118095 Iteration 3 Error: 0.026375 Align patch 23 2 left Iteration 1 Error: 1.779609 Iteration 2 Error: 0.346703 Iteration 3 Error: 0.042592 Align patch 24 1 left Iteration 1 Error: 0.775809 Iteration 2 Error: 0.133726 Iteration 3 Error: 0.034582 Align patch 25 0 left Iteration 1 Error: 0.686818 Iteration 2 Error: 0.070053 Iteration 3 Error: 0.033063 3D Fitting completed. Patch alignment time: 16.81(sec) Local motion has been corrected. Process thread exits. Computational time: 31.595955 sec Total time: 41.348255 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00003hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00003hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.243991s Reading file: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00003hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.849281s ........................................ >>>>>>TIME<<<<<< FFT: 1.526778s Defocus_U Defocus_V Angle CCC 26261.83 25546.86 82.97 0.034848 Final Values Defocus_U Defocus_V Angle CCC 26260.27 25548.42 82.97 0.050558 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00001sq_v01_00003hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00003hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.994e-02 CC threshold: 0.734 Mean Std: 31.72 6.00 Num Hot pixels: 181 Hot pixel threshold: 67.69 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.002943 Iteration 2 Error: 0.196477 Iteration 3 Error: 0.049274 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.31 0.04 ...... Frame ( 3) shift: 0.62 0.09 ...... Frame ( 4) shift: 0.93 0.13 ...... Frame ( 5) shift: 1.24 0.17 ...... Frame ( 6) shift: 1.52 0.24 ...... Frame ( 7) shift: 1.79 0.34 ...... Frame ( 8) shift: 2.05 0.44 ...... Frame ( 9) shift: 2.20 0.48 ...... Frame ( 10) shift: 2.21 0.47 ...... Frame ( 11) shift: 2.23 0.46 ...... Frame ( 12) shift: 2.26 0.45 ...... Frame ( 13) shift: 2.32 0.44 ...... Frame ( 14) shift: 2.37 0.43 ...... Frame ( 15) shift: 2.41 0.45 ...... Frame ( 16) shift: 2.42 0.50 ...... Frame ( 17) shift: 2.44 0.55 ...... Frame ( 18) shift: 2.49 0.53 ...... Frame ( 19) shift: 2.57 0.44 ...... Frame ( 20) shift: 2.66 0.35 ...... Frame ( 21) shift: 2.73 0.31 ...... Frame ( 22) shift: 2.79 0.31 ...... Frame ( 23) shift: 2.85 0.32 ...... Frame ( 24) shift: 2.92 0.34 ...... Frame ( 25) shift: 2.99 0.39 ...... Frame ( 26) shift: 3.07 0.43 ...... Frame ( 27) shift: 3.11 0.44 ...... Frame ( 28) shift: 3.12 0.41 ...... Frame ( 29) shift: 3.14 0.38 ...... Frame ( 30) shift: 3.16 0.38 ...... Frame ( 31) shift: 3.19 0.42 ...... Frame ( 32) shift: 3.21 0.47 ...... Frame ( 33) shift: 3.25 0.53 ...... Frame ( 34) shift: 3.29 0.62 ...... Frame ( 35) shift: 3.33 0.71 ...... Frame ( 36) shift: 3.36 0.76 ...... Frame ( 37) shift: 3.37 0.76 ...... Frame ( 38) shift: 3.38 0.76 ...... Frame ( 39) shift: 3.39 0.76 ...... Frame ( 40) shift: 3.40 0.76 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.920832 Iteration 2 Error: 0.178942 Iteration 3 Error: 0.060068 Iteration 4 Error: 0.026576 Align patch 2 23 left Iteration 1 Error: 1.505167 Iteration 2 Error: 0.148252 Iteration 3 Error: 0.033068 Align patch 3 22 left Iteration 1 Error: 0.883632 Iteration 2 Error: 0.173563 Iteration 3 Error: 0.045247 Align patch 4 21 left Iteration 1 Error: 1.566646 Iteration 2 Error: 0.234157 Iteration 3 Error: 0.113291 Iteration 4 Error: 0.021852 Align patch 5 20 left Iteration 1 Error: 1.743451 Iteration 2 Error: 0.233182 Iteration 3 Error: 0.073018 Iteration 4 Error: 0.025120 Align patch 6 19 left Iteration 1 Error: 0.821406 Iteration 2 Error: 0.217080 Iteration 3 Error: 0.061153 Iteration 4 Error: 0.018667 Align patch 7 18 left Iteration 1 Error: 1.007723 Iteration 2 Error: 0.177402 Iteration 3 Error: 0.063984 Iteration 4 Error: 0.019863 Align patch 8 17 left Iteration 1 Error: 0.854807 Iteration 2 Error: 0.211143 Iteration 3 Error: 0.065697 Iteration 4 Error: 0.017947 Align patch 9 16 left Iteration 1 Error: 1.073357 Iteration 2 Error: 0.212841 Iteration 3 Error: 0.074151 Iteration 4 Error: 0.030463 Align patch 10 15 left Iteration 1 Error: 0.831947 Iteration 2 Error: 0.164537 Iteration 3 Error: 0.034899 Align patch 11 14 left Iteration 1 Error: 0.880282 Iteration 2 Error: 0.254526 Iteration 3 Error: 0.070422 Iteration 4 Error: 0.035078 Align patch 12 13 left Iteration 1 Error: 0.820192 Iteration 2 Error: 0.204597 Iteration 3 Error: 0.057377 Iteration 4 Error: 0.020683 Align patch 13 12 left Iteration 1 Error: 0.701622 Iteration 2 Error: 0.115438 Iteration 3 Error: 0.025428 Align patch 14 11 left Iteration 1 Error: 1.115974 Iteration 2 Error: 0.165085 Iteration 3 Error: 0.044649 Align patch 15 10 left Iteration 1 Error: 1.242105 Iteration 2 Error: 0.183192 Iteration 3 Error: 0.047397 Align patch 16 9 left Iteration 1 Error: 1.412915 Iteration 2 Error: 0.325588 Iteration 3 Error: 0.079775 Iteration 4 Error: 0.025533 Align patch 17 8 left Iteration 1 Error: 1.398506 Iteration 2 Error: 0.284713 Iteration 3 Error: 0.086386 Iteration 4 Error: 0.032421 Align patch 18 7 left Iteration 1 Error: 0.813891 Iteration 2 Error: 0.197420 Iteration 3 Error: 0.044760 Align patch 19 6 left Iteration 1 Error: 1.016031 Iteration 2 Error: 0.161039 Iteration 3 Error: 0.038644 Align patch 20 5 left Iteration 1 Error: 0.699484 Iteration 2 Error: 0.116567 Iteration 3 Error: 0.029652 Align patch 21 4 left Iteration 1 Error: 1.725796 Iteration 2 Error: 0.291033 Iteration 3 Error: 0.063298 Iteration 4 Error: 0.021171 Align patch 22 3 left Iteration 1 Error: 1.424381 Iteration 2 Error: 0.283193 Iteration 3 Error: 0.078541 Iteration 4 Error: 0.020753 Align patch 23 2 left Iteration 1 Error: 1.324686 Iteration 2 Error: 0.279783 Iteration 3 Error: 0.072113 Iteration 4 Error: 0.017317 Align patch 24 1 left Iteration 1 Error: 0.970555 Iteration 2 Error: 0.266692 Iteration 3 Error: 0.106999 Iteration 4 Error: 0.040574 Align patch 25 0 left Iteration 1 Error: 0.784804 Iteration 2 Error: 0.104987 Iteration 3 Error: 0.033058 3D Fitting completed. Patch alignment time: 13.24(sec) Local motion has been corrected. Process thread exits. Computational time: 23.963610 sec Total time: 32.909904 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00003hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00003hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.531281s Reading file: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00003hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.064536s ........................................ >>>>>>TIME<<<<<< FFT: 0.969342s Defocus_U Defocus_V Angle CCC 23843.73 24675.79 7.08 0.020754 Final Values Defocus_U Defocus_V Angle CCC 23765.59 24635.19 6.14 0.029738 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00001sq_v01_00004hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00004hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.997e-02 CC threshold: 0.734 Mean Std: 32.53 6.11 Num Hot pixels: 185 Hot pixel threshold: 69.17 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.810020 Iteration 2 Error: 0.258064 Iteration 3 Error: 0.080007 Iteration 4 Error: 0.023722 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.32 0.05 ...... Frame ( 3) shift: 0.65 0.09 ...... Frame ( 4) shift: 0.97 0.14 ...... Frame ( 5) shift: 1.29 0.19 ...... Frame ( 6) shift: 1.48 0.27 ...... Frame ( 7) shift: 1.55 0.39 ...... Frame ( 8) shift: 1.61 0.51 ...... Frame ( 9) shift: 1.67 0.58 ...... Frame ( 10) shift: 1.72 0.59 ...... Frame ( 11) shift: 1.77 0.61 ...... Frame ( 12) shift: 1.84 0.63 ...... Frame ( 13) shift: 1.93 0.66 ...... Frame ( 14) shift: 2.02 0.70 ...... Frame ( 15) shift: 2.09 0.71 ...... Frame ( 16) shift: 2.12 0.69 ...... Frame ( 17) shift: 2.15 0.68 ...... Frame ( 18) shift: 2.24 0.71 ...... Frame ( 19) shift: 2.37 0.80 ...... Frame ( 20) shift: 2.51 0.88 ...... Frame ( 21) shift: 2.58 0.92 ...... Frame ( 22) shift: 2.59 0.92 ...... Frame ( 23) shift: 2.59 0.91 ...... Frame ( 24) shift: 2.60 0.93 ...... Frame ( 25) shift: 2.62 0.98 ...... Frame ( 26) shift: 2.65 1.03 ...... Frame ( 27) shift: 2.72 1.05 ...... Frame ( 28) shift: 2.83 1.05 ...... Frame ( 29) shift: 2.95 1.06 ...... Frame ( 30) shift: 3.02 1.06 ...... Frame ( 31) shift: 3.04 1.05 ...... Frame ( 32) shift: 3.07 1.05 ...... Frame ( 33) shift: 3.14 1.09 ...... Frame ( 34) shift: 3.25 1.18 ...... Frame ( 35) shift: 3.37 1.27 ...... Frame ( 36) shift: 3.46 1.36 ...... Frame ( 37) shift: 3.52 1.46 ...... Frame ( 38) shift: 3.59 1.56 ...... Frame ( 39) shift: 3.66 1.66 ...... Frame ( 40) shift: 3.72 1.76 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.770629 Iteration 2 Error: 0.202487 Iteration 3 Error: 0.047128 Align patch 2 23 left Iteration 1 Error: 0.931781 Iteration 2 Error: 0.220930 Iteration 3 Error: 0.077189 Iteration 4 Error: 0.025377 Align patch 3 22 left Iteration 1 Error: 0.663936 Iteration 2 Error: 0.090319 Iteration 3 Error: 0.035261 Align patch 4 21 left Iteration 1 Error: 1.064548 Iteration 2 Error: 0.342804 Iteration 3 Error: 0.103348 Iteration 4 Error: 0.026724 Align patch 5 20 left Iteration 1 Error: 0.962022 Iteration 2 Error: 0.216134 Iteration 3 Error: 0.059628 Iteration 4 Error: 0.019485 Align patch 6 19 left Iteration 1 Error: 1.091149 Iteration 2 Error: 0.191958 Iteration 3 Error: 0.030494 Align patch 7 18 left Iteration 1 Error: 0.819593 Iteration 2 Error: 0.158500 Iteration 3 Error: 0.035457 Align patch 8 17 left Iteration 1 Error: 0.568068 Iteration 2 Error: 0.128197 Iteration 3 Error: 0.060576 Iteration 4 Error: 0.020106 Align patch 9 16 left Iteration 1 Error: 1.006069 Iteration 2 Error: 0.193709 Iteration 3 Error: 0.066125 Iteration 4 Error: 0.019342 Align patch 10 15 left Iteration 1 Error: 1.205279 Iteration 2 Error: 0.226279 Iteration 3 Error: 0.056942 Iteration 4 Error: 0.035591 Align patch 11 14 left Iteration 1 Error: 1.708871 Iteration 2 Error: 0.238032 Iteration 3 Error: 0.061155 Iteration 4 Error: 0.018290 Align patch 12 13 left Iteration 1 Error: 1.013233 Iteration 2 Error: 0.187230 Iteration 3 Error: 0.066439 Iteration 4 Error: 0.020295 Align patch 13 12 left Iteration 1 Error: 0.812955 Iteration 2 Error: 0.162195 Iteration 3 Error: 0.035573 Align patch 14 11 left Iteration 1 Error: 0.758724 Iteration 2 Error: 0.138851 Iteration 3 Error: 0.051704 Iteration 4 Error: 0.016934 Align patch 15 10 left Iteration 1 Error: 1.379307 Iteration 2 Error: 0.235483 Iteration 3 Error: 0.048910 Align patch 16 9 left Iteration 1 Error: 1.154717 Iteration 2 Error: 0.340682 Iteration 3 Error: 0.137092 Iteration 4 Error: 0.070842 Iteration 5 Error: 0.035718 Align patch 17 8 left Iteration 1 Error: 1.145396 Iteration 2 Error: 0.247611 Iteration 3 Error: 0.095844 Iteration 4 Error: 0.027996 Align patch 18 7 left Iteration 1 Error: 1.044248 Iteration 2 Error: 0.163993 Iteration 3 Error: 0.048449 Align patch 19 6 left Iteration 1 Error: 0.819183 Iteration 2 Error: 0.174636 Iteration 3 Error: 0.054928 Iteration 4 Error: 0.011895 Align patch 20 5 left Iteration 1 Error: 1.822401 Iteration 2 Error: 0.251372 Iteration 3 Error: 0.054315 Iteration 4 Error: 0.022010 Align patch 21 4 left Iteration 1 Error: 1.177337 Iteration 2 Error: 0.161175 Iteration 3 Error: 0.030665 Align patch 22 3 left Iteration 1 Error: 1.166021 Iteration 2 Error: 0.221234 Iteration 3 Error: 0.064433 Iteration 4 Error: 0.028145 Align patch 23 2 left Iteration 1 Error: 0.951340 Iteration 2 Error: 0.207849 Iteration 3 Error: 0.052521 Iteration 4 Error: 0.022043 Align patch 24 1 left Iteration 1 Error: 0.572436 Iteration 2 Error: 0.106405 Iteration 3 Error: 0.025231 Align patch 25 0 left Iteration 1 Error: 1.075186 Iteration 2 Error: 0.181490 Iteration 3 Error: 0.058408 Iteration 4 Error: 0.013150 3D Fitting completed. Patch alignment time: 13.65(sec) Local motion has been corrected. Process thread exits. Computational time: 23.914511 sec Total time: 29.845901 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00004hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00004hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.437621s Reading file: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00004hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.920760s ........................................ >>>>>>TIME<<<<<< FFT: 0.905506s Defocus_U Defocus_V Angle CCC 27146.55 26732.36 50.45 0.016557 Final Values Defocus_U Defocus_V Angle CCC 27154.36 26740.21 43.76 0.020665 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00001sq_v01_00004hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00004hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.342e-01 9.988e-02 CC threshold: 0.734 Mean Std: 30.40 5.88 Num Hot pixels: 187 Hot pixel threshold: 65.65 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.675858 Iteration 2 Error: 0.118994 Iteration 3 Error: 0.028974 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.10 -0.10 ...... Frame ( 3) shift: 0.19 -0.19 ...... Frame ( 4) shift: 0.29 -0.29 ...... Frame ( 5) shift: 0.39 -0.38 ...... Frame ( 6) shift: 0.46 -0.40 ...... Frame ( 7) shift: 0.51 -0.35 ...... Frame ( 8) shift: 0.55 -0.30 ...... Frame ( 9) shift: 0.58 -0.25 ...... Frame ( 10) shift: 0.60 -0.20 ...... Frame ( 11) shift: 0.61 -0.15 ...... Frame ( 12) shift: 0.69 -0.11 ...... Frame ( 13) shift: 0.82 -0.09 ...... Frame ( 14) shift: 0.96 -0.07 ...... Frame ( 15) shift: 1.00 -0.04 ...... Frame ( 16) shift: 0.94 -0.01 ...... Frame ( 17) shift: 0.88 0.03 ...... Frame ( 18) shift: 0.85 0.03 ...... Frame ( 19) shift: 0.86 0.00 ...... Frame ( 20) shift: 0.86 -0.03 ...... Frame ( 21) shift: 0.86 0.00 ...... Frame ( 22) shift: 0.86 0.09 ...... Frame ( 23) shift: 0.87 0.18 ...... Frame ( 24) shift: 0.91 0.21 ...... Frame ( 25) shift: 0.99 0.18 ...... Frame ( 26) shift: 1.07 0.15 ...... Frame ( 27) shift: 1.11 0.16 ...... Frame ( 28) shift: 1.10 0.22 ...... Frame ( 29) shift: 1.10 0.27 ...... Frame ( 30) shift: 1.10 0.29 ...... Frame ( 31) shift: 1.13 0.26 ...... Frame ( 32) shift: 1.15 0.24 ...... Frame ( 33) shift: 1.18 0.24 ...... Frame ( 34) shift: 1.23 0.25 ...... Frame ( 35) shift: 1.27 0.26 ...... Frame ( 36) shift: 1.26 0.32 ...... Frame ( 37) shift: 1.20 0.40 ...... Frame ( 38) shift: 1.14 0.49 ...... Frame ( 39) shift: 1.08 0.58 ...... Frame ( 40) shift: 1.02 0.66 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.913147 Iteration 2 Error: 0.315492 Iteration 3 Error: 0.102900 Iteration 4 Error: 0.040323 Align patch 2 23 left Iteration 1 Error: 1.149434 Iteration 2 Error: 0.240943 Iteration 3 Error: 0.101492 Iteration 4 Error: 0.043638 Align patch 3 22 left Iteration 1 Error: 1.227564 Iteration 2 Error: 0.257375 Iteration 3 Error: 0.050341 Iteration 4 Error: 0.027615 Align patch 4 21 left Iteration 1 Error: 1.568391 Iteration 2 Error: 0.388819 Iteration 3 Error: 0.112413 Iteration 4 Error: 0.056692 Iteration 5 Error: 0.027199 Align patch 5 20 left Iteration 1 Error: 0.670376 Iteration 2 Error: 0.215273 Iteration 3 Error: 0.053125 Iteration 4 Error: 0.025445 Align patch 6 19 left Iteration 1 Error: 1.105692 Iteration 2 Error: 0.251188 Iteration 3 Error: 0.073130 Iteration 4 Error: 0.043825 Align patch 7 18 left Iteration 1 Error: 0.586304 Iteration 2 Error: 0.247256 Iteration 3 Error: 0.093545 Iteration 4 Error: 0.053093 Iteration 5 Error: 0.017865 Align patch 8 17 left Iteration 1 Error: 0.732055 Iteration 2 Error: 0.370479 Iteration 3 Error: 0.154789 Iteration 4 Error: 0.074778 Iteration 5 Error: 0.036276 Align patch 9 16 left Iteration 1 Error: 0.735568 Iteration 2 Error: 0.182016 Iteration 3 Error: 0.062112 Iteration 4 Error: 0.024786 Align patch 10 15 left Iteration 1 Error: 1.285649 Iteration 2 Error: 0.365476 Iteration 3 Error: 0.153037 Iteration 4 Error: 0.095212 Iteration 5 Error: 0.052701 Align patch 10 15 left Iteration 1 Error: 0.849500 Iteration 2 Error: 0.150834 Iteration 3 Error: 0.026350 Align patch 11 14 left Iteration 1 Error: 0.995548 Iteration 2 Error: 0.268919 Iteration 3 Error: 0.123117 Iteration 4 Error: 0.046062 Align patch 12 13 left Iteration 1 Error: 0.957476 Iteration 2 Error: 0.170542 Iteration 3 Error: 0.051696 Iteration 4 Error: 0.030887 Align patch 13 12 left Iteration 1 Error: 1.089436 Iteration 2 Error: 0.311742 Iteration 3 Error: 0.111766 Iteration 4 Error: 0.038700 Align patch 14 11 left Iteration 1 Error: 0.670037 Iteration 2 Error: 0.178718 Iteration 3 Error: 0.065405 Iteration 4 Error: 0.024040 Align patch 15 10 left Iteration 1 Error: 1.283903 Iteration 2 Error: 0.547685 Iteration 3 Error: 0.137463 Iteration 4 Error: 0.087165 Iteration 5 Error: 0.036205 Align patch 16 9 left Iteration 1 Error: 1.032807 Iteration 2 Error: 0.340447 Iteration 3 Error: 0.126201 Iteration 4 Error: 0.064236 Iteration 5 Error: 0.029888 Align patch 17 8 left Iteration 1 Error: 0.855046 Iteration 2 Error: 0.427283 Iteration 3 Error: 0.089958 Iteration 4 Error: 0.041746 Align patch 18 7 left Iteration 1 Error: 1.051090 Iteration 2 Error: 0.210909 Iteration 3 Error: 0.065834 Iteration 4 Error: 0.018149 Align patch 19 6 left Iteration 1 Error: 1.139343 Iteration 2 Error: 0.203274 Iteration 3 Error: 0.090753 Iteration 4 Error: 0.030831 Align patch 20 5 left Iteration 1 Error: 1.028738 Iteration 2 Error: 0.311555 Iteration 3 Error: 0.116782 Iteration 4 Error: 0.041785 Align patch 21 4 left Iteration 1 Error: 1.015373 Iteration 2 Error: 0.130466 Iteration 3 Error: 0.065309 Iteration 4 Error: 0.016619 Align patch 22 3 left Iteration 1 Error: 1.126750 Iteration 2 Error: 0.189199 Iteration 3 Error: 0.059719 Iteration 4 Error: 0.019269 Align patch 23 2 left Iteration 1 Error: 1.294947 Iteration 2 Error: 0.286779 Iteration 3 Error: 0.164230 Iteration 4 Error: 0.069462 Iteration 5 Error: 0.038614 Align patch 24 1 left Iteration 1 Error: 1.091324 Iteration 2 Error: 0.295226 Iteration 3 Error: 0.104446 Iteration 4 Error: 0.043931 Align patch 25 0 left Iteration 1 Error: 0.842188 Iteration 2 Error: 0.153697 Iteration 3 Error: 0.077610 Iteration 4 Error: 0.031601 3D Fitting completed. Patch alignment time: 13.82(sec) Local motion has been corrected. Process thread exits. Computational time: 24.099751 sec Total time: 30.155596 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00004hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00004hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.638095s Reading file: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00004hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.666442s ........................................ >>>>>>TIME<<<<<< FFT: 0.896086s Defocus_U Defocus_V Angle CCC 26515.63 27476.57 29.91 0.015141 Final Values Defocus_U Defocus_V Angle CCC 26489.07 27640.65 30.22 0.018942 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00001sq_v01_00004hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00004hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.997e-02 CC threshold: 0.734 Mean Std: 21.60 7.79 Num Hot pixels: 48 Hot pixel threshold: 68.31 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.078802 Iteration 2 Error: 0.084971 Iteration 3 Error: 0.014232 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.18 0.03 ...... Frame ( 3) shift: 0.36 0.05 ...... Frame ( 4) shift: 0.55 0.08 ...... Frame ( 5) shift: 0.73 0.10 ...... Frame ( 6) shift: 0.82 0.12 ...... Frame ( 7) shift: 0.83 0.12 ...... Frame ( 8) shift: 0.83 0.12 ...... Frame ( 9) shift: 0.85 0.06 ...... Frame ( 10) shift: 0.89 -0.06 ...... Frame ( 11) shift: 0.93 -0.19 ...... Frame ( 12) shift: 0.97 -0.28 ...... Frame ( 13) shift: 1.01 -0.36 ...... Frame ( 14) shift: 1.06 -0.43 ...... Frame ( 15) shift: 1.10 -0.47 ...... Frame ( 16) shift: 1.14 -0.49 ...... Frame ( 17) shift: 1.17 -0.50 ...... Frame ( 18) shift: 1.21 -0.53 ...... Frame ( 19) shift: 1.24 -0.58 ...... Frame ( 20) shift: 1.28 -0.63 ...... Frame ( 21) shift: 1.29 -0.66 ...... Frame ( 22) shift: 1.28 -0.67 ...... Frame ( 23) shift: 1.27 -0.68 ...... Frame ( 24) shift: 1.29 -0.66 ...... Frame ( 25) shift: 1.34 -0.61 ...... Frame ( 26) shift: 1.39 -0.56 ...... Frame ( 27) shift: 1.44 -0.55 ...... Frame ( 28) shift: 1.48 -0.57 ...... Frame ( 29) shift: 1.52 -0.60 ...... Frame ( 30) shift: 1.55 -0.59 ...... Frame ( 31) shift: 1.57 -0.54 ...... Frame ( 32) shift: 1.58 -0.50 ...... Frame ( 33) shift: 1.61 -0.48 ...... Frame ( 34) shift: 1.64 -0.49 ...... Frame ( 35) shift: 1.67 -0.49 ...... Frame ( 36) shift: 1.72 -0.49 ...... Frame ( 37) shift: 1.80 -0.49 ...... Frame ( 38) shift: 1.88 -0.49 ...... Frame ( 39) shift: 1.96 -0.48 ...... Frame ( 40) shift: 2.04 -0.48 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 13.213559 Iteration 2 Error: 1.238196 Iteration 3 Error: 0.411626 Iteration 4 Error: 0.108375 Iteration 5 Error: 0.053261 Align patch 1 24 left Iteration 1 Error: 12.567721 Iteration 2 Error: 0.657263 Iteration 3 Error: 0.092510 Iteration 4 Error: 0.019580 Align patch 2 23 left Iteration 1 Error: 11.934248 Iteration 2 Error: 1.548402 Iteration 3 Error: 0.610266 Iteration 4 Error: 0.164450 Iteration 5 Error: 0.065105 Align patch 2 23 left Iteration 1 Error: 11.775384 Iteration 2 Error: 0.687263 Iteration 3 Error: 0.094875 Iteration 4 Error: 0.029976 Align patch 3 22 left Iteration 1 Error: 7.207749 Iteration 2 Error: 1.406892 Iteration 3 Error: 0.553645 Iteration 4 Error: 0.296380 Iteration 5 Error: 0.106526 Align patch 3 22 left Iteration 1 Error: 8.266122 Iteration 2 Error: 0.840542 Iteration 3 Error: 0.145999 Iteration 4 Error: 0.038532 Align patch 4 21 left Iteration 1 Error: 3.183439 Iteration 2 Error: 0.959870 Iteration 3 Error: 0.173905 Iteration 4 Error: 0.097539 Iteration 5 Error: 0.026665 Align patch 5 20 left Iteration 1 Error: 1.582550 Iteration 2 Error: 0.264412 Iteration 3 Error: 0.058785 Iteration 4 Error: 0.016176 Align patch 6 19 left Iteration 1 Error: 13.533602 Iteration 2 Error: 2.686907 Iteration 3 Error: 0.551043 Iteration 4 Error: 0.263968 Iteration 5 Error: 0.116434 Align patch 6 19 left Iteration 1 Error: 12.413033 Iteration 2 Error: 0.619708 Iteration 3 Error: 0.116903 Iteration 4 Error: 0.022164 Align patch 7 18 left Iteration 1 Error: 10.897364 Iteration 2 Error: 2.641853 Iteration 3 Error: 0.306158 Iteration 4 Error: 0.129564 Iteration 5 Error: 0.046910 Align patch 8 17 left Iteration 1 Error: 8.902571 Iteration 2 Error: 2.247489 Iteration 3 Error: 0.810033 Iteration 4 Error: 0.341767 Iteration 5 Error: 0.101795 Align patch 8 17 left Iteration 1 Error: 8.823203 Iteration 2 Error: 0.677055 Iteration 3 Error: 0.101680 Iteration 4 Error: 0.018298 Align patch 9 16 left Iteration 1 Error: 8.278960 Iteration 2 Error: 0.909957 Iteration 3 Error: 0.343252 Iteration 4 Error: 0.162681 Iteration 5 Error: 0.092149 Align patch 9 16 left Iteration 1 Error: 0.470296 Iteration 2 Error: 0.160363 Iteration 3 Error: 0.023048 Align patch 10 15 left Iteration 1 Error: 1.384921 Iteration 2 Error: 0.313115 Iteration 3 Error: 0.094209 Iteration 4 Error: 0.028299 Align patch 11 14 left Iteration 1 Error: 11.093379 Iteration 2 Error: 1.957175 Iteration 3 Error: 0.533167 Iteration 4 Error: 0.269682 Iteration 5 Error: 0.159589 Align patch 11 14 left Iteration 1 Error: 10.954949 Iteration 2 Error: 0.861059 Iteration 3 Error: 0.162017 Iteration 4 Error: 0.049269 Align patch 12 13 left Iteration 1 Error: 10.743122 Iteration 2 Error: 1.770308 Iteration 3 Error: 0.452896 Iteration 4 Error: 0.160180 Iteration 5 Error: 0.058461 Align patch 12 13 left Iteration 1 Error: 11.612986 Iteration 2 Error: 0.823741 Iteration 3 Error: 0.161353 Iteration 4 Error: 0.036938 Align patch 13 12 left Iteration 1 Error: 11.035678 Iteration 2 Error: 1.305977 Iteration 3 Error: 0.435591 Iteration 4 Error: 0.174657 Iteration 5 Error: 0.068754 Align patch 13 12 left Iteration 1 Error: 9.657076 Iteration 2 Error: 0.840939 Iteration 3 Error: 0.181935 Iteration 4 Error: 0.026649 Align patch 14 11 left Iteration 1 Error: 6.545711 Iteration 2 Error: 1.317874 Iteration 3 Error: 0.382027 Iteration 4 Error: 0.146904 Iteration 5 Error: 0.088691 Align patch 14 11 left Iteration 1 Error: 7.133456 Iteration 2 Error: 0.491054 Iteration 3 Error: 0.108239 Iteration 4 Error: 0.025319 Align patch 15 10 left Iteration 1 Error: 2.001653 Iteration 2 Error: 0.141214 Iteration 3 Error: 0.013108 Align patch 16 9 left Iteration 1 Error: 6.942764 Iteration 2 Error: 3.140919 Iteration 3 Error: 0.857391 Iteration 4 Error: 0.351623 Iteration 5 Error: 0.173486 Align patch 16 9 left Iteration 1 Error: 8.978692 Iteration 2 Error: 1.100159 Iteration 3 Error: 0.298985 Iteration 4 Error: 0.077610 Iteration 5 Error: 0.025348 Align patch 17 8 left Iteration 1 Error: 11.388425 Iteration 2 Error: 1.079894 Iteration 3 Error: 0.370178 Iteration 4 Error: 0.123600 Iteration 5 Error: 0.072477 Align patch 17 8 left Iteration 1 Error: 10.638906 Iteration 2 Error: 0.744391 Iteration 3 Error: 0.122139 Iteration 4 Error: 0.031710 Align patch 18 7 left Iteration 1 Error: 9.908161 Iteration 2 Error: 1.445830 Iteration 3 Error: 0.523695 Iteration 4 Error: 0.199727 Iteration 5 Error: 0.128113 Align patch 18 7 left Iteration 1 Error: 9.399258 Iteration 2 Error: 0.710730 Iteration 3 Error: 0.101856 Iteration 4 Error: 0.027387 Align patch 19 6 left Iteration 1 Error: 6.414934 Iteration 2 Error: 1.700298 Iteration 3 Error: 0.380966 Iteration 4 Error: 0.102487 Iteration 5 Error: 0.043368 Align patch 20 5 left Iteration 1 Error: 1.227202 Iteration 2 Error: 0.051411 Iteration 3 Error: 0.006727 Align patch 21 4 left Iteration 1 Error: 8.208119 Iteration 2 Error: 2.590260 Iteration 3 Error: 0.698457 Iteration 4 Error: 0.310872 Iteration 5 Error: 0.098488 Align patch 21 4 left Iteration 1 Error: 8.568970 Iteration 2 Error: 1.329411 Iteration 3 Error: 0.249041 Iteration 4 Error: 0.053873 Iteration 5 Error: 0.013514 Align patch 22 3 left Iteration 1 Error: 9.950237 Iteration 2 Error: 1.736457 Iteration 3 Error: 0.451346 Iteration 4 Error: 0.144445 Iteration 5 Error: 0.072963 Align patch 22 3 left Iteration 1 Error: 10.282578 Iteration 2 Error: 0.642591 Iteration 3 Error: 0.073238 Iteration 4 Error: 0.016924 Align patch 23 2 left Iteration 1 Error: 9.460050 Iteration 2 Error: 1.583556 Iteration 3 Error: 0.281306 Iteration 4 Error: 0.078904 Iteration 5 Error: 0.032381 Align patch 24 1 left Iteration 1 Error: 7.581598 Iteration 2 Error: 1.771879 Iteration 3 Error: 0.279499 Iteration 4 Error: 0.103590 Iteration 5 Error: 0.037659 Align patch 25 0 left Iteration 1 Error: 1.029188 Iteration 2 Error: 0.053033 Iteration 3 Error: 0.009948 3D Fitting completed. Patch alignment time: 23.19(sec) Local motion has been corrected. Process thread exits. Computational time: 33.307034 sec Total time: 39.140327 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00004hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00004hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.565308s Reading file: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00004hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.451880s ........................................ >>>>>>TIME<<<<<< FFT: 1.003314s Defocus_U Defocus_V Angle CCC 28371.10 30621.26 3.30 -0.034507 Final Values Defocus_U Defocus_V Angle CCC 28347.64 30644.72 3.62 -0.104103 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00001sq_v01_00005hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00005hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 40.78 6.93 Num Hot pixels: 218 Hot pixel threshold: 82.34 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.969456 Iteration 2 Error: 0.104463 Iteration 3 Error: 0.017867 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.25 -0.04 ...... Frame ( 3) shift: -0.50 -0.09 ...... Frame ( 4) shift: -0.76 -0.13 ...... Frame ( 5) shift: -1.01 -0.18 ...... Frame ( 6) shift: -1.16 -0.22 ...... Frame ( 7) shift: -1.23 -0.25 ...... Frame ( 8) shift: -1.29 -0.29 ...... Frame ( 9) shift: -1.32 -0.23 ...... Frame ( 10) shift: -1.32 -0.09 ...... Frame ( 11) shift: -1.33 0.06 ...... Frame ( 12) shift: -1.35 0.16 ...... Frame ( 13) shift: -1.39 0.21 ...... Frame ( 14) shift: -1.43 0.26 ...... Frame ( 15) shift: -1.41 0.28 ...... Frame ( 16) shift: -1.35 0.26 ...... Frame ( 17) shift: -1.28 0.24 ...... Frame ( 18) shift: -1.21 0.28 ...... Frame ( 19) shift: -1.14 0.37 ...... Frame ( 20) shift: -1.06 0.47 ...... Frame ( 21) shift: -1.03 0.52 ...... Frame ( 22) shift: -1.05 0.52 ...... Frame ( 23) shift: -1.06 0.52 ...... Frame ( 24) shift: -1.08 0.52 ...... Frame ( 25) shift: -1.08 0.53 ...... Frame ( 26) shift: -1.09 0.54 ...... Frame ( 27) shift: -1.08 0.56 ...... Frame ( 28) shift: -1.05 0.59 ...... Frame ( 29) shift: -1.02 0.62 ...... Frame ( 30) shift: -0.97 0.68 ...... Frame ( 31) shift: -0.91 0.78 ...... Frame ( 32) shift: -0.84 0.87 ...... Frame ( 33) shift: -0.80 0.95 ...... Frame ( 34) shift: -0.80 1.00 ...... Frame ( 35) shift: -0.79 1.06 ...... Frame ( 36) shift: -0.75 1.12 ...... Frame ( 37) shift: -0.67 1.19 ...... Frame ( 38) shift: -0.60 1.25 ...... Frame ( 39) shift: -0.52 1.32 ...... Frame ( 40) shift: -0.45 1.39 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.746310 Iteration 2 Error: 0.139883 Iteration 3 Error: 0.046901 Align patch 2 23 left Iteration 1 Error: 0.454104 Iteration 2 Error: 0.122047 Iteration 3 Error: 0.024631 Align patch 3 22 left Iteration 1 Error: 0.577869 Iteration 2 Error: 0.111136 Iteration 3 Error: 0.022485 Align patch 4 21 left Iteration 1 Error: 0.630952 Iteration 2 Error: 0.088753 Iteration 3 Error: 0.021512 Align patch 5 20 left Iteration 1 Error: 1.027702 Iteration 2 Error: 0.106897 Iteration 3 Error: 0.016309 Align patch 6 19 left Iteration 1 Error: 0.574887 Iteration 2 Error: 0.067834 Iteration 3 Error: 0.013480 Align patch 7 18 left Iteration 1 Error: 0.639411 Iteration 2 Error: 0.068926 Iteration 3 Error: 0.014836 Align patch 8 17 left Iteration 1 Error: 0.729785 Iteration 2 Error: 0.081442 Iteration 3 Error: 0.025374 Align patch 9 16 left Iteration 1 Error: 0.682114 Iteration 2 Error: 0.087812 Iteration 3 Error: 0.015777 Align patch 10 15 left Iteration 1 Error: 0.591862 Iteration 2 Error: 0.078361 Iteration 3 Error: 0.024545 Align patch 11 14 left Iteration 1 Error: 0.809552 Iteration 2 Error: 0.115471 Iteration 3 Error: 0.027294 Align patch 12 13 left Iteration 1 Error: 0.488932 Iteration 2 Error: 0.067797 Iteration 3 Error: 0.014577 Align patch 13 12 left Iteration 1 Error: 0.426124 Iteration 2 Error: 0.035817 Align patch 14 11 left Iteration 1 Error: 0.604798 Iteration 2 Error: 0.101116 Iteration 3 Error: 0.022053 Align patch 15 10 left Iteration 1 Error: 0.541683 Iteration 2 Error: 0.098486 Iteration 3 Error: 0.014409 Align patch 16 9 left Iteration 1 Error: 0.823910 Iteration 2 Error: 0.092175 Iteration 3 Error: 0.017578 Align patch 17 8 left Iteration 1 Error: 0.481770 Iteration 2 Error: 0.070636 Iteration 3 Error: 0.011625 Align patch 18 7 left Iteration 1 Error: 0.749960 Iteration 2 Error: 0.078213 Iteration 3 Error: 0.013905 Align patch 19 6 left Iteration 1 Error: 0.533090 Iteration 2 Error: 0.060472 Iteration 3 Error: 0.007096 Align patch 20 5 left Iteration 1 Error: 0.563792 Iteration 2 Error: 0.094523 Iteration 3 Error: 0.020850 Align patch 21 4 left Iteration 1 Error: 1.043364 Iteration 2 Error: 0.106764 Iteration 3 Error: 0.028219 Align patch 22 3 left Iteration 1 Error: 0.684306 Iteration 2 Error: 0.087885 Iteration 3 Error: 0.018808 Align patch 23 2 left Iteration 1 Error: 0.689740 Iteration 2 Error: 0.083243 Iteration 3 Error: 0.021226 Align patch 24 1 left Iteration 1 Error: 0.818001 Iteration 2 Error: 0.104230 Iteration 3 Error: 0.021907 Align patch 25 0 left Iteration 1 Error: 0.761576 Iteration 2 Error: 0.109849 Iteration 3 Error: 0.021751 3D Fitting completed. Patch alignment time: 10.72(sec) Local motion has been corrected. Process thread exits. Computational time: 21.419111 sec Total time: 27.776167 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00005hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00005hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.574048s Reading file: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00005hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.845784s ........................................ >>>>>>TIME<<<<<< FFT: 1.135549s Defocus_U Defocus_V Angle CCC 25265.65 26128.94 10.03 0.051791 Final Values Defocus_U Defocus_V Angle CCC 25268.77 26125.81 10.03 0.080811 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00001sq_v01_00005hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00005hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.995e-02 CC threshold: 0.734 Mean Std: 39.41 6.81 Num Hot pixels: 220 Hot pixel threshold: 80.27 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.258698 Iteration 2 Error: 0.302976 Iteration 3 Error: 0.072082 Iteration 4 Error: 0.025583 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.14 0.06 ...... Frame ( 3) shift: -0.27 0.13 ...... Frame ( 4) shift: -0.41 0.19 ...... Frame ( 5) shift: -0.54 0.25 ...... Frame ( 6) shift: -0.59 0.32 ...... Frame ( 7) shift: -0.54 0.38 ...... Frame ( 8) shift: -0.50 0.45 ...... Frame ( 9) shift: -0.47 0.52 ...... Frame ( 10) shift: -0.46 0.61 ...... Frame ( 11) shift: -0.45 0.69 ...... Frame ( 12) shift: -0.41 0.74 ...... Frame ( 13) shift: -0.34 0.76 ...... Frame ( 14) shift: -0.28 0.78 ...... Frame ( 15) shift: -0.22 0.81 ...... Frame ( 16) shift: -0.18 0.87 ...... Frame ( 17) shift: -0.14 0.92 ...... Frame ( 18) shift: -0.09 0.98 ...... Frame ( 19) shift: -0.01 1.05 ...... Frame ( 20) shift: 0.06 1.13 ...... Frame ( 21) shift: 0.15 1.21 ...... Frame ( 22) shift: 0.27 1.30 ...... Frame ( 23) shift: 0.39 1.40 ...... Frame ( 24) shift: 0.45 1.46 ...... Frame ( 25) shift: 0.47 1.49 ...... Frame ( 26) shift: 0.48 1.52 ...... Frame ( 27) shift: 0.52 1.60 ...... Frame ( 28) shift: 0.60 1.72 ...... Frame ( 29) shift: 0.67 1.85 ...... Frame ( 30) shift: 0.73 1.90 ...... Frame ( 31) shift: 0.79 1.88 ...... Frame ( 32) shift: 0.85 1.86 ...... Frame ( 33) shift: 0.89 1.89 ...... Frame ( 34) shift: 0.91 1.99 ...... Frame ( 35) shift: 0.94 2.08 ...... Frame ( 36) shift: 0.96 2.16 ...... Frame ( 37) shift: 0.99 2.22 ...... Frame ( 38) shift: 1.02 2.29 ...... Frame ( 39) shift: 1.05 2.36 ...... Frame ( 40) shift: 1.08 2.43 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.723519 Iteration 2 Error: 0.177647 Iteration 3 Error: 0.056149 Iteration 4 Error: 0.011969 Align patch 2 23 left Iteration 1 Error: 0.942347 Iteration 2 Error: 0.171745 Iteration 3 Error: 0.038895 Align patch 3 22 left Iteration 1 Error: 1.365977 Iteration 2 Error: 0.176379 Iteration 3 Error: 0.054300 Iteration 4 Error: 0.012484 Align patch 4 21 left Iteration 1 Error: 1.430638 Iteration 2 Error: 0.200538 Iteration 3 Error: 0.042627 Align patch 5 20 left Iteration 1 Error: 0.878503 Iteration 2 Error: 0.153184 Iteration 3 Error: 0.040635 Align patch 6 19 left Iteration 1 Error: 0.726799 Iteration 2 Error: 0.192362 Iteration 3 Error: 0.064184 Iteration 4 Error: 0.027808 Align patch 7 18 left Iteration 1 Error: 0.743725 Iteration 2 Error: 0.206070 Iteration 3 Error: 0.063366 Iteration 4 Error: 0.023106 Align patch 8 17 left Iteration 1 Error: 2.307525 Iteration 2 Error: 0.513610 Iteration 3 Error: 0.159597 Iteration 4 Error: 0.055499 Iteration 5 Error: 0.022805 Align patch 9 16 left Iteration 1 Error: 3.481385 Iteration 2 Error: 1.324126 Iteration 3 Error: 0.464651 Iteration 4 Error: 0.297921 Iteration 5 Error: 0.183828 Align patch 9 16 left Iteration 1 Error: 3.953876 Iteration 2 Error: 0.792159 Iteration 3 Error: 0.186644 Iteration 4 Error: 0.049854 Align patch 10 15 left Iteration 1 Error: 3.087159 Iteration 2 Error: 1.282709 Iteration 3 Error: 0.660229 Iteration 4 Error: 0.398525 Iteration 5 Error: 0.241888 Align patch 10 15 left Iteration 1 Error: 3.085864 Iteration 2 Error: 0.866099 Iteration 3 Error: 0.281338 Iteration 4 Error: 0.107964 Iteration 5 Error: 0.043107 Align patch 11 14 left Iteration 1 Error: 0.844930 Iteration 2 Error: 0.297646 Iteration 3 Error: 0.083323 Iteration 4 Error: 0.027624 Align patch 12 13 left Iteration 1 Error: 1.129065 Iteration 2 Error: 0.187796 Iteration 3 Error: 0.046194 Align patch 13 12 left Iteration 1 Error: 0.821643 Iteration 2 Error: 0.114989 Iteration 3 Error: 0.042464 Align patch 14 11 left Iteration 1 Error: 0.826298 Iteration 2 Error: 0.264655 Iteration 3 Error: 0.053564 Iteration 4 Error: 0.019290 Align patch 15 10 left Iteration 1 Error: 1.486646 Iteration 2 Error: 0.377819 Iteration 3 Error: 0.115694 Iteration 4 Error: 0.044582 Align patch 16 9 left Iteration 1 Error: 1.287460 Iteration 2 Error: 0.168495 Iteration 3 Error: 0.043405 Align patch 17 8 left Iteration 1 Error: 1.168377 Iteration 2 Error: 0.126278 Iteration 3 Error: 0.042926 Align patch 18 7 left Iteration 1 Error: 0.716416 Iteration 2 Error: 0.116121 Iteration 3 Error: 0.032115 Align patch 19 6 left Iteration 1 Error: 0.713743 Iteration 2 Error: 0.171459 Iteration 3 Error: 0.030929 Align patch 20 5 left Iteration 1 Error: 0.719534 Iteration 2 Error: 0.168707 Iteration 3 Error: 0.038864 Align patch 21 4 left Iteration 1 Error: 0.754684 Iteration 2 Error: 0.102819 Iteration 3 Error: 0.020611 Align patch 22 3 left Iteration 1 Error: 0.792905 Iteration 2 Error: 0.134375 Iteration 3 Error: 0.030945 Align patch 23 2 left Iteration 1 Error: 0.984415 Iteration 2 Error: 0.196848 Iteration 3 Error: 0.066757 Iteration 4 Error: 0.025520 Align patch 24 1 left Iteration 1 Error: 0.521825 Iteration 2 Error: 0.097662 Iteration 3 Error: 0.034619 Align patch 25 0 left Iteration 1 Error: 0.854416 Iteration 2 Error: 0.262154 Iteration 3 Error: 0.055015 Iteration 4 Error: 0.024611 3D Fitting completed. Patch alignment time: 22.23(sec) Local motion has been corrected. Process thread exits. Computational time: 38.363136 sec Total time: 46.345711 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00005hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00005hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.858431s Reading file: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00005hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.525876s ........................................ >>>>>>TIME<<<<<< FFT: 1.571335s Defocus_U Defocus_V Angle CCC 25912.16 26451.22 0.38 0.031927 Final Values Defocus_U Defocus_V Angle CCC 25923.10 26449.66 1.32 0.048237 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00001sq_v01_00005hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00005hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 40.90 7.01 Num Hot pixels: 220 Hot pixel threshold: 82.97 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.090010 Iteration 2 Error: 0.089670 Iteration 3 Error: 0.015979 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.09 0.10 ...... Frame ( 3) shift: -0.17 0.21 ...... Frame ( 4) shift: -0.26 0.31 ...... Frame ( 5) shift: -0.35 0.41 ...... Frame ( 6) shift: -0.39 0.52 ...... Frame ( 7) shift: -0.38 0.62 ...... Frame ( 8) shift: -0.38 0.73 ...... Frame ( 9) shift: -0.36 0.84 ...... Frame ( 10) shift: -0.34 0.97 ...... Frame ( 11) shift: -0.32 1.09 ...... Frame ( 12) shift: -0.30 1.18 ...... Frame ( 13) shift: -0.29 1.24 ...... Frame ( 14) shift: -0.27 1.30 ...... Frame ( 15) shift: -0.24 1.36 ...... Frame ( 16) shift: -0.19 1.40 ...... Frame ( 17) shift: -0.14 1.44 ...... Frame ( 18) shift: -0.12 1.48 ...... Frame ( 19) shift: -0.11 1.51 ...... Frame ( 20) shift: -0.10 1.55 ...... Frame ( 21) shift: -0.08 1.56 ...... Frame ( 22) shift: -0.04 1.54 ...... Frame ( 23) shift: -0.00 1.53 ...... Frame ( 24) shift: 0.04 1.54 ...... Frame ( 25) shift: 0.08 1.57 ...... Frame ( 26) shift: 0.12 1.61 ...... Frame ( 27) shift: 0.16 1.60 ...... Frame ( 28) shift: 0.20 1.55 ...... Frame ( 29) shift: 0.23 1.50 ...... Frame ( 30) shift: 0.25 1.50 ...... Frame ( 31) shift: 0.27 1.55 ...... Frame ( 32) shift: 0.29 1.60 ...... Frame ( 33) shift: 0.35 1.64 ...... Frame ( 34) shift: 0.44 1.66 ...... Frame ( 35) shift: 0.53 1.67 ...... Frame ( 36) shift: 0.57 1.67 ...... Frame ( 37) shift: 0.56 1.64 ...... Frame ( 38) shift: 0.56 1.61 ...... Frame ( 39) shift: 0.55 1.58 ...... Frame ( 40) shift: 0.55 1.56 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.837985 Iteration 2 Error: 0.092107 Iteration 3 Error: 0.026342 Align patch 2 23 left Iteration 1 Error: 0.713828 Iteration 2 Error: 0.131432 Iteration 3 Error: 0.023251 Align patch 3 22 left Iteration 1 Error: 0.738017 Iteration 2 Error: 0.054788 Iteration 3 Error: 0.009198 Align patch 4 21 left Iteration 1 Error: 0.464222 Iteration 2 Error: 0.051662 Iteration 3 Error: 0.008343 Align patch 5 20 left Iteration 1 Error: 0.503397 Iteration 2 Error: 0.059793 Iteration 3 Error: 0.010600 Align patch 6 19 left Iteration 1 Error: 0.544334 Iteration 2 Error: 0.073979 Iteration 3 Error: 0.016047 Align patch 7 18 left Iteration 1 Error: 0.963377 Iteration 2 Error: 0.099375 Iteration 3 Error: 0.024716 Align patch 8 17 left Iteration 1 Error: 0.530334 Iteration 2 Error: 0.069955 Iteration 3 Error: 0.020378 Align patch 9 16 left Iteration 1 Error: 0.436348 Iteration 2 Error: 0.073142 Iteration 3 Error: 0.007767 Align patch 10 15 left Iteration 1 Error: 0.514203 Iteration 2 Error: 0.037676 Align patch 11 14 left Iteration 1 Error: 0.763327 Iteration 2 Error: 0.105055 Iteration 3 Error: 0.021750 Align patch 12 13 left Iteration 1 Error: 0.973309 Iteration 2 Error: 0.078122 Iteration 3 Error: 0.013318 Align patch 13 12 left Iteration 1 Error: 0.505082 Iteration 2 Error: 0.065099 Iteration 3 Error: 0.014708 Align patch 14 11 left Iteration 1 Error: 0.473833 Iteration 2 Error: 0.080839 Iteration 3 Error: 0.016487 Align patch 15 10 left Iteration 1 Error: 0.443212 Iteration 2 Error: 0.039916 Align patch 16 9 left Iteration 1 Error: 0.747989 Iteration 2 Error: 0.098858 Iteration 3 Error: 0.028578 Align patch 17 8 left Iteration 1 Error: 0.460098 Iteration 2 Error: 0.068305 Iteration 3 Error: 0.013228 Align patch 18 7 left Iteration 1 Error: 0.512205 Iteration 2 Error: 0.054055 Iteration 3 Error: 0.007742 Align patch 19 6 left Iteration 1 Error: 0.521436 Iteration 2 Error: 0.053184 Iteration 3 Error: 0.008749 Align patch 20 5 left Iteration 1 Error: 0.631620 Iteration 2 Error: 0.065273 Iteration 3 Error: 0.010619 Align patch 21 4 left Iteration 1 Error: 0.821633 Iteration 2 Error: 0.110060 Iteration 3 Error: 0.028892 Align patch 22 3 left Iteration 1 Error: 1.080673 Iteration 2 Error: 0.098148 Iteration 3 Error: 0.016314 Align patch 23 2 left Iteration 1 Error: 0.366561 Iteration 2 Error: 0.068885 Iteration 3 Error: 0.010455 Align patch 24 1 left Iteration 1 Error: 0.521164 Iteration 2 Error: 0.045347 Align patch 25 0 left Iteration 1 Error: 0.465640 Iteration 2 Error: 0.050513 Iteration 3 Error: 0.007184 3D Fitting completed. Patch alignment time: 17.60(sec) Local motion has been corrected. Process thread exits. Computational time: 34.914867 sec Total time: 44.679916 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00005hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00005hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.514177s Reading file: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00005hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.072628s ........................................ >>>>>>TIME<<<<<< FFT: 1.192918s Defocus_U Defocus_V Angle CCC 23404.30 24369.14 5.26 0.056627 Final Values Defocus_U Defocus_V Angle CCC 23416.79 24369.15 4.94 0.090398 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00001sq_v01_00005hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00005hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.355e-01 1.007e-01 CC threshold: 0.740 Mean Std: 40.63 7.01 Num Hot pixels: 224 Hot pixel threshold: 82.69 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.314180 Iteration 2 Error: 0.094894 Iteration 3 Error: 0.014938 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.06 0.13 ...... Frame ( 3) shift: -0.11 0.27 ...... Frame ( 4) shift: -0.17 0.40 ...... Frame ( 5) shift: -0.23 0.54 ...... Frame ( 6) shift: -0.25 0.64 ...... Frame ( 7) shift: -0.22 0.72 ...... Frame ( 8) shift: -0.20 0.80 ...... Frame ( 9) shift: -0.17 0.88 ...... Frame ( 10) shift: -0.14 0.96 ...... Frame ( 11) shift: -0.10 1.03 ...... Frame ( 12) shift: -0.07 1.14 ...... Frame ( 13) shift: -0.03 1.27 ...... Frame ( 14) shift: 0.00 1.40 ...... Frame ( 15) shift: 0.02 1.50 ...... Frame ( 16) shift: 0.01 1.57 ...... Frame ( 17) shift: 0.00 1.64 ...... Frame ( 18) shift: -0.00 1.68 ...... Frame ( 19) shift: -0.01 1.68 ...... Frame ( 20) shift: -0.01 1.68 ...... Frame ( 21) shift: 0.02 1.69 ...... Frame ( 22) shift: 0.07 1.73 ...... Frame ( 23) shift: 0.12 1.76 ...... Frame ( 24) shift: 0.15 1.80 ...... Frame ( 25) shift: 0.16 1.84 ...... Frame ( 26) shift: 0.17 1.88 ...... Frame ( 27) shift: 0.18 1.93 ...... Frame ( 28) shift: 0.18 1.99 ...... Frame ( 29) shift: 0.19 2.05 ...... Frame ( 30) shift: 0.21 2.10 ...... Frame ( 31) shift: 0.26 2.16 ...... Frame ( 32) shift: 0.30 2.22 ...... Frame ( 33) shift: 0.33 2.24 ...... Frame ( 34) shift: 0.34 2.24 ...... Frame ( 35) shift: 0.35 2.24 ...... Frame ( 36) shift: 0.36 2.24 ...... Frame ( 37) shift: 0.38 2.26 ...... Frame ( 38) shift: 0.40 2.27 ...... Frame ( 39) shift: 0.41 2.28 ...... Frame ( 40) shift: 0.43 2.29 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.148478 Iteration 2 Error: 0.103866 Iteration 3 Error: 0.017828 Align patch 2 23 left Iteration 1 Error: 0.791491 Iteration 2 Error: 0.078039 Iteration 3 Error: 0.015111 Align patch 3 22 left Iteration 1 Error: 0.542001 Iteration 2 Error: 0.060116 Iteration 3 Error: 0.010024 Align patch 4 21 left Iteration 1 Error: 0.673173 Iteration 2 Error: 0.081637 Iteration 3 Error: 0.014621 Align patch 5 20 left Iteration 1 Error: 0.485645 Iteration 2 Error: 0.037470 Align patch 6 19 left Iteration 1 Error: 0.757241 Iteration 2 Error: 0.093553 Iteration 3 Error: 0.024302 Align patch 7 18 left Iteration 1 Error: 0.455963 Iteration 2 Error: 0.039699 Align patch 8 17 left Iteration 1 Error: 0.713851 Iteration 2 Error: 0.065488 Iteration 3 Error: 0.010617 Align patch 9 16 left Iteration 1 Error: 0.335294 Iteration 2 Error: 0.033183 Align patch 10 15 left Iteration 1 Error: 0.367853 Iteration 2 Error: 0.033799 Align patch 11 14 left Iteration 1 Error: 0.404085 Iteration 2 Error: 0.046930 Align patch 12 13 left Iteration 1 Error: 0.385605 Iteration 2 Error: 0.041445 Align patch 13 12 left Iteration 1 Error: 0.635308 Iteration 2 Error: 0.034153 Align patch 14 11 left Iteration 1 Error: 0.394382 Iteration 2 Error: 0.055285 Iteration 3 Error: 0.009174 Align patch 15 10 left Iteration 1 Error: 0.428323 Iteration 2 Error: 0.042647 Align patch 16 9 left Iteration 1 Error: 0.416906 Iteration 2 Error: 0.057385 Iteration 3 Error: 0.009969 Align patch 17 8 left Iteration 1 Error: 0.527571 Iteration 2 Error: 0.042099 Align patch 18 7 left Iteration 1 Error: 0.713689 Iteration 2 Error: 0.069383 Iteration 3 Error: 0.010399 Align patch 19 6 left Iteration 1 Error: 0.600500 Iteration 2 Error: 0.100399 Iteration 3 Error: 0.017079 Align patch 20 5 left Iteration 1 Error: 0.299762 Iteration 2 Error: 0.034880 Align patch 21 4 left Iteration 1 Error: 0.331851 Iteration 2 Error: 0.031267 Align patch 22 3 left Iteration 1 Error: 0.512479 Iteration 2 Error: 0.040802 Align patch 23 2 left Iteration 1 Error: 1.073383 Iteration 2 Error: 0.109705 Iteration 3 Error: 0.019049 Align patch 24 1 left Iteration 1 Error: 0.974516 Iteration 2 Error: 0.134939 Iteration 3 Error: 0.019116 Align patch 25 0 left Iteration 1 Error: 0.700044 Iteration 2 Error: 0.101582 Iteration 3 Error: 0.012101 3D Fitting completed. Patch alignment time: 18.02(sec) Local motion has been corrected. Process thread exits. Computational time: 33.793636 sec Total time: 44.311378 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00005hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00005hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.854350s Reading file: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00005hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.514347s ........................................ >>>>>>TIME<<<<<< FFT: 1.382302s Defocus_U Defocus_V Angle CCC 27697.27 27021.48 82.16 0.079991 Final Values Defocus_U Defocus_V Angle CCC 27701.96 27019.92 82.16 0.123399 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00001sq_v01_00006hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00006hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.350e-01 1.003e-01 CC threshold: 0.737 Mean Std: 39.57 6.88 Num Hot pixels: 189 Hot pixel threshold: 80.83 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.433179 Iteration 2 Error: 0.373754 Iteration 3 Error: 0.062077 Iteration 4 Error: 0.015996 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.11 -0.02 ...... Frame ( 3) shift: -0.22 -0.04 ...... Frame ( 4) shift: -0.32 -0.06 ...... Frame ( 5) shift: -0.43 -0.07 ...... Frame ( 6) shift: -0.46 -0.04 ...... Frame ( 7) shift: -0.42 0.04 ...... Frame ( 8) shift: -0.38 0.12 ...... Frame ( 9) shift: -0.30 0.23 ...... Frame ( 10) shift: -0.19 0.37 ...... Frame ( 11) shift: -0.08 0.51 ...... Frame ( 12) shift: 0.02 0.64 ...... Frame ( 13) shift: 0.12 0.77 ...... Frame ( 14) shift: 0.21 0.90 ...... Frame ( 15) shift: 0.33 1.01 ...... Frame ( 16) shift: 0.46 1.09 ...... Frame ( 17) shift: 0.60 1.18 ...... Frame ( 18) shift: 0.71 1.25 ...... Frame ( 19) shift: 0.79 1.32 ...... Frame ( 20) shift: 0.88 1.39 ...... Frame ( 21) shift: 0.95 1.46 ...... Frame ( 22) shift: 1.01 1.54 ...... Frame ( 23) shift: 1.06 1.61 ...... Frame ( 24) shift: 1.12 1.70 ...... Frame ( 25) shift: 1.17 1.82 ...... Frame ( 26) shift: 1.22 1.94 ...... Frame ( 27) shift: 1.35 2.05 ...... Frame ( 28) shift: 1.56 2.16 ...... Frame ( 29) shift: 1.77 2.27 ...... Frame ( 30) shift: 1.89 2.38 ...... Frame ( 31) shift: 1.92 2.49 ...... Frame ( 32) shift: 1.96 2.60 ...... Frame ( 33) shift: 1.98 2.71 ...... Frame ( 34) shift: 1.98 2.81 ...... Frame ( 35) shift: 1.99 2.92 ...... Frame ( 36) shift: 2.05 3.04 ...... Frame ( 37) shift: 2.16 3.19 ...... Frame ( 38) shift: 2.27 3.33 ...... Frame ( 39) shift: 2.38 3.47 ...... Frame ( 40) shift: 2.48 3.62 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.848277 Iteration 2 Error: 0.315421 Iteration 3 Error: 0.059936 Iteration 4 Error: 0.014352 Align patch 2 23 left Iteration 1 Error: 0.813587 Iteration 2 Error: 0.157316 Iteration 3 Error: 0.061161 Iteration 4 Error: 0.020478 Align patch 3 22 left Iteration 1 Error: 0.407544 Iteration 2 Error: 0.054459 Iteration 3 Error: 0.012131 Align patch 4 21 left Iteration 1 Error: 0.589961 Iteration 2 Error: 0.090527 Iteration 3 Error: 0.013771 Align patch 5 20 left Iteration 1 Error: 0.794122 Iteration 2 Error: 0.103976 Iteration 3 Error: 0.021564 Align patch 6 19 left Iteration 1 Error: 1.962848 Iteration 2 Error: 0.423171 Iteration 3 Error: 0.074588 Iteration 4 Error: 0.015650 Align patch 7 18 left Iteration 1 Error: 0.696435 Iteration 2 Error: 0.227186 Iteration 3 Error: 0.074913 Iteration 4 Error: 0.028147 Align patch 8 17 left Iteration 1 Error: 0.585916 Iteration 2 Error: 0.076305 Iteration 3 Error: 0.010856 Align patch 9 16 left Iteration 1 Error: 0.436141 Iteration 2 Error: 0.068823 Iteration 3 Error: 0.011170 Align patch 10 15 left Iteration 1 Error: 0.713566 Iteration 2 Error: 0.109001 Iteration 3 Error: 0.019545 Align patch 11 14 left Iteration 1 Error: 0.925950 Iteration 2 Error: 0.221998 Iteration 3 Error: 0.048832 Align patch 12 13 left Iteration 1 Error: 0.816229 Iteration 2 Error: 0.277178 Iteration 3 Error: 0.078186 Iteration 4 Error: 0.027562 Align patch 13 12 left Iteration 1 Error: 0.394583 Iteration 2 Error: 0.092563 Iteration 3 Error: 0.024979 Align patch 14 11 left Iteration 1 Error: 0.583186 Iteration 2 Error: 0.106219 Iteration 3 Error: 0.023451 Align patch 15 10 left Iteration 1 Error: 0.783294 Iteration 2 Error: 0.107852 Iteration 3 Error: 0.025008 Align patch 16 9 left Iteration 1 Error: 0.705252 Iteration 2 Error: 0.162735 Iteration 3 Error: 0.051550 Iteration 4 Error: 0.021145 Align patch 17 8 left Iteration 1 Error: 0.713066 Iteration 2 Error: 0.144248 Iteration 3 Error: 0.055281 Iteration 4 Error: 0.020877 Align patch 18 7 left Iteration 1 Error: 0.678963 Iteration 2 Error: 0.093922 Iteration 3 Error: 0.021147 Align patch 19 6 left Iteration 1 Error: 0.865707 Iteration 2 Error: 0.221846 Iteration 3 Error: 0.056073 Iteration 4 Error: 0.018051 Align patch 20 5 left Iteration 1 Error: 0.789190 Iteration 2 Error: 0.154364 Iteration 3 Error: 0.050046 Iteration 4 Error: 0.014936 Align patch 21 4 left Iteration 1 Error: 0.780608 Iteration 2 Error: 0.154159 Iteration 3 Error: 0.040183 Align patch 22 3 left Iteration 1 Error: 0.542682 Iteration 2 Error: 0.098328 Iteration 3 Error: 0.022216 Align patch 23 2 left Iteration 1 Error: 0.666889 Iteration 2 Error: 0.136066 Iteration 3 Error: 0.039324 Align patch 24 1 left Iteration 1 Error: 1.034742 Iteration 2 Error: 0.193618 Iteration 3 Error: 0.056365 Iteration 4 Error: 0.015338 Align patch 25 0 left Iteration 1 Error: 0.884747 Iteration 2 Error: 0.176932 Iteration 3 Error: 0.042820 3D Fitting completed. Patch alignment time: 18.64(sec) Local motion has been corrected. Process thread exits. Computational time: 30.149670 sec Total time: 38.839268 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00006hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00006hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.567257s Reading file: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00006hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 4.278725s ........................................ >>>>>>TIME<<<<<< FFT: 1.322502s Defocus_U Defocus_V Angle CCC 26113.28 26945.31 10.88 0.070365 Final Values Defocus_U Defocus_V Angle CCC 26114.84 26950.00 11.19 0.106731 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00001sq_v01_00006hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00006hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.001e-01 CC threshold: 0.735 Mean Std: 40.04 7.02 Num Hot pixels: 223 Hot pixel threshold: 82.19 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.508457 Iteration 2 Error: 0.425886 Iteration 3 Error: 0.118109 Iteration 4 Error: 0.043031 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.15 0.23 ...... Frame ( 3) shift: 0.30 0.46 ...... Frame ( 4) shift: 0.46 0.69 ...... Frame ( 5) shift: 0.61 0.91 ...... Frame ( 6) shift: 0.73 1.09 ...... Frame ( 7) shift: 0.84 1.20 ...... Frame ( 8) shift: 0.94 1.31 ...... Frame ( 9) shift: 1.05 1.43 ...... Frame ( 10) shift: 1.16 1.56 ...... Frame ( 11) shift: 1.28 1.69 ...... Frame ( 12) shift: 1.41 1.79 ...... Frame ( 13) shift: 1.55 1.88 ...... Frame ( 14) shift: 1.69 1.97 ...... Frame ( 15) shift: 1.81 2.05 ...... Frame ( 16) shift: 1.91 2.12 ...... Frame ( 17) shift: 2.01 2.19 ...... Frame ( 18) shift: 2.07 2.27 ...... Frame ( 19) shift: 2.09 2.36 ...... Frame ( 20) shift: 2.11 2.45 ...... Frame ( 21) shift: 2.15 2.52 ...... Frame ( 22) shift: 2.23 2.56 ...... Frame ( 23) shift: 2.30 2.59 ...... Frame ( 24) shift: 2.38 2.67 ...... Frame ( 25) shift: 2.45 2.78 ...... Frame ( 26) shift: 2.53 2.90 ...... Frame ( 27) shift: 2.63 3.00 ...... Frame ( 28) shift: 2.77 3.10 ...... Frame ( 29) shift: 2.90 3.20 ...... Frame ( 30) shift: 3.00 3.27 ...... Frame ( 31) shift: 3.08 3.30 ...... Frame ( 32) shift: 3.15 3.34 ...... Frame ( 33) shift: 3.26 3.37 ...... Frame ( 34) shift: 3.42 3.41 ...... Frame ( 35) shift: 3.58 3.44 ...... Frame ( 36) shift: 3.70 3.52 ...... Frame ( 37) shift: 3.80 3.62 ...... Frame ( 38) shift: 3.89 3.73 ...... Frame ( 39) shift: 3.98 3.83 ...... Frame ( 40) shift: 4.07 3.94 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 4.838940 Iteration 2 Error: 1.753126 Iteration 3 Error: 0.552141 Iteration 4 Error: 0.211921 Iteration 5 Error: 0.095373 Align patch 1 24 left Iteration 1 Error: 4.902404 Iteration 2 Error: 0.901662 Iteration 3 Error: 0.368736 Iteration 4 Error: 0.160065 Iteration 5 Error: 0.072193 Align patch 2 23 left Iteration 1 Error: 10.523161 Iteration 2 Error: 5.128020 Iteration 3 Error: 3.099977 Iteration 4 Error: 1.334307 Iteration 5 Error: 0.464542 Align patch 2 23 left Iteration 1 Error: 7.374340 Iteration 2 Error: 2.654596 Iteration 3 Error: 1.179246 Iteration 4 Error: 0.648809 Iteration 5 Error: 0.480395 Align patch 3 22 left Iteration 1 Error: 4.589072 Iteration 2 Error: 1.926077 Iteration 3 Error: 1.800086 Iteration 4 Error: 1.056574 Iteration 5 Error: 0.674910 Align patch 3 22 left Iteration 1 Error: 5.824170 Iteration 2 Error: 1.969138 Iteration 3 Error: 1.278800 Iteration 4 Error: 1.041617 Iteration 5 Error: 0.959795 Align patch 4 21 left Iteration 1 Error: 2.347152 Iteration 2 Error: 0.680484 Iteration 3 Error: 0.246340 Iteration 4 Error: 0.128112 Iteration 5 Error: 0.068406 Align patch 4 21 left Iteration 1 Error: 1.359008 Iteration 2 Error: 0.275486 Iteration 3 Error: 0.087123 Iteration 4 Error: 0.040442 Align patch 5 20 left Iteration 1 Error: 1.314025 Iteration 2 Error: 0.147986 Iteration 3 Error: 0.015133 Align patch 6 19 left Iteration 1 Error: 3.318572 Iteration 2 Error: 0.598998 Iteration 3 Error: 0.220198 Iteration 4 Error: 0.067063 Iteration 5 Error: 0.022988 Align patch 7 18 left Iteration 1 Error: 1.387406 Iteration 2 Error: 0.318030 Iteration 3 Error: 0.130927 Iteration 4 Error: 0.056741 Iteration 5 Error: 0.027124 Align patch 8 17 left Iteration 1 Error: 1.083887 Iteration 2 Error: 0.244698 Iteration 3 Error: 0.106555 Iteration 4 Error: 0.042425 Align patch 9 16 left Iteration 1 Error: 0.879881 Iteration 2 Error: 0.232765 Iteration 3 Error: 0.067993 Iteration 4 Error: 0.023753 Align patch 10 15 left Iteration 1 Error: 1.536269 Iteration 2 Error: 0.297644 Iteration 3 Error: 0.118156 Iteration 4 Error: 0.027009 Align patch 11 14 left Iteration 1 Error: 4.002760 Iteration 2 Error: 0.621691 Iteration 3 Error: 0.122268 Iteration 4 Error: 0.039302 Align patch 12 13 left Iteration 1 Error: 0.938535 Iteration 2 Error: 0.205637 Iteration 3 Error: 0.081290 Iteration 4 Error: 0.031849 Align patch 13 12 left Iteration 1 Error: 1.333017 Iteration 2 Error: 0.320449 Iteration 3 Error: 0.085284 Iteration 4 Error: 0.030222 Align patch 14 11 left Iteration 1 Error: 1.268511 Iteration 2 Error: 0.416460 Iteration 3 Error: 0.115213 Iteration 4 Error: 0.041790 Align patch 15 10 left Iteration 1 Error: 1.601398 Iteration 2 Error: 0.340068 Iteration 3 Error: 0.087720 Iteration 4 Error: 0.028371 Align patch 16 9 left Iteration 1 Error: 1.453241 Iteration 2 Error: 0.368953 Iteration 3 Error: 0.083664 Iteration 4 Error: 0.030855 Align patch 17 8 left Iteration 1 Error: 1.556040 Iteration 2 Error: 0.472900 Iteration 3 Error: 0.093140 Iteration 4 Error: 0.033161 Align patch 18 7 left Iteration 1 Error: 1.273488 Iteration 2 Error: 0.252711 Iteration 3 Error: 0.078763 Iteration 4 Error: 0.022960 Align patch 19 6 left Iteration 1 Error: 1.374350 Iteration 2 Error: 0.273063 Iteration 3 Error: 0.050869 Iteration 4 Error: 0.014257 Align patch 20 5 left Iteration 1 Error: 1.555125 Iteration 2 Error: 0.251911 Iteration 3 Error: 0.045590 Align patch 21 4 left Iteration 1 Error: 2.289353 Iteration 2 Error: 0.401340 Iteration 3 Error: 0.075622 Iteration 4 Error: 0.014382 Align patch 22 3 left Iteration 1 Error: 1.955886 Iteration 2 Error: 0.316360 Iteration 3 Error: 0.094071 Iteration 4 Error: 0.028000 Align patch 23 2 left Iteration 1 Error: 2.440023 Iteration 2 Error: 0.327257 Iteration 3 Error: 0.091039 Iteration 4 Error: 0.026181 Align patch 24 1 left Iteration 1 Error: 2.333624 Iteration 2 Error: 0.373209 Iteration 3 Error: 0.081351 Iteration 4 Error: 0.033884 Align patch 25 0 left Iteration 1 Error: 1.687706 Iteration 2 Error: 0.285535 Iteration 3 Error: 0.055664 Iteration 4 Error: 0.021898 3D Fitting completed. Patch alignment time: 27.62(sec) Local motion has been corrected. Process thread exits. Computational time: 42.780552 sec Total time: 51.838493 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00006hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00006hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.367787s Reading file: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00006hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.546711s ........................................ >>>>>>TIME<<<<<< FFT: 1.316634s Defocus_U Defocus_V Angle CCC 27054.69 26539.06 85.11 0.045086 Final Values Defocus_U Defocus_V Angle CCC 27056.25 26537.50 85.11 0.067906 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00001sq_v01_00006hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00006hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.351e-01 1.004e-01 CC threshold: 0.738 Mean Std: 38.63 6.87 Num Hot pixels: 193 Hot pixel threshold: 79.86 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.046900 Iteration 2 Error: 0.135541 Iteration 3 Error: 0.025433 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.22 -0.19 ...... Frame ( 3) shift: -0.43 -0.37 ...... Frame ( 4) shift: -0.65 -0.56 ...... Frame ( 5) shift: -0.87 -0.75 ...... Frame ( 6) shift: -1.01 -0.85 ...... Frame ( 7) shift: -1.07 -0.86 ...... Frame ( 8) shift: -1.14 -0.88 ...... Frame ( 9) shift: -1.16 -0.81 ...... Frame ( 10) shift: -1.15 -0.66 ...... Frame ( 11) shift: -1.14 -0.50 ...... Frame ( 12) shift: -1.10 -0.38 ...... Frame ( 13) shift: -1.05 -0.29 ...... Frame ( 14) shift: -1.00 -0.20 ...... Frame ( 15) shift: -0.96 -0.12 ...... Frame ( 16) shift: -0.93 -0.04 ...... Frame ( 17) shift: -0.89 0.03 ...... Frame ( 18) shift: -0.85 0.12 ...... Frame ( 19) shift: -0.79 0.22 ...... Frame ( 20) shift: -0.73 0.33 ...... Frame ( 21) shift: -0.68 0.39 ...... Frame ( 22) shift: -0.65 0.42 ...... Frame ( 23) shift: -0.62 0.46 ...... Frame ( 24) shift: -0.62 0.50 ...... Frame ( 25) shift: -0.63 0.55 ...... Frame ( 26) shift: -0.65 0.60 ...... Frame ( 27) shift: -0.63 0.66 ...... Frame ( 28) shift: -0.56 0.72 ...... Frame ( 29) shift: -0.50 0.78 ...... Frame ( 30) shift: -0.48 0.83 ...... Frame ( 31) shift: -0.50 0.86 ...... Frame ( 32) shift: -0.51 0.88 ...... Frame ( 33) shift: -0.50 0.88 ...... Frame ( 34) shift: -0.44 0.85 ...... Frame ( 35) shift: -0.38 0.82 ...... Frame ( 36) shift: -0.38 0.82 ...... Frame ( 37) shift: -0.42 0.83 ...... Frame ( 38) shift: -0.47 0.85 ...... Frame ( 39) shift: -0.51 0.86 ...... Frame ( 40) shift: -0.56 0.88 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.865971 Iteration 2 Error: 0.188039 Iteration 3 Error: 0.058227 Iteration 4 Error: 0.013798 Align patch 2 23 left Iteration 1 Error: 1.391294 Iteration 2 Error: 0.193408 Iteration 3 Error: 0.040463 Align patch 3 22 left Iteration 1 Error: 0.426966 Iteration 2 Error: 0.047072 Align patch 4 21 left Iteration 1 Error: 0.497141 Iteration 2 Error: 0.081930 Iteration 3 Error: 0.012955 Align patch 5 20 left Iteration 1 Error: 0.708593 Iteration 2 Error: 0.057594 Iteration 3 Error: 0.008922 Align patch 6 19 left Iteration 1 Error: 1.158141 Iteration 2 Error: 0.192897 Iteration 3 Error: 0.055987 Iteration 4 Error: 0.020086 Align patch 7 18 left Iteration 1 Error: 0.918168 Iteration 2 Error: 0.196594 Iteration 3 Error: 0.052069 Iteration 4 Error: 0.018635 Align patch 8 17 left Iteration 1 Error: 0.409393 Iteration 2 Error: 0.053841 Iteration 3 Error: 0.014644 Align patch 9 16 left Iteration 1 Error: 0.405293 Iteration 2 Error: 0.056705 Iteration 3 Error: 0.012559 Align patch 10 15 left Iteration 1 Error: 0.637253 Iteration 2 Error: 0.073261 Iteration 3 Error: 0.008395 Align patch 11 14 left Iteration 1 Error: 0.855468 Iteration 2 Error: 0.143461 Iteration 3 Error: 0.041351 Align patch 12 13 left Iteration 1 Error: 1.024889 Iteration 2 Error: 0.196956 Iteration 3 Error: 0.055549 Iteration 4 Error: 0.016463 Align patch 13 12 left Iteration 1 Error: 0.436378 Iteration 2 Error: 0.077885 Iteration 3 Error: 0.013623 Align patch 14 11 left Iteration 1 Error: 0.465654 Iteration 2 Error: 0.081808 Iteration 3 Error: 0.016300 Align patch 15 10 left Iteration 1 Error: 0.665813 Iteration 2 Error: 0.103453 Iteration 3 Error: 0.011719 Align patch 16 9 left Iteration 1 Error: 0.985450 Iteration 2 Error: 0.222815 Iteration 3 Error: 0.076673 Iteration 4 Error: 0.023881 Align patch 17 8 left Iteration 1 Error: 0.703393 Iteration 2 Error: 0.098556 Iteration 3 Error: 0.027424 Align patch 18 7 left Iteration 1 Error: 0.454957 Iteration 2 Error: 0.073739 Iteration 3 Error: 0.013087 Align patch 19 6 left Iteration 1 Error: 0.778885 Iteration 2 Error: 0.110315 Iteration 3 Error: 0.021643 Align patch 20 5 left Iteration 1 Error: 0.724007 Iteration 2 Error: 0.093523 Iteration 3 Error: 0.010708 Align patch 21 4 left Iteration 1 Error: 0.827253 Iteration 2 Error: 0.185446 Iteration 3 Error: 0.070828 Iteration 4 Error: 0.020485 Align patch 22 3 left Iteration 1 Error: 0.577365 Iteration 2 Error: 0.106193 Iteration 3 Error: 0.026338 Align patch 23 2 left Iteration 1 Error: 0.506884 Iteration 2 Error: 0.075983 Iteration 3 Error: 0.017727 Align patch 24 1 left Iteration 1 Error: 0.655895 Iteration 2 Error: 0.108789 Iteration 3 Error: 0.012258 Align patch 25 0 left Iteration 1 Error: 0.691232 Iteration 2 Error: 0.095321 Iteration 3 Error: 0.011220 3D Fitting completed. Patch alignment time: 20.31(sec) Local motion has been corrected. Process thread exits. Computational time: 35.709881 sec Total time: 43.426178 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00006hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00006hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.633263s Reading file: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00006hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.295218s ........................................ >>>>>>TIME<<<<<< FFT: 1.389486s Defocus_U Defocus_V Angle CCC 25910.16 26828.13 5.06 0.059509 Final Values Defocus_U Defocus_V Angle CCC 25894.49 26828.18 5.06 0.085185 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00001sq_v01_00006hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00006hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.003e-01 CC threshold: 0.736 Mean Std: 41.21 7.02 Num Hot pixels: 199 Hot pixel threshold: 83.35 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.902838 Iteration 2 Error: 0.137113 Iteration 3 Error: 0.025039 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.16 -0.22 ...... Frame ( 3) shift: -0.32 -0.45 ...... Frame ( 4) shift: -0.48 -0.67 ...... Frame ( 5) shift: -0.64 -0.89 ...... Frame ( 6) shift: -0.74 -1.01 ...... Frame ( 7) shift: -0.78 -1.02 ...... Frame ( 8) shift: -0.82 -1.02 ...... Frame ( 9) shift: -0.85 -0.98 ...... Frame ( 10) shift: -0.84 -0.89 ...... Frame ( 11) shift: -0.84 -0.80 ...... Frame ( 12) shift: -0.86 -0.71 ...... Frame ( 13) shift: -0.89 -0.62 ...... Frame ( 14) shift: -0.92 -0.52 ...... Frame ( 15) shift: -0.90 -0.42 ...... Frame ( 16) shift: -0.82 -0.31 ...... Frame ( 17) shift: -0.75 -0.21 ...... Frame ( 18) shift: -0.71 -0.13 ...... Frame ( 19) shift: -0.70 -0.09 ...... Frame ( 20) shift: -0.70 -0.06 ...... Frame ( 21) shift: -0.68 0.00 ...... Frame ( 22) shift: -0.65 0.08 ...... Frame ( 23) shift: -0.61 0.16 ...... Frame ( 24) shift: -0.55 0.25 ...... Frame ( 25) shift: -0.45 0.34 ...... Frame ( 26) shift: -0.36 0.43 ...... Frame ( 27) shift: -0.28 0.50 ...... Frame ( 28) shift: -0.23 0.55 ...... Frame ( 29) shift: -0.17 0.60 ...... Frame ( 30) shift: -0.18 0.63 ...... Frame ( 31) shift: -0.25 0.64 ...... Frame ( 32) shift: -0.32 0.66 ...... Frame ( 33) shift: -0.35 0.69 ...... Frame ( 34) shift: -0.33 0.74 ...... Frame ( 35) shift: -0.32 0.79 ...... Frame ( 36) shift: -0.31 0.81 ...... Frame ( 37) shift: -0.32 0.81 ...... Frame ( 38) shift: -0.33 0.82 ...... Frame ( 39) shift: -0.34 0.82 ...... Frame ( 40) shift: -0.35 0.82 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.431488 Iteration 2 Error: 0.222882 Iteration 3 Error: 0.071946 Iteration 4 Error: 0.020827 Align patch 2 23 left Iteration 1 Error: 1.053717 Iteration 2 Error: 0.100239 Iteration 3 Error: 0.021493 Align patch 3 22 left Iteration 1 Error: 0.753274 Iteration 2 Error: 0.077243 Iteration 3 Error: 0.014877 Align patch 4 21 left Iteration 1 Error: 0.930413 Iteration 2 Error: 0.115942 Iteration 3 Error: 0.024297 Align patch 5 20 left Iteration 1 Error: 0.725426 Iteration 2 Error: 0.123961 Iteration 3 Error: 0.016955 Align patch 6 19 left Iteration 1 Error: 1.017791 Iteration 2 Error: 0.158767 Iteration 3 Error: 0.029502 Align patch 7 18 left Iteration 1 Error: 0.482568 Iteration 2 Error: 0.105238 Iteration 3 Error: 0.029589 Align patch 8 17 left Iteration 1 Error: 0.655940 Iteration 2 Error: 0.060479 Iteration 3 Error: 0.012478 Align patch 9 16 left Iteration 1 Error: 0.471945 Iteration 2 Error: 0.047768 Align patch 10 15 left Iteration 1 Error: 0.555035 Iteration 2 Error: 0.068999 Iteration 3 Error: 0.014608 Align patch 11 14 left Iteration 1 Error: 0.870450 Iteration 2 Error: 0.111921 Iteration 3 Error: 0.024244 Align patch 12 13 left Iteration 1 Error: 0.749677 Iteration 2 Error: 0.115200 Iteration 3 Error: 0.019401 Align patch 13 12 left Iteration 1 Error: 0.545038 Iteration 2 Error: 0.070801 Iteration 3 Error: 0.015732 Align patch 14 11 left Iteration 1 Error: 0.502077 Iteration 2 Error: 0.058436 Iteration 3 Error: 0.008751 Align patch 15 10 left Iteration 1 Error: 0.386572 Iteration 2 Error: 0.049816 Align patch 16 9 left Iteration 1 Error: 0.609306 Iteration 2 Error: 0.052645 Iteration 3 Error: 0.016273 Align patch 17 8 left Iteration 1 Error: 0.858530 Iteration 2 Error: 0.105452 Iteration 3 Error: 0.014802 Align patch 18 7 left Iteration 1 Error: 0.549042 Iteration 2 Error: 0.106699 Iteration 3 Error: 0.023016 Align patch 19 6 left Iteration 1 Error: 0.495843 Iteration 2 Error: 0.071002 Iteration 3 Error: 0.016087 Align patch 20 5 left Iteration 1 Error: 0.379975 Iteration 2 Error: 0.060710 Iteration 3 Error: 0.011608 Align patch 21 4 left Iteration 1 Error: 0.757544 Iteration 2 Error: 0.149121 Iteration 3 Error: 0.038097 Align patch 22 3 left Iteration 1 Error: 0.701390 Iteration 2 Error: 0.093652 Iteration 3 Error: 0.023628 Align patch 23 2 left Iteration 1 Error: 0.443914 Iteration 2 Error: 0.067469 Iteration 3 Error: 0.010391 Align patch 24 1 left Iteration 1 Error: 0.334284 Iteration 2 Error: 0.055691 Iteration 3 Error: 0.010706 Align patch 25 0 left Iteration 1 Error: 0.404436 Iteration 2 Error: 0.068866 Iteration 3 Error: 0.014378 3D Fitting completed. Patch alignment time: 13.71(sec) Local motion has been corrected. Process thread exits. Computational time: 32.377155 sec Total time: 40.018978 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00006hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00006hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.589784s Reading file: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00006hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 6.106776s ........................................ >>>>>>TIME<<<<<< FFT: 1.687098s Defocus_U Defocus_V Angle CCC 25818.62 25161.88 82.07 0.057541 Final Values Defocus_U Defocus_V Angle CCC 25810.81 25135.31 80.84 0.088645 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00001sq_v01_00007hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00007hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 41.76 7.06 Num Hot pixels: 234 Hot pixel threshold: 84.15 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.226397 Iteration 2 Error: 0.150288 Iteration 3 Error: 0.022971 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.08 0.13 ...... Frame ( 3) shift: -0.16 0.26 ...... Frame ( 4) shift: -0.24 0.39 ...... Frame ( 5) shift: -0.32 0.52 ...... Frame ( 6) shift: -0.34 0.61 ...... Frame ( 7) shift: -0.30 0.66 ...... Frame ( 8) shift: -0.26 0.70 ...... Frame ( 9) shift: -0.21 0.77 ...... Frame ( 10) shift: -0.15 0.87 ...... Frame ( 11) shift: -0.09 0.96 ...... Frame ( 12) shift: 0.01 1.02 ...... Frame ( 13) shift: 0.14 1.05 ...... Frame ( 14) shift: 0.27 1.08 ...... Frame ( 15) shift: 0.34 1.10 ...... Frame ( 16) shift: 0.33 1.10 ...... Frame ( 17) shift: 0.33 1.11 ...... Frame ( 18) shift: 0.35 1.11 ...... Frame ( 19) shift: 0.40 1.10 ...... Frame ( 20) shift: 0.45 1.10 ...... Frame ( 21) shift: 0.50 1.12 ...... Frame ( 22) shift: 0.55 1.16 ...... Frame ( 23) shift: 0.60 1.19 ...... Frame ( 24) shift: 0.64 1.22 ...... Frame ( 25) shift: 0.66 1.25 ...... Frame ( 26) shift: 0.68 1.27 ...... Frame ( 27) shift: 0.71 1.29 ...... Frame ( 28) shift: 0.76 1.31 ...... Frame ( 29) shift: 0.80 1.32 ...... Frame ( 30) shift: 0.86 1.40 ...... Frame ( 31) shift: 0.96 1.52 ...... Frame ( 32) shift: 1.05 1.65 ...... Frame ( 33) shift: 1.11 1.74 ...... Frame ( 34) shift: 1.15 1.80 ...... Frame ( 35) shift: 1.18 1.86 ...... Frame ( 36) shift: 1.23 1.92 ...... Frame ( 37) shift: 1.28 1.98 ...... Frame ( 38) shift: 1.33 2.04 ...... Frame ( 39) shift: 1.39 2.10 ...... Frame ( 40) shift: 1.44 2.16 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.704379 Iteration 2 Error: 0.178567 Iteration 3 Error: 0.020541 Align patch 2 23 left Iteration 1 Error: 0.760379 Iteration 2 Error: 0.104070 Iteration 3 Error: 0.022793 Align patch 3 22 left Iteration 1 Error: 0.490550 Iteration 2 Error: 0.105094 Iteration 3 Error: 0.029519 Align patch 4 21 left Iteration 1 Error: 0.487465 Iteration 2 Error: 0.078800 Iteration 3 Error: 0.013857 Align patch 5 20 left Iteration 1 Error: 0.633292 Iteration 2 Error: 0.082510 Iteration 3 Error: 0.013325 Align patch 6 19 left Iteration 1 Error: 0.733750 Iteration 2 Error: 0.141889 Iteration 3 Error: 0.032522 Align patch 7 18 left Iteration 1 Error: 0.717054 Iteration 2 Error: 0.076294 Iteration 3 Error: 0.020294 Align patch 8 17 left Iteration 1 Error: 0.568947 Iteration 2 Error: 0.048512 Align patch 9 16 left Iteration 1 Error: 0.489634 Iteration 2 Error: 0.049856 Align patch 10 15 left Iteration 1 Error: 0.673247 Iteration 2 Error: 0.092739 Iteration 3 Error: 0.017451 Align patch 11 14 left Iteration 1 Error: 0.827119 Iteration 2 Error: 0.083139 Iteration 3 Error: 0.018126 Align patch 12 13 left Iteration 1 Error: 0.697046 Iteration 2 Error: 0.068683 Iteration 3 Error: 0.021106 Align patch 13 12 left Iteration 1 Error: 0.398909 Iteration 2 Error: 0.029353 Align patch 14 11 left Iteration 1 Error: 0.418079 Iteration 2 Error: 0.056175 Iteration 3 Error: 0.010386 Align patch 15 10 left Iteration 1 Error: 0.392606 Iteration 2 Error: 0.065840 Iteration 3 Error: 0.010626 Align patch 16 9 left Iteration 1 Error: 0.884244 Iteration 2 Error: 0.084055 Iteration 3 Error: 0.022637 Align patch 17 8 left Iteration 1 Error: 0.746872 Iteration 2 Error: 0.118284 Iteration 3 Error: 0.025198 Align patch 18 7 left Iteration 1 Error: 0.522815 Iteration 2 Error: 0.051694 Iteration 3 Error: 0.013080 Align patch 19 6 left Iteration 1 Error: 0.532553 Iteration 2 Error: 0.092069 Iteration 3 Error: 0.015899 Align patch 20 5 left Iteration 1 Error: 0.285853 Iteration 2 Error: 0.028694 Align patch 21 4 left Iteration 1 Error: 0.824604 Iteration 2 Error: 0.149722 Iteration 3 Error: 0.036276 Align patch 22 3 left Iteration 1 Error: 0.975399 Iteration 2 Error: 0.106718 Iteration 3 Error: 0.015133 Align patch 23 2 left Iteration 1 Error: 0.667418 Iteration 2 Error: 0.079989 Iteration 3 Error: 0.016314 Align patch 24 1 left Iteration 1 Error: 0.761785 Iteration 2 Error: 0.064291 Iteration 3 Error: 0.010639 Align patch 25 0 left Iteration 1 Error: 0.468317 Iteration 2 Error: 0.054737 Iteration 3 Error: 0.008072 3D Fitting completed. Patch alignment time: 18.29(sec) Local motion has been corrected. Process thread exits. Computational time: 30.179253 sec Total time: 39.298466 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00007hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00007hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.573129s Reading file: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00007hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.829378s ........................................ >>>>>>TIME<<<<<< FFT: 1.308181s Defocus_U Defocus_V Angle CCC 26789.07 27628.93 10.38 0.062386 Final Values Defocus_U Defocus_V Angle CCC 26793.76 27621.12 9.75 0.097242 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00001sq_v01_00007hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00007hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.002e-01 CC threshold: 0.736 Mean Std: 40.65 6.93 Num Hot pixels: 233 Hot pixel threshold: 82.24 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.881727 Iteration 2 Error: 0.146965 Iteration 3 Error: 0.028289 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.02 -0.01 ...... Frame ( 3) shift: 0.03 -0.01 ...... Frame ( 4) shift: 0.05 -0.02 ...... Frame ( 5) shift: 0.07 -0.02 ...... Frame ( 6) shift: 0.09 0.00 ...... Frame ( 7) shift: 0.12 0.05 ...... Frame ( 8) shift: 0.14 0.11 ...... Frame ( 9) shift: 0.14 0.12 ...... Frame ( 10) shift: 0.11 0.08 ...... Frame ( 11) shift: 0.07 0.05 ...... Frame ( 12) shift: 0.04 0.02 ...... Frame ( 13) shift: -0.01 0.00 ...... Frame ( 14) shift: -0.05 -0.02 ...... Frame ( 15) shift: -0.05 -0.01 ...... Frame ( 16) shift: -0.01 0.01 ...... Frame ( 17) shift: 0.04 0.04 ...... Frame ( 18) shift: 0.09 0.11 ...... Frame ( 19) shift: 0.14 0.23 ...... Frame ( 20) shift: 0.19 0.35 ...... Frame ( 21) shift: 0.22 0.42 ...... Frame ( 22) shift: 0.23 0.45 ...... Frame ( 23) shift: 0.24 0.48 ...... Frame ( 24) shift: 0.27 0.52 ...... Frame ( 25) shift: 0.31 0.57 ...... Frame ( 26) shift: 0.36 0.62 ...... Frame ( 27) shift: 0.41 0.68 ...... Frame ( 28) shift: 0.45 0.73 ...... Frame ( 29) shift: 0.49 0.78 ...... Frame ( 30) shift: 0.49 0.83 ...... Frame ( 31) shift: 0.46 0.87 ...... Frame ( 32) shift: 0.43 0.90 ...... Frame ( 33) shift: 0.46 0.93 ...... Frame ( 34) shift: 0.56 0.93 ...... Frame ( 35) shift: 0.65 0.94 ...... Frame ( 36) shift: 0.70 0.99 ...... Frame ( 37) shift: 0.70 1.08 ...... Frame ( 38) shift: 0.70 1.18 ...... Frame ( 39) shift: 0.69 1.28 ...... Frame ( 40) shift: 0.69 1.37 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.650643 Iteration 2 Error: 0.170929 Iteration 3 Error: 0.039155 Align patch 2 23 left Iteration 1 Error: 0.623680 Iteration 2 Error: 0.110425 Iteration 3 Error: 0.025350 Align patch 3 22 left Iteration 1 Error: 0.678815 Iteration 2 Error: 0.132242 Iteration 3 Error: 0.027624 Align patch 4 21 left Iteration 1 Error: 0.687388 Iteration 2 Error: 0.072203 Iteration 3 Error: 0.019703 Align patch 5 20 left Iteration 1 Error: 1.017510 Iteration 2 Error: 0.118332 Iteration 3 Error: 0.028709 Align patch 6 19 left Iteration 1 Error: 0.801987 Iteration 2 Error: 0.179062 Iteration 3 Error: 0.043069 Align patch 7 18 left Iteration 1 Error: 0.774626 Iteration 2 Error: 0.098008 Iteration 3 Error: 0.032987 Align patch 8 17 left Iteration 1 Error: 0.506230 Iteration 2 Error: 0.075463 Iteration 3 Error: 0.017583 Align patch 9 16 left Iteration 1 Error: 0.575626 Iteration 2 Error: 0.096031 Iteration 3 Error: 0.020094 Align patch 10 15 left Iteration 1 Error: 0.570108 Iteration 2 Error: 0.071956 Iteration 3 Error: 0.006658 Align patch 11 14 left Iteration 1 Error: 1.352883 Iteration 2 Error: 0.305774 Iteration 3 Error: 0.067530 Iteration 4 Error: 0.021857 Align patch 12 13 left Iteration 1 Error: 0.646939 Iteration 2 Error: 0.104482 Iteration 3 Error: 0.054856 Iteration 4 Error: 0.016641 Align patch 13 12 left Iteration 1 Error: 0.378478 Iteration 2 Error: 0.069124 Iteration 3 Error: 0.014359 Align patch 14 11 left Iteration 1 Error: 0.842046 Iteration 2 Error: 0.093746 Iteration 3 Error: 0.025473 Align patch 15 10 left Iteration 1 Error: 0.545113 Iteration 2 Error: 0.105394 Iteration 3 Error: 0.017887 Align patch 16 9 left Iteration 1 Error: 0.609658 Iteration 2 Error: 0.085435 Iteration 3 Error: 0.020241 Align patch 17 8 left Iteration 1 Error: 0.511544 Iteration 2 Error: 0.137827 Iteration 3 Error: 0.036639 Align patch 18 7 left Iteration 1 Error: 0.989265 Iteration 2 Error: 0.113440 Iteration 3 Error: 0.017583 Align patch 19 6 left Iteration 1 Error: 1.008237 Iteration 2 Error: 0.091924 Iteration 3 Error: 0.011598 Align patch 20 5 left Iteration 1 Error: 0.517574 Iteration 2 Error: 0.051397 Iteration 3 Error: 0.007293 Align patch 21 4 left Iteration 1 Error: 0.670310 Iteration 2 Error: 0.109362 Iteration 3 Error: 0.048185 Align patch 22 3 left Iteration 1 Error: 0.620302 Iteration 2 Error: 0.081099 Iteration 3 Error: 0.016032 Align patch 23 2 left Iteration 1 Error: 0.687414 Iteration 2 Error: 0.095341 Iteration 3 Error: 0.022964 Align patch 24 1 left Iteration 1 Error: 0.650898 Iteration 2 Error: 0.136745 Iteration 3 Error: 0.028693 Align patch 25 0 left Iteration 1 Error: 0.737381 Iteration 2 Error: 0.188121 Iteration 3 Error: 0.041546 3D Fitting completed. Patch alignment time: 18.57(sec) Local motion has been corrected. Process thread exits. Computational time: 30.711662 sec Total time: 38.379238 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00007hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00007hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.593849s Reading file: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00007hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.074873s ........................................ >>>>>>TIME<<<<<< FFT: 1.637237s Defocus_U Defocus_V Angle CCC 23628.96 23023.39 86.70 0.045787 Final Values Defocus_U Defocus_V Angle CCC 23658.63 23024.97 87.96 0.071664 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00001sq_v01_00007hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00007hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.003e-01 CC threshold: 0.736 Mean Std: 41.94 7.20 Num Hot pixels: 222 Hot pixel threshold: 85.15 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.626503 Iteration 2 Error: 0.042674 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.02 0.07 ...... Frame ( 3) shift: 0.03 0.13 ...... Frame ( 4) shift: 0.05 0.20 ...... Frame ( 5) shift: 0.07 0.27 ...... Frame ( 6) shift: 0.12 0.31 ...... Frame ( 7) shift: 0.21 0.34 ...... Frame ( 8) shift: 0.30 0.36 ...... Frame ( 9) shift: 0.36 0.39 ...... Frame ( 10) shift: 0.37 0.42 ...... Frame ( 11) shift: 0.38 0.46 ...... Frame ( 12) shift: 0.42 0.48 ...... Frame ( 13) shift: 0.50 0.50 ...... Frame ( 14) shift: 0.57 0.52 ...... Frame ( 15) shift: 0.65 0.53 ...... Frame ( 16) shift: 0.72 0.52 ...... Frame ( 17) shift: 0.80 0.51 ...... Frame ( 18) shift: 0.82 0.49 ...... Frame ( 19) shift: 0.80 0.48 ...... Frame ( 20) shift: 0.78 0.46 ...... Frame ( 21) shift: 0.80 0.48 ...... Frame ( 22) shift: 0.86 0.52 ...... Frame ( 23) shift: 0.92 0.56 ...... Frame ( 24) shift: 0.92 0.56 ...... Frame ( 25) shift: 0.88 0.53 ...... Frame ( 26) shift: 0.83 0.49 ...... Frame ( 27) shift: 0.78 0.45 ...... Frame ( 28) shift: 0.74 0.40 ...... Frame ( 29) shift: 0.70 0.36 ...... Frame ( 30) shift: 0.68 0.32 ...... Frame ( 31) shift: 0.68 0.28 ...... Frame ( 32) shift: 0.67 0.24 ...... Frame ( 33) shift: 0.70 0.23 ...... Frame ( 34) shift: 0.75 0.24 ...... Frame ( 35) shift: 0.80 0.26 ...... Frame ( 36) shift: 0.84 0.29 ...... Frame ( 37) shift: 0.87 0.33 ...... Frame ( 38) shift: 0.89 0.38 ...... Frame ( 39) shift: 0.92 0.43 ...... Frame ( 40) shift: 0.95 0.47 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.332037 Iteration 2 Error: 0.126494 Iteration 3 Error: 0.025445 Align patch 2 23 left Iteration 1 Error: 0.894432 Iteration 2 Error: 0.124256 Iteration 3 Error: 0.029188 Align patch 3 22 left Iteration 1 Error: 0.738600 Iteration 2 Error: 0.065158 Iteration 3 Error: 0.016120 Align patch 4 21 left Iteration 1 Error: 0.567769 Iteration 2 Error: 0.079553 Iteration 3 Error: 0.012481 Align patch 5 20 left Iteration 1 Error: 0.550311 Iteration 2 Error: 0.076487 Iteration 3 Error: 0.010745 Align patch 6 19 left Iteration 1 Error: 0.893736 Iteration 2 Error: 0.087591 Iteration 3 Error: 0.017230 Align patch 7 18 left Iteration 1 Error: 0.774858 Iteration 2 Error: 0.135738 Iteration 3 Error: 0.024740 Align patch 8 17 left Iteration 1 Error: 0.526062 Iteration 2 Error: 0.070687 Iteration 3 Error: 0.014915 Align patch 9 16 left Iteration 1 Error: 0.431816 Iteration 2 Error: 0.037220 Align patch 10 15 left Iteration 1 Error: 0.600886 Iteration 2 Error: 0.057259 Iteration 3 Error: 0.008077 Align patch 11 14 left Iteration 1 Error: 0.887683 Iteration 2 Error: 0.111099 Iteration 3 Error: 0.026139 Align patch 12 13 left Iteration 1 Error: 0.604330 Iteration 2 Error: 0.065722 Iteration 3 Error: 0.015816 Align patch 13 12 left Iteration 1 Error: 0.482463 Iteration 2 Error: 0.099943 Iteration 3 Error: 0.015873 Align patch 14 11 left Iteration 1 Error: 0.380027 Iteration 2 Error: 0.052186 Iteration 3 Error: 0.008325 Align patch 15 10 left Iteration 1 Error: 2.288391 Iteration 2 Error: 0.500588 Iteration 3 Error: 0.327534 Iteration 4 Error: 0.177797 Iteration 5 Error: 0.115414 Align patch 15 10 left Iteration 1 Error: 1.416666 Iteration 2 Error: 0.169415 Iteration 3 Error: 0.036745 Align patch 16 9 left Iteration 1 Error: 0.633824 Iteration 2 Error: 0.082611 Iteration 3 Error: 0.018628 Align patch 17 8 left Iteration 1 Error: 0.797007 Iteration 2 Error: 0.078851 Iteration 3 Error: 0.017870 Align patch 18 7 left Iteration 1 Error: 0.533306 Iteration 2 Error: 0.083780 Iteration 3 Error: 0.022292 Align patch 19 6 left Iteration 1 Error: 0.843874 Iteration 2 Error: 0.108949 Iteration 3 Error: 0.016762 Align patch 20 5 left Iteration 1 Error: 1.164001 Iteration 2 Error: 0.222307 Iteration 3 Error: 0.057655 Iteration 4 Error: 0.021719 Align patch 21 4 left Iteration 1 Error: 1.040546 Iteration 2 Error: 0.109104 Iteration 3 Error: 0.029106 Align patch 22 3 left Iteration 1 Error: 0.670508 Iteration 2 Error: 0.060901 Iteration 3 Error: 0.010726 Align patch 23 2 left Iteration 1 Error: 0.563084 Iteration 2 Error: 0.075403 Iteration 3 Error: 0.019310 Align patch 24 1 left Iteration 1 Error: 0.546408 Iteration 2 Error: 0.085619 Iteration 3 Error: 0.023599 Align patch 25 0 left Iteration 1 Error: 1.314296 Iteration 2 Error: 0.253711 Iteration 3 Error: 0.067752 Iteration 4 Error: 0.023191 3D Fitting completed. Patch alignment time: 18.57(sec) Local motion has been corrected. Process thread exits. Computational time: 34.450989 sec Total time: 43.316029 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00007hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00007hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.623443s Reading file: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00007hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.225708s ........................................ >>>>>>TIME<<<<<< FFT: 1.337398s Defocus_U Defocus_V Angle CCC 26191.43 27066.43 2.42 0.054891 Final Values Defocus_U Defocus_V Angle CCC 26199.23 27043.02 3.36 0.085932 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00001sq_v01_00007hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00007hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.002e-01 CC threshold: 0.736 Mean Std: 40.76 6.92 Num Hot pixels: 205 Hot pixel threshold: 82.27 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.627413 Iteration 2 Error: 0.144442 Iteration 3 Error: 0.022917 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.05 0.25 ...... Frame ( 3) shift: 0.10 0.50 ...... Frame ( 4) shift: 0.16 0.75 ...... Frame ( 5) shift: 0.21 1.01 ...... Frame ( 6) shift: 0.29 1.15 ...... Frame ( 7) shift: 0.40 1.18 ...... Frame ( 8) shift: 0.51 1.22 ...... Frame ( 9) shift: 0.62 1.24 ...... Frame ( 10) shift: 0.71 1.23 ...... Frame ( 11) shift: 0.80 1.22 ...... Frame ( 12) shift: 0.90 1.21 ...... Frame ( 13) shift: 1.03 1.20 ...... Frame ( 14) shift: 1.16 1.19 ...... Frame ( 15) shift: 1.25 1.18 ...... Frame ( 16) shift: 1.32 1.18 ...... Frame ( 17) shift: 1.39 1.18 ...... Frame ( 18) shift: 1.43 1.19 ...... Frame ( 19) shift: 1.43 1.22 ...... Frame ( 20) shift: 1.43 1.24 ...... Frame ( 21) shift: 1.46 1.31 ...... Frame ( 22) shift: 1.51 1.41 ...... Frame ( 23) shift: 1.56 1.50 ...... Frame ( 24) shift: 1.64 1.56 ...... Frame ( 25) shift: 1.75 1.57 ...... Frame ( 26) shift: 1.86 1.57 ...... Frame ( 27) shift: 1.93 1.59 ...... Frame ( 28) shift: 1.94 1.62 ...... Frame ( 29) shift: 1.96 1.65 ...... Frame ( 30) shift: 2.00 1.70 ...... Frame ( 31) shift: 2.06 1.79 ...... Frame ( 32) shift: 2.13 1.87 ...... Frame ( 33) shift: 2.18 1.92 ...... Frame ( 34) shift: 2.20 1.91 ...... Frame ( 35) shift: 2.23 1.91 ...... Frame ( 36) shift: 2.27 1.91 ...... Frame ( 37) shift: 2.31 1.90 ...... Frame ( 38) shift: 2.35 1.90 ...... Frame ( 39) shift: 2.39 1.89 ...... Frame ( 40) shift: 2.43 1.89 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.120740 Iteration 2 Error: 0.118252 Iteration 3 Error: 0.029829 Align patch 2 23 left Iteration 1 Error: 0.767174 Iteration 2 Error: 0.113675 Iteration 3 Error: 0.033965 Align patch 3 22 left Iteration 1 Error: 0.788568 Iteration 2 Error: 0.060001 Iteration 3 Error: 0.010583 Align patch 4 21 left Iteration 1 Error: 0.464215 Iteration 2 Error: 0.080228 Iteration 3 Error: 0.016544 Align patch 5 20 left Iteration 1 Error: 0.437760 Iteration 2 Error: 0.070352 Iteration 3 Error: 0.011034 Align patch 6 19 left Iteration 1 Error: 1.064413 Iteration 2 Error: 0.219856 Iteration 3 Error: 0.060967 Iteration 4 Error: 0.018126 Align patch 7 18 left Iteration 1 Error: 0.591715 Iteration 2 Error: 0.105231 Iteration 3 Error: 0.035733 Align patch 8 17 left Iteration 1 Error: 0.607333 Iteration 2 Error: 0.072573 Iteration 3 Error: 0.012758 Align patch 9 16 left Iteration 1 Error: 0.507869 Iteration 2 Error: 0.048448 Align patch 10 15 left Iteration 1 Error: 0.642683 Iteration 2 Error: 0.149702 Iteration 3 Error: 0.045712 Align patch 11 14 left Iteration 1 Error: 0.687142 Iteration 2 Error: 0.100997 Iteration 3 Error: 0.018275 Align patch 12 13 left Iteration 1 Error: 0.413308 Iteration 2 Error: 0.055840 Iteration 3 Error: 0.017567 Align patch 13 12 left Iteration 1 Error: 0.437010 Iteration 2 Error: 0.046871 Align patch 14 11 left Iteration 1 Error: 0.553882 Iteration 2 Error: 0.069697 Iteration 3 Error: 0.015405 Align patch 15 10 left Iteration 1 Error: 0.465458 Iteration 2 Error: 0.102782 Iteration 3 Error: 0.027730 Align patch 16 9 left Iteration 1 Error: 0.472326 Iteration 2 Error: 0.064485 Iteration 3 Error: 0.015801 Align patch 17 8 left Iteration 1 Error: 0.607070 Iteration 2 Error: 0.054571 Iteration 3 Error: 0.011099 Align patch 18 7 left Iteration 1 Error: 0.498293 Iteration 2 Error: 0.147806 Iteration 3 Error: 0.044707 Align patch 19 6 left Iteration 1 Error: 0.656141 Iteration 2 Error: 0.070769 Iteration 3 Error: 0.015772 Align patch 20 5 left Iteration 1 Error: 0.753156 Iteration 2 Error: 0.057040 Iteration 3 Error: 0.009219 Align patch 21 4 left Iteration 1 Error: 1.074125 Iteration 2 Error: 0.100840 Iteration 3 Error: 0.020727 Align patch 22 3 left Iteration 1 Error: 0.859196 Iteration 2 Error: 0.106935 Iteration 3 Error: 0.017265 Align patch 23 2 left Iteration 1 Error: 0.870247 Iteration 2 Error: 0.085619 Iteration 3 Error: 0.021713 Align patch 24 1 left Iteration 1 Error: 0.653721 Iteration 2 Error: 0.079436 Iteration 3 Error: 0.014810 Align patch 25 0 left Iteration 1 Error: 0.566023 Iteration 2 Error: 0.061400 Iteration 3 Error: 0.017164 3D Fitting completed. Patch alignment time: 17.52(sec) Local motion has been corrected. Process thread exits. Computational time: 31.196077 sec Total time: 39.055523 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00007hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00007hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.569460s Reading file: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00007hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.074405s ........................................ >>>>>>TIME<<<<<< FFT: 1.261365s Defocus_U Defocus_V Angle CCC 26183.59 25523.44 81.77 0.058527 Final Values Defocus_U Defocus_V Angle CCC 26182.06 25534.41 81.77 0.090423 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00001sq_v01_00008hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00008hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.990e-02 CC threshold: 0.734 Mean Std: 37.06 6.57 Num Hot pixels: 208 Hot pixel threshold: 76.45 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.671372 Iteration 2 Error: 0.325956 Iteration 3 Error: 0.074841 Iteration 4 Error: 0.023635 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.17 0.19 ...... Frame ( 3) shift: -0.34 0.38 ...... Frame ( 4) shift: -0.52 0.57 ...... Frame ( 5) shift: -0.69 0.76 ...... Frame ( 6) shift: -0.75 0.86 ...... Frame ( 7) shift: -0.69 0.88 ...... Frame ( 8) shift: -0.63 0.90 ...... Frame ( 9) shift: -0.55 0.97 ...... Frame ( 10) shift: -0.43 1.07 ...... Frame ( 11) shift: -0.32 1.18 ...... Frame ( 12) shift: -0.22 1.29 ...... Frame ( 13) shift: -0.14 1.40 ...... Frame ( 14) shift: -0.06 1.51 ...... Frame ( 15) shift: -0.04 1.56 ...... Frame ( 16) shift: -0.09 1.56 ...... Frame ( 17) shift: -0.14 1.55 ...... Frame ( 18) shift: -0.15 1.55 ...... Frame ( 19) shift: -0.12 1.55 ...... Frame ( 20) shift: -0.08 1.54 ...... Frame ( 21) shift: -0.04 1.55 ...... Frame ( 22) shift: -0.00 1.57 ...... Frame ( 23) shift: 0.04 1.59 ...... Frame ( 24) shift: 0.11 1.62 ...... Frame ( 25) shift: 0.22 1.66 ...... Frame ( 26) shift: 0.34 1.70 ...... Frame ( 27) shift: 0.43 1.77 ...... Frame ( 28) shift: 0.51 1.86 ...... Frame ( 29) shift: 0.59 1.96 ...... Frame ( 30) shift: 0.67 2.01 ...... Frame ( 31) shift: 0.77 2.00 ...... Frame ( 32) shift: 0.86 2.00 ...... Frame ( 33) shift: 0.97 2.05 ...... Frame ( 34) shift: 1.09 2.16 ...... Frame ( 35) shift: 1.21 2.27 ...... Frame ( 36) shift: 1.32 2.38 ...... Frame ( 37) shift: 1.40 2.48 ...... Frame ( 38) shift: 1.49 2.58 ...... Frame ( 39) shift: 1.58 2.69 ...... Frame ( 40) shift: 1.66 2.79 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.032354 Iteration 2 Error: 0.258503 Iteration 3 Error: 0.143304 Iteration 4 Error: 0.078257 Iteration 5 Error: 0.047926 Align patch 2 23 left Iteration 1 Error: 1.073795 Iteration 2 Error: 0.255992 Iteration 3 Error: 0.087417 Iteration 4 Error: 0.032011 Align patch 3 22 left Iteration 1 Error: 1.215534 Iteration 2 Error: 0.403747 Iteration 3 Error: 0.092226 Iteration 4 Error: 0.036083 Align patch 4 21 left Iteration 1 Error: 1.898831 Iteration 2 Error: 0.303737 Iteration 3 Error: 0.037101 Align patch 5 20 left Iteration 1 Error: 1.411322 Iteration 2 Error: 0.135889 Iteration 3 Error: 0.024133 Align patch 6 19 left Iteration 1 Error: 1.050341 Iteration 2 Error: 0.260745 Iteration 3 Error: 0.111221 Iteration 4 Error: 0.039672 Align patch 7 18 left Iteration 1 Error: 1.122863 Iteration 2 Error: 0.239601 Iteration 3 Error: 0.078668 Iteration 4 Error: 0.033915 Align patch 8 17 left Iteration 1 Error: 0.875388 Iteration 2 Error: 0.246771 Iteration 3 Error: 0.067644 Iteration 4 Error: 0.036161 Align patch 9 16 left Iteration 1 Error: 0.970715 Iteration 2 Error: 0.203005 Iteration 3 Error: 0.078493 Iteration 4 Error: 0.026114 Align patch 10 15 left Iteration 1 Error: 0.909697 Iteration 2 Error: 0.231980 Iteration 3 Error: 0.070685 Iteration 4 Error: 0.031528 Align patch 11 14 left Iteration 1 Error: 1.013727 Iteration 2 Error: 0.266426 Iteration 3 Error: 0.079442 Iteration 4 Error: 0.033931 Align patch 12 13 left Iteration 1 Error: 0.872360 Iteration 2 Error: 0.313599 Iteration 3 Error: 0.095875 Iteration 4 Error: 0.043170 Align patch 13 12 left Iteration 1 Error: 1.020767 Iteration 2 Error: 0.196436 Iteration 3 Error: 0.044146 Align patch 14 11 left Iteration 1 Error: 1.223272 Iteration 2 Error: 0.315570 Iteration 3 Error: 0.063192 Iteration 4 Error: 0.022912 Align patch 15 10 left Iteration 1 Error: 1.275813 Iteration 2 Error: 0.158635 Iteration 3 Error: 0.027012 Align patch 16 9 left Iteration 1 Error: 1.477063 Iteration 2 Error: 0.131062 Iteration 3 Error: 0.054228 Iteration 4 Error: 0.020684 Align patch 17 8 left Iteration 1 Error: 1.004806 Iteration 2 Error: 0.348275 Iteration 3 Error: 0.089349 Iteration 4 Error: 0.042229 Align patch 18 7 left Iteration 1 Error: 1.008865 Iteration 2 Error: 0.299801 Iteration 3 Error: 0.093665 Iteration 4 Error: 0.034510 Align patch 19 6 left Iteration 1 Error: 1.160625 Iteration 2 Error: 0.176660 Iteration 3 Error: 0.062200 Iteration 4 Error: 0.026746 Align patch 20 5 left Iteration 1 Error: 1.021183 Iteration 2 Error: 0.211544 Iteration 3 Error: 0.061332 Iteration 4 Error: 0.020107 Align patch 21 4 left Iteration 1 Error: 1.228151 Iteration 2 Error: 0.220085 Iteration 3 Error: 0.071961 Iteration 4 Error: 0.031656 Align patch 22 3 left Iteration 1 Error: 1.907020 Iteration 2 Error: 0.249272 Iteration 3 Error: 0.093711 Iteration 4 Error: 0.071241 Iteration 5 Error: 0.031459 Align patch 23 2 left Iteration 1 Error: 1.375483 Iteration 2 Error: 0.336898 Iteration 3 Error: 0.112228 Iteration 4 Error: 0.111731 Iteration 5 Error: 0.050662 Align patch 23 2 left Iteration 1 Error: 0.836992 Iteration 2 Error: 0.154592 Iteration 3 Error: 0.038385 Align patch 24 1 left Iteration 1 Error: 1.055118 Iteration 2 Error: 0.360924 Iteration 3 Error: 0.117639 Iteration 4 Error: 0.034556 Align patch 25 0 left Iteration 1 Error: 0.781765 Iteration 2 Error: 0.205114 Iteration 3 Error: 0.054816 Iteration 4 Error: 0.023017 3D Fitting completed. Patch alignment time: 21.22(sec) Local motion has been corrected. Process thread exits. Computational time: 37.169987 sec Total time: 45.382828 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00008hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00008hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.655404s Reading file: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00008hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.975431s ........................................ >>>>>>TIME<<<<<< FFT: 1.490145s Defocus_U Defocus_V Angle CCC 26855.48 28058.62 7.23 0.029052 Final Values Defocus_U Defocus_V Angle CCC 26824.20 28102.41 6.61 0.040838 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00001sq_v01_00008hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00008hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 38.37 6.77 Num Hot pixels: 186 Hot pixel threshold: 79.01 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.183372 Iteration 2 Error: 0.198921 Iteration 3 Error: 0.038134 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.02 0.00 ...... Frame ( 3) shift: -0.04 0.00 ...... Frame ( 4) shift: -0.07 0.00 ...... Frame ( 5) shift: -0.09 0.00 ...... Frame ( 6) shift: -0.10 0.04 ...... Frame ( 7) shift: -0.11 0.10 ...... Frame ( 8) shift: -0.12 0.16 ...... Frame ( 9) shift: -0.12 0.25 ...... Frame ( 10) shift: -0.11 0.36 ...... Frame ( 11) shift: -0.10 0.47 ...... Frame ( 12) shift: -0.08 0.55 ...... Frame ( 13) shift: -0.04 0.61 ...... Frame ( 14) shift: 0.00 0.66 ...... Frame ( 15) shift: 0.01 0.74 ...... Frame ( 16) shift: -0.00 0.84 ...... Frame ( 17) shift: -0.01 0.95 ...... Frame ( 18) shift: -0.06 1.02 ...... Frame ( 19) shift: -0.14 1.05 ...... Frame ( 20) shift: -0.21 1.09 ...... Frame ( 21) shift: -0.20 1.10 ...... Frame ( 22) shift: -0.09 1.10 ...... Frame ( 23) shift: 0.01 1.10 ...... Frame ( 24) shift: 0.06 1.12 ...... Frame ( 25) shift: 0.04 1.14 ...... Frame ( 26) shift: 0.03 1.17 ...... Frame ( 27) shift: 0.09 1.24 ...... Frame ( 28) shift: 0.22 1.36 ...... Frame ( 29) shift: 0.35 1.49 ...... Frame ( 30) shift: 0.43 1.55 ...... Frame ( 31) shift: 0.48 1.55 ...... Frame ( 32) shift: 0.52 1.54 ...... Frame ( 33) shift: 0.56 1.57 ...... Frame ( 34) shift: 0.61 1.63 ...... Frame ( 35) shift: 0.66 1.69 ...... Frame ( 36) shift: 0.69 1.77 ...... Frame ( 37) shift: 0.72 1.88 ...... Frame ( 38) shift: 0.74 2.00 ...... Frame ( 39) shift: 0.77 2.11 ...... Frame ( 40) shift: 0.80 2.22 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.769160 Iteration 2 Error: 0.194521 Iteration 3 Error: 0.043511 Align patch 2 23 left Iteration 1 Error: 0.642856 Iteration 2 Error: 0.074189 Iteration 3 Error: 0.017917 Align patch 3 22 left Iteration 1 Error: 0.731826 Iteration 2 Error: 0.107848 Iteration 3 Error: 0.016879 Align patch 4 21 left Iteration 1 Error: 0.763911 Iteration 2 Error: 0.151849 Iteration 3 Error: 0.031644 Align patch 5 20 left Iteration 1 Error: 0.453426 Iteration 2 Error: 0.058310 Iteration 3 Error: 0.012046 Align patch 6 19 left Iteration 1 Error: 0.569832 Iteration 2 Error: 0.158408 Iteration 3 Error: 0.036081 Align patch 7 18 left Iteration 1 Error: 0.628482 Iteration 2 Error: 0.127808 Iteration 3 Error: 0.052787 Iteration 4 Error: 0.024352 Align patch 8 17 left Iteration 1 Error: 0.690456 Iteration 2 Error: 0.115187 Iteration 3 Error: 0.027945 Align patch 9 16 left Iteration 1 Error: 0.619734 Iteration 2 Error: 0.094274 Iteration 3 Error: 0.023634 Align patch 10 15 left Iteration 1 Error: 0.488510 Iteration 2 Error: 0.058183 Iteration 3 Error: 0.013575 Align patch 11 14 left Iteration 1 Error: 1.147170 Iteration 2 Error: 0.103834 Iteration 3 Error: 0.021783 Align patch 12 13 left Iteration 1 Error: 0.906464 Iteration 2 Error: 0.123844 Iteration 3 Error: 0.034577 Align patch 13 12 left Iteration 1 Error: 0.966201 Iteration 2 Error: 0.227978 Iteration 3 Error: 0.066716 Iteration 4 Error: 0.019656 Align patch 14 11 left Iteration 1 Error: 0.719857 Iteration 2 Error: 0.097695 Iteration 3 Error: 0.020427 Align patch 15 10 left Iteration 1 Error: 0.596228 Iteration 2 Error: 0.081682 Iteration 3 Error: 0.019100 Align patch 16 9 left Iteration 1 Error: 0.440722 Iteration 2 Error: 0.069380 Iteration 3 Error: 0.012351 Align patch 17 8 left Iteration 1 Error: 0.855797 Iteration 2 Error: 0.122388 Iteration 3 Error: 0.026398 Align patch 18 7 left Iteration 1 Error: 0.991639 Iteration 2 Error: 0.058540 Iteration 3 Error: 0.012083 Align patch 19 6 left Iteration 1 Error: 0.567368 Iteration 2 Error: 0.082512 Iteration 3 Error: 0.015256 Align patch 20 5 left Iteration 1 Error: 0.641262 Iteration 2 Error: 0.078600 Iteration 3 Error: 0.017672 Align patch 21 4 left Iteration 1 Error: 1.179426 Iteration 2 Error: 0.124236 Iteration 3 Error: 0.039205 Align patch 22 3 left Iteration 1 Error: 0.636964 Iteration 2 Error: 0.116459 Iteration 3 Error: 0.024805 Align patch 23 2 left Iteration 1 Error: 0.693077 Iteration 2 Error: 0.124147 Iteration 3 Error: 0.038051 Align patch 24 1 left Iteration 1 Error: 0.852201 Iteration 2 Error: 0.128505 Iteration 3 Error: 0.028993 Align patch 25 0 left Iteration 1 Error: 0.486899 Iteration 2 Error: 0.093482 Iteration 3 Error: 0.027725 3D Fitting completed. Patch alignment time: 17.51(sec) Local motion has been corrected. Process thread exits. Computational time: 29.538443 sec Total time: 38.121456 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00008hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00008hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.325406s Reading file: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00008hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 4.400931s ........................................ >>>>>>TIME<<<<<< FFT: 1.524401s Defocus_U Defocus_V Angle CCC 26953.25 26425.89 83.14 0.048354 Final Values Defocus_U Defocus_V Angle CCC 26961.08 26471.23 82.52 0.071567 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00001sq_v01_00008hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00008hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.351e-01 1.004e-01 CC threshold: 0.738 Mean Std: 38.40 6.77 Num Hot pixels: 208 Hot pixel threshold: 79.02 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.944555 Iteration 2 Error: 0.164647 Iteration 3 Error: 0.029155 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.01 -0.01 ...... Frame ( 3) shift: -0.01 -0.02 ...... Frame ( 4) shift: -0.02 -0.02 ...... Frame ( 5) shift: -0.03 -0.03 ...... Frame ( 6) shift: -0.06 -0.01 ...... Frame ( 7) shift: -0.10 0.02 ...... Frame ( 8) shift: -0.15 0.06 ...... Frame ( 9) shift: -0.11 0.10 ...... Frame ( 10) shift: 0.00 0.13 ...... Frame ( 11) shift: 0.12 0.17 ...... Frame ( 12) shift: 0.18 0.22 ...... Frame ( 13) shift: 0.20 0.29 ...... Frame ( 14) shift: 0.22 0.36 ...... Frame ( 15) shift: 0.27 0.43 ...... Frame ( 16) shift: 0.34 0.49 ...... Frame ( 17) shift: 0.42 0.55 ...... Frame ( 18) shift: 0.48 0.61 ...... Frame ( 19) shift: 0.54 0.67 ...... Frame ( 20) shift: 0.60 0.72 ...... Frame ( 21) shift: 0.63 0.76 ...... Frame ( 22) shift: 0.62 0.77 ...... Frame ( 23) shift: 0.62 0.78 ...... Frame ( 24) shift: 0.66 0.80 ...... Frame ( 25) shift: 0.75 0.82 ...... Frame ( 26) shift: 0.83 0.84 ...... Frame ( 27) shift: 0.88 0.89 ...... Frame ( 28) shift: 0.90 0.97 ...... Frame ( 29) shift: 0.91 1.05 ...... Frame ( 30) shift: 0.96 1.10 ...... Frame ( 31) shift: 1.05 1.14 ...... Frame ( 32) shift: 1.14 1.17 ...... Frame ( 33) shift: 1.15 1.19 ...... Frame ( 34) shift: 1.10 1.21 ...... Frame ( 35) shift: 1.05 1.23 ...... Frame ( 36) shift: 1.04 1.27 ...... Frame ( 37) shift: 1.09 1.33 ...... Frame ( 38) shift: 1.14 1.40 ...... Frame ( 39) shift: 1.19 1.47 ...... Frame ( 40) shift: 1.24 1.54 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.557484 Iteration 2 Error: 0.365531 Iteration 3 Error: 0.082337 Iteration 4 Error: 0.025396 Align patch 2 23 left Iteration 1 Error: 1.046119 Iteration 2 Error: 0.193692 Iteration 3 Error: 0.047325 Align patch 3 22 left Iteration 1 Error: 0.524403 Iteration 2 Error: 0.057794 Iteration 3 Error: 0.009106 Align patch 4 21 left Iteration 1 Error: 0.477325 Iteration 2 Error: 0.081156 Iteration 3 Error: 0.014941 Align patch 5 20 left Iteration 1 Error: 0.678897 Iteration 2 Error: 0.062713 Iteration 3 Error: 0.012177 Align patch 6 19 left Iteration 1 Error: 1.132244 Iteration 2 Error: 0.272142 Iteration 3 Error: 0.062439 Iteration 4 Error: 0.017711 Align patch 7 18 left Iteration 1 Error: 0.957150 Iteration 2 Error: 0.162628 Iteration 3 Error: 0.046988 Align patch 8 17 left Iteration 1 Error: 0.408409 Iteration 2 Error: 0.045843 Align patch 9 16 left Iteration 1 Error: 0.671960 Iteration 2 Error: 0.141267 Iteration 3 Error: 0.024263 Align patch 10 15 left Iteration 1 Error: 0.746088 Iteration 2 Error: 0.074098 Iteration 3 Error: 0.012947 Align patch 11 14 left Iteration 1 Error: 0.755778 Iteration 2 Error: 0.131411 Iteration 3 Error: 0.037876 Align patch 12 13 left Iteration 1 Error: 0.784772 Iteration 2 Error: 0.090814 Iteration 3 Error: 0.022467 Align patch 13 12 left Iteration 1 Error: 0.671881 Iteration 2 Error: 0.050591 Iteration 3 Error: 0.011899 Align patch 14 11 left Iteration 1 Error: 0.426613 Iteration 2 Error: 0.079509 Iteration 3 Error: 0.011818 Align patch 15 10 left Iteration 1 Error: 0.862059 Iteration 2 Error: 0.085726 Iteration 3 Error: 0.015362 Align patch 16 9 left Iteration 1 Error: 0.732410 Iteration 2 Error: 0.151802 Iteration 3 Error: 0.032556 Align patch 17 8 left Iteration 1 Error: 0.617134 Iteration 2 Error: 0.104409 Iteration 3 Error: 0.047620 Align patch 18 7 left Iteration 1 Error: 0.661715 Iteration 2 Error: 0.091457 Iteration 3 Error: 0.018859 Align patch 19 6 left Iteration 1 Error: 0.724582 Iteration 2 Error: 0.132331 Iteration 3 Error: 0.023190 Align patch 20 5 left Iteration 1 Error: 0.591947 Iteration 2 Error: 0.101402 Iteration 3 Error: 0.024107 Align patch 21 4 left Iteration 1 Error: 0.743514 Iteration 2 Error: 0.074179 Iteration 3 Error: 0.018659 Align patch 22 3 left Iteration 1 Error: 0.810629 Iteration 2 Error: 0.068698 Iteration 3 Error: 0.011790 Align patch 23 2 left Iteration 1 Error: 0.511882 Iteration 2 Error: 0.069236 Iteration 3 Error: 0.015510 Align patch 24 1 left Iteration 1 Error: 0.889143 Iteration 2 Error: 0.081160 Iteration 3 Error: 0.013718 Align patch 25 0 left Iteration 1 Error: 1.090390 Iteration 2 Error: 0.136953 Iteration 3 Error: 0.017771 3D Fitting completed. Patch alignment time: 17.76(sec) Local motion has been corrected. Process thread exits. Computational time: 32.081722 sec Total time: 40.581181 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00008hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00008hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.465610s Reading file: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00008hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 4.230096s ........................................ >>>>>>TIME<<<<<< FFT: 1.617465s Defocus_U Defocus_V Angle CCC 23634.77 24537.11 0.49 0.058395 Final Values Defocus_U Defocus_V Angle CCC 23623.85 24526.19 1.43 0.088181 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00001sq_v01_00008hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00008hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 41.78 7.06 Num Hot pixels: 223 Hot pixel threshold: 84.16 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.224694 Iteration 2 Error: 0.107653 Iteration 3 Error: 0.019656 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.00 0.08 ...... Frame ( 3) shift: -0.00 0.17 ...... Frame ( 4) shift: -0.00 0.25 ...... Frame ( 5) shift: -0.00 0.33 ...... Frame ( 6) shift: 0.00 0.43 ...... Frame ( 7) shift: 0.02 0.55 ...... Frame ( 8) shift: 0.03 0.66 ...... Frame ( 9) shift: 0.02 0.74 ...... Frame ( 10) shift: -0.01 0.78 ...... Frame ( 11) shift: -0.05 0.82 ...... Frame ( 12) shift: -0.07 0.90 ...... Frame ( 13) shift: -0.06 1.03 ...... Frame ( 14) shift: -0.06 1.16 ...... Frame ( 15) shift: -0.05 1.25 ...... Frame ( 16) shift: -0.02 1.31 ...... Frame ( 17) shift: 0.01 1.36 ...... Frame ( 18) shift: 0.01 1.42 ...... Frame ( 19) shift: -0.03 1.47 ...... Frame ( 20) shift: -0.06 1.53 ...... Frame ( 21) shift: -0.04 1.64 ...... Frame ( 22) shift: 0.05 1.81 ...... Frame ( 23) shift: 0.13 1.97 ...... Frame ( 24) shift: 0.16 2.08 ...... Frame ( 25) shift: 0.14 2.15 ...... Frame ( 26) shift: 0.12 2.21 ...... Frame ( 27) shift: 0.08 2.22 ...... Frame ( 28) shift: 0.01 2.19 ...... Frame ( 29) shift: -0.06 2.15 ...... Frame ( 30) shift: -0.10 2.12 ...... Frame ( 31) shift: -0.12 2.09 ...... Frame ( 32) shift: -0.13 2.06 ...... Frame ( 33) shift: -0.15 2.01 ...... Frame ( 34) shift: -0.18 1.93 ...... Frame ( 35) shift: -0.20 1.86 ...... Frame ( 36) shift: -0.23 1.81 ...... Frame ( 37) shift: -0.25 1.79 ...... Frame ( 38) shift: -0.27 1.77 ...... Frame ( 39) shift: -0.29 1.75 ...... Frame ( 40) shift: -0.31 1.73 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.010235 Iteration 2 Error: 0.104973 Iteration 3 Error: 0.024822 Align patch 2 23 left Iteration 1 Error: 0.997807 Iteration 2 Error: 0.119231 Iteration 3 Error: 0.021019 Align patch 3 22 left Iteration 1 Error: 0.527053 Iteration 2 Error: 0.102364 Iteration 3 Error: 0.017248 Align patch 4 21 left Iteration 1 Error: 0.363423 Iteration 2 Error: 0.052457 Iteration 3 Error: 0.009251 Align patch 5 20 left Iteration 1 Error: 0.521636 Iteration 2 Error: 0.053115 Iteration 3 Error: 0.009055 Align patch 6 19 left Iteration 1 Error: 1.156581 Iteration 2 Error: 0.077345 Iteration 3 Error: 0.017453 Align patch 7 18 left Iteration 1 Error: 0.556836 Iteration 2 Error: 0.071304 Iteration 3 Error: 0.019723 Align patch 8 17 left Iteration 1 Error: 0.478844 Iteration 2 Error: 0.062341 Iteration 3 Error: 0.015169 Align patch 9 16 left Iteration 1 Error: 0.522422 Iteration 2 Error: 0.062008 Iteration 3 Error: 0.011231 Align patch 10 15 left Iteration 1 Error: 0.597576 Iteration 2 Error: 0.068979 Iteration 3 Error: 0.016793 Align patch 11 14 left Iteration 1 Error: 0.799871 Iteration 2 Error: 0.104490 Iteration 3 Error: 0.019753 Align patch 12 13 left Iteration 1 Error: 0.749827 Iteration 2 Error: 0.073505 Iteration 3 Error: 0.011701 Align patch 13 12 left Iteration 1 Error: 0.651577 Iteration 2 Error: 0.075362 Iteration 3 Error: 0.016761 Align patch 14 11 left Iteration 1 Error: 0.408869 Iteration 2 Error: 0.069050 Iteration 3 Error: 0.012487 Align patch 15 10 left Iteration 1 Error: 0.517326 Iteration 2 Error: 0.067983 Iteration 3 Error: 0.012624 Align patch 16 9 left Iteration 1 Error: 0.487163 Iteration 2 Error: 0.037737 Align patch 17 8 left Iteration 1 Error: 0.731289 Iteration 2 Error: 0.097329 Iteration 3 Error: 0.026239 Align patch 18 7 left Iteration 1 Error: 0.485850 Iteration 2 Error: 0.058011 Iteration 3 Error: 0.013799 Align patch 19 6 left Iteration 1 Error: 0.988840 Iteration 2 Error: 0.111317 Iteration 3 Error: 0.023946 Align patch 20 5 left Iteration 1 Error: 0.816567 Iteration 2 Error: 0.094675 Iteration 3 Error: 0.013063 Align patch 21 4 left Iteration 1 Error: 0.472184 Iteration 2 Error: 0.048270 Align patch 22 3 left Iteration 1 Error: 0.576886 Iteration 2 Error: 0.073995 Iteration 3 Error: 0.018582 Align patch 23 2 left Iteration 1 Error: 1.306678 Iteration 2 Error: 0.099318 Iteration 3 Error: 0.019316 Align patch 24 1 left Iteration 1 Error: 0.600520 Iteration 2 Error: 0.074320 Iteration 3 Error: 0.009158 Align patch 25 0 left Iteration 1 Error: 0.640745 Iteration 2 Error: 0.079370 Iteration 3 Error: 0.009357 3D Fitting completed. Patch alignment time: 13.74(sec) Local motion has been corrected. Process thread exits. Computational time: 25.813883 sec Total time: 32.500332 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00008hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00008hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.752739s Reading file: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00008hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.882862s ........................................ >>>>>>TIME<<<<<< FFT: 1.186440s Defocus_U Defocus_V Angle CCC 27349.70 26646.48 78.53 0.060421 Final Values Defocus_U Defocus_V Angle CCC 27335.63 26654.30 79.47 0.095887 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00001sq_v01_00009hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00009hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 40.86 6.98 Num Hot pixels: 223 Hot pixel threshold: 82.72 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.210729 Iteration 2 Error: 0.141306 Iteration 3 Error: 0.030598 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.05 0.16 ...... Frame ( 3) shift: -0.10 0.32 ...... Frame ( 4) shift: -0.15 0.48 ...... Frame ( 5) shift: -0.20 0.64 ...... Frame ( 6) shift: -0.22 0.76 ...... Frame ( 7) shift: -0.21 0.84 ...... Frame ( 8) shift: -0.21 0.91 ...... Frame ( 9) shift: -0.19 0.99 ...... Frame ( 10) shift: -0.14 1.07 ...... Frame ( 11) shift: -0.10 1.15 ...... Frame ( 12) shift: -0.05 1.27 ...... Frame ( 13) shift: 0.01 1.43 ...... Frame ( 14) shift: 0.07 1.59 ...... Frame ( 15) shift: 0.10 1.66 ...... Frame ( 16) shift: 0.09 1.64 ...... Frame ( 17) shift: 0.08 1.63 ...... Frame ( 18) shift: 0.09 1.61 ...... Frame ( 19) shift: 0.11 1.58 ...... Frame ( 20) shift: 0.14 1.55 ...... Frame ( 21) shift: 0.13 1.53 ...... Frame ( 22) shift: 0.10 1.53 ...... Frame ( 23) shift: 0.06 1.53 ...... Frame ( 24) shift: 0.07 1.57 ...... Frame ( 25) shift: 0.12 1.65 ...... Frame ( 26) shift: 0.16 1.74 ...... Frame ( 27) shift: 0.22 1.79 ...... Frame ( 28) shift: 0.27 1.80 ...... Frame ( 29) shift: 0.33 1.82 ...... Frame ( 30) shift: 0.39 1.84 ...... Frame ( 31) shift: 0.45 1.86 ...... Frame ( 32) shift: 0.50 1.89 ...... Frame ( 33) shift: 0.52 1.94 ...... Frame ( 34) shift: 0.49 2.02 ...... Frame ( 35) shift: 0.47 2.10 ...... Frame ( 36) shift: 0.47 2.14 ...... Frame ( 37) shift: 0.49 2.15 ...... Frame ( 38) shift: 0.51 2.15 ...... Frame ( 39) shift: 0.53 2.16 ...... Frame ( 40) shift: 0.55 2.17 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.152561 Iteration 2 Error: 0.271454 Iteration 3 Error: 0.097770 Iteration 4 Error: 0.035489 Align patch 2 23 left Iteration 1 Error: 0.750980 Iteration 2 Error: 0.110286 Iteration 3 Error: 0.025487 Align patch 3 22 left Iteration 1 Error: 0.981663 Iteration 2 Error: 0.153981 Iteration 3 Error: 0.049837 Align patch 4 21 left Iteration 1 Error: 1.011869 Iteration 2 Error: 0.093212 Iteration 3 Error: 0.024536 Align patch 5 20 left Iteration 1 Error: 0.521697 Iteration 2 Error: 0.054488 Iteration 3 Error: 0.013593 Align patch 6 19 left Iteration 1 Error: 1.036888 Iteration 2 Error: 0.247037 Iteration 3 Error: 0.053093 Iteration 4 Error: 0.039125 Align patch 7 18 left Iteration 1 Error: 0.599209 Iteration 2 Error: 0.114369 Iteration 3 Error: 0.026607 Align patch 8 17 left Iteration 1 Error: 0.683094 Iteration 2 Error: 0.096728 Iteration 3 Error: 0.031498 Align patch 9 16 left Iteration 1 Error: 0.837505 Iteration 2 Error: 0.096194 Iteration 3 Error: 0.019096 Align patch 10 15 left Iteration 1 Error: 0.677917 Iteration 2 Error: 0.070699 Iteration 3 Error: 0.016709 Align patch 11 14 left Iteration 1 Error: 0.845559 Iteration 2 Error: 0.228153 Iteration 3 Error: 0.081953 Iteration 4 Error: 0.039893 Align patch 12 13 left Iteration 1 Error: 0.755010 Iteration 2 Error: 0.195069 Iteration 3 Error: 0.066310 Iteration 4 Error: 0.019667 Align patch 13 12 left Iteration 1 Error: 0.544313 Iteration 2 Error: 0.084167 Iteration 3 Error: 0.026593 Align patch 14 11 left Iteration 1 Error: 0.677609 Iteration 2 Error: 0.114775 Iteration 3 Error: 0.031308 Align patch 15 10 left Iteration 1 Error: 0.784126 Iteration 2 Error: 0.090257 Iteration 3 Error: 0.019923 Align patch 16 9 left Iteration 1 Error: 0.566027 Iteration 2 Error: 0.088630 Iteration 3 Error: 0.025079 Align patch 17 8 left Iteration 1 Error: 0.677864 Iteration 2 Error: 0.138847 Iteration 3 Error: 0.030661 Align patch 18 7 left Iteration 1 Error: 0.776777 Iteration 2 Error: 0.097768 Iteration 3 Error: 0.019957 Align patch 19 6 left Iteration 1 Error: 0.492689 Iteration 2 Error: 0.088663 Iteration 3 Error: 0.029472 Align patch 20 5 left Iteration 1 Error: 0.523921 Iteration 2 Error: 0.134872 Iteration 3 Error: 0.024448 Align patch 21 4 left Iteration 1 Error: 1.607497 Iteration 2 Error: 0.252018 Iteration 3 Error: 0.065351 Iteration 4 Error: 0.023314 Align patch 22 3 left Iteration 1 Error: 1.330362 Iteration 2 Error: 0.295041 Iteration 3 Error: 0.063776 Iteration 4 Error: 0.027106 Align patch 23 2 left Iteration 1 Error: 0.835782 Iteration 2 Error: 0.123199 Iteration 3 Error: 0.022985 Align patch 24 1 left Iteration 1 Error: 0.595061 Iteration 2 Error: 0.087997 Iteration 3 Error: 0.028865 Align patch 25 0 left Iteration 1 Error: 0.474173 Iteration 2 Error: 0.055946 Iteration 3 Error: 0.011580 3D Fitting completed. Patch alignment time: 16.17(sec) Local motion has been corrected. Process thread exits. Computational time: 29.310337 sec Total time: 36.952610 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00009hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00009hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.205261s Reading file: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00009hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 4.549231s ........................................ >>>>>>TIME<<<<<< FFT: 1.780164s Defocus_U Defocus_V Angle CCC 26439.45 27287.11 9.04 0.043993 Final Values Defocus_U Defocus_V Angle CCC 26455.04 27280.90 9.35 0.068112 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00001sq_v01_00009hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00009hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.001e-01 CC threshold: 0.735 Mean Std: 41.40 7.13 Num Hot pixels: 205 Hot pixel threshold: 84.18 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.727340 Iteration 2 Error: 0.091468 Iteration 3 Error: 0.020368 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.03 0.05 ...... Frame ( 3) shift: 0.06 0.09 ...... Frame ( 4) shift: 0.09 0.14 ...... Frame ( 5) shift: 0.12 0.18 ...... Frame ( 6) shift: 0.13 0.24 ...... Frame ( 7) shift: 0.11 0.29 ...... Frame ( 8) shift: 0.09 0.35 ...... Frame ( 9) shift: 0.06 0.38 ...... Frame ( 10) shift: 0.02 0.40 ...... Frame ( 11) shift: -0.02 0.42 ...... Frame ( 12) shift: -0.02 0.44 ...... Frame ( 13) shift: 0.03 0.46 ...... Frame ( 14) shift: 0.07 0.48 ...... Frame ( 15) shift: 0.09 0.54 ...... Frame ( 16) shift: 0.10 0.62 ...... Frame ( 17) shift: 0.11 0.70 ...... Frame ( 18) shift: 0.10 0.74 ...... Frame ( 19) shift: 0.09 0.72 ...... Frame ( 20) shift: 0.08 0.71 ...... Frame ( 21) shift: 0.08 0.76 ...... Frame ( 22) shift: 0.10 0.86 ...... Frame ( 23) shift: 0.12 0.97 ...... Frame ( 24) shift: 0.11 1.01 ...... Frame ( 25) shift: 0.06 0.97 ...... Frame ( 26) shift: 0.02 0.93 ...... Frame ( 27) shift: 0.05 0.92 ...... Frame ( 28) shift: 0.14 0.92 ...... Frame ( 29) shift: 0.23 0.92 ...... Frame ( 30) shift: 0.29 0.93 ...... Frame ( 31) shift: 0.33 0.93 ...... Frame ( 32) shift: 0.37 0.94 ...... Frame ( 33) shift: 0.37 1.01 ...... Frame ( 34) shift: 0.34 1.13 ...... Frame ( 35) shift: 0.31 1.26 ...... Frame ( 36) shift: 0.30 1.35 ...... Frame ( 37) shift: 0.32 1.40 ...... Frame ( 38) shift: 0.33 1.44 ...... Frame ( 39) shift: 0.35 1.49 ...... Frame ( 40) shift: 0.37 1.53 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.016085 Iteration 2 Error: 0.293688 Iteration 3 Error: 0.099658 Iteration 4 Error: 0.036768 Align patch 2 23 left Iteration 1 Error: 0.926088 Iteration 2 Error: 0.129070 Iteration 3 Error: 0.032370 Align patch 3 22 left Iteration 1 Error: 0.973625 Iteration 2 Error: 0.210552 Iteration 3 Error: 0.046856 Align patch 4 21 left Iteration 1 Error: 0.772455 Iteration 2 Error: 0.186753 Iteration 3 Error: 0.036687 Align patch 5 20 left Iteration 1 Error: 1.118342 Iteration 2 Error: 0.103233 Iteration 3 Error: 0.026693 Align patch 6 19 left Iteration 1 Error: 0.735079 Iteration 2 Error: 0.161623 Iteration 3 Error: 0.039290 Align patch 7 18 left Iteration 1 Error: 0.609360 Iteration 2 Error: 0.071560 Iteration 3 Error: 0.018096 Align patch 8 17 left Iteration 1 Error: 1.012550 Iteration 2 Error: 0.218927 Iteration 3 Error: 0.051671 Iteration 4 Error: 0.020674 Align patch 9 16 left Iteration 1 Error: 1.249023 Iteration 2 Error: 0.241850 Iteration 3 Error: 0.061725 Iteration 4 Error: 0.017423 Align patch 10 15 left Iteration 1 Error: 0.940318 Iteration 2 Error: 0.176605 Iteration 3 Error: 0.036494 Align patch 11 14 left Iteration 1 Error: 0.762199 Iteration 2 Error: 0.124319 Iteration 3 Error: 0.036836 Align patch 12 13 left Iteration 1 Error: 1.003511 Iteration 2 Error: 0.183790 Iteration 3 Error: 0.044662 Align patch 13 12 left Iteration 1 Error: 0.991405 Iteration 2 Error: 0.090837 Iteration 3 Error: 0.027617 Align patch 14 11 left Iteration 1 Error: 1.775557 Iteration 2 Error: 0.409606 Iteration 3 Error: 0.174561 Iteration 4 Error: 0.073895 Iteration 5 Error: 0.036324 Align patch 15 10 left Iteration 1 Error: 0.984558 Iteration 2 Error: 0.177527 Iteration 3 Error: 0.054950 Iteration 4 Error: 0.015447 Align patch 16 9 left Iteration 1 Error: 0.955049 Iteration 2 Error: 0.126430 Iteration 3 Error: 0.036850 Align patch 17 8 left Iteration 1 Error: 0.766389 Iteration 2 Error: 0.106779 Iteration 3 Error: 0.024365 Align patch 18 7 left Iteration 1 Error: 0.979607 Iteration 2 Error: 0.151480 Iteration 3 Error: 0.026388 Align patch 19 6 left Iteration 1 Error: 1.173560 Iteration 2 Error: 0.258379 Iteration 3 Error: 0.093538 Iteration 4 Error: 0.040376 Align patch 20 5 left Iteration 1 Error: 5.564670 Iteration 2 Error: 3.317148 Iteration 3 Error: 1.416394 Iteration 4 Error: 0.799343 Iteration 5 Error: 0.553245 Align patch 20 5 left Iteration 1 Error: 3.826314 Iteration 2 Error: 1.202069 Iteration 3 Error: 0.668826 Iteration 4 Error: 0.344299 Iteration 5 Error: 0.210768 Align patch 21 4 left Iteration 1 Error: 0.903336 Iteration 2 Error: 0.194001 Iteration 3 Error: 0.047113 Align patch 22 3 left Iteration 1 Error: 0.686216 Iteration 2 Error: 0.095796 Iteration 3 Error: 0.037287 Align patch 23 2 left Iteration 1 Error: 0.970393 Iteration 2 Error: 0.222185 Iteration 3 Error: 0.054056 Iteration 4 Error: 0.014812 Align patch 24 1 left Iteration 1 Error: 1.863412 Iteration 2 Error: 0.326710 Iteration 3 Error: 0.102225 Iteration 4 Error: 0.018660 Align patch 25 0 left Iteration 1 Error: 1.878089 Iteration 2 Error: 0.427818 Iteration 3 Error: 0.183987 Iteration 4 Error: 0.087774 Iteration 5 Error: 0.041985 3D Fitting completed. Patch alignment time: 16.32(sec) Local motion has been corrected. Process thread exits. Computational time: 30.366121 sec Total time: 39.799061 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00009hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00009hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.202691s Reading file: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00009hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 4.309520s ........................................ >>>>>>TIME<<<<<< FFT: 1.650338s Defocus_U Defocus_V Angle CCC 27375.02 26757.82 83.73 0.037546 Final Values Defocus_U Defocus_V Angle CCC 27373.46 26753.14 83.11 0.057622 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00001sq_v01_00009hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00009hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 42.57 7.09 Num Hot pixels: 222 Hot pixel threshold: 85.10 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.475023 Iteration 2 Error: 0.244408 Iteration 3 Error: 0.043069 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.06 -0.15 ...... Frame ( 3) shift: -0.11 -0.30 ...... Frame ( 4) shift: -0.17 -0.44 ...... Frame ( 5) shift: -0.22 -0.59 ...... Frame ( 6) shift: -0.18 -0.65 ...... Frame ( 7) shift: -0.05 -0.63 ...... Frame ( 8) shift: 0.08 -0.61 ...... Frame ( 9) shift: 0.19 -0.56 ...... Frame ( 10) shift: 0.29 -0.49 ...... Frame ( 11) shift: 0.38 -0.41 ...... Frame ( 12) shift: 0.47 -0.33 ...... Frame ( 13) shift: 0.54 -0.23 ...... Frame ( 14) shift: 0.60 -0.14 ...... Frame ( 15) shift: 0.68 -0.06 ...... Frame ( 16) shift: 0.75 -0.01 ...... Frame ( 17) shift: 0.83 0.05 ...... Frame ( 18) shift: 0.92 0.06 ...... Frame ( 19) shift: 1.02 0.01 ...... Frame ( 20) shift: 1.13 -0.03 ...... Frame ( 21) shift: 1.23 -0.07 ...... Frame ( 22) shift: 1.34 -0.10 ...... Frame ( 23) shift: 1.45 -0.12 ...... Frame ( 24) shift: 1.57 -0.14 ...... Frame ( 25) shift: 1.73 -0.16 ...... Frame ( 26) shift: 1.88 -0.18 ...... Frame ( 27) shift: 2.01 -0.16 ...... Frame ( 28) shift: 2.11 -0.08 ...... Frame ( 29) shift: 2.21 -0.01 ...... Frame ( 30) shift: 2.29 0.06 ...... Frame ( 31) shift: 2.35 0.12 ...... Frame ( 32) shift: 2.41 0.18 ...... Frame ( 33) shift: 2.46 0.20 ...... Frame ( 34) shift: 2.51 0.18 ...... Frame ( 35) shift: 2.57 0.16 ...... Frame ( 36) shift: 2.62 0.14 ...... Frame ( 37) shift: 2.68 0.13 ...... Frame ( 38) shift: 2.74 0.12 ...... Frame ( 39) shift: 2.81 0.11 ...... Frame ( 40) shift: 2.87 0.10 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.561903 Iteration 2 Error: 0.157219 Iteration 3 Error: 0.078851 Iteration 4 Error: 0.030984 Align patch 2 23 left Iteration 1 Error: 1.240505 Iteration 2 Error: 0.261911 Iteration 3 Error: 0.058800 Iteration 4 Error: 0.019942 Align patch 3 22 left Iteration 1 Error: 1.062029 Iteration 2 Error: 0.253492 Iteration 3 Error: 0.100407 Iteration 4 Error: 0.027000 Align patch 4 21 left Iteration 1 Error: 0.724985 Iteration 2 Error: 0.192787 Iteration 3 Error: 0.040582 Align patch 5 20 left Iteration 1 Error: 0.462088 Iteration 2 Error: 0.078053 Iteration 3 Error: 0.012141 Align patch 6 19 left Iteration 1 Error: 1.278166 Iteration 2 Error: 0.150353 Iteration 3 Error: 0.040047 Align patch 7 18 left Iteration 1 Error: 1.247680 Iteration 2 Error: 0.181450 Iteration 3 Error: 0.043285 Align patch 8 17 left Iteration 1 Error: 1.168927 Iteration 2 Error: 0.206999 Iteration 3 Error: 0.083363 Iteration 4 Error: 0.026996 Align patch 9 16 left Iteration 1 Error: 0.723906 Iteration 2 Error: 0.100011 Iteration 3 Error: 0.018261 Align patch 10 15 left Iteration 1 Error: 0.521019 Iteration 2 Error: 0.093776 Iteration 3 Error: 0.016985 Align patch 11 14 left Iteration 1 Error: 1.117013 Iteration 2 Error: 0.122707 Iteration 3 Error: 0.039423 Align patch 12 13 left Iteration 1 Error: 0.982673 Iteration 2 Error: 0.139211 Iteration 3 Error: 0.029200 Align patch 13 12 left Iteration 1 Error: 0.449319 Iteration 2 Error: 0.048721 Align patch 14 11 left Iteration 1 Error: 0.496342 Iteration 2 Error: 0.079393 Iteration 3 Error: 0.014172 Align patch 15 10 left Iteration 1 Error: 0.430502 Iteration 2 Error: 0.033472 Align patch 16 9 left Iteration 1 Error: 0.783025 Iteration 2 Error: 0.134680 Iteration 3 Error: 0.025658 Align patch 17 8 left Iteration 1 Error: 0.700181 Iteration 2 Error: 0.104904 Iteration 3 Error: 0.022996 Align patch 18 7 left Iteration 1 Error: 0.759152 Iteration 2 Error: 0.080687 Iteration 3 Error: 0.024867 Align patch 19 6 left Iteration 1 Error: 0.484316 Iteration 2 Error: 0.051279 Iteration 3 Error: 0.010410 Align patch 20 5 left Iteration 1 Error: 1.020410 Iteration 2 Error: 0.155495 Iteration 3 Error: 0.037463 Align patch 21 4 left Iteration 1 Error: 1.021128 Iteration 2 Error: 0.224794 Iteration 3 Error: 0.058455 Iteration 4 Error: 0.021273 Align patch 22 3 left Iteration 1 Error: 0.778153 Iteration 2 Error: 0.128939 Iteration 3 Error: 0.027683 Align patch 23 2 left Iteration 1 Error: 1.162616 Iteration 2 Error: 0.152648 Iteration 3 Error: 0.027019 Align patch 24 1 left Iteration 1 Error: 0.642952 Iteration 2 Error: 0.097470 Iteration 3 Error: 0.021668 Align patch 25 0 left Iteration 1 Error: 0.631863 Iteration 2 Error: 0.096509 Iteration 3 Error: 0.018728 3D Fitting completed. Patch alignment time: 17.50(sec) Local motion has been corrected. Process thread exits. Computational time: 29.568413 sec Total time: 37.464260 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00009hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00009hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.391757s Reading file: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00009hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.917231s ........................................ >>>>>>TIME<<<<<< FFT: 1.124849s Defocus_U Defocus_V Angle CCC 28544.93 29439.46 2.10 0.049098 Final Values Defocus_U Defocus_V Angle CCC 28549.62 29444.15 1.47 0.081636 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00001sq_v01_00009hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00009hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.002e-01 CC threshold: 0.736 Mean Std: 41.90 7.06 Num Hot pixels: 204 Hot pixel threshold: 84.27 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.357131 Iteration 2 Error: 0.189921 Iteration 3 Error: 0.044806 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.18 -0.07 ...... Frame ( 3) shift: -0.35 -0.14 ...... Frame ( 4) shift: -0.53 -0.21 ...... Frame ( 5) shift: -0.71 -0.27 ...... Frame ( 6) shift: -0.75 -0.28 ...... Frame ( 7) shift: -0.67 -0.22 ...... Frame ( 8) shift: -0.59 -0.16 ...... Frame ( 9) shift: -0.51 -0.06 ...... Frame ( 10) shift: -0.44 0.08 ...... Frame ( 11) shift: -0.36 0.22 ...... Frame ( 12) shift: -0.29 0.34 ...... Frame ( 13) shift: -0.23 0.44 ...... Frame ( 14) shift: -0.16 0.54 ...... Frame ( 15) shift: -0.07 0.64 ...... Frame ( 16) shift: 0.04 0.75 ...... Frame ( 17) shift: 0.15 0.86 ...... Frame ( 18) shift: 0.22 0.94 ...... Frame ( 19) shift: 0.26 0.99 ...... Frame ( 20) shift: 0.30 1.05 ...... Frame ( 21) shift: 0.35 1.08 ...... Frame ( 22) shift: 0.40 1.11 ...... Frame ( 23) shift: 0.46 1.13 ...... Frame ( 24) shift: 0.51 1.16 ...... Frame ( 25) shift: 0.55 1.21 ...... Frame ( 26) shift: 0.59 1.26 ...... Frame ( 27) shift: 0.61 1.31 ...... Frame ( 28) shift: 0.61 1.37 ...... Frame ( 29) shift: 0.61 1.44 ...... Frame ( 30) shift: 0.63 1.49 ...... Frame ( 31) shift: 0.69 1.55 ...... Frame ( 32) shift: 0.74 1.60 ...... Frame ( 33) shift: 0.77 1.63 ...... Frame ( 34) shift: 0.76 1.63 ...... Frame ( 35) shift: 0.76 1.63 ...... Frame ( 36) shift: 0.77 1.64 ...... Frame ( 37) shift: 0.79 1.68 ...... Frame ( 38) shift: 0.82 1.71 ...... Frame ( 39) shift: 0.84 1.75 ...... Frame ( 40) shift: 0.86 1.79 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.361953 Iteration 2 Error: 0.142541 Iteration 3 Error: 0.048179 Align patch 2 23 left Iteration 1 Error: 1.076942 Iteration 2 Error: 0.096468 Iteration 3 Error: 0.020740 Align patch 3 22 left Iteration 1 Error: 0.675114 Iteration 2 Error: 0.066199 Iteration 3 Error: 0.020591 Align patch 4 21 left Iteration 1 Error: 0.439397 Iteration 2 Error: 0.070995 Iteration 3 Error: 0.012104 Align patch 5 20 left Iteration 1 Error: 0.409182 Iteration 2 Error: 0.074454 Iteration 3 Error: 0.012628 Align patch 6 19 left Iteration 1 Error: 1.695428 Iteration 2 Error: 0.228410 Iteration 3 Error: 0.040381 Align patch 7 18 left Iteration 1 Error: 1.436992 Iteration 2 Error: 0.078502 Iteration 3 Error: 0.018303 Align patch 8 17 left Iteration 1 Error: 0.610310 Iteration 2 Error: 0.083865 Iteration 3 Error: 0.022205 Align patch 9 16 left Iteration 1 Error: 0.524989 Iteration 2 Error: 0.078567 Iteration 3 Error: 0.015437 Align patch 10 15 left Iteration 1 Error: 0.583808 Iteration 2 Error: 0.066380 Iteration 3 Error: 0.012145 Align patch 11 14 left Iteration 1 Error: 0.649857 Iteration 2 Error: 0.191180 Iteration 3 Error: 0.067117 Iteration 4 Error: 0.030025 Align patch 12 13 left Iteration 1 Error: 0.597032 Iteration 2 Error: 0.070056 Iteration 3 Error: 0.010970 Align patch 13 12 left Iteration 1 Error: 0.509014 Iteration 2 Error: 0.072035 Iteration 3 Error: 0.020079 Align patch 14 11 left Iteration 1 Error: 0.541199 Iteration 2 Error: 0.048711 Align patch 15 10 left Iteration 1 Error: 0.538293 Iteration 2 Error: 0.076937 Iteration 3 Error: 0.016346 Align patch 16 9 left Iteration 1 Error: 0.701543 Iteration 2 Error: 0.136564 Iteration 3 Error: 0.023492 Align patch 17 8 left Iteration 1 Error: 0.692788 Iteration 2 Error: 0.067912 Iteration 3 Error: 0.018804 Align patch 18 7 left Iteration 1 Error: 0.532377 Iteration 2 Error: 0.098644 Iteration 3 Error: 0.020305 Align patch 19 6 left Iteration 1 Error: 0.738069 Iteration 2 Error: 0.115238 Iteration 3 Error: 0.013404 Align patch 20 5 left Iteration 1 Error: 0.420117 Iteration 2 Error: 0.055411 Iteration 3 Error: 0.006815 Align patch 21 4 left Iteration 1 Error: 0.827951 Iteration 2 Error: 0.116288 Iteration 3 Error: 0.028307 Align patch 22 3 left Iteration 1 Error: 0.477949 Iteration 2 Error: 0.066506 Iteration 3 Error: 0.016318 Align patch 23 2 left Iteration 1 Error: 0.738734 Iteration 2 Error: 0.083662 Iteration 3 Error: 0.016672 Align patch 24 1 left Iteration 1 Error: 0.417179 Iteration 2 Error: 0.044716 Align patch 25 0 left Iteration 1 Error: 0.967033 Iteration 2 Error: 0.103346 Iteration 3 Error: 0.021478 3D Fitting completed. Patch alignment time: 13.63(sec) Local motion has been corrected. Process thread exits. Computational time: 25.768723 sec Total time: 32.548691 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00009hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00009hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.644168s Reading file: gc_18feb27f_CTD_g1_00012gr_00001sq_v01_00009hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 4.341325s ........................................ >>>>>>TIME<<<<<< FFT: 1.142597s Defocus_U Defocus_V Angle CCC 25580.15 24962.91 79.96 0.055692 Final Values Defocus_U Defocus_V Angle CCC 25573.90 24959.79 80.28 0.087978 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00002sq_v01_00002hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00002hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.325e-01 9.875e-02 CC threshold: 0.725 Mean Std: 41.40 7.11 Num Hot pixels: 215 Hot pixel threshold: 84.07 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.920612 Iteration 2 Error: 0.231785 Iteration 3 Error: 0.042390 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.10 0.23 ...... Frame ( 3) shift: 0.21 0.46 ...... Frame ( 4) shift: 0.31 0.70 ...... Frame ( 5) shift: 0.42 0.93 ...... Frame ( 6) shift: 0.44 1.07 ...... Frame ( 7) shift: 0.38 1.14 ...... Frame ( 8) shift: 0.32 1.20 ...... Frame ( 9) shift: 0.31 1.24 ...... Frame ( 10) shift: 0.35 1.26 ...... Frame ( 11) shift: 0.38 1.29 ...... Frame ( 12) shift: 0.43 1.33 ...... Frame ( 13) shift: 0.49 1.39 ...... Frame ( 14) shift: 0.54 1.45 ...... Frame ( 15) shift: 0.56 1.54 ...... Frame ( 16) shift: 0.53 1.67 ...... Frame ( 17) shift: 0.51 1.79 ...... Frame ( 18) shift: 0.50 1.94 ...... Frame ( 19) shift: 0.51 2.11 ...... Frame ( 20) shift: 0.52 2.28 ...... Frame ( 21) shift: 0.54 2.42 ...... Frame ( 22) shift: 0.58 2.54 ...... Frame ( 23) shift: 0.61 2.66 ...... Frame ( 24) shift: 0.64 2.79 ...... Frame ( 25) shift: 0.64 2.91 ...... Frame ( 26) shift: 0.65 3.03 ...... Frame ( 27) shift: 0.66 3.13 ...... Frame ( 28) shift: 0.66 3.21 ...... Frame ( 29) shift: 0.67 3.29 ...... Frame ( 30) shift: 0.69 3.37 ...... Frame ( 31) shift: 0.71 3.47 ...... Frame ( 32) shift: 0.74 3.56 ...... Frame ( 33) shift: 0.72 3.66 ...... Frame ( 34) shift: 0.66 3.77 ...... Frame ( 35) shift: 0.59 3.88 ...... Frame ( 36) shift: 0.55 4.00 ...... Frame ( 37) shift: 0.52 4.12 ...... Frame ( 38) shift: 0.49 4.25 ...... Frame ( 39) shift: 0.46 4.38 ...... Frame ( 40) shift: 0.43 4.51 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.302956 Iteration 2 Error: 0.205368 Iteration 3 Error: 0.047631 Align patch 2 23 left Iteration 1 Error: 1.052318 Iteration 2 Error: 0.175385 Iteration 3 Error: 0.029505 Align patch 3 22 left Iteration 1 Error: 0.629421 Iteration 2 Error: 0.069775 Iteration 3 Error: 0.013173 Align patch 4 21 left Iteration 1 Error: 0.794680 Iteration 2 Error: 0.174632 Iteration 3 Error: 0.033095 Align patch 5 20 left Iteration 1 Error: 0.979481 Iteration 2 Error: 0.160273 Iteration 3 Error: 0.031947 Align patch 6 19 left Iteration 1 Error: 1.667057 Iteration 2 Error: 0.246147 Iteration 3 Error: 0.042503 Align patch 7 18 left Iteration 1 Error: 1.136393 Iteration 2 Error: 0.172780 Iteration 3 Error: 0.029753 Align patch 8 17 left Iteration 1 Error: 0.539292 Iteration 2 Error: 0.073965 Iteration 3 Error: 0.017790 Align patch 9 16 left Iteration 1 Error: 0.681996 Iteration 2 Error: 0.082031 Iteration 3 Error: 0.024499 Align patch 10 15 left Iteration 1 Error: 1.454331 Iteration 2 Error: 0.122444 Iteration 3 Error: 0.029092 Align patch 11 14 left Iteration 1 Error: 0.983021 Iteration 2 Error: 0.158521 Iteration 3 Error: 0.031411 Align patch 12 13 left Iteration 1 Error: 1.401244 Iteration 2 Error: 0.146174 Iteration 3 Error: 0.029892 Align patch 13 12 left Iteration 1 Error: 0.848621 Iteration 2 Error: 0.077773 Iteration 3 Error: 0.008981 Align patch 14 11 left Iteration 1 Error: 0.637313 Iteration 2 Error: 0.095220 Iteration 3 Error: 0.015881 Align patch 15 10 left Iteration 1 Error: 1.072474 Iteration 2 Error: 0.132256 Iteration 3 Error: 0.020986 Align patch 16 9 left Iteration 1 Error: 1.487639 Iteration 2 Error: 0.168851 Iteration 3 Error: 0.033844 Align patch 17 8 left Iteration 1 Error: 1.325520 Iteration 2 Error: 0.155776 Iteration 3 Error: 0.027668 Align patch 18 7 left Iteration 1 Error: 0.609555 Iteration 2 Error: 0.097033 Iteration 3 Error: 0.025821 Align patch 19 6 left Iteration 1 Error: 0.747907 Iteration 2 Error: 0.099324 Iteration 3 Error: 0.017964 Align patch 20 5 left Iteration 1 Error: 0.823642 Iteration 2 Error: 0.085301 Iteration 3 Error: 0.019101 Align patch 21 4 left Iteration 1 Error: 0.740913 Iteration 2 Error: 0.086373 Iteration 3 Error: 0.021370 Align patch 22 3 left Iteration 1 Error: 0.828179 Iteration 2 Error: 0.106247 Iteration 3 Error: 0.021619 Align patch 23 2 left Iteration 1 Error: 0.408421 Iteration 2 Error: 0.059909 Iteration 3 Error: 0.018902 Align patch 24 1 left Iteration 1 Error: 0.958251 Iteration 2 Error: 0.160296 Iteration 3 Error: 0.037423 Align patch 25 0 left Iteration 1 Error: 1.277763 Iteration 2 Error: 0.231976 Iteration 3 Error: 0.035884 3D Fitting completed. Patch alignment time: 12.67(sec) Local motion has been corrected. Process thread exits. Computational time: 23.201721 sec Total time: 29.332642 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00002hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00002hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.565369s Reading file: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00002hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.616079s ........................................ >>>>>>TIME<<<<<< FFT: 1.007580s Defocus_U Defocus_V Angle CCC 25791.05 26666.05 10.72 -0.012081 Final Values Defocus_U Defocus_V Angle CCC 25786.36 26670.74 10.72 -0.175941 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00002sq_v01_00002hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00002hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.321e-01 9.848e-02 CC threshold: 0.723 Mean Std: 41.34 7.08 Num Hot pixels: 211 Hot pixel threshold: 83.85 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.262801 Iteration 2 Error: 0.332511 Iteration 3 Error: 0.084824 Iteration 4 Error: 0.027757 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.01 0.21 ...... Frame ( 3) shift: 0.02 0.42 ...... Frame ( 4) shift: 0.03 0.62 ...... Frame ( 5) shift: 0.04 0.83 ...... Frame ( 6) shift: 0.07 1.03 ...... Frame ( 7) shift: 0.12 1.23 ...... Frame ( 8) shift: 0.17 1.43 ...... Frame ( 9) shift: 0.21 1.59 ...... Frame ( 10) shift: 0.25 1.70 ...... Frame ( 11) shift: 0.28 1.81 ...... Frame ( 12) shift: 0.32 1.89 ...... Frame ( 13) shift: 0.36 1.95 ...... Frame ( 14) shift: 0.40 2.01 ...... Frame ( 15) shift: 0.45 2.09 ...... Frame ( 16) shift: 0.49 2.19 ...... Frame ( 17) shift: 0.54 2.29 ...... Frame ( 18) shift: 0.62 2.41 ...... Frame ( 19) shift: 0.74 2.54 ...... Frame ( 20) shift: 0.85 2.68 ...... Frame ( 21) shift: 0.93 2.82 ...... Frame ( 22) shift: 0.98 2.95 ...... Frame ( 23) shift: 1.03 3.09 ...... Frame ( 24) shift: 1.08 3.23 ...... Frame ( 25) shift: 1.14 3.37 ...... Frame ( 26) shift: 1.20 3.51 ...... Frame ( 27) shift: 1.29 3.65 ...... Frame ( 28) shift: 1.39 3.79 ...... Frame ( 29) shift: 1.49 3.93 ...... Frame ( 30) shift: 1.58 4.05 ...... Frame ( 31) shift: 1.66 4.14 ...... Frame ( 32) shift: 1.74 4.23 ...... Frame ( 33) shift: 1.82 4.31 ...... Frame ( 34) shift: 1.88 4.39 ...... Frame ( 35) shift: 1.95 4.47 ...... Frame ( 36) shift: 1.99 4.58 ...... Frame ( 37) shift: 2.01 4.71 ...... Frame ( 38) shift: 2.02 4.84 ...... Frame ( 39) shift: 2.04 4.97 ...... Frame ( 40) shift: 2.05 5.11 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.686101 Iteration 2 Error: 0.129232 Iteration 3 Error: 0.035808 Align patch 2 23 left Iteration 1 Error: 0.573738 Iteration 2 Error: 0.102259 Iteration 3 Error: 0.017218 Align patch 3 22 left Iteration 1 Error: 0.655285 Iteration 2 Error: 0.132357 Iteration 3 Error: 0.036106 Align patch 4 21 left Iteration 1 Error: 0.711372 Iteration 2 Error: 0.112697 Iteration 3 Error: 0.029955 Align patch 5 20 left Iteration 1 Error: 0.491102 Iteration 2 Error: 0.037997 Align patch 6 19 left Iteration 1 Error: 0.764282 Iteration 2 Error: 0.114590 Iteration 3 Error: 0.029154 Align patch 7 18 left Iteration 1 Error: 1.002510 Iteration 2 Error: 0.334494 Iteration 3 Error: 0.119334 Iteration 4 Error: 0.048811 Align patch 8 17 left Iteration 1 Error: 0.469577 Iteration 2 Error: 0.103959 Iteration 3 Error: 0.029616 Align patch 9 16 left Iteration 1 Error: 0.752902 Iteration 2 Error: 0.136727 Iteration 3 Error: 0.053662 Iteration 4 Error: 0.013380 Align patch 10 15 left Iteration 1 Error: 0.767333 Iteration 2 Error: 0.092109 Iteration 3 Error: 0.015742 Align patch 11 14 left Iteration 1 Error: 0.789472 Iteration 2 Error: 0.231955 Iteration 3 Error: 0.059240 Iteration 4 Error: 0.029688 Align patch 12 13 left Iteration 1 Error: 0.553995 Iteration 2 Error: 0.071598 Iteration 3 Error: 0.017105 Align patch 13 12 left Iteration 1 Error: 0.499940 Iteration 2 Error: 0.074758 Iteration 3 Error: 0.018522 Align patch 14 11 left Iteration 1 Error: 0.399523 Iteration 2 Error: 0.065969 Iteration 3 Error: 0.016609 Align patch 15 10 left Iteration 1 Error: 0.682014 Iteration 2 Error: 0.126412 Iteration 3 Error: 0.017836 Align patch 16 9 left Iteration 1 Error: 0.818890 Iteration 2 Error: 0.132542 Iteration 3 Error: 0.050725 Iteration 4 Error: 0.017177 Align patch 17 8 left Iteration 1 Error: 0.694248 Iteration 2 Error: 0.181488 Iteration 3 Error: 0.031404 Align patch 18 7 left Iteration 1 Error: 0.855560 Iteration 2 Error: 0.275477 Iteration 3 Error: 0.087477 Iteration 4 Error: 0.029093 Align patch 19 6 left Iteration 1 Error: 0.622773 Iteration 2 Error: 0.105339 Iteration 3 Error: 0.034611 Align patch 20 5 left Iteration 1 Error: 0.686083 Iteration 2 Error: 0.215440 Iteration 3 Error: 0.061375 Iteration 4 Error: 0.024163 Align patch 21 4 left Iteration 1 Error: 0.965423 Iteration 2 Error: 0.174411 Iteration 3 Error: 0.037495 Align patch 22 3 left Iteration 1 Error: 0.855536 Iteration 2 Error: 0.169227 Iteration 3 Error: 0.039647 Align patch 23 2 left Iteration 1 Error: 0.534627 Iteration 2 Error: 0.064639 Iteration 3 Error: 0.015179 Align patch 24 1 left Iteration 1 Error: 0.754726 Iteration 2 Error: 0.084765 Iteration 3 Error: 0.017230 Align patch 25 0 left Iteration 1 Error: 0.875270 Iteration 2 Error: 0.173148 Iteration 3 Error: 0.053845 Iteration 4 Error: 0.016848 3D Fitting completed. Patch alignment time: 11.48(sec) Local motion has been corrected. Process thread exits. Computational time: 22.641981 sec Total time: 29.254000 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00002hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00002hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.594788s Reading file: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00002hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 4.306334s ........................................ >>>>>>TIME<<<<<< FFT: 1.092309s Defocus_U Defocus_V Angle CCC 22461.00 21910.17 82.06 -0.028513 Final Values Defocus_U Defocus_V Angle CCC 22503.23 21899.29 83.74 -0.201969 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00002sq_v01_00002hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00002hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 9.999e-02 CC threshold: 0.734 Mean Std: 41.15 8.84 Num Hot pixels: 120 Hot pixel threshold: 94.19 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 37.480755 Iteration 2 Error: 37.483196 Iteration 3 Error: 37.485672 Iteration 4 Error: 39.238132 Iteration 5 Error: 37.885025 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.10 -9.89 ...... Frame ( 3) shift: -0.21 -19.78 ...... Frame ( 4) shift: -0.31 -29.66 ...... Frame ( 5) shift: -0.41 -39.55 ...... Frame ( 6) shift: -0.55 -50.40 ...... Frame ( 7) shift: -0.71 -62.22 ...... Frame ( 8) shift: -0.87 -74.03 ...... Frame ( 9) shift: -1.01 -86.13 ...... Frame ( 10) shift: -1.14 -98.51 ...... Frame ( 11) shift: -1.27 -110.88 ...... Frame ( 12) shift: -1.18 -129.82 ...... Frame ( 13) shift: -0.89 -155.30 ...... Frame ( 14) shift: -0.59 -180.79 ...... Frame ( 15) shift: -0.44 -193.57 ...... Frame ( 16) shift: -0.44 -193.65 ...... Frame ( 17) shift: -0.44 -193.73 ...... Frame ( 18) shift: -0.47 -193.77 ...... Frame ( 19) shift: -0.55 -193.77 ...... Frame ( 20) shift: -0.63 -193.77 ...... Frame ( 21) shift: -0.71 -193.83 ...... Frame ( 22) shift: -0.79 -193.95 ...... Frame ( 23) shift: -0.87 -194.07 ...... Frame ( 24) shift: -0.93 -194.18 ...... Frame ( 25) shift: -0.99 -194.30 ...... Frame ( 26) shift: -1.05 -194.42 ...... Frame ( 27) shift: -1.13 -194.56 ...... Frame ( 28) shift: -1.24 -194.73 ...... Frame ( 29) shift: -1.34 -194.90 ...... Frame ( 30) shift: -1.45 -195.02 ...... Frame ( 31) shift: -1.58 -195.09 ...... Frame ( 32) shift: -1.70 -195.16 ...... Frame ( 33) shift: -1.83 -195.26 ...... Frame ( 34) shift: -1.96 -195.41 ...... Frame ( 35) shift: -2.08 -195.55 ...... Frame ( 36) shift: -2.20 -195.71 ...... Frame ( 37) shift: -2.30 -195.90 ...... Frame ( 38) shift: -2.40 -196.09 ...... Frame ( 39) shift: -2.50 -196.27 ...... Frame ( 40) shift: -2.60 -196.46 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 39.102722 Iteration 2 Error: 31.071665 Iteration 3 Error: 9.429749 Iteration 4 Error: 11.827659 Iteration 5 Error: 11.178089 Align patch 1 24 left Iteration 1 Error: 57.548027 Iteration 2 Error: 40.789379 Iteration 3 Error: 58.994854 Iteration 4 Error: 56.893764 Iteration 5 Error: 56.670696 Align patch 2 23 left Iteration 1 Error: 37.449360 Iteration 2 Error: 38.583206 Iteration 3 Error: 32.892731 Iteration 4 Error: 30.625359 Iteration 5 Error: 14.436146 Align patch 2 23 left Iteration 1 Error: 57.550575 Iteration 2 Error: 49.916183 Iteration 3 Error: 8.040418 Iteration 4 Error: 6.281455 Iteration 5 Error: 4.642332 Align patch 3 22 left Iteration 1 Error: 22.001347 Iteration 2 Error: 35.959625 Iteration 3 Error: 23.238100 Iteration 4 Error: 33.453751 Iteration 5 Error: 35.959339 Align patch 3 22 left Iteration 1 Error: 15.061882 Iteration 2 Error: 0.466840 Iteration 3 Error: 0.199720 Iteration 4 Error: 0.026351 Align patch 4 21 left Iteration 1 Error: 1.733538 Iteration 2 Error: 0.087581 Iteration 3 Error: 0.019012 Align patch 5 20 left Iteration 1 Error: 5.929410 Iteration 2 Error: 0.370143 Iteration 3 Error: 0.054200 Iteration 4 Error: 0.012781 Align patch 6 19 left Iteration 1 Error: 34.896431 Iteration 2 Error: 46.588985 Iteration 3 Error: 34.595562 Iteration 4 Error: 35.629860 Iteration 5 Error: 36.104626 Align patch 6 19 left Iteration 1 Error: 57.525093 Iteration 2 Error: 57.501995 Iteration 3 Error: 56.314224 Iteration 4 Error: 59.669876 Iteration 5 Error: 59.332870 Align patch 7 18 left Iteration 1 Error: 47.648220 Iteration 2 Error: 38.019131 Iteration 3 Error: 25.426998 Iteration 4 Error: 3.594468 Iteration 5 Error: 0.777164 Align patch 7 18 left Iteration 1 Error: 57.560677 Iteration 2 Error: 47.703568 Iteration 3 Error: 46.485615 Iteration 4 Error: 46.144142 Iteration 5 Error: 57.643780 Align patch 8 17 left Iteration 1 Error: 36.033195 Iteration 2 Error: 35.359055 Iteration 3 Error: 36.168404 Iteration 4 Error: 15.392086 Iteration 5 Error: 34.791553 Align patch 8 17 left Iteration 1 Error: 57.523273 Iteration 2 Error: 57.586769 Iteration 3 Error: 42.533375 Iteration 4 Error: 43.468388 Iteration 5 Error: 44.933815 Align patch 9 16 left Iteration 1 Error: 43.982925 Iteration 2 Error: 44.388634 Iteration 3 Error: 37.096397 Iteration 4 Error: 36.038803 Iteration 5 Error: 36.498398 Align patch 9 16 left Iteration 1 Error: 3.343568 Iteration 2 Error: 0.573404 Iteration 3 Error: 0.120936 Iteration 4 Error: 0.050372 Iteration 5 Error: 0.042501 Align patch 10 15 left Iteration 1 Error: 4.267078 Iteration 2 Error: 0.818375 Iteration 3 Error: 0.177235 Iteration 4 Error: 0.058901 Iteration 5 Error: 0.030044 Align patch 11 14 left Iteration 1 Error: 37.099083 Iteration 2 Error: 37.651390 Iteration 3 Error: 35.447514 Iteration 4 Error: 30.316021 Iteration 5 Error: 2.709642 Align patch 11 14 left Iteration 1 Error: 58.728863 Iteration 2 Error: 42.096405 Iteration 3 Error: 9.067492 Iteration 4 Error: 2.044605 Iteration 5 Error: 3.154862 Align patch 12 13 left Iteration 1 Error: 39.836460 Iteration 2 Error: 38.973553 Iteration 3 Error: 38.084938 Iteration 4 Error: 0.878627 Iteration 5 Error: 0.458116 Align patch 12 13 left Iteration 1 Error: 60.029449 Iteration 2 Error: 44.618702 Iteration 3 Error: 20.881834 Iteration 4 Error: 6.719350 Iteration 5 Error: 0.821447 Align patch 13 12 left Iteration 1 Error: 40.229797 Iteration 2 Error: 38.391136 Iteration 3 Error: 30.089575 Iteration 4 Error: 28.923916 Iteration 5 Error: 1.007654 Align patch 13 12 left Iteration 1 Error: 58.654095 Iteration 2 Error: 57.703724 Iteration 3 Error: 11.052891 Iteration 4 Error: 2.899660 Iteration 5 Error: 1.236873 Align patch 14 11 left Iteration 1 Error: 43.718597 Iteration 2 Error: 37.974560 Iteration 3 Error: 1.600535 Iteration 4 Error: 0.414942 Iteration 5 Error: 0.443309 Align patch 14 11 left Iteration 1 Error: 57.560802 Iteration 2 Error: 43.382996 Iteration 3 Error: 42.408817 Iteration 4 Error: 44.646461 Iteration 5 Error: 44.186966 Align patch 15 10 left Iteration 1 Error: 49.189762 Iteration 2 Error: 43.071499 Iteration 3 Error: 37.202759 Iteration 4 Error: 7.045081 Iteration 5 Error: 2.074664 Align patch 15 10 left Iteration 1 Error: 57.585133 Iteration 2 Error: 42.542778 Iteration 3 Error: 40.620384 Iteration 4 Error: 42.532013 Iteration 5 Error: 45.492809 Align patch 16 9 left Iteration 1 Error: 31.182842 Iteration 2 Error: 44.118851 Iteration 3 Error: 39.931385 Iteration 4 Error: 4.186188 Iteration 5 Error: 1.069523 Align patch 16 9 left Iteration 1 Error: 57.764870 Iteration 2 Error: 59.019306 Iteration 3 Error: 45.036766 Iteration 4 Error: 14.496860 Iteration 5 Error: 1.147114 Align patch 17 8 left Iteration 1 Error: 37.765072 Iteration 2 Error: 40.251675 Iteration 3 Error: 42.844681 Iteration 4 Error: 44.138466 Iteration 5 Error: 43.062973 Align patch 17 8 left Iteration 1 Error: 57.726009 Iteration 2 Error: 41.643135 Iteration 3 Error: 19.009686 Iteration 4 Error: 2.702002 Iteration 5 Error: 1.988964 Align patch 18 7 left Iteration 1 Error: 37.583420 Iteration 2 Error: 27.716515 Iteration 3 Error: 38.603462 Iteration 4 Error: 20.219864 Iteration 5 Error: 34.058235 Align patch 18 7 left Iteration 1 Error: 57.825111 Iteration 2 Error: 42.270866 Iteration 3 Error: 20.774799 Iteration 4 Error: 18.200344 Iteration 5 Error: 1.190920 Align patch 19 6 left Iteration 1 Error: 7.751578 Iteration 2 Error: 3.778069 Iteration 3 Error: 4.967689 Iteration 4 Error: 0.651917 Iteration 5 Error: 0.246463 Align patch 19 6 left Iteration 1 Error: 6.471463 Iteration 2 Error: 1.402826 Iteration 3 Error: 0.588389 Iteration 4 Error: 0.156859 Iteration 5 Error: 0.073572 Align patch 20 5 left Iteration 1 Error: 33.130001 Iteration 2 Error: 12.046577 Iteration 3 Error: 1.384238 Iteration 4 Error: 22.769066 Iteration 5 Error: 1.011755 Align patch 20 5 left Iteration 1 Error: 5.356458 Iteration 2 Error: 1.379252 Iteration 3 Error: 0.539315 Iteration 4 Error: 0.224862 Iteration 5 Error: 0.054011 Align patch 21 4 left Iteration 1 Error: 35.938835 Iteration 2 Error: 44.170078 Iteration 3 Error: 1.717012 Iteration 4 Error: 0.623253 Iteration 5 Error: 0.304905 Align patch 21 4 left Iteration 1 Error: 57.775307 Iteration 2 Error: 43.148849 Iteration 3 Error: 3.449820 Iteration 4 Error: 1.276085 Iteration 5 Error: 0.409498 Align patch 22 3 left Iteration 1 Error: 35.963451 Iteration 2 Error: 37.863735 Iteration 3 Error: 35.173878 Iteration 4 Error: 30.049290 Iteration 5 Error: 37.093662 Align patch 22 3 left Iteration 1 Error: 57.724739 Iteration 2 Error: 42.410683 Iteration 3 Error: 19.919632 Iteration 4 Error: 17.716629 Iteration 5 Error: 17.168892 Align patch 23 2 left Iteration 1 Error: 36.045826 Iteration 2 Error: 22.032349 Iteration 3 Error: 17.296886 Iteration 4 Error: 25.614418 Iteration 5 Error: 28.979143 Align patch 23 2 left Iteration 1 Error: 57.652779 Iteration 2 Error: 42.812679 Iteration 3 Error: 3.511660 Iteration 4 Error: 0.979112 Iteration 5 Error: 0.337103 Align patch 24 1 left Iteration 1 Error: 4.608575 Iteration 2 Error: 1.662413 Iteration 3 Error: 0.530594 Iteration 4 Error: 0.277482 Iteration 5 Error: 0.177753 Align patch 24 1 left Iteration 1 Error: 57.532024 Iteration 2 Error: 22.761133 Iteration 3 Error: 5.236791 Iteration 4 Error: 0.575383 Iteration 5 Error: 0.152422 Align patch 25 0 left Iteration 1 Error: 35.999901 Iteration 2 Error: 35.938961 Iteration 3 Error: 35.938583 Iteration 4 Error: 35.940044 Iteration 5 Error: 35.940701 Align patch 25 0 left Iteration 1 Error: 57.550953 Iteration 2 Error: 57.501846 Iteration 3 Error: 57.500538 Iteration 4 Error: 57.500439 Iteration 5 Error: 57.500050 3D Fitting completed. Patch alignment time: 29.28(sec) Local motion has been corrected. Process thread exits. Computational time: 41.710335 sec Total time: 47.916359 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00002hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00002hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.702888s Reading file: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00002hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.373977s ........................................ >>>>>>TIME<<<<<< FFT: 0.916571s Defocus_U Defocus_V Angle CCC 22771.59 23591.92 13.10 0.078822 Final Values Defocus_U Defocus_V Angle CCC 22774.71 23585.68 15.60 0.159995 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00002sq_v01_00002hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00002hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.339e-01 9.964e-02 CC threshold: 0.732 Mean Std: 41.76 7.07 Num Hot pixels: 222 Hot pixel threshold: 84.17 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.508375 Iteration 2 Error: 0.228603 Iteration 3 Error: 0.043923 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.27 0.19 ...... Frame ( 3) shift: -0.53 0.39 ...... Frame ( 4) shift: -0.80 0.58 ...... Frame ( 5) shift: -1.07 0.78 ...... Frame ( 6) shift: -1.26 0.92 ...... Frame ( 7) shift: -1.39 1.01 ...... Frame ( 8) shift: -1.51 1.11 ...... Frame ( 9) shift: -1.62 1.23 ...... Frame ( 10) shift: -1.72 1.39 ...... Frame ( 11) shift: -1.81 1.56 ...... Frame ( 12) shift: -1.88 1.70 ...... Frame ( 13) shift: -1.92 1.82 ...... Frame ( 14) shift: -1.95 1.95 ...... Frame ( 15) shift: -2.02 2.04 ...... Frame ( 16) shift: -2.12 2.10 ...... Frame ( 17) shift: -2.22 2.16 ...... Frame ( 18) shift: -2.30 2.20 ...... Frame ( 19) shift: -2.37 2.21 ...... Frame ( 20) shift: -2.43 2.23 ...... Frame ( 21) shift: -2.49 2.28 ...... Frame ( 22) shift: -2.55 2.38 ...... Frame ( 23) shift: -2.60 2.47 ...... Frame ( 24) shift: -2.65 2.55 ...... Frame ( 25) shift: -2.69 2.61 ...... Frame ( 26) shift: -2.73 2.67 ...... Frame ( 27) shift: -2.78 2.71 ...... Frame ( 28) shift: -2.85 2.75 ...... Frame ( 29) shift: -2.91 2.78 ...... Frame ( 30) shift: -2.95 2.81 ...... Frame ( 31) shift: -2.96 2.83 ...... Frame ( 32) shift: -2.97 2.86 ...... Frame ( 33) shift: -3.01 2.89 ...... Frame ( 34) shift: -3.06 2.95 ...... Frame ( 35) shift: -3.12 3.00 ...... Frame ( 36) shift: -3.14 3.03 ...... Frame ( 37) shift: -3.14 3.04 ...... Frame ( 38) shift: -3.13 3.06 ...... Frame ( 39) shift: -3.12 3.07 ...... Frame ( 40) shift: -3.11 3.08 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.775585 Iteration 2 Error: 0.136184 Iteration 3 Error: 0.034816 Align patch 2 23 left Iteration 1 Error: 0.796863 Iteration 2 Error: 0.106218 Iteration 3 Error: 0.027408 Align patch 3 22 left Iteration 1 Error: 0.883136 Iteration 2 Error: 0.114288 Iteration 3 Error: 0.032843 Align patch 4 21 left Iteration 1 Error: 0.732227 Iteration 2 Error: 0.118492 Iteration 3 Error: 0.023106 Align patch 5 20 left Iteration 1 Error: 1.351533 Iteration 2 Error: 0.114167 Iteration 3 Error: 0.024596 Align patch 6 19 left Iteration 1 Error: 0.925430 Iteration 2 Error: 0.213566 Iteration 3 Error: 0.074792 Iteration 4 Error: 0.026527 Align patch 7 18 left Iteration 1 Error: 0.742627 Iteration 2 Error: 0.101507 Iteration 3 Error: 0.023478 Align patch 8 17 left Iteration 1 Error: 0.518048 Iteration 2 Error: 0.089567 Iteration 3 Error: 0.022503 Align patch 9 16 left Iteration 1 Error: 0.501878 Iteration 2 Error: 0.041867 Align patch 10 15 left Iteration 1 Error: 1.223894 Iteration 2 Error: 0.144313 Iteration 3 Error: 0.028778 Align patch 11 14 left Iteration 1 Error: 0.856016 Iteration 2 Error: 0.127244 Iteration 3 Error: 0.022575 Align patch 12 13 left Iteration 1 Error: 0.647436 Iteration 2 Error: 0.084636 Iteration 3 Error: 0.016890 Align patch 13 12 left Iteration 1 Error: 0.614003 Iteration 2 Error: 0.049136 Align patch 14 11 left Iteration 1 Error: 0.602588 Iteration 2 Error: 0.065488 Iteration 3 Error: 0.014953 Align patch 15 10 left Iteration 1 Error: 0.602753 Iteration 2 Error: 0.072271 Iteration 3 Error: 0.014150 Align patch 16 9 left Iteration 1 Error: 0.753914 Iteration 2 Error: 0.090662 Iteration 3 Error: 0.029668 Align patch 17 8 left Iteration 1 Error: 0.987492 Iteration 2 Error: 0.130820 Iteration 3 Error: 0.022972 Align patch 18 7 left Iteration 1 Error: 0.985829 Iteration 2 Error: 0.156777 Iteration 3 Error: 0.026045 Align patch 19 6 left Iteration 1 Error: 0.529060 Iteration 2 Error: 0.046699 Align patch 20 5 left Iteration 1 Error: 1.018315 Iteration 2 Error: 0.120360 Iteration 3 Error: 0.018194 Align patch 21 4 left Iteration 1 Error: 1.009944 Iteration 2 Error: 0.099620 Iteration 3 Error: 0.015482 Align patch 22 3 left Iteration 1 Error: 1.315778 Iteration 2 Error: 0.118293 Iteration 3 Error: 0.019951 Align patch 23 2 left Iteration 1 Error: 0.717426 Iteration 2 Error: 0.104302 Iteration 3 Error: 0.022153 Align patch 24 1 left Iteration 1 Error: 0.561449 Iteration 2 Error: 0.073438 Iteration 3 Error: 0.014243 Align patch 25 0 left Iteration 1 Error: 1.002231 Iteration 2 Error: 0.103463 Iteration 3 Error: 0.015862 3D Fitting completed. Patch alignment time: 11.19(sec) Local motion has been corrected. Process thread exits. Computational time: 21.133873 sec Total time: 27.409290 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00002hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00002hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.716647s Reading file: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00002hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.265798s ........................................ >>>>>>TIME<<<<<< FFT: 1.006575s Defocus_U Defocus_V Angle CCC 27511.79 26781.23 76.70 0.034448 Final Values Defocus_U Defocus_V Angle CCC 27507.10 26789.05 76.70 -0.002532 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00002sq_v01_00003hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00003hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 41.84 7.08 Num Hot pixels: 212 Hot pixel threshold: 84.33 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.395450 Iteration 2 Error: 0.168396 Iteration 3 Error: 0.029582 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.11 0.32 ...... Frame ( 3) shift: -0.22 0.64 ...... Frame ( 4) shift: -0.33 0.96 ...... Frame ( 5) shift: -0.44 1.29 ...... Frame ( 6) shift: -0.49 1.53 ...... Frame ( 7) shift: -0.46 1.70 ...... Frame ( 8) shift: -0.44 1.87 ...... Frame ( 9) shift: -0.42 2.05 ...... Frame ( 10) shift: -0.41 2.24 ...... Frame ( 11) shift: -0.40 2.43 ...... Frame ( 12) shift: -0.38 2.60 ...... Frame ( 13) shift: -0.37 2.75 ...... Frame ( 14) shift: -0.35 2.90 ...... Frame ( 15) shift: -0.30 2.99 ...... Frame ( 16) shift: -0.21 3.01 ...... Frame ( 17) shift: -0.13 3.03 ...... Frame ( 18) shift: -0.07 3.07 ...... Frame ( 19) shift: -0.04 3.14 ...... Frame ( 20) shift: -0.01 3.21 ...... Frame ( 21) shift: -0.03 3.27 ...... Frame ( 22) shift: -0.09 3.32 ...... Frame ( 23) shift: -0.14 3.37 ...... Frame ( 24) shift: -0.13 3.42 ...... Frame ( 25) shift: -0.03 3.47 ...... Frame ( 26) shift: 0.06 3.51 ...... Frame ( 27) shift: 0.09 3.55 ...... Frame ( 28) shift: 0.07 3.57 ...... Frame ( 29) shift: 0.05 3.59 ...... Frame ( 30) shift: 0.03 3.61 ...... Frame ( 31) shift: 0.03 3.63 ...... Frame ( 32) shift: 0.02 3.65 ...... Frame ( 33) shift: 0.04 3.71 ...... Frame ( 34) shift: 0.06 3.81 ...... Frame ( 35) shift: 0.09 3.92 ...... Frame ( 36) shift: 0.12 3.98 ...... Frame ( 37) shift: 0.14 3.98 ...... Frame ( 38) shift: 0.16 3.98 ...... Frame ( 39) shift: 0.18 3.98 ...... Frame ( 40) shift: 0.20 3.98 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.634403 Iteration 2 Error: 0.081519 Iteration 3 Error: 0.013279 Align patch 2 23 left Iteration 1 Error: 0.540611 Iteration 2 Error: 0.053183 Iteration 3 Error: 0.013483 Align patch 3 22 left Iteration 1 Error: 0.729399 Iteration 2 Error: 0.078293 Iteration 3 Error: 0.018990 Align patch 4 21 left Iteration 1 Error: 0.454153 Iteration 2 Error: 0.072180 Iteration 3 Error: 0.020731 Align patch 5 20 left Iteration 1 Error: 0.640246 Iteration 2 Error: 0.063189 Iteration 3 Error: 0.016723 Align patch 6 19 left Iteration 1 Error: 0.648795 Iteration 2 Error: 0.118962 Iteration 3 Error: 0.023177 Align patch 7 18 left Iteration 1 Error: 0.606365 Iteration 2 Error: 0.096333 Iteration 3 Error: 0.025152 Align patch 8 17 left Iteration 1 Error: 0.495317 Iteration 2 Error: 0.076781 Iteration 3 Error: 0.013739 Align patch 9 16 left Iteration 1 Error: 0.482226 Iteration 2 Error: 0.055341 Iteration 3 Error: 0.012050 Align patch 10 15 left Iteration 1 Error: 0.473924 Iteration 2 Error: 0.064865 Iteration 3 Error: 0.015064 Align patch 11 14 left Iteration 1 Error: 1.069610 Iteration 2 Error: 0.092906 Iteration 3 Error: 0.022528 Align patch 12 13 left Iteration 1 Error: 0.623210 Iteration 2 Error: 0.072537 Iteration 3 Error: 0.020245 Align patch 13 12 left Iteration 1 Error: 0.519957 Iteration 2 Error: 0.063636 Iteration 3 Error: 0.016761 Align patch 14 11 left Iteration 1 Error: 0.421178 Iteration 2 Error: 0.054564 Iteration 3 Error: 0.015259 Align patch 15 10 left Iteration 1 Error: 0.835033 Iteration 2 Error: 0.081202 Iteration 3 Error: 0.021297 Align patch 16 9 left Iteration 1 Error: 0.926080 Iteration 2 Error: 0.158343 Iteration 3 Error: 0.042890 Align patch 17 8 left Iteration 1 Error: 0.607951 Iteration 2 Error: 0.060293 Iteration 3 Error: 0.015730 Align patch 18 7 left Iteration 1 Error: 0.520299 Iteration 2 Error: 0.065201 Iteration 3 Error: 0.017050 Align patch 19 6 left Iteration 1 Error: 0.446796 Iteration 2 Error: 0.063447 Iteration 3 Error: 0.011098 Align patch 20 5 left Iteration 1 Error: 0.536744 Iteration 2 Error: 0.080619 Iteration 3 Error: 0.019918 Align patch 21 4 left Iteration 1 Error: 0.627290 Iteration 2 Error: 0.090162 Iteration 3 Error: 0.021537 Align patch 22 3 left Iteration 1 Error: 0.641889 Iteration 2 Error: 0.062935 Iteration 3 Error: 0.011850 Align patch 23 2 left Iteration 1 Error: 0.592606 Iteration 2 Error: 0.040165 Align patch 24 1 left Iteration 1 Error: 0.507485 Iteration 2 Error: 0.061429 Iteration 3 Error: 0.010436 Align patch 25 0 left Iteration 1 Error: 0.557934 Iteration 2 Error: 0.057906 Iteration 3 Error: 0.009804 3D Fitting completed. Patch alignment time: 13.25(sec) Local motion has been corrected. Process thread exits. Computational time: 30.174347 sec Total time: 37.771999 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00003hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00003hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.601164s Reading file: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00003hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.712310s ........................................ >>>>>>TIME<<<<<< FFT: 1.577931s Defocus_U Defocus_V Angle CCC 25720.71 26548.83 7.08 0.062257 Final Values Defocus_U Defocus_V Angle CCC 25728.52 26541.02 7.40 0.096573 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00002sq_v01_00003hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00003hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 41.74 7.02 Num Hot pixels: 220 Hot pixel threshold: 83.85 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.503647 Iteration 2 Error: 0.176630 Iteration 3 Error: 0.031292 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.09 0.15 ...... Frame ( 3) shift: -0.18 0.30 ...... Frame ( 4) shift: -0.27 0.45 ...... Frame ( 5) shift: -0.36 0.60 ...... Frame ( 6) shift: -0.40 0.73 ...... Frame ( 7) shift: -0.39 0.82 ...... Frame ( 8) shift: -0.37 0.92 ...... Frame ( 9) shift: -0.36 1.03 ...... Frame ( 10) shift: -0.34 1.17 ...... Frame ( 11) shift: -0.33 1.30 ...... Frame ( 12) shift: -0.30 1.41 ...... Frame ( 13) shift: -0.26 1.51 ...... Frame ( 14) shift: -0.22 1.61 ...... Frame ( 15) shift: -0.20 1.68 ...... Frame ( 16) shift: -0.20 1.72 ...... Frame ( 17) shift: -0.20 1.75 ...... Frame ( 18) shift: -0.14 1.79 ...... Frame ( 19) shift: -0.04 1.84 ...... Frame ( 20) shift: 0.06 1.88 ...... Frame ( 21) shift: 0.11 1.95 ...... Frame ( 22) shift: 0.11 2.06 ...... Frame ( 23) shift: 0.10 2.17 ...... Frame ( 24) shift: 0.11 2.22 ...... Frame ( 25) shift: 0.14 2.23 ...... Frame ( 26) shift: 0.16 2.24 ...... Frame ( 27) shift: 0.19 2.25 ...... Frame ( 28) shift: 0.23 2.26 ...... Frame ( 29) shift: 0.26 2.26 ...... Frame ( 30) shift: 0.28 2.31 ...... Frame ( 31) shift: 0.27 2.41 ...... Frame ( 32) shift: 0.27 2.51 ...... Frame ( 33) shift: 0.31 2.57 ...... Frame ( 34) shift: 0.39 2.61 ...... Frame ( 35) shift: 0.48 2.66 ...... Frame ( 36) shift: 0.52 2.70 ...... Frame ( 37) shift: 0.53 2.76 ...... Frame ( 38) shift: 0.54 2.82 ...... Frame ( 39) shift: 0.55 2.88 ...... Frame ( 40) shift: 0.56 2.93 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.093068 Iteration 2 Error: 0.158409 Iteration 3 Error: 0.036585 Align patch 2 23 left Iteration 1 Error: 0.717816 Iteration 2 Error: 0.160284 Iteration 3 Error: 0.050345 Iteration 4 Error: 0.014398 Align patch 3 22 left Iteration 1 Error: 0.499273 Iteration 2 Error: 0.076839 Iteration 3 Error: 0.014578 Align patch 4 21 left Iteration 1 Error: 0.444017 Iteration 2 Error: 0.065802 Iteration 3 Error: 0.018019 Align patch 5 20 left Iteration 1 Error: 0.780402 Iteration 2 Error: 0.084260 Iteration 3 Error: 0.021531 Align patch 6 19 left Iteration 1 Error: 0.754986 Iteration 2 Error: 0.111155 Iteration 3 Error: 0.025940 Align patch 7 18 left Iteration 1 Error: 0.530933 Iteration 2 Error: 0.058916 Iteration 3 Error: 0.020352 Align patch 8 17 left Iteration 1 Error: 0.634347 Iteration 2 Error: 0.070213 Iteration 3 Error: 0.021139 Align patch 9 16 left Iteration 1 Error: 0.480561 Iteration 2 Error: 0.050375 Iteration 3 Error: 0.006784 Align patch 10 15 left Iteration 1 Error: 0.621823 Iteration 2 Error: 0.102944 Iteration 3 Error: 0.023508 Align patch 11 14 left Iteration 1 Error: 0.698361 Iteration 2 Error: 0.097444 Iteration 3 Error: 0.020380 Align patch 12 13 left Iteration 1 Error: 0.759865 Iteration 2 Error: 0.080280 Iteration 3 Error: 0.019598 Align patch 13 12 left Iteration 1 Error: 0.897051 Iteration 2 Error: 0.105625 Iteration 3 Error: 0.022683 Align patch 14 11 left Iteration 1 Error: 0.589224 Iteration 2 Error: 0.078786 Iteration 3 Error: 0.020428 Align patch 15 10 left Iteration 1 Error: 0.574751 Iteration 2 Error: 0.046276 Align patch 16 9 left Iteration 1 Error: 0.698889 Iteration 2 Error: 0.059075 Iteration 3 Error: 0.014018 Align patch 17 8 left Iteration 1 Error: 0.675375 Iteration 2 Error: 0.066764 Iteration 3 Error: 0.016545 Align patch 18 7 left Iteration 1 Error: 0.608211 Iteration 2 Error: 0.062373 Iteration 3 Error: 0.020037 Align patch 19 6 left Iteration 1 Error: 0.666438 Iteration 2 Error: 0.147184 Iteration 3 Error: 0.023580 Align patch 20 5 left Iteration 1 Error: 0.505244 Iteration 2 Error: 0.079939 Iteration 3 Error: 0.014369 Align patch 21 4 left Iteration 1 Error: 0.895160 Iteration 2 Error: 0.147837 Iteration 3 Error: 0.032992 Align patch 22 3 left Iteration 1 Error: 0.725387 Iteration 2 Error: 0.103722 Iteration 3 Error: 0.030772 Align patch 23 2 left Iteration 1 Error: 0.661261 Iteration 2 Error: 0.149698 Iteration 3 Error: 0.027199 Align patch 24 1 left Iteration 1 Error: 0.553608 Iteration 2 Error: 0.085328 Iteration 3 Error: 0.020961 Align patch 25 0 left Iteration 1 Error: 0.710118 Iteration 2 Error: 0.083288 Iteration 3 Error: 0.016093 3D Fitting completed. Patch alignment time: 19.97(sec) Local motion has been corrected. Process thread exits. Computational time: 35.611416 sec Total time: 44.450176 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00003hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00003hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.564706s Reading file: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00003hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 4.357058s ........................................ >>>>>>TIME<<<<<< FFT: 1.479382s Defocus_U Defocus_V Angle CCC 25003.96 25535.22 0.18 0.050543 Final Values Defocus_U Defocus_V Angle CCC 25574.32 24989.88 89.86 0.079571 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00002sq_v01_00003hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00003hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 41.98 7.08 Num Hot pixels: 202 Hot pixel threshold: 84.44 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.682069 Iteration 2 Error: 0.436453 Iteration 3 Error: 0.155736 Iteration 4 Error: 0.056861 Iteration 5 Error: 0.024686 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.13 0.22 ...... Frame ( 3) shift: -0.26 0.44 ...... Frame ( 4) shift: -0.39 0.65 ...... Frame ( 5) shift: -0.52 0.87 ...... Frame ( 6) shift: -0.55 1.04 ...... Frame ( 7) shift: -0.47 1.15 ...... Frame ( 8) shift: -0.40 1.26 ...... Frame ( 9) shift: -0.32 1.35 ...... Frame ( 10) shift: -0.23 1.40 ...... Frame ( 11) shift: -0.14 1.45 ...... Frame ( 12) shift: -0.07 1.54 ...... Frame ( 13) shift: -0.02 1.67 ...... Frame ( 14) shift: 0.02 1.80 ...... Frame ( 15) shift: 0.11 1.97 ...... Frame ( 16) shift: 0.25 2.18 ...... Frame ( 17) shift: 0.39 2.38 ...... Frame ( 18) shift: 0.47 2.53 ...... Frame ( 19) shift: 0.50 2.61 ...... Frame ( 20) shift: 0.53 2.69 ...... Frame ( 21) shift: 0.57 2.76 ...... Frame ( 22) shift: 0.62 2.81 ...... Frame ( 23) shift: 0.68 2.87 ...... Frame ( 24) shift: 0.77 2.95 ...... Frame ( 25) shift: 0.91 3.06 ...... Frame ( 26) shift: 1.06 3.16 ...... Frame ( 27) shift: 1.20 3.30 ...... Frame ( 28) shift: 1.35 3.47 ...... Frame ( 29) shift: 1.49 3.64 ...... Frame ( 30) shift: 1.58 3.80 ...... Frame ( 31) shift: 1.61 3.93 ...... Frame ( 32) shift: 1.63 4.07 ...... Frame ( 33) shift: 1.70 4.21 ...... Frame ( 34) shift: 1.82 4.35 ...... Frame ( 35) shift: 1.93 4.49 ...... Frame ( 36) shift: 2.07 4.65 ...... Frame ( 37) shift: 2.24 4.81 ...... Frame ( 38) shift: 2.40 4.97 ...... Frame ( 39) shift: 2.57 5.13 ...... Frame ( 40) shift: 2.73 5.29 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 7.393866 Iteration 2 Error: 1.915224 Iteration 3 Error: 0.786841 Iteration 4 Error: 0.223133 Iteration 5 Error: 0.104020 Align patch 1 24 left Iteration 1 Error: 5.237118 Iteration 2 Error: 0.768377 Iteration 3 Error: 0.210444 Iteration 4 Error: 0.056694 Iteration 5 Error: 0.020268 Align patch 2 23 left Iteration 1 Error: 2.855549 Iteration 2 Error: 0.753401 Iteration 3 Error: 0.346021 Iteration 4 Error: 0.193171 Iteration 5 Error: 0.101449 Align patch 2 23 left Iteration 1 Error: 3.668732 Iteration 2 Error: 0.682234 Iteration 3 Error: 0.151036 Iteration 4 Error: 0.040004 Align patch 3 22 left Iteration 1 Error: 0.996904 Iteration 2 Error: 0.132432 Iteration 3 Error: 0.031447 Align patch 4 21 left Iteration 1 Error: 0.731258 Iteration 2 Error: 0.191775 Iteration 3 Error: 0.029546 Align patch 5 20 left Iteration 1 Error: 0.998100 Iteration 2 Error: 0.230539 Iteration 3 Error: 0.050119 Iteration 4 Error: 0.013048 Align patch 6 19 left Iteration 1 Error: 5.502288 Iteration 2 Error: 1.525916 Iteration 3 Error: 0.351429 Iteration 4 Error: 0.155706 Iteration 5 Error: 0.054268 Align patch 6 19 left Iteration 1 Error: 4.833143 Iteration 2 Error: 0.613131 Iteration 3 Error: 0.166697 Iteration 4 Error: 0.040236 Align patch 7 18 left Iteration 1 Error: 2.182838 Iteration 2 Error: 0.535936 Iteration 3 Error: 0.243468 Iteration 4 Error: 0.113892 Iteration 5 Error: 0.063300 Align patch 7 18 left Iteration 1 Error: 3.189599 Iteration 2 Error: 0.695473 Iteration 3 Error: 0.138500 Iteration 4 Error: 0.044669 Align patch 8 17 left Iteration 1 Error: 1.078136 Iteration 2 Error: 0.151236 Iteration 3 Error: 0.050368 Iteration 4 Error: 0.022543 Align patch 9 16 left Iteration 1 Error: 0.910615 Iteration 2 Error: 0.199471 Iteration 3 Error: 0.039684 Align patch 10 15 left Iteration 1 Error: 1.279034 Iteration 2 Error: 0.279786 Iteration 3 Error: 0.058174 Iteration 4 Error: 0.012835 Align patch 11 14 left Iteration 1 Error: 3.671802 Iteration 2 Error: 1.061932 Iteration 3 Error: 0.215531 Iteration 4 Error: 0.116188 Iteration 5 Error: 0.048134 Align patch 12 13 left Iteration 1 Error: 1.556473 Iteration 2 Error: 0.275803 Iteration 3 Error: 0.103238 Iteration 4 Error: 0.049873 Align patch 13 12 left Iteration 1 Error: 0.712783 Iteration 2 Error: 0.087921 Iteration 3 Error: 0.030404 Align patch 14 11 left Iteration 1 Error: 0.562803 Iteration 2 Error: 0.150951 Iteration 3 Error: 0.031341 Align patch 15 10 left Iteration 1 Error: 1.673335 Iteration 2 Error: 0.351991 Iteration 3 Error: 0.067850 Iteration 4 Error: 0.017231 Align patch 16 9 left Iteration 1 Error: 1.773543 Iteration 2 Error: 0.622036 Iteration 3 Error: 0.202986 Iteration 4 Error: 0.077823 Iteration 5 Error: 0.031808 Align patch 17 8 left Iteration 1 Error: 1.224284 Iteration 2 Error: 0.186483 Iteration 3 Error: 0.094302 Iteration 4 Error: 0.027653 Align patch 18 7 left Iteration 1 Error: 0.805246 Iteration 2 Error: 0.139464 Iteration 3 Error: 0.049840 Align patch 19 6 left Iteration 1 Error: 1.159750 Iteration 2 Error: 0.322661 Iteration 3 Error: 0.077628 Iteration 4 Error: 0.032752 Align patch 20 5 left Iteration 1 Error: 1.963160 Iteration 2 Error: 0.374369 Iteration 3 Error: 0.068531 Iteration 4 Error: 0.015032 Align patch 21 4 left Iteration 1 Error: 0.884693 Iteration 2 Error: 0.281818 Iteration 3 Error: 0.072925 Iteration 4 Error: 0.035535 Align patch 22 3 left Iteration 1 Error: 0.797018 Iteration 2 Error: 0.211612 Iteration 3 Error: 0.059693 Iteration 4 Error: 0.018788 Align patch 23 2 left Iteration 1 Error: 1.021229 Iteration 2 Error: 0.231496 Iteration 3 Error: 0.050396 Iteration 4 Error: 0.019352 Align patch 24 1 left Iteration 1 Error: 1.021241 Iteration 2 Error: 0.244637 Iteration 3 Error: 0.062273 Iteration 4 Error: 0.016546 Align patch 25 0 left Iteration 1 Error: 1.996391 Iteration 2 Error: 0.400732 Iteration 3 Error: 0.057961 Iteration 4 Error: 0.012335 3D Fitting completed. Patch alignment time: 26.31(sec) Local motion has been corrected. Process thread exits. Computational time: 42.182037 sec Total time: 51.820084 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00003hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00003hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.615004s Reading file: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00003hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.426165s ........................................ >>>>>>TIME<<<<<< FFT: 1.618368s Defocus_U Defocus_V Angle CCC 25115.24 26013.68 2.20 0.054291 Final Values Defocus_U Defocus_V Angle CCC 25126.20 26005.89 1.57 0.088208 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00002sq_v01_00003hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00003hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.002e-01 CC threshold: 0.736 Mean Std: 42.54 7.16 Num Hot pixels: 214 Hot pixel threshold: 85.50 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.744971 Iteration 2 Error: 0.128689 Iteration 3 Error: 0.023513 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.17 0.23 ...... Frame ( 3) shift: -0.34 0.46 ...... Frame ( 4) shift: -0.52 0.69 ...... Frame ( 5) shift: -0.69 0.92 ...... Frame ( 6) shift: -0.79 1.09 ...... Frame ( 7) shift: -0.81 1.22 ...... Frame ( 8) shift: -0.82 1.34 ...... Frame ( 9) shift: -0.86 1.45 ...... Frame ( 10) shift: -0.90 1.56 ...... Frame ( 11) shift: -0.95 1.67 ...... Frame ( 12) shift: -0.99 1.77 ...... Frame ( 13) shift: -1.01 1.85 ...... Frame ( 14) shift: -1.04 1.94 ...... Frame ( 15) shift: -1.08 1.98 ...... Frame ( 16) shift: -1.15 1.98 ...... Frame ( 17) shift: -1.21 1.98 ...... Frame ( 18) shift: -1.26 2.01 ...... Frame ( 19) shift: -1.30 2.07 ...... Frame ( 20) shift: -1.34 2.13 ...... Frame ( 21) shift: -1.36 2.16 ...... Frame ( 22) shift: -1.34 2.14 ...... Frame ( 23) shift: -1.33 2.13 ...... Frame ( 24) shift: -1.35 2.13 ...... Frame ( 25) shift: -1.40 2.14 ...... Frame ( 26) shift: -1.45 2.16 ...... Frame ( 27) shift: -1.47 2.15 ...... Frame ( 28) shift: -1.46 2.11 ...... Frame ( 29) shift: -1.45 2.08 ...... Frame ( 30) shift: -1.43 2.08 ...... Frame ( 31) shift: -1.39 2.13 ...... Frame ( 32) shift: -1.35 2.17 ...... Frame ( 33) shift: -1.38 2.23 ...... Frame ( 34) shift: -1.47 2.30 ...... Frame ( 35) shift: -1.56 2.38 ...... Frame ( 36) shift: -1.62 2.42 ...... Frame ( 37) shift: -1.63 2.44 ...... Frame ( 38) shift: -1.65 2.46 ...... Frame ( 39) shift: -1.67 2.47 ...... Frame ( 40) shift: -1.69 2.49 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.127327 Iteration 2 Error: 0.112243 Iteration 3 Error: 0.033159 Align patch 2 23 left Iteration 1 Error: 0.863699 Iteration 2 Error: 0.085236 Iteration 3 Error: 0.019820 Align patch 3 22 left Iteration 1 Error: 0.685991 Iteration 2 Error: 0.082832 Iteration 3 Error: 0.022944 Align patch 4 21 left Iteration 1 Error: 0.785273 Iteration 2 Error: 0.070440 Iteration 3 Error: 0.017252 Align patch 5 20 left Iteration 1 Error: 0.780940 Iteration 2 Error: 0.145085 Iteration 3 Error: 0.029606 Align patch 6 19 left Iteration 1 Error: 0.884450 Iteration 2 Error: 0.135153 Iteration 3 Error: 0.036741 Align patch 7 18 left Iteration 1 Error: 0.551992 Iteration 2 Error: 0.094202 Iteration 3 Error: 0.014409 Align patch 8 17 left Iteration 1 Error: 0.682506 Iteration 2 Error: 0.084392 Iteration 3 Error: 0.026748 Align patch 9 16 left Iteration 1 Error: 1.728585 Iteration 2 Error: 0.363773 Iteration 3 Error: 0.083754 Iteration 4 Error: 0.026487 Align patch 10 15 left Iteration 1 Error: 1.624501 Iteration 2 Error: 0.384955 Iteration 3 Error: 0.105391 Iteration 4 Error: 0.034840 Align patch 11 14 left Iteration 1 Error: 0.771773 Iteration 2 Error: 0.080548 Iteration 3 Error: 0.021776 Align patch 12 13 left Iteration 1 Error: 0.591828 Iteration 2 Error: 0.114229 Iteration 3 Error: 0.025886 Align patch 13 12 left Iteration 1 Error: 0.655826 Iteration 2 Error: 0.056400 Iteration 3 Error: 0.015698 Align patch 14 11 left Iteration 1 Error: 1.295997 Iteration 2 Error: 0.332836 Iteration 3 Error: 0.140181 Iteration 4 Error: 0.050378 Iteration 5 Error: 0.022667 Align patch 15 10 left Iteration 1 Error: 2.007660 Iteration 2 Error: 0.535883 Iteration 3 Error: 0.179548 Iteration 4 Error: 0.068324 Iteration 5 Error: 0.036189 Align patch 16 9 left Iteration 1 Error: 0.802303 Iteration 2 Error: 0.137076 Iteration 3 Error: 0.025782 Align patch 17 8 left Iteration 1 Error: 0.899443 Iteration 2 Error: 0.089822 Iteration 3 Error: 0.021886 Align patch 18 7 left Iteration 1 Error: 0.575604 Iteration 2 Error: 0.054902 Iteration 3 Error: 0.014107 Align patch 19 6 left Iteration 1 Error: 0.708485 Iteration 2 Error: 0.059530 Iteration 3 Error: 0.014470 Align patch 20 5 left Iteration 1 Error: 0.846659 Iteration 2 Error: 0.114259 Iteration 3 Error: 0.024158 Align patch 21 4 left Iteration 1 Error: 0.958466 Iteration 2 Error: 0.172308 Iteration 3 Error: 0.024475 Align patch 22 3 left Iteration 1 Error: 1.070266 Iteration 2 Error: 0.100779 Iteration 3 Error: 0.026678 Align patch 23 2 left Iteration 1 Error: 1.102589 Iteration 2 Error: 0.144374 Iteration 3 Error: 0.023136 Align patch 24 1 left Iteration 1 Error: 0.762559 Iteration 2 Error: 0.135345 Iteration 3 Error: 0.022044 Align patch 25 0 left Iteration 1 Error: 0.782634 Iteration 2 Error: 0.111493 Iteration 3 Error: 0.020618 3D Fitting completed. Patch alignment time: 18.34(sec) Local motion has been corrected. Process thread exits. Computational time: 33.096668 sec Total time: 42.401501 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00003hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00003hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.546830s Reading file: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00003hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 4.032773s ........................................ >>>>>>TIME<<<<<< FFT: 1.468651s Defocus_U Defocus_V Angle CCC 28186.04 27513.38 80.04 0.043503 Final Values Defocus_U Defocus_V Angle CCC 28187.60 27514.94 79.10 0.071424 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00002sq_v01_00004hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00004hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.001e-01 CC threshold: 0.735 Mean Std: 41.24 6.95 Num Hot pixels: 219 Hot pixel threshold: 82.96 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.549524 Iteration 2 Error: 0.257210 Iteration 3 Error: 0.042987 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.26 -0.08 ...... Frame ( 3) shift: -0.53 -0.16 ...... Frame ( 4) shift: -0.79 -0.24 ...... Frame ( 5) shift: -1.06 -0.31 ...... Frame ( 6) shift: -1.13 -0.33 ...... Frame ( 7) shift: -1.02 -0.29 ...... Frame ( 8) shift: -0.90 -0.24 ...... Frame ( 9) shift: -0.81 -0.19 ...... Frame ( 10) shift: -0.74 -0.12 ...... Frame ( 11) shift: -0.67 -0.06 ...... Frame ( 12) shift: -0.62 0.02 ...... Frame ( 13) shift: -0.58 0.09 ...... Frame ( 14) shift: -0.54 0.17 ...... Frame ( 15) shift: -0.51 0.23 ...... Frame ( 16) shift: -0.47 0.28 ...... Frame ( 17) shift: -0.43 0.32 ...... Frame ( 18) shift: -0.38 0.33 ...... Frame ( 19) shift: -0.31 0.30 ...... Frame ( 20) shift: -0.25 0.27 ...... Frame ( 21) shift: -0.18 0.31 ...... Frame ( 22) shift: -0.12 0.43 ...... Frame ( 23) shift: -0.06 0.55 ...... Frame ( 24) shift: -0.01 0.68 ...... Frame ( 25) shift: 0.04 0.81 ...... Frame ( 26) shift: 0.09 0.95 ...... Frame ( 27) shift: 0.14 1.07 ...... Frame ( 28) shift: 0.21 1.18 ...... Frame ( 29) shift: 0.27 1.30 ...... Frame ( 30) shift: 0.35 1.38 ...... Frame ( 31) shift: 0.43 1.42 ...... Frame ( 32) shift: 0.52 1.47 ...... Frame ( 33) shift: 0.56 1.50 ...... Frame ( 34) shift: 0.55 1.51 ...... Frame ( 35) shift: 0.55 1.52 ...... Frame ( 36) shift: 0.59 1.56 ...... Frame ( 37) shift: 0.67 1.65 ...... Frame ( 38) shift: 0.75 1.73 ...... Frame ( 39) shift: 0.84 1.82 ...... Frame ( 40) shift: 0.92 1.91 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.020793 Iteration 2 Error: 0.163987 Iteration 3 Error: 0.020777 Align patch 2 23 left Iteration 1 Error: 0.882968 Iteration 2 Error: 0.139468 Iteration 3 Error: 0.047928 Align patch 3 22 left Iteration 1 Error: 1.004394 Iteration 2 Error: 0.242093 Iteration 3 Error: 0.087752 Iteration 4 Error: 0.040676 Align patch 4 21 left Iteration 1 Error: 1.004480 Iteration 2 Error: 0.236678 Iteration 3 Error: 0.098176 Iteration 4 Error: 0.030484 Align patch 5 20 left Iteration 1 Error: 0.666003 Iteration 2 Error: 0.083008 Iteration 3 Error: 0.024046 Align patch 6 19 left Iteration 1 Error: 0.684464 Iteration 2 Error: 0.166487 Iteration 3 Error: 0.071667 Iteration 4 Error: 0.027601 Align patch 7 18 left Iteration 1 Error: 0.793121 Iteration 2 Error: 0.162013 Iteration 3 Error: 0.037103 Align patch 8 17 left Iteration 1 Error: 0.457706 Iteration 2 Error: 0.072426 Iteration 3 Error: 0.032784 Align patch 9 16 left Iteration 1 Error: 1.165236 Iteration 2 Error: 0.180452 Iteration 3 Error: 0.029622 Align patch 10 15 left Iteration 1 Error: 1.268030 Iteration 2 Error: 0.269508 Iteration 3 Error: 0.064554 Iteration 4 Error: 0.023251 Align patch 11 14 left Iteration 1 Error: 0.502639 Iteration 2 Error: 0.096137 Iteration 3 Error: 0.027976 Align patch 12 13 left Iteration 1 Error: 0.615511 Iteration 2 Error: 0.138985 Iteration 3 Error: 0.034355 Align patch 13 12 left Iteration 1 Error: 0.651876 Iteration 2 Error: 0.064597 Iteration 3 Error: 0.014192 Align patch 14 11 left Iteration 1 Error: 0.699862 Iteration 2 Error: 0.214598 Iteration 3 Error: 0.042534 Align patch 15 10 left Iteration 1 Error: 0.630152 Iteration 2 Error: 0.121458 Iteration 3 Error: 0.028163 Align patch 16 9 left Iteration 1 Error: 0.750994 Iteration 2 Error: 0.182770 Iteration 3 Error: 0.077211 Iteration 4 Error: 0.028737 Align patch 17 8 left Iteration 1 Error: 0.812153 Iteration 2 Error: 0.103256 Iteration 3 Error: 0.031598 Align patch 18 7 left Iteration 1 Error: 0.792731 Iteration 2 Error: 0.172511 Iteration 3 Error: 0.091453 Iteration 4 Error: 0.029160 Align patch 19 6 left Iteration 1 Error: 1.267960 Iteration 2 Error: 0.148353 Iteration 3 Error: 0.042119 Align patch 20 5 left Iteration 1 Error: 0.818005 Iteration 2 Error: 0.136989 Iteration 3 Error: 0.043800 Align patch 21 4 left Iteration 1 Error: 0.623460 Iteration 2 Error: 0.131489 Iteration 3 Error: 0.048130 Align patch 22 3 left Iteration 1 Error: 0.675720 Iteration 2 Error: 0.088149 Iteration 3 Error: 0.011057 Align patch 23 2 left Iteration 1 Error: 0.841797 Iteration 2 Error: 0.138183 Iteration 3 Error: 0.019431 Align patch 24 1 left Iteration 1 Error: 0.687162 Iteration 2 Error: 0.152317 Iteration 3 Error: 0.026299 Align patch 25 0 left Iteration 1 Error: 1.137376 Iteration 2 Error: 0.107423 Iteration 3 Error: 0.022373 3D Fitting completed. Patch alignment time: 19.43(sec) Local motion has been corrected. Process thread exits. Computational time: 33.705330 sec Total time: 41.624577 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00004hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00004hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.681110s Reading file: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00004hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.385657s ........................................ >>>>>>TIME<<<<<< FFT: 1.408028s Defocus_U Defocus_V Angle CCC 25437.48 26242.21 9.22 0.043010 Final Values Defocus_U Defocus_V Angle CCC 25448.41 26225.03 6.10 0.067915 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00002sq_v01_00004hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00004hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 9.998e-02 CC threshold: 0.734 Mean Std: 41.95 7.01 Num Hot pixels: 215 Hot pixel threshold: 84.04 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.806231 Iteration 2 Error: 0.773518 Iteration 3 Error: 0.285282 Iteration 4 Error: 0.115306 Iteration 5 Error: 0.049354 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.08 0.09 ...... Frame ( 3) shift: 0.15 0.18 ...... Frame ( 4) shift: 0.23 0.26 ...... Frame ( 5) shift: 0.31 0.35 ...... Frame ( 6) shift: 0.43 0.51 ...... Frame ( 7) shift: 0.61 0.72 ...... Frame ( 8) shift: 0.79 0.94 ...... Frame ( 9) shift: 0.97 1.20 ...... Frame ( 10) shift: 1.14 1.51 ...... Frame ( 11) shift: 1.31 1.81 ...... Frame ( 12) shift: 1.40 2.08 ...... Frame ( 13) shift: 1.41 2.32 ...... Frame ( 14) shift: 1.42 2.56 ...... Frame ( 15) shift: 1.44 2.77 ...... Frame ( 16) shift: 1.49 2.94 ...... Frame ( 17) shift: 1.53 3.11 ...... Frame ( 18) shift: 1.57 3.31 ...... Frame ( 19) shift: 1.58 3.53 ...... Frame ( 20) shift: 1.60 3.75 ...... Frame ( 21) shift: 1.62 3.98 ...... Frame ( 22) shift: 1.64 4.21 ...... Frame ( 23) shift: 1.65 4.45 ...... Frame ( 24) shift: 1.65 4.70 ...... Frame ( 25) shift: 1.65 4.95 ...... Frame ( 26) shift: 1.64 5.21 ...... Frame ( 27) shift: 1.63 5.43 ...... Frame ( 28) shift: 1.62 5.60 ...... Frame ( 29) shift: 1.60 5.78 ...... Frame ( 30) shift: 1.56 5.96 ...... Frame ( 31) shift: 1.47 6.16 ...... Frame ( 32) shift: 1.39 6.35 ...... Frame ( 33) shift: 1.30 6.50 ...... Frame ( 34) shift: 1.22 6.60 ...... Frame ( 35) shift: 1.13 6.70 ...... Frame ( 36) shift: 1.10 6.85 ...... Frame ( 37) shift: 1.10 7.04 ...... Frame ( 38) shift: 1.11 7.22 ...... Frame ( 39) shift: 1.11 7.41 ...... Frame ( 40) shift: 1.12 7.60 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 5.194686 Iteration 2 Error: 1.181771 Iteration 3 Error: 0.397452 Iteration 4 Error: 0.187810 Iteration 5 Error: 0.054790 Align patch 1 24 left Iteration 1 Error: 4.060979 Iteration 2 Error: 0.415619 Iteration 3 Error: 0.052027 Iteration 4 Error: 0.008937 Align patch 2 23 left Iteration 1 Error: 3.938109 Iteration 2 Error: 1.005633 Iteration 3 Error: 0.257479 Iteration 4 Error: 0.063892 Iteration 5 Error: 0.044392 Align patch 3 22 left Iteration 1 Error: 2.580123 Iteration 2 Error: 0.623933 Iteration 3 Error: 0.191792 Iteration 4 Error: 0.062501 Iteration 5 Error: 0.023469 Align patch 4 21 left Iteration 1 Error: 2.505388 Iteration 2 Error: 0.751804 Iteration 3 Error: 0.262286 Iteration 4 Error: 0.071612 Iteration 5 Error: 0.031913 Align patch 5 20 left Iteration 1 Error: 1.073616 Iteration 2 Error: 0.303502 Iteration 3 Error: 0.136713 Iteration 4 Error: 0.056591 Iteration 5 Error: 0.036866 Align patch 6 19 left Iteration 1 Error: 2.587785 Iteration 2 Error: 0.662528 Iteration 3 Error: 0.175694 Iteration 4 Error: 0.050150 Iteration 5 Error: 0.019254 Align patch 7 18 left Iteration 1 Error: 1.776599 Iteration 2 Error: 0.577795 Iteration 3 Error: 0.144405 Iteration 4 Error: 0.051308 Iteration 5 Error: 0.022844 Align patch 8 17 left Iteration 1 Error: 0.901768 Iteration 2 Error: 0.352593 Iteration 3 Error: 0.140410 Iteration 4 Error: 0.058304 Iteration 5 Error: 0.032322 Align patch 9 16 left Iteration 1 Error: 0.911607 Iteration 2 Error: 0.449523 Iteration 3 Error: 0.109344 Iteration 4 Error: 0.062846 Iteration 5 Error: 0.031897 Align patch 10 15 left Iteration 1 Error: 1.733991 Iteration 2 Error: 0.481883 Iteration 3 Error: 0.184829 Iteration 4 Error: 0.107394 Iteration 5 Error: 0.062179 Align patch 10 15 left Iteration 1 Error: 0.949156 Iteration 2 Error: 0.145963 Iteration 3 Error: 0.027844 Align patch 11 14 left Iteration 1 Error: 1.294862 Iteration 2 Error: 0.390743 Iteration 3 Error: 0.114830 Iteration 4 Error: 0.049270 Align patch 12 13 left Iteration 1 Error: 1.453139 Iteration 2 Error: 0.475566 Iteration 3 Error: 0.125465 Iteration 4 Error: 0.070594 Iteration 5 Error: 0.033085 Align patch 13 12 left Iteration 1 Error: 0.908980 Iteration 2 Error: 0.354923 Iteration 3 Error: 0.150402 Iteration 4 Error: 0.065608 Iteration 5 Error: 0.025612 Align patch 14 11 left Iteration 1 Error: 1.065270 Iteration 2 Error: 0.263442 Iteration 3 Error: 0.068514 Iteration 4 Error: 0.036318 Align patch 15 10 left Iteration 1 Error: 1.254040 Iteration 2 Error: 0.293407 Iteration 3 Error: 0.094396 Iteration 4 Error: 0.046719 Align patch 16 9 left Iteration 1 Error: 1.040213 Iteration 2 Error: 0.215770 Iteration 3 Error: 0.076997 Iteration 4 Error: 0.033412 Align patch 17 8 left Iteration 1 Error: 0.846577 Iteration 2 Error: 0.181010 Iteration 3 Error: 0.042098 Align patch 18 7 left Iteration 1 Error: 1.054497 Iteration 2 Error: 0.198818 Iteration 3 Error: 0.047179 Align patch 19 6 left Iteration 1 Error: 1.699169 Iteration 2 Error: 0.490340 Iteration 3 Error: 0.168766 Iteration 4 Error: 0.075404 Iteration 5 Error: 0.033465 Align patch 20 5 left Iteration 1 Error: 1.721751 Iteration 2 Error: 0.344933 Iteration 3 Error: 0.104599 Iteration 4 Error: 0.036544 Align patch 21 4 left Iteration 1 Error: 1.272901 Iteration 2 Error: 0.397916 Iteration 3 Error: 0.088546 Iteration 4 Error: 0.029846 Align patch 22 3 left Iteration 1 Error: 1.807693 Iteration 2 Error: 0.493445 Iteration 3 Error: 0.082816 Iteration 4 Error: 0.027418 Align patch 23 2 left Iteration 1 Error: 2.119446 Iteration 2 Error: 0.669474 Iteration 3 Error: 0.195059 Iteration 4 Error: 0.096587 Iteration 5 Error: 0.045268 Align patch 24 1 left Iteration 1 Error: 1.501335 Iteration 2 Error: 0.588844 Iteration 3 Error: 0.120846 Iteration 4 Error: 0.050346 Iteration 5 Error: 0.018704 Align patch 25 0 left Iteration 1 Error: 1.805719 Iteration 2 Error: 0.356585 Iteration 3 Error: 0.084753 Iteration 4 Error: 0.024030 3D Fitting completed. Patch alignment time: 22.51(sec) Local motion has been corrected. Process thread exits. Computational time: 38.750847 sec Total time: 47.463905 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00004hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00004hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.687328s Reading file: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00004hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.365121s ........................................ >>>>>>TIME<<<<<< FFT: 1.455630s Defocus_U Defocus_V Angle CCC 26447.29 26048.84 86.01 0.055468 Final Values Defocus_U Defocus_V Angle CCC 26441.03 26064.47 86.95 0.093833 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00002sq_v01_00004hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00004hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 41.74 6.98 Num Hot pixels: 226 Hot pixel threshold: 83.63 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.158928 Iteration 2 Error: 0.148791 Iteration 3 Error: 0.035573 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.21 -0.20 ...... Frame ( 3) shift: -0.42 -0.40 ...... Frame ( 4) shift: -0.63 -0.59 ...... Frame ( 5) shift: -0.84 -0.79 ...... Frame ( 6) shift: -0.87 -0.90 ...... Frame ( 7) shift: -0.72 -0.91 ...... Frame ( 8) shift: -0.58 -0.93 ...... Frame ( 9) shift: -0.47 -0.94 ...... Frame ( 10) shift: -0.38 -0.93 ...... Frame ( 11) shift: -0.30 -0.93 ...... Frame ( 12) shift: -0.21 -0.88 ...... Frame ( 13) shift: -0.12 -0.78 ...... Frame ( 14) shift: -0.02 -0.69 ...... Frame ( 15) shift: 0.08 -0.64 ...... Frame ( 16) shift: 0.18 -0.63 ...... Frame ( 17) shift: 0.28 -0.63 ...... Frame ( 18) shift: 0.36 -0.66 ...... Frame ( 19) shift: 0.41 -0.73 ...... Frame ( 20) shift: 0.46 -0.80 ...... Frame ( 21) shift: 0.49 -0.82 ...... Frame ( 22) shift: 0.49 -0.79 ...... Frame ( 23) shift: 0.50 -0.75 ...... Frame ( 24) shift: 0.52 -0.71 ...... Frame ( 25) shift: 0.56 -0.68 ...... Frame ( 26) shift: 0.61 -0.64 ...... Frame ( 27) shift: 0.65 -0.62 ...... Frame ( 28) shift: 0.70 -0.61 ...... Frame ( 29) shift: 0.75 -0.59 ...... Frame ( 30) shift: 0.81 -0.53 ...... Frame ( 31) shift: 0.89 -0.41 ...... Frame ( 32) shift: 0.96 -0.30 ...... Frame ( 33) shift: 1.01 -0.21 ...... Frame ( 34) shift: 1.03 -0.15 ...... Frame ( 35) shift: 1.05 -0.09 ...... Frame ( 36) shift: 1.09 -0.03 ...... Frame ( 37) shift: 1.16 0.03 ...... Frame ( 38) shift: 1.22 0.09 ...... Frame ( 39) shift: 1.29 0.15 ...... Frame ( 40) shift: 1.35 0.20 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.675904 Iteration 2 Error: 0.117465 Iteration 3 Error: 0.033585 Align patch 2 23 left Iteration 1 Error: 0.876235 Iteration 2 Error: 0.211656 Iteration 3 Error: 0.069553 Iteration 4 Error: 0.030955 Align patch 3 22 left Iteration 1 Error: 0.814329 Iteration 2 Error: 0.135492 Iteration 3 Error: 0.028869 Align patch 4 21 left Iteration 1 Error: 0.666434 Iteration 2 Error: 0.080477 Iteration 3 Error: 0.020540 Align patch 5 20 left Iteration 1 Error: 1.000073 Iteration 2 Error: 0.107834 Iteration 3 Error: 0.028256 Align patch 6 19 left Iteration 1 Error: 0.736593 Iteration 2 Error: 0.080999 Iteration 3 Error: 0.028937 Align patch 7 18 left Iteration 1 Error: 0.535716 Iteration 2 Error: 0.115483 Iteration 3 Error: 0.027775 Align patch 8 17 left Iteration 1 Error: 1.003412 Iteration 2 Error: 0.139470 Iteration 3 Error: 0.046603 Align patch 9 16 left Iteration 1 Error: 0.575879 Iteration 2 Error: 0.121565 Iteration 3 Error: 0.035532 Align patch 10 15 left Iteration 1 Error: 0.978858 Iteration 2 Error: 0.136787 Iteration 3 Error: 0.038635 Align patch 11 14 left Iteration 1 Error: 1.048770 Iteration 2 Error: 0.177258 Iteration 3 Error: 0.035194 Align patch 12 13 left Iteration 1 Error: 0.475507 Iteration 2 Error: 0.090263 Iteration 3 Error: 0.025424 Align patch 13 12 left Iteration 1 Error: 0.874294 Iteration 2 Error: 0.136934 Iteration 3 Error: 0.035954 Align patch 14 11 left Iteration 1 Error: 0.838098 Iteration 2 Error: 0.140515 Iteration 3 Error: 0.019720 Align patch 15 10 left Iteration 1 Error: 0.759159 Iteration 2 Error: 0.102893 Iteration 3 Error: 0.030055 Align patch 16 9 left Iteration 1 Error: 0.770264 Iteration 2 Error: 0.119526 Iteration 3 Error: 0.030816 Align patch 17 8 left Iteration 1 Error: 0.481943 Iteration 2 Error: 0.087781 Iteration 3 Error: 0.014770 Align patch 18 7 left Iteration 1 Error: 0.680846 Iteration 2 Error: 0.119547 Iteration 3 Error: 0.033241 Align patch 19 6 left Iteration 1 Error: 0.716085 Iteration 2 Error: 0.096361 Iteration 3 Error: 0.029150 Align patch 20 5 left Iteration 1 Error: 0.558381 Iteration 2 Error: 0.157518 Iteration 3 Error: 0.030226 Align patch 21 4 left Iteration 1 Error: 0.691063 Iteration 2 Error: 0.147439 Iteration 3 Error: 0.044220 Align patch 22 3 left Iteration 1 Error: 0.771252 Iteration 2 Error: 0.170168 Iteration 3 Error: 0.039789 Align patch 23 2 left Iteration 1 Error: 0.610172 Iteration 2 Error: 0.193480 Iteration 3 Error: 0.044843 Align patch 24 1 left Iteration 1 Error: 0.549022 Iteration 2 Error: 0.115809 Iteration 3 Error: 0.035519 Align patch 25 0 left Iteration 1 Error: 1.059497 Iteration 2 Error: 0.193585 Iteration 3 Error: 0.041270 3D Fitting completed. Patch alignment time: 13.51(sec) Local motion has been corrected. Process thread exits. Computational time: 27.804382 sec Total time: 35.561153 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00004hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00004hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.685457s Reading file: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00004hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 5.209440s ........................................ >>>>>>TIME<<<<<< FFT: 1.743935s Defocus_U Defocus_V Angle CCC 25033.21 25939.46 3.70 0.045902 Final Values Defocus_U Defocus_V Angle CCC 25033.21 25939.46 4.02 0.072548 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00002sq_v01_00004hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00004hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 42.27 7.06 Num Hot pixels: 213 Hot pixel threshold: 84.63 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.026877 Iteration 2 Error: 0.141256 Iteration 3 Error: 0.030923 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.02 0.04 ...... Frame ( 3) shift: -0.03 0.09 ...... Frame ( 4) shift: -0.05 0.13 ...... Frame ( 5) shift: -0.07 0.18 ...... Frame ( 6) shift: -0.03 0.24 ...... Frame ( 7) shift: 0.07 0.32 ...... Frame ( 8) shift: 0.16 0.40 ...... Frame ( 9) shift: 0.24 0.50 ...... Frame ( 10) shift: 0.31 0.63 ...... Frame ( 11) shift: 0.38 0.76 ...... Frame ( 12) shift: 0.43 0.87 ...... Frame ( 13) shift: 0.45 0.96 ...... Frame ( 14) shift: 0.47 1.04 ...... Frame ( 15) shift: 0.49 1.12 ...... Frame ( 16) shift: 0.51 1.19 ...... Frame ( 17) shift: 0.53 1.26 ...... Frame ( 18) shift: 0.55 1.32 ...... Frame ( 19) shift: 0.57 1.37 ...... Frame ( 20) shift: 0.59 1.41 ...... Frame ( 21) shift: 0.64 1.44 ...... Frame ( 22) shift: 0.71 1.44 ...... Frame ( 23) shift: 0.79 1.44 ...... Frame ( 24) shift: 0.83 1.44 ...... Frame ( 25) shift: 0.84 1.45 ...... Frame ( 26) shift: 0.84 1.46 ...... Frame ( 27) shift: 0.83 1.47 ...... Frame ( 28) shift: 0.80 1.47 ...... Frame ( 29) shift: 0.77 1.47 ...... Frame ( 30) shift: 0.77 1.47 ...... Frame ( 31) shift: 0.80 1.48 ...... Frame ( 32) shift: 0.83 1.49 ...... Frame ( 33) shift: 0.86 1.50 ...... Frame ( 34) shift: 0.88 1.52 ...... Frame ( 35) shift: 0.90 1.54 ...... Frame ( 36) shift: 0.90 1.57 ...... Frame ( 37) shift: 0.86 1.61 ...... Frame ( 38) shift: 0.82 1.65 ...... Frame ( 39) shift: 0.78 1.69 ...... Frame ( 40) shift: 0.74 1.73 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.067221 Iteration 2 Error: 0.162194 Iteration 3 Error: 0.025773 Align patch 2 23 left Iteration 1 Error: 0.993602 Iteration 2 Error: 0.088982 Iteration 3 Error: 0.030215 Align patch 3 22 left Iteration 1 Error: 0.404372 Iteration 2 Error: 0.048481 Align patch 4 21 left Iteration 1 Error: 0.747048 Iteration 2 Error: 0.100704 Iteration 3 Error: 0.019401 Align patch 5 20 left Iteration 1 Error: 0.656844 Iteration 2 Error: 0.098929 Iteration 3 Error: 0.025345 Align patch 6 19 left Iteration 1 Error: 0.985883 Iteration 2 Error: 0.173414 Iteration 3 Error: 0.051406 Iteration 4 Error: 0.017306 Align patch 7 18 left Iteration 1 Error: 0.762446 Iteration 2 Error: 0.162097 Iteration 3 Error: 0.044033 Align patch 8 17 left Iteration 1 Error: 0.814455 Iteration 2 Error: 0.079317 Iteration 3 Error: 0.018076 Align patch 9 16 left Iteration 1 Error: 0.658858 Iteration 2 Error: 0.088022 Iteration 3 Error: 0.017361 Align patch 10 15 left Iteration 1 Error: 0.883062 Iteration 2 Error: 0.138101 Iteration 3 Error: 0.018732 Align patch 11 14 left Iteration 1 Error: 1.112351 Iteration 2 Error: 0.102366 Iteration 3 Error: 0.033683 Align patch 12 13 left Iteration 1 Error: 0.849256 Iteration 2 Error: 0.136078 Iteration 3 Error: 0.057259 Iteration 4 Error: 0.017003 Align patch 13 12 left Iteration 1 Error: 0.550946 Iteration 2 Error: 0.079561 Iteration 3 Error: 0.020560 Align patch 14 11 left Iteration 1 Error: 0.618331 Iteration 2 Error: 0.141807 Iteration 3 Error: 0.026645 Align patch 15 10 left Iteration 1 Error: 0.802010 Iteration 2 Error: 0.143540 Iteration 3 Error: 0.035193 Align patch 16 9 left Iteration 1 Error: 0.805329 Iteration 2 Error: 0.081031 Iteration 3 Error: 0.016633 Align patch 17 8 left Iteration 1 Error: 0.689590 Iteration 2 Error: 0.088803 Iteration 3 Error: 0.020235 Align patch 18 7 left Iteration 1 Error: 0.647834 Iteration 2 Error: 0.049492 Align patch 19 6 left Iteration 1 Error: 0.460028 Iteration 2 Error: 0.060128 Iteration 3 Error: 0.014273 Align patch 20 5 left Iteration 1 Error: 0.527889 Iteration 2 Error: 0.118723 Iteration 3 Error: 0.022836 Align patch 21 4 left Iteration 1 Error: 1.009367 Iteration 2 Error: 0.122696 Iteration 3 Error: 0.024382 Align patch 22 3 left Iteration 1 Error: 0.773388 Iteration 2 Error: 0.093318 Iteration 3 Error: 0.022751 Align patch 23 2 left Iteration 1 Error: 0.478545 Iteration 2 Error: 0.039481 Align patch 24 1 left Iteration 1 Error: 1.056959 Iteration 2 Error: 0.138812 Iteration 3 Error: 0.028227 Align patch 25 0 left Iteration 1 Error: 0.706648 Iteration 2 Error: 0.078074 Iteration 3 Error: 0.017923 3D Fitting completed. Patch alignment time: 19.06(sec) Local motion has been corrected. Process thread exits. Computational time: 38.449303 sec Total time: 47.788155 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00004hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00004hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.620693s Reading file: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00004hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 4.376333s ........................................ >>>>>>TIME<<<<<< FFT: 1.459830s Defocus_U Defocus_V Angle CCC 27381.61 26731.70 81.52 0.051279 Final Values Defocus_U Defocus_V Angle CCC 27362.85 26737.95 80.89 0.080983 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00002sq_v01_00005hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00005hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.993e-02 CC threshold: 0.734 Mean Std: 40.60 6.81 Num Hot pixels: 222 Hot pixel threshold: 81.48 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.238204 Iteration 2 Error: 0.324779 Iteration 3 Error: 0.084928 Iteration 4 Error: 0.029627 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.02 -0.01 ...... Frame ( 3) shift: -0.04 -0.03 ...... Frame ( 4) shift: -0.06 -0.04 ...... Frame ( 5) shift: -0.08 -0.06 ...... Frame ( 6) shift: -0.02 0.00 ...... Frame ( 7) shift: 0.11 0.14 ...... Frame ( 8) shift: 0.24 0.27 ...... Frame ( 9) shift: 0.31 0.38 ...... Frame ( 10) shift: 0.32 0.45 ...... Frame ( 11) shift: 0.33 0.53 ...... Frame ( 12) shift: 0.33 0.63 ...... Frame ( 13) shift: 0.29 0.75 ...... Frame ( 14) shift: 0.26 0.87 ...... Frame ( 15) shift: 0.27 0.99 ...... Frame ( 16) shift: 0.32 1.09 ...... Frame ( 17) shift: 0.38 1.19 ...... Frame ( 18) shift: 0.42 1.29 ...... Frame ( 19) shift: 0.47 1.38 ...... Frame ( 20) shift: 0.51 1.47 ...... Frame ( 21) shift: 0.56 1.54 ...... Frame ( 22) shift: 0.62 1.60 ...... Frame ( 23) shift: 0.67 1.67 ...... Frame ( 24) shift: 0.71 1.75 ...... Frame ( 25) shift: 0.74 1.86 ...... Frame ( 26) shift: 0.76 1.97 ...... Frame ( 27) shift: 0.76 2.07 ...... Frame ( 28) shift: 0.75 2.16 ...... Frame ( 29) shift: 0.74 2.25 ...... Frame ( 30) shift: 0.76 2.30 ...... Frame ( 31) shift: 0.80 2.30 ...... Frame ( 32) shift: 0.84 2.31 ...... Frame ( 33) shift: 0.90 2.34 ...... Frame ( 34) shift: 0.99 2.40 ...... Frame ( 35) shift: 1.08 2.46 ...... Frame ( 36) shift: 1.12 2.52 ...... Frame ( 37) shift: 1.10 2.60 ...... Frame ( 38) shift: 1.09 2.68 ...... Frame ( 39) shift: 1.07 2.76 ...... Frame ( 40) shift: 1.06 2.83 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.905909 Iteration 2 Error: 0.140481 Iteration 3 Error: 0.069204 Iteration 4 Error: 0.030749 Align patch 2 23 left Iteration 1 Error: 1.200704 Iteration 2 Error: 0.235589 Iteration 3 Error: 0.103844 Iteration 4 Error: 0.046231 Align patch 3 22 left Iteration 1 Error: 0.683645 Iteration 2 Error: 0.236345 Iteration 3 Error: 0.096381 Iteration 4 Error: 0.046043 Align patch 4 21 left Iteration 1 Error: 0.627047 Iteration 2 Error: 0.133862 Iteration 3 Error: 0.035665 Align patch 5 20 left Iteration 1 Error: 0.677804 Iteration 2 Error: 0.134687 Iteration 3 Error: 0.049638 Align patch 6 19 left Iteration 1 Error: 0.737326 Iteration 2 Error: 0.134227 Iteration 3 Error: 0.052924 Iteration 4 Error: 0.021598 Align patch 7 18 left Iteration 1 Error: 0.795607 Iteration 2 Error: 0.207018 Iteration 3 Error: 0.084379 Iteration 4 Error: 0.040704 Align patch 8 17 left Iteration 1 Error: 0.651663 Iteration 2 Error: 0.222064 Iteration 3 Error: 0.087291 Iteration 4 Error: 0.042283 Align patch 9 16 left Iteration 1 Error: 0.921001 Iteration 2 Error: 0.159542 Iteration 3 Error: 0.059152 Iteration 4 Error: 0.020408 Align patch 10 15 left Iteration 1 Error: 0.807354 Iteration 2 Error: 0.146211 Iteration 3 Error: 0.046449 Align patch 11 14 left Iteration 1 Error: 1.405386 Iteration 2 Error: 0.231765 Iteration 3 Error: 0.043085 Align patch 12 13 left Iteration 1 Error: 0.769440 Iteration 2 Error: 0.124989 Iteration 3 Error: 0.074546 Iteration 4 Error: 0.022230 Align patch 13 12 left Iteration 1 Error: 1.036541 Iteration 2 Error: 0.175221 Iteration 3 Error: 0.076586 Iteration 4 Error: 0.040984 Align patch 14 11 left Iteration 1 Error: 0.695123 Iteration 2 Error: 0.143619 Iteration 3 Error: 0.065738 Iteration 4 Error: 0.019252 Align patch 15 10 left Iteration 1 Error: 0.547606 Iteration 2 Error: 0.106735 Iteration 3 Error: 0.034556 Align patch 16 9 left Iteration 1 Error: 0.823864 Iteration 2 Error: 0.150282 Iteration 3 Error: 0.028284 Align patch 17 8 left Iteration 1 Error: 1.233218 Iteration 2 Error: 0.215942 Iteration 3 Error: 0.063552 Iteration 4 Error: 0.029228 Align patch 18 7 left Iteration 1 Error: 0.934701 Iteration 2 Error: 0.221461 Iteration 3 Error: 0.046546 Align patch 19 6 left Iteration 1 Error: 0.869052 Iteration 2 Error: 0.149697 Iteration 3 Error: 0.029135 Align patch 20 5 left Iteration 1 Error: 1.065275 Iteration 2 Error: 0.195777 Iteration 3 Error: 0.069206 Iteration 4 Error: 0.041857 Align patch 21 4 left Iteration 1 Error: 0.668198 Iteration 2 Error: 0.146645 Iteration 3 Error: 0.053664 Iteration 4 Error: 0.024261 Align patch 22 3 left Iteration 1 Error: 0.770823 Iteration 2 Error: 0.158995 Iteration 3 Error: 0.038421 Align patch 23 2 left Iteration 1 Error: 0.779891 Iteration 2 Error: 0.114873 Iteration 3 Error: 0.054654 Iteration 4 Error: 0.022771 Align patch 24 1 left Iteration 1 Error: 1.198888 Iteration 2 Error: 0.181806 Iteration 3 Error: 0.094393 Iteration 4 Error: 0.020714 Align patch 25 0 left Iteration 1 Error: 1.248850 Iteration 2 Error: 0.183278 Iteration 3 Error: 0.071980 Iteration 4 Error: 0.017806 3D Fitting completed. Patch alignment time: 14.96(sec) Local motion has been corrected. Process thread exits. Computational time: 26.899462 sec Total time: 34.891968 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00005hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00005hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.556893s Reading file: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00005hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 5.111988s ........................................ >>>>>>TIME<<<<<< FFT: 1.719736s Defocus_U Defocus_V Angle CCC 27599.86 26834.04 79.67 0.031732 Final Values Defocus_U Defocus_V Angle CCC 27595.17 26823.10 79.67 0.048953 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00002sq_v01_00005hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00005hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.995e-02 CC threshold: 0.734 Mean Std: 38.08 6.60 Num Hot pixels: 215 Hot pixel threshold: 77.68 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.504900 Iteration 2 Error: 0.084216 Iteration 3 Error: 0.016176 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.02 -0.08 ...... Frame ( 3) shift: -0.05 -0.16 ...... Frame ( 4) shift: -0.07 -0.24 ...... Frame ( 5) shift: -0.09 -0.32 ...... Frame ( 6) shift: -0.12 -0.34 ...... Frame ( 7) shift: -0.15 -0.28 ...... Frame ( 8) shift: -0.18 -0.23 ...... Frame ( 9) shift: -0.21 -0.20 ...... Frame ( 10) shift: -0.25 -0.20 ...... Frame ( 11) shift: -0.29 -0.20 ...... Frame ( 12) shift: -0.29 -0.15 ...... Frame ( 13) shift: -0.24 -0.06 ...... Frame ( 14) shift: -0.19 0.03 ...... Frame ( 15) shift: -0.14 0.08 ...... Frame ( 16) shift: -0.11 0.10 ...... Frame ( 17) shift: -0.07 0.11 ...... Frame ( 18) shift: -0.06 0.13 ...... Frame ( 19) shift: -0.09 0.16 ...... Frame ( 20) shift: -0.11 0.19 ...... Frame ( 21) shift: -0.14 0.23 ...... Frame ( 22) shift: -0.18 0.27 ...... Frame ( 23) shift: -0.22 0.32 ...... Frame ( 24) shift: -0.23 0.34 ...... Frame ( 25) shift: -0.21 0.33 ...... Frame ( 26) shift: -0.18 0.32 ...... Frame ( 27) shift: -0.16 0.37 ...... Frame ( 28) shift: -0.14 0.48 ...... Frame ( 29) shift: -0.11 0.59 ...... Frame ( 30) shift: -0.11 0.63 ...... Frame ( 31) shift: -0.14 0.60 ...... Frame ( 32) shift: -0.16 0.58 ...... Frame ( 33) shift: -0.20 0.57 ...... Frame ( 34) shift: -0.27 0.58 ...... Frame ( 35) shift: -0.34 0.59 ...... Frame ( 36) shift: -0.37 0.60 ...... Frame ( 37) shift: -0.36 0.63 ...... Frame ( 38) shift: -0.34 0.65 ...... Frame ( 39) shift: -0.33 0.67 ...... Frame ( 40) shift: -0.32 0.70 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.915181 Iteration 2 Error: 0.191073 Iteration 3 Error: 0.032296 Align patch 2 23 left Iteration 1 Error: 0.943888 Iteration 2 Error: 0.168609 Iteration 3 Error: 0.039433 Align patch 3 22 left Iteration 1 Error: 0.819970 Iteration 2 Error: 0.139280 Iteration 3 Error: 0.028307 Align patch 4 21 left Iteration 1 Error: 0.757379 Iteration 2 Error: 0.108374 Iteration 3 Error: 0.035374 Align patch 5 20 left Iteration 1 Error: 0.618069 Iteration 2 Error: 0.099586 Iteration 3 Error: 0.019973 Align patch 6 19 left Iteration 1 Error: 0.595192 Iteration 2 Error: 0.130039 Iteration 3 Error: 0.029727 Align patch 7 18 left Iteration 1 Error: 0.934728 Iteration 2 Error: 0.124081 Iteration 3 Error: 0.037814 Align patch 8 17 left Iteration 1 Error: 0.852733 Iteration 2 Error: 0.142580 Iteration 3 Error: 0.019345 Align patch 9 16 left Iteration 1 Error: 0.986282 Iteration 2 Error: 0.152470 Iteration 3 Error: 0.036316 Align patch 10 15 left Iteration 1 Error: 0.826549 Iteration 2 Error: 0.151837 Iteration 3 Error: 0.043624 Align patch 11 14 left Iteration 1 Error: 0.971433 Iteration 2 Error: 0.155881 Iteration 3 Error: 0.035990 Align patch 12 13 left Iteration 1 Error: 0.622487 Iteration 2 Error: 0.115546 Iteration 3 Error: 0.049683 Align patch 13 12 left Iteration 1 Error: 0.841213 Iteration 2 Error: 0.136228 Iteration 3 Error: 0.026759 Align patch 14 11 left Iteration 1 Error: 0.903481 Iteration 2 Error: 0.098407 Iteration 3 Error: 0.024875 Align patch 15 10 left Iteration 1 Error: 0.522774 Iteration 2 Error: 0.090605 Iteration 3 Error: 0.022275 Align patch 16 9 left Iteration 1 Error: 0.752255 Iteration 2 Error: 0.159358 Iteration 3 Error: 0.073700 Iteration 4 Error: 0.021293 Align patch 17 8 left Iteration 1 Error: 0.940853 Iteration 2 Error: 0.194542 Iteration 3 Error: 0.033274 Align patch 18 7 left Iteration 1 Error: 0.610423 Iteration 2 Error: 0.063331 Iteration 3 Error: 0.009459 Align patch 19 6 left Iteration 1 Error: 0.709637 Iteration 2 Error: 0.208463 Iteration 3 Error: 0.060139 Iteration 4 Error: 0.023177 Align patch 20 5 left Iteration 1 Error: 0.988703 Iteration 2 Error: 0.237521 Iteration 3 Error: 0.070006 Iteration 4 Error: 0.026984 Align patch 21 4 left Iteration 1 Error: 0.623366 Iteration 2 Error: 0.107272 Iteration 3 Error: 0.026863 Align patch 22 3 left Iteration 1 Error: 0.905722 Iteration 2 Error: 0.182028 Iteration 3 Error: 0.043125 Align patch 23 2 left Iteration 1 Error: 0.887852 Iteration 2 Error: 0.101997 Iteration 3 Error: 0.030544 Align patch 24 1 left Iteration 1 Error: 1.014459 Iteration 2 Error: 0.198508 Iteration 3 Error: 0.050214 Iteration 4 Error: 0.011022 Align patch 25 0 left Iteration 1 Error: 0.588763 Iteration 2 Error: 0.082695 Iteration 3 Error: 0.026194 3D Fitting completed. Patch alignment time: 18.18(sec) Local motion has been corrected. Process thread exits. Computational time: 39.321651 sec Total time: 48.018005 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00005hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00005hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.374907s Reading file: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00005hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.593328s ........................................ >>>>>>TIME<<<<<< FFT: 1.428757s Defocus_U Defocus_V Angle CCC 23963.50 23403.04 86.94 0.024149 Final Values Defocus_U Defocus_V Angle CCC 24049.50 23523.45 89.14 0.033890 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00002sq_v01_00006hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00006hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.338e-01 9.959e-02 CC threshold: 0.731 Mean Std: 41.41 7.04 Num Hot pixels: 193 Hot pixel threshold: 83.62 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.272306 Iteration 2 Error: 0.392473 Iteration 3 Error: 0.120209 Iteration 4 Error: 0.046539 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.29 -0.10 ...... Frame ( 3) shift: -0.58 -0.19 ...... Frame ( 4) shift: -0.87 -0.29 ...... Frame ( 5) shift: -1.16 -0.38 ...... Frame ( 6) shift: -1.36 -0.36 ...... Frame ( 7) shift: -1.48 -0.22 ...... Frame ( 8) shift: -1.60 -0.08 ...... Frame ( 9) shift: -1.70 0.05 ...... Frame ( 10) shift: -1.79 0.16 ...... Frame ( 11) shift: -1.88 0.28 ...... Frame ( 12) shift: -1.94 0.40 ...... Frame ( 13) shift: -1.96 0.54 ...... Frame ( 14) shift: -1.98 0.68 ...... Frame ( 15) shift: -1.95 0.80 ...... Frame ( 16) shift: -1.87 0.91 ...... Frame ( 17) shift: -1.80 1.02 ...... Frame ( 18) shift: -1.72 1.12 ...... Frame ( 19) shift: -1.64 1.19 ...... Frame ( 20) shift: -1.56 1.26 ...... Frame ( 21) shift: -1.46 1.36 ...... Frame ( 22) shift: -1.35 1.50 ...... Frame ( 23) shift: -1.24 1.63 ...... Frame ( 24) shift: -1.20 1.77 ...... Frame ( 25) shift: -1.22 1.91 ...... Frame ( 26) shift: -1.25 2.06 ...... Frame ( 27) shift: -1.26 2.21 ...... Frame ( 28) shift: -1.26 2.37 ...... Frame ( 29) shift: -1.25 2.53 ...... Frame ( 30) shift: -1.21 2.66 ...... Frame ( 31) shift: -1.13 2.77 ...... Frame ( 32) shift: -1.05 2.87 ...... Frame ( 33) shift: -0.96 3.00 ...... Frame ( 34) shift: -0.86 3.14 ...... Frame ( 35) shift: -0.75 3.28 ...... Frame ( 36) shift: -0.67 3.45 ...... Frame ( 37) shift: -0.60 3.63 ...... Frame ( 38) shift: -0.53 3.82 ...... Frame ( 39) shift: -0.47 4.01 ...... Frame ( 40) shift: -0.40 4.20 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 3.224394 Iteration 2 Error: 1.140079 Iteration 3 Error: 0.314731 Iteration 4 Error: 0.111337 Iteration 5 Error: 0.051662 Align patch 1 24 left Iteration 1 Error: 2.781323 Iteration 2 Error: 0.363312 Iteration 3 Error: 0.074713 Iteration 4 Error: 0.029854 Align patch 2 23 left Iteration 1 Error: 1.363379 Iteration 2 Error: 0.328997 Iteration 3 Error: 0.101953 Iteration 4 Error: 0.040110 Align patch 3 22 left Iteration 1 Error: 0.522656 Iteration 2 Error: 0.056235 Iteration 3 Error: 0.015290 Align patch 4 21 left Iteration 1 Error: 1.530702 Iteration 2 Error: 0.189411 Iteration 3 Error: 0.037315 Align patch 5 20 left Iteration 1 Error: 1.319166 Iteration 2 Error: 0.224138 Iteration 3 Error: 0.027111 Align patch 6 19 left Iteration 1 Error: 2.012115 Iteration 2 Error: 1.074871 Iteration 3 Error: 0.695118 Iteration 4 Error: 0.295559 Iteration 5 Error: 0.154818 Align patch 6 19 left Iteration 1 Error: 3.017807 Iteration 2 Error: 0.492370 Iteration 3 Error: 0.105036 Iteration 4 Error: 0.033073 Align patch 7 18 left Iteration 1 Error: 2.506740 Iteration 2 Error: 0.674186 Iteration 3 Error: 0.192080 Iteration 4 Error: 0.089054 Iteration 5 Error: 0.026861 Align patch 8 17 left Iteration 1 Error: 0.667413 Iteration 2 Error: 0.092955 Iteration 3 Error: 0.021825 Align patch 9 16 left Iteration 1 Error: 1.328942 Iteration 2 Error: 0.203033 Iteration 3 Error: 0.047226 Align patch 10 15 left Iteration 1 Error: 1.500770 Iteration 2 Error: 0.239322 Iteration 3 Error: 0.033603 Align patch 11 14 left Iteration 1 Error: 2.685822 Iteration 2 Error: 1.435358 Iteration 3 Error: 0.636034 Iteration 4 Error: 0.250402 Iteration 5 Error: 0.115117 Align patch 11 14 left Iteration 1 Error: 2.712532 Iteration 2 Error: 0.602053 Iteration 3 Error: 0.149274 Iteration 4 Error: 0.040914 Align patch 12 13 left Iteration 1 Error: 1.623692 Iteration 2 Error: 0.671970 Iteration 3 Error: 0.296580 Iteration 4 Error: 0.139246 Iteration 5 Error: 0.067694 Align patch 12 13 left Iteration 1 Error: 2.103014 Iteration 2 Error: 0.363713 Iteration 3 Error: 0.056524 Iteration 4 Error: 0.018162 Align patch 13 12 left Iteration 1 Error: 0.752431 Iteration 2 Error: 0.246517 Iteration 3 Error: 0.053824 Iteration 4 Error: 0.028472 Align patch 14 11 left Iteration 1 Error: 0.881614 Iteration 2 Error: 0.201108 Iteration 3 Error: 0.035073 Align patch 15 10 left Iteration 1 Error: 1.168349 Iteration 2 Error: 0.241057 Iteration 3 Error: 0.059399 Iteration 4 Error: 0.017146 Align patch 16 9 left Iteration 1 Error: 2.163608 Iteration 2 Error: 0.904930 Iteration 3 Error: 0.460609 Iteration 4 Error: 0.187385 Iteration 5 Error: 0.094755 Align patch 16 9 left Iteration 1 Error: 2.433235 Iteration 2 Error: 0.474733 Iteration 3 Error: 0.072246 Iteration 4 Error: 0.024391 Align patch 17 8 left Iteration 1 Error: 1.554595 Iteration 2 Error: 0.375332 Iteration 3 Error: 0.189197 Iteration 4 Error: 0.076463 Iteration 5 Error: 0.024977 Align patch 18 7 left Iteration 1 Error: 0.610736 Iteration 2 Error: 0.111416 Iteration 3 Error: 0.023639 Align patch 19 6 left Iteration 1 Error: 1.144885 Iteration 2 Error: 0.191814 Iteration 3 Error: 0.033414 Align patch 20 5 left Iteration 1 Error: 2.083916 Iteration 2 Error: 0.216934 Iteration 3 Error: 0.046208 Align patch 21 4 left Iteration 1 Error: 2.033622 Iteration 2 Error: 0.822700 Iteration 3 Error: 0.307155 Iteration 4 Error: 0.176167 Iteration 5 Error: 0.072651 Align patch 21 4 left Iteration 1 Error: 1.967277 Iteration 2 Error: 0.327709 Iteration 3 Error: 0.056630 Iteration 4 Error: 0.013924 Align patch 22 3 left Iteration 1 Error: 0.810880 Iteration 2 Error: 0.275086 Iteration 3 Error: 0.094247 Iteration 4 Error: 0.033281 Align patch 23 2 left Iteration 1 Error: 0.686606 Iteration 2 Error: 0.071264 Iteration 3 Error: 0.023048 Align patch 24 1 left Iteration 1 Error: 0.778320 Iteration 2 Error: 0.161667 Iteration 3 Error: 0.036419 Align patch 25 0 left Iteration 1 Error: 1.391157 Iteration 2 Error: 0.220542 Iteration 3 Error: 0.054402 Iteration 4 Error: 0.011965 3D Fitting completed. Patch alignment time: 28.19(sec) Local motion has been corrected. Process thread exits. Computational time: 43.659866 sec Total time: 52.250221 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00006hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00006hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.592844s Reading file: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00006hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.775445s ........................................ >>>>>>TIME<<<<<< FFT: 1.714657s Defocus_U Defocus_V Angle CCC 12968.75 13804.69 12.48 0.038120 Final Values Defocus_U Defocus_V Angle CCC 12957.81 13815.63 11.54 0.013759 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00002sq_v01_00006hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00006hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.003e-01 CC threshold: 0.736 Mean Std: 39.42 6.93 Num Hot pixels: 198 Hot pixel threshold: 81.00 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 5.027931 Iteration 2 Error: 0.750760 Iteration 3 Error: 0.371620 Iteration 4 Error: 0.189950 Iteration 5 Error: 0.102151 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.80 -0.34 ...... Frame ( 3) shift: 1.59 -0.67 ...... Frame ( 4) shift: 2.39 -1.01 ...... Frame ( 5) shift: 3.18 -1.35 ...... Frame ( 6) shift: 3.91 -1.61 ...... Frame ( 7) shift: 4.57 -1.80 ...... Frame ( 8) shift: 5.23 -2.00 ...... Frame ( 9) shift: 5.71 -2.16 ...... Frame ( 10) shift: 6.01 -2.31 ...... Frame ( 11) shift: 6.32 -2.45 ...... Frame ( 12) shift: 6.56 -2.54 ...... Frame ( 13) shift: 6.73 -2.59 ...... Frame ( 14) shift: 6.91 -2.63 ...... Frame ( 15) shift: 7.05 -2.65 ...... Frame ( 16) shift: 7.16 -2.65 ...... Frame ( 17) shift: 7.26 -2.65 ...... Frame ( 18) shift: 7.32 -2.63 ...... Frame ( 19) shift: 7.33 -2.60 ...... Frame ( 20) shift: 7.35 -2.57 ...... Frame ( 21) shift: 7.40 -2.56 ...... Frame ( 22) shift: 7.50 -2.56 ...... Frame ( 23) shift: 7.60 -2.56 ...... Frame ( 24) shift: 7.67 -2.56 ...... Frame ( 25) shift: 7.71 -2.58 ...... Frame ( 26) shift: 7.75 -2.59 ...... Frame ( 27) shift: 7.79 -2.57 ...... Frame ( 28) shift: 7.84 -2.54 ...... Frame ( 29) shift: 7.89 -2.50 ...... Frame ( 30) shift: 7.92 -2.50 ...... Frame ( 31) shift: 7.94 -2.55 ...... Frame ( 32) shift: 7.97 -2.59 ...... Frame ( 33) shift: 8.02 -2.61 ...... Frame ( 34) shift: 8.10 -2.59 ...... Frame ( 35) shift: 8.18 -2.58 ...... Frame ( 36) shift: 8.23 -2.58 ...... Frame ( 37) shift: 8.27 -2.59 ...... Frame ( 38) shift: 8.30 -2.61 ...... Frame ( 39) shift: 8.33 -2.62 ...... Frame ( 40) shift: 8.37 -2.63 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 3.466171 Iteration 2 Error: 1.028930 Iteration 3 Error: 0.346287 Iteration 4 Error: 0.118829 Iteration 5 Error: 0.034271 Align patch 2 23 left Iteration 1 Error: 4.007798 Iteration 2 Error: 1.813113 Iteration 3 Error: 0.621918 Iteration 4 Error: 0.223917 Iteration 5 Error: 0.120806 Align patch 2 23 left Iteration 1 Error: 3.260192 Iteration 2 Error: 0.702627 Iteration 3 Error: 0.192614 Iteration 4 Error: 0.076353 Iteration 5 Error: 0.026786 Align patch 3 22 left Iteration 1 Error: 5.560595 Iteration 2 Error: 3.728759 Iteration 3 Error: 1.192650 Iteration 4 Error: 0.670688 Iteration 5 Error: 0.318084 Align patch 3 22 left Iteration 1 Error: 4.364759 Iteration 2 Error: 1.650574 Iteration 3 Error: 1.021803 Iteration 4 Error: 0.658089 Iteration 5 Error: 0.393150 Align patch 4 21 left Iteration 1 Error: 6.905645 Iteration 2 Error: 4.684638 Iteration 3 Error: 2.307313 Iteration 4 Error: 1.824247 Iteration 5 Error: 0.859571 Align patch 4 21 left Iteration 1 Error: 5.650197 Iteration 2 Error: 3.330007 Iteration 3 Error: 1.252157 Iteration 4 Error: 0.846275 Iteration 5 Error: 0.670381 Align patch 5 20 left Iteration 1 Error: 4.982876 Iteration 2 Error: 3.836376 Iteration 3 Error: 3.121556 Iteration 4 Error: 2.336562 Iteration 5 Error: 2.161678 Align patch 5 20 left Iteration 1 Error: 5.747103 Iteration 2 Error: 3.265702 Iteration 3 Error: 1.235073 Iteration 4 Error: 0.880252 Iteration 5 Error: 0.731495 Align patch 6 19 left Iteration 1 Error: 1.677696 Iteration 2 Error: 0.283020 Iteration 3 Error: 0.084916 Iteration 4 Error: 0.025883 Align patch 7 18 left Iteration 1 Error: 1.683657 Iteration 2 Error: 0.251998 Iteration 3 Error: 0.062853 Iteration 4 Error: 0.018360 Align patch 8 17 left Iteration 1 Error: 2.175389 Iteration 2 Error: 0.558848 Iteration 3 Error: 0.158078 Iteration 4 Error: 0.082833 Iteration 5 Error: 0.028301 Align patch 9 16 left Iteration 1 Error: 3.404600 Iteration 2 Error: 0.887152 Iteration 3 Error: 0.461651 Iteration 4 Error: 0.429941 Iteration 5 Error: 0.254407 Align patch 9 16 left Iteration 1 Error: 2.986902 Iteration 2 Error: 0.703138 Iteration 3 Error: 0.342573 Iteration 4 Error: 0.261905 Iteration 5 Error: 0.174700 Align patch 10 15 left Iteration 1 Error: 4.454939 Iteration 2 Error: 1.825759 Iteration 3 Error: 1.451393 Iteration 4 Error: 1.116014 Iteration 5 Error: 0.911058 Align patch 10 15 left Iteration 1 Error: 3.297475 Iteration 2 Error: 0.748599 Iteration 3 Error: 0.613749 Iteration 4 Error: 0.295933 Iteration 5 Error: 0.233038 Align patch 11 14 left Iteration 1 Error: 1.628415 Iteration 2 Error: 0.369951 Iteration 3 Error: 0.091520 Iteration 4 Error: 0.021940 Align patch 12 13 left Iteration 1 Error: 2.029608 Iteration 2 Error: 0.349760 Iteration 3 Error: 0.114051 Iteration 4 Error: 0.036595 Align patch 13 12 left Iteration 1 Error: 3.906491 Iteration 2 Error: 1.020707 Iteration 3 Error: 0.285640 Iteration 4 Error: 0.108994 Iteration 5 Error: 0.044231 Align patch 14 11 left Iteration 1 Error: 2.487923 Iteration 2 Error: 1.333741 Iteration 3 Error: 0.897847 Iteration 4 Error: 0.731073 Iteration 5 Error: 0.606659 Align patch 14 11 left Iteration 1 Error: 2.266608 Iteration 2 Error: 1.024866 Iteration 3 Error: 0.625882 Iteration 4 Error: 0.452721 Iteration 5 Error: 0.298160 Align patch 15 10 left Iteration 1 Error: 5.376153 Iteration 2 Error: 2.848780 Iteration 3 Error: 2.420682 Iteration 4 Error: 1.380633 Iteration 5 Error: 0.718252 Align patch 15 10 left Iteration 1 Error: 3.497902 Iteration 2 Error: 1.463459 Iteration 3 Error: 1.316317 Iteration 4 Error: 1.097918 Iteration 5 Error: 0.861516 Align patch 16 9 left Iteration 1 Error: 1.630163 Iteration 2 Error: 0.160855 Iteration 3 Error: 0.039881 Align patch 17 8 left Iteration 1 Error: 2.575874 Iteration 2 Error: 0.549809 Iteration 3 Error: 0.104072 Iteration 4 Error: 0.027698 Align patch 18 7 left Iteration 1 Error: 2.065762 Iteration 2 Error: 0.357954 Iteration 3 Error: 0.121942 Iteration 4 Error: 0.040044 Align patch 19 6 left Iteration 1 Error: 2.236040 Iteration 2 Error: 0.477753 Iteration 3 Error: 0.271214 Iteration 4 Error: 0.126756 Iteration 5 Error: 0.074866 Align patch 19 6 left Iteration 1 Error: 2.567288 Iteration 2 Error: 0.527519 Iteration 3 Error: 0.270038 Iteration 4 Error: 0.144139 Iteration 5 Error: 0.076173 Align patch 20 5 left Iteration 1 Error: 5.838250 Iteration 2 Error: 3.921404 Iteration 3 Error: 2.395832 Iteration 4 Error: 1.657100 Iteration 5 Error: 1.139900 Align patch 20 5 left Iteration 1 Error: 5.146908 Iteration 2 Error: 1.995255 Iteration 3 Error: 1.340969 Iteration 4 Error: 0.902161 Iteration 5 Error: 0.610779 Align patch 21 4 left Iteration 1 Error: 1.007001 Iteration 2 Error: 0.203140 Iteration 3 Error: 0.039053 Align patch 22 3 left Iteration 1 Error: 1.756650 Iteration 2 Error: 0.408047 Iteration 3 Error: 0.104437 Iteration 4 Error: 0.047214 Align patch 23 2 left Iteration 1 Error: 1.362578 Iteration 2 Error: 0.168366 Iteration 3 Error: 0.030786 Align patch 24 1 left Iteration 1 Error: 1.814776 Iteration 2 Error: 0.384943 Iteration 3 Error: 0.158595 Iteration 4 Error: 0.061278 Iteration 5 Error: 0.027705 Align patch 25 0 left Iteration 1 Error: 3.481972 Iteration 2 Error: 1.317168 Iteration 3 Error: 0.393350 Iteration 4 Error: 0.136428 Iteration 5 Error: 0.048612 3D Fitting completed. Patch alignment time: 31.65(sec) Local motion has been corrected. Process thread exits. Computational time: 44.903378 sec Total time: 52.802589 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00006hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00006hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.563802s Reading file: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00006hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.315611s ........................................ >>>>>>TIME<<<<<< FFT: 1.395485s Defocus_U Defocus_V Angle CCC 13457.04 13910.17 4.47 0.076256 Final Values Defocus_U Defocus_V Angle CCC 13460.17 13913.29 5.10 0.126997 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00002sq_v01_00006hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00006hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.995e-02 CC threshold: 0.734 Mean Std: 43.10 7.09 Num Hot pixels: 233 Hot pixel threshold: 85.63 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.945377 Iteration 2 Error: 0.151271 Iteration 3 Error: 0.027263 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.11 -0.19 ...... Frame ( 3) shift: -0.22 -0.37 ...... Frame ( 4) shift: -0.33 -0.56 ...... Frame ( 5) shift: -0.44 -0.75 ...... Frame ( 6) shift: -0.50 -0.86 ...... Frame ( 7) shift: -0.49 -0.91 ...... Frame ( 8) shift: -0.49 -0.96 ...... Frame ( 9) shift: -0.48 -0.92 ...... Frame ( 10) shift: -0.46 -0.79 ...... Frame ( 11) shift: -0.45 -0.66 ...... Frame ( 12) shift: -0.43 -0.57 ...... Frame ( 13) shift: -0.40 -0.52 ...... Frame ( 14) shift: -0.37 -0.47 ...... Frame ( 15) shift: -0.36 -0.36 ...... Frame ( 16) shift: -0.37 -0.18 ...... Frame ( 17) shift: -0.38 -0.00 ...... Frame ( 18) shift: -0.41 0.14 ...... Frame ( 19) shift: -0.44 0.24 ...... Frame ( 20) shift: -0.48 0.34 ...... Frame ( 21) shift: -0.51 0.40 ...... Frame ( 22) shift: -0.51 0.44 ...... Frame ( 23) shift: -0.52 0.47 ...... Frame ( 24) shift: -0.54 0.49 ...... Frame ( 25) shift: -0.58 0.51 ...... Frame ( 26) shift: -0.61 0.53 ...... Frame ( 27) shift: -0.62 0.55 ...... Frame ( 28) shift: -0.60 0.59 ...... Frame ( 29) shift: -0.58 0.62 ...... Frame ( 30) shift: -0.61 0.65 ...... Frame ( 31) shift: -0.69 0.67 ...... Frame ( 32) shift: -0.77 0.69 ...... Frame ( 33) shift: -0.81 0.68 ...... Frame ( 34) shift: -0.79 0.65 ...... Frame ( 35) shift: -0.78 0.61 ...... Frame ( 36) shift: -0.73 0.63 ...... Frame ( 37) shift: -0.66 0.70 ...... Frame ( 38) shift: -0.58 0.78 ...... Frame ( 39) shift: -0.51 0.85 ...... Frame ( 40) shift: -0.43 0.92 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.858849 Iteration 2 Error: 0.082712 Iteration 3 Error: 0.021322 Align patch 2 23 left Iteration 1 Error: 0.844339 Iteration 2 Error: 0.137971 Iteration 3 Error: 0.055617 Iteration 4 Error: 0.023969 Align patch 3 22 left Iteration 1 Error: 0.807275 Iteration 2 Error: 0.126320 Iteration 3 Error: 0.028468 Align patch 4 21 left Iteration 1 Error: 0.909831 Iteration 2 Error: 0.213917 Iteration 3 Error: 0.048503 Align patch 5 20 left Iteration 1 Error: 1.091619 Iteration 2 Error: 0.239301 Iteration 3 Error: 0.057598 Iteration 4 Error: 0.027593 Align patch 6 19 left Iteration 1 Error: 1.357763 Iteration 2 Error: 0.117542 Iteration 3 Error: 0.029334 Align patch 7 18 left Iteration 1 Error: 0.857284 Iteration 2 Error: 0.203535 Iteration 3 Error: 0.034139 Align patch 8 17 left Iteration 1 Error: 0.783683 Iteration 2 Error: 0.148558 Iteration 3 Error: 0.026350 Align patch 9 16 left Iteration 1 Error: 0.643888 Iteration 2 Error: 0.094984 Iteration 3 Error: 0.025509 Align patch 10 15 left Iteration 1 Error: 0.425917 Iteration 2 Error: 0.078509 Iteration 3 Error: 0.014449 Align patch 11 14 left Iteration 1 Error: 1.104848 Iteration 2 Error: 0.164511 Iteration 3 Error: 0.043642 Align patch 12 13 left Iteration 1 Error: 1.001176 Iteration 2 Error: 0.177197 Iteration 3 Error: 0.074691 Iteration 4 Error: 0.022639 Align patch 13 12 left Iteration 1 Error: 0.729144 Iteration 2 Error: 0.102901 Iteration 3 Error: 0.023153 Align patch 14 11 left Iteration 1 Error: 0.901513 Iteration 2 Error: 0.176746 Iteration 3 Error: 0.038297 Align patch 15 10 left Iteration 1 Error: 1.070157 Iteration 2 Error: 0.111042 Iteration 3 Error: 0.024071 Align patch 16 9 left Iteration 1 Error: 0.647636 Iteration 2 Error: 0.120756 Iteration 3 Error: 0.023667 Align patch 17 8 left Iteration 1 Error: 0.706204 Iteration 2 Error: 0.128489 Iteration 3 Error: 0.022628 Align patch 18 7 left Iteration 1 Error: 0.744080 Iteration 2 Error: 0.085556 Iteration 3 Error: 0.014218 Align patch 19 6 left Iteration 1 Error: 1.233623 Iteration 2 Error: 0.134432 Iteration 3 Error: 0.047269 Align patch 20 5 left Iteration 1 Error: 0.799101 Iteration 2 Error: 0.136922 Iteration 3 Error: 0.028432 Align patch 21 4 left Iteration 1 Error: 0.757851 Iteration 2 Error: 0.143836 Iteration 3 Error: 0.032017 Align patch 22 3 left Iteration 1 Error: 0.868944 Iteration 2 Error: 0.123718 Iteration 3 Error: 0.027031 Align patch 23 2 left Iteration 1 Error: 0.511405 Iteration 2 Error: 0.117566 Iteration 3 Error: 0.018666 Align patch 24 1 left Iteration 1 Error: 1.035398 Iteration 2 Error: 0.175257 Iteration 3 Error: 0.045885 Align patch 25 0 left Iteration 1 Error: 0.685598 Iteration 2 Error: 0.176066 Iteration 3 Error: 0.030992 3D Fitting completed. Patch alignment time: 18.64(sec) Local motion has been corrected. Process thread exits. Computational time: 32.377033 sec Total time: 39.380665 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00006hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00006hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.623737s Reading file: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00006hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.461191s ........................................ >>>>>>TIME<<<<<< FFT: 1.436723s Defocus_U Defocus_V Angle CCC 15070.31 15976.56 4.79 0.056828 Final Values Defocus_U Defocus_V Angle CCC 15081.25 15987.50 5.10 0.079786 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00002sq_v01_00006hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00006hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.001e-01 CC threshold: 0.735 Mean Std: 40.47 6.94 Num Hot pixels: 211 Hot pixel threshold: 82.10 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.971715 Iteration 2 Error: 0.371400 Iteration 3 Error: 0.115081 Iteration 4 Error: 0.046390 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.24 -0.35 ...... Frame ( 3) shift: -0.48 -0.69 ...... Frame ( 4) shift: -0.72 -1.04 ...... Frame ( 5) shift: -0.95 -1.38 ...... Frame ( 6) shift: -1.00 -1.54 ...... Frame ( 7) shift: -0.86 -1.51 ...... Frame ( 8) shift: -0.72 -1.49 ...... Frame ( 9) shift: -0.63 -1.46 ...... Frame ( 10) shift: -0.59 -1.44 ...... Frame ( 11) shift: -0.54 -1.42 ...... Frame ( 12) shift: -0.49 -1.37 ...... Frame ( 13) shift: -0.44 -1.29 ...... Frame ( 14) shift: -0.39 -1.21 ...... Frame ( 15) shift: -0.32 -1.20 ...... Frame ( 16) shift: -0.23 -1.25 ...... Frame ( 17) shift: -0.14 -1.30 ...... Frame ( 18) shift: -0.02 -1.38 ...... Frame ( 19) shift: 0.11 -1.47 ...... Frame ( 20) shift: 0.25 -1.56 ...... Frame ( 21) shift: 0.34 -1.64 ...... Frame ( 22) shift: 0.41 -1.70 ...... Frame ( 23) shift: 0.47 -1.75 ...... Frame ( 24) shift: 0.54 -1.86 ...... Frame ( 25) shift: 0.62 -2.01 ...... Frame ( 26) shift: 0.69 -2.16 ...... Frame ( 27) shift: 0.75 -2.31 ...... Frame ( 28) shift: 0.78 -2.46 ...... Frame ( 29) shift: 0.81 -2.61 ...... Frame ( 30) shift: 0.89 -2.74 ...... Frame ( 31) shift: 1.02 -2.86 ...... Frame ( 32) shift: 1.15 -2.97 ...... Frame ( 33) shift: 1.25 -3.07 ...... Frame ( 34) shift: 1.32 -3.15 ...... Frame ( 35) shift: 1.39 -3.24 ...... Frame ( 36) shift: 1.46 -3.33 ...... Frame ( 37) shift: 1.51 -3.44 ...... Frame ( 38) shift: 1.57 -3.55 ...... Frame ( 39) shift: 1.63 -3.66 ...... Frame ( 40) shift: 1.69 -3.77 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.919917 Iteration 2 Error: 0.360292 Iteration 3 Error: 0.126125 Iteration 4 Error: 0.051097 Iteration 5 Error: 0.032804 Align patch 2 23 left Iteration 1 Error: 0.708735 Iteration 2 Error: 0.170151 Iteration 3 Error: 0.040054 Align patch 3 22 left Iteration 1 Error: 0.983851 Iteration 2 Error: 0.127619 Iteration 3 Error: 0.042614 Align patch 4 21 left Iteration 1 Error: 1.427362 Iteration 2 Error: 0.226471 Iteration 3 Error: 0.058940 Iteration 4 Error: 0.015184 Align patch 5 20 left Iteration 1 Error: 1.488590 Iteration 2 Error: 0.201247 Iteration 3 Error: 0.029363 Align patch 6 19 left Iteration 1 Error: 1.492300 Iteration 2 Error: 0.782326 Iteration 3 Error: 0.364574 Iteration 4 Error: 0.183994 Iteration 5 Error: 0.088342 Align patch 6 19 left Iteration 1 Error: 1.684610 Iteration 2 Error: 0.341689 Iteration 3 Error: 0.066245 Iteration 4 Error: 0.015199 Align patch 7 18 left Iteration 1 Error: 0.981654 Iteration 2 Error: 0.280585 Iteration 3 Error: 0.131753 Iteration 4 Error: 0.068847 Iteration 5 Error: 0.025648 Align patch 8 17 left Iteration 1 Error: 1.153882 Iteration 2 Error: 0.148255 Iteration 3 Error: 0.037311 Align patch 9 16 left Iteration 1 Error: 1.343650 Iteration 2 Error: 0.212194 Iteration 3 Error: 0.043732 Align patch 10 15 left Iteration 1 Error: 1.243412 Iteration 2 Error: 0.248186 Iteration 3 Error: 0.035267 Align patch 11 14 left Iteration 1 Error: 2.499923 Iteration 2 Error: 0.888793 Iteration 3 Error: 0.409976 Iteration 4 Error: 0.241379 Iteration 5 Error: 0.133222 Align patch 11 14 left Iteration 1 Error: 2.620027 Iteration 2 Error: 0.415643 Iteration 3 Error: 0.097511 Iteration 4 Error: 0.026877 Align patch 12 13 left Iteration 1 Error: 1.215242 Iteration 2 Error: 0.362647 Iteration 3 Error: 0.154243 Iteration 4 Error: 0.058618 Iteration 5 Error: 0.029672 Align patch 13 12 left Iteration 1 Error: 0.605906 Iteration 2 Error: 0.065136 Iteration 3 Error: 0.011354 Align patch 14 11 left Iteration 1 Error: 0.774453 Iteration 2 Error: 0.147789 Iteration 3 Error: 0.031399 Align patch 15 10 left Iteration 1 Error: 1.163502 Iteration 2 Error: 0.154751 Iteration 3 Error: 0.037047 Align patch 16 9 left Iteration 1 Error: 3.161937 Iteration 2 Error: 1.275579 Iteration 3 Error: 0.609424 Iteration 4 Error: 0.542500 Iteration 5 Error: 0.410697 Align patch 16 9 left Iteration 1 Error: 3.259831 Iteration 2 Error: 0.636023 Iteration 3 Error: 0.196361 Iteration 4 Error: 0.060561 Iteration 5 Error: 0.019715 Align patch 17 8 left Iteration 1 Error: 2.048963 Iteration 2 Error: 0.622884 Iteration 3 Error: 0.254268 Iteration 4 Error: 0.142181 Iteration 5 Error: 0.080451 Align patch 17 8 left Iteration 1 Error: 2.460341 Iteration 2 Error: 0.350018 Iteration 3 Error: 0.079337 Iteration 4 Error: 0.024281 Align patch 18 7 left Iteration 1 Error: 0.620649 Iteration 2 Error: 0.149215 Iteration 3 Error: 0.036996 Align patch 19 6 left Iteration 1 Error: 0.597152 Iteration 2 Error: 0.089784 Iteration 3 Error: 0.017619 Align patch 20 5 left Iteration 1 Error: 1.372322 Iteration 2 Error: 0.325365 Iteration 3 Error: 0.063671 Iteration 4 Error: 0.031402 Align patch 21 4 left Iteration 1 Error: 8.923871 Iteration 2 Error: 4.406510 Iteration 3 Error: 1.023970 Iteration 4 Error: 0.284413 Iteration 5 Error: 0.089982 Align patch 21 4 left Iteration 1 Error: 4.045235 Iteration 2 Error: 0.844350 Iteration 3 Error: 0.265421 Iteration 4 Error: 0.077818 Iteration 5 Error: 0.026843 Align patch 22 3 left Iteration 1 Error: 3.413711 Iteration 2 Error: 0.873112 Iteration 3 Error: 0.246917 Iteration 4 Error: 0.158798 Iteration 5 Error: 0.077120 Align patch 22 3 left Iteration 1 Error: 2.862137 Iteration 2 Error: 0.425017 Iteration 3 Error: 0.102337 Iteration 4 Error: 0.035207 Align patch 23 2 left Iteration 1 Error: 1.579934 Iteration 2 Error: 0.389597 Iteration 3 Error: 0.132561 Iteration 4 Error: 0.047958 Align patch 24 1 left Iteration 1 Error: 0.691480 Iteration 2 Error: 0.116904 Iteration 3 Error: 0.028186 Align patch 25 0 left Iteration 1 Error: 1.252166 Iteration 2 Error: 0.276398 Iteration 3 Error: 0.072988 Iteration 4 Error: 0.023149 3D Fitting completed. Patch alignment time: 27.15(sec) Local motion has been corrected. Process thread exits. Computational time: 38.487213 sec Total time: 46.855076 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00006hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00006hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.564092s Reading file: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00006hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 4.531362s ........................................ >>>>>>TIME<<<<<< FFT: 1.639760s Defocus_U Defocus_V Angle CCC 17301.02 16663.88 81.01 0.049558 Final Values Defocus_U Defocus_V Angle CCC 17307.27 16663.88 81.01 0.082565 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00002sq_v01_00007hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00007hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 42.10 7.08 Num Hot pixels: 235 Hot pixel threshold: 84.57 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.115732 Iteration 2 Error: 0.216993 Iteration 3 Error: 0.037271 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.16 0.27 ...... Frame ( 3) shift: -0.31 0.53 ...... Frame ( 4) shift: -0.47 0.80 ...... Frame ( 5) shift: -0.62 1.06 ...... Frame ( 6) shift: -0.69 1.31 ...... Frame ( 7) shift: -0.66 1.52 ...... Frame ( 8) shift: -0.63 1.73 ...... Frame ( 9) shift: -0.63 1.90 ...... Frame ( 10) shift: -0.64 2.02 ...... Frame ( 11) shift: -0.66 2.13 ...... Frame ( 12) shift: -0.67 2.26 ...... Frame ( 13) shift: -0.67 2.38 ...... Frame ( 14) shift: -0.67 2.51 ...... Frame ( 15) shift: -0.61 2.62 ...... Frame ( 16) shift: -0.49 2.70 ...... Frame ( 17) shift: -0.37 2.79 ...... Frame ( 18) shift: -0.30 2.84 ...... Frame ( 19) shift: -0.28 2.86 ...... Frame ( 20) shift: -0.27 2.88 ...... Frame ( 21) shift: -0.24 2.93 ...... Frame ( 22) shift: -0.19 3.03 ...... Frame ( 23) shift: -0.15 3.13 ...... Frame ( 24) shift: -0.11 3.18 ...... Frame ( 25) shift: -0.08 3.18 ...... Frame ( 26) shift: -0.05 3.18 ...... Frame ( 27) shift: -0.01 3.20 ...... Frame ( 28) shift: 0.02 3.22 ...... Frame ( 29) shift: 0.06 3.25 ...... Frame ( 30) shift: 0.09 3.25 ...... Frame ( 31) shift: 0.11 3.22 ...... Frame ( 32) shift: 0.13 3.19 ...... Frame ( 33) shift: 0.19 3.22 ...... Frame ( 34) shift: 0.29 3.31 ...... Frame ( 35) shift: 0.39 3.40 ...... Frame ( 36) shift: 0.42 3.46 ...... Frame ( 37) shift: 0.38 3.50 ...... Frame ( 38) shift: 0.35 3.53 ...... Frame ( 39) shift: 0.31 3.57 ...... Frame ( 40) shift: 0.28 3.61 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.069933 Iteration 2 Error: 0.112985 Iteration 3 Error: 0.026315 Align patch 2 23 left Iteration 1 Error: 1.245189 Iteration 2 Error: 0.140327 Iteration 3 Error: 0.038741 Align patch 3 22 left Iteration 1 Error: 0.983679 Iteration 2 Error: 0.238616 Iteration 3 Error: 0.050143 Iteration 4 Error: 0.016858 Align patch 4 21 left Iteration 1 Error: 0.972874 Iteration 2 Error: 0.219197 Iteration 3 Error: 0.046363 Align patch 5 20 left Iteration 1 Error: 0.734519 Iteration 2 Error: 0.064850 Iteration 3 Error: 0.018018 Align patch 6 19 left Iteration 1 Error: 0.590307 Iteration 2 Error: 0.076955 Iteration 3 Error: 0.034561 Align patch 7 18 left Iteration 1 Error: 0.580710 Iteration 2 Error: 0.086877 Iteration 3 Error: 0.019474 Align patch 8 17 left Iteration 1 Error: 0.785580 Iteration 2 Error: 0.074326 Iteration 3 Error: 0.013784 Align patch 9 16 left Iteration 1 Error: 0.827176 Iteration 2 Error: 0.093893 Iteration 3 Error: 0.028345 Align patch 10 15 left Iteration 1 Error: 0.647687 Iteration 2 Error: 0.112554 Iteration 3 Error: 0.030402 Align patch 11 14 left Iteration 1 Error: 0.955688 Iteration 2 Error: 0.147197 Iteration 3 Error: 0.042583 Align patch 12 13 left Iteration 1 Error: 0.683363 Iteration 2 Error: 0.098399 Iteration 3 Error: 0.021574 Align patch 13 12 left Iteration 1 Error: 0.410483 Iteration 2 Error: 0.065602 Iteration 3 Error: 0.015933 Align patch 14 11 left Iteration 1 Error: 0.608703 Iteration 2 Error: 0.121925 Iteration 3 Error: 0.016165 Align patch 15 10 left Iteration 1 Error: 0.919542 Iteration 2 Error: 0.198412 Iteration 3 Error: 0.034232 Align patch 16 9 left Iteration 1 Error: 1.126567 Iteration 2 Error: 0.141232 Iteration 3 Error: 0.029043 Align patch 17 8 left Iteration 1 Error: 0.811655 Iteration 2 Error: 0.110576 Iteration 3 Error: 0.022433 Align patch 18 7 left Iteration 1 Error: 0.588927 Iteration 2 Error: 0.111514 Iteration 3 Error: 0.024210 Align patch 19 6 left Iteration 1 Error: 0.572251 Iteration 2 Error: 0.055035 Iteration 3 Error: 0.011830 Align patch 20 5 left Iteration 1 Error: 0.628775 Iteration 2 Error: 0.171572 Iteration 3 Error: 0.066917 Iteration 4 Error: 0.024599 Align patch 21 4 left Iteration 1 Error: 0.985530 Iteration 2 Error: 0.141721 Iteration 3 Error: 0.052007 Iteration 4 Error: 0.009487 Align patch 22 3 left Iteration 1 Error: 1.509930 Iteration 2 Error: 0.115113 Iteration 3 Error: 0.025089 Align patch 23 2 left Iteration 1 Error: 0.776792 Iteration 2 Error: 0.100969 Iteration 3 Error: 0.025949 Align patch 24 1 left Iteration 1 Error: 0.543786 Iteration 2 Error: 0.124046 Iteration 3 Error: 0.018486 Align patch 25 0 left Iteration 1 Error: 0.439225 Iteration 2 Error: 0.057039 Iteration 3 Error: 0.009001 3D Fitting completed. Patch alignment time: 15.14(sec) Local motion has been corrected. Process thread exits. Computational time: 27.108143 sec Total time: 36.503365 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00007hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00007hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.661417s Reading file: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00007hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.461356s ........................................ >>>>>>TIME<<<<<< FFT: 1.062090s Defocus_U Defocus_V Angle CCC 13507.81 14347.66 11.54 0.060290 Final Values Defocus_U Defocus_V Angle CCC 13506.24 14352.36 11.54 0.100985 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00002sq_v01_00007hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00007hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 41.30 6.93 Num Hot pixels: 196 Hot pixel threshold: 82.85 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.118429 Iteration 2 Error: 0.144430 Iteration 3 Error: 0.036301 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.06 -0.19 ...... Frame ( 3) shift: -0.12 -0.38 ...... Frame ( 4) shift: -0.18 -0.57 ...... Frame ( 5) shift: -0.24 -0.76 ...... Frame ( 6) shift: -0.29 -0.82 ...... Frame ( 7) shift: -0.32 -0.76 ...... Frame ( 8) shift: -0.35 -0.71 ...... Frame ( 9) shift: -0.38 -0.61 ...... Frame ( 10) shift: -0.40 -0.48 ...... Frame ( 11) shift: -0.43 -0.35 ...... Frame ( 12) shift: -0.45 -0.22 ...... Frame ( 13) shift: -0.47 -0.09 ...... Frame ( 14) shift: -0.50 0.04 ...... Frame ( 15) shift: -0.47 0.13 ...... Frame ( 16) shift: -0.41 0.17 ...... Frame ( 17) shift: -0.34 0.22 ...... Frame ( 18) shift: -0.32 0.29 ...... Frame ( 19) shift: -0.33 0.39 ...... Frame ( 20) shift: -0.34 0.48 ...... Frame ( 21) shift: -0.33 0.57 ...... Frame ( 22) shift: -0.30 0.64 ...... Frame ( 23) shift: -0.26 0.71 ...... Frame ( 24) shift: -0.24 0.78 ...... Frame ( 25) shift: -0.23 0.85 ...... Frame ( 26) shift: -0.23 0.92 ...... Frame ( 27) shift: -0.22 0.97 ...... Frame ( 28) shift: -0.21 1.00 ...... Frame ( 29) shift: -0.20 1.03 ...... Frame ( 30) shift: -0.20 1.08 ...... Frame ( 31) shift: -0.23 1.14 ...... Frame ( 32) shift: -0.25 1.21 ...... Frame ( 33) shift: -0.26 1.26 ...... Frame ( 34) shift: -0.25 1.29 ...... Frame ( 35) shift: -0.25 1.33 ...... Frame ( 36) shift: -0.24 1.33 ...... Frame ( 37) shift: -0.24 1.30 ...... Frame ( 38) shift: -0.23 1.27 ...... Frame ( 39) shift: -0.23 1.24 ...... Frame ( 40) shift: -0.22 1.21 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.813423 Iteration 2 Error: 0.168636 Iteration 3 Error: 0.043716 Align patch 2 23 left Iteration 1 Error: 0.903615 Iteration 2 Error: 0.137205 Iteration 3 Error: 0.036823 Align patch 3 22 left Iteration 1 Error: 0.613127 Iteration 2 Error: 0.108591 Iteration 3 Error: 0.026010 Align patch 4 21 left Iteration 1 Error: 0.912699 Iteration 2 Error: 0.158849 Iteration 3 Error: 0.033285 Align patch 5 20 left Iteration 1 Error: 1.037374 Iteration 2 Error: 0.126444 Iteration 3 Error: 0.026046 Align patch 6 19 left Iteration 1 Error: 0.901288 Iteration 2 Error: 0.116947 Iteration 3 Error: 0.019310 Align patch 7 18 left Iteration 1 Error: 0.742816 Iteration 2 Error: 0.089429 Iteration 3 Error: 0.020063 Align patch 8 17 left Iteration 1 Error: 0.569875 Iteration 2 Error: 0.056156 Iteration 3 Error: 0.012192 Align patch 9 16 left Iteration 1 Error: 0.657830 Iteration 2 Error: 0.156980 Iteration 3 Error: 0.031570 Align patch 10 15 left Iteration 1 Error: 0.487494 Iteration 2 Error: 0.060627 Iteration 3 Error: 0.011431 Align patch 11 14 left Iteration 1 Error: 0.815456 Iteration 2 Error: 0.238639 Iteration 3 Error: 0.054203 Iteration 4 Error: 0.022089 Align patch 12 13 left Iteration 1 Error: 0.707252 Iteration 2 Error: 0.148625 Iteration 3 Error: 0.046303 Align patch 13 12 left Iteration 1 Error: 0.777625 Iteration 2 Error: 0.074500 Iteration 3 Error: 0.018776 Align patch 14 11 left Iteration 1 Error: 0.532191 Iteration 2 Error: 0.070557 Iteration 3 Error: 0.018800 Align patch 15 10 left Iteration 1 Error: 0.555732 Iteration 2 Error: 0.074250 Iteration 3 Error: 0.017295 Align patch 16 9 left Iteration 1 Error: 0.805020 Iteration 2 Error: 0.111668 Iteration 3 Error: 0.027985 Align patch 17 8 left Iteration 1 Error: 0.647936 Iteration 2 Error: 0.101283 Iteration 3 Error: 0.035239 Align patch 18 7 left Iteration 1 Error: 0.454564 Iteration 2 Error: 0.059855 Iteration 3 Error: 0.018403 Align patch 19 6 left Iteration 1 Error: 0.525979 Iteration 2 Error: 0.077369 Iteration 3 Error: 0.019124 Align patch 20 5 left Iteration 1 Error: 0.650071 Iteration 2 Error: 0.099427 Iteration 3 Error: 0.033201 Align patch 21 4 left Iteration 1 Error: 0.834304 Iteration 2 Error: 0.157427 Iteration 3 Error: 0.046011 Align patch 22 3 left Iteration 1 Error: 0.577187 Iteration 2 Error: 0.080403 Iteration 3 Error: 0.021963 Align patch 23 2 left Iteration 1 Error: 0.534985 Iteration 2 Error: 0.131264 Iteration 3 Error: 0.024478 Align patch 24 1 left Iteration 1 Error: 0.661539 Iteration 2 Error: 0.065884 Iteration 3 Error: 0.012461 Align patch 25 0 left Iteration 1 Error: 0.622655 Iteration 2 Error: 0.083542 Iteration 3 Error: 0.012259 3D Fitting completed. Patch alignment time: 18.68(sec) Local motion has been corrected. Process thread exits. Computational time: 32.276920 sec Total time: 45.565670 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00007hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00007hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.519964s Reading file: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00007hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.173826s ........................................ >>>>>>TIME<<<<<< FFT: 1.389422s Defocus_U Defocus_V Angle CCC 13105.47 12527.34 89.94 0.048743 Final Values Defocus_U Defocus_V Angle CCC 12547.67 13110.17 0.58 0.079396 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00002sq_v01_00007hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00007hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 40.96 7.06 Num Hot pixels: 189 Hot pixel threshold: 83.32 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.765731 Iteration 2 Error: 0.110270 Iteration 3 Error: 0.022554 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.13 0.32 ...... Frame ( 3) shift: -0.27 0.65 ...... Frame ( 4) shift: -0.40 0.97 ...... Frame ( 5) shift: -0.54 1.29 ...... Frame ( 6) shift: -0.60 1.52 ...... Frame ( 7) shift: -0.59 1.66 ...... Frame ( 8) shift: -0.58 1.79 ...... Frame ( 9) shift: -0.57 1.93 ...... Frame ( 10) shift: -0.55 2.07 ...... Frame ( 11) shift: -0.53 2.21 ...... Frame ( 12) shift: -0.50 2.30 ...... Frame ( 13) shift: -0.47 2.33 ...... Frame ( 14) shift: -0.43 2.36 ...... Frame ( 15) shift: -0.41 2.39 ...... Frame ( 16) shift: -0.39 2.43 ...... Frame ( 17) shift: -0.37 2.47 ...... Frame ( 18) shift: -0.39 2.50 ...... Frame ( 19) shift: -0.42 2.53 ...... Frame ( 20) shift: -0.46 2.55 ...... Frame ( 21) shift: -0.47 2.56 ...... Frame ( 22) shift: -0.44 2.55 ...... Frame ( 23) shift: -0.41 2.53 ...... Frame ( 24) shift: -0.40 2.54 ...... Frame ( 25) shift: -0.41 2.56 ...... Frame ( 26) shift: -0.41 2.59 ...... Frame ( 27) shift: -0.40 2.57 ...... Frame ( 28) shift: -0.37 2.51 ...... Frame ( 29) shift: -0.33 2.45 ...... Frame ( 30) shift: -0.34 2.44 ...... Frame ( 31) shift: -0.40 2.48 ...... Frame ( 32) shift: -0.46 2.52 ...... Frame ( 33) shift: -0.51 2.54 ...... Frame ( 34) shift: -0.54 2.55 ...... Frame ( 35) shift: -0.57 2.56 ...... Frame ( 36) shift: -0.55 2.55 ...... Frame ( 37) shift: -0.49 2.52 ...... Frame ( 38) shift: -0.42 2.49 ...... Frame ( 39) shift: -0.36 2.46 ...... Frame ( 40) shift: -0.29 2.43 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.665845 Iteration 2 Error: 0.223578 Iteration 3 Error: 0.055661 Iteration 4 Error: 0.014882 Align patch 2 23 left Iteration 1 Error: 0.828518 Iteration 2 Error: 0.121356 Iteration 3 Error: 0.053116 Iteration 4 Error: 0.011026 Align patch 3 22 left Iteration 1 Error: 0.646119 Iteration 2 Error: 0.085673 Iteration 3 Error: 0.022935 Align patch 4 21 left Iteration 1 Error: 0.471300 Iteration 2 Error: 0.067442 Iteration 3 Error: 0.018026 Align patch 5 20 left Iteration 1 Error: 0.654087 Iteration 2 Error: 0.110891 Iteration 3 Error: 0.020213 Align patch 6 19 left Iteration 1 Error: 1.801884 Iteration 2 Error: 0.191696 Iteration 3 Error: 0.056380 Iteration 4 Error: 0.023759 Align patch 7 18 left Iteration 1 Error: 1.802754 Iteration 2 Error: 0.122746 Iteration 3 Error: 0.050139 Iteration 4 Error: 0.011910 Align patch 8 17 left Iteration 1 Error: 0.991671 Iteration 2 Error: 0.103044 Iteration 3 Error: 0.030990 Align patch 9 16 left Iteration 1 Error: 0.704720 Iteration 2 Error: 0.123468 Iteration 3 Error: 0.015889 Align patch 10 15 left Iteration 1 Error: 1.638051 Iteration 2 Error: 0.096702 Iteration 3 Error: 0.014919 Align patch 11 14 left Iteration 1 Error: 0.582157 Iteration 2 Error: 0.114544 Iteration 3 Error: 0.019284 Align patch 12 13 left Iteration 1 Error: 0.623214 Iteration 2 Error: 0.073614 Iteration 3 Error: 0.018072 Align patch 13 12 left Iteration 1 Error: 0.491250 Iteration 2 Error: 0.060742 Iteration 3 Error: 0.009000 Align patch 14 11 left Iteration 1 Error: 0.796726 Iteration 2 Error: 0.092193 Iteration 3 Error: 0.020357 Align patch 15 10 left Iteration 1 Error: 1.409028 Iteration 2 Error: 0.129043 Iteration 3 Error: 0.021085 Align patch 16 9 left Iteration 1 Error: 0.733164 Iteration 2 Error: 0.082523 Iteration 3 Error: 0.015646 Align patch 17 8 left Iteration 1 Error: 0.567807 Iteration 2 Error: 0.072179 Iteration 3 Error: 0.029928 Align patch 18 7 left Iteration 1 Error: 0.898396 Iteration 2 Error: 0.116085 Iteration 3 Error: 0.033632 Align patch 19 6 left Iteration 1 Error: 0.739524 Iteration 2 Error: 0.114216 Iteration 3 Error: 0.025756 Align patch 20 5 left Iteration 1 Error: 0.816970 Iteration 2 Error: 0.120917 Iteration 3 Error: 0.018664 Align patch 21 4 left Iteration 1 Error: 0.668151 Iteration 2 Error: 0.120136 Iteration 3 Error: 0.014299 Align patch 22 3 left Iteration 1 Error: 0.771682 Iteration 2 Error: 0.153389 Iteration 3 Error: 0.031943 Align patch 23 2 left Iteration 1 Error: 0.876347 Iteration 2 Error: 0.133151 Iteration 3 Error: 0.034424 Align patch 24 1 left Iteration 1 Error: 0.732873 Iteration 2 Error: 0.132304 Iteration 3 Error: 0.026507 Align patch 25 0 left Iteration 1 Error: 0.610740 Iteration 2 Error: 0.071430 Iteration 3 Error: 0.009999 3D Fitting completed. Patch alignment time: 17.45(sec) Local motion has been corrected. Process thread exits. Computational time: 29.171074 sec Total time: 37.983433 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00007hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00007hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.398635s Reading file: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00007hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.804714s ........................................ >>>>>>TIME<<<<<< FFT: 1.076727s Defocus_U Defocus_V Angle CCC 15005.86 15748.05 6.48 0.051325 Final Values Defocus_U Defocus_V Angle CCC 15010.55 15749.61 6.80 0.080596 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00002sq_v01_00008hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00008hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 40.93 7.08 Num Hot pixels: 204 Hot pixel threshold: 83.43 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.843058 Iteration 2 Error: 0.300660 Iteration 3 Error: 0.066935 Iteration 4 Error: 0.020064 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.00 0.09 ...... Frame ( 3) shift: 0.01 0.18 ...... Frame ( 4) shift: 0.01 0.26 ...... Frame ( 5) shift: 0.02 0.35 ...... Frame ( 6) shift: 0.09 0.44 ...... Frame ( 7) shift: 0.22 0.54 ...... Frame ( 8) shift: 0.34 0.64 ...... Frame ( 9) shift: 0.48 0.78 ...... Frame ( 10) shift: 0.61 0.97 ...... Frame ( 11) shift: 0.74 1.16 ...... Frame ( 12) shift: 0.83 1.32 ...... Frame ( 13) shift: 0.86 1.45 ...... Frame ( 14) shift: 0.89 1.57 ...... Frame ( 15) shift: 0.94 1.69 ...... Frame ( 16) shift: 1.01 1.78 ...... Frame ( 17) shift: 1.07 1.88 ...... Frame ( 18) shift: 1.12 1.98 ...... Frame ( 19) shift: 1.15 2.08 ...... Frame ( 20) shift: 1.18 2.18 ...... Frame ( 21) shift: 1.22 2.25 ...... Frame ( 22) shift: 1.27 2.27 ...... Frame ( 23) shift: 1.33 2.30 ...... Frame ( 24) shift: 1.36 2.31 ...... Frame ( 25) shift: 1.37 2.30 ...... Frame ( 26) shift: 1.38 2.29 ...... Frame ( 27) shift: 1.42 2.30 ...... Frame ( 28) shift: 1.49 2.34 ...... Frame ( 29) shift: 1.57 2.38 ...... Frame ( 30) shift: 1.63 2.43 ...... Frame ( 31) shift: 1.68 2.48 ...... Frame ( 32) shift: 1.74 2.54 ...... Frame ( 33) shift: 1.78 2.58 ...... Frame ( 34) shift: 1.82 2.60 ...... Frame ( 35) shift: 1.86 2.63 ...... Frame ( 36) shift: 1.91 2.69 ...... Frame ( 37) shift: 1.96 2.78 ...... Frame ( 38) shift: 2.02 2.86 ...... Frame ( 39) shift: 2.07 2.95 ...... Frame ( 40) shift: 2.13 3.04 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.596999 Iteration 2 Error: 0.382690 Iteration 3 Error: 0.196416 Iteration 4 Error: 0.115781 Iteration 5 Error: 0.066108 Align patch 1 24 left Iteration 1 Error: 1.414463 Iteration 2 Error: 0.297357 Iteration 3 Error: 0.052808 Iteration 4 Error: 0.013586 Align patch 2 23 left Iteration 1 Error: 0.684083 Iteration 2 Error: 0.226228 Iteration 3 Error: 0.068442 Iteration 4 Error: 0.038821 Align patch 3 22 left Iteration 1 Error: 0.852465 Iteration 2 Error: 0.089132 Iteration 3 Error: 0.039948 Align patch 4 21 left Iteration 1 Error: 0.511854 Iteration 2 Error: 0.086528 Iteration 3 Error: 0.012876 Align patch 5 20 left Iteration 1 Error: 0.973092 Iteration 2 Error: 0.138270 Iteration 3 Error: 0.040071 Align patch 6 19 left Iteration 1 Error: 2.389517 Iteration 2 Error: 0.342459 Iteration 3 Error: 0.128340 Iteration 4 Error: 0.063084 Iteration 5 Error: 0.033824 Align patch 7 18 left Iteration 1 Error: 0.770380 Iteration 2 Error: 0.361734 Iteration 3 Error: 0.103279 Iteration 4 Error: 0.047955 Align patch 8 17 left Iteration 1 Error: 0.491116 Iteration 2 Error: 0.129519 Iteration 3 Error: 0.044429 Align patch 9 16 left Iteration 1 Error: 0.627522 Iteration 2 Error: 0.128473 Iteration 3 Error: 0.047130 Align patch 10 15 left Iteration 1 Error: 0.770848 Iteration 2 Error: 0.181395 Iteration 3 Error: 0.046941 Align patch 11 14 left Iteration 1 Error: 0.965904 Iteration 2 Error: 0.147880 Iteration 3 Error: 0.049115 Align patch 12 13 left Iteration 1 Error: 0.940098 Iteration 2 Error: 0.099142 Iteration 3 Error: 0.024476 Align patch 13 12 left Iteration 1 Error: 0.488230 Iteration 2 Error: 0.077545 Iteration 3 Error: 0.018791 Align patch 14 11 left Iteration 1 Error: 0.556678 Iteration 2 Error: 0.098950 Iteration 3 Error: 0.036741 Align patch 15 10 left Iteration 1 Error: 0.749124 Iteration 2 Error: 0.094067 Iteration 3 Error: 0.026705 Align patch 16 9 left Iteration 1 Error: 1.205379 Iteration 2 Error: 0.202881 Iteration 3 Error: 0.041369 Align patch 17 8 left Iteration 1 Error: 0.709872 Iteration 2 Error: 0.168342 Iteration 3 Error: 0.050092 Iteration 4 Error: 0.014064 Align patch 18 7 left Iteration 1 Error: 0.668524 Iteration 2 Error: 0.151008 Iteration 3 Error: 0.029680 Align patch 19 6 left Iteration 1 Error: 0.617905 Iteration 2 Error: 0.050818 Iteration 3 Error: 0.017444 Align patch 20 5 left Iteration 1 Error: 0.476248 Iteration 2 Error: 0.085322 Iteration 3 Error: 0.014847 Align patch 21 4 left Iteration 1 Error: 1.306113 Iteration 2 Error: 0.177715 Iteration 3 Error: 0.045344 Align patch 22 3 left Iteration 1 Error: 1.340976 Iteration 2 Error: 0.152812 Iteration 3 Error: 0.023388 Align patch 23 2 left Iteration 1 Error: 0.681587 Iteration 2 Error: 0.099214 Iteration 3 Error: 0.025110 Align patch 24 1 left Iteration 1 Error: 0.470570 Iteration 2 Error: 0.067308 Iteration 3 Error: 0.014351 Align patch 25 0 left Iteration 1 Error: 0.395722 Iteration 2 Error: 0.050075 Iteration 3 Error: 0.009391 3D Fitting completed. Patch alignment time: 14.43(sec) Local motion has been corrected. Process thread exits. Computational time: 24.923038 sec Total time: 32.713009 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00008hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00008hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.734034s Reading file: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00008hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.585986s ........................................ >>>>>>TIME<<<<<< FFT: 0.951717s Defocus_U Defocus_V Angle CCC 11330.13 12228.57 13.41 0.052488 Final Values Defocus_U Defocus_V Angle CCC 11375.49 12264.54 12.78 0.088374 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00002sq_v01_00008hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00008hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.001e-01 CC threshold: 0.736 Mean Std: 42.17 7.10 Num Hot pixels: 222 Hot pixel threshold: 84.78 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.143453 Iteration 2 Error: 0.149592 Iteration 3 Error: 0.030909 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.07 0.08 ...... Frame ( 3) shift: -0.15 0.16 ...... Frame ( 4) shift: -0.22 0.24 ...... Frame ( 5) shift: -0.30 0.32 ...... Frame ( 6) shift: -0.28 0.39 ...... Frame ( 7) shift: -0.16 0.46 ...... Frame ( 8) shift: -0.04 0.54 ...... Frame ( 9) shift: 0.02 0.62 ...... Frame ( 10) shift: 0.03 0.72 ...... Frame ( 11) shift: 0.04 0.81 ...... Frame ( 12) shift: 0.06 0.90 ...... Frame ( 13) shift: 0.09 0.98 ...... Frame ( 14) shift: 0.12 1.06 ...... Frame ( 15) shift: 0.13 1.13 ...... Frame ( 16) shift: 0.11 1.21 ...... Frame ( 17) shift: 0.09 1.28 ...... Frame ( 18) shift: 0.12 1.35 ...... Frame ( 19) shift: 0.19 1.39 ...... Frame ( 20) shift: 0.27 1.44 ...... Frame ( 21) shift: 0.31 1.48 ...... Frame ( 22) shift: 0.33 1.51 ...... Frame ( 23) shift: 0.35 1.54 ...... Frame ( 24) shift: 0.37 1.58 ...... Frame ( 25) shift: 0.38 1.63 ...... Frame ( 26) shift: 0.39 1.67 ...... Frame ( 27) shift: 0.42 1.70 ...... Frame ( 28) shift: 0.47 1.71 ...... Frame ( 29) shift: 0.52 1.72 ...... Frame ( 30) shift: 0.52 1.76 ...... Frame ( 31) shift: 0.48 1.83 ...... Frame ( 32) shift: 0.43 1.90 ...... Frame ( 33) shift: 0.41 1.99 ...... Frame ( 34) shift: 0.40 2.08 ...... Frame ( 35) shift: 0.40 2.18 ...... Frame ( 36) shift: 0.42 2.20 ...... Frame ( 37) shift: 0.48 2.16 ...... Frame ( 38) shift: 0.54 2.11 ...... Frame ( 39) shift: 0.60 2.07 ...... Frame ( 40) shift: 0.66 2.03 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.906158 Iteration 2 Error: 0.094332 Iteration 3 Error: 0.021504 Align patch 2 23 left Iteration 1 Error: 1.078990 Iteration 2 Error: 0.136915 Iteration 3 Error: 0.045586 Align patch 3 22 left Iteration 1 Error: 0.597821 Iteration 2 Error: 0.068595 Iteration 3 Error: 0.017115 Align patch 4 21 left Iteration 1 Error: 0.381858 Iteration 2 Error: 0.055956 Iteration 3 Error: 0.010995 Align patch 5 20 left Iteration 1 Error: 0.913470 Iteration 2 Error: 0.099677 Iteration 3 Error: 0.017596 Align patch 6 19 left Iteration 1 Error: 0.752636 Iteration 2 Error: 0.100326 Iteration 3 Error: 0.029571 Align patch 7 18 left Iteration 1 Error: 0.851190 Iteration 2 Error: 0.145771 Iteration 3 Error: 0.050607 Iteration 4 Error: 0.018067 Align patch 8 17 left Iteration 1 Error: 0.758661 Iteration 2 Error: 0.152382 Iteration 3 Error: 0.034621 Align patch 9 16 left Iteration 1 Error: 0.548705 Iteration 2 Error: 0.102346 Iteration 3 Error: 0.031237 Align patch 10 15 left Iteration 1 Error: 0.574088 Iteration 2 Error: 0.094083 Iteration 3 Error: 0.015634 Align patch 11 14 left Iteration 1 Error: 0.839255 Iteration 2 Error: 0.200611 Iteration 3 Error: 0.055390 Iteration 4 Error: 0.016671 Align patch 12 13 left Iteration 1 Error: 0.803006 Iteration 2 Error: 0.081144 Iteration 3 Error: 0.024823 Align patch 13 12 left Iteration 1 Error: 0.535908 Iteration 2 Error: 0.052880 Iteration 3 Error: 0.018070 Align patch 14 11 left Iteration 1 Error: 0.926512 Iteration 2 Error: 0.120957 Iteration 3 Error: 0.037707 Align patch 15 10 left Iteration 1 Error: 0.560152 Iteration 2 Error: 0.072378 Iteration 3 Error: 0.013958 Align patch 16 9 left Iteration 1 Error: 0.945138 Iteration 2 Error: 0.155460 Iteration 3 Error: 0.044953 Align patch 17 8 left Iteration 1 Error: 0.447246 Iteration 2 Error: 0.051440 Iteration 3 Error: 0.026225 Align patch 18 7 left Iteration 1 Error: 0.559401 Iteration 2 Error: 0.077240 Iteration 3 Error: 0.020306 Align patch 19 6 left Iteration 1 Error: 0.981593 Iteration 2 Error: 0.113289 Iteration 3 Error: 0.024693 Align patch 20 5 left Iteration 1 Error: 0.625695 Iteration 2 Error: 0.064062 Iteration 3 Error: 0.014601 Align patch 21 4 left Iteration 1 Error: 1.630870 Iteration 2 Error: 0.174266 Iteration 3 Error: 0.029789 Align patch 22 3 left Iteration 1 Error: 0.763271 Iteration 2 Error: 0.146155 Iteration 3 Error: 0.024516 Align patch 23 2 left Iteration 1 Error: 0.557661 Iteration 2 Error: 0.084873 Iteration 3 Error: 0.016149 Align patch 24 1 left Iteration 1 Error: 0.622258 Iteration 2 Error: 0.099080 Iteration 3 Error: 0.013897 Align patch 25 0 left Iteration 1 Error: 0.718760 Iteration 2 Error: 0.101109 Iteration 3 Error: 0.023161 3D Fitting completed. Patch alignment time: 12.07(sec) Local motion has been corrected. Process thread exits. Computational time: 22.438248 sec Total time: 29.774307 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00008hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00008hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.611096s Reading file: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00008hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.542424s ........................................ >>>>>>TIME<<<<<< FFT: 0.927448s Defocus_U Defocus_V Angle CCC 15992.19 15507.82 83.81 0.056488 Final Values Defocus_U Defocus_V Angle CCC 15998.44 15498.44 83.81 0.091901 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00002sq_v01_00008hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00008hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.002e-01 CC threshold: 0.736 Mean Std: 42.55 7.07 Num Hot pixels: 222 Hot pixel threshold: 84.98 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.763058 Iteration 2 Error: 0.137417 Iteration 3 Error: 0.027560 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.10 0.01 ...... Frame ( 3) shift: -0.20 0.01 ...... Frame ( 4) shift: -0.30 0.02 ...... Frame ( 5) shift: -0.40 0.03 ...... Frame ( 6) shift: -0.43 0.06 ...... Frame ( 7) shift: -0.39 0.12 ...... Frame ( 8) shift: -0.35 0.19 ...... Frame ( 9) shift: -0.30 0.25 ...... Frame ( 10) shift: -0.23 0.31 ...... Frame ( 11) shift: -0.17 0.36 ...... Frame ( 12) shift: -0.11 0.44 ...... Frame ( 13) shift: -0.05 0.54 ...... Frame ( 14) shift: 0.01 0.64 ...... Frame ( 15) shift: 0.07 0.73 ...... Frame ( 16) shift: 0.13 0.79 ...... Frame ( 17) shift: 0.19 0.86 ...... Frame ( 18) shift: 0.22 0.89 ...... Frame ( 19) shift: 0.21 0.89 ...... Frame ( 20) shift: 0.21 0.89 ...... Frame ( 21) shift: 0.26 0.90 ...... Frame ( 22) shift: 0.35 0.91 ...... Frame ( 23) shift: 0.44 0.92 ...... Frame ( 24) shift: 0.47 0.93 ...... Frame ( 25) shift: 0.43 0.94 ...... Frame ( 26) shift: 0.39 0.94 ...... Frame ( 27) shift: 0.35 0.96 ...... Frame ( 28) shift: 0.32 0.99 ...... Frame ( 29) shift: 0.29 1.02 ...... Frame ( 30) shift: 0.31 1.04 ...... Frame ( 31) shift: 0.38 1.06 ...... Frame ( 32) shift: 0.45 1.08 ...... Frame ( 33) shift: 0.47 1.13 ...... Frame ( 34) shift: 0.43 1.21 ...... Frame ( 35) shift: 0.39 1.30 ...... Frame ( 36) shift: 0.37 1.30 ...... Frame ( 37) shift: 0.38 1.23 ...... Frame ( 38) shift: 0.38 1.16 ...... Frame ( 39) shift: 0.39 1.09 ...... Frame ( 40) shift: 0.39 1.02 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.202756 Iteration 2 Error: 0.344177 Iteration 3 Error: 0.133917 Iteration 4 Error: 0.047173 Align patch 2 23 left Iteration 1 Error: 1.432310 Iteration 2 Error: 0.186875 Iteration 3 Error: 0.080995 Iteration 4 Error: 0.026445 Align patch 3 22 left Iteration 1 Error: 0.778049 Iteration 2 Error: 0.090539 Iteration 3 Error: 0.014368 Align patch 4 21 left Iteration 1 Error: 0.530697 Iteration 2 Error: 0.068710 Iteration 3 Error: 0.017146 Align patch 5 20 left Iteration 1 Error: 0.608108 Iteration 2 Error: 0.062598 Iteration 3 Error: 0.007278 Align patch 6 19 left Iteration 1 Error: 1.298300 Iteration 2 Error: 0.246198 Iteration 3 Error: 0.110290 Iteration 4 Error: 0.041755 Align patch 7 18 left Iteration 1 Error: 0.772592 Iteration 2 Error: 0.130315 Iteration 3 Error: 0.019277 Align patch 8 17 left Iteration 1 Error: 0.943462 Iteration 2 Error: 0.141817 Iteration 3 Error: 0.034845 Align patch 9 16 left Iteration 1 Error: 0.707741 Iteration 2 Error: 0.100707 Iteration 3 Error: 0.024972 Align patch 10 15 left Iteration 1 Error: 0.646354 Iteration 2 Error: 0.070346 Iteration 3 Error: 0.017605 Align patch 11 14 left Iteration 1 Error: 0.848351 Iteration 2 Error: 0.173815 Iteration 3 Error: 0.040862 Align patch 12 13 left Iteration 1 Error: 0.658915 Iteration 2 Error: 0.139420 Iteration 3 Error: 0.044473 Align patch 13 12 left Iteration 1 Error: 0.509947 Iteration 2 Error: 0.073532 Iteration 3 Error: 0.021112 Align patch 14 11 left Iteration 1 Error: 0.967026 Iteration 2 Error: 0.139137 Iteration 3 Error: 0.021982 Align patch 15 10 left Iteration 1 Error: 0.568579 Iteration 2 Error: 0.075439 Iteration 3 Error: 0.016248 Align patch 16 9 left Iteration 1 Error: 1.068193 Iteration 2 Error: 0.094978 Iteration 3 Error: 0.034335 Align patch 17 8 left Iteration 1 Error: 0.575142 Iteration 2 Error: 0.077111 Iteration 3 Error: 0.012630 Align patch 18 7 left Iteration 1 Error: 0.633309 Iteration 2 Error: 0.101314 Iteration 3 Error: 0.019916 Align patch 19 6 left Iteration 1 Error: 0.860314 Iteration 2 Error: 0.109150 Iteration 3 Error: 0.017834 Align patch 20 5 left Iteration 1 Error: 0.662597 Iteration 2 Error: 0.091357 Iteration 3 Error: 0.021741 Align patch 21 4 left Iteration 1 Error: 0.815701 Iteration 2 Error: 0.168106 Iteration 3 Error: 0.041874 Align patch 22 3 left Iteration 1 Error: 0.590704 Iteration 2 Error: 0.099025 Iteration 3 Error: 0.023772 Align patch 23 2 left Iteration 1 Error: 0.616926 Iteration 2 Error: 0.095961 Iteration 3 Error: 0.014726 Align patch 24 1 left Iteration 1 Error: 0.627404 Iteration 2 Error: 0.076460 Iteration 3 Error: 0.012137 Align patch 25 0 left Iteration 1 Error: 1.047009 Iteration 2 Error: 0.133279 Iteration 3 Error: 0.021050 3D Fitting completed. Patch alignment time: 11.68(sec) Local motion has been corrected. Process thread exits. Computational time: 21.452822 sec Total time: 27.512205 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00008hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00008hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.654384s Reading file: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00008hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.570325s ........................................ >>>>>>TIME<<<<<< FFT: 0.948313s Defocus_U Defocus_V Angle CCC 17048.85 17865.25 5.98 0.049139 Final Values Defocus_U Defocus_V Angle CCC 17031.66 17879.32 5.36 0.084836 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00002sq_v01_00008hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00008hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.002e-01 CC threshold: 0.736 Mean Std: 41.00 7.23 Num Hot pixels: 201 Hot pixel threshold: 84.35 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.995191 Iteration 2 Error: 0.096330 Iteration 3 Error: 0.019553 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.11 0.11 ...... Frame ( 3) shift: -0.22 0.21 ...... Frame ( 4) shift: -0.34 0.32 ...... Frame ( 5) shift: -0.45 0.43 ...... Frame ( 6) shift: -0.47 0.54 ...... Frame ( 7) shift: -0.39 0.66 ...... Frame ( 8) shift: -0.31 0.78 ...... Frame ( 9) shift: -0.25 0.86 ...... Frame ( 10) shift: -0.22 0.91 ...... Frame ( 11) shift: -0.18 0.97 ...... Frame ( 12) shift: -0.16 1.02 ...... Frame ( 13) shift: -0.16 1.07 ...... Frame ( 14) shift: -0.16 1.11 ...... Frame ( 15) shift: -0.15 1.18 ...... Frame ( 16) shift: -0.14 1.25 ...... Frame ( 17) shift: -0.12 1.32 ...... Frame ( 18) shift: -0.12 1.38 ...... Frame ( 19) shift: -0.14 1.42 ...... Frame ( 20) shift: -0.15 1.46 ...... Frame ( 21) shift: -0.17 1.48 ...... Frame ( 22) shift: -0.18 1.47 ...... Frame ( 23) shift: -0.20 1.46 ...... Frame ( 24) shift: -0.18 1.48 ...... Frame ( 25) shift: -0.12 1.52 ...... Frame ( 26) shift: -0.06 1.56 ...... Frame ( 27) shift: 0.01 1.57 ...... Frame ( 28) shift: 0.09 1.57 ...... Frame ( 29) shift: 0.18 1.56 ...... Frame ( 30) shift: 0.26 1.56 ...... Frame ( 31) shift: 0.35 1.58 ...... Frame ( 32) shift: 0.43 1.59 ...... Frame ( 33) shift: 0.49 1.59 ...... Frame ( 34) shift: 0.52 1.57 ...... Frame ( 35) shift: 0.54 1.55 ...... Frame ( 36) shift: 0.54 1.55 ...... Frame ( 37) shift: 0.50 1.55 ...... Frame ( 38) shift: 0.45 1.55 ...... Frame ( 39) shift: 0.41 1.55 ...... Frame ( 40) shift: 0.37 1.55 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.167110 Iteration 2 Error: 0.173668 Iteration 3 Error: 0.038392 Align patch 2 23 left Iteration 1 Error: 1.176097 Iteration 2 Error: 0.120664 Iteration 3 Error: 0.017645 Align patch 3 22 left Iteration 1 Error: 0.622226 Iteration 2 Error: 0.142521 Iteration 3 Error: 0.039405 Align patch 4 21 left Iteration 1 Error: 0.577916 Iteration 2 Error: 0.112385 Iteration 3 Error: 0.024168 Align patch 5 20 left Iteration 1 Error: 0.778508 Iteration 2 Error: 0.118726 Iteration 3 Error: 0.023284 Align patch 6 19 left Iteration 1 Error: 1.221523 Iteration 2 Error: 0.188507 Iteration 3 Error: 0.041852 Align patch 7 18 left Iteration 1 Error: 0.703652 Iteration 2 Error: 0.213351 Iteration 3 Error: 0.079039 Iteration 4 Error: 0.026064 Align patch 8 17 left Iteration 1 Error: 1.007230 Iteration 2 Error: 0.156204 Iteration 3 Error: 0.039512 Align patch 9 16 left Iteration 1 Error: 0.554114 Iteration 2 Error: 0.051189 Iteration 3 Error: 0.011179 Align patch 10 15 left Iteration 1 Error: 0.775439 Iteration 2 Error: 0.093046 Iteration 3 Error: 0.019184 Align patch 11 14 left Iteration 1 Error: 0.648505 Iteration 2 Error: 0.159872 Iteration 3 Error: 0.047963 Align patch 12 13 left Iteration 1 Error: 0.666870 Iteration 2 Error: 0.083335 Iteration 3 Error: 0.015184 Align patch 13 12 left Iteration 1 Error: 0.622028 Iteration 2 Error: 0.059076 Iteration 3 Error: 0.010084 Align patch 14 11 left Iteration 1 Error: 0.572514 Iteration 2 Error: 0.050451 Iteration 3 Error: 0.009892 Align patch 15 10 left Iteration 1 Error: 1.126066 Iteration 2 Error: 0.082055 Iteration 3 Error: 0.013853 Align patch 16 9 left Iteration 1 Error: 0.797562 Iteration 2 Error: 0.103576 Iteration 3 Error: 0.028784 Align patch 17 8 left Iteration 1 Error: 0.740158 Iteration 2 Error: 0.145166 Iteration 3 Error: 0.026548 Align patch 18 7 left Iteration 1 Error: 1.346138 Iteration 2 Error: 0.143083 Iteration 3 Error: 0.027771 Align patch 19 6 left Iteration 1 Error: 0.434822 Iteration 2 Error: 0.064179 Iteration 3 Error: 0.009742 Align patch 20 5 left Iteration 1 Error: 0.653911 Iteration 2 Error: 0.081000 Iteration 3 Error: 0.016176 Align patch 21 4 left Iteration 1 Error: 1.299441 Iteration 2 Error: 0.252336 Iteration 3 Error: 0.052206 Iteration 4 Error: 0.016958 Align patch 22 3 left Iteration 1 Error: 1.283716 Iteration 2 Error: 0.139076 Iteration 3 Error: 0.032377 Align patch 23 2 left Iteration 1 Error: 1.699013 Iteration 2 Error: 0.280085 Iteration 3 Error: 0.090986 Iteration 4 Error: 0.025242 Align patch 24 1 left Iteration 1 Error: 0.610724 Iteration 2 Error: 0.120564 Iteration 3 Error: 0.022469 Align patch 25 0 left Iteration 1 Error: 0.926142 Iteration 2 Error: 0.113800 Iteration 3 Error: 0.024352 3D Fitting completed. Patch alignment time: 12.37(sec) Local motion has been corrected. Process thread exits. Computational time: 23.182697 sec Total time: 28.737391 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00008hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00008hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.834211s Reading file: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00008hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.551026s ........................................ >>>>>>TIME<<<<<< FFT: 1.054346s Defocus_U Defocus_V Angle CCC 13860.38 13178.69 86.39 0.050942 Final Values Defocus_U Defocus_V Angle CCC 13869.76 13191.20 86.39 0.083757 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00002sq_v01_00009hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00009hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.993e-02 CC threshold: 0.734 Mean Std: 40.93 6.91 Num Hot pixels: 220 Hot pixel threshold: 82.39 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.993337 Iteration 2 Error: 0.493309 Iteration 3 Error: 0.162882 Iteration 4 Error: 0.076330 Iteration 5 Error: 0.035551 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.13 0.04 ...... Frame ( 3) shift: -0.26 0.08 ...... Frame ( 4) shift: -0.39 0.11 ...... Frame ( 5) shift: -0.52 0.15 ...... Frame ( 6) shift: -0.53 0.22 ...... Frame ( 7) shift: -0.43 0.32 ...... Frame ( 8) shift: -0.33 0.42 ...... Frame ( 9) shift: -0.26 0.48 ...... Frame ( 10) shift: -0.23 0.50 ...... Frame ( 11) shift: -0.20 0.51 ...... Frame ( 12) shift: -0.12 0.51 ...... Frame ( 13) shift: 0.01 0.49 ...... Frame ( 14) shift: 0.14 0.47 ...... Frame ( 15) shift: 0.24 0.52 ...... Frame ( 16) shift: 0.32 0.65 ...... Frame ( 17) shift: 0.40 0.78 ...... Frame ( 18) shift: 0.52 0.92 ...... Frame ( 19) shift: 0.70 1.06 ...... Frame ( 20) shift: 0.88 1.20 ...... Frame ( 21) shift: 1.00 1.33 ...... Frame ( 22) shift: 1.05 1.46 ...... Frame ( 23) shift: 1.11 1.59 ...... Frame ( 24) shift: 1.20 1.73 ...... Frame ( 25) shift: 1.34 1.89 ...... Frame ( 26) shift: 1.48 2.05 ...... Frame ( 27) shift: 1.57 2.16 ...... Frame ( 28) shift: 1.62 2.24 ...... Frame ( 29) shift: 1.66 2.31 ...... Frame ( 30) shift: 1.70 2.43 ...... Frame ( 31) shift: 1.73 2.58 ...... Frame ( 32) shift: 1.76 2.73 ...... Frame ( 33) shift: 1.76 2.85 ...... Frame ( 34) shift: 1.72 2.92 ...... Frame ( 35) shift: 1.68 3.00 ...... Frame ( 36) shift: 1.73 3.08 ...... Frame ( 37) shift: 1.88 3.15 ...... Frame ( 38) shift: 2.02 3.23 ...... Frame ( 39) shift: 2.16 3.31 ...... Frame ( 40) shift: 2.31 3.39 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.071003 Iteration 2 Error: 0.217990 Iteration 3 Error: 0.077897 Iteration 4 Error: 0.029182 Align patch 2 23 left Iteration 1 Error: 1.419598 Iteration 2 Error: 0.348630 Iteration 3 Error: 0.121821 Iteration 4 Error: 0.052740 Iteration 5 Error: 0.018214 Align patch 3 22 left Iteration 1 Error: 1.188690 Iteration 2 Error: 0.281977 Iteration 3 Error: 0.118651 Iteration 4 Error: 0.054315 Iteration 5 Error: 0.028203 Align patch 4 21 left Iteration 1 Error: 1.050122 Iteration 2 Error: 0.255153 Iteration 3 Error: 0.111000 Iteration 4 Error: 0.056098 Iteration 5 Error: 0.033532 Align patch 5 20 left Iteration 1 Error: 1.926990 Iteration 2 Error: 0.313311 Iteration 3 Error: 0.099381 Iteration 4 Error: 0.045101 Align patch 6 19 left Iteration 1 Error: 1.171044 Iteration 2 Error: 0.239416 Iteration 3 Error: 0.063158 Iteration 4 Error: 0.037197 Align patch 7 18 left Iteration 1 Error: 0.837416 Iteration 2 Error: 0.335353 Iteration 3 Error: 0.146018 Iteration 4 Error: 0.068800 Iteration 5 Error: 0.027295 Align patch 8 17 left Iteration 1 Error: 1.596960 Iteration 2 Error: 0.311649 Iteration 3 Error: 0.088964 Iteration 4 Error: 0.042882 Align patch 9 16 left Iteration 1 Error: 0.708501 Iteration 2 Error: 0.131982 Iteration 3 Error: 0.045333 Align patch 10 15 left Iteration 1 Error: 0.775461 Iteration 2 Error: 0.213515 Iteration 3 Error: 0.069846 Iteration 4 Error: 0.031796 Align patch 11 14 left Iteration 1 Error: 0.763060 Iteration 2 Error: 0.199102 Iteration 3 Error: 0.053145 Iteration 4 Error: 0.027001 Align patch 12 13 left Iteration 1 Error: 0.670365 Iteration 2 Error: 0.155234 Iteration 3 Error: 0.073238 Iteration 4 Error: 0.032671 Align patch 13 12 left Iteration 1 Error: 0.850438 Iteration 2 Error: 0.196335 Iteration 3 Error: 0.059662 Iteration 4 Error: 0.017894 Align patch 14 11 left Iteration 1 Error: 0.647890 Iteration 2 Error: 0.101750 Iteration 3 Error: 0.025499 Align patch 15 10 left Iteration 1 Error: 1.040079 Iteration 2 Error: 0.238332 Iteration 3 Error: 0.057563 Iteration 4 Error: 0.024226 Align patch 16 9 left Iteration 1 Error: 0.849234 Iteration 2 Error: 0.171903 Iteration 3 Error: 0.040916 Align patch 17 8 left Iteration 1 Error: 0.458946 Iteration 2 Error: 0.107587 Iteration 3 Error: 0.049188 Align patch 18 7 left Iteration 1 Error: 0.811594 Iteration 2 Error: 0.173860 Iteration 3 Error: 0.041010 Align patch 19 6 left Iteration 1 Error: 0.918723 Iteration 2 Error: 0.185045 Iteration 3 Error: 0.045718 Align patch 20 5 left Iteration 1 Error: 0.944002 Iteration 2 Error: 0.238935 Iteration 3 Error: 0.075961 Iteration 4 Error: 0.023612 Align patch 21 4 left Iteration 1 Error: 1.526438 Iteration 2 Error: 0.207484 Iteration 3 Error: 0.050192 Iteration 4 Error: 0.012425 Align patch 22 3 left Iteration 1 Error: 1.134885 Iteration 2 Error: 0.160810 Iteration 3 Error: 0.049980 Align patch 23 2 left Iteration 1 Error: 0.910878 Iteration 2 Error: 0.184856 Iteration 3 Error: 0.078968 Iteration 4 Error: 0.031901 Align patch 24 1 left Iteration 1 Error: 0.793173 Iteration 2 Error: 0.115233 Iteration 3 Error: 0.065800 Iteration 4 Error: 0.014004 Align patch 25 0 left Iteration 1 Error: 0.816285 Iteration 2 Error: 0.340377 Iteration 3 Error: 0.120598 Iteration 4 Error: 0.052414 Iteration 5 Error: 0.022998 3D Fitting completed. Patch alignment time: 13.26(sec) Local motion has been corrected. Process thread exits. Computational time: 24.116192 sec Total time: 30.413260 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00009hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00009hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.843928s Reading file: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00009hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.235361s ........................................ >>>>>>TIME<<<<<< FFT: 1.035148s Defocus_U Defocus_V Angle CCC 14431.64 15384.77 12.83 0.046221 Final Values Defocus_U Defocus_V Angle CCC 14439.45 15367.58 12.52 0.075457 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00002sq_v01_00009hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00009hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.002e-01 CC threshold: 0.736 Mean Std: 41.21 6.97 Num Hot pixels: 219 Hot pixel threshold: 83.02 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.367852 Iteration 2 Error: 0.189424 Iteration 3 Error: 0.048615 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.04 0.15 ...... Frame ( 3) shift: -0.08 0.29 ...... Frame ( 4) shift: -0.12 0.44 ...... Frame ( 5) shift: -0.15 0.59 ...... Frame ( 6) shift: -0.10 0.70 ...... Frame ( 7) shift: 0.04 0.79 ...... Frame ( 8) shift: 0.18 0.88 ...... Frame ( 9) shift: 0.27 0.97 ...... Frame ( 10) shift: 0.31 1.08 ...... Frame ( 11) shift: 0.35 1.18 ...... Frame ( 12) shift: 0.41 1.26 ...... Frame ( 13) shift: 0.48 1.31 ...... Frame ( 14) shift: 0.55 1.36 ...... Frame ( 15) shift: 0.61 1.42 ...... Frame ( 16) shift: 0.64 1.47 ...... Frame ( 17) shift: 0.68 1.53 ...... Frame ( 18) shift: 0.73 1.59 ...... Frame ( 19) shift: 0.80 1.66 ...... Frame ( 20) shift: 0.88 1.72 ...... Frame ( 21) shift: 0.95 1.74 ...... Frame ( 22) shift: 1.02 1.70 ...... Frame ( 23) shift: 1.09 1.67 ...... Frame ( 24) shift: 1.14 1.69 ...... Frame ( 25) shift: 1.17 1.77 ...... Frame ( 26) shift: 1.19 1.84 ...... Frame ( 27) shift: 1.20 1.90 ...... Frame ( 28) shift: 1.18 1.95 ...... Frame ( 29) shift: 1.16 2.00 ...... Frame ( 30) shift: 1.17 2.03 ...... Frame ( 31) shift: 1.20 2.03 ...... Frame ( 32) shift: 1.23 2.04 ...... Frame ( 33) shift: 1.22 2.09 ...... Frame ( 34) shift: 1.15 2.18 ...... Frame ( 35) shift: 1.09 2.26 ...... Frame ( 36) shift: 1.07 2.31 ...... Frame ( 37) shift: 1.11 2.31 ...... Frame ( 38) shift: 1.14 2.31 ...... Frame ( 39) shift: 1.17 2.32 ...... Frame ( 40) shift: 1.20 2.32 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.281571 Iteration 2 Error: 0.362289 Iteration 3 Error: 0.087193 Iteration 4 Error: 0.034700 Align patch 2 23 left Iteration 1 Error: 1.454787 Iteration 2 Error: 0.214352 Iteration 3 Error: 0.076028 Iteration 4 Error: 0.029650 Align patch 3 22 left Iteration 1 Error: 0.651769 Iteration 2 Error: 0.102171 Iteration 3 Error: 0.018776 Align patch 4 21 left Iteration 1 Error: 0.591810 Iteration 2 Error: 0.104925 Iteration 3 Error: 0.023988 Align patch 5 20 left Iteration 1 Error: 0.661525 Iteration 2 Error: 0.094199 Iteration 3 Error: 0.023538 Align patch 6 19 left Iteration 1 Error: 1.855527 Iteration 2 Error: 0.226635 Iteration 3 Error: 0.054346 Iteration 4 Error: 0.020152 Align patch 7 18 left Iteration 1 Error: 0.784338 Iteration 2 Error: 0.262325 Iteration 3 Error: 0.069679 Iteration 4 Error: 0.028246 Align patch 8 17 left Iteration 1 Error: 0.971371 Iteration 2 Error: 0.106365 Iteration 3 Error: 0.031774 Align patch 9 16 left Iteration 1 Error: 0.845534 Iteration 2 Error: 0.116390 Iteration 3 Error: 0.029258 Align patch 10 15 left Iteration 1 Error: 0.813949 Iteration 2 Error: 0.167778 Iteration 3 Error: 0.026297 Align patch 11 14 left Iteration 1 Error: 1.204138 Iteration 2 Error: 0.195472 Iteration 3 Error: 0.053649 Iteration 4 Error: 0.022500 Align patch 12 13 left Iteration 1 Error: 0.792135 Iteration 2 Error: 0.177533 Iteration 3 Error: 0.073989 Iteration 4 Error: 0.026299 Align patch 13 12 left Iteration 1 Error: 0.735369 Iteration 2 Error: 0.134471 Iteration 3 Error: 0.031156 Align patch 14 11 left Iteration 1 Error: 1.044796 Iteration 2 Error: 0.128003 Iteration 3 Error: 0.034563 Align patch 15 10 left Iteration 1 Error: 0.585883 Iteration 2 Error: 0.109535 Iteration 3 Error: 0.026628 Align patch 16 9 left Iteration 1 Error: 0.650097 Iteration 2 Error: 0.090863 Iteration 3 Error: 0.024638 Align patch 17 8 left Iteration 1 Error: 1.107307 Iteration 2 Error: 0.120653 Iteration 3 Error: 0.033755 Align patch 18 7 left Iteration 1 Error: 0.544453 Iteration 2 Error: 0.084753 Iteration 3 Error: 0.015142 Align patch 19 6 left Iteration 1 Error: 0.622922 Iteration 2 Error: 0.126903 Iteration 3 Error: 0.031306 Align patch 20 5 left Iteration 1 Error: 0.797046 Iteration 2 Error: 0.120538 Iteration 3 Error: 0.029332 Align patch 21 4 left Iteration 1 Error: 0.512547 Iteration 2 Error: 0.219144 Iteration 3 Error: 0.051204 Iteration 4 Error: 0.015412 Align patch 22 3 left Iteration 1 Error: 0.722468 Iteration 2 Error: 0.115180 Iteration 3 Error: 0.029247 Align patch 23 2 left Iteration 1 Error: 1.318495 Iteration 2 Error: 0.307217 Iteration 3 Error: 0.069817 Iteration 4 Error: 0.017069 Align patch 24 1 left Iteration 1 Error: 1.272578 Iteration 2 Error: 0.124642 Iteration 3 Error: 0.018401 Align patch 25 0 left Iteration 1 Error: 0.800507 Iteration 2 Error: 0.129383 Iteration 3 Error: 0.032653 3D Fitting completed. Patch alignment time: 12.28(sec) Local motion has been corrected. Process thread exits. Computational time: 22.402037 sec Total time: 28.437279 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00009hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00009hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.463125s Reading file: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00009hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.445453s ........................................ >>>>>>TIME<<<<<< FFT: 0.885965s Defocus_U Defocus_V Angle CCC 15306.65 14818.37 88.97 0.058086 Final Values Defocus_U Defocus_V Angle CCC 15317.59 14810.56 89.59 0.093675 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00002sq_v01_00009hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00009hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.998e-02 CC threshold: 0.734 Mean Std: 41.49 6.94 Num Hot pixels: 222 Hot pixel threshold: 83.11 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.400794 Iteration 2 Error: 0.255503 Iteration 3 Error: 0.077326 Iteration 4 Error: 0.035733 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.06 0.06 ...... Frame ( 3) shift: -0.13 0.13 ...... Frame ( 4) shift: -0.19 0.19 ...... Frame ( 5) shift: -0.25 0.25 ...... Frame ( 6) shift: -0.23 0.39 ...... Frame ( 7) shift: -0.13 0.59 ...... Frame ( 8) shift: -0.03 0.80 ...... Frame ( 9) shift: 0.05 0.93 ...... Frame ( 10) shift: 0.10 1.00 ...... Frame ( 11) shift: 0.15 1.07 ...... Frame ( 12) shift: 0.19 1.17 ...... Frame ( 13) shift: 0.21 1.30 ...... Frame ( 14) shift: 0.23 1.42 ...... Frame ( 15) shift: 0.29 1.52 ...... Frame ( 16) shift: 0.37 1.60 ...... Frame ( 17) shift: 0.46 1.67 ...... Frame ( 18) shift: 0.51 1.75 ...... Frame ( 19) shift: 0.52 1.83 ...... Frame ( 20) shift: 0.54 1.91 ...... Frame ( 21) shift: 0.55 1.97 ...... Frame ( 22) shift: 0.57 2.02 ...... Frame ( 23) shift: 0.59 2.06 ...... Frame ( 24) shift: 0.62 2.14 ...... Frame ( 25) shift: 0.68 2.26 ...... Frame ( 26) shift: 0.74 2.39 ...... Frame ( 27) shift: 0.79 2.44 ...... Frame ( 28) shift: 0.83 2.44 ...... Frame ( 29) shift: 0.87 2.44 ...... Frame ( 30) shift: 0.93 2.46 ...... Frame ( 31) shift: 1.02 2.51 ...... Frame ( 32) shift: 1.10 2.56 ...... Frame ( 33) shift: 1.12 2.57 ...... Frame ( 34) shift: 1.06 2.54 ...... Frame ( 35) shift: 0.99 2.51 ...... Frame ( 36) shift: 0.97 2.52 ...... Frame ( 37) shift: 0.99 2.58 ...... Frame ( 38) shift: 1.01 2.63 ...... Frame ( 39) shift: 1.03 2.68 ...... Frame ( 40) shift: 1.05 2.73 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.541643 Iteration 2 Error: 0.274216 Iteration 3 Error: 0.069066 Iteration 4 Error: 0.022578 Align patch 2 23 left Iteration 1 Error: 1.138215 Iteration 2 Error: 0.275269 Iteration 3 Error: 0.144961 Iteration 4 Error: 0.069048 Iteration 5 Error: 0.030075 Align patch 3 22 left Iteration 1 Error: 1.067904 Iteration 2 Error: 0.218180 Iteration 3 Error: 0.095829 Iteration 4 Error: 0.045429 Align patch 4 21 left Iteration 1 Error: 1.071273 Iteration 2 Error: 0.125832 Iteration 3 Error: 0.046804 Align patch 5 20 left Iteration 1 Error: 0.514145 Iteration 2 Error: 0.096953 Iteration 3 Error: 0.040056 Align patch 6 19 left Iteration 1 Error: 0.833176 Iteration 2 Error: 0.326764 Iteration 3 Error: 0.099136 Iteration 4 Error: 0.040570 Align patch 7 18 left Iteration 1 Error: 1.124588 Iteration 2 Error: 0.164466 Iteration 3 Error: 0.058406 Iteration 4 Error: 0.016178 Align patch 8 17 left Iteration 1 Error: 0.998764 Iteration 2 Error: 0.223951 Iteration 3 Error: 0.069198 Iteration 4 Error: 0.034551 Align patch 9 16 left Iteration 1 Error: 0.787360 Iteration 2 Error: 0.121425 Iteration 3 Error: 0.041508 Align patch 10 15 left Iteration 1 Error: 0.995672 Iteration 2 Error: 0.132139 Iteration 3 Error: 0.032830 Align patch 11 14 left Iteration 1 Error: 0.855285 Iteration 2 Error: 0.179069 Iteration 3 Error: 0.044331 Align patch 12 13 left Iteration 1 Error: 0.812872 Iteration 2 Error: 0.192710 Iteration 3 Error: 0.049442 Align patch 13 12 left Iteration 1 Error: 1.177479 Iteration 2 Error: 0.179665 Iteration 3 Error: 0.030974 Align patch 14 11 left Iteration 1 Error: 0.861260 Iteration 2 Error: 0.158987 Iteration 3 Error: 0.043360 Align patch 15 10 left Iteration 1 Error: 0.747197 Iteration 2 Error: 0.171257 Iteration 3 Error: 0.048506 Align patch 16 9 left Iteration 1 Error: 1.010224 Iteration 2 Error: 0.182956 Iteration 3 Error: 0.034400 Align patch 17 8 left Iteration 1 Error: 0.730235 Iteration 2 Error: 0.186724 Iteration 3 Error: 0.046047 Align patch 18 7 left Iteration 1 Error: 0.799602 Iteration 2 Error: 0.213414 Iteration 3 Error: 0.083077 Iteration 4 Error: 0.038826 Align patch 19 6 left Iteration 1 Error: 0.627771 Iteration 2 Error: 0.155290 Iteration 3 Error: 0.041885 Align patch 20 5 left Iteration 1 Error: 0.621975 Iteration 2 Error: 0.092765 Iteration 3 Error: 0.019128 Align patch 21 4 left Iteration 1 Error: 0.655642 Iteration 2 Error: 0.121541 Iteration 3 Error: 0.054199 Iteration 4 Error: 0.022460 Align patch 22 3 left Iteration 1 Error: 0.515626 Iteration 2 Error: 0.083630 Iteration 3 Error: 0.021638 Align patch 23 2 left Iteration 1 Error: 1.389712 Iteration 2 Error: 0.160362 Iteration 3 Error: 0.044792 Align patch 24 1 left Iteration 1 Error: 0.635222 Iteration 2 Error: 0.217274 Iteration 3 Error: 0.097887 Iteration 4 Error: 0.042510 Align patch 25 0 left Iteration 1 Error: 1.269454 Iteration 2 Error: 0.239045 Iteration 3 Error: 0.048756 3D Fitting completed. Patch alignment time: 12.05(sec) Local motion has been corrected. Process thread exits. Computational time: 21.853512 sec Total time: 28.424128 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00009hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00009hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.848320s Reading file: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00009hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.708470s ........................................ >>>>>>TIME<<<<<< FFT: 0.962110s Defocus_U Defocus_V Angle CCC 15189.46 16189.46 6.64 0.043489 Final Values Defocus_U Defocus_V Angle CCC 15186.33 16195.71 5.71 0.069723 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00002sq_v01_00010hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00010hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.001e-01 CC threshold: 0.735 Mean Std: 41.20 6.93 Num Hot pixels: 238 Hot pixel threshold: 82.80 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.214728 Iteration 2 Error: 0.192203 Iteration 3 Error: 0.044174 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.08 -0.06 ...... Frame ( 3) shift: -0.16 -0.11 ...... Frame ( 4) shift: -0.24 -0.17 ...... Frame ( 5) shift: -0.32 -0.23 ...... Frame ( 6) shift: -0.32 -0.18 ...... Frame ( 7) shift: -0.26 -0.01 ...... Frame ( 8) shift: -0.19 0.15 ...... Frame ( 9) shift: -0.13 0.26 ...... Frame ( 10) shift: -0.09 0.31 ...... Frame ( 11) shift: -0.05 0.36 ...... Frame ( 12) shift: 0.01 0.46 ...... Frame ( 13) shift: 0.09 0.61 ...... Frame ( 14) shift: 0.16 0.76 ...... Frame ( 15) shift: 0.23 0.86 ...... Frame ( 16) shift: 0.29 0.89 ...... Frame ( 17) shift: 0.34 0.93 ...... Frame ( 18) shift: 0.35 0.99 ...... Frame ( 19) shift: 0.32 1.07 ...... Frame ( 20) shift: 0.29 1.16 ...... Frame ( 21) shift: 0.27 1.23 ...... Frame ( 22) shift: 0.25 1.31 ...... Frame ( 23) shift: 0.23 1.38 ...... Frame ( 24) shift: 0.26 1.44 ...... Frame ( 25) shift: 0.34 1.50 ...... Frame ( 26) shift: 0.42 1.55 ...... Frame ( 27) shift: 0.46 1.59 ...... Frame ( 28) shift: 0.47 1.60 ...... Frame ( 29) shift: 0.47 1.62 ...... Frame ( 30) shift: 0.49 1.62 ...... Frame ( 31) shift: 0.53 1.60 ...... Frame ( 32) shift: 0.57 1.58 ...... Frame ( 33) shift: 0.57 1.58 ...... Frame ( 34) shift: 0.53 1.58 ...... Frame ( 35) shift: 0.50 1.59 ...... Frame ( 36) shift: 0.48 1.59 ...... Frame ( 37) shift: 0.48 1.59 ...... Frame ( 38) shift: 0.48 1.60 ...... Frame ( 39) shift: 0.48 1.60 ...... Frame ( 40) shift: 0.48 1.60 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.832449 Iteration 2 Error: 0.137022 Iteration 3 Error: 0.073584 Iteration 4 Error: 0.022531 Align patch 2 23 left Iteration 1 Error: 0.804595 Iteration 2 Error: 0.196485 Iteration 3 Error: 0.047882 Align patch 3 22 left Iteration 1 Error: 0.572501 Iteration 2 Error: 0.075284 Iteration 3 Error: 0.014104 Align patch 4 21 left Iteration 1 Error: 0.761600 Iteration 2 Error: 0.130895 Iteration 3 Error: 0.020345 Align patch 5 20 left Iteration 1 Error: 0.503305 Iteration 2 Error: 0.045010 Align patch 6 19 left Iteration 1 Error: 0.736457 Iteration 2 Error: 0.123423 Iteration 3 Error: 0.038085 Align patch 7 18 left Iteration 1 Error: 0.422309 Iteration 2 Error: 0.073426 Iteration 3 Error: 0.023548 Align patch 8 17 left Iteration 1 Error: 0.490965 Iteration 2 Error: 0.102150 Iteration 3 Error: 0.042402 Align patch 9 16 left Iteration 1 Error: 0.908090 Iteration 2 Error: 0.158339 Iteration 3 Error: 0.037350 Align patch 10 15 left Iteration 1 Error: 0.621053 Iteration 2 Error: 0.070419 Iteration 3 Error: 0.015778 Align patch 11 14 left Iteration 1 Error: 0.980515 Iteration 2 Error: 0.170438 Iteration 3 Error: 0.051172 Iteration 4 Error: 0.017317 Align patch 12 13 left Iteration 1 Error: 0.689890 Iteration 2 Error: 0.121629 Iteration 3 Error: 0.036688 Align patch 13 12 left Iteration 1 Error: 0.737097 Iteration 2 Error: 0.109150 Iteration 3 Error: 0.024125 Align patch 14 11 left Iteration 1 Error: 0.737995 Iteration 2 Error: 0.072154 Iteration 3 Error: 0.021098 Align patch 15 10 left Iteration 1 Error: 0.729742 Iteration 2 Error: 0.071064 Iteration 3 Error: 0.016079 Align patch 16 9 left Iteration 1 Error: 0.807885 Iteration 2 Error: 0.172015 Iteration 3 Error: 0.049057 Align patch 17 8 left Iteration 1 Error: 0.526875 Iteration 2 Error: 0.068535 Iteration 3 Error: 0.017383 Align patch 18 7 left Iteration 1 Error: 0.501123 Iteration 2 Error: 0.081922 Iteration 3 Error: 0.012735 Align patch 19 6 left Iteration 1 Error: 0.611952 Iteration 2 Error: 0.105343 Iteration 3 Error: 0.029746 Align patch 20 5 left Iteration 1 Error: 0.565051 Iteration 2 Error: 0.154543 Iteration 3 Error: 0.030891 Align patch 21 4 left Iteration 1 Error: 0.724110 Iteration 2 Error: 0.155196 Iteration 3 Error: 0.042084 Align patch 22 3 left Iteration 1 Error: 0.942950 Iteration 2 Error: 0.154578 Iteration 3 Error: 0.039250 Align patch 23 2 left Iteration 1 Error: 0.697169 Iteration 2 Error: 0.090467 Iteration 3 Error: 0.026836 Align patch 24 1 left Iteration 1 Error: 0.822252 Iteration 2 Error: 0.149995 Iteration 3 Error: 0.038650 Align patch 25 0 left Iteration 1 Error: 0.727069 Iteration 2 Error: 0.145727 Iteration 3 Error: 0.051074 Iteration 4 Error: 0.013778 3D Fitting completed. Patch alignment time: 11.79(sec) Local motion has been corrected. Process thread exits. Computational time: 21.856501 sec Total time: 28.353245 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00010hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00010hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.582475s Reading file: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00010hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.507351s ........................................ >>>>>>TIME<<<<<< FFT: 0.888798s Defocus_U Defocus_V Angle CCC 11435.54 12337.91 12.86 0.047727 Final Values Defocus_U Defocus_V Angle CCC 11460.54 12341.05 12.86 0.082358 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00002sq_v01_00010hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00010hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 40.58 7.36 Num Hot pixels: 172 Hot pixel threshold: 84.76 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.716898 Iteration 2 Error: 0.085733 Iteration 3 Error: 0.019793 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.12 -0.02 ...... Frame ( 3) shift: -0.23 -0.03 ...... Frame ( 4) shift: -0.35 -0.05 ...... Frame ( 5) shift: -0.46 -0.07 ...... Frame ( 6) shift: -0.50 -0.05 ...... Frame ( 7) shift: -0.46 -0.00 ...... Frame ( 8) shift: -0.42 0.04 ...... Frame ( 9) shift: -0.38 0.11 ...... Frame ( 10) shift: -0.34 0.18 ...... Frame ( 11) shift: -0.30 0.26 ...... Frame ( 12) shift: -0.25 0.31 ...... Frame ( 13) shift: -0.18 0.33 ...... Frame ( 14) shift: -0.11 0.35 ...... Frame ( 15) shift: -0.05 0.40 ...... Frame ( 16) shift: -0.01 0.47 ...... Frame ( 17) shift: 0.04 0.55 ...... Frame ( 18) shift: 0.07 0.59 ...... Frame ( 19) shift: 0.08 0.61 ...... Frame ( 20) shift: 0.09 0.63 ...... Frame ( 21) shift: 0.14 0.64 ...... Frame ( 22) shift: 0.23 0.66 ...... Frame ( 23) shift: 0.31 0.67 ...... Frame ( 24) shift: 0.37 0.67 ...... Frame ( 25) shift: 0.40 0.64 ...... Frame ( 26) shift: 0.42 0.62 ...... Frame ( 27) shift: 0.46 0.59 ...... Frame ( 28) shift: 0.51 0.55 ...... Frame ( 29) shift: 0.55 0.51 ...... Frame ( 30) shift: 0.58 0.48 ...... Frame ( 31) shift: 0.60 0.45 ...... Frame ( 32) shift: 0.62 0.43 ...... Frame ( 33) shift: 0.61 0.41 ...... Frame ( 34) shift: 0.59 0.41 ...... Frame ( 35) shift: 0.57 0.42 ...... Frame ( 36) shift: 0.57 0.46 ...... Frame ( 37) shift: 0.58 0.56 ...... Frame ( 38) shift: 0.60 0.65 ...... Frame ( 39) shift: 0.61 0.75 ...... Frame ( 40) shift: 0.63 0.84 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.111181 Iteration 2 Error: 0.104936 Iteration 3 Error: 0.026086 Align patch 2 23 left Iteration 1 Error: 1.211824 Iteration 2 Error: 0.231657 Iteration 3 Error: 0.061459 Iteration 4 Error: 0.025655 Align patch 3 22 left Iteration 1 Error: 0.803544 Iteration 2 Error: 0.071224 Iteration 3 Error: 0.018611 Align patch 4 21 left Iteration 1 Error: 0.339045 Iteration 2 Error: 0.050707 Iteration 3 Error: 0.007104 Align patch 5 20 left Iteration 1 Error: 0.354312 Iteration 2 Error: 0.099097 Iteration 3 Error: 0.027794 Align patch 6 19 left Iteration 1 Error: 1.068911 Iteration 2 Error: 0.128961 Iteration 3 Error: 0.022410 Align patch 7 18 left Iteration 1 Error: 0.582599 Iteration 2 Error: 0.079751 Iteration 3 Error: 0.016122 Align patch 8 17 left Iteration 1 Error: 0.630001 Iteration 2 Error: 0.072962 Iteration 3 Error: 0.018298 Align patch 9 16 left Iteration 1 Error: 0.535197 Iteration 2 Error: 0.071662 Iteration 3 Error: 0.013398 Align patch 10 15 left Iteration 1 Error: 0.600133 Iteration 2 Error: 0.087635 Iteration 3 Error: 0.017761 Align patch 11 14 left Iteration 1 Error: 0.627776 Iteration 2 Error: 0.108336 Iteration 3 Error: 0.014944 Align patch 12 13 left Iteration 1 Error: 0.532790 Iteration 2 Error: 0.096332 Iteration 3 Error: 0.023531 Align patch 13 12 left Iteration 1 Error: 0.365397 Iteration 2 Error: 0.042296 Align patch 14 11 left Iteration 1 Error: 0.640300 Iteration 2 Error: 0.068986 Iteration 3 Error: 0.011821 Align patch 15 10 left Iteration 1 Error: 0.613573 Iteration 2 Error: 0.100485 Iteration 3 Error: 0.012822 Align patch 16 9 left Iteration 1 Error: 0.601236 Iteration 2 Error: 0.139047 Iteration 3 Error: 0.027700 Align patch 17 8 left Iteration 1 Error: 0.735816 Iteration 2 Error: 0.093874 Iteration 3 Error: 0.024344 Align patch 18 7 left Iteration 1 Error: 0.382906 Iteration 2 Error: 0.092865 Iteration 3 Error: 0.017754 Align patch 19 6 left Iteration 1 Error: 0.546742 Iteration 2 Error: 0.108963 Iteration 3 Error: 0.020160 Align patch 20 5 left Iteration 1 Error: 0.563164 Iteration 2 Error: 0.068321 Iteration 3 Error: 0.015961 Align patch 21 4 left Iteration 1 Error: 0.538099 Iteration 2 Error: 0.069668 Iteration 3 Error: 0.011063 Align patch 22 3 left Iteration 1 Error: 0.598362 Iteration 2 Error: 0.112354 Iteration 3 Error: 0.019752 Align patch 23 2 left Iteration 1 Error: 0.696879 Iteration 2 Error: 0.081887 Iteration 3 Error: 0.015697 Align patch 24 1 left Iteration 1 Error: 0.681022 Iteration 2 Error: 0.148879 Iteration 3 Error: 0.022961 Align patch 25 0 left Iteration 1 Error: 0.773445 Iteration 2 Error: 0.113575 Iteration 3 Error: 0.028805 3D Fitting completed. Patch alignment time: 10.92(sec) Local motion has been corrected. Process thread exits. Computational time: 21.174307 sec Total time: 27.779543 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00010hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00010hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.488963s Reading file: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00010hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.029554s ........................................ >>>>>>TIME<<<<<< FFT: 1.290059s Defocus_U Defocus_V Angle CCC 14876.96 15318.36 0.40 0.055379 Final Values Defocus_U Defocus_V Angle CCC 14875.39 15313.69 1.98 0.086396 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00002sq_v01_00010hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00010hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 39.89 6.95 Num Hot pixels: 222 Hot pixel threshold: 81.59 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.362329 Iteration 2 Error: 0.244237 Iteration 3 Error: 0.048052 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.26 -0.31 ...... Frame ( 3) shift: -0.53 -0.62 ...... Frame ( 4) shift: -0.79 -0.93 ...... Frame ( 5) shift: -1.06 -1.24 ...... Frame ( 6) shift: -1.20 -1.38 ...... Frame ( 7) shift: -1.21 -1.37 ...... Frame ( 8) shift: -1.23 -1.35 ...... Frame ( 9) shift: -1.25 -1.32 ...... Frame ( 10) shift: -1.28 -1.27 ...... Frame ( 11) shift: -1.31 -1.22 ...... Frame ( 12) shift: -1.30 -1.15 ...... Frame ( 13) shift: -1.24 -1.06 ...... Frame ( 14) shift: -1.18 -0.98 ...... Frame ( 15) shift: -1.11 -0.91 ...... Frame ( 16) shift: -1.04 -0.85 ...... Frame ( 17) shift: -0.96 -0.80 ...... Frame ( 18) shift: -0.91 -0.74 ...... Frame ( 19) shift: -0.90 -0.67 ...... Frame ( 20) shift: -0.88 -0.61 ...... Frame ( 21) shift: -0.88 -0.54 ...... Frame ( 22) shift: -0.90 -0.45 ...... Frame ( 23) shift: -0.92 -0.36 ...... Frame ( 24) shift: -0.91 -0.26 ...... Frame ( 25) shift: -0.88 -0.14 ...... Frame ( 26) shift: -0.85 -0.03 ...... Frame ( 27) shift: -0.83 0.06 ...... Frame ( 28) shift: -0.80 0.13 ...... Frame ( 29) shift: -0.77 0.20 ...... Frame ( 30) shift: -0.76 0.28 ...... Frame ( 31) shift: -0.78 0.35 ...... Frame ( 32) shift: -0.80 0.43 ...... Frame ( 33) shift: -0.80 0.52 ...... Frame ( 34) shift: -0.77 0.62 ...... Frame ( 35) shift: -0.75 0.72 ...... Frame ( 36) shift: -0.71 0.82 ...... Frame ( 37) shift: -0.67 0.90 ...... Frame ( 38) shift: -0.62 0.99 ...... Frame ( 39) shift: -0.58 1.07 ...... Frame ( 40) shift: -0.53 1.16 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.467357 Iteration 2 Error: 0.165075 Iteration 3 Error: 0.054224 Iteration 4 Error: 0.023064 Align patch 2 23 left Iteration 1 Error: 0.584251 Iteration 2 Error: 0.128263 Iteration 3 Error: 0.059324 Iteration 4 Error: 0.022173 Align patch 3 22 left Iteration 1 Error: 0.752966 Iteration 2 Error: 0.107998 Iteration 3 Error: 0.036963 Align patch 4 21 left Iteration 1 Error: 0.499539 Iteration 2 Error: 0.059636 Iteration 3 Error: 0.018189 Align patch 5 20 left Iteration 1 Error: 0.606251 Iteration 2 Error: 0.080846 Iteration 3 Error: 0.019890 Align patch 6 19 left Iteration 1 Error: 0.744462 Iteration 2 Error: 0.197242 Iteration 3 Error: 0.047078 Align patch 7 18 left Iteration 1 Error: 0.869069 Iteration 2 Error: 0.106833 Iteration 3 Error: 0.026134 Align patch 8 17 left Iteration 1 Error: 0.560557 Iteration 2 Error: 0.077271 Iteration 3 Error: 0.026269 Align patch 9 16 left Iteration 1 Error: 0.617742 Iteration 2 Error: 0.063231 Iteration 3 Error: 0.012556 Align patch 10 15 left Iteration 1 Error: 0.720418 Iteration 2 Error: 0.127162 Iteration 3 Error: 0.025243 Align patch 11 14 left Iteration 1 Error: 0.877609 Iteration 2 Error: 0.154834 Iteration 3 Error: 0.037348 Align patch 12 13 left Iteration 1 Error: 1.540863 Iteration 2 Error: 0.396639 Iteration 3 Error: 0.125051 Iteration 4 Error: 0.047525 Align patch 13 12 left Iteration 1 Error: 1.082718 Iteration 2 Error: 0.205919 Iteration 3 Error: 0.049163 Align patch 14 11 left Iteration 1 Error: 1.004085 Iteration 2 Error: 0.136964 Iteration 3 Error: 0.030833 Align patch 15 10 left Iteration 1 Error: 0.420887 Iteration 2 Error: 0.052971 Iteration 3 Error: 0.011807 Align patch 16 9 left Iteration 1 Error: 0.927139 Iteration 2 Error: 0.122335 Iteration 3 Error: 0.039002 Align patch 17 8 left Iteration 1 Error: 0.800228 Iteration 2 Error: 0.228235 Iteration 3 Error: 0.076629 Iteration 4 Error: 0.023989 Align patch 18 7 left Iteration 1 Error: 0.936045 Iteration 2 Error: 0.228909 Iteration 3 Error: 0.053955 Iteration 4 Error: 0.023177 Align patch 19 6 left Iteration 1 Error: 0.780251 Iteration 2 Error: 0.066758 Iteration 3 Error: 0.015977 Align patch 20 5 left Iteration 1 Error: 0.823356 Iteration 2 Error: 0.135048 Iteration 3 Error: 0.037539 Align patch 21 4 left Iteration 1 Error: 0.853048 Iteration 2 Error: 0.142528 Iteration 3 Error: 0.034027 Align patch 22 3 left Iteration 1 Error: 1.018266 Iteration 2 Error: 0.189356 Iteration 3 Error: 0.028500 Align patch 23 2 left Iteration 1 Error: 0.830494 Iteration 2 Error: 0.146355 Iteration 3 Error: 0.060358 Iteration 4 Error: 0.015185 Align patch 24 1 left Iteration 1 Error: 1.071241 Iteration 2 Error: 0.228981 Iteration 3 Error: 0.038316 Align patch 25 0 left Iteration 1 Error: 0.530169 Iteration 2 Error: 0.113746 Iteration 3 Error: 0.016052 3D Fitting completed. Patch alignment time: 12.10(sec) Local motion has been corrected. Process thread exits. Computational time: 22.924074 sec Total time: 29.481775 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00010hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00010hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.619513s Reading file: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00010hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.732657s ........................................ >>>>>>TIME<<<<<< FFT: 0.915431s Defocus_U Defocus_V Angle CCC 14418.87 15225.71 3.80 0.045935 Final Values Defocus_U Defocus_V Angle CCC 14414.19 15202.30 4.11 0.070769 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00002sq_v01_00010hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00010hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 40.23 7.08 Num Hot pixels: 209 Hot pixel threshold: 82.68 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.045795 Iteration 2 Error: 0.136117 Iteration 3 Error: 0.028988 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.30 -0.04 ...... Frame ( 3) shift: -0.59 -0.07 ...... Frame ( 4) shift: -0.89 -0.11 ...... Frame ( 5) shift: -1.18 -0.14 ...... Frame ( 6) shift: -1.34 -0.12 ...... Frame ( 7) shift: -1.37 -0.03 ...... Frame ( 8) shift: -1.39 0.06 ...... Frame ( 9) shift: -1.40 0.13 ...... Frame ( 10) shift: -1.40 0.18 ...... Frame ( 11) shift: -1.39 0.23 ...... Frame ( 12) shift: -1.38 0.34 ...... Frame ( 13) shift: -1.38 0.49 ...... Frame ( 14) shift: -1.37 0.64 ...... Frame ( 15) shift: -1.35 0.75 ...... Frame ( 16) shift: -1.30 0.80 ...... Frame ( 17) shift: -1.25 0.86 ...... Frame ( 18) shift: -1.21 0.93 ...... Frame ( 19) shift: -1.16 1.03 ...... Frame ( 20) shift: -1.11 1.12 ...... Frame ( 21) shift: -1.06 1.21 ...... Frame ( 22) shift: -1.01 1.30 ...... Frame ( 23) shift: -0.96 1.39 ...... Frame ( 24) shift: -0.92 1.42 ...... Frame ( 25) shift: -0.90 1.41 ...... Frame ( 26) shift: -0.87 1.39 ...... Frame ( 27) shift: -0.85 1.38 ...... Frame ( 28) shift: -0.83 1.36 ...... Frame ( 29) shift: -0.82 1.35 ...... Frame ( 30) shift: -0.78 1.36 ...... Frame ( 31) shift: -0.74 1.39 ...... Frame ( 32) shift: -0.69 1.42 ...... Frame ( 33) shift: -0.69 1.42 ...... Frame ( 34) shift: -0.75 1.39 ...... Frame ( 35) shift: -0.81 1.35 ...... Frame ( 36) shift: -0.84 1.34 ...... Frame ( 37) shift: -0.83 1.35 ...... Frame ( 38) shift: -0.83 1.37 ...... Frame ( 39) shift: -0.82 1.38 ...... Frame ( 40) shift: -0.82 1.39 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 3.238915 Iteration 2 Error: 0.858727 Iteration 3 Error: 0.483389 Iteration 4 Error: 0.400362 Iteration 5 Error: 0.312138 Align patch 1 24 left Iteration 1 Error: 2.367658 Iteration 2 Error: 0.365323 Iteration 3 Error: 0.111076 Iteration 4 Error: 0.026852 Align patch 2 23 left Iteration 1 Error: 1.837305 Iteration 2 Error: 0.410154 Iteration 3 Error: 0.095755 Iteration 4 Error: 0.027469 Align patch 3 22 left Iteration 1 Error: 0.793602 Iteration 2 Error: 0.147949 Iteration 3 Error: 0.031535 Align patch 4 21 left Iteration 1 Error: 0.532857 Iteration 2 Error: 0.087813 Iteration 3 Error: 0.019849 Align patch 5 20 left Iteration 1 Error: 0.736956 Iteration 2 Error: 0.134522 Iteration 3 Error: 0.024192 Align patch 6 19 left Iteration 1 Error: 1.192297 Iteration 2 Error: 0.326198 Iteration 3 Error: 0.120274 Iteration 4 Error: 0.057130 Iteration 5 Error: 0.024512 Align patch 7 18 left Iteration 1 Error: 1.797132 Iteration 2 Error: 0.422082 Iteration 3 Error: 0.150653 Iteration 4 Error: 0.071641 Iteration 5 Error: 0.032001 Align patch 8 17 left Iteration 1 Error: 0.618209 Iteration 2 Error: 0.068443 Iteration 3 Error: 0.019318 Align patch 9 16 left Iteration 1 Error: 0.752983 Iteration 2 Error: 0.146092 Iteration 3 Error: 0.042138 Align patch 10 15 left Iteration 1 Error: 0.886218 Iteration 2 Error: 0.139806 Iteration 3 Error: 0.039829 Align patch 11 14 left Iteration 1 Error: 0.652100 Iteration 2 Error: 0.101483 Iteration 3 Error: 0.018466 Align patch 12 13 left Iteration 1 Error: 0.610654 Iteration 2 Error: 0.121892 Iteration 3 Error: 0.027487 Align patch 13 12 left Iteration 1 Error: 0.586186 Iteration 2 Error: 0.083556 Iteration 3 Error: 0.016895 Align patch 14 11 left Iteration 1 Error: 0.721532 Iteration 2 Error: 0.087880 Iteration 3 Error: 0.019296 Align patch 15 10 left Iteration 1 Error: 0.732884 Iteration 2 Error: 0.147706 Iteration 3 Error: 0.029468 Align patch 16 9 left Iteration 1 Error: 0.678073 Iteration 2 Error: 0.092815 Iteration 3 Error: 0.018901 Align patch 17 8 left Iteration 1 Error: 0.851113 Iteration 2 Error: 0.127564 Iteration 3 Error: 0.030789 Align patch 18 7 left Iteration 1 Error: 0.629260 Iteration 2 Error: 0.056365 Iteration 3 Error: 0.009752 Align patch 19 6 left Iteration 1 Error: 0.923281 Iteration 2 Error: 0.068091 Iteration 3 Error: 0.017402 Align patch 20 5 left Iteration 1 Error: 0.970240 Iteration 2 Error: 0.140217 Iteration 3 Error: 0.023073 Align patch 21 4 left Iteration 1 Error: 0.686069 Iteration 2 Error: 0.103283 Iteration 3 Error: 0.017065 Align patch 22 3 left Iteration 1 Error: 0.665427 Iteration 2 Error: 0.102655 Iteration 3 Error: 0.022681 Align patch 23 2 left Iteration 1 Error: 0.611109 Iteration 2 Error: 0.091416 Iteration 3 Error: 0.031288 Align patch 24 1 left Iteration 1 Error: 0.956940 Iteration 2 Error: 0.132000 Iteration 3 Error: 0.024776 Align patch 25 0 left Iteration 1 Error: 1.129077 Iteration 2 Error: 0.101314 Iteration 3 Error: 0.022796 3D Fitting completed. Patch alignment time: 12.15(sec) Local motion has been corrected. Process thread exits. Computational time: 22.434902 sec Total time: 29.316004 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00010hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00010hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.640409s Reading file: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00010hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.211506s ........................................ >>>>>>TIME<<<<<< FFT: 0.942279s Defocus_U Defocus_V Angle CCC 17310.71 16646.36 80.81 0.044359 Final Values Defocus_U Defocus_V Angle CCC 17301.34 16661.98 80.81 0.070695 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00002sq_v01_00011hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00011hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 39.96 6.87 Num Hot pixels: 223 Hot pixel threshold: 81.18 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.584902 Iteration 2 Error: 0.243508 Iteration 3 Error: 0.062329 Iteration 4 Error: 0.022531 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.01 0.12 ...... Frame ( 3) shift: -0.02 0.25 ...... Frame ( 4) shift: -0.03 0.37 ...... Frame ( 5) shift: -0.04 0.49 ...... Frame ( 6) shift: 0.00 0.59 ...... Frame ( 7) shift: 0.09 0.67 ...... Frame ( 8) shift: 0.18 0.75 ...... Frame ( 9) shift: 0.28 0.85 ...... Frame ( 10) shift: 0.37 0.97 ...... Frame ( 11) shift: 0.46 1.09 ...... Frame ( 12) shift: 0.54 1.21 ...... Frame ( 13) shift: 0.63 1.33 ...... Frame ( 14) shift: 0.71 1.46 ...... Frame ( 15) shift: 0.78 1.56 ...... Frame ( 16) shift: 0.84 1.64 ...... Frame ( 17) shift: 0.91 1.71 ...... Frame ( 18) shift: 1.02 1.73 ...... Frame ( 19) shift: 1.18 1.69 ...... Frame ( 20) shift: 1.34 1.65 ...... Frame ( 21) shift: 1.48 1.61 ...... Frame ( 22) shift: 1.59 1.56 ...... Frame ( 23) shift: 1.70 1.52 ...... Frame ( 24) shift: 1.78 1.48 ...... Frame ( 25) shift: 1.83 1.44 ...... Frame ( 26) shift: 1.87 1.41 ...... Frame ( 27) shift: 1.95 1.41 ...... Frame ( 28) shift: 2.06 1.45 ...... Frame ( 29) shift: 2.17 1.48 ...... Frame ( 30) shift: 2.30 1.49 ...... Frame ( 31) shift: 2.44 1.47 ...... Frame ( 32) shift: 2.59 1.45 ...... Frame ( 33) shift: 2.70 1.46 ...... Frame ( 34) shift: 2.79 1.52 ...... Frame ( 35) shift: 2.88 1.57 ...... Frame ( 36) shift: 2.94 1.59 ...... Frame ( 37) shift: 2.98 1.59 ...... Frame ( 38) shift: 3.02 1.59 ...... Frame ( 39) shift: 3.06 1.59 ...... Frame ( 40) shift: 3.10 1.59 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.660898 Iteration 2 Error: 0.149126 Iteration 3 Error: 0.031136 Align patch 2 23 left Iteration 1 Error: 0.618065 Iteration 2 Error: 0.083038 Iteration 3 Error: 0.015114 Align patch 3 22 left Iteration 1 Error: 1.025450 Iteration 2 Error: 0.235742 Iteration 3 Error: 0.066098 Iteration 4 Error: 0.021804 Align patch 4 21 left Iteration 1 Error: 0.599785 Iteration 2 Error: 0.118350 Iteration 3 Error: 0.032976 Align patch 5 20 left Iteration 1 Error: 0.877775 Iteration 2 Error: 0.195615 Iteration 3 Error: 0.050233 Iteration 4 Error: 0.015690 Align patch 6 19 left Iteration 1 Error: 0.790906 Iteration 2 Error: 0.121330 Iteration 3 Error: 0.024139 Align patch 7 18 left Iteration 1 Error: 0.573056 Iteration 2 Error: 0.118721 Iteration 3 Error: 0.028778 Align patch 8 17 left Iteration 1 Error: 0.806649 Iteration 2 Error: 0.175002 Iteration 3 Error: 0.040120 Align patch 9 16 left Iteration 1 Error: 0.810779 Iteration 2 Error: 0.142687 Iteration 3 Error: 0.050643 Iteration 4 Error: 0.020170 Align patch 10 15 left Iteration 1 Error: 0.650911 Iteration 2 Error: 0.102975 Iteration 3 Error: 0.028829 Align patch 11 14 left Iteration 1 Error: 1.249789 Iteration 2 Error: 0.213439 Iteration 3 Error: 0.073030 Iteration 4 Error: 0.034783 Align patch 12 13 left Iteration 1 Error: 1.330149 Iteration 2 Error: 0.187217 Iteration 3 Error: 0.065444 Iteration 4 Error: 0.021220 Align patch 13 12 left Iteration 1 Error: 0.777605 Iteration 2 Error: 0.135964 Iteration 3 Error: 0.019622 Align patch 14 11 left Iteration 1 Error: 0.870485 Iteration 2 Error: 0.084318 Iteration 3 Error: 0.034061 Align patch 15 10 left Iteration 1 Error: 0.635811 Iteration 2 Error: 0.100245 Iteration 3 Error: 0.035027 Align patch 16 9 left Iteration 1 Error: 1.170113 Iteration 2 Error: 0.208537 Iteration 3 Error: 0.050247 Iteration 4 Error: 0.020443 Align patch 17 8 left Iteration 1 Error: 1.315960 Iteration 2 Error: 0.200024 Iteration 3 Error: 0.040762 Align patch 18 7 left Iteration 1 Error: 0.583819 Iteration 2 Error: 0.152244 Iteration 3 Error: 0.044341 Align patch 19 6 left Iteration 1 Error: 0.885173 Iteration 2 Error: 0.133102 Iteration 3 Error: 0.028938 Align patch 20 5 left Iteration 1 Error: 0.590519 Iteration 2 Error: 0.125924 Iteration 3 Error: 0.025883 Align patch 21 4 left Iteration 1 Error: 1.756051 Iteration 2 Error: 0.430300 Iteration 3 Error: 0.098792 Iteration 4 Error: 0.039709 Align patch 22 3 left Iteration 1 Error: 0.770948 Iteration 2 Error: 0.124815 Iteration 3 Error: 0.027035 Align patch 23 2 left Iteration 1 Error: 0.851144 Iteration 2 Error: 0.169606 Iteration 3 Error: 0.050620 Iteration 4 Error: 0.016020 Align patch 24 1 left Iteration 1 Error: 0.818460 Iteration 2 Error: 0.139123 Iteration 3 Error: 0.037860 Align patch 25 0 left Iteration 1 Error: 0.886783 Iteration 2 Error: 0.157935 Iteration 3 Error: 0.085205 Iteration 4 Error: 0.033926 3D Fitting completed. Patch alignment time: 11.62(sec) Local motion has been corrected. Process thread exits. Computational time: 23.277185 sec Total time: 29.946980 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00011hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00011hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.491961s Reading file: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00011hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.676897s ........................................ >>>>>>TIME<<<<<< FFT: 0.874955s Defocus_U Defocus_V Angle CCC 15734.40 16609.40 11.62 0.050050 Final Values Defocus_U Defocus_V Angle CCC 15725.03 16606.28 10.68 0.078166 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00002sq_v01_00011hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00011hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.001e-01 CC threshold: 0.735 Mean Std: 41.23 6.93 Num Hot pixels: 220 Hot pixel threshold: 82.79 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.376410 Iteration 2 Error: 0.258274 Iteration 3 Error: 0.057314 Iteration 4 Error: 0.017620 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.12 -0.14 ...... Frame ( 3) shift: -0.25 -0.28 ...... Frame ( 4) shift: -0.37 -0.42 ...... Frame ( 5) shift: -0.49 -0.56 ...... Frame ( 6) shift: -0.52 -0.57 ...... Frame ( 7) shift: -0.47 -0.46 ...... Frame ( 8) shift: -0.41 -0.35 ...... Frame ( 9) shift: -0.37 -0.21 ...... Frame ( 10) shift: -0.36 -0.06 ...... Frame ( 11) shift: -0.35 0.09 ...... Frame ( 12) shift: -0.32 0.22 ...... Frame ( 13) shift: -0.28 0.34 ...... Frame ( 14) shift: -0.24 0.45 ...... Frame ( 15) shift: -0.20 0.55 ...... Frame ( 16) shift: -0.18 0.63 ...... Frame ( 17) shift: -0.16 0.71 ...... Frame ( 18) shift: -0.16 0.78 ...... Frame ( 19) shift: -0.16 0.84 ...... Frame ( 20) shift: -0.17 0.90 ...... Frame ( 21) shift: -0.16 0.96 ...... Frame ( 22) shift: -0.14 1.03 ...... Frame ( 23) shift: -0.11 1.09 ...... Frame ( 24) shift: -0.07 1.18 ...... Frame ( 25) shift: -0.02 1.31 ...... Frame ( 26) shift: 0.04 1.44 ...... Frame ( 27) shift: 0.12 1.51 ...... Frame ( 28) shift: 0.22 1.54 ...... Frame ( 29) shift: 0.31 1.57 ...... Frame ( 30) shift: 0.38 1.60 ...... Frame ( 31) shift: 0.41 1.66 ...... Frame ( 32) shift: 0.43 1.71 ...... Frame ( 33) shift: 0.47 1.74 ...... Frame ( 34) shift: 0.51 1.74 ...... Frame ( 35) shift: 0.54 1.75 ...... Frame ( 36) shift: 0.65 1.75 ...... Frame ( 37) shift: 0.83 1.75 ...... Frame ( 38) shift: 1.01 1.74 ...... Frame ( 39) shift: 1.19 1.74 ...... Frame ( 40) shift: 1.37 1.74 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.840886 Iteration 2 Error: 0.217968 Iteration 3 Error: 0.053273 Iteration 4 Error: 0.017878 Align patch 2 23 left Iteration 1 Error: 0.766247 Iteration 2 Error: 0.136891 Iteration 3 Error: 0.041643 Align patch 3 22 left Iteration 1 Error: 0.568385 Iteration 2 Error: 0.092787 Iteration 3 Error: 0.024016 Align patch 4 21 left Iteration 1 Error: 0.758690 Iteration 2 Error: 0.113719 Iteration 3 Error: 0.036409 Align patch 5 20 left Iteration 1 Error: 0.510839 Iteration 2 Error: 0.055934 Iteration 3 Error: 0.017554 Align patch 6 19 left Iteration 1 Error: 1.463527 Iteration 2 Error: 0.159510 Iteration 3 Error: 0.058131 Iteration 4 Error: 0.031650 Align patch 7 18 left Iteration 1 Error: 0.684142 Iteration 2 Error: 0.128477 Iteration 3 Error: 0.032377 Align patch 8 17 left Iteration 1 Error: 0.908614 Iteration 2 Error: 0.145256 Iteration 3 Error: 0.040604 Align patch 9 16 left Iteration 1 Error: 0.591086 Iteration 2 Error: 0.130609 Iteration 3 Error: 0.039473 Align patch 10 15 left Iteration 1 Error: 0.430477 Iteration 2 Error: 0.060285 Iteration 3 Error: 0.015133 Align patch 11 14 left Iteration 1 Error: 1.184846 Iteration 2 Error: 0.225987 Iteration 3 Error: 0.068828 Iteration 4 Error: 0.031576 Align patch 12 13 left Iteration 1 Error: 0.965124 Iteration 2 Error: 0.201141 Iteration 3 Error: 0.068913 Iteration 4 Error: 0.020726 Align patch 13 12 left Iteration 1 Error: 0.768531 Iteration 2 Error: 0.154108 Iteration 3 Error: 0.029800 Align patch 14 11 left Iteration 1 Error: 0.581043 Iteration 2 Error: 0.076506 Iteration 3 Error: 0.024613 Align patch 15 10 left Iteration 1 Error: 0.876439 Iteration 2 Error: 0.136109 Iteration 3 Error: 0.038742 Align patch 16 9 left Iteration 1 Error: 0.454297 Iteration 2 Error: 0.055313 Iteration 3 Error: 0.015723 Align patch 17 8 left Iteration 1 Error: 0.383040 Iteration 2 Error: 0.033580 Align patch 18 7 left Iteration 1 Error: 0.761430 Iteration 2 Error: 0.147620 Iteration 3 Error: 0.045874 Align patch 19 6 left Iteration 1 Error: 0.609988 Iteration 2 Error: 0.097616 Iteration 3 Error: 0.016048 Align patch 20 5 left Iteration 1 Error: 0.604018 Iteration 2 Error: 0.179721 Iteration 3 Error: 0.028113 Align patch 21 4 left Iteration 1 Error: 0.754224 Iteration 2 Error: 0.102420 Iteration 3 Error: 0.026553 Align patch 22 3 left Iteration 1 Error: 0.387073 Iteration 2 Error: 0.094745 Iteration 3 Error: 0.019768 Align patch 23 2 left Iteration 1 Error: 0.520652 Iteration 2 Error: 0.080442 Iteration 3 Error: 0.017995 Align patch 24 1 left Iteration 1 Error: 0.754089 Iteration 2 Error: 0.092509 Iteration 3 Error: 0.023170 Align patch 25 0 left Iteration 1 Error: 0.992172 Iteration 2 Error: 0.130270 Iteration 3 Error: 0.018926 3D Fitting completed. Patch alignment time: 11.51(sec) Local motion has been corrected. Process thread exits. Computational time: 22.266600 sec Total time: 28.784412 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00011hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00011hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.660153s Reading file: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00011hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.534509s ........................................ >>>>>>TIME<<<<<< FFT: 0.914462s Defocus_U Defocus_V Angle CCC 13236.32 13794.94 0.03 0.053419 Final Values Defocus_U Defocus_V Angle CCC 13231.63 13790.25 0.03 0.087162 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00002sq_v01_00011hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00011hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 39.29 6.81 Num Hot pixels: 205 Hot pixel threshold: 80.17 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.556968 Iteration 2 Error: 0.144990 Iteration 3 Error: 0.025302 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.12 0.28 ...... Frame ( 3) shift: -0.24 0.57 ...... Frame ( 4) shift: -0.36 0.85 ...... Frame ( 5) shift: -0.48 1.14 ...... Frame ( 6) shift: -0.55 1.33 ...... Frame ( 7) shift: -0.58 1.43 ...... Frame ( 8) shift: -0.61 1.53 ...... Frame ( 9) shift: -0.62 1.62 ...... Frame ( 10) shift: -0.60 1.72 ...... Frame ( 11) shift: -0.58 1.82 ...... Frame ( 12) shift: -0.56 1.89 ...... Frame ( 13) shift: -0.53 1.94 ...... Frame ( 14) shift: -0.51 1.99 ...... Frame ( 15) shift: -0.47 2.03 ...... Frame ( 16) shift: -0.44 2.06 ...... Frame ( 17) shift: -0.40 2.09 ...... Frame ( 18) shift: -0.33 2.10 ...... Frame ( 19) shift: -0.23 2.09 ...... Frame ( 20) shift: -0.14 2.08 ...... Frame ( 21) shift: -0.07 2.09 ...... Frame ( 22) shift: -0.02 2.12 ...... Frame ( 23) shift: 0.02 2.16 ...... Frame ( 24) shift: 0.07 2.20 ...... Frame ( 25) shift: 0.12 2.26 ...... Frame ( 26) shift: 0.17 2.31 ...... Frame ( 27) shift: 0.20 2.33 ...... Frame ( 28) shift: 0.21 2.32 ...... Frame ( 29) shift: 0.21 2.31 ...... Frame ( 30) shift: 0.24 2.33 ...... Frame ( 31) shift: 0.27 2.37 ...... Frame ( 32) shift: 0.31 2.41 ...... Frame ( 33) shift: 0.37 2.45 ...... Frame ( 34) shift: 0.44 2.48 ...... Frame ( 35) shift: 0.51 2.51 ...... Frame ( 36) shift: 0.53 2.51 ...... Frame ( 37) shift: 0.50 2.48 ...... Frame ( 38) shift: 0.47 2.45 ...... Frame ( 39) shift: 0.45 2.41 ...... Frame ( 40) shift: 0.42 2.38 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.694436 Iteration 2 Error: 0.122745 Iteration 3 Error: 0.016255 Align patch 2 23 left Iteration 1 Error: 0.544708 Iteration 2 Error: 0.076076 Iteration 3 Error: 0.019301 Align patch 3 22 left Iteration 1 Error: 0.549052 Iteration 2 Error: 0.132912 Iteration 3 Error: 0.029034 Align patch 4 21 left Iteration 1 Error: 0.847121 Iteration 2 Error: 0.107605 Iteration 3 Error: 0.023801 Align patch 5 20 left Iteration 1 Error: 0.612630 Iteration 2 Error: 0.067385 Iteration 3 Error: 0.011690 Align patch 6 19 left Iteration 1 Error: 0.915739 Iteration 2 Error: 0.126995 Iteration 3 Error: 0.032617 Align patch 7 18 left Iteration 1 Error: 0.457954 Iteration 2 Error: 0.078322 Iteration 3 Error: 0.014167 Align patch 8 17 left Iteration 1 Error: 0.959469 Iteration 2 Error: 0.120261 Iteration 3 Error: 0.036358 Align patch 9 16 left Iteration 1 Error: 0.497175 Iteration 2 Error: 0.061392 Iteration 3 Error: 0.011071 Align patch 10 15 left Iteration 1 Error: 0.680484 Iteration 2 Error: 0.078240 Iteration 3 Error: 0.018132 Align patch 11 14 left Iteration 1 Error: 1.083460 Iteration 2 Error: 0.121873 Iteration 3 Error: 0.024235 Align patch 12 13 left Iteration 1 Error: 0.885937 Iteration 2 Error: 0.130534 Iteration 3 Error: 0.021716 Align patch 13 12 left Iteration 1 Error: 0.513569 Iteration 2 Error: 0.069295 Iteration 3 Error: 0.013847 Align patch 14 11 left Iteration 1 Error: 0.534461 Iteration 2 Error: 0.057899 Iteration 3 Error: 0.013040 Align patch 15 10 left Iteration 1 Error: 0.478175 Iteration 2 Error: 0.085008 Iteration 3 Error: 0.021142 Align patch 16 9 left Iteration 1 Error: 0.894077 Iteration 2 Error: 0.123972 Iteration 3 Error: 0.030217 Align patch 17 8 left Iteration 1 Error: 0.692087 Iteration 2 Error: 0.104516 Iteration 3 Error: 0.027226 Align patch 18 7 left Iteration 1 Error: 0.849299 Iteration 2 Error: 0.131289 Iteration 3 Error: 0.029928 Align patch 19 6 left Iteration 1 Error: 0.664654 Iteration 2 Error: 0.059743 Iteration 3 Error: 0.019702 Align patch 20 5 left Iteration 1 Error: 0.557900 Iteration 2 Error: 0.071513 Iteration 3 Error: 0.018229 Align patch 21 4 left Iteration 1 Error: 0.839850 Iteration 2 Error: 0.090533 Iteration 3 Error: 0.027256 Align patch 22 3 left Iteration 1 Error: 0.659568 Iteration 2 Error: 0.124487 Iteration 3 Error: 0.017675 Align patch 23 2 left Iteration 1 Error: 0.918673 Iteration 2 Error: 0.110506 Iteration 3 Error: 0.028128 Align patch 24 1 left Iteration 1 Error: 0.429060 Iteration 2 Error: 0.036817 Align patch 25 0 left Iteration 1 Error: 0.702116 Iteration 2 Error: 0.155554 Iteration 3 Error: 0.031258 3D Fitting completed. Patch alignment time: 11.43(sec) Local motion has been corrected. Process thread exits. Computational time: 21.799047 sec Total time: 29.891060 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00011hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00011hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.767387s Reading file: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00011hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.574036s ........................................ >>>>>>TIME<<<<<< FFT: 0.915305s Defocus_U Defocus_V Angle CCC 14292.96 15144.56 3.89 0.053008 Final Values Defocus_U Defocus_V Angle CCC 14292.93 15135.21 3.89 0.081020 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00002sq_v01_00011hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00011hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.003e-01 CC threshold: 0.737 Mean Std: 40.67 6.97 Num Hot pixels: 212 Hot pixel threshold: 82.52 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.544661 Iteration 2 Error: 0.086674 Iteration 3 Error: 0.013041 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.04 -0.08 ...... Frame ( 3) shift: -0.08 -0.16 ...... Frame ( 4) shift: -0.11 -0.24 ...... Frame ( 5) shift: -0.15 -0.32 ...... Frame ( 6) shift: -0.18 -0.35 ...... Frame ( 7) shift: -0.20 -0.35 ...... Frame ( 8) shift: -0.23 -0.35 ...... Frame ( 9) shift: -0.25 -0.33 ...... Frame ( 10) shift: -0.26 -0.30 ...... Frame ( 11) shift: -0.28 -0.27 ...... Frame ( 12) shift: -0.29 -0.25 ...... Frame ( 13) shift: -0.29 -0.24 ...... Frame ( 14) shift: -0.29 -0.23 ...... Frame ( 15) shift: -0.27 -0.20 ...... Frame ( 16) shift: -0.22 -0.15 ...... Frame ( 17) shift: -0.16 -0.09 ...... Frame ( 18) shift: -0.15 -0.06 ...... Frame ( 19) shift: -0.16 -0.03 ...... Frame ( 20) shift: -0.18 -0.01 ...... Frame ( 21) shift: -0.17 0.04 ...... Frame ( 22) shift: -0.14 0.12 ...... Frame ( 23) shift: -0.10 0.21 ...... Frame ( 24) shift: -0.11 0.23 ...... Frame ( 25) shift: -0.15 0.21 ...... Frame ( 26) shift: -0.20 0.18 ...... Frame ( 27) shift: -0.17 0.18 ...... Frame ( 28) shift: -0.09 0.21 ...... Frame ( 29) shift: 0.00 0.23 ...... Frame ( 30) shift: 0.06 0.26 ...... Frame ( 31) shift: 0.09 0.31 ...... Frame ( 32) shift: 0.13 0.35 ...... Frame ( 33) shift: 0.13 0.36 ...... Frame ( 34) shift: 0.11 0.34 ...... Frame ( 35) shift: 0.09 0.32 ...... Frame ( 36) shift: 0.12 0.32 ...... Frame ( 37) shift: 0.19 0.35 ...... Frame ( 38) shift: 0.26 0.37 ...... Frame ( 39) shift: 0.33 0.40 ...... Frame ( 40) shift: 0.40 0.43 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.745649 Iteration 2 Error: 0.111429 Iteration 3 Error: 0.037754 Align patch 2 23 left Iteration 1 Error: 0.607291 Iteration 2 Error: 0.103087 Iteration 3 Error: 0.017481 Align patch 3 22 left Iteration 1 Error: 0.949806 Iteration 2 Error: 0.107696 Iteration 3 Error: 0.021166 Align patch 4 21 left Iteration 1 Error: 0.972696 Iteration 2 Error: 0.128789 Iteration 3 Error: 0.020900 Align patch 5 20 left Iteration 1 Error: 0.756508 Iteration 2 Error: 0.103702 Iteration 3 Error: 0.029633 Align patch 6 19 left Iteration 1 Error: 0.925043 Iteration 2 Error: 0.145771 Iteration 3 Error: 0.033549 Align patch 7 18 left Iteration 1 Error: 1.014282 Iteration 2 Error: 0.104493 Iteration 3 Error: 0.024366 Align patch 8 17 left Iteration 1 Error: 0.732221 Iteration 2 Error: 0.077350 Iteration 3 Error: 0.015900 Align patch 9 16 left Iteration 1 Error: 0.651057 Iteration 2 Error: 0.077990 Iteration 3 Error: 0.025103 Align patch 10 15 left Iteration 1 Error: 1.024458 Iteration 2 Error: 0.121749 Iteration 3 Error: 0.026950 Align patch 11 14 left Iteration 1 Error: 0.945223 Iteration 2 Error: 0.103977 Iteration 3 Error: 0.022162 Align patch 12 13 left Iteration 1 Error: 0.548898 Iteration 2 Error: 0.084832 Iteration 3 Error: 0.019551 Align patch 13 12 left Iteration 1 Error: 0.425771 Iteration 2 Error: 0.090665 Iteration 3 Error: 0.026743 Align patch 14 11 left Iteration 1 Error: 0.833867 Iteration 2 Error: 0.084224 Iteration 3 Error: 0.020636 Align patch 15 10 left Iteration 1 Error: 0.487400 Iteration 2 Error: 0.070649 Iteration 3 Error: 0.017493 Align patch 16 9 left Iteration 1 Error: 0.612987 Iteration 2 Error: 0.063167 Iteration 3 Error: 0.014385 Align patch 17 8 left Iteration 1 Error: 0.662885 Iteration 2 Error: 0.114335 Iteration 3 Error: 0.018780 Align patch 18 7 left Iteration 1 Error: 0.401686 Iteration 2 Error: 0.045135 Align patch 19 6 left Iteration 1 Error: 0.761430 Iteration 2 Error: 0.102577 Iteration 3 Error: 0.020760 Align patch 20 5 left Iteration 1 Error: 0.623611 Iteration 2 Error: 0.080867 Iteration 3 Error: 0.014483 Align patch 21 4 left Iteration 1 Error: 0.544602 Iteration 2 Error: 0.093244 Iteration 3 Error: 0.020222 Align patch 22 3 left Iteration 1 Error: 0.787741 Iteration 2 Error: 0.094255 Iteration 3 Error: 0.021939 Align patch 23 2 left Iteration 1 Error: 0.531242 Iteration 2 Error: 0.051391 Iteration 3 Error: 0.011811 Align patch 24 1 left Iteration 1 Error: 0.687214 Iteration 2 Error: 0.091355 Iteration 3 Error: 0.015793 Align patch 25 0 left Iteration 1 Error: 1.160651 Iteration 2 Error: 0.118289 Iteration 3 Error: 0.016342 3D Fitting completed. Patch alignment time: 10.87(sec) Local motion has been corrected. Process thread exits. Computational time: 23.249817 sec Total time: 30.617802 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00011hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00011hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.681934s Reading file: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00011hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.939776s ........................................ >>>>>>TIME<<<<<< FFT: 1.025762s Defocus_U Defocus_V Angle CCC 17010.00 16306.48 80.18 0.046750 Final Values Defocus_U Defocus_V Angle CCC 17014.69 16308.06 80.18 0.075090 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00002sq_v01_00012hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00012hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 41.43 7.02 Num Hot pixels: 199 Hot pixel threshold: 83.53 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.267165 Iteration 2 Error: 0.211624 Iteration 3 Error: 0.055572 Iteration 4 Error: 0.014721 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.08 0.10 ...... Frame ( 3) shift: -0.15 0.21 ...... Frame ( 4) shift: -0.23 0.31 ...... Frame ( 5) shift: -0.31 0.42 ...... Frame ( 6) shift: -0.31 0.48 ...... Frame ( 7) shift: -0.25 0.50 ...... Frame ( 8) shift: -0.18 0.52 ...... Frame ( 9) shift: -0.14 0.57 ...... Frame ( 10) shift: -0.12 0.65 ...... Frame ( 11) shift: -0.10 0.73 ...... Frame ( 12) shift: -0.07 0.79 ...... Frame ( 13) shift: -0.02 0.83 ...... Frame ( 14) shift: 0.03 0.87 ...... Frame ( 15) shift: 0.10 0.92 ...... Frame ( 16) shift: 0.17 0.96 ...... Frame ( 17) shift: 0.25 1.00 ...... Frame ( 18) shift: 0.31 1.05 ...... Frame ( 19) shift: 0.36 1.09 ...... Frame ( 20) shift: 0.41 1.13 ...... Frame ( 21) shift: 0.46 1.16 ...... Frame ( 22) shift: 0.52 1.18 ...... Frame ( 23) shift: 0.58 1.19 ...... Frame ( 24) shift: 0.66 1.25 ...... Frame ( 25) shift: 0.76 1.34 ...... Frame ( 26) shift: 0.86 1.43 ...... Frame ( 27) shift: 0.93 1.50 ...... Frame ( 28) shift: 0.96 1.56 ...... Frame ( 29) shift: 0.99 1.62 ...... Frame ( 30) shift: 1.02 1.67 ...... Frame ( 31) shift: 1.04 1.71 ...... Frame ( 32) shift: 1.06 1.75 ...... Frame ( 33) shift: 1.11 1.80 ...... Frame ( 34) shift: 1.18 1.88 ...... Frame ( 35) shift: 1.25 1.95 ...... Frame ( 36) shift: 1.32 2.02 ...... Frame ( 37) shift: 1.38 2.07 ...... Frame ( 38) shift: 1.44 2.12 ...... Frame ( 39) shift: 1.51 2.17 ...... Frame ( 40) shift: 1.57 2.22 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.932360 Iteration 2 Error: 0.093832 Iteration 3 Error: 0.020440 Align patch 2 23 left Iteration 1 Error: 0.709465 Iteration 2 Error: 0.135002 Iteration 3 Error: 0.031613 Align patch 3 22 left Iteration 1 Error: 0.720114 Iteration 2 Error: 0.117753 Iteration 3 Error: 0.049654 Align patch 4 21 left Iteration 1 Error: 0.615134 Iteration 2 Error: 0.109060 Iteration 3 Error: 0.038186 Align patch 5 20 left Iteration 1 Error: 0.716106 Iteration 2 Error: 0.141911 Iteration 3 Error: 0.040139 Align patch 6 19 left Iteration 1 Error: 0.833997 Iteration 2 Error: 0.164815 Iteration 3 Error: 0.060029 Iteration 4 Error: 0.014719 Align patch 7 18 left Iteration 1 Error: 0.652385 Iteration 2 Error: 0.187556 Iteration 3 Error: 0.064082 Iteration 4 Error: 0.031578 Align patch 8 17 left Iteration 1 Error: 0.705088 Iteration 2 Error: 0.109598 Iteration 3 Error: 0.030307 Align patch 9 16 left Iteration 1 Error: 1.172275 Iteration 2 Error: 0.111611 Iteration 3 Error: 0.018568 Align patch 10 15 left Iteration 1 Error: 0.454497 Iteration 2 Error: 0.066446 Iteration 3 Error: 0.012009 Align patch 11 14 left Iteration 1 Error: 0.596544 Iteration 2 Error: 0.147879 Iteration 3 Error: 0.046531 Align patch 12 13 left Iteration 1 Error: 0.750037 Iteration 2 Error: 0.123895 Iteration 3 Error: 0.018614 Align patch 13 12 left Iteration 1 Error: 0.582641 Iteration 2 Error: 0.106317 Iteration 3 Error: 0.040371 Align patch 14 11 left Iteration 1 Error: 0.616367 Iteration 2 Error: 0.112267 Iteration 3 Error: 0.020494 Align patch 15 10 left Iteration 1 Error: 0.574290 Iteration 2 Error: 0.078661 Iteration 3 Error: 0.019878 Align patch 16 9 left Iteration 1 Error: 1.099873 Iteration 2 Error: 0.109786 Iteration 3 Error: 0.026546 Align patch 17 8 left Iteration 1 Error: 0.565601 Iteration 2 Error: 0.105861 Iteration 3 Error: 0.024660 Align patch 18 7 left Iteration 1 Error: 0.693450 Iteration 2 Error: 0.081382 Iteration 3 Error: 0.024831 Align patch 19 6 left Iteration 1 Error: 0.537406 Iteration 2 Error: 0.080653 Iteration 3 Error: 0.014792 Align patch 20 5 left Iteration 1 Error: 0.893712 Iteration 2 Error: 0.113227 Iteration 3 Error: 0.026600 Align patch 21 4 left Iteration 1 Error: 1.492995 Iteration 2 Error: 0.126421 Iteration 3 Error: 0.037860 Align patch 22 3 left Iteration 1 Error: 0.764125 Iteration 2 Error: 0.087909 Iteration 3 Error: 0.027645 Align patch 23 2 left Iteration 1 Error: 0.685366 Iteration 2 Error: 0.086269 Iteration 3 Error: 0.016287 Align patch 24 1 left Iteration 1 Error: 0.648224 Iteration 2 Error: 0.101276 Iteration 3 Error: 0.026224 Align patch 25 0 left Iteration 1 Error: 0.578782 Iteration 2 Error: 0.064044 Iteration 3 Error: 0.013311 3D Fitting completed. Patch alignment time: 11.19(sec) Local motion has been corrected. Process thread exits. Computational time: 22.090900 sec Total time: 28.995117 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00012hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00012hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.601636s Reading file: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00012hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.963603s ........................................ >>>>>>TIME<<<<<< FFT: 1.135619s Defocus_U Defocus_V Angle CCC 13673.83 14529.33 9.70 0.056970 Final Values Defocus_U Defocus_V Angle CCC 13676.93 14526.22 9.39 0.090988 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00002sq_v01_00012hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00012hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 41.35 6.96 Num Hot pixels: 189 Hot pixel threshold: 83.11 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.815389 Iteration 2 Error: 0.174397 Iteration 3 Error: 0.036609 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.15 0.20 ...... Frame ( 3) shift: -0.30 0.41 ...... Frame ( 4) shift: -0.45 0.61 ...... Frame ( 5) shift: -0.60 0.81 ...... Frame ( 6) shift: -0.66 0.96 ...... Frame ( 7) shift: -0.64 1.04 ...... Frame ( 8) shift: -0.62 1.12 ...... Frame ( 9) shift: -0.57 1.18 ...... Frame ( 10) shift: -0.48 1.22 ...... Frame ( 11) shift: -0.39 1.26 ...... Frame ( 12) shift: -0.34 1.29 ...... Frame ( 13) shift: -0.33 1.31 ...... Frame ( 14) shift: -0.31 1.33 ...... Frame ( 15) shift: -0.27 1.30 ...... Frame ( 16) shift: -0.20 1.23 ...... Frame ( 17) shift: -0.12 1.15 ...... Frame ( 18) shift: -0.06 1.08 ...... Frame ( 19) shift: -0.03 1.03 ...... Frame ( 20) shift: 0.01 0.97 ...... Frame ( 21) shift: 0.08 0.94 ...... Frame ( 22) shift: 0.19 0.93 ...... Frame ( 23) shift: 0.30 0.92 ...... Frame ( 24) shift: 0.39 0.88 ...... Frame ( 25) shift: 0.46 0.80 ...... Frame ( 26) shift: 0.54 0.73 ...... Frame ( 27) shift: 0.60 0.64 ...... Frame ( 28) shift: 0.64 0.53 ...... Frame ( 29) shift: 0.69 0.43 ...... Frame ( 30) shift: 0.75 0.38 ...... Frame ( 31) shift: 0.83 0.40 ...... Frame ( 32) shift: 0.91 0.42 ...... Frame ( 33) shift: 0.94 0.41 ...... Frame ( 34) shift: 0.94 0.36 ...... Frame ( 35) shift: 0.93 0.32 ...... Frame ( 36) shift: 0.93 0.29 ...... Frame ( 37) shift: 0.92 0.26 ...... Frame ( 38) shift: 0.92 0.23 ...... Frame ( 39) shift: 0.91 0.20 ...... Frame ( 40) shift: 0.91 0.18 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.659394 Iteration 2 Error: 0.086958 Iteration 3 Error: 0.017199 Align patch 2 23 left Iteration 1 Error: 0.438099 Iteration 2 Error: 0.061787 Iteration 3 Error: 0.020144 Align patch 3 22 left Iteration 1 Error: 1.058321 Iteration 2 Error: 0.099903 Iteration 3 Error: 0.018802 Align patch 4 21 left Iteration 1 Error: 1.062846 Iteration 2 Error: 0.181327 Iteration 3 Error: 0.053442 Iteration 4 Error: 0.012326 Align patch 5 20 left Iteration 1 Error: 1.174659 Iteration 2 Error: 0.230057 Iteration 3 Error: 0.060999 Iteration 4 Error: 0.015211 Align patch 6 19 left Iteration 1 Error: 1.067740 Iteration 2 Error: 0.289571 Iteration 3 Error: 0.102049 Iteration 4 Error: 0.034321 Align patch 7 18 left Iteration 1 Error: 1.255292 Iteration 2 Error: 0.164470 Iteration 3 Error: 0.024694 Align patch 8 17 left Iteration 1 Error: 0.703358 Iteration 2 Error: 0.097152 Iteration 3 Error: 0.015828 Align patch 9 16 left Iteration 1 Error: 0.750607 Iteration 2 Error: 0.152242 Iteration 3 Error: 0.026888 Align patch 10 15 left Iteration 1 Error: 1.172475 Iteration 2 Error: 0.148275 Iteration 3 Error: 0.031712 Align patch 11 14 left Iteration 1 Error: 1.230563 Iteration 2 Error: 0.308378 Iteration 3 Error: 0.096200 Iteration 4 Error: 0.038166 Align patch 12 13 left Iteration 1 Error: 1.054377 Iteration 2 Error: 0.241560 Iteration 3 Error: 0.069863 Iteration 4 Error: 0.019414 Align patch 13 12 left Iteration 1 Error: 0.480657 Iteration 2 Error: 0.112628 Iteration 3 Error: 0.038806 Align patch 14 11 left Iteration 1 Error: 0.681191 Iteration 2 Error: 0.153663 Iteration 3 Error: 0.023125 Align patch 15 10 left Iteration 1 Error: 1.188280 Iteration 2 Error: 0.224753 Iteration 3 Error: 0.042238 Align patch 16 9 left Iteration 1 Error: 1.601399 Iteration 2 Error: 0.564335 Iteration 3 Error: 0.668921 Iteration 4 Error: 0.684848 Iteration 5 Error: 0.576364 Align patch 16 9 left Iteration 1 Error: 3.226762 Iteration 2 Error: 0.627183 Iteration 3 Error: 0.268956 Iteration 4 Error: 0.146236 Iteration 5 Error: 0.067532 Align patch 17 8 left Iteration 1 Error: 1.411263 Iteration 2 Error: 0.360977 Iteration 3 Error: 0.132702 Iteration 4 Error: 0.079064 Iteration 5 Error: 0.035919 Align patch 18 7 left Iteration 1 Error: 0.883630 Iteration 2 Error: 0.232625 Iteration 3 Error: 0.086639 Iteration 4 Error: 0.024499 Align patch 19 6 left Iteration 1 Error: 0.657412 Iteration 2 Error: 0.113681 Iteration 3 Error: 0.030978 Align patch 20 5 left Iteration 1 Error: 1.252893 Iteration 2 Error: 0.193157 Iteration 3 Error: 0.053150 Iteration 4 Error: 0.016898 Align patch 21 4 left Iteration 1 Error: 7.032976 Iteration 2 Error: 2.962764 Iteration 3 Error: 0.619029 Iteration 4 Error: 0.764575 Iteration 5 Error: 0.403280 Align patch 21 4 left Iteration 1 Error: 4.672919 Iteration 2 Error: 1.160888 Iteration 3 Error: 0.454867 Iteration 4 Error: 0.265592 Iteration 5 Error: 0.136189 Align patch 22 3 left Iteration 1 Error: 1.891050 Iteration 2 Error: 0.531558 Iteration 3 Error: 0.303674 Iteration 4 Error: 0.137134 Iteration 5 Error: 0.059481 Align patch 22 3 left Iteration 1 Error: 3.114358 Iteration 2 Error: 0.729594 Iteration 3 Error: 0.184445 Iteration 4 Error: 0.091351 Iteration 5 Error: 0.041795 Align patch 23 2 left Iteration 1 Error: 1.445830 Iteration 2 Error: 0.315408 Iteration 3 Error: 0.139929 Iteration 4 Error: 0.070945 Iteration 5 Error: 0.032043 Align patch 24 1 left Iteration 1 Error: 0.619385 Iteration 2 Error: 0.088191 Iteration 3 Error: 0.014058 Align patch 25 0 left Iteration 1 Error: 1.063604 Iteration 2 Error: 0.142715 Iteration 3 Error: 0.024419 3D Fitting completed. Patch alignment time: 13.94(sec) Local motion has been corrected. Process thread exits. Computational time: 27.206905 sec Total time: 33.879761 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00012hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00012hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.607782s Reading file: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00012hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.612479s ........................................ >>>>>>TIME<<<<<< FFT: 0.956796s Defocus_U Defocus_V Angle CCC 16312.56 15773.38 86.93 0.049189 Final Values Defocus_U Defocus_V Angle CCC 16309.44 15770.26 86.93 0.081326 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00002sq_v01_00012hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00012hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.001e-01 CC threshold: 0.736 Mean Std: 41.64 7.02 Num Hot pixels: 212 Hot pixel threshold: 83.78 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.057849 Iteration 2 Error: 0.126381 Iteration 3 Error: 0.027138 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.08 0.10 ...... Frame ( 3) shift: -0.15 0.19 ...... Frame ( 4) shift: -0.23 0.29 ...... Frame ( 5) shift: -0.31 0.39 ...... Frame ( 6) shift: -0.33 0.48 ...... Frame ( 7) shift: -0.31 0.57 ...... Frame ( 8) shift: -0.29 0.66 ...... Frame ( 9) shift: -0.30 0.77 ...... Frame ( 10) shift: -0.34 0.91 ...... Frame ( 11) shift: -0.39 1.05 ...... Frame ( 12) shift: -0.41 1.10 ...... Frame ( 13) shift: -0.40 1.05 ...... Frame ( 14) shift: -0.38 1.00 ...... Frame ( 15) shift: -0.37 1.00 ...... Frame ( 16) shift: -0.36 1.04 ...... Frame ( 17) shift: -0.35 1.09 ...... Frame ( 18) shift: -0.35 1.14 ...... Frame ( 19) shift: -0.36 1.19 ...... Frame ( 20) shift: -0.36 1.25 ...... Frame ( 21) shift: -0.34 1.32 ...... Frame ( 22) shift: -0.29 1.42 ...... Frame ( 23) shift: -0.24 1.52 ...... Frame ( 24) shift: -0.24 1.57 ...... Frame ( 25) shift: -0.28 1.57 ...... Frame ( 26) shift: -0.32 1.57 ...... Frame ( 27) shift: -0.30 1.60 ...... Frame ( 28) shift: -0.23 1.66 ...... Frame ( 29) shift: -0.17 1.71 ...... Frame ( 30) shift: -0.15 1.74 ...... Frame ( 31) shift: -0.19 1.74 ...... Frame ( 32) shift: -0.22 1.74 ...... Frame ( 33) shift: -0.22 1.78 ...... Frame ( 34) shift: -0.18 1.88 ...... Frame ( 35) shift: -0.13 1.97 ...... Frame ( 36) shift: -0.12 2.03 ...... Frame ( 37) shift: -0.12 2.05 ...... Frame ( 38) shift: -0.13 2.07 ...... Frame ( 39) shift: -0.14 2.09 ...... Frame ( 40) shift: -0.15 2.12 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.662001 Iteration 2 Error: 0.088089 Iteration 3 Error: 0.030900 Align patch 2 23 left Iteration 1 Error: 1.256138 Iteration 2 Error: 0.233749 Iteration 3 Error: 0.089946 Iteration 4 Error: 0.031049 Align patch 3 22 left Iteration 1 Error: 0.833265 Iteration 2 Error: 0.155246 Iteration 3 Error: 0.039702 Align patch 4 21 left Iteration 1 Error: 0.468452 Iteration 2 Error: 0.058953 Iteration 3 Error: 0.013646 Align patch 5 20 left Iteration 1 Error: 0.561636 Iteration 2 Error: 0.054742 Iteration 3 Error: 0.021808 Align patch 6 19 left Iteration 1 Error: 0.625321 Iteration 2 Error: 0.097102 Iteration 3 Error: 0.041699 Align patch 7 18 left Iteration 1 Error: 1.122236 Iteration 2 Error: 0.159978 Iteration 3 Error: 0.046054 Align patch 8 17 left Iteration 1 Error: 0.586684 Iteration 2 Error: 0.146258 Iteration 3 Error: 0.021597 Align patch 9 16 left Iteration 1 Error: 0.786410 Iteration 2 Error: 0.081012 Iteration 3 Error: 0.021642 Align patch 10 15 left Iteration 1 Error: 0.652832 Iteration 2 Error: 0.145727 Iteration 3 Error: 0.022728 Align patch 11 14 left Iteration 1 Error: 0.722597 Iteration 2 Error: 0.108200 Iteration 3 Error: 0.029869 Align patch 12 13 left Iteration 1 Error: 1.058679 Iteration 2 Error: 0.120291 Iteration 3 Error: 0.020637 Align patch 13 12 left Iteration 1 Error: 0.612456 Iteration 2 Error: 0.085169 Iteration 3 Error: 0.016216 Align patch 14 11 left Iteration 1 Error: 0.487783 Iteration 2 Error: 0.043483 Align patch 15 10 left Iteration 1 Error: 0.791456 Iteration 2 Error: 0.202793 Iteration 3 Error: 0.051178 Iteration 4 Error: 0.015491 Align patch 16 9 left Iteration 1 Error: 0.688686 Iteration 2 Error: 0.123297 Iteration 3 Error: 0.035589 Align patch 17 8 left Iteration 1 Error: 0.579970 Iteration 2 Error: 0.081980 Iteration 3 Error: 0.019696 Align patch 18 7 left Iteration 1 Error: 0.682146 Iteration 2 Error: 0.089373 Iteration 3 Error: 0.023796 Align patch 19 6 left Iteration 1 Error: 0.607839 Iteration 2 Error: 0.088346 Iteration 3 Error: 0.027856 Align patch 20 5 left Iteration 1 Error: 0.480411 Iteration 2 Error: 0.068577 Iteration 3 Error: 0.011747 Align patch 21 4 left Iteration 1 Error: 0.892999 Iteration 2 Error: 0.150674 Iteration 3 Error: 0.040877 Align patch 22 3 left Iteration 1 Error: 0.750319 Iteration 2 Error: 0.119009 Iteration 3 Error: 0.017811 Align patch 23 2 left Iteration 1 Error: 0.822291 Iteration 2 Error: 0.119427 Iteration 3 Error: 0.024258 Align patch 24 1 left Iteration 1 Error: 0.662344 Iteration 2 Error: 0.101811 Iteration 3 Error: 0.016080 Align patch 25 0 left Iteration 1 Error: 1.086266 Iteration 2 Error: 0.189403 Iteration 3 Error: 0.031138 3D Fitting completed. Patch alignment time: 11.88(sec) Local motion has been corrected. Process thread exits. Computational time: 22.355234 sec Total time: 29.147411 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00012hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00012hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.451804s Reading file: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00012hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.903805s ........................................ >>>>>>TIME<<<<<< FFT: 0.947136s Defocus_U Defocus_V Angle CCC 13636.74 14449.24 3.63 0.051650 Final Values Defocus_U Defocus_V Angle CCC 13641.43 14438.31 3.32 0.084667 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00002sq_v01_00012hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00012hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 40.59 6.99 Num Hot pixels: 209 Hot pixel threshold: 82.56 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.911010 Iteration 2 Error: 0.072209 Iteration 3 Error: 0.015758 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.16 0.19 ...... Frame ( 3) shift: -0.33 0.37 ...... Frame ( 4) shift: -0.49 0.56 ...... Frame ( 5) shift: -0.66 0.74 ...... Frame ( 6) shift: -0.74 0.87 ...... Frame ( 7) shift: -0.74 0.92 ...... Frame ( 8) shift: -0.73 0.98 ...... Frame ( 9) shift: -0.74 1.04 ...... Frame ( 10) shift: -0.75 1.10 ...... Frame ( 11) shift: -0.77 1.16 ...... Frame ( 12) shift: -0.76 1.18 ...... Frame ( 13) shift: -0.73 1.16 ...... Frame ( 14) shift: -0.71 1.14 ...... Frame ( 15) shift: -0.70 1.16 ...... Frame ( 16) shift: -0.70 1.19 ...... Frame ( 17) shift: -0.70 1.23 ...... Frame ( 18) shift: -0.71 1.23 ...... Frame ( 19) shift: -0.72 1.17 ...... Frame ( 20) shift: -0.73 1.12 ...... Frame ( 21) shift: -0.71 1.10 ...... Frame ( 22) shift: -0.66 1.09 ...... Frame ( 23) shift: -0.61 1.09 ...... Frame ( 24) shift: -0.56 1.12 ...... Frame ( 25) shift: -0.52 1.17 ...... Frame ( 26) shift: -0.47 1.22 ...... Frame ( 27) shift: -0.43 1.27 ...... Frame ( 28) shift: -0.42 1.31 ...... Frame ( 29) shift: -0.40 1.35 ...... Frame ( 30) shift: -0.38 1.37 ...... Frame ( 31) shift: -0.38 1.39 ...... Frame ( 32) shift: -0.37 1.41 ...... Frame ( 33) shift: -0.37 1.42 ...... Frame ( 34) shift: -0.37 1.42 ...... Frame ( 35) shift: -0.37 1.42 ...... Frame ( 36) shift: -0.34 1.41 ...... Frame ( 37) shift: -0.28 1.40 ...... Frame ( 38) shift: -0.22 1.39 ...... Frame ( 39) shift: -0.16 1.39 ...... Frame ( 40) shift: -0.10 1.38 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.689271 Iteration 2 Error: 0.117933 Iteration 3 Error: 0.029047 Align patch 2 23 left Iteration 1 Error: 0.617728 Iteration 2 Error: 0.061161 Iteration 3 Error: 0.018128 Align patch 3 22 left Iteration 1 Error: 0.505374 Iteration 2 Error: 0.066175 Iteration 3 Error: 0.013541 Align patch 4 21 left Iteration 1 Error: 0.392503 Iteration 2 Error: 0.094057 Iteration 3 Error: 0.011811 Align patch 5 20 left Iteration 1 Error: 0.561766 Iteration 2 Error: 0.139491 Iteration 3 Error: 0.038432 Align patch 6 19 left Iteration 1 Error: 0.911403 Iteration 2 Error: 0.121345 Iteration 3 Error: 0.057610 Iteration 4 Error: 0.019167 Align patch 7 18 left Iteration 1 Error: 0.646533 Iteration 2 Error: 0.074650 Iteration 3 Error: 0.016941 Align patch 8 17 left Iteration 1 Error: 0.930724 Iteration 2 Error: 0.103439 Iteration 3 Error: 0.019213 Align patch 9 16 left Iteration 1 Error: 0.576907 Iteration 2 Error: 0.100924 Iteration 3 Error: 0.021384 Align patch 10 15 left Iteration 1 Error: 0.410924 Iteration 2 Error: 0.062299 Iteration 3 Error: 0.020471 Align patch 11 14 left Iteration 1 Error: 0.742842 Iteration 2 Error: 0.187343 Iteration 3 Error: 0.050434 Iteration 4 Error: 0.025152 Align patch 12 13 left Iteration 1 Error: 0.803858 Iteration 2 Error: 0.158367 Iteration 3 Error: 0.041284 Align patch 13 12 left Iteration 1 Error: 0.544916 Iteration 2 Error: 0.089690 Iteration 3 Error: 0.020152 Align patch 14 11 left Iteration 1 Error: 0.461429 Iteration 2 Error: 0.051338 Iteration 3 Error: 0.007435 Align patch 15 10 left Iteration 1 Error: 0.562616 Iteration 2 Error: 0.129077 Iteration 3 Error: 0.022896 Align patch 16 9 left Iteration 1 Error: 0.699258 Iteration 2 Error: 0.093681 Iteration 3 Error: 0.018009 Align patch 17 8 left Iteration 1 Error: 0.434914 Iteration 2 Error: 0.119758 Iteration 3 Error: 0.022772 Align patch 18 7 left Iteration 1 Error: 0.821335 Iteration 2 Error: 0.088533 Iteration 3 Error: 0.028002 Align patch 19 6 left Iteration 1 Error: 0.704638 Iteration 2 Error: 0.136224 Iteration 3 Error: 0.036926 Align patch 20 5 left Iteration 1 Error: 0.696460 Iteration 2 Error: 0.099795 Iteration 3 Error: 0.029612 Align patch 21 4 left Iteration 1 Error: 0.792183 Iteration 2 Error: 0.105839 Iteration 3 Error: 0.021127 Align patch 22 3 left Iteration 1 Error: 1.256445 Iteration 2 Error: 0.197720 Iteration 3 Error: 0.025434 Align patch 23 2 left Iteration 1 Error: 0.823193 Iteration 2 Error: 0.101683 Iteration 3 Error: 0.023712 Align patch 24 1 left Iteration 1 Error: 1.613294 Iteration 2 Error: 0.536864 Iteration 3 Error: 0.203343 Iteration 4 Error: 0.091742 Iteration 5 Error: 0.045397 Align patch 25 0 left Iteration 1 Error: 1.134536 Iteration 2 Error: 0.259211 Iteration 3 Error: 0.080502 Iteration 4 Error: 0.029041 3D Fitting completed. Patch alignment time: 12.83(sec) Local motion has been corrected. Process thread exits. Computational time: 27.394897 sec Total time: 34.586552 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00012hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00012hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.449133s Reading file: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00012hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.917905s ........................................ >>>>>>TIME<<<<<< FFT: 0.920859s Defocus_U Defocus_V Angle CCC 14521.23 13845.99 81.62 0.051023 Final Values Defocus_U Defocus_V Angle CCC 14527.48 13846.00 81.62 0.080827 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00002sq_v01_00013hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00013hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 40.65 6.88 Num Hot pixels: 226 Hot pixel threshold: 81.93 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.357112 Iteration 2 Error: 0.303570 Iteration 3 Error: 0.088408 Iteration 4 Error: 0.026628 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.04 0.27 ...... Frame ( 3) shift: 0.09 0.54 ...... Frame ( 4) shift: 0.13 0.82 ...... Frame ( 5) shift: 0.18 1.09 ...... Frame ( 6) shift: 0.25 1.31 ...... Frame ( 7) shift: 0.34 1.47 ...... Frame ( 8) shift: 0.44 1.63 ...... Frame ( 9) shift: 0.56 1.80 ...... Frame ( 10) shift: 0.70 1.97 ...... Frame ( 11) shift: 0.84 2.15 ...... Frame ( 12) shift: 0.93 2.24 ...... Frame ( 13) shift: 0.97 2.27 ...... Frame ( 14) shift: 1.00 2.30 ...... Frame ( 15) shift: 1.07 2.36 ...... Frame ( 16) shift: 1.16 2.44 ...... Frame ( 17) shift: 1.25 2.53 ...... Frame ( 18) shift: 1.31 2.65 ...... Frame ( 19) shift: 1.35 2.79 ...... Frame ( 20) shift: 1.39 2.94 ...... Frame ( 21) shift: 1.43 3.02 ...... Frame ( 22) shift: 1.48 3.03 ...... Frame ( 23) shift: 1.52 3.05 ...... Frame ( 24) shift: 1.57 3.08 ...... Frame ( 25) shift: 1.62 3.12 ...... Frame ( 26) shift: 1.67 3.16 ...... Frame ( 27) shift: 1.73 3.22 ...... Frame ( 28) shift: 1.81 3.29 ...... Frame ( 29) shift: 1.88 3.37 ...... Frame ( 30) shift: 1.94 3.40 ...... Frame ( 31) shift: 1.96 3.37 ...... Frame ( 32) shift: 1.99 3.34 ...... Frame ( 33) shift: 2.02 3.35 ...... Frame ( 34) shift: 2.06 3.42 ...... Frame ( 35) shift: 2.11 3.49 ...... Frame ( 36) shift: 2.15 3.57 ...... Frame ( 37) shift: 2.19 3.67 ...... Frame ( 38) shift: 2.23 3.77 ...... Frame ( 39) shift: 2.27 3.87 ...... Frame ( 40) shift: 2.31 3.97 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.058441 Iteration 2 Error: 0.380819 Iteration 3 Error: 0.123129 Iteration 4 Error: 0.052087 Iteration 5 Error: 0.027883 Align patch 2 23 left Iteration 1 Error: 0.874031 Iteration 2 Error: 0.253593 Iteration 3 Error: 0.113223 Iteration 4 Error: 0.047896 Align patch 3 22 left Iteration 1 Error: 0.647438 Iteration 2 Error: 0.125639 Iteration 3 Error: 0.032211 Align patch 4 21 left Iteration 1 Error: 0.755145 Iteration 2 Error: 0.118259 Iteration 3 Error: 0.032906 Align patch 5 20 left Iteration 1 Error: 0.785995 Iteration 2 Error: 0.123422 Iteration 3 Error: 0.023851 Align patch 6 19 left Iteration 1 Error: 2.221318 Iteration 2 Error: 0.366128 Iteration 3 Error: 0.171648 Iteration 4 Error: 0.073655 Iteration 5 Error: 0.040354 Align patch 7 18 left Iteration 1 Error: 1.159633 Iteration 2 Error: 0.290801 Iteration 3 Error: 0.120728 Iteration 4 Error: 0.037442 Align patch 8 17 left Iteration 1 Error: 0.706969 Iteration 2 Error: 0.133046 Iteration 3 Error: 0.049096 Align patch 9 16 left Iteration 1 Error: 0.643554 Iteration 2 Error: 0.114318 Iteration 3 Error: 0.027976 Align patch 10 15 left Iteration 1 Error: 0.579660 Iteration 2 Error: 0.083808 Iteration 3 Error: 0.020987 Align patch 11 14 left Iteration 1 Error: 1.722110 Iteration 2 Error: 0.382333 Iteration 3 Error: 0.111284 Iteration 4 Error: 0.047855 Align patch 12 13 left Iteration 1 Error: 1.082339 Iteration 2 Error: 0.200877 Iteration 3 Error: 0.072941 Iteration 4 Error: 0.029192 Align patch 13 12 left Iteration 1 Error: 0.651681 Iteration 2 Error: 0.123116 Iteration 3 Error: 0.036857 Align patch 14 11 left Iteration 1 Error: 1.011978 Iteration 2 Error: 0.119946 Iteration 3 Error: 0.040795 Align patch 15 10 left Iteration 1 Error: 0.945812 Iteration 2 Error: 0.111514 Iteration 3 Error: 0.023538 Align patch 16 9 left Iteration 1 Error: 0.867989 Iteration 2 Error: 0.202050 Iteration 3 Error: 0.074770 Iteration 4 Error: 0.022977 Align patch 17 8 left Iteration 1 Error: 0.492303 Iteration 2 Error: 0.125178 Iteration 3 Error: 0.037750 Align patch 18 7 left Iteration 1 Error: 0.784957 Iteration 2 Error: 0.096047 Iteration 3 Error: 0.040568 Align patch 19 6 left Iteration 1 Error: 0.626612 Iteration 2 Error: 0.149660 Iteration 3 Error: 0.049322 Align patch 20 5 left Iteration 1 Error: 0.785746 Iteration 2 Error: 0.174499 Iteration 3 Error: 0.047538 Align patch 21 4 left Iteration 1 Error: 0.746009 Iteration 2 Error: 0.100847 Iteration 3 Error: 0.033962 Align patch 22 3 left Iteration 1 Error: 0.735190 Iteration 2 Error: 0.168310 Iteration 3 Error: 0.059140 Iteration 4 Error: 0.024523 Align patch 23 2 left Iteration 1 Error: 0.678046 Iteration 2 Error: 0.182158 Iteration 3 Error: 0.062354 Iteration 4 Error: 0.018101 Align patch 24 1 left Iteration 1 Error: 0.702624 Iteration 2 Error: 0.151179 Iteration 3 Error: 0.054865 Iteration 4 Error: 0.015717 Align patch 25 0 left Iteration 1 Error: 0.624760 Iteration 2 Error: 0.116092 Iteration 3 Error: 0.023948 3D Fitting completed. Patch alignment time: 11.72(sec) Local motion has been corrected. Process thread exits. Computational time: 23.687973 sec Total time: 29.877834 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00013hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00013hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.046507s Reading file: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00013hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.862877s ........................................ >>>>>>TIME<<<<<< FFT: 0.963695s Defocus_U Defocus_V Angle CCC 11888.69 12810.57 10.72 0.054260 Final Values Defocus_U Defocus_V Angle CCC 11909.03 12812.15 11.35 0.087588 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00002sq_v01_00013hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00013hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 41.33 7.13 Num Hot pixels: 215 Hot pixel threshold: 84.11 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.646990 Iteration 2 Error: 0.331679 Iteration 3 Error: 0.066006 Iteration 4 Error: 0.016428 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.09 0.18 ...... Frame ( 3) shift: -0.17 0.36 ...... Frame ( 4) shift: -0.26 0.55 ...... Frame ( 5) shift: -0.35 0.73 ...... Frame ( 6) shift: -0.32 0.85 ...... Frame ( 7) shift: -0.19 0.91 ...... Frame ( 8) shift: -0.05 0.96 ...... Frame ( 9) shift: 0.03 1.05 ...... Frame ( 10) shift: 0.05 1.15 ...... Frame ( 11) shift: 0.07 1.26 ...... Frame ( 12) shift: 0.11 1.34 ...... Frame ( 13) shift: 0.17 1.41 ...... Frame ( 14) shift: 0.23 1.48 ...... Frame ( 15) shift: 0.27 1.57 ...... Frame ( 16) shift: 0.30 1.71 ...... Frame ( 17) shift: 0.32 1.84 ...... Frame ( 18) shift: 0.36 1.95 ...... Frame ( 19) shift: 0.41 2.05 ...... Frame ( 20) shift: 0.46 2.15 ...... Frame ( 21) shift: 0.50 2.22 ...... Frame ( 22) shift: 0.54 2.28 ...... Frame ( 23) shift: 0.57 2.33 ...... Frame ( 24) shift: 0.61 2.39 ...... Frame ( 25) shift: 0.64 2.46 ...... Frame ( 26) shift: 0.67 2.53 ...... Frame ( 27) shift: 0.71 2.61 ...... Frame ( 28) shift: 0.76 2.69 ...... Frame ( 29) shift: 0.81 2.78 ...... Frame ( 30) shift: 0.86 2.88 ...... Frame ( 31) shift: 0.92 3.00 ...... Frame ( 32) shift: 0.97 3.11 ...... Frame ( 33) shift: 1.04 3.19 ...... Frame ( 34) shift: 1.10 3.25 ...... Frame ( 35) shift: 1.17 3.30 ...... Frame ( 36) shift: 1.18 3.37 ...... Frame ( 37) shift: 1.13 3.44 ...... Frame ( 38) shift: 1.08 3.51 ...... Frame ( 39) shift: 1.04 3.58 ...... Frame ( 40) shift: 0.99 3.66 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.632822 Iteration 2 Error: 0.329973 Iteration 3 Error: 0.103921 Iteration 4 Error: 0.030690 Align patch 2 23 left Iteration 1 Error: 0.701585 Iteration 2 Error: 0.176388 Iteration 3 Error: 0.084143 Iteration 4 Error: 0.043101 Align patch 3 22 left Iteration 1 Error: 0.806953 Iteration 2 Error: 0.155847 Iteration 3 Error: 0.036790 Align patch 4 21 left Iteration 1 Error: 0.641614 Iteration 2 Error: 0.082973 Iteration 3 Error: 0.019309 Align patch 5 20 left Iteration 1 Error: 0.518992 Iteration 2 Error: 0.107189 Iteration 3 Error: 0.026313 Align patch 6 19 left Iteration 1 Error: 2.000261 Iteration 2 Error: 0.486936 Iteration 3 Error: 0.094421 Iteration 4 Error: 0.033242 Align patch 7 18 left Iteration 1 Error: 0.937931 Iteration 2 Error: 0.196665 Iteration 3 Error: 0.072235 Iteration 4 Error: 0.032995 Align patch 8 17 left Iteration 1 Error: 0.684090 Iteration 2 Error: 0.084332 Iteration 3 Error: 0.021497 Align patch 9 16 left Iteration 1 Error: 0.565461 Iteration 2 Error: 0.070075 Iteration 3 Error: 0.013448 Align patch 10 15 left Iteration 1 Error: 0.588076 Iteration 2 Error: 0.126729 Iteration 3 Error: 0.022793 Align patch 11 14 left Iteration 1 Error: 1.700080 Iteration 2 Error: 0.216710 Iteration 3 Error: 0.065893 Iteration 4 Error: 0.027627 Align patch 12 13 left Iteration 1 Error: 0.610420 Iteration 2 Error: 0.151160 Iteration 3 Error: 0.043553 Align patch 13 12 left Iteration 1 Error: 0.567762 Iteration 2 Error: 0.161617 Iteration 3 Error: 0.038647 Align patch 14 11 left Iteration 1 Error: 0.527974 Iteration 2 Error: 0.059731 Iteration 3 Error: 0.010867 Align patch 15 10 left Iteration 1 Error: 0.445983 Iteration 2 Error: 0.061917 Iteration 3 Error: 0.013453 Align patch 16 9 left Iteration 1 Error: 0.693008 Iteration 2 Error: 0.113104 Iteration 3 Error: 0.019279 Align patch 17 8 left Iteration 1 Error: 0.475036 Iteration 2 Error: 0.092614 Iteration 3 Error: 0.020932 Align patch 18 7 left Iteration 1 Error: 0.619955 Iteration 2 Error: 0.087550 Iteration 3 Error: 0.023886 Align patch 19 6 left Iteration 1 Error: 0.412595 Iteration 2 Error: 0.071463 Iteration 3 Error: 0.021310 Align patch 20 5 left Iteration 1 Error: 0.577050 Iteration 2 Error: 0.093706 Iteration 3 Error: 0.025738 Align patch 21 4 left Iteration 1 Error: 0.616525 Iteration 2 Error: 0.098363 Iteration 3 Error: 0.030910 Align patch 22 3 left Iteration 1 Error: 0.692400 Iteration 2 Error: 0.127327 Iteration 3 Error: 0.041562 Align patch 23 2 left Iteration 1 Error: 0.769595 Iteration 2 Error: 0.182101 Iteration 3 Error: 0.044255 Align patch 24 1 left Iteration 1 Error: 0.586825 Iteration 2 Error: 0.152302 Iteration 3 Error: 0.048363 Align patch 25 0 left Iteration 1 Error: 0.497875 Iteration 2 Error: 0.110435 Iteration 3 Error: 0.023820 3D Fitting completed. Patch alignment time: 11.04(sec) Local motion has been corrected. Process thread exits. Computational time: 22.112621 sec Total time: 29.131353 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00013hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00013hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.912410s Reading file: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00013hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.584269s ........................................ >>>>>>TIME<<<<<< FFT: 1.023118s Defocus_U Defocus_V Angle CCC 15644.52 16199.23 2.46 0.052771 Final Values Defocus_U Defocus_V Angle CCC 15641.40 16205.50 2.15 0.084144 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00002sq_v01_00013hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00013hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 40.93 6.85 Num Hot pixels: 215 Hot pixel threshold: 82.06 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.188772 Iteration 2 Error: 0.355363 Iteration 3 Error: 0.118836 Iteration 4 Error: 0.038253 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.10 -0.05 ...... Frame ( 3) shift: -0.20 -0.09 ...... Frame ( 4) shift: -0.30 -0.14 ...... Frame ( 5) shift: -0.39 -0.19 ...... Frame ( 6) shift: -0.43 -0.23 ...... Frame ( 7) shift: -0.40 -0.25 ...... Frame ( 8) shift: -0.38 -0.28 ...... Frame ( 9) shift: -0.29 -0.23 ...... Frame ( 10) shift: -0.16 -0.11 ...... Frame ( 11) shift: -0.02 0.01 ...... Frame ( 12) shift: 0.12 0.13 ...... Frame ( 13) shift: 0.28 0.25 ...... Frame ( 14) shift: 0.43 0.37 ...... Frame ( 15) shift: 0.55 0.50 ...... Frame ( 16) shift: 0.63 0.62 ...... Frame ( 17) shift: 0.71 0.74 ...... Frame ( 18) shift: 0.74 0.85 ...... Frame ( 19) shift: 0.71 0.95 ...... Frame ( 20) shift: 0.69 1.05 ...... Frame ( 21) shift: 0.67 1.15 ...... Frame ( 22) shift: 0.67 1.26 ...... Frame ( 23) shift: 0.66 1.37 ...... Frame ( 24) shift: 0.71 1.46 ...... Frame ( 25) shift: 0.82 1.53 ...... Frame ( 26) shift: 0.92 1.59 ...... Frame ( 27) shift: 1.01 1.62 ...... Frame ( 28) shift: 1.07 1.60 ...... Frame ( 29) shift: 1.14 1.58 ...... Frame ( 30) shift: 1.16 1.60 ...... Frame ( 31) shift: 1.15 1.66 ...... Frame ( 32) shift: 1.13 1.72 ...... Frame ( 33) shift: 1.19 1.77 ...... Frame ( 34) shift: 1.31 1.80 ...... Frame ( 35) shift: 1.43 1.84 ...... Frame ( 36) shift: 1.50 1.87 ...... Frame ( 37) shift: 1.51 1.89 ...... Frame ( 38) shift: 1.53 1.91 ...... Frame ( 39) shift: 1.54 1.93 ...... Frame ( 40) shift: 1.56 1.95 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.632406 Iteration 2 Error: 0.378378 Iteration 3 Error: 0.118605 Iteration 4 Error: 0.054467 Iteration 5 Error: 0.022882 Align patch 2 23 left Iteration 1 Error: 1.083235 Iteration 2 Error: 0.469193 Iteration 3 Error: 0.235457 Iteration 4 Error: 0.110433 Iteration 5 Error: 0.043864 Align patch 3 22 left Iteration 1 Error: 1.529653 Iteration 2 Error: 0.338679 Iteration 3 Error: 0.139242 Iteration 4 Error: 0.064080 Iteration 5 Error: 0.021916 Align patch 4 21 left Iteration 1 Error: 0.628005 Iteration 2 Error: 0.108742 Iteration 3 Error: 0.021002 Align patch 5 20 left Iteration 1 Error: 1.401621 Iteration 2 Error: 0.194533 Iteration 3 Error: 0.056204 Iteration 4 Error: 0.013892 Align patch 6 19 left Iteration 1 Error: 2.351578 Iteration 2 Error: 0.618922 Iteration 3 Error: 0.246168 Iteration 4 Error: 0.134978 Iteration 5 Error: 0.054151 Align patch 6 19 left Iteration 1 Error: 2.269194 Iteration 2 Error: 0.395712 Iteration 3 Error: 0.076392 Iteration 4 Error: 0.017524 Align patch 7 18 left Iteration 1 Error: 0.717987 Iteration 2 Error: 0.314477 Iteration 3 Error: 0.144527 Iteration 4 Error: 0.073762 Iteration 5 Error: 0.041158 Align patch 8 17 left Iteration 1 Error: 0.995988 Iteration 2 Error: 0.310452 Iteration 3 Error: 0.129964 Iteration 4 Error: 0.073331 Iteration 5 Error: 0.037593 Align patch 9 16 left Iteration 1 Error: 0.514411 Iteration 2 Error: 0.162100 Iteration 3 Error: 0.043172 Align patch 10 15 left Iteration 1 Error: 0.848149 Iteration 2 Error: 0.135906 Iteration 3 Error: 0.031663 Align patch 11 14 left Iteration 1 Error: 2.343043 Iteration 2 Error: 0.518936 Iteration 3 Error: 0.202178 Iteration 4 Error: 0.064080 Iteration 5 Error: 0.040116 Align patch 12 13 left Iteration 1 Error: 1.151248 Iteration 2 Error: 0.340736 Iteration 3 Error: 0.171848 Iteration 4 Error: 0.093369 Iteration 5 Error: 0.047466 Align patch 13 12 left Iteration 1 Error: 0.896502 Iteration 2 Error: 0.187611 Iteration 3 Error: 0.076031 Iteration 4 Error: 0.032698 Align patch 14 11 left Iteration 1 Error: 0.745150 Iteration 2 Error: 0.085990 Iteration 3 Error: 0.027033 Align patch 15 10 left Iteration 1 Error: 1.036580 Iteration 2 Error: 0.166680 Iteration 3 Error: 0.045675 Align patch 16 9 left Iteration 1 Error: 1.358999 Iteration 2 Error: 0.348094 Iteration 3 Error: 0.125118 Iteration 4 Error: 0.076764 Iteration 5 Error: 0.035394 Align patch 17 8 left Iteration 1 Error: 1.146402 Iteration 2 Error: 0.229918 Iteration 3 Error: 0.081438 Iteration 4 Error: 0.030173 Align patch 18 7 left Iteration 1 Error: 0.737185 Iteration 2 Error: 0.176721 Iteration 3 Error: 0.058420 Iteration 4 Error: 0.018411 Align patch 19 6 left Iteration 1 Error: 0.578817 Iteration 2 Error: 0.195785 Iteration 3 Error: 0.066806 Iteration 4 Error: 0.031625 Align patch 20 5 left Iteration 1 Error: 1.093427 Iteration 2 Error: 0.293407 Iteration 3 Error: 0.094788 Iteration 4 Error: 0.045075 Align patch 21 4 left Iteration 1 Error: 1.050091 Iteration 2 Error: 0.278603 Iteration 3 Error: 0.070473 Iteration 4 Error: 0.011507 Align patch 22 3 left Iteration 1 Error: 1.038595 Iteration 2 Error: 0.136608 Iteration 3 Error: 0.028260 Align patch 23 2 left Iteration 1 Error: 1.157285 Iteration 2 Error: 0.190441 Iteration 3 Error: 0.078267 Iteration 4 Error: 0.018556 Align patch 24 1 left Iteration 1 Error: 1.131603 Iteration 2 Error: 0.174439 Iteration 3 Error: 0.043084 Align patch 25 0 left Iteration 1 Error: 1.235016 Iteration 2 Error: 0.195901 Iteration 3 Error: 0.063928 Iteration 4 Error: 0.028206 3D Fitting completed. Patch alignment time: 13.10(sec) Local motion has been corrected. Process thread exits. Computational time: 24.869469 sec Total time: 32.378090 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00013hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00013hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.604321s Reading file: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00013hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.674964s ........................................ >>>>>>TIME<<<<<< FFT: 0.911713s Defocus_U Defocus_V Angle CCC 14537.11 15427.74 4.82 0.048208 Final Values Defocus_U Defocus_V Angle CCC 14538.68 15426.18 4.82 0.075127 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00002sq_v01_00013hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00013hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.002e-01 CC threshold: 0.736 Mean Std: 41.55 7.01 Num Hot pixels: 213 Hot pixel threshold: 83.63 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.578356 Iteration 2 Error: 0.063918 Iteration 3 Error: 0.014181 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.08 0.13 ...... Frame ( 3) shift: -0.16 0.25 ...... Frame ( 4) shift: -0.24 0.38 ...... Frame ( 5) shift: -0.31 0.51 ...... Frame ( 6) shift: -0.31 0.57 ...... Frame ( 7) shift: -0.23 0.58 ...... Frame ( 8) shift: -0.14 0.59 ...... Frame ( 9) shift: -0.05 0.56 ...... Frame ( 10) shift: 0.05 0.50 ...... Frame ( 11) shift: 0.16 0.44 ...... Frame ( 12) shift: 0.21 0.40 ...... Frame ( 13) shift: 0.22 0.36 ...... Frame ( 14) shift: 0.22 0.32 ...... Frame ( 15) shift: 0.26 0.30 ...... Frame ( 16) shift: 0.31 0.28 ...... Frame ( 17) shift: 0.37 0.27 ...... Frame ( 18) shift: 0.39 0.26 ...... Frame ( 19) shift: 0.37 0.26 ...... Frame ( 20) shift: 0.34 0.26 ...... Frame ( 21) shift: 0.33 0.25 ...... Frame ( 22) shift: 0.32 0.24 ...... Frame ( 23) shift: 0.31 0.22 ...... Frame ( 24) shift: 0.35 0.27 ...... Frame ( 25) shift: 0.42 0.38 ...... Frame ( 26) shift: 0.49 0.49 ...... Frame ( 27) shift: 0.52 0.53 ...... Frame ( 28) shift: 0.51 0.52 ...... Frame ( 29) shift: 0.50 0.51 ...... Frame ( 30) shift: 0.51 0.52 ...... Frame ( 31) shift: 0.52 0.56 ...... Frame ( 32) shift: 0.54 0.59 ...... Frame ( 33) shift: 0.50 0.64 ...... Frame ( 34) shift: 0.42 0.72 ...... Frame ( 35) shift: 0.34 0.79 ...... Frame ( 36) shift: 0.32 0.80 ...... Frame ( 37) shift: 0.37 0.76 ...... Frame ( 38) shift: 0.41 0.72 ...... Frame ( 39) shift: 0.45 0.68 ...... Frame ( 40) shift: 0.50 0.63 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.644360 Iteration 2 Error: 0.168057 Iteration 3 Error: 0.045217 Align patch 2 23 left Iteration 1 Error: 0.873542 Iteration 2 Error: 0.146464 Iteration 3 Error: 0.046975 Align patch 3 22 left Iteration 1 Error: 0.518182 Iteration 2 Error: 0.090060 Iteration 3 Error: 0.024851 Align patch 4 21 left Iteration 1 Error: 0.455370 Iteration 2 Error: 0.073310 Iteration 3 Error: 0.014255 Align patch 5 20 left Iteration 1 Error: 0.618927 Iteration 2 Error: 0.099791 Iteration 3 Error: 0.011665 Align patch 6 19 left Iteration 1 Error: 0.873970 Iteration 2 Error: 0.238850 Iteration 3 Error: 0.061875 Iteration 4 Error: 0.016864 Align patch 7 18 left Iteration 1 Error: 0.836196 Iteration 2 Error: 0.221572 Iteration 3 Error: 0.051626 Iteration 4 Error: 0.016079 Align patch 8 17 left Iteration 1 Error: 0.395338 Iteration 2 Error: 0.065779 Iteration 3 Error: 0.021270 Align patch 9 16 left Iteration 1 Error: 0.655252 Iteration 2 Error: 0.081882 Iteration 3 Error: 0.016900 Align patch 10 15 left Iteration 1 Error: 0.762181 Iteration 2 Error: 0.091384 Iteration 3 Error: 0.014514 Align patch 11 14 left Iteration 1 Error: 0.756603 Iteration 2 Error: 0.120477 Iteration 3 Error: 0.034057 Align patch 12 13 left Iteration 1 Error: 0.644654 Iteration 2 Error: 0.092178 Iteration 3 Error: 0.027659 Align patch 13 12 left Iteration 1 Error: 0.575281 Iteration 2 Error: 0.068724 Iteration 3 Error: 0.011256 Align patch 14 11 left Iteration 1 Error: 0.833917 Iteration 2 Error: 0.125800 Iteration 3 Error: 0.019395 Align patch 15 10 left Iteration 1 Error: 0.569090 Iteration 2 Error: 0.058008 Iteration 3 Error: 0.016583 Align patch 16 9 left Iteration 1 Error: 0.713112 Iteration 2 Error: 0.165144 Iteration 3 Error: 0.037926 Align patch 17 8 left Iteration 1 Error: 0.329666 Iteration 2 Error: 0.033688 Align patch 18 7 left Iteration 1 Error: 0.502986 Iteration 2 Error: 0.077281 Iteration 3 Error: 0.012989 Align patch 19 6 left Iteration 1 Error: 0.718302 Iteration 2 Error: 0.104348 Iteration 3 Error: 0.019467 Align patch 20 5 left Iteration 1 Error: 0.661340 Iteration 2 Error: 0.114230 Iteration 3 Error: 0.025575 Align patch 21 4 left Iteration 1 Error: 0.606611 Iteration 2 Error: 0.100420 Iteration 3 Error: 0.024424 Align patch 22 3 left Iteration 1 Error: 0.621811 Iteration 2 Error: 0.073145 Iteration 3 Error: 0.019379 Align patch 23 2 left Iteration 1 Error: 0.657980 Iteration 2 Error: 0.071336 Iteration 3 Error: 0.017674 Align patch 24 1 left Iteration 1 Error: 0.898078 Iteration 2 Error: 0.104904 Iteration 3 Error: 0.019741 Align patch 25 0 left Iteration 1 Error: 0.589156 Iteration 2 Error: 0.060907 Iteration 3 Error: 0.014769 3D Fitting completed. Patch alignment time: 11.22(sec) Local motion has been corrected. Process thread exits. Computational time: 22.350885 sec Total time: 32.134834 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00013hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00013hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.716282s Reading file: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00013hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.158063s ........................................ >>>>>>TIME<<<<<< FFT: 1.020357s Defocus_U Defocus_V Angle CCC 15265.62 14585.94 85.97 0.065468 Final Values Defocus_U Defocus_V Angle CCC 15262.50 14585.94 85.35 0.104470 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00002sq_v01_00014hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00014hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.001e-01 CC threshold: 0.735 Mean Std: 41.75 6.97 Num Hot pixels: 243 Hot pixel threshold: 83.55 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.081228 Iteration 2 Error: 0.489827 Iteration 3 Error: 0.119013 Iteration 4 Error: 0.046899 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.13 -0.07 ...... Frame ( 3) shift: -0.26 -0.15 ...... Frame ( 4) shift: -0.39 -0.22 ...... Frame ( 5) shift: -0.51 -0.30 ...... Frame ( 6) shift: -0.55 -0.30 ...... Frame ( 7) shift: -0.48 -0.23 ...... Frame ( 8) shift: -0.41 -0.17 ...... Frame ( 9) shift: -0.37 -0.07 ...... Frame ( 10) shift: -0.36 0.06 ...... Frame ( 11) shift: -0.35 0.19 ...... Frame ( 12) shift: -0.28 0.31 ...... Frame ( 13) shift: -0.16 0.42 ...... Frame ( 14) shift: -0.03 0.52 ...... Frame ( 15) shift: 0.10 0.66 ...... Frame ( 16) shift: 0.24 0.84 ...... Frame ( 17) shift: 0.37 1.01 ...... Frame ( 18) shift: 0.40 1.14 ...... Frame ( 19) shift: 0.33 1.22 ...... Frame ( 20) shift: 0.25 1.31 ...... Frame ( 21) shift: 0.23 1.37 ...... Frame ( 22) shift: 0.27 1.42 ...... Frame ( 23) shift: 0.31 1.47 ...... Frame ( 24) shift: 0.34 1.49 ...... Frame ( 25) shift: 0.37 1.47 ...... Frame ( 26) shift: 0.40 1.46 ...... Frame ( 27) shift: 0.45 1.45 ...... Frame ( 28) shift: 0.52 1.45 ...... Frame ( 29) shift: 0.59 1.45 ...... Frame ( 30) shift: 0.74 1.51 ...... Frame ( 31) shift: 0.95 1.64 ...... Frame ( 32) shift: 1.16 1.76 ...... Frame ( 33) shift: 1.33 1.89 ...... Frame ( 34) shift: 1.45 2.02 ...... Frame ( 35) shift: 1.58 2.15 ...... Frame ( 36) shift: 1.66 2.29 ...... Frame ( 37) shift: 1.72 2.45 ...... Frame ( 38) shift: 1.77 2.61 ...... Frame ( 39) shift: 1.82 2.77 ...... Frame ( 40) shift: 1.87 2.92 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.437118 Iteration 2 Error: 0.170375 Iteration 3 Error: 0.058293 Iteration 4 Error: 0.026020 Align patch 2 23 left Iteration 1 Error: 0.628498 Iteration 2 Error: 0.184530 Iteration 3 Error: 0.053299 Iteration 4 Error: 0.021898 Align patch 3 22 left Iteration 1 Error: 0.890249 Iteration 2 Error: 0.113458 Iteration 3 Error: 0.031504 Align patch 4 21 left Iteration 1 Error: 1.085878 Iteration 2 Error: 0.123293 Iteration 3 Error: 0.030370 Align patch 5 20 left Iteration 1 Error: 0.534102 Iteration 2 Error: 0.139484 Iteration 3 Error: 0.033807 Align patch 6 19 left Iteration 1 Error: 1.435510 Iteration 2 Error: 0.191154 Iteration 3 Error: 0.065934 Iteration 4 Error: 0.020314 Align patch 7 18 left Iteration 1 Error: 0.854578 Iteration 2 Error: 0.216659 Iteration 3 Error: 0.076413 Iteration 4 Error: 0.035705 Align patch 8 17 left Iteration 1 Error: 0.704724 Iteration 2 Error: 0.221354 Iteration 3 Error: 0.073425 Iteration 4 Error: 0.031035 Align patch 9 16 left Iteration 1 Error: 0.848880 Iteration 2 Error: 0.143374 Iteration 3 Error: 0.024527 Align patch 10 15 left Iteration 1 Error: 0.736762 Iteration 2 Error: 0.177564 Iteration 3 Error: 0.055656 Iteration 4 Error: 0.026022 Align patch 11 14 left Iteration 1 Error: 0.822135 Iteration 2 Error: 0.156851 Iteration 3 Error: 0.072193 Iteration 4 Error: 0.029596 Align patch 12 13 left Iteration 1 Error: 1.015779 Iteration 2 Error: 0.380696 Iteration 3 Error: 0.155034 Iteration 4 Error: 0.057718 Iteration 5 Error: 0.032347 Align patch 13 12 left Iteration 1 Error: 0.966677 Iteration 2 Error: 0.105694 Iteration 3 Error: 0.018298 Align patch 14 11 left Iteration 1 Error: 0.697872 Iteration 2 Error: 0.111808 Iteration 3 Error: 0.028169 Align patch 15 10 left Iteration 1 Error: 0.514948 Iteration 2 Error: 0.126317 Iteration 3 Error: 0.037839 Align patch 16 9 left Iteration 1 Error: 0.633728 Iteration 2 Error: 0.163682 Iteration 3 Error: 0.062757 Iteration 4 Error: 0.023963 Align patch 17 8 left Iteration 1 Error: 0.619462 Iteration 2 Error: 0.170996 Iteration 3 Error: 0.052372 Iteration 4 Error: 0.025615 Align patch 18 7 left Iteration 1 Error: 0.741343 Iteration 2 Error: 0.189633 Iteration 3 Error: 0.077736 Iteration 4 Error: 0.030171 Align patch 19 6 left Iteration 1 Error: 1.214440 Iteration 2 Error: 0.196064 Iteration 3 Error: 0.044514 Align patch 20 5 left Iteration 1 Error: 1.088236 Iteration 2 Error: 0.322837 Iteration 3 Error: 0.067758 Iteration 4 Error: 0.024347 Align patch 21 4 left Iteration 1 Error: 0.987925 Iteration 2 Error: 0.236411 Iteration 3 Error: 0.054667 Iteration 4 Error: 0.025310 Align patch 22 3 left Iteration 1 Error: 0.554400 Iteration 2 Error: 0.162005 Iteration 3 Error: 0.051288 Iteration 4 Error: 0.012467 Align patch 23 2 left Iteration 1 Error: 0.526968 Iteration 2 Error: 0.115753 Iteration 3 Error: 0.029464 Align patch 24 1 left Iteration 1 Error: 0.921241 Iteration 2 Error: 0.196143 Iteration 3 Error: 0.062923 Iteration 4 Error: 0.020106 Align patch 25 0 left Iteration 1 Error: 0.690130 Iteration 2 Error: 0.196130 Iteration 3 Error: 0.044875 3D Fitting completed. Patch alignment time: 11.91(sec) Local motion has been corrected. Process thread exits. Computational time: 23.190075 sec Total time: 30.696518 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00014hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00014hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.471013s Reading file: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00014hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.340225s ........................................ >>>>>>TIME<<<<<< FFT: 0.949163s Defocus_U Defocus_V Angle CCC 9226.56 10058.60 12.32 0.045849 Final Values Defocus_U Defocus_V Angle CCC 9226.58 10055.48 12.32 0.085166 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00002sq_v01_00014hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00014hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 40.13 6.90 Num Hot pixels: 219 Hot pixel threshold: 81.55 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.759338 Iteration 2 Error: 0.113779 Iteration 3 Error: 0.027130 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.20 -0.15 ...... Frame ( 3) shift: -0.41 -0.31 ...... Frame ( 4) shift: -0.61 -0.46 ...... Frame ( 5) shift: -0.82 -0.61 ...... Frame ( 6) shift: -0.92 -0.68 ...... Frame ( 7) shift: -0.91 -0.66 ...... Frame ( 8) shift: -0.91 -0.63 ...... Frame ( 9) shift: -0.86 -0.59 ...... Frame ( 10) shift: -0.75 -0.52 ...... Frame ( 11) shift: -0.64 -0.45 ...... Frame ( 12) shift: -0.58 -0.36 ...... Frame ( 13) shift: -0.57 -0.25 ...... Frame ( 14) shift: -0.56 -0.14 ...... Frame ( 15) shift: -0.54 -0.08 ...... Frame ( 16) shift: -0.53 -0.08 ...... Frame ( 17) shift: -0.52 -0.07 ...... Frame ( 18) shift: -0.50 -0.07 ...... Frame ( 19) shift: -0.46 -0.07 ...... Frame ( 20) shift: -0.43 -0.08 ...... Frame ( 21) shift: -0.42 -0.06 ...... Frame ( 22) shift: -0.43 -0.01 ...... Frame ( 23) shift: -0.44 0.03 ...... Frame ( 24) shift: -0.44 0.08 ...... Frame ( 25) shift: -0.45 0.13 ...... Frame ( 26) shift: -0.45 0.18 ...... Frame ( 27) shift: -0.45 0.21 ...... Frame ( 28) shift: -0.45 0.23 ...... Frame ( 29) shift: -0.45 0.24 ...... Frame ( 30) shift: -0.42 0.28 ...... Frame ( 31) shift: -0.38 0.33 ...... Frame ( 32) shift: -0.33 0.38 ...... Frame ( 33) shift: -0.28 0.44 ...... Frame ( 34) shift: -0.21 0.50 ...... Frame ( 35) shift: -0.15 0.57 ...... Frame ( 36) shift: -0.10 0.62 ...... Frame ( 37) shift: -0.06 0.64 ...... Frame ( 38) shift: -0.03 0.67 ...... Frame ( 39) shift: 0.01 0.70 ...... Frame ( 40) shift: 0.05 0.72 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.367570 Iteration 2 Error: 0.149368 Iteration 3 Error: 0.043207 Align patch 2 23 left Iteration 1 Error: 0.896413 Iteration 2 Error: 0.172546 Iteration 3 Error: 0.053697 Iteration 4 Error: 0.017506 Align patch 3 22 left Iteration 1 Error: 0.660166 Iteration 2 Error: 0.127321 Iteration 3 Error: 0.032438 Align patch 4 21 left Iteration 1 Error: 0.509935 Iteration 2 Error: 0.097700 Iteration 3 Error: 0.018019 Align patch 5 20 left Iteration 1 Error: 0.537465 Iteration 2 Error: 0.055340 Iteration 3 Error: 0.010792 Align patch 6 19 left Iteration 1 Error: 1.685382 Iteration 2 Error: 0.241725 Iteration 3 Error: 0.068643 Iteration 4 Error: 0.025362 Align patch 7 18 left Iteration 1 Error: 0.893126 Iteration 2 Error: 0.095558 Iteration 3 Error: 0.040081 Align patch 8 17 left Iteration 1 Error: 0.734727 Iteration 2 Error: 0.127010 Iteration 3 Error: 0.034491 Align patch 9 16 left Iteration 1 Error: 0.621667 Iteration 2 Error: 0.131665 Iteration 3 Error: 0.027802 Align patch 10 15 left Iteration 1 Error: 0.571290 Iteration 2 Error: 0.094565 Iteration 3 Error: 0.012688 Align patch 11 14 left Iteration 1 Error: 0.857664 Iteration 2 Error: 0.149504 Iteration 3 Error: 0.050233 Iteration 4 Error: 0.020319 Align patch 12 13 left Iteration 1 Error: 0.712339 Iteration 2 Error: 0.096663 Iteration 3 Error: 0.036208 Align patch 13 12 left Iteration 1 Error: 0.595107 Iteration 2 Error: 0.052065 Iteration 3 Error: 0.006299 Align patch 14 11 left Iteration 1 Error: 0.504738 Iteration 2 Error: 0.055319 Iteration 3 Error: 0.011461 Align patch 15 10 left Iteration 1 Error: 0.652248 Iteration 2 Error: 0.057400 Iteration 3 Error: 0.016679 Align patch 16 9 left Iteration 1 Error: 0.620485 Iteration 2 Error: 0.230984 Iteration 3 Error: 0.096125 Iteration 4 Error: 0.035662 Align patch 17 8 left Iteration 1 Error: 0.945017 Iteration 2 Error: 0.148994 Iteration 3 Error: 0.045230 Align patch 18 7 left Iteration 1 Error: 0.663440 Iteration 2 Error: 0.093140 Iteration 3 Error: 0.021256 Align patch 19 6 left Iteration 1 Error: 0.459259 Iteration 2 Error: 0.066352 Iteration 3 Error: 0.012714 Align patch 20 5 left Iteration 1 Error: 0.388102 Iteration 2 Error: 0.062256 Iteration 3 Error: 0.014279 Align patch 21 4 left Iteration 1 Error: 0.720391 Iteration 2 Error: 0.112957 Iteration 3 Error: 0.042608 Align patch 22 3 left Iteration 1 Error: 0.492437 Iteration 2 Error: 0.094631 Iteration 3 Error: 0.032461 Align patch 23 2 left Iteration 1 Error: 0.691906 Iteration 2 Error: 0.077153 Iteration 3 Error: 0.018249 Align patch 24 1 left Iteration 1 Error: 0.565145 Iteration 2 Error: 0.063280 Iteration 3 Error: 0.009250 Align patch 25 0 left Iteration 1 Error: 0.585686 Iteration 2 Error: 0.053013 Iteration 3 Error: 0.009955 3D Fitting completed. Patch alignment time: 12.02(sec) Local motion has been corrected. Process thread exits. Computational time: 23.917027 sec Total time: 31.216316 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00014hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00014hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.498028s Reading file: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00014hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.890190s ........................................ >>>>>>TIME<<<<<< FFT: 1.006794s Defocus_U Defocus_V Angle CCC 12923.85 13416.04 0.24 0.051873 Final Values Defocus_U Defocus_V Angle CCC 13420.74 12944.17 88.68 0.084175 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00002sq_v01_00014hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00014hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 40.55 6.93 Num Hot pixels: 227 Hot pixel threshold: 82.13 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.665792 Iteration 2 Error: 0.093365 Iteration 3 Error: 0.019797 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.18 -0.15 ...... Frame ( 3) shift: -0.35 -0.30 ...... Frame ( 4) shift: -0.53 -0.45 ...... Frame ( 5) shift: -0.70 -0.60 ...... Frame ( 6) shift: -0.78 -0.70 ...... Frame ( 7) shift: -0.76 -0.73 ...... Frame ( 8) shift: -0.75 -0.77 ...... Frame ( 9) shift: -0.74 -0.76 ...... Frame ( 10) shift: -0.75 -0.72 ...... Frame ( 11) shift: -0.75 -0.67 ...... Frame ( 12) shift: -0.75 -0.61 ...... Frame ( 13) shift: -0.74 -0.55 ...... Frame ( 14) shift: -0.73 -0.48 ...... Frame ( 15) shift: -0.70 -0.42 ...... Frame ( 16) shift: -0.66 -0.38 ...... Frame ( 17) shift: -0.63 -0.33 ...... Frame ( 18) shift: -0.61 -0.30 ...... Frame ( 19) shift: -0.62 -0.30 ...... Frame ( 20) shift: -0.63 -0.29 ...... Frame ( 21) shift: -0.63 -0.26 ...... Frame ( 22) shift: -0.62 -0.19 ...... Frame ( 23) shift: -0.61 -0.13 ...... Frame ( 24) shift: -0.63 -0.11 ...... Frame ( 25) shift: -0.68 -0.13 ...... Frame ( 26) shift: -0.73 -0.14 ...... Frame ( 27) shift: -0.75 -0.16 ...... Frame ( 28) shift: -0.72 -0.17 ...... Frame ( 29) shift: -0.69 -0.18 ...... Frame ( 30) shift: -0.63 -0.13 ...... Frame ( 31) shift: -0.55 -0.01 ...... Frame ( 32) shift: -0.47 0.11 ...... Frame ( 33) shift: -0.42 0.22 ...... Frame ( 34) shift: -0.42 0.34 ...... Frame ( 35) shift: -0.42 0.45 ...... Frame ( 36) shift: -0.43 0.49 ...... Frame ( 37) shift: -0.44 0.44 ...... Frame ( 38) shift: -0.46 0.40 ...... Frame ( 39) shift: -0.48 0.36 ...... Frame ( 40) shift: -0.49 0.32 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.634824 Iteration 2 Error: 0.133330 Iteration 3 Error: 0.033658 Align patch 2 23 left Iteration 1 Error: 0.577176 Iteration 2 Error: 0.099004 Iteration 3 Error: 0.018821 Align patch 3 22 left Iteration 1 Error: 0.659769 Iteration 2 Error: 0.061568 Iteration 3 Error: 0.014670 Align patch 4 21 left Iteration 1 Error: 0.716288 Iteration 2 Error: 0.079810 Iteration 3 Error: 0.015191 Align patch 5 20 left Iteration 1 Error: 0.672115 Iteration 2 Error: 0.045387 Align patch 6 19 left Iteration 1 Error: 0.748022 Iteration 2 Error: 0.153641 Iteration 3 Error: 0.034115 Align patch 7 18 left Iteration 1 Error: 1.113907 Iteration 2 Error: 0.173422 Iteration 3 Error: 0.044597 Align patch 8 17 left Iteration 1 Error: 0.847110 Iteration 2 Error: 0.121064 Iteration 3 Error: 0.037921 Align patch 9 16 left Iteration 1 Error: 0.925118 Iteration 2 Error: 0.181188 Iteration 3 Error: 0.050145 Iteration 4 Error: 0.011223 Align patch 10 15 left Iteration 1 Error: 0.853188 Iteration 2 Error: 0.079704 Iteration 3 Error: 0.017704 Align patch 11 14 left Iteration 1 Error: 0.631240 Iteration 2 Error: 0.126672 Iteration 3 Error: 0.031942 Align patch 12 13 left Iteration 1 Error: 0.626478 Iteration 2 Error: 0.107921 Iteration 3 Error: 0.034291 Align patch 13 12 left Iteration 1 Error: 0.508942 Iteration 2 Error: 0.108711 Iteration 3 Error: 0.021127 Align patch 14 11 left Iteration 1 Error: 0.533575 Iteration 2 Error: 0.111010 Iteration 3 Error: 0.023411 Align patch 15 10 left Iteration 1 Error: 0.559348 Iteration 2 Error: 0.107249 Iteration 3 Error: 0.032935 Align patch 16 9 left Iteration 1 Error: 0.610406 Iteration 2 Error: 0.118294 Iteration 3 Error: 0.026026 Align patch 17 8 left Iteration 1 Error: 0.882076 Iteration 2 Error: 0.072733 Iteration 3 Error: 0.021280 Align patch 18 7 left Iteration 1 Error: 0.692807 Iteration 2 Error: 0.106625 Iteration 3 Error: 0.035060 Align patch 19 6 left Iteration 1 Error: 0.611607 Iteration 2 Error: 0.125273 Iteration 3 Error: 0.020184 Align patch 20 5 left Iteration 1 Error: 0.640228 Iteration 2 Error: 0.097473 Iteration 3 Error: 0.019627 Align patch 21 4 left Iteration 1 Error: 0.793166 Iteration 2 Error: 0.159505 Iteration 3 Error: 0.034164 Align patch 22 3 left Iteration 1 Error: 0.828520 Iteration 2 Error: 0.101685 Iteration 3 Error: 0.021889 Align patch 23 2 left Iteration 1 Error: 0.730791 Iteration 2 Error: 0.160142 Iteration 3 Error: 0.054644 Iteration 4 Error: 0.017900 Align patch 24 1 left Iteration 1 Error: 0.808154 Iteration 2 Error: 0.112141 Iteration 3 Error: 0.031947 Align patch 25 0 left Iteration 1 Error: 1.044792 Iteration 2 Error: 0.165927 Iteration 3 Error: 0.030093 3D Fitting completed. Patch alignment time: 13.20(sec) Local motion has been corrected. Process thread exits. Computational time: 23.583000 sec Total time: 29.853088 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00014hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00014hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.493747s Reading file: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00014hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.362683s ........................................ >>>>>>TIME<<<<<< FFT: 1.037286s Defocus_U Defocus_V Angle CCC 11611.33 12525.39 5.48 0.045632 Final Values Defocus_U Defocus_V Angle CCC 11620.71 12534.77 5.17 0.080013 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00002sq_v01_00014hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00014hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 40.09 6.88 Num Hot pixels: 222 Hot pixel threshold: 81.39 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.192959 Iteration 2 Error: 0.171896 Iteration 3 Error: 0.036518 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.28 -0.06 ...... Frame ( 3) shift: -0.56 -0.12 ...... Frame ( 4) shift: -0.84 -0.17 ...... Frame ( 5) shift: -1.12 -0.23 ...... Frame ( 6) shift: -1.26 -0.30 ...... Frame ( 7) shift: -1.25 -0.37 ...... Frame ( 8) shift: -1.25 -0.45 ...... Frame ( 9) shift: -1.19 -0.41 ...... Frame ( 10) shift: -1.09 -0.27 ...... Frame ( 11) shift: -0.99 -0.12 ...... Frame ( 12) shift: -0.91 0.01 ...... Frame ( 13) shift: -0.85 0.14 ...... Frame ( 14) shift: -0.78 0.26 ...... Frame ( 15) shift: -0.73 0.38 ...... Frame ( 16) shift: -0.68 0.50 ...... Frame ( 17) shift: -0.64 0.61 ...... Frame ( 18) shift: -0.60 0.71 ...... Frame ( 19) shift: -0.57 0.77 ...... Frame ( 20) shift: -0.54 0.84 ...... Frame ( 21) shift: -0.54 0.90 ...... Frame ( 22) shift: -0.56 0.94 ...... Frame ( 23) shift: -0.58 0.98 ...... Frame ( 24) shift: -0.59 1.05 ...... Frame ( 25) shift: -0.59 1.13 ...... Frame ( 26) shift: -0.59 1.21 ...... Frame ( 27) shift: -0.57 1.26 ...... Frame ( 28) shift: -0.51 1.29 ...... Frame ( 29) shift: -0.46 1.32 ...... Frame ( 30) shift: -0.40 1.35 ...... Frame ( 31) shift: -0.32 1.38 ...... Frame ( 32) shift: -0.24 1.40 ...... Frame ( 33) shift: -0.21 1.43 ...... Frame ( 34) shift: -0.23 1.47 ...... Frame ( 35) shift: -0.25 1.50 ...... Frame ( 36) shift: -0.27 1.50 ...... Frame ( 37) shift: -0.29 1.47 ...... Frame ( 38) shift: -0.32 1.43 ...... Frame ( 39) shift: -0.35 1.40 ...... Frame ( 40) shift: -0.37 1.37 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.191762 Iteration 2 Error: 0.168478 Iteration 3 Error: 0.054766 Iteration 4 Error: 0.019217 Align patch 2 23 left Iteration 1 Error: 0.655756 Iteration 2 Error: 0.089763 Iteration 3 Error: 0.022315 Align patch 3 22 left Iteration 1 Error: 0.697554 Iteration 2 Error: 0.120850 Iteration 3 Error: 0.045963 Align patch 4 21 left Iteration 1 Error: 0.373538 Iteration 2 Error: 0.039384 Align patch 5 20 left Iteration 1 Error: 0.874518 Iteration 2 Error: 0.157704 Iteration 3 Error: 0.054865 Iteration 4 Error: 0.010248 Align patch 6 19 left Iteration 1 Error: 0.815367 Iteration 2 Error: 0.166076 Iteration 3 Error: 0.076195 Iteration 4 Error: 0.023158 Align patch 7 18 left Iteration 1 Error: 0.668504 Iteration 2 Error: 0.120943 Iteration 3 Error: 0.028736 Align patch 8 17 left Iteration 1 Error: 0.719269 Iteration 2 Error: 0.153228 Iteration 3 Error: 0.058846 Iteration 4 Error: 0.022387 Align patch 9 16 left Iteration 1 Error: 0.534424 Iteration 2 Error: 0.141842 Iteration 3 Error: 0.041450 Align patch 10 15 left Iteration 1 Error: 0.468846 Iteration 2 Error: 0.061603 Iteration 3 Error: 0.016501 Align patch 11 14 left Iteration 1 Error: 0.891878 Iteration 2 Error: 0.116339 Iteration 3 Error: 0.025769 Align patch 12 13 left Iteration 1 Error: 0.667047 Iteration 2 Error: 0.137749 Iteration 3 Error: 0.035443 Align patch 13 12 left Iteration 1 Error: 0.644932 Iteration 2 Error: 0.103787 Iteration 3 Error: 0.031127 Align patch 14 11 left Iteration 1 Error: 0.615325 Iteration 2 Error: 0.080187 Iteration 3 Error: 0.023104 Align patch 15 10 left Iteration 1 Error: 0.678574 Iteration 2 Error: 0.112043 Iteration 3 Error: 0.019747 Align patch 16 9 left Iteration 1 Error: 0.760355 Iteration 2 Error: 0.102368 Iteration 3 Error: 0.022284 Align patch 17 8 left Iteration 1 Error: 0.752457 Iteration 2 Error: 0.107929 Iteration 3 Error: 0.021432 Align patch 18 7 left Iteration 1 Error: 0.891127 Iteration 2 Error: 0.179768 Iteration 3 Error: 0.046169 Align patch 19 6 left Iteration 1 Error: 0.648447 Iteration 2 Error: 0.083537 Iteration 3 Error: 0.022535 Align patch 20 5 left Iteration 1 Error: 0.697297 Iteration 2 Error: 0.121044 Iteration 3 Error: 0.036242 Align patch 21 4 left Iteration 1 Error: 0.867692 Iteration 2 Error: 0.151754 Iteration 3 Error: 0.018637 Align patch 22 3 left Iteration 1 Error: 0.731442 Iteration 2 Error: 0.141643 Iteration 3 Error: 0.041211 Align patch 23 2 left Iteration 1 Error: 0.774646 Iteration 2 Error: 0.142794 Iteration 3 Error: 0.037600 Align patch 24 1 left Iteration 1 Error: 0.545390 Iteration 2 Error: 0.071303 Iteration 3 Error: 0.012238 Align patch 25 0 left Iteration 1 Error: 0.478174 Iteration 2 Error: 0.097341 Iteration 3 Error: 0.020079 3D Fitting completed. Patch alignment time: 11.17(sec) Local motion has been corrected. Process thread exits. Computational time: 22.066347 sec Total time: 28.208969 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00014hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00014hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.628925s Reading file: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00014hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.912737s ........................................ >>>>>>TIME<<<<<< FFT: 0.972247s Defocus_U Defocus_V Angle CCC 11591.88 10896.50 81.09 0.046039 Final Values Defocus_U Defocus_V Angle CCC 11620.00 10905.91 82.98 0.077818 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00002sq_v01_00015hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00015hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 40.21 6.88 Num Hot pixels: 240 Hot pixel threshold: 81.49 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.460170 Iteration 2 Error: 0.223121 Iteration 3 Error: 0.043550 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.07 0.07 ...... Frame ( 3) shift: -0.14 0.15 ...... Frame ( 4) shift: -0.21 0.22 ...... Frame ( 5) shift: -0.28 0.30 ...... Frame ( 6) shift: -0.33 0.36 ...... Frame ( 7) shift: -0.35 0.40 ...... Frame ( 8) shift: -0.36 0.44 ...... Frame ( 9) shift: -0.36 0.49 ...... Frame ( 10) shift: -0.34 0.56 ...... Frame ( 11) shift: -0.32 0.62 ...... Frame ( 12) shift: -0.32 0.70 ...... Frame ( 13) shift: -0.35 0.78 ...... Frame ( 14) shift: -0.37 0.87 ...... Frame ( 15) shift: -0.38 0.92 ...... Frame ( 16) shift: -0.36 0.94 ...... Frame ( 17) shift: -0.34 0.96 ...... Frame ( 18) shift: -0.29 0.98 ...... Frame ( 19) shift: -0.21 1.02 ...... Frame ( 20) shift: -0.12 1.05 ...... Frame ( 21) shift: -0.06 1.11 ...... Frame ( 22) shift: -0.01 1.19 ...... Frame ( 23) shift: 0.03 1.27 ...... Frame ( 24) shift: 0.07 1.33 ...... Frame ( 25) shift: 0.10 1.37 ...... Frame ( 26) shift: 0.13 1.40 ...... Frame ( 27) shift: 0.15 1.44 ...... Frame ( 28) shift: 0.16 1.46 ...... Frame ( 29) shift: 0.16 1.49 ...... Frame ( 30) shift: 0.19 1.58 ...... Frame ( 31) shift: 0.25 1.74 ...... Frame ( 32) shift: 0.31 1.90 ...... Frame ( 33) shift: 0.35 2.00 ...... Frame ( 34) shift: 0.39 2.06 ...... Frame ( 35) shift: 0.43 2.12 ...... Frame ( 36) shift: 0.46 2.21 ...... Frame ( 37) shift: 0.49 2.34 ...... Frame ( 38) shift: 0.52 2.48 ...... Frame ( 39) shift: 0.55 2.61 ...... Frame ( 40) shift: 0.58 2.74 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.354488 Iteration 2 Error: 0.080554 Iteration 3 Error: 0.034013 Align patch 2 23 left Iteration 1 Error: 0.769479 Iteration 2 Error: 0.110851 Iteration 3 Error: 0.027052 Align patch 3 22 left Iteration 1 Error: 0.333348 Iteration 2 Error: 0.067567 Iteration 3 Error: 0.024456 Align patch 4 21 left Iteration 1 Error: 0.681801 Iteration 2 Error: 0.128139 Iteration 3 Error: 0.024629 Align patch 5 20 left Iteration 1 Error: 0.743331 Iteration 2 Error: 0.095043 Iteration 3 Error: 0.035393 Align patch 6 19 left Iteration 1 Error: 1.054326 Iteration 2 Error: 0.240947 Iteration 3 Error: 0.028425 Align patch 7 18 left Iteration 1 Error: 0.762693 Iteration 2 Error: 0.090402 Iteration 3 Error: 0.019960 Align patch 8 17 left Iteration 1 Error: 0.497675 Iteration 2 Error: 0.079432 Iteration 3 Error: 0.021352 Align patch 9 16 left Iteration 1 Error: 0.612706 Iteration 2 Error: 0.090521 Iteration 3 Error: 0.022512 Align patch 10 15 left Iteration 1 Error: 0.841433 Iteration 2 Error: 0.115318 Iteration 3 Error: 0.024898 Align patch 11 14 left Iteration 1 Error: 0.455552 Iteration 2 Error: 0.067450 Iteration 3 Error: 0.014621 Align patch 12 13 left Iteration 1 Error: 0.752634 Iteration 2 Error: 0.137155 Iteration 3 Error: 0.029299 Align patch 13 12 left Iteration 1 Error: 0.523490 Iteration 2 Error: 0.095246 Iteration 3 Error: 0.018135 Align patch 14 11 left Iteration 1 Error: 0.496694 Iteration 2 Error: 0.071419 Iteration 3 Error: 0.012692 Align patch 15 10 left Iteration 1 Error: 0.426952 Iteration 2 Error: 0.116638 Iteration 3 Error: 0.027975 Align patch 16 9 left Iteration 1 Error: 0.689209 Iteration 2 Error: 0.139148 Iteration 3 Error: 0.043174 Align patch 17 8 left Iteration 1 Error: 0.629443 Iteration 2 Error: 0.121683 Iteration 3 Error: 0.028520 Align patch 18 7 left Iteration 1 Error: 0.432980 Iteration 2 Error: 0.055231 Iteration 3 Error: 0.019896 Align patch 19 6 left Iteration 1 Error: 0.556823 Iteration 2 Error: 0.080916 Iteration 3 Error: 0.014550 Align patch 20 5 left Iteration 1 Error: 0.898788 Iteration 2 Error: 0.166005 Iteration 3 Error: 0.017429 Align patch 21 4 left Iteration 1 Error: 0.596761 Iteration 2 Error: 0.108729 Iteration 3 Error: 0.037538 Align patch 22 3 left Iteration 1 Error: 0.656483 Iteration 2 Error: 0.166649 Iteration 3 Error: 0.035980 Align patch 23 2 left Iteration 1 Error: 1.108976 Iteration 2 Error: 0.183108 Iteration 3 Error: 0.039858 Align patch 24 1 left Iteration 1 Error: 0.629092 Iteration 2 Error: 0.069305 Iteration 3 Error: 0.019128 Align patch 25 0 left Iteration 1 Error: 0.484963 Iteration 2 Error: 0.070324 Iteration 3 Error: 0.011207 3D Fitting completed. Patch alignment time: 12.92(sec) Local motion has been corrected. Process thread exits. Computational time: 23.185539 sec Total time: 30.150242 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00015hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00015hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.539048s Reading file: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00015hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.621191s ........................................ >>>>>>TIME<<<<<< FFT: 0.933970s Defocus_U Defocus_V Angle CCC 8992.19 9863.28 11.84 0.035349 Final Values Defocus_U Defocus_V Angle CCC 8987.50 9871.10 12.15 0.066663 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00002sq_v01_00015hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00015hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 39.89 6.87 Num Hot pixels: 204 Hot pixel threshold: 81.09 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.858712 Iteration 2 Error: 0.149736 Iteration 3 Error: 0.033153 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.21 -0.16 ...... Frame ( 3) shift: -0.42 -0.31 ...... Frame ( 4) shift: -0.62 -0.47 ...... Frame ( 5) shift: -0.83 -0.62 ...... Frame ( 6) shift: -0.97 -0.67 ...... Frame ( 7) shift: -1.03 -0.60 ...... Frame ( 8) shift: -1.09 -0.53 ...... Frame ( 9) shift: -1.14 -0.45 ...... Frame ( 10) shift: -1.18 -0.36 ...... Frame ( 11) shift: -1.22 -0.28 ...... Frame ( 12) shift: -1.21 -0.20 ...... Frame ( 13) shift: -1.15 -0.13 ...... Frame ( 14) shift: -1.09 -0.06 ...... Frame ( 15) shift: -1.05 -0.01 ...... Frame ( 16) shift: -1.04 0.02 ...... Frame ( 17) shift: -1.03 0.05 ...... Frame ( 18) shift: -1.03 0.10 ...... Frame ( 19) shift: -1.03 0.16 ...... Frame ( 20) shift: -1.04 0.21 ...... Frame ( 21) shift: -1.03 0.29 ...... Frame ( 22) shift: -1.00 0.38 ...... Frame ( 23) shift: -0.96 0.46 ...... Frame ( 24) shift: -0.93 0.52 ...... Frame ( 25) shift: -0.90 0.55 ...... Frame ( 26) shift: -0.88 0.58 ...... Frame ( 27) shift: -0.86 0.62 ...... Frame ( 28) shift: -0.85 0.69 ...... Frame ( 29) shift: -0.85 0.75 ...... Frame ( 30) shift: -0.85 0.81 ...... Frame ( 31) shift: -0.88 0.85 ...... Frame ( 32) shift: -0.90 0.90 ...... Frame ( 33) shift: -0.87 0.95 ...... Frame ( 34) shift: -0.78 0.99 ...... Frame ( 35) shift: -0.69 1.04 ...... Frame ( 36) shift: -0.63 1.07 ...... Frame ( 37) shift: -0.61 1.11 ...... Frame ( 38) shift: -0.58 1.14 ...... Frame ( 39) shift: -0.56 1.17 ...... Frame ( 40) shift: -0.54 1.20 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.131373 Iteration 2 Error: 0.121380 Iteration 3 Error: 0.029262 Align patch 2 23 left Iteration 1 Error: 0.615704 Iteration 2 Error: 0.117615 Iteration 3 Error: 0.030901 Align patch 3 22 left Iteration 1 Error: 0.731359 Iteration 2 Error: 0.116513 Iteration 3 Error: 0.038195 Align patch 4 21 left Iteration 1 Error: 0.625497 Iteration 2 Error: 0.103633 Iteration 3 Error: 0.022784 Align patch 5 20 left Iteration 1 Error: 0.719836 Iteration 2 Error: 0.122626 Iteration 3 Error: 0.026472 Align patch 6 19 left Iteration 1 Error: 0.544473 Iteration 2 Error: 0.115053 Iteration 3 Error: 0.024857 Align patch 7 18 left Iteration 1 Error: 0.412834 Iteration 2 Error: 0.061704 Iteration 3 Error: 0.014419 Align patch 8 17 left Iteration 1 Error: 0.591409 Iteration 2 Error: 0.094189 Iteration 3 Error: 0.019935 Align patch 9 16 left Iteration 1 Error: 0.860643 Iteration 2 Error: 0.146206 Iteration 3 Error: 0.032683 Align patch 10 15 left Iteration 1 Error: 0.499118 Iteration 2 Error: 0.062303 Iteration 3 Error: 0.012712 Align patch 11 14 left Iteration 1 Error: 0.618115 Iteration 2 Error: 0.099223 Iteration 3 Error: 0.027948 Align patch 12 13 left Iteration 1 Error: 0.610828 Iteration 2 Error: 0.082524 Iteration 3 Error: 0.017972 Align patch 13 12 left Iteration 1 Error: 0.706529 Iteration 2 Error: 0.107063 Iteration 3 Error: 0.032094 Align patch 14 11 left Iteration 1 Error: 0.670490 Iteration 2 Error: 0.129218 Iteration 3 Error: 0.027177 Align patch 15 10 left Iteration 1 Error: 0.426627 Iteration 2 Error: 0.077688 Iteration 3 Error: 0.023808 Align patch 16 9 left Iteration 1 Error: 0.819279 Iteration 2 Error: 0.061886 Iteration 3 Error: 0.011035 Align patch 17 8 left Iteration 1 Error: 0.987922 Iteration 2 Error: 0.126068 Iteration 3 Error: 0.030797 Align patch 18 7 left Iteration 1 Error: 0.684713 Iteration 2 Error: 0.121648 Iteration 3 Error: 0.036867 Align patch 19 6 left Iteration 1 Error: 0.654452 Iteration 2 Error: 0.107053 Iteration 3 Error: 0.037554 Align patch 20 5 left Iteration 1 Error: 0.665176 Iteration 2 Error: 0.062761 Iteration 3 Error: 0.009350 Align patch 21 4 left Iteration 1 Error: 0.706015 Iteration 2 Error: 0.145077 Iteration 3 Error: 0.023133 Align patch 22 3 left Iteration 1 Error: 1.149920 Iteration 2 Error: 0.145704 Iteration 3 Error: 0.028282 Align patch 23 2 left Iteration 1 Error: 0.359162 Iteration 2 Error: 0.050348 Iteration 3 Error: 0.010889 Align patch 24 1 left Iteration 1 Error: 0.712315 Iteration 2 Error: 0.071564 Iteration 3 Error: 0.019130 Align patch 25 0 left Iteration 1 Error: 0.673207 Iteration 2 Error: 0.075797 Iteration 3 Error: 0.016594 3D Fitting completed. Patch alignment time: 11.02(sec) Local motion has been corrected. Process thread exits. Computational time: 23.069965 sec Total time: 31.370872 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00015hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00015hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.598597s Reading file: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00015hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.438067s ........................................ >>>>>>TIME<<<<<< FFT: 1.052764s Defocus_U Defocus_V Angle CCC 10472.68 10058.60 88.26 0.042397 Final Values Defocus_U Defocus_V Angle CCC 10510.18 10049.23 88.58 0.070284 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00002sq_v01_00015hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00015hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 41.08 6.94 Num Hot pixels: 220 Hot pixel threshold: 82.74 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.492011 Iteration 2 Error: 0.058398 Iteration 3 Error: 0.016205 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.04 0.13 ...... Frame ( 3) shift: -0.09 0.27 ...... Frame ( 4) shift: -0.13 0.40 ...... Frame ( 5) shift: -0.18 0.54 ...... Frame ( 6) shift: -0.20 0.62 ...... Frame ( 7) shift: -0.21 0.65 ...... Frame ( 8) shift: -0.21 0.68 ...... Frame ( 9) shift: -0.21 0.71 ...... Frame ( 10) shift: -0.21 0.73 ...... Frame ( 11) shift: -0.20 0.75 ...... Frame ( 12) shift: -0.19 0.73 ...... Frame ( 13) shift: -0.17 0.67 ...... Frame ( 14) shift: -0.15 0.61 ...... Frame ( 15) shift: -0.12 0.58 ...... Frame ( 16) shift: -0.08 0.59 ...... Frame ( 17) shift: -0.03 0.60 ...... Frame ( 18) shift: 0.00 0.60 ...... Frame ( 19) shift: 0.03 0.59 ...... Frame ( 20) shift: 0.06 0.59 ...... Frame ( 21) shift: 0.09 0.60 ...... Frame ( 22) shift: 0.13 0.64 ...... Frame ( 23) shift: 0.17 0.67 ...... Frame ( 24) shift: 0.20 0.71 ...... Frame ( 25) shift: 0.22 0.77 ...... Frame ( 26) shift: 0.23 0.83 ...... Frame ( 27) shift: 0.24 0.87 ...... Frame ( 28) shift: 0.25 0.91 ...... Frame ( 29) shift: 0.26 0.94 ...... Frame ( 30) shift: 0.25 0.94 ...... Frame ( 31) shift: 0.23 0.90 ...... Frame ( 32) shift: 0.21 0.86 ...... Frame ( 33) shift: 0.23 0.84 ...... Frame ( 34) shift: 0.29 0.85 ...... Frame ( 35) shift: 0.35 0.86 ...... Frame ( 36) shift: 0.38 0.86 ...... Frame ( 37) shift: 0.37 0.84 ...... Frame ( 38) shift: 0.37 0.83 ...... Frame ( 39) shift: 0.37 0.81 ...... Frame ( 40) shift: 0.37 0.79 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.644977 Iteration 2 Error: 0.105369 Iteration 3 Error: 0.013895 Align patch 2 23 left Iteration 1 Error: 0.905714 Iteration 2 Error: 0.069912 Iteration 3 Error: 0.022365 Align patch 3 22 left Iteration 1 Error: 0.712439 Iteration 2 Error: 0.120191 Iteration 3 Error: 0.029887 Align patch 4 21 left Iteration 1 Error: 0.608933 Iteration 2 Error: 0.078056 Iteration 3 Error: 0.024231 Align patch 5 20 left Iteration 1 Error: 0.807184 Iteration 2 Error: 0.123619 Iteration 3 Error: 0.022005 Align patch 6 19 left Iteration 1 Error: 0.521872 Iteration 2 Error: 0.095173 Iteration 3 Error: 0.015992 Align patch 7 18 left Iteration 1 Error: 0.520754 Iteration 2 Error: 0.066106 Iteration 3 Error: 0.007969 Align patch 8 17 left Iteration 1 Error: 0.805441 Iteration 2 Error: 0.134820 Iteration 3 Error: 0.057577 Iteration 4 Error: 0.019960 Align patch 9 16 left Iteration 1 Error: 0.845316 Iteration 2 Error: 0.181097 Iteration 3 Error: 0.026738 Align patch 10 15 left Iteration 1 Error: 0.550653 Iteration 2 Error: 0.112420 Iteration 3 Error: 0.022517 Align patch 11 14 left Iteration 1 Error: 0.667590 Iteration 2 Error: 0.064072 Iteration 3 Error: 0.024063 Align patch 12 13 left Iteration 1 Error: 0.765154 Iteration 2 Error: 0.107371 Iteration 3 Error: 0.033986 Align patch 13 12 left Iteration 1 Error: 0.436932 Iteration 2 Error: 0.079606 Iteration 3 Error: 0.019930 Align patch 14 11 left Iteration 1 Error: 0.727680 Iteration 2 Error: 0.163713 Iteration 3 Error: 0.024383 Align patch 15 10 left Iteration 1 Error: 0.632034 Iteration 2 Error: 0.060063 Iteration 3 Error: 0.012777 Align patch 16 9 left Iteration 1 Error: 0.663066 Iteration 2 Error: 0.130446 Iteration 3 Error: 0.026974 Align patch 17 8 left Iteration 1 Error: 0.755788 Iteration 2 Error: 0.074986 Iteration 3 Error: 0.018589 Align patch 18 7 left Iteration 1 Error: 0.486252 Iteration 2 Error: 0.058194 Iteration 3 Error: 0.018419 Align patch 19 6 left Iteration 1 Error: 0.848996 Iteration 2 Error: 0.105210 Iteration 3 Error: 0.015285 Align patch 20 5 left Iteration 1 Error: 0.765032 Iteration 2 Error: 0.119369 Iteration 3 Error: 0.030194 Align patch 21 4 left Iteration 1 Error: 0.668455 Iteration 2 Error: 0.168730 Iteration 3 Error: 0.040609 Align patch 22 3 left Iteration 1 Error: 0.945597 Iteration 2 Error: 0.137174 Iteration 3 Error: 0.022570 Align patch 23 2 left Iteration 1 Error: 0.660562 Iteration 2 Error: 0.072229 Iteration 3 Error: 0.011391 Align patch 24 1 left Iteration 1 Error: 0.823332 Iteration 2 Error: 0.056836 Iteration 3 Error: 0.009567 Align patch 25 0 left Iteration 1 Error: 0.591841 Iteration 2 Error: 0.087501 Iteration 3 Error: 0.019324 3D Fitting completed. Patch alignment time: 11.11(sec) Local motion has been corrected. Process thread exits. Computational time: 25.667007 sec Total time: 32.690063 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00015hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00015hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.470135s Reading file: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00015hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.241870s ........................................ >>>>>>TIME<<<<<< FFT: 1.063679s Defocus_U Defocus_V Angle CCC 9021.48 9884.77 3.41 0.035862 Final Values Defocus_U Defocus_V Angle CCC 9015.22 9891.03 4.04 0.070759 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00002sq_v01_00015hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00015hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.351e-01 1.004e-01 CC threshold: 0.738 Mean Std: 39.93 6.95 Num Hot pixels: 221 Hot pixel threshold: 81.65 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.776000 Iteration 2 Error: 0.100832 Iteration 3 Error: 0.020942 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.12 -0.12 ...... Frame ( 3) shift: -0.24 -0.24 ...... Frame ( 4) shift: -0.35 -0.35 ...... Frame ( 5) shift: -0.47 -0.47 ...... Frame ( 6) shift: -0.49 -0.57 ...... Frame ( 7) shift: -0.42 -0.67 ...... Frame ( 8) shift: -0.35 -0.76 ...... Frame ( 9) shift: -0.27 -0.78 ...... Frame ( 10) shift: -0.20 -0.75 ...... Frame ( 11) shift: -0.12 -0.71 ...... Frame ( 12) shift: -0.07 -0.74 ...... Frame ( 13) shift: -0.03 -0.83 ...... Frame ( 14) shift: 0.01 -0.92 ...... Frame ( 15) shift: 0.05 -0.96 ...... Frame ( 16) shift: 0.08 -0.96 ...... Frame ( 17) shift: 0.12 -0.95 ...... Frame ( 18) shift: 0.12 -0.97 ...... Frame ( 19) shift: 0.09 -1.03 ...... Frame ( 20) shift: 0.06 -1.09 ...... Frame ( 21) shift: 0.09 -1.11 ...... Frame ( 22) shift: 0.18 -1.10 ...... Frame ( 23) shift: 0.27 -1.09 ...... Frame ( 24) shift: 0.32 -1.09 ...... Frame ( 25) shift: 0.33 -1.10 ...... Frame ( 26) shift: 0.34 -1.11 ...... Frame ( 27) shift: 0.34 -1.12 ...... Frame ( 28) shift: 0.32 -1.15 ...... Frame ( 29) shift: 0.31 -1.17 ...... Frame ( 30) shift: 0.31 -1.19 ...... Frame ( 31) shift: 0.32 -1.20 ...... Frame ( 32) shift: 0.33 -1.20 ...... Frame ( 33) shift: 0.36 -1.22 ...... Frame ( 34) shift: 0.41 -1.24 ...... Frame ( 35) shift: 0.47 -1.26 ...... Frame ( 36) shift: 0.53 -1.29 ...... Frame ( 37) shift: 0.59 -1.30 ...... Frame ( 38) shift: 0.65 -1.32 ...... Frame ( 39) shift: 0.71 -1.34 ...... Frame ( 40) shift: 0.77 -1.36 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.760473 Iteration 2 Error: 0.111891 Iteration 3 Error: 0.026176 Align patch 2 23 left Iteration 1 Error: 0.929855 Iteration 2 Error: 0.201662 Iteration 3 Error: 0.054795 Iteration 4 Error: 0.010696 Align patch 3 22 left Iteration 1 Error: 0.964041 Iteration 2 Error: 0.099802 Iteration 3 Error: 0.025801 Align patch 4 21 left Iteration 1 Error: 1.779754 Iteration 2 Error: 0.274707 Iteration 3 Error: 0.074352 Iteration 4 Error: 0.015651 Align patch 5 20 left Iteration 1 Error: 2.394606 Iteration 2 Error: 0.307533 Iteration 3 Error: 0.045468 Align patch 6 19 left Iteration 1 Error: 0.599405 Iteration 2 Error: 0.118674 Iteration 3 Error: 0.031142 Align patch 7 18 left Iteration 1 Error: 0.682294 Iteration 2 Error: 0.106710 Iteration 3 Error: 0.027931 Align patch 8 17 left Iteration 1 Error: 0.445180 Iteration 2 Error: 0.064276 Iteration 3 Error: 0.009534 Align patch 9 16 left Iteration 1 Error: 0.409150 Iteration 2 Error: 0.049905 Align patch 10 15 left Iteration 1 Error: 0.589479 Iteration 2 Error: 0.077027 Iteration 3 Error: 0.015960 Align patch 11 14 left Iteration 1 Error: 0.777430 Iteration 2 Error: 0.121467 Iteration 3 Error: 0.029722 Align patch 12 13 left Iteration 1 Error: 1.114902 Iteration 2 Error: 0.152334 Iteration 3 Error: 0.034299 Align patch 13 12 left Iteration 1 Error: 0.354351 Iteration 2 Error: 0.068386 Iteration 3 Error: 0.013031 Align patch 14 11 left Iteration 1 Error: 0.576892 Iteration 2 Error: 0.072439 Iteration 3 Error: 0.013585 Align patch 15 10 left Iteration 1 Error: 0.681636 Iteration 2 Error: 0.095515 Iteration 3 Error: 0.018235 Align patch 16 9 left Iteration 1 Error: 0.860098 Iteration 2 Error: 0.182708 Iteration 3 Error: 0.054167 Iteration 4 Error: 0.019765 Align patch 17 8 left Iteration 1 Error: 0.688212 Iteration 2 Error: 0.140230 Iteration 3 Error: 0.026541 Align patch 18 7 left Iteration 1 Error: 0.625563 Iteration 2 Error: 0.087457 Iteration 3 Error: 0.027651 Align patch 19 6 left Iteration 1 Error: 0.549825 Iteration 2 Error: 0.052861 Iteration 3 Error: 0.009725 Align patch 20 5 left Iteration 1 Error: 0.635284 Iteration 2 Error: 0.096000 Iteration 3 Error: 0.013058 Align patch 21 4 left Iteration 1 Error: 0.687891 Iteration 2 Error: 0.120084 Iteration 3 Error: 0.019851 Align patch 22 3 left Iteration 1 Error: 0.800394 Iteration 2 Error: 0.127684 Iteration 3 Error: 0.016594 Align patch 23 2 left Iteration 1 Error: 0.947788 Iteration 2 Error: 0.118160 Iteration 3 Error: 0.036173 Align patch 24 1 left Iteration 1 Error: 0.853161 Iteration 2 Error: 0.127560 Iteration 3 Error: 0.027397 Align patch 25 0 left Iteration 1 Error: 0.912471 Iteration 2 Error: 0.083383 Iteration 3 Error: 0.012100 3D Fitting completed. Patch alignment time: 11.32(sec) Local motion has been corrected. Process thread exits. Computational time: 24.191940 sec Total time: 30.611364 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00015hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00015hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.560096s Reading file: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00015hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.639370s ........................................ >>>>>>TIME<<<<<< FFT: 1.007020s Defocus_U Defocus_V Angle CCC 14914.08 14218.76 83.69 0.070755 Final Values Defocus_U Defocus_V Angle CCC 14918.76 14210.95 84.01 0.107481 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00002sq_v01_00016hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00016hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 40.15 6.94 Num Hot pixels: 213 Hot pixel threshold: 81.81 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.417077 Iteration 2 Error: 0.046234 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.06 0.11 ...... Frame ( 3) shift: -0.13 0.22 ...... Frame ( 4) shift: -0.19 0.34 ...... Frame ( 5) shift: -0.25 0.45 ...... Frame ( 6) shift: -0.26 0.51 ...... Frame ( 7) shift: -0.21 0.53 ...... Frame ( 8) shift: -0.16 0.54 ...... Frame ( 9) shift: -0.13 0.55 ...... Frame ( 10) shift: -0.12 0.53 ...... Frame ( 11) shift: -0.10 0.52 ...... Frame ( 12) shift: -0.06 0.50 ...... Frame ( 13) shift: 0.00 0.48 ...... Frame ( 14) shift: 0.07 0.46 ...... Frame ( 15) shift: 0.07 0.45 ...... Frame ( 16) shift: 0.03 0.44 ...... Frame ( 17) shift: -0.02 0.44 ...... Frame ( 18) shift: -0.00 0.45 ...... Frame ( 19) shift: 0.09 0.48 ...... Frame ( 20) shift: 0.17 0.51 ...... Frame ( 21) shift: 0.24 0.54 ...... Frame ( 22) shift: 0.28 0.57 ...... Frame ( 23) shift: 0.32 0.60 ...... Frame ( 24) shift: 0.33 0.60 ...... Frame ( 25) shift: 0.29 0.59 ...... Frame ( 26) shift: 0.25 0.58 ...... Frame ( 27) shift: 0.26 0.59 ...... Frame ( 28) shift: 0.30 0.64 ...... Frame ( 29) shift: 0.34 0.68 ...... Frame ( 30) shift: 0.34 0.71 ...... Frame ( 31) shift: 0.29 0.73 ...... Frame ( 32) shift: 0.25 0.75 ...... Frame ( 33) shift: 0.23 0.75 ...... Frame ( 34) shift: 0.23 0.74 ...... Frame ( 35) shift: 0.23 0.73 ...... Frame ( 36) shift: 0.24 0.73 ...... Frame ( 37) shift: 0.24 0.76 ...... Frame ( 38) shift: 0.25 0.79 ...... Frame ( 39) shift: 0.25 0.82 ...... Frame ( 40) shift: 0.26 0.84 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.804879 Iteration 2 Error: 0.272253 Iteration 3 Error: 0.119544 Iteration 4 Error: 0.052365 Iteration 5 Error: 0.019618 Align patch 2 23 left Iteration 1 Error: 0.545564 Iteration 2 Error: 0.087926 Iteration 3 Error: 0.020301 Align patch 3 22 left Iteration 1 Error: 0.735293 Iteration 2 Error: 0.107958 Iteration 3 Error: 0.024049 Align patch 4 21 left Iteration 1 Error: 0.634502 Iteration 2 Error: 0.083735 Iteration 3 Error: 0.020796 Align patch 5 20 left Iteration 1 Error: 0.459929 Iteration 2 Error: 0.055063 Iteration 3 Error: 0.011575 Align patch 6 19 left Iteration 1 Error: 0.332766 Iteration 2 Error: 0.055491 Iteration 3 Error: 0.014906 Align patch 7 18 left Iteration 1 Error: 0.598139 Iteration 2 Error: 0.064445 Iteration 3 Error: 0.017179 Align patch 8 17 left Iteration 1 Error: 0.680887 Iteration 2 Error: 0.093137 Iteration 3 Error: 0.021769 Align patch 9 16 left Iteration 1 Error: 0.373849 Iteration 2 Error: 0.038706 Align patch 10 15 left Iteration 1 Error: 0.498341 Iteration 2 Error: 0.060215 Iteration 3 Error: 0.020453 Align patch 11 14 left Iteration 1 Error: 0.660740 Iteration 2 Error: 0.098713 Iteration 3 Error: 0.024297 Align patch 12 13 left Iteration 1 Error: 0.590870 Iteration 2 Error: 0.049445 Align patch 13 12 left Iteration 1 Error: 0.496330 Iteration 2 Error: 0.090289 Iteration 3 Error: 0.016561 Align patch 14 11 left Iteration 1 Error: 0.541623 Iteration 2 Error: 0.037322 Align patch 15 10 left Iteration 1 Error: 0.817781 Iteration 2 Error: 0.122369 Iteration 3 Error: 0.018867 Align patch 16 9 left Iteration 1 Error: 0.854163 Iteration 2 Error: 0.091100 Iteration 3 Error: 0.034115 Align patch 17 8 left Iteration 1 Error: 0.780905 Iteration 2 Error: 0.170415 Iteration 3 Error: 0.043503 Align patch 18 7 left Iteration 1 Error: 0.518067 Iteration 2 Error: 0.085534 Iteration 3 Error: 0.016249 Align patch 19 6 left Iteration 1 Error: 0.636288 Iteration 2 Error: 0.119486 Iteration 3 Error: 0.024949 Align patch 20 5 left Iteration 1 Error: 0.589102 Iteration 2 Error: 0.046241 Align patch 21 4 left Iteration 1 Error: 0.782657 Iteration 2 Error: 0.096673 Iteration 3 Error: 0.025599 Align patch 22 3 left Iteration 1 Error: 0.611815 Iteration 2 Error: 0.087689 Iteration 3 Error: 0.017596 Align patch 23 2 left Iteration 1 Error: 0.694437 Iteration 2 Error: 0.111747 Iteration 3 Error: 0.018648 Align patch 24 1 left Iteration 1 Error: 0.622844 Iteration 2 Error: 0.065419 Iteration 3 Error: 0.015638 Align patch 25 0 left Iteration 1 Error: 0.658392 Iteration 2 Error: 0.080327 Iteration 3 Error: 0.016413 3D Fitting completed. Patch alignment time: 10.74(sec) Local motion has been corrected. Process thread exits. Computational time: 22.795391 sec Total time: 29.513428 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00016hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00016hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.698116s Reading file: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00016hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 4.168391s ........................................ >>>>>>TIME<<<<<< FFT: 0.991139s Defocus_U Defocus_V Angle CCC 9488.28 10371.09 12.96 0.038952 Final Values Defocus_U Defocus_V Angle CCC 9494.53 10371.10 12.34 0.068833 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00002sq_v01_00016hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00016hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.002e-01 CC threshold: 0.736 Mean Std: 39.49 6.93 Num Hot pixels: 209 Hot pixel threshold: 81.08 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.825169 Iteration 2 Error: 0.095760 Iteration 3 Error: 0.015047 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.08 0.23 ...... Frame ( 3) shift: -0.15 0.46 ...... Frame ( 4) shift: -0.23 0.68 ...... Frame ( 5) shift: -0.30 0.91 ...... Frame ( 6) shift: -0.35 1.05 ...... Frame ( 7) shift: -0.37 1.09 ...... Frame ( 8) shift: -0.39 1.13 ...... Frame ( 9) shift: -0.40 1.17 ...... Frame ( 10) shift: -0.40 1.21 ...... Frame ( 11) shift: -0.40 1.25 ...... Frame ( 12) shift: -0.35 1.28 ...... Frame ( 13) shift: -0.25 1.30 ...... Frame ( 14) shift: -0.14 1.32 ...... Frame ( 15) shift: -0.08 1.31 ...... Frame ( 16) shift: -0.05 1.27 ...... Frame ( 17) shift: -0.02 1.23 ...... Frame ( 18) shift: 0.00 1.23 ...... Frame ( 19) shift: 0.02 1.27 ...... Frame ( 20) shift: 0.03 1.30 ...... Frame ( 21) shift: 0.06 1.30 ...... Frame ( 22) shift: 0.10 1.25 ...... Frame ( 23) shift: 0.15 1.21 ...... Frame ( 24) shift: 0.18 1.17 ...... Frame ( 25) shift: 0.21 1.12 ...... Frame ( 26) shift: 0.24 1.08 ...... Frame ( 27) shift: 0.28 1.07 ...... Frame ( 28) shift: 0.34 1.09 ...... Frame ( 29) shift: 0.39 1.11 ...... Frame ( 30) shift: 0.42 1.11 ...... Frame ( 31) shift: 0.41 1.09 ...... Frame ( 32) shift: 0.41 1.06 ...... Frame ( 33) shift: 0.44 1.06 ...... Frame ( 34) shift: 0.50 1.08 ...... Frame ( 35) shift: 0.56 1.10 ...... Frame ( 36) shift: 0.61 1.12 ...... Frame ( 37) shift: 0.63 1.13 ...... Frame ( 38) shift: 0.66 1.14 ...... Frame ( 39) shift: 0.68 1.15 ...... Frame ( 40) shift: 0.71 1.16 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.759626 Iteration 2 Error: 0.157435 Iteration 3 Error: 0.047107 Align patch 2 23 left Iteration 1 Error: 0.764289 Iteration 2 Error: 0.179926 Iteration 3 Error: 0.061235 Iteration 4 Error: 0.022894 Align patch 3 22 left Iteration 1 Error: 0.777800 Iteration 2 Error: 0.126242 Iteration 3 Error: 0.037782 Align patch 4 21 left Iteration 1 Error: 0.500247 Iteration 2 Error: 0.111337 Iteration 3 Error: 0.028405 Align patch 5 20 left Iteration 1 Error: 0.308887 Iteration 2 Error: 0.037718 Align patch 6 19 left Iteration 1 Error: 0.689487 Iteration 2 Error: 0.102961 Iteration 3 Error: 0.030636 Align patch 7 18 left Iteration 1 Error: 0.471245 Iteration 2 Error: 0.056232 Iteration 3 Error: 0.013368 Align patch 8 17 left Iteration 1 Error: 0.841754 Iteration 2 Error: 0.219567 Iteration 3 Error: 0.038606 Align patch 9 16 left Iteration 1 Error: 0.548113 Iteration 2 Error: 0.102918 Iteration 3 Error: 0.017629 Align patch 10 15 left Iteration 1 Error: 0.535221 Iteration 2 Error: 0.075159 Iteration 3 Error: 0.015592 Align patch 11 14 left Iteration 1 Error: 0.716259 Iteration 2 Error: 0.095115 Iteration 3 Error: 0.031041 Align patch 12 13 left Iteration 1 Error: 0.619416 Iteration 2 Error: 0.108388 Iteration 3 Error: 0.027795 Align patch 13 12 left Iteration 1 Error: 0.467906 Iteration 2 Error: 0.056270 Iteration 3 Error: 0.011247 Align patch 14 11 left Iteration 1 Error: 0.887669 Iteration 2 Error: 0.135360 Iteration 3 Error: 0.034152 Align patch 15 10 left Iteration 1 Error: 0.665932 Iteration 2 Error: 0.075565 Iteration 3 Error: 0.029353 Align patch 16 9 left Iteration 1 Error: 0.689655 Iteration 2 Error: 0.074415 Iteration 3 Error: 0.020841 Align patch 17 8 left Iteration 1 Error: 0.748589 Iteration 2 Error: 0.145199 Iteration 3 Error: 0.034525 Align patch 18 7 left Iteration 1 Error: 0.531066 Iteration 2 Error: 0.091708 Iteration 3 Error: 0.018973 Align patch 19 6 left Iteration 1 Error: 0.849251 Iteration 2 Error: 0.084891 Iteration 3 Error: 0.019194 Align patch 20 5 left Iteration 1 Error: 0.551808 Iteration 2 Error: 0.110939 Iteration 3 Error: 0.020310 Align patch 21 4 left Iteration 1 Error: 1.243370 Iteration 2 Error: 0.138184 Iteration 3 Error: 0.034779 Align patch 22 3 left Iteration 1 Error: 0.877438 Iteration 2 Error: 0.134483 Iteration 3 Error: 0.024945 Align patch 23 2 left Iteration 1 Error: 0.524037 Iteration 2 Error: 0.045109 Align patch 24 1 left Iteration 1 Error: 0.669030 Iteration 2 Error: 0.117131 Iteration 3 Error: 0.033037 Align patch 25 0 left Iteration 1 Error: 0.397446 Iteration 2 Error: 0.068747 Iteration 3 Error: 0.012828 3D Fitting completed. Patch alignment time: 11.37(sec) Local motion has been corrected. Process thread exits. Computational time: 22.166452 sec Total time: 30.434170 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00016hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00016hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.580064s Reading file: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00016hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.573949s ........................................ >>>>>>TIME<<<<<< FFT: 1.004889s Defocus_U Defocus_V Angle CCC 10384.79 10853.54 3.65 0.037582 Final Values Defocus_U Defocus_V Angle CCC 10394.20 10878.59 3.65 0.064215 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00002sq_v01_00016hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00016hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.002e-01 CC threshold: 0.736 Mean Std: 40.47 6.95 Num Hot pixels: 227 Hot pixel threshold: 82.17 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.407950 Iteration 2 Error: 0.047357 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.21 -0.09 ...... Frame ( 3) shift: -0.42 -0.18 ...... Frame ( 4) shift: -0.64 -0.27 ...... Frame ( 5) shift: -0.85 -0.37 ...... Frame ( 6) shift: -0.95 -0.39 ...... Frame ( 7) shift: -0.93 -0.34 ...... Frame ( 8) shift: -0.91 -0.30 ...... Frame ( 9) shift: -0.87 -0.27 ...... Frame ( 10) shift: -0.78 -0.26 ...... Frame ( 11) shift: -0.70 -0.25 ...... Frame ( 12) shift: -0.68 -0.25 ...... Frame ( 13) shift: -0.74 -0.28 ...... Frame ( 14) shift: -0.79 -0.31 ...... Frame ( 15) shift: -0.78 -0.31 ...... Frame ( 16) shift: -0.71 -0.28 ...... Frame ( 17) shift: -0.64 -0.25 ...... Frame ( 18) shift: -0.62 -0.23 ...... Frame ( 19) shift: -0.65 -0.22 ...... Frame ( 20) shift: -0.68 -0.21 ...... Frame ( 21) shift: -0.69 -0.21 ...... Frame ( 22) shift: -0.68 -0.20 ...... Frame ( 23) shift: -0.66 -0.19 ...... Frame ( 24) shift: -0.63 -0.21 ...... Frame ( 25) shift: -0.56 -0.26 ...... Frame ( 26) shift: -0.50 -0.31 ...... Frame ( 27) shift: -0.49 -0.35 ...... Frame ( 28) shift: -0.51 -0.39 ...... Frame ( 29) shift: -0.54 -0.42 ...... Frame ( 30) shift: -0.56 -0.46 ...... Frame ( 31) shift: -0.57 -0.49 ...... Frame ( 32) shift: -0.57 -0.53 ...... Frame ( 33) shift: -0.56 -0.53 ...... Frame ( 34) shift: -0.54 -0.49 ...... Frame ( 35) shift: -0.51 -0.45 ...... Frame ( 36) shift: -0.49 -0.43 ...... Frame ( 37) shift: -0.48 -0.43 ...... Frame ( 38) shift: -0.46 -0.43 ...... Frame ( 39) shift: -0.44 -0.43 ...... Frame ( 40) shift: -0.43 -0.43 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.883773 Iteration 2 Error: 0.140845 Iteration 3 Error: 0.028588 Align patch 2 23 left Iteration 1 Error: 0.646166 Iteration 2 Error: 0.081502 Iteration 3 Error: 0.018187 Align patch 3 22 left Iteration 1 Error: 0.952660 Iteration 2 Error: 0.112629 Iteration 3 Error: 0.025908 Align patch 4 21 left Iteration 1 Error: 0.532993 Iteration 2 Error: 0.086022 Iteration 3 Error: 0.012055 Align patch 5 20 left Iteration 1 Error: 0.803309 Iteration 2 Error: 0.117272 Iteration 3 Error: 0.020701 Align patch 6 19 left Iteration 1 Error: 0.847131 Iteration 2 Error: 0.107058 Iteration 3 Error: 0.026910 Align patch 7 18 left Iteration 1 Error: 0.734232 Iteration 2 Error: 0.101485 Iteration 3 Error: 0.022058 Align patch 8 17 left Iteration 1 Error: 0.494515 Iteration 2 Error: 0.057552 Iteration 3 Error: 0.013292 Align patch 9 16 left Iteration 1 Error: 0.476015 Iteration 2 Error: 0.049530 Align patch 10 15 left Iteration 1 Error: 0.386631 Iteration 2 Error: 0.043025 Align patch 11 14 left Iteration 1 Error: 0.818728 Iteration 2 Error: 0.178289 Iteration 3 Error: 0.038167 Align patch 12 13 left Iteration 1 Error: 0.571766 Iteration 2 Error: 0.099210 Iteration 3 Error: 0.013218 Align patch 13 12 left Iteration 1 Error: 0.398567 Iteration 2 Error: 0.048691 Align patch 14 11 left Iteration 1 Error: 0.478599 Iteration 2 Error: 0.095210 Iteration 3 Error: 0.021870 Align patch 15 10 left Iteration 1 Error: 0.834094 Iteration 2 Error: 0.071012 Iteration 3 Error: 0.019584 Align patch 16 9 left Iteration 1 Error: 0.480569 Iteration 2 Error: 0.089948 Iteration 3 Error: 0.015986 Align patch 17 8 left Iteration 1 Error: 0.364703 Iteration 2 Error: 0.050867 Iteration 3 Error: 0.012371 Align patch 18 7 left Iteration 1 Error: 1.048488 Iteration 2 Error: 0.104314 Iteration 3 Error: 0.020680 Align patch 19 6 left Iteration 1 Error: 0.757370 Iteration 2 Error: 0.113142 Iteration 3 Error: 0.025314 Align patch 20 5 left Iteration 1 Error: 0.486839 Iteration 2 Error: 0.093497 Iteration 3 Error: 0.023539 Align patch 21 4 left Iteration 1 Error: 0.785175 Iteration 2 Error: 0.140467 Iteration 3 Error: 0.027337 Align patch 22 3 left Iteration 1 Error: 0.688925 Iteration 2 Error: 0.108532 Iteration 3 Error: 0.021095 Align patch 23 2 left Iteration 1 Error: 1.032158 Iteration 2 Error: 0.099724 Iteration 3 Error: 0.025650 Align patch 24 1 left Iteration 1 Error: 0.881442 Iteration 2 Error: 0.092258 Iteration 3 Error: 0.028702 Align patch 25 0 left Iteration 1 Error: 0.703616 Iteration 2 Error: 0.091348 Iteration 3 Error: 0.027003 3D Fitting completed. Patch alignment time: 11.29(sec) Local motion has been corrected. Process thread exits. Computational time: 24.674643 sec Total time: 31.971037 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00016hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00016hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.788561s Reading file: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00016hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.524194s ........................................ >>>>>>TIME<<<<<< FFT: 1.047567s Defocus_U Defocus_V Angle CCC 11121.09 12000.02 6.93 0.044177 Final Values Defocus_U Defocus_V Angle CCC 11171.11 12018.83 7.87 0.073315 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00002sq_v01_00016hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00016hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 41.26 6.97 Num Hot pixels: 237 Hot pixel threshold: 83.08 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.467747 Iteration 2 Error: 0.039821 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.02 0.13 ...... Frame ( 3) shift: 0.04 0.25 ...... Frame ( 4) shift: 0.06 0.38 ...... Frame ( 5) shift: 0.09 0.51 ...... Frame ( 6) shift: 0.10 0.62 ...... Frame ( 7) shift: 0.12 0.71 ...... Frame ( 8) shift: 0.14 0.81 ...... Frame ( 9) shift: 0.16 0.83 ...... Frame ( 10) shift: 0.20 0.79 ...... Frame ( 11) shift: 0.23 0.74 ...... Frame ( 12) shift: 0.27 0.72 ...... Frame ( 13) shift: 0.30 0.72 ...... Frame ( 14) shift: 0.34 0.71 ...... Frame ( 15) shift: 0.35 0.68 ...... Frame ( 16) shift: 0.33 0.62 ...... Frame ( 17) shift: 0.31 0.55 ...... Frame ( 18) shift: 0.29 0.55 ...... Frame ( 19) shift: 0.28 0.60 ...... Frame ( 20) shift: 0.27 0.66 ...... Frame ( 21) shift: 0.27 0.63 ...... Frame ( 22) shift: 0.28 0.52 ...... Frame ( 23) shift: 0.30 0.41 ...... Frame ( 24) shift: 0.30 0.37 ...... Frame ( 25) shift: 0.29 0.41 ...... Frame ( 26) shift: 0.28 0.44 ...... Frame ( 27) shift: 0.29 0.47 ...... Frame ( 28) shift: 0.32 0.52 ...... Frame ( 29) shift: 0.35 0.56 ...... Frame ( 30) shift: 0.37 0.57 ...... Frame ( 31) shift: 0.36 0.56 ...... Frame ( 32) shift: 0.36 0.54 ...... Frame ( 33) shift: 0.38 0.54 ...... Frame ( 34) shift: 0.44 0.57 ...... Frame ( 35) shift: 0.50 0.59 ...... Frame ( 36) shift: 0.53 0.58 ...... Frame ( 37) shift: 0.53 0.52 ...... Frame ( 38) shift: 0.52 0.46 ...... Frame ( 39) shift: 0.52 0.40 ...... Frame ( 40) shift: 0.52 0.34 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.558984 Iteration 2 Error: 0.067297 Iteration 3 Error: 0.029703 Align patch 2 23 left Iteration 1 Error: 0.826272 Iteration 2 Error: 0.125261 Iteration 3 Error: 0.029228 Align patch 3 22 left Iteration 1 Error: 0.514321 Iteration 2 Error: 0.081277 Iteration 3 Error: 0.014114 Align patch 4 21 left Iteration 1 Error: 0.462339 Iteration 2 Error: 0.063850 Iteration 3 Error: 0.011664 Align patch 5 20 left Iteration 1 Error: 0.437790 Iteration 2 Error: 0.084792 Iteration 3 Error: 0.013780 Align patch 6 19 left Iteration 1 Error: 0.440280 Iteration 2 Error: 0.087119 Iteration 3 Error: 0.023091 Align patch 7 18 left Iteration 1 Error: 0.642328 Iteration 2 Error: 0.151165 Iteration 3 Error: 0.027332 Align patch 8 17 left Iteration 1 Error: 0.684551 Iteration 2 Error: 0.163491 Iteration 3 Error: 0.038748 Align patch 9 16 left Iteration 1 Error: 0.482238 Iteration 2 Error: 0.064273 Iteration 3 Error: 0.015391 Align patch 10 15 left Iteration 1 Error: 0.345238 Iteration 2 Error: 0.029376 Align patch 11 14 left Iteration 1 Error: 0.617554 Iteration 2 Error: 0.089816 Iteration 3 Error: 0.021203 Align patch 12 13 left Iteration 1 Error: 0.472488 Iteration 2 Error: 0.132202 Iteration 3 Error: 0.019996 Align patch 13 12 left Iteration 1 Error: 0.668903 Iteration 2 Error: 0.065780 Iteration 3 Error: 0.018606 Align patch 14 11 left Iteration 1 Error: 0.636318 Iteration 2 Error: 0.083715 Iteration 3 Error: 0.020901 Align patch 15 10 left Iteration 1 Error: 0.440852 Iteration 2 Error: 0.082259 Iteration 3 Error: 0.022598 Align patch 16 9 left Iteration 1 Error: 0.818529 Iteration 2 Error: 0.071291 Iteration 3 Error: 0.014359 Align patch 17 8 left Iteration 1 Error: 0.501389 Iteration 2 Error: 0.059523 Iteration 3 Error: 0.015394 Align patch 18 7 left Iteration 1 Error: 0.537490 Iteration 2 Error: 0.088131 Iteration 3 Error: 0.030329 Align patch 19 6 left Iteration 1 Error: 0.361643 Iteration 2 Error: 0.037677 Align patch 20 5 left Iteration 1 Error: 0.728381 Iteration 2 Error: 0.069698 Iteration 3 Error: 0.019861 Align patch 21 4 left Iteration 1 Error: 0.526290 Iteration 2 Error: 0.112819 Iteration 3 Error: 0.025463 Align patch 22 3 left Iteration 1 Error: 0.589846 Iteration 2 Error: 0.090401 Iteration 3 Error: 0.026372 Align patch 23 2 left Iteration 1 Error: 0.772558 Iteration 2 Error: 0.130924 Iteration 3 Error: 0.032338 Align patch 24 1 left Iteration 1 Error: 0.761709 Iteration 2 Error: 0.109789 Iteration 3 Error: 0.016392 Align patch 25 0 left Iteration 1 Error: 0.723639 Iteration 2 Error: 0.122276 Iteration 3 Error: 0.028021 3D Fitting completed. Patch alignment time: 11.09(sec) Local motion has been corrected. Process thread exits. Computational time: 25.874407 sec Total time: 35.444107 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00016hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00016hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.635528s Reading file: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00016hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.882085s ........................................ >>>>>>TIME<<<<<< FFT: 0.950221s Defocus_U Defocus_V Angle CCC 12087.93 11384.80 86.10 0.050997 Final Values Defocus_U Defocus_V Angle CCC 12109.81 11394.20 85.16 0.088418 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00002sq_v01_00017hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00017hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.001e-01 CC threshold: 0.735 Mean Std: 39.68 6.85 Num Hot pixels: 221 Hot pixel threshold: 80.79 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.228274 Iteration 2 Error: 0.189985 Iteration 3 Error: 0.047839 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.33 -0.20 ...... Frame ( 3) shift: -0.66 -0.41 ...... Frame ( 4) shift: -0.99 -0.61 ...... Frame ( 5) shift: -1.32 -0.82 ...... Frame ( 6) shift: -1.48 -0.89 ...... Frame ( 7) shift: -1.48 -0.84 ...... Frame ( 8) shift: -1.48 -0.79 ...... Frame ( 9) shift: -1.43 -0.67 ...... Frame ( 10) shift: -1.32 -0.49 ...... Frame ( 11) shift: -1.21 -0.31 ...... Frame ( 12) shift: -1.12 -0.19 ...... Frame ( 13) shift: -1.03 -0.14 ...... Frame ( 14) shift: -0.94 -0.08 ...... Frame ( 15) shift: -0.85 -0.00 ...... Frame ( 16) shift: -0.75 0.10 ...... Frame ( 17) shift: -0.66 0.20 ...... Frame ( 18) shift: -0.60 0.28 ...... Frame ( 19) shift: -0.58 0.34 ...... Frame ( 20) shift: -0.57 0.40 ...... Frame ( 21) shift: -0.55 0.47 ...... Frame ( 22) shift: -0.52 0.55 ...... Frame ( 23) shift: -0.50 0.63 ...... Frame ( 24) shift: -0.47 0.67 ...... Frame ( 25) shift: -0.44 0.69 ...... Frame ( 26) shift: -0.41 0.71 ...... Frame ( 27) shift: -0.41 0.71 ...... Frame ( 28) shift: -0.43 0.69 ...... Frame ( 29) shift: -0.46 0.67 ...... Frame ( 30) shift: -0.47 0.68 ...... Frame ( 31) shift: -0.46 0.72 ...... Frame ( 32) shift: -0.45 0.76 ...... Frame ( 33) shift: -0.41 0.76 ...... Frame ( 34) shift: -0.33 0.73 ...... Frame ( 35) shift: -0.25 0.70 ...... Frame ( 36) shift: -0.21 0.67 ...... Frame ( 37) shift: -0.20 0.66 ...... Frame ( 38) shift: -0.19 0.65 ...... Frame ( 39) shift: -0.18 0.63 ...... Frame ( 40) shift: -0.17 0.62 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.982671 Iteration 2 Error: 0.224936 Iteration 3 Error: 0.090043 Iteration 4 Error: 0.042230 Align patch 2 23 left Iteration 1 Error: 0.838729 Iteration 2 Error: 0.195632 Iteration 3 Error: 0.065221 Iteration 4 Error: 0.026326 Align patch 3 22 left Iteration 1 Error: 0.795870 Iteration 2 Error: 0.129686 Iteration 3 Error: 0.049744 Align patch 4 21 left Iteration 1 Error: 0.663709 Iteration 2 Error: 0.132938 Iteration 3 Error: 0.035016 Align patch 5 20 left Iteration 1 Error: 0.480404 Iteration 2 Error: 0.080225 Iteration 3 Error: 0.026535 Align patch 6 19 left Iteration 1 Error: 1.765094 Iteration 2 Error: 0.283496 Iteration 3 Error: 0.064766 Iteration 4 Error: 0.018112 Align patch 7 18 left Iteration 1 Error: 0.694095 Iteration 2 Error: 0.188634 Iteration 3 Error: 0.038711 Align patch 8 17 left Iteration 1 Error: 0.680931 Iteration 2 Error: 0.142384 Iteration 3 Error: 0.041714 Align patch 9 16 left Iteration 1 Error: 0.792588 Iteration 2 Error: 0.107751 Iteration 3 Error: 0.028329 Align patch 10 15 left Iteration 1 Error: 0.686002 Iteration 2 Error: 0.101661 Iteration 3 Error: 0.024848 Align patch 11 14 left Iteration 1 Error: 0.801170 Iteration 2 Error: 0.178844 Iteration 3 Error: 0.041003 Align patch 12 13 left Iteration 1 Error: 0.777969 Iteration 2 Error: 0.174864 Iteration 3 Error: 0.063657 Iteration 4 Error: 0.031846 Align patch 13 12 left Iteration 1 Error: 0.502132 Iteration 2 Error: 0.111103 Iteration 3 Error: 0.029037 Align patch 14 11 left Iteration 1 Error: 0.717160 Iteration 2 Error: 0.201574 Iteration 3 Error: 0.042886 Align patch 15 10 left Iteration 1 Error: 0.692014 Iteration 2 Error: 0.203251 Iteration 3 Error: 0.050143 Iteration 4 Error: 0.025475 Align patch 16 9 left Iteration 1 Error: 1.152552 Iteration 2 Error: 0.211106 Iteration 3 Error: 0.062451 Iteration 4 Error: 0.028198 Align patch 17 8 left Iteration 1 Error: 1.074122 Iteration 2 Error: 0.108938 Iteration 3 Error: 0.021948 Align patch 18 7 left Iteration 1 Error: 0.620999 Iteration 2 Error: 0.080073 Iteration 3 Error: 0.027770 Align patch 19 6 left Iteration 1 Error: 0.539855 Iteration 2 Error: 0.144062 Iteration 3 Error: 0.020847 Align patch 20 5 left Iteration 1 Error: 0.534048 Iteration 2 Error: 0.168536 Iteration 3 Error: 0.054203 Iteration 4 Error: 0.015191 Align patch 21 4 left Iteration 1 Error: 0.578575 Iteration 2 Error: 0.151837 Iteration 3 Error: 0.038440 Align patch 22 3 left Iteration 1 Error: 0.879199 Iteration 2 Error: 0.161913 Iteration 3 Error: 0.038893 Align patch 23 2 left Iteration 1 Error: 0.789004 Iteration 2 Error: 0.074253 Iteration 3 Error: 0.010890 Align patch 24 1 left Iteration 1 Error: 0.792476 Iteration 2 Error: 0.139280 Iteration 3 Error: 0.039780 Align patch 25 0 left Iteration 1 Error: 0.593831 Iteration 2 Error: 0.071101 Iteration 3 Error: 0.025636 3D Fitting completed. Patch alignment time: 12.71(sec) Local motion has been corrected. Process thread exits. Computational time: 27.082352 sec Total time: 34.943260 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00017hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00017hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.535355s Reading file: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00017hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.079255s ........................................ >>>>>>TIME<<<<<< FFT: 1.083179s Defocus_U Defocus_V Angle CCC 9630.89 10544.96 11.79 0.031208 Final Values Defocus_U Defocus_V Angle CCC 9652.79 10557.53 12.11 0.054896 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00002sq_v01_00017hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00017hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.002e-01 CC threshold: 0.736 Mean Std: 38.79 7.20 Num Hot pixels: 182 Hot pixel threshold: 82.00 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.262065 Iteration 2 Error: 0.232618 Iteration 3 Error: 0.072556 Iteration 4 Error: 0.025117 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.24 -0.06 ...... Frame ( 3) shift: -0.49 -0.12 ...... Frame ( 4) shift: -0.73 -0.18 ...... Frame ( 5) shift: -0.98 -0.24 ...... Frame ( 6) shift: -1.12 -0.24 ...... Frame ( 7) shift: -1.15 -0.19 ...... Frame ( 8) shift: -1.18 -0.13 ...... Frame ( 9) shift: -1.20 -0.05 ...... Frame ( 10) shift: -1.20 0.05 ...... Frame ( 11) shift: -1.20 0.15 ...... Frame ( 12) shift: -1.24 0.23 ...... Frame ( 13) shift: -1.30 0.29 ...... Frame ( 14) shift: -1.36 0.35 ...... Frame ( 15) shift: -1.41 0.45 ...... Frame ( 16) shift: -1.46 0.56 ...... Frame ( 17) shift: -1.50 0.68 ...... Frame ( 18) shift: -1.54 0.75 ...... Frame ( 19) shift: -1.57 0.76 ...... Frame ( 20) shift: -1.59 0.78 ...... Frame ( 21) shift: -1.62 0.82 ...... Frame ( 22) shift: -1.65 0.89 ...... Frame ( 23) shift: -1.68 0.97 ...... Frame ( 24) shift: -1.74 0.99 ...... Frame ( 25) shift: -1.85 0.96 ...... Frame ( 26) shift: -1.96 0.94 ...... Frame ( 27) shift: -2.04 0.90 ...... Frame ( 28) shift: -2.10 0.84 ...... Frame ( 29) shift: -2.15 0.79 ...... Frame ( 30) shift: -2.22 0.75 ...... Frame ( 31) shift: -2.30 0.72 ...... Frame ( 32) shift: -2.38 0.69 ...... Frame ( 33) shift: -2.44 0.69 ...... Frame ( 34) shift: -2.47 0.70 ...... Frame ( 35) shift: -2.51 0.72 ...... Frame ( 36) shift: -2.56 0.72 ...... Frame ( 37) shift: -2.64 0.72 ...... Frame ( 38) shift: -2.71 0.72 ...... Frame ( 39) shift: -2.79 0.72 ...... Frame ( 40) shift: -2.87 0.73 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.363516 Iteration 2 Error: 0.221756 Iteration 3 Error: 0.062063 Iteration 4 Error: 0.024178 Align patch 2 23 left Iteration 1 Error: 0.993663 Iteration 2 Error: 0.213086 Iteration 3 Error: 0.052332 Iteration 4 Error: 0.015946 Align patch 3 22 left Iteration 1 Error: 1.054040 Iteration 2 Error: 0.134961 Iteration 3 Error: 0.051710 Iteration 4 Error: 0.018252 Align patch 4 21 left Iteration 1 Error: 1.209292 Iteration 2 Error: 0.261038 Iteration 3 Error: 0.055480 Iteration 4 Error: 0.017339 Align patch 5 20 left Iteration 1 Error: 1.739054 Iteration 2 Error: 0.184164 Iteration 3 Error: 0.027352 Align patch 6 19 left Iteration 1 Error: 0.811763 Iteration 2 Error: 0.271702 Iteration 3 Error: 0.112127 Iteration 4 Error: 0.043172 Align patch 7 18 left Iteration 1 Error: 0.796181 Iteration 2 Error: 0.379739 Iteration 3 Error: 0.182533 Iteration 4 Error: 0.092984 Iteration 5 Error: 0.049448 Align patch 8 17 left Iteration 1 Error: 1.055851 Iteration 2 Error: 0.420512 Iteration 3 Error: 0.135026 Iteration 4 Error: 0.072533 Iteration 5 Error: 0.036623 Align patch 9 16 left Iteration 1 Error: 1.253094 Iteration 2 Error: 0.306227 Iteration 3 Error: 0.077933 Iteration 4 Error: 0.026154 Align patch 10 15 left Iteration 1 Error: 1.892382 Iteration 2 Error: 0.614686 Iteration 3 Error: 0.182656 Iteration 4 Error: 0.079520 Iteration 5 Error: 0.035163 Align patch 11 14 left Iteration 1 Error: 1.382442 Iteration 2 Error: 0.256842 Iteration 3 Error: 0.085996 Iteration 4 Error: 0.026894 Align patch 12 13 left Iteration 1 Error: 1.877161 Iteration 2 Error: 0.693408 Iteration 3 Error: 0.439301 Iteration 4 Error: 0.269823 Iteration 5 Error: 0.138426 Align patch 12 13 left Iteration 1 Error: 2.078360 Iteration 2 Error: 0.453110 Iteration 3 Error: 0.085632 Iteration 4 Error: 0.031147 Align patch 13 12 left Iteration 1 Error: 1.339649 Iteration 2 Error: 0.474206 Iteration 3 Error: 0.186628 Iteration 4 Error: 0.106393 Iteration 5 Error: 0.063589 Align patch 13 12 left Iteration 1 Error: 2.422731 Iteration 2 Error: 0.567038 Iteration 3 Error: 0.153494 Iteration 4 Error: 0.055597 Iteration 5 Error: 0.032463 Align patch 14 11 left Iteration 1 Error: 1.387258 Iteration 2 Error: 0.325268 Iteration 3 Error: 0.083037 Iteration 4 Error: 0.035471 Align patch 15 10 left Iteration 1 Error: 1.686854 Iteration 2 Error: 0.547477 Iteration 3 Error: 0.314616 Iteration 4 Error: 0.145188 Iteration 5 Error: 0.118202 Align patch 15 10 left Iteration 1 Error: 3.211873 Iteration 2 Error: 0.739860 Iteration 3 Error: 0.233036 Iteration 4 Error: 0.109193 Iteration 5 Error: 0.055719 Align patch 16 9 left Iteration 1 Error: 1.662194 Iteration 2 Error: 0.688852 Iteration 3 Error: 0.295699 Iteration 4 Error: 0.115537 Iteration 5 Error: 0.052181 Align patch 16 9 left Iteration 1 Error: 2.870595 Iteration 2 Error: 0.490110 Iteration 3 Error: 0.070546 Iteration 4 Error: 0.021618 Align patch 17 8 left Iteration 1 Error: 3.537190 Iteration 2 Error: 1.065057 Iteration 3 Error: 0.463820 Iteration 4 Error: 0.246193 Iteration 5 Error: 0.114521 Align patch 17 8 left Iteration 1 Error: 3.095408 Iteration 2 Error: 0.720530 Iteration 3 Error: 0.133871 Iteration 4 Error: 0.031020 Align patch 18 7 left Iteration 1 Error: 2.712255 Iteration 2 Error: 1.003871 Iteration 3 Error: 0.526590 Iteration 4 Error: 0.418909 Iteration 5 Error: 0.267303 Align patch 18 7 left Iteration 1 Error: 3.143454 Iteration 2 Error: 0.743972 Iteration 3 Error: 0.249002 Iteration 4 Error: 0.080439 Iteration 5 Error: 0.060544 Align patch 19 6 left Iteration 1 Error: 8.354318 Iteration 2 Error: 2.333373 Iteration 3 Error: 0.479915 Iteration 4 Error: 0.530278 Iteration 5 Error: 0.280524 Align patch 19 6 left Iteration 1 Error: 4.083591 Iteration 2 Error: 1.044637 Iteration 3 Error: 0.384463 Iteration 4 Error: 0.195700 Iteration 5 Error: 0.092115 Align patch 20 5 left Iteration 1 Error: 5.279380 Iteration 2 Error: 1.944671 Iteration 3 Error: 0.892656 Iteration 4 Error: 0.773938 Iteration 5 Error: 0.509156 Align patch 20 5 left Iteration 1 Error: 3.466834 Iteration 2 Error: 1.094699 Iteration 3 Error: 0.607608 Iteration 4 Error: 0.359879 Iteration 5 Error: 0.214064 Align patch 21 4 left Iteration 1 Error: 1.623464 Iteration 2 Error: 0.538257 Iteration 3 Error: 0.304715 Iteration 4 Error: 0.151594 Iteration 5 Error: 0.089507 Align patch 21 4 left Iteration 1 Error: 2.885899 Iteration 2 Error: 0.603897 Iteration 3 Error: 0.135759 Iteration 4 Error: 0.049194 Align patch 22 3 left Iteration 1 Error: 2.279094 Iteration 2 Error: 0.731260 Iteration 3 Error: 0.515013 Iteration 4 Error: 0.314615 Iteration 5 Error: 0.227999 Align patch 22 3 left Iteration 1 Error: 3.315475 Iteration 2 Error: 0.626907 Iteration 3 Error: 0.139747 Iteration 4 Error: 0.046437 Align patch 23 2 left Iteration 1 Error: 5.176734 Iteration 2 Error: 1.767897 Iteration 3 Error: 0.748078 Iteration 4 Error: 0.514568 Iteration 5 Error: 0.269561 Align patch 23 2 left Iteration 1 Error: 3.548749 Iteration 2 Error: 0.856839 Iteration 3 Error: 0.277279 Iteration 4 Error: 0.080878 Iteration 5 Error: 0.030924 Align patch 24 1 left Iteration 1 Error: 3.721797 Iteration 2 Error: 0.972013 Iteration 3 Error: 0.550136 Iteration 4 Error: 0.367545 Iteration 5 Error: 0.233550 Align patch 24 1 left Iteration 1 Error: 4.514686 Iteration 2 Error: 1.229666 Iteration 3 Error: 0.547218 Iteration 4 Error: 0.305506 Iteration 5 Error: 0.186668 Align patch 25 0 left Iteration 1 Error: 4.385730 Iteration 2 Error: 3.410877 Iteration 3 Error: 1.843519 Iteration 4 Error: 8.882673 Iteration 5 Error: 3.046678 Align patch 25 0 left Iteration 1 Error: 4.919272 Iteration 2 Error: 2.080594 Iteration 3 Error: 1.204082 Iteration 4 Error: 0.894781 Iteration 5 Error: 0.629689 3D Fitting completed. Patch alignment time: 22.06(sec) Local motion has been corrected. Process thread exits. Computational time: 37.655216 sec Total time: 47.169617 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00017hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00017hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.941818s Reading file: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00017hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.966173s ........................................ >>>>>>TIME<<<<<< FFT: 0.969231s Defocus_U Defocus_V Angle CCC 11554.67 12148.46 2.05 0.041730 Final Values Defocus_U Defocus_V Angle CCC 11568.73 12153.15 2.99 0.076900 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00002sq_v01_00017hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00017hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.996e-02 CC threshold: 0.734 Mean Std: 38.90 6.67 Num Hot pixels: 220 Hot pixel threshold: 78.93 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.811427 Iteration 2 Error: 0.180289 Iteration 3 Error: 0.052925 Iteration 4 Error: 0.025045 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.23 -0.19 ...... Frame ( 3) shift: -0.45 -0.39 ...... Frame ( 4) shift: -0.68 -0.58 ...... Frame ( 5) shift: -0.91 -0.77 ...... Frame ( 6) shift: -1.01 -0.89 ...... Frame ( 7) shift: -0.99 -0.92 ...... Frame ( 8) shift: -0.97 -0.96 ...... Frame ( 9) shift: -0.91 -0.94 ...... Frame ( 10) shift: -0.81 -0.86 ...... Frame ( 11) shift: -0.71 -0.79 ...... Frame ( 12) shift: -0.66 -0.71 ...... Frame ( 13) shift: -0.67 -0.63 ...... Frame ( 14) shift: -0.67 -0.55 ...... Frame ( 15) shift: -0.61 -0.49 ...... Frame ( 16) shift: -0.49 -0.45 ...... Frame ( 17) shift: -0.37 -0.41 ...... Frame ( 18) shift: -0.28 -0.39 ...... Frame ( 19) shift: -0.23 -0.38 ...... Frame ( 20) shift: -0.19 -0.38 ...... Frame ( 21) shift: -0.16 -0.37 ...... Frame ( 22) shift: -0.14 -0.34 ...... Frame ( 23) shift: -0.12 -0.30 ...... Frame ( 24) shift: -0.10 -0.27 ...... Frame ( 25) shift: -0.07 -0.24 ...... Frame ( 26) shift: -0.03 -0.21 ...... Frame ( 27) shift: -0.02 -0.19 ...... Frame ( 28) shift: -0.02 -0.18 ...... Frame ( 29) shift: -0.02 -0.17 ...... Frame ( 30) shift: -0.03 -0.15 ...... Frame ( 31) shift: -0.03 -0.13 ...... Frame ( 32) shift: -0.04 -0.10 ...... Frame ( 33) shift: 0.01 -0.05 ...... Frame ( 34) shift: 0.12 0.03 ...... Frame ( 35) shift: 0.23 0.11 ...... Frame ( 36) shift: 0.31 0.15 ...... Frame ( 37) shift: 0.38 0.16 ...... Frame ( 38) shift: 0.45 0.16 ...... Frame ( 39) shift: 0.52 0.17 ...... Frame ( 40) shift: 0.59 0.18 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.193310 Iteration 2 Error: 0.294867 Iteration 3 Error: 0.090084 Iteration 4 Error: 0.039691 Align patch 2 23 left Iteration 1 Error: 0.977239 Iteration 2 Error: 0.313325 Iteration 3 Error: 0.084647 Iteration 4 Error: 0.040307 Align patch 3 22 left Iteration 1 Error: 0.702457 Iteration 2 Error: 0.141166 Iteration 3 Error: 0.041641 Align patch 4 21 left Iteration 1 Error: 0.882013 Iteration 2 Error: 0.214544 Iteration 3 Error: 0.053114 Iteration 4 Error: 0.013646 Align patch 5 20 left Iteration 1 Error: 0.974961 Iteration 2 Error: 0.103105 Iteration 3 Error: 0.021027 Align patch 6 19 left Iteration 1 Error: 0.838228 Iteration 2 Error: 0.230242 Iteration 3 Error: 0.111461 Iteration 4 Error: 0.037023 Align patch 7 18 left Iteration 1 Error: 2.036481 Iteration 2 Error: 0.447184 Iteration 3 Error: 0.144830 Iteration 4 Error: 0.061492 Iteration 5 Error: 0.025910 Align patch 8 17 left Iteration 1 Error: 0.805473 Iteration 2 Error: 0.224308 Iteration 3 Error: 0.052210 Iteration 4 Error: 0.023251 Align patch 9 16 left Iteration 1 Error: 0.694656 Iteration 2 Error: 0.111165 Iteration 3 Error: 0.043957 Align patch 10 15 left Iteration 1 Error: 0.610587 Iteration 2 Error: 0.070110 Iteration 3 Error: 0.016133 Align patch 11 14 left Iteration 1 Error: 0.767758 Iteration 2 Error: 0.226107 Iteration 3 Error: 0.079830 Iteration 4 Error: 0.035472 Align patch 12 13 left Iteration 1 Error: 0.852058 Iteration 2 Error: 0.119280 Iteration 3 Error: 0.051086 Iteration 4 Error: 0.017492 Align patch 13 12 left Iteration 1 Error: 0.777477 Iteration 2 Error: 0.131572 Iteration 3 Error: 0.050224 Iteration 4 Error: 0.013938 Align patch 14 11 left Iteration 1 Error: 0.757812 Iteration 2 Error: 0.106434 Iteration 3 Error: 0.033061 Align patch 15 10 left Iteration 1 Error: 0.667319 Iteration 2 Error: 0.165446 Iteration 3 Error: 0.050070 Iteration 4 Error: 0.017677 Align patch 16 9 left Iteration 1 Error: 1.280392 Iteration 2 Error: 0.180738 Iteration 3 Error: 0.038858 Align patch 17 8 left Iteration 1 Error: 1.058779 Iteration 2 Error: 0.258890 Iteration 3 Error: 0.049801 Align patch 18 7 left Iteration 1 Error: 1.051748 Iteration 2 Error: 0.201803 Iteration 3 Error: 0.059147 Iteration 4 Error: 0.035414 Align patch 19 6 left Iteration 1 Error: 1.254651 Iteration 2 Error: 0.226504 Iteration 3 Error: 0.054015 Iteration 4 Error: 0.014799 Align patch 20 5 left Iteration 1 Error: 0.604116 Iteration 2 Error: 0.141163 Iteration 3 Error: 0.038351 Align patch 21 4 left Iteration 1 Error: 1.393501 Iteration 2 Error: 0.260364 Iteration 3 Error: 0.094942 Iteration 4 Error: 0.030416 Align patch 22 3 left Iteration 1 Error: 0.938719 Iteration 2 Error: 0.226698 Iteration 3 Error: 0.075851 Iteration 4 Error: 0.021898 Align patch 23 2 left Iteration 1 Error: 1.666758 Iteration 2 Error: 0.272966 Iteration 3 Error: 0.050660 Iteration 4 Error: 0.020363 Align patch 24 1 left Iteration 1 Error: 0.842719 Iteration 2 Error: 0.179539 Iteration 3 Error: 0.045034 Align patch 25 0 left Iteration 1 Error: 0.913947 Iteration 2 Error: 0.262681 Iteration 3 Error: 0.063299 Iteration 4 Error: 0.028393 3D Fitting completed. Patch alignment time: 11.90(sec) Local motion has been corrected. Process thread exits. Computational time: 26.917496 sec Total time: 34.536736 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00017hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00017hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.139641s Reading file: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00017hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.051097s ........................................ >>>>>>TIME<<<<<< FFT: 0.984692s Defocus_U Defocus_V Angle CCC 14248.07 15169.93 5.96 0.032673 Final Values Defocus_U Defocus_V Angle CCC 14251.19 15191.81 6.58 0.049571 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00002sq_v01_00017hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00017hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 38.17 6.73 Num Hot pixels: 212 Hot pixel threshold: 78.56 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.036366 Iteration 2 Error: 0.162964 Iteration 3 Error: 0.043033 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.29 -0.27 ...... Frame ( 3) shift: -0.59 -0.55 ...... Frame ( 4) shift: -0.88 -0.82 ...... Frame ( 5) shift: -1.17 -1.09 ...... Frame ( 6) shift: -1.32 -1.21 ...... Frame ( 7) shift: -1.32 -1.19 ...... Frame ( 8) shift: -1.32 -1.16 ...... Frame ( 9) shift: -1.24 -1.08 ...... Frame ( 10) shift: -1.08 -0.94 ...... Frame ( 11) shift: -0.92 -0.81 ...... Frame ( 12) shift: -0.83 -0.70 ...... Frame ( 13) shift: -0.81 -0.61 ...... Frame ( 14) shift: -0.79 -0.53 ...... Frame ( 15) shift: -0.75 -0.45 ...... Frame ( 16) shift: -0.68 -0.37 ...... Frame ( 17) shift: -0.62 -0.29 ...... Frame ( 18) shift: -0.56 -0.24 ...... Frame ( 19) shift: -0.50 -0.23 ...... Frame ( 20) shift: -0.44 -0.21 ...... Frame ( 21) shift: -0.38 -0.19 ...... Frame ( 22) shift: -0.31 -0.15 ...... Frame ( 23) shift: -0.24 -0.12 ...... Frame ( 24) shift: -0.21 -0.10 ...... Frame ( 25) shift: -0.22 -0.09 ...... Frame ( 26) shift: -0.22 -0.08 ...... Frame ( 27) shift: -0.20 -0.09 ...... Frame ( 28) shift: -0.15 -0.12 ...... Frame ( 29) shift: -0.10 -0.14 ...... Frame ( 30) shift: -0.03 -0.09 ...... Frame ( 31) shift: 0.06 0.04 ...... Frame ( 32) shift: 0.14 0.16 ...... Frame ( 33) shift: 0.16 0.22 ...... Frame ( 34) shift: 0.11 0.20 ...... Frame ( 35) shift: 0.06 0.18 ...... Frame ( 36) shift: 0.05 0.15 ...... Frame ( 37) shift: 0.09 0.11 ...... Frame ( 38) shift: 0.13 0.07 ...... Frame ( 39) shift: 0.16 0.03 ...... Frame ( 40) shift: 0.20 -0.01 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.985839 Iteration 2 Error: 0.280967 Iteration 3 Error: 0.050262 Iteration 4 Error: 0.029461 Align patch 2 23 left Iteration 1 Error: 0.861064 Iteration 2 Error: 0.310376 Iteration 3 Error: 0.077202 Iteration 4 Error: 0.025014 Align patch 3 22 left Iteration 1 Error: 0.607077 Iteration 2 Error: 0.162774 Iteration 3 Error: 0.038323 Align patch 4 21 left Iteration 1 Error: 0.457730 Iteration 2 Error: 0.091301 Iteration 3 Error: 0.027721 Align patch 5 20 left Iteration 1 Error: 0.839975 Iteration 2 Error: 0.145973 Iteration 3 Error: 0.029125 Align patch 6 19 left Iteration 1 Error: 0.864597 Iteration 2 Error: 0.263836 Iteration 3 Error: 0.118509 Iteration 4 Error: 0.060448 Iteration 5 Error: 0.028280 Align patch 7 18 left Iteration 1 Error: 0.564024 Iteration 2 Error: 0.112390 Iteration 3 Error: 0.023569 Align patch 8 17 left Iteration 1 Error: 0.821889 Iteration 2 Error: 0.258454 Iteration 3 Error: 0.058222 Iteration 4 Error: 0.020006 Align patch 9 16 left Iteration 1 Error: 0.692793 Iteration 2 Error: 0.090994 Iteration 3 Error: 0.026059 Align patch 10 15 left Iteration 1 Error: 0.504965 Iteration 2 Error: 0.118192 Iteration 3 Error: 0.024990 Align patch 11 14 left Iteration 1 Error: 0.697545 Iteration 2 Error: 0.150741 Iteration 3 Error: 0.055752 Iteration 4 Error: 0.025308 Align patch 12 13 left Iteration 1 Error: 0.758249 Iteration 2 Error: 0.263218 Iteration 3 Error: 0.077346 Iteration 4 Error: 0.026512 Align patch 13 12 left Iteration 1 Error: 0.778514 Iteration 2 Error: 0.144606 Iteration 3 Error: 0.022723 Align patch 14 11 left Iteration 1 Error: 0.841799 Iteration 2 Error: 0.122127 Iteration 3 Error: 0.042635 Align patch 15 10 left Iteration 1 Error: 0.542645 Iteration 2 Error: 0.061236 Iteration 3 Error: 0.018466 Align patch 16 9 left Iteration 1 Error: 0.605802 Iteration 2 Error: 0.164635 Iteration 3 Error: 0.073166 Iteration 4 Error: 0.024032 Align patch 17 8 left Iteration 1 Error: 0.899749 Iteration 2 Error: 0.161202 Iteration 3 Error: 0.039099 Align patch 18 7 left Iteration 1 Error: 0.941407 Iteration 2 Error: 0.166561 Iteration 3 Error: 0.021885 Align patch 19 6 left Iteration 1 Error: 0.648005 Iteration 2 Error: 0.131840 Iteration 3 Error: 0.042731 Align patch 20 5 left Iteration 1 Error: 0.935926 Iteration 2 Error: 0.177056 Iteration 3 Error: 0.053475 Iteration 4 Error: 0.015320 Align patch 21 4 left Iteration 1 Error: 0.641582 Iteration 2 Error: 0.104273 Iteration 3 Error: 0.029380 Align patch 22 3 left Iteration 1 Error: 0.549486 Iteration 2 Error: 0.115763 Iteration 3 Error: 0.026663 Align patch 23 2 left Iteration 1 Error: 1.013085 Iteration 2 Error: 0.232633 Iteration 3 Error: 0.050872 Iteration 4 Error: 0.015406 Align patch 24 1 left Iteration 1 Error: 0.960292 Iteration 2 Error: 0.136430 Iteration 3 Error: 0.029866 Align patch 25 0 left Iteration 1 Error: 0.883307 Iteration 2 Error: 0.222340 Iteration 3 Error: 0.073080 Iteration 4 Error: 0.021703 3D Fitting completed. Patch alignment time: 13.70(sec) Local motion has been corrected. Process thread exits. Computational time: 22.005161 sec Total time: 27.633244 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00017hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00017hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.845252s Reading file: gc_18feb27f_CTD_g1_00012gr_00002sq_v01_00017hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.235081s ........................................ >>>>>>TIME<<<<<< FFT: 0.793268s Defocus_U Defocus_V Angle CCC 11662.13 10994.13 83.83 0.027799 Final Values Defocus_U Defocus_V Angle CCC 11679.33 11033.22 86.68 0.044315 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00002hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00002hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.993e-02 CC threshold: 0.734 Mean Std: 37.30 6.48 Num Hot pixels: 221 Hot pixel threshold: 76.17 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.645354 Iteration 2 Error: 0.366926 Iteration 3 Error: 0.106289 Iteration 4 Error: 0.050296 Iteration 5 Error: 0.018688 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.14 -0.15 ...... Frame ( 3) shift: 0.28 -0.29 ...... Frame ( 4) shift: 0.42 -0.44 ...... Frame ( 5) shift: 0.56 -0.59 ...... Frame ( 6) shift: 0.63 -0.66 ...... Frame ( 7) shift: 0.63 -0.66 ...... Frame ( 8) shift: 0.63 -0.67 ...... Frame ( 9) shift: 0.67 -0.66 ...... Frame ( 10) shift: 0.77 -0.64 ...... Frame ( 11) shift: 0.87 -0.62 ...... Frame ( 12) shift: 0.94 -0.53 ...... Frame ( 13) shift: 0.98 -0.36 ...... Frame ( 14) shift: 1.02 -0.19 ...... Frame ( 15) shift: 1.07 -0.07 ...... Frame ( 16) shift: 1.11 -0.00 ...... Frame ( 17) shift: 1.16 0.06 ...... Frame ( 18) shift: 1.21 0.15 ...... Frame ( 19) shift: 1.26 0.26 ...... Frame ( 20) shift: 1.31 0.38 ...... Frame ( 21) shift: 1.37 0.47 ...... Frame ( 22) shift: 1.44 0.54 ...... Frame ( 23) shift: 1.51 0.61 ...... Frame ( 24) shift: 1.55 0.69 ...... Frame ( 25) shift: 1.58 0.78 ...... Frame ( 26) shift: 1.60 0.87 ...... Frame ( 27) shift: 1.64 0.93 ...... Frame ( 28) shift: 1.69 0.96 ...... Frame ( 29) shift: 1.75 0.98 ...... Frame ( 30) shift: 1.82 1.06 ...... Frame ( 31) shift: 1.90 1.19 ...... Frame ( 32) shift: 1.99 1.32 ...... Frame ( 33) shift: 2.03 1.42 ...... Frame ( 34) shift: 2.03 1.49 ...... Frame ( 35) shift: 2.02 1.56 ...... Frame ( 36) shift: 2.10 1.61 ...... Frame ( 37) shift: 2.26 1.64 ...... Frame ( 38) shift: 2.41 1.66 ...... Frame ( 39) shift: 2.57 1.69 ...... Frame ( 40) shift: 2.73 1.72 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.218319 Iteration 2 Error: 0.381502 Iteration 3 Error: 0.155427 Iteration 4 Error: 0.091822 Iteration 5 Error: 0.041897 Align patch 2 23 left Iteration 1 Error: 0.899241 Iteration 2 Error: 0.139434 Iteration 3 Error: 0.038266 Align patch 3 22 left Iteration 1 Error: 0.760907 Iteration 2 Error: 0.242733 Iteration 3 Error: 0.091377 Iteration 4 Error: 0.043485 Align patch 4 21 left Iteration 1 Error: 0.945927 Iteration 2 Error: 0.221602 Iteration 3 Error: 0.054448 Iteration 4 Error: 0.037743 Align patch 5 20 left Iteration 1 Error: 0.811905 Iteration 2 Error: 0.162197 Iteration 3 Error: 0.064789 Iteration 4 Error: 0.023470 Align patch 6 19 left Iteration 1 Error: 1.052842 Iteration 2 Error: 0.161632 Iteration 3 Error: 0.058166 Iteration 4 Error: 0.021458 Align patch 7 18 left Iteration 1 Error: 1.219877 Iteration 2 Error: 0.286392 Iteration 3 Error: 0.090972 Iteration 4 Error: 0.064709 Iteration 5 Error: 0.037766 Align patch 8 17 left Iteration 1 Error: 0.825723 Iteration 2 Error: 0.130298 Iteration 3 Error: 0.047949 Align patch 9 16 left Iteration 1 Error: 0.970186 Iteration 2 Error: 0.378799 Iteration 3 Error: 0.083438 Iteration 4 Error: 0.047033 Align patch 10 15 left Iteration 1 Error: 1.100369 Iteration 2 Error: 0.262706 Iteration 3 Error: 0.073722 Iteration 4 Error: 0.047849 Align patch 11 14 left Iteration 1 Error: 1.122209 Iteration 2 Error: 0.258114 Iteration 3 Error: 0.070769 Iteration 4 Error: 0.024271 Align patch 12 13 left Iteration 1 Error: 0.734721 Iteration 2 Error: 0.211394 Iteration 3 Error: 0.053212 Iteration 4 Error: 0.033061 Align patch 13 12 left Iteration 1 Error: 1.003628 Iteration 2 Error: 0.252757 Iteration 3 Error: 0.068323 Iteration 4 Error: 0.032957 Align patch 14 11 left Iteration 1 Error: 0.797078 Iteration 2 Error: 0.162173 Iteration 3 Error: 0.052474 Iteration 4 Error: 0.018805 Align patch 15 10 left Iteration 1 Error: 0.977539 Iteration 2 Error: 0.144387 Iteration 3 Error: 0.059295 Iteration 4 Error: 0.031657 Align patch 16 9 left Iteration 1 Error: 1.369477 Iteration 2 Error: 0.383492 Iteration 3 Error: 0.142446 Iteration 4 Error: 0.061826 Iteration 5 Error: 0.037232 Align patch 17 8 left Iteration 1 Error: 0.750312 Iteration 2 Error: 0.175001 Iteration 3 Error: 0.054557 Iteration 4 Error: 0.020554 Align patch 18 7 left Iteration 1 Error: 0.736757 Iteration 2 Error: 0.238229 Iteration 3 Error: 0.049980 Align patch 19 6 left Iteration 1 Error: 1.270955 Iteration 2 Error: 0.362467 Iteration 3 Error: 0.078597 Iteration 4 Error: 0.037999 Align patch 20 5 left Iteration 1 Error: 0.748337 Iteration 2 Error: 0.185804 Iteration 3 Error: 0.109168 Iteration 4 Error: 0.039456 Align patch 21 4 left Iteration 1 Error: 1.345434 Iteration 2 Error: 0.191120 Iteration 3 Error: 0.080982 Iteration 4 Error: 0.029459 Align patch 22 3 left Iteration 1 Error: 0.884124 Iteration 2 Error: 0.147237 Iteration 3 Error: 0.050570 Iteration 4 Error: 0.017493 Align patch 23 2 left Iteration 1 Error: 0.667645 Iteration 2 Error: 0.104903 Iteration 3 Error: 0.027032 Align patch 24 1 left Iteration 1 Error: 0.853713 Iteration 2 Error: 0.179617 Iteration 3 Error: 0.069711 Iteration 4 Error: 0.018911 Align patch 25 0 left Iteration 1 Error: 1.454260 Iteration 2 Error: 0.265349 Iteration 3 Error: 0.116001 Iteration 4 Error: 0.034426 3D Fitting completed. Patch alignment time: 13.24(sec) Local motion has been corrected. Process thread exits. Computational time: 22.994986 sec Total time: 28.161856 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00002hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00002hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.524312s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00002hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.220937s ........................................ >>>>>>TIME<<<<<< FFT: 1.231274s Defocus_U Defocus_V Angle CCC 8820.33 9683.62 16.71 0.019175 Final Values Defocus_U Defocus_V Angle CCC 8826.58 9646.12 20.47 0.032483 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00002hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00002hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.993e-02 CC threshold: 0.734 Mean Std: 42.41 7.07 Num Hot pixels: 228 Hot pixel threshold: 84.82 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.641221 Iteration 2 Error: 0.522682 Iteration 3 Error: 0.166249 Iteration 4 Error: 0.067586 Iteration 5 Error: 0.036119 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.15 0.10 ...... Frame ( 3) shift: -0.31 0.20 ...... Frame ( 4) shift: -0.46 0.30 ...... Frame ( 5) shift: -0.62 0.41 ...... Frame ( 6) shift: -0.70 0.50 ...... Frame ( 7) shift: -0.69 0.58 ...... Frame ( 8) shift: -0.69 0.67 ...... Frame ( 9) shift: -0.64 0.80 ...... Frame ( 10) shift: -0.55 0.97 ...... Frame ( 11) shift: -0.45 1.14 ...... Frame ( 12) shift: -0.36 1.30 ...... Frame ( 13) shift: -0.28 1.46 ...... Frame ( 14) shift: -0.20 1.62 ...... Frame ( 15) shift: -0.15 1.75 ...... Frame ( 16) shift: -0.14 1.85 ...... Frame ( 17) shift: -0.12 1.95 ...... Frame ( 18) shift: -0.07 2.07 ...... Frame ( 19) shift: 0.01 2.20 ...... Frame ( 20) shift: 0.09 2.33 ...... Frame ( 21) shift: 0.19 2.46 ...... Frame ( 22) shift: 0.31 2.59 ...... Frame ( 23) shift: 0.43 2.73 ...... Frame ( 24) shift: 0.52 2.85 ...... Frame ( 25) shift: 0.57 2.95 ...... Frame ( 26) shift: 0.62 3.06 ...... Frame ( 27) shift: 0.65 3.15 ...... Frame ( 28) shift: 0.67 3.22 ...... Frame ( 29) shift: 0.70 3.29 ...... Frame ( 30) shift: 0.74 3.37 ...... Frame ( 31) shift: 0.80 3.46 ...... Frame ( 32) shift: 0.86 3.56 ...... Frame ( 33) shift: 0.92 3.62 ...... Frame ( 34) shift: 0.97 3.66 ...... Frame ( 35) shift: 1.02 3.70 ...... Frame ( 36) shift: 1.02 3.78 ...... Frame ( 37) shift: 0.97 3.90 ...... Frame ( 38) shift: 0.91 4.03 ...... Frame ( 39) shift: 0.86 4.16 ...... Frame ( 40) shift: 0.80 4.29 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.510905 Iteration 2 Error: 0.495727 Iteration 3 Error: 0.164988 Iteration 4 Error: 0.087549 Iteration 5 Error: 0.056848 Align patch 1 24 left Iteration 1 Error: 1.625203 Iteration 2 Error: 0.443042 Iteration 3 Error: 0.092905 Iteration 4 Error: 0.031675 Align patch 2 23 left Iteration 1 Error: 1.281849 Iteration 2 Error: 0.434363 Iteration 3 Error: 0.263614 Iteration 4 Error: 0.102397 Iteration 5 Error: 0.047947 Align patch 3 22 left Iteration 1 Error: 1.568906 Iteration 2 Error: 0.261029 Iteration 3 Error: 0.081980 Iteration 4 Error: 0.039032 Align patch 4 21 left Iteration 1 Error: 1.056890 Iteration 2 Error: 0.248771 Iteration 3 Error: 0.073385 Iteration 4 Error: 0.024052 Align patch 5 20 left Iteration 1 Error: 1.395736 Iteration 2 Error: 0.460783 Iteration 3 Error: 0.133556 Iteration 4 Error: 0.058685 Iteration 5 Error: 0.021845 Align patch 6 19 left Iteration 1 Error: 1.909928 Iteration 2 Error: 0.564439 Iteration 3 Error: 0.270304 Iteration 4 Error: 0.083628 Iteration 5 Error: 0.051975 Align patch 6 19 left Iteration 1 Error: 1.881306 Iteration 2 Error: 0.309109 Iteration 3 Error: 0.083669 Iteration 4 Error: 0.026870 Align patch 7 18 left Iteration 1 Error: 0.917185 Iteration 2 Error: 0.283646 Iteration 3 Error: 0.065255 Iteration 4 Error: 0.028578 Align patch 8 17 left Iteration 1 Error: 0.817851 Iteration 2 Error: 0.230384 Iteration 3 Error: 0.097855 Iteration 4 Error: 0.045244 Align patch 9 16 left Iteration 1 Error: 0.545933 Iteration 2 Error: 0.151653 Iteration 3 Error: 0.038698 Align patch 10 15 left Iteration 1 Error: 0.647973 Iteration 2 Error: 0.166167 Iteration 3 Error: 0.059083 Iteration 4 Error: 0.023714 Align patch 11 14 left Iteration 1 Error: 1.268734 Iteration 2 Error: 0.339206 Iteration 3 Error: 0.153255 Iteration 4 Error: 0.066116 Iteration 5 Error: 0.029361 Align patch 12 13 left Iteration 1 Error: 1.060073 Iteration 2 Error: 0.227643 Iteration 3 Error: 0.058666 Iteration 4 Error: 0.012652 Align patch 13 12 left Iteration 1 Error: 0.935109 Iteration 2 Error: 0.245906 Iteration 3 Error: 0.042771 Align patch 14 11 left Iteration 1 Error: 0.629763 Iteration 2 Error: 0.182464 Iteration 3 Error: 0.064413 Iteration 4 Error: 0.018239 Align patch 15 10 left Iteration 1 Error: 0.875377 Iteration 2 Error: 0.168395 Iteration 3 Error: 0.038673 Align patch 16 9 left Iteration 1 Error: 0.814455 Iteration 2 Error: 0.390369 Iteration 3 Error: 0.083047 Iteration 4 Error: 0.045679 Align patch 17 8 left Iteration 1 Error: 0.663222 Iteration 2 Error: 0.184556 Iteration 3 Error: 0.056535 Iteration 4 Error: 0.020333 Align patch 18 7 left Iteration 1 Error: 0.573151 Iteration 2 Error: 0.108712 Iteration 3 Error: 0.029921 Align patch 19 6 left Iteration 1 Error: 1.234216 Iteration 2 Error: 0.251468 Iteration 3 Error: 0.053677 Iteration 4 Error: 0.023376 Align patch 20 5 left Iteration 1 Error: 0.793513 Iteration 2 Error: 0.155139 Iteration 3 Error: 0.042691 Align patch 21 4 left Iteration 1 Error: 0.869052 Iteration 2 Error: 0.234911 Iteration 3 Error: 0.062172 Iteration 4 Error: 0.025313 Align patch 22 3 left Iteration 1 Error: 0.787299 Iteration 2 Error: 0.091043 Iteration 3 Error: 0.051743 Iteration 4 Error: 0.024260 Align patch 23 2 left Iteration 1 Error: 0.799794 Iteration 2 Error: 0.231502 Iteration 3 Error: 0.123852 Iteration 4 Error: 0.060800 Iteration 5 Error: 0.043043 Align patch 24 1 left Iteration 1 Error: 1.120114 Iteration 2 Error: 0.354034 Iteration 3 Error: 0.123553 Iteration 4 Error: 0.059227 Iteration 5 Error: 0.032767 Align patch 25 0 left Iteration 1 Error: 1.470724 Iteration 2 Error: 0.326532 Iteration 3 Error: 0.117608 Iteration 4 Error: 0.043780 3D Fitting completed. Patch alignment time: 14.74(sec) Local motion has been corrected. Process thread exits. Computational time: 24.182293 sec Total time: 30.103109 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00002hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00002hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.620624s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00002hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.236509s ........................................ >>>>>>TIME<<<<<< FFT: 1.133749s Defocus_U Defocus_V Angle CCC 12601.54 13050.83 4.71 0.047712 Final Values Defocus_U Defocus_V Angle CCC 12621.86 13049.27 5.65 0.081683 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00002hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00002hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 39.14 6.77 Num Hot pixels: 231 Hot pixel threshold: 79.74 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.990416 Iteration 2 Error: 0.226622 Iteration 3 Error: 0.060213 Iteration 4 Error: 0.015831 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.09 -0.14 ...... Frame ( 3) shift: -0.18 -0.29 ...... Frame ( 4) shift: -0.28 -0.43 ...... Frame ( 5) shift: -0.37 -0.57 ...... Frame ( 6) shift: -0.40 -0.62 ...... Frame ( 7) shift: -0.38 -0.57 ...... Frame ( 8) shift: -0.35 -0.53 ...... Frame ( 9) shift: -0.28 -0.48 ...... Frame ( 10) shift: -0.17 -0.44 ...... Frame ( 11) shift: -0.06 -0.40 ...... Frame ( 12) shift: -0.00 -0.36 ...... Frame ( 13) shift: 0.02 -0.30 ...... Frame ( 14) shift: 0.04 -0.25 ...... Frame ( 15) shift: 0.09 -0.18 ...... Frame ( 16) shift: 0.17 -0.11 ...... Frame ( 17) shift: 0.25 -0.04 ...... Frame ( 18) shift: 0.28 0.01 ...... Frame ( 19) shift: 0.25 0.04 ...... Frame ( 20) shift: 0.22 0.06 ...... Frame ( 21) shift: 0.21 0.08 ...... Frame ( 22) shift: 0.23 0.11 ...... Frame ( 23) shift: 0.25 0.13 ...... Frame ( 24) shift: 0.32 0.17 ...... Frame ( 25) shift: 0.44 0.21 ...... Frame ( 26) shift: 0.56 0.25 ...... Frame ( 27) shift: 0.64 0.30 ...... Frame ( 28) shift: 0.68 0.37 ...... Frame ( 29) shift: 0.73 0.44 ...... Frame ( 30) shift: 0.75 0.52 ...... Frame ( 31) shift: 0.76 0.63 ...... Frame ( 32) shift: 0.77 0.73 ...... Frame ( 33) shift: 0.77 0.78 ...... Frame ( 34) shift: 0.76 0.76 ...... Frame ( 35) shift: 0.75 0.74 ...... Frame ( 36) shift: 0.79 0.78 ...... Frame ( 37) shift: 0.88 0.87 ...... Frame ( 38) shift: 0.97 0.95 ...... Frame ( 39) shift: 1.06 1.04 ...... Frame ( 40) shift: 1.15 1.13 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.141648 Iteration 2 Error: 0.179162 Iteration 3 Error: 0.067448 Iteration 4 Error: 0.035205 Align patch 2 23 left Iteration 1 Error: 0.811562 Iteration 2 Error: 0.270794 Iteration 3 Error: 0.047458 Align patch 3 22 left Iteration 1 Error: 0.789625 Iteration 2 Error: 0.203374 Iteration 3 Error: 0.062031 Iteration 4 Error: 0.018401 Align patch 4 21 left Iteration 1 Error: 0.921230 Iteration 2 Error: 0.209579 Iteration 3 Error: 0.070223 Iteration 4 Error: 0.018161 Align patch 5 20 left Iteration 1 Error: 0.842523 Iteration 2 Error: 0.155876 Iteration 3 Error: 0.038709 Align patch 6 19 left Iteration 1 Error: 0.701080 Iteration 2 Error: 0.107825 Iteration 3 Error: 0.040631 Align patch 7 18 left Iteration 1 Error: 0.499971 Iteration 2 Error: 0.061538 Iteration 3 Error: 0.020902 Align patch 8 17 left Iteration 1 Error: 0.949673 Iteration 2 Error: 0.124686 Iteration 3 Error: 0.035224 Align patch 9 16 left Iteration 1 Error: 0.697675 Iteration 2 Error: 0.156357 Iteration 3 Error: 0.043316 Align patch 10 15 left Iteration 1 Error: 1.374933 Iteration 2 Error: 0.153231 Iteration 3 Error: 0.038303 Align patch 11 14 left Iteration 1 Error: 0.756393 Iteration 2 Error: 0.194953 Iteration 3 Error: 0.053195 Iteration 4 Error: 0.021317 Align patch 12 13 left Iteration 1 Error: 1.123048 Iteration 2 Error: 0.144326 Iteration 3 Error: 0.026861 Align patch 13 12 left Iteration 1 Error: 0.572969 Iteration 2 Error: 0.151179 Iteration 3 Error: 0.049243 Align patch 14 11 left Iteration 1 Error: 1.768033 Iteration 2 Error: 0.253524 Iteration 3 Error: 0.128887 Iteration 4 Error: 0.058064 Iteration 5 Error: 0.038155 Align patch 15 10 left Iteration 1 Error: 1.012018 Iteration 2 Error: 0.158913 Iteration 3 Error: 0.028991 Align patch 16 9 left Iteration 1 Error: 0.857970 Iteration 2 Error: 0.201884 Iteration 3 Error: 0.071102 Iteration 4 Error: 0.020588 Align patch 17 8 left Iteration 1 Error: 0.893704 Iteration 2 Error: 0.183111 Iteration 3 Error: 0.039361 Align patch 18 7 left Iteration 1 Error: 0.832965 Iteration 2 Error: 0.121351 Iteration 3 Error: 0.041552 Align patch 19 6 left Iteration 1 Error: 0.663622 Iteration 2 Error: 0.145570 Iteration 3 Error: 0.041317 Align patch 20 5 left Iteration 1 Error: 0.872188 Iteration 2 Error: 0.162084 Iteration 3 Error: 0.040768 Align patch 21 4 left Iteration 1 Error: 0.973697 Iteration 2 Error: 0.147425 Iteration 3 Error: 0.026083 Align patch 22 3 left Iteration 1 Error: 0.917177 Iteration 2 Error: 0.247022 Iteration 3 Error: 0.096612 Iteration 4 Error: 0.029254 Align patch 23 2 left Iteration 1 Error: 0.748325 Iteration 2 Error: 0.152238 Iteration 3 Error: 0.035911 Align patch 24 1 left Iteration 1 Error: 0.604585 Iteration 2 Error: 0.087452 Iteration 3 Error: 0.028627 Align patch 25 0 left Iteration 1 Error: 0.788382 Iteration 2 Error: 0.182059 Iteration 3 Error: 0.049143 3D Fitting completed. Patch alignment time: 11.97(sec) Local motion has been corrected. Process thread exits. Computational time: 22.035437 sec Total time: 27.815483 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00002hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00002hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.640046s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00002hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.595787s ........................................ >>>>>>TIME<<<<<< FFT: 1.044975s Defocus_U Defocus_V Angle CCC 14179.68 15027.35 6.49 0.042132 Final Values Defocus_U Defocus_V Angle CCC 14198.43 15039.85 4.92 0.061675 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00002hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00002hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.994e-02 CC threshold: 0.734 Mean Std: 42.94 7.14 Num Hot pixels: 231 Hot pixel threshold: 85.81 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.807180 Iteration 2 Error: 0.338800 Iteration 3 Error: 0.117654 Iteration 4 Error: 0.038416 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.18 -0.03 ...... Frame ( 3) shift: -0.37 -0.06 ...... Frame ( 4) shift: -0.55 -0.09 ...... Frame ( 5) shift: -0.74 -0.12 ...... Frame ( 6) shift: -0.78 -0.05 ...... Frame ( 7) shift: -0.68 0.14 ...... Frame ( 8) shift: -0.57 0.32 ...... Frame ( 9) shift: -0.49 0.51 ...... Frame ( 10) shift: -0.43 0.69 ...... Frame ( 11) shift: -0.37 0.88 ...... Frame ( 12) shift: -0.29 1.06 ...... Frame ( 13) shift: -0.20 1.23 ...... Frame ( 14) shift: -0.10 1.40 ...... Frame ( 15) shift: -0.04 1.57 ...... Frame ( 16) shift: -0.01 1.73 ...... Frame ( 17) shift: 0.02 1.89 ...... Frame ( 18) shift: 0.07 2.00 ...... Frame ( 19) shift: 0.16 2.06 ...... Frame ( 20) shift: 0.25 2.12 ...... Frame ( 21) shift: 0.30 2.20 ...... Frame ( 22) shift: 0.31 2.30 ...... Frame ( 23) shift: 0.33 2.40 ...... Frame ( 24) shift: 0.35 2.49 ...... Frame ( 25) shift: 0.38 2.57 ...... Frame ( 26) shift: 0.41 2.65 ...... Frame ( 27) shift: 0.44 2.73 ...... Frame ( 28) shift: 0.48 2.80 ...... Frame ( 29) shift: 0.51 2.87 ...... Frame ( 30) shift: 0.52 2.93 ...... Frame ( 31) shift: 0.52 2.96 ...... Frame ( 32) shift: 0.51 3.00 ...... Frame ( 33) shift: 0.53 3.07 ...... Frame ( 34) shift: 0.56 3.17 ...... Frame ( 35) shift: 0.59 3.27 ...... Frame ( 36) shift: 0.61 3.35 ...... Frame ( 37) shift: 0.63 3.41 ...... Frame ( 38) shift: 0.64 3.47 ...... Frame ( 39) shift: 0.65 3.53 ...... Frame ( 40) shift: 0.67 3.58 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.407295 Iteration 2 Error: 0.167518 Iteration 3 Error: 0.054547 Iteration 4 Error: 0.016835 Align patch 2 23 left Iteration 1 Error: 0.740638 Iteration 2 Error: 0.149861 Iteration 3 Error: 0.044911 Align patch 3 22 left Iteration 1 Error: 0.837524 Iteration 2 Error: 0.212576 Iteration 3 Error: 0.069699 Iteration 4 Error: 0.030982 Align patch 4 21 left Iteration 1 Error: 1.064256 Iteration 2 Error: 0.179072 Iteration 3 Error: 0.031369 Align patch 5 20 left Iteration 1 Error: 0.929015 Iteration 2 Error: 0.208765 Iteration 3 Error: 0.061385 Iteration 4 Error: 0.012119 Align patch 6 19 left Iteration 1 Error: 2.420401 Iteration 2 Error: 0.416378 Iteration 3 Error: 0.260539 Iteration 4 Error: 0.081020 Iteration 5 Error: 0.090796 Align patch 6 19 left Iteration 1 Error: 2.451245 Iteration 2 Error: 0.373715 Iteration 3 Error: 0.096014 Iteration 4 Error: 0.030709 Align patch 7 18 left Iteration 1 Error: 1.717216 Iteration 2 Error: 0.260163 Iteration 3 Error: 0.150239 Iteration 4 Error: 0.083691 Iteration 5 Error: 0.047177 Align patch 8 17 left Iteration 1 Error: 1.170280 Iteration 2 Error: 0.225893 Iteration 3 Error: 0.061312 Iteration 4 Error: 0.027125 Align patch 9 16 left Iteration 1 Error: 0.756445 Iteration 2 Error: 0.144607 Iteration 3 Error: 0.048194 Align patch 10 15 left Iteration 1 Error: 0.928029 Iteration 2 Error: 0.172500 Iteration 3 Error: 0.049636 Align patch 11 14 left Iteration 1 Error: 1.449948 Iteration 2 Error: 0.266965 Iteration 3 Error: 0.092343 Iteration 4 Error: 0.026241 Align patch 12 13 left Iteration 1 Error: 1.302851 Iteration 2 Error: 0.227247 Iteration 3 Error: 0.082353 Iteration 4 Error: 0.026850 Align patch 13 12 left Iteration 1 Error: 1.420692 Iteration 2 Error: 0.245249 Iteration 3 Error: 0.074601 Iteration 4 Error: 0.022575 Align patch 14 11 left Iteration 1 Error: 1.186719 Iteration 2 Error: 0.212026 Iteration 3 Error: 0.063738 Iteration 4 Error: 0.021384 Align patch 15 10 left Iteration 1 Error: 1.093491 Iteration 2 Error: 0.217671 Iteration 3 Error: 0.092880 Iteration 4 Error: 0.021768 Align patch 16 9 left Iteration 1 Error: 1.001613 Iteration 2 Error: 0.203471 Iteration 3 Error: 0.062942 Iteration 4 Error: 0.030780 Align patch 17 8 left Iteration 1 Error: 0.866038 Iteration 2 Error: 0.211846 Iteration 3 Error: 0.079047 Iteration 4 Error: 0.035644 Align patch 18 7 left Iteration 1 Error: 1.152637 Iteration 2 Error: 0.158963 Iteration 3 Error: 0.044735 Align patch 19 6 left Iteration 1 Error: 0.783675 Iteration 2 Error: 0.265951 Iteration 3 Error: 0.063586 Iteration 4 Error: 0.026789 Align patch 20 5 left Iteration 1 Error: 0.926980 Iteration 2 Error: 0.124885 Iteration 3 Error: 0.031978 Align patch 21 4 left Iteration 1 Error: 1.170466 Iteration 2 Error: 0.236903 Iteration 3 Error: 0.083888 Iteration 4 Error: 0.043459 Align patch 22 3 left Iteration 1 Error: 1.244658 Iteration 2 Error: 0.180467 Iteration 3 Error: 0.031940 Align patch 23 2 left Iteration 1 Error: 0.861358 Iteration 2 Error: 0.101929 Iteration 3 Error: 0.026699 Align patch 24 1 left Iteration 1 Error: 0.873666 Iteration 2 Error: 0.175843 Iteration 3 Error: 0.047786 Align patch 25 0 left Iteration 1 Error: 0.901582 Iteration 2 Error: 0.180670 Iteration 3 Error: 0.049341 3D Fitting completed. Patch alignment time: 13.08(sec) Local motion has been corrected. Process thread exits. Computational time: 22.951393 sec Total time: 28.987595 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00002hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00002hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.635613s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00002hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.519073s ........................................ >>>>>>TIME<<<<<< FFT: 1.085126s Defocus_U Defocus_V Angle CCC 15005.87 14322.26 84.29 0.051622 Final Values Defocus_U Defocus_V Angle CCC 14990.21 14325.42 83.35 0.086793 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00003hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00003hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.002e-01 CC threshold: 0.736 Mean Std: 45.15 7.48 Num Hot pixels: 223 Hot pixel threshold: 90.02 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.758640 Iteration 2 Error: 0.065639 Iteration 3 Error: 0.018927 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.16 0.07 ...... Frame ( 3) shift: -0.33 0.15 ...... Frame ( 4) shift: -0.49 0.22 ...... Frame ( 5) shift: -0.65 0.30 ...... Frame ( 6) shift: -0.72 0.34 ...... Frame ( 7) shift: -0.69 0.36 ...... Frame ( 8) shift: -0.66 0.37 ...... Frame ( 9) shift: -0.65 0.42 ...... Frame ( 10) shift: -0.66 0.51 ...... Frame ( 11) shift: -0.66 0.59 ...... Frame ( 12) shift: -0.63 0.67 ...... Frame ( 13) shift: -0.57 0.74 ...... Frame ( 14) shift: -0.51 0.81 ...... Frame ( 15) shift: -0.48 0.87 ...... Frame ( 16) shift: -0.48 0.93 ...... Frame ( 17) shift: -0.49 0.99 ...... Frame ( 18) shift: -0.49 1.03 ...... Frame ( 19) shift: -0.50 1.04 ...... Frame ( 20) shift: -0.50 1.05 ...... Frame ( 21) shift: -0.51 1.08 ...... Frame ( 22) shift: -0.54 1.12 ...... Frame ( 23) shift: -0.56 1.15 ...... Frame ( 24) shift: -0.56 1.15 ...... Frame ( 25) shift: -0.53 1.11 ...... Frame ( 26) shift: -0.51 1.07 ...... Frame ( 27) shift: -0.49 1.05 ...... Frame ( 28) shift: -0.47 1.06 ...... Frame ( 29) shift: -0.44 1.07 ...... Frame ( 30) shift: -0.43 1.09 ...... Frame ( 31) shift: -0.43 1.11 ...... Frame ( 32) shift: -0.43 1.13 ...... Frame ( 33) shift: -0.39 1.15 ...... Frame ( 34) shift: -0.31 1.16 ...... Frame ( 35) shift: -0.23 1.17 ...... Frame ( 36) shift: -0.19 1.17 ...... Frame ( 37) shift: -0.22 1.15 ...... Frame ( 38) shift: -0.24 1.13 ...... Frame ( 39) shift: -0.26 1.11 ...... Frame ( 40) shift: -0.28 1.09 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.815585 Iteration 2 Error: 0.097610 Iteration 3 Error: 0.018610 Align patch 2 23 left Iteration 1 Error: 0.929089 Iteration 2 Error: 0.162975 Iteration 3 Error: 0.035864 Align patch 3 22 left Iteration 1 Error: 1.037953 Iteration 2 Error: 0.108718 Iteration 3 Error: 0.026241 Align patch 4 21 left Iteration 1 Error: 0.846515 Iteration 2 Error: 0.092181 Iteration 3 Error: 0.028965 Align patch 5 20 left Iteration 1 Error: 1.101852 Iteration 2 Error: 0.142215 Iteration 3 Error: 0.021148 Align patch 6 19 left Iteration 1 Error: 1.026145 Iteration 2 Error: 0.153766 Iteration 3 Error: 0.033544 Align patch 7 18 left Iteration 1 Error: 0.823162 Iteration 2 Error: 0.151749 Iteration 3 Error: 0.032271 Align patch 8 17 left Iteration 1 Error: 0.631583 Iteration 2 Error: 0.145538 Iteration 3 Error: 0.026181 Align patch 9 16 left Iteration 1 Error: 0.997586 Iteration 2 Error: 0.088874 Iteration 3 Error: 0.014589 Align patch 10 15 left Iteration 1 Error: 1.228745 Iteration 2 Error: 0.142408 Iteration 3 Error: 0.022772 Align patch 11 14 left Iteration 1 Error: 1.143323 Iteration 2 Error: 0.143125 Iteration 3 Error: 0.042836 Align patch 12 13 left Iteration 1 Error: 1.271672 Iteration 2 Error: 0.163138 Iteration 3 Error: 0.024568 Align patch 13 12 left Iteration 1 Error: 0.606644 Iteration 2 Error: 0.119986 Iteration 3 Error: 0.032091 Align patch 14 11 left Iteration 1 Error: 0.456948 Iteration 2 Error: 0.050227 Iteration 3 Error: 0.007799 Align patch 15 10 left Iteration 1 Error: 0.778603 Iteration 2 Error: 0.154405 Iteration 3 Error: 0.039878 Align patch 16 9 left Iteration 1 Error: 1.651035 Iteration 2 Error: 0.155237 Iteration 3 Error: 0.048568 Align patch 17 8 left Iteration 1 Error: 1.591381 Iteration 2 Error: 0.191027 Iteration 3 Error: 0.053054 Iteration 4 Error: 0.010664 Align patch 18 7 left Iteration 1 Error: 1.075606 Iteration 2 Error: 0.172878 Iteration 3 Error: 0.047241 Align patch 19 6 left Iteration 1 Error: 0.794886 Iteration 2 Error: 0.085782 Iteration 3 Error: 0.023064 Align patch 20 5 left Iteration 1 Error: 0.942257 Iteration 2 Error: 0.182767 Iteration 3 Error: 0.050498 Iteration 4 Error: 0.019441 Align patch 21 4 left Iteration 1 Error: 1.752512 Iteration 2 Error: 0.183145 Iteration 3 Error: 0.042402 Align patch 22 3 left Iteration 1 Error: 0.697545 Iteration 2 Error: 0.149966 Iteration 3 Error: 0.034796 Align patch 23 2 left Iteration 1 Error: 1.096759 Iteration 2 Error: 0.153116 Iteration 3 Error: 0.029350 Align patch 24 1 left Iteration 1 Error: 0.600465 Iteration 2 Error: 0.080993 Iteration 3 Error: 0.014285 Align patch 25 0 left Iteration 1 Error: 0.721397 Iteration 2 Error: 0.186697 Iteration 3 Error: 0.024135 3D Fitting completed. Patch alignment time: 12.09(sec) Local motion has been corrected. Process thread exits. Computational time: 22.474123 sec Total time: 29.451754 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00003hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00003hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.617030s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00003hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.155133s ........................................ >>>>>>TIME<<<<<< FFT: 0.943045s Defocus_U Defocus_V Angle CCC 12662.12 13572.27 10.89 0.061099 Final Values Defocus_U Defocus_V Angle CCC 12671.49 13566.02 10.89 0.103680 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00003hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00003hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.003e-01 CC threshold: 0.736 Mean Std: 44.98 7.47 Num Hot pixels: 217 Hot pixel threshold: 89.82 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.005430 Iteration 2 Error: 0.063746 Iteration 3 Error: 0.009883 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.36 0.04 ...... Frame ( 3) shift: -0.72 0.09 ...... Frame ( 4) shift: -1.08 0.13 ...... Frame ( 5) shift: -1.43 0.18 ...... Frame ( 6) shift: -1.63 0.20 ...... Frame ( 7) shift: -1.66 0.19 ...... Frame ( 8) shift: -1.69 0.19 ...... Frame ( 9) shift: -1.69 0.12 ...... Frame ( 10) shift: -1.66 -0.01 ...... Frame ( 11) shift: -1.63 -0.13 ...... Frame ( 12) shift: -1.61 -0.22 ...... Frame ( 13) shift: -1.60 -0.27 ...... Frame ( 14) shift: -1.60 -0.31 ...... Frame ( 15) shift: -1.60 -0.32 ...... Frame ( 16) shift: -1.60 -0.29 ...... Frame ( 17) shift: -1.61 -0.26 ...... Frame ( 18) shift: -1.59 -0.25 ...... Frame ( 19) shift: -1.55 -0.25 ...... Frame ( 20) shift: -1.52 -0.26 ...... Frame ( 21) shift: -1.51 -0.28 ...... Frame ( 22) shift: -1.53 -0.31 ...... Frame ( 23) shift: -1.56 -0.34 ...... Frame ( 24) shift: -1.58 -0.36 ...... Frame ( 25) shift: -1.59 -0.36 ...... Frame ( 26) shift: -1.60 -0.36 ...... Frame ( 27) shift: -1.61 -0.37 ...... Frame ( 28) shift: -1.61 -0.39 ...... Frame ( 29) shift: -1.61 -0.41 ...... Frame ( 30) shift: -1.56 -0.43 ...... Frame ( 31) shift: -1.47 -0.47 ...... Frame ( 32) shift: -1.38 -0.50 ...... Frame ( 33) shift: -1.33 -0.53 ...... Frame ( 34) shift: -1.32 -0.57 ...... Frame ( 35) shift: -1.31 -0.61 ...... Frame ( 36) shift: -1.26 -0.58 ...... Frame ( 37) shift: -1.15 -0.47 ...... Frame ( 38) shift: -1.04 -0.36 ...... Frame ( 39) shift: -0.94 -0.25 ...... Frame ( 40) shift: -0.83 -0.14 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.176560 Iteration 2 Error: 0.115237 Iteration 3 Error: 0.020604 Align patch 2 23 left Iteration 1 Error: 0.986811 Iteration 2 Error: 0.162278 Iteration 3 Error: 0.052295 Iteration 4 Error: 0.019315 Align patch 3 22 left Iteration 1 Error: 0.780886 Iteration 2 Error: 0.080424 Iteration 3 Error: 0.015593 Align patch 4 21 left Iteration 1 Error: 0.620374 Iteration 2 Error: 0.081372 Iteration 3 Error: 0.022040 Align patch 5 20 left Iteration 1 Error: 0.619167 Iteration 2 Error: 0.093154 Iteration 3 Error: 0.024402 Align patch 6 19 left Iteration 1 Error: 0.927510 Iteration 2 Error: 0.079570 Iteration 3 Error: 0.029680 Align patch 7 18 left Iteration 1 Error: 0.644337 Iteration 2 Error: 0.087331 Iteration 3 Error: 0.025374 Align patch 8 17 left Iteration 1 Error: 0.714241 Iteration 2 Error: 0.115257 Iteration 3 Error: 0.020123 Align patch 9 16 left Iteration 1 Error: 0.704505 Iteration 2 Error: 0.072352 Iteration 3 Error: 0.025042 Align patch 10 15 left Iteration 1 Error: 0.715604 Iteration 2 Error: 0.071823 Iteration 3 Error: 0.012176 Align patch 11 14 left Iteration 1 Error: 1.378431 Iteration 2 Error: 0.132911 Iteration 3 Error: 0.020874 Align patch 12 13 left Iteration 1 Error: 0.959662 Iteration 2 Error: 0.124439 Iteration 3 Error: 0.028654 Align patch 13 12 left Iteration 1 Error: 0.644930 Iteration 2 Error: 0.114700 Iteration 3 Error: 0.035979 Align patch 14 11 left Iteration 1 Error: 0.874390 Iteration 2 Error: 0.179971 Iteration 3 Error: 0.039368 Align patch 15 10 left Iteration 1 Error: 0.711870 Iteration 2 Error: 0.090007 Iteration 3 Error: 0.018492 Align patch 16 9 left Iteration 1 Error: 0.681997 Iteration 2 Error: 0.128091 Iteration 3 Error: 0.033262 Align patch 17 8 left Iteration 1 Error: 0.683829 Iteration 2 Error: 0.102963 Iteration 3 Error: 0.026815 Align patch 18 7 left Iteration 1 Error: 0.444004 Iteration 2 Error: 0.105650 Iteration 3 Error: 0.025302 Align patch 19 6 left Iteration 1 Error: 0.706390 Iteration 2 Error: 0.142865 Iteration 3 Error: 0.035848 Align patch 20 5 left Iteration 1 Error: 0.707087 Iteration 2 Error: 0.088940 Iteration 3 Error: 0.017257 Align patch 21 4 left Iteration 1 Error: 1.955271 Iteration 2 Error: 0.179275 Iteration 3 Error: 0.051260 Iteration 4 Error: 0.022797 Align patch 22 3 left Iteration 1 Error: 1.852972 Iteration 2 Error: 0.165508 Iteration 3 Error: 0.038124 Align patch 23 2 left Iteration 1 Error: 1.459221 Iteration 2 Error: 0.133973 Iteration 3 Error: 0.022366 Align patch 24 1 left Iteration 1 Error: 0.883650 Iteration 2 Error: 0.113591 Iteration 3 Error: 0.039834 Align patch 25 0 left Iteration 1 Error: 1.270350 Iteration 2 Error: 0.114689 Iteration 3 Error: 0.028076 3D Fitting completed. Patch alignment time: 11.15(sec) Local motion has been corrected. Process thread exits. Computational time: 21.532978 sec Total time: 31.119619 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00003hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00003hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.039332s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00003hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.774684s ........................................ >>>>>>TIME<<<<<< FFT: 1.078546s Defocus_U Defocus_V Angle CCC 10355.49 9843.77 89.12 0.054980 Final Values Defocus_U Defocus_V Angle CCC 10361.73 9846.90 89.12 0.102869 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00003hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00003hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.002e-01 CC threshold: 0.736 Mean Std: 45.99 7.53 Num Hot pixels: 209 Hot pixel threshold: 91.20 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.365026 Iteration 2 Error: 0.038508 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.15 0.05 ...... Frame ( 3) shift: -0.30 0.11 ...... Frame ( 4) shift: -0.45 0.16 ...... Frame ( 5) shift: -0.60 0.21 ...... Frame ( 6) shift: -0.69 0.24 ...... Frame ( 7) shift: -0.70 0.26 ...... Frame ( 8) shift: -0.71 0.27 ...... Frame ( 9) shift: -0.66 0.32 ...... Frame ( 10) shift: -0.54 0.40 ...... Frame ( 11) shift: -0.42 0.47 ...... Frame ( 12) shift: -0.33 0.50 ...... Frame ( 13) shift: -0.27 0.46 ...... Frame ( 14) shift: -0.22 0.43 ...... Frame ( 15) shift: -0.19 0.41 ...... Frame ( 16) shift: -0.19 0.40 ...... Frame ( 17) shift: -0.19 0.39 ...... Frame ( 18) shift: -0.19 0.40 ...... Frame ( 19) shift: -0.18 0.42 ...... Frame ( 20) shift: -0.17 0.44 ...... Frame ( 21) shift: -0.17 0.41 ...... Frame ( 22) shift: -0.17 0.33 ...... Frame ( 23) shift: -0.17 0.25 ...... Frame ( 24) shift: -0.21 0.19 ...... Frame ( 25) shift: -0.29 0.14 ...... Frame ( 26) shift: -0.36 0.10 ...... Frame ( 27) shift: -0.38 0.10 ...... Frame ( 28) shift: -0.33 0.15 ...... Frame ( 29) shift: -0.28 0.21 ...... Frame ( 30) shift: -0.26 0.21 ...... Frame ( 31) shift: -0.28 0.16 ...... Frame ( 32) shift: -0.29 0.12 ...... Frame ( 33) shift: -0.32 0.10 ...... Frame ( 34) shift: -0.37 0.11 ...... Frame ( 35) shift: -0.41 0.12 ...... Frame ( 36) shift: -0.44 0.15 ...... Frame ( 37) shift: -0.46 0.18 ...... Frame ( 38) shift: -0.47 0.21 ...... Frame ( 39) shift: -0.48 0.24 ...... Frame ( 40) shift: -0.50 0.27 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.079059 Iteration 2 Error: 0.175296 Iteration 3 Error: 0.074222 Iteration 4 Error: 0.013667 Align patch 2 23 left Iteration 1 Error: 0.776744 Iteration 2 Error: 0.130932 Iteration 3 Error: 0.038627 Align patch 3 22 left Iteration 1 Error: 0.622139 Iteration 2 Error: 0.090899 Iteration 3 Error: 0.018877 Align patch 4 21 left Iteration 1 Error: 0.500668 Iteration 2 Error: 0.084219 Iteration 3 Error: 0.011363 Align patch 5 20 left Iteration 1 Error: 0.466743 Iteration 2 Error: 0.060799 Iteration 3 Error: 0.013183 Align patch 6 19 left Iteration 1 Error: 0.806958 Iteration 2 Error: 0.099865 Iteration 3 Error: 0.033189 Align patch 7 18 left Iteration 1 Error: 0.811199 Iteration 2 Error: 0.121722 Iteration 3 Error: 0.039007 Align patch 8 17 left Iteration 1 Error: 0.648853 Iteration 2 Error: 0.060115 Iteration 3 Error: 0.016002 Align patch 9 16 left Iteration 1 Error: 0.484266 Iteration 2 Error: 0.061529 Iteration 3 Error: 0.012290 Align patch 10 15 left Iteration 1 Error: 0.760121 Iteration 2 Error: 0.075729 Iteration 3 Error: 0.013276 Align patch 11 14 left Iteration 1 Error: 0.680652 Iteration 2 Error: 0.187322 Iteration 3 Error: 0.043567 Align patch 12 13 left Iteration 1 Error: 0.602698 Iteration 2 Error: 0.090748 Iteration 3 Error: 0.027144 Align patch 13 12 left Iteration 1 Error: 1.065346 Iteration 2 Error: 0.136397 Iteration 3 Error: 0.035012 Align patch 14 11 left Iteration 1 Error: 1.067465 Iteration 2 Error: 0.090650 Iteration 3 Error: 0.015652 Align patch 15 10 left Iteration 1 Error: 0.762732 Iteration 2 Error: 0.100666 Iteration 3 Error: 0.016270 Align patch 16 9 left Iteration 1 Error: 0.826238 Iteration 2 Error: 0.142815 Iteration 3 Error: 0.027569 Align patch 17 8 left Iteration 1 Error: 0.903479 Iteration 2 Error: 0.147398 Iteration 3 Error: 0.028302 Align patch 18 7 left Iteration 1 Error: 0.959231 Iteration 2 Error: 0.127172 Iteration 3 Error: 0.033219 Align patch 19 6 left Iteration 1 Error: 0.599435 Iteration 2 Error: 0.107654 Iteration 3 Error: 0.024694 Align patch 20 5 left Iteration 1 Error: 0.589993 Iteration 2 Error: 0.077740 Iteration 3 Error: 0.013772 Align patch 21 4 left Iteration 1 Error: 0.887145 Iteration 2 Error: 0.127452 Iteration 3 Error: 0.036109 Align patch 22 3 left Iteration 1 Error: 0.672632 Iteration 2 Error: 0.077245 Iteration 3 Error: 0.018914 Align patch 23 2 left Iteration 1 Error: 0.669336 Iteration 2 Error: 0.084586 Iteration 3 Error: 0.025662 Align patch 24 1 left Iteration 1 Error: 1.388388 Iteration 2 Error: 0.147248 Iteration 3 Error: 0.024568 Align patch 25 0 left Iteration 1 Error: 0.606186 Iteration 2 Error: 0.053607 Iteration 3 Error: 0.011284 3D Fitting completed. Patch alignment time: 11.32(sec) Local motion has been corrected. Process thread exits. Computational time: 21.922508 sec Total time: 27.887989 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00003hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00003hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.593874s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00003hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.699044s ........................................ >>>>>>TIME<<<<<< FFT: 0.883675s Defocus_U Defocus_V Angle CCC 11460.94 12394.53 3.87 0.055108 Final Values Defocus_U Defocus_V Angle CCC 11464.06 12397.66 3.56 0.098384 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00003hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00003hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 45.32 7.51 Num Hot pixels: 218 Hot pixel threshold: 90.39 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.963052 Iteration 2 Error: 0.218892 Iteration 3 Error: 0.057716 Iteration 4 Error: 0.018863 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.37 0.06 ...... Frame ( 3) shift: -0.73 0.13 ...... Frame ( 4) shift: -1.10 0.19 ...... Frame ( 5) shift: -1.46 0.25 ...... Frame ( 6) shift: -1.68 0.30 ...... Frame ( 7) shift: -1.75 0.32 ...... Frame ( 8) shift: -1.82 0.34 ...... Frame ( 9) shift: -1.81 0.34 ...... Frame ( 10) shift: -1.73 0.33 ...... Frame ( 11) shift: -1.66 0.32 ...... Frame ( 12) shift: -1.60 0.29 ...... Frame ( 13) shift: -1.58 0.22 ...... Frame ( 14) shift: -1.55 0.16 ...... Frame ( 15) shift: -1.48 0.11 ...... Frame ( 16) shift: -1.38 0.07 ...... Frame ( 17) shift: -1.27 0.04 ...... Frame ( 18) shift: -1.17 -0.03 ...... Frame ( 19) shift: -1.10 -0.13 ...... Frame ( 20) shift: -1.02 -0.23 ...... Frame ( 21) shift: -0.96 -0.33 ...... Frame ( 22) shift: -0.90 -0.42 ...... Frame ( 23) shift: -0.85 -0.52 ...... Frame ( 24) shift: -0.76 -0.55 ...... Frame ( 25) shift: -0.65 -0.52 ...... Frame ( 26) shift: -0.53 -0.48 ...... Frame ( 27) shift: -0.49 -0.47 ...... Frame ( 28) shift: -0.50 -0.47 ...... Frame ( 29) shift: -0.52 -0.47 ...... Frame ( 30) shift: -0.48 -0.46 ...... Frame ( 31) shift: -0.37 -0.44 ...... Frame ( 32) shift: -0.27 -0.42 ...... Frame ( 33) shift: -0.17 -0.47 ...... Frame ( 34) shift: -0.08 -0.58 ...... Frame ( 35) shift: 0.01 -0.69 ...... Frame ( 36) shift: 0.04 -0.79 ...... Frame ( 37) shift: 0.00 -0.88 ...... Frame ( 38) shift: -0.03 -0.97 ...... Frame ( 39) shift: -0.06 -1.06 ...... Frame ( 40) shift: -0.10 -1.15 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.604629 Iteration 2 Error: 0.093101 Iteration 3 Error: 0.023680 Align patch 2 23 left Iteration 1 Error: 0.803781 Iteration 2 Error: 0.095007 Iteration 3 Error: 0.023929 Align patch 3 22 left Iteration 1 Error: 0.888047 Iteration 2 Error: 0.165611 Iteration 3 Error: 0.044743 Align patch 4 21 left Iteration 1 Error: 1.612685 Iteration 2 Error: 0.118911 Iteration 3 Error: 0.032756 Align patch 5 20 left Iteration 1 Error: 1.695259 Iteration 2 Error: 0.184654 Iteration 3 Error: 0.053557 Iteration 4 Error: 0.011954 Align patch 6 19 left Iteration 1 Error: 2.078867 Iteration 2 Error: 0.317229 Iteration 3 Error: 0.123274 Iteration 4 Error: 0.030395 Align patch 7 18 left Iteration 1 Error: 1.278161 Iteration 2 Error: 0.307655 Iteration 3 Error: 0.113261 Iteration 4 Error: 0.066044 Iteration 5 Error: 0.022883 Align patch 8 17 left Iteration 1 Error: 0.855963 Iteration 2 Error: 0.183156 Iteration 3 Error: 0.055998 Iteration 4 Error: 0.020965 Align patch 9 16 left Iteration 1 Error: 0.680203 Iteration 2 Error: 0.117422 Iteration 3 Error: 0.036869 Align patch 10 15 left Iteration 1 Error: 1.096290 Iteration 2 Error: 0.223268 Iteration 3 Error: 0.064741 Iteration 4 Error: 0.020537 Align patch 11 14 left Iteration 1 Error: 1.597276 Iteration 2 Error: 0.351059 Iteration 3 Error: 0.166501 Iteration 4 Error: 0.109654 Iteration 5 Error: 0.058259 Align patch 11 14 left Iteration 1 Error: 2.981156 Iteration 2 Error: 0.775264 Iteration 3 Error: 0.372952 Iteration 4 Error: 0.151117 Iteration 5 Error: 0.068855 Align patch 12 13 left Iteration 1 Error: 1.031412 Iteration 2 Error: 0.549915 Iteration 3 Error: 0.394701 Iteration 4 Error: 0.434446 Iteration 5 Error: 0.436372 Align patch 12 13 left Iteration 1 Error: 2.591832 Iteration 2 Error: 0.824093 Iteration 3 Error: 0.294181 Iteration 4 Error: 0.121532 Iteration 5 Error: 0.049628 Align patch 13 12 left Iteration 1 Error: 0.648980 Iteration 2 Error: 0.187466 Iteration 3 Error: 0.054199 Iteration 4 Error: 0.021694 Align patch 14 11 left Iteration 1 Error: 0.737119 Iteration 2 Error: 0.105091 Iteration 3 Error: 0.033861 Align patch 15 10 left Iteration 1 Error: 0.511762 Iteration 2 Error: 0.085763 Iteration 3 Error: 0.014231 Align patch 16 9 left Iteration 1 Error: 2.576560 Iteration 2 Error: 4.943757 Iteration 3 Error: 3.583805 Iteration 4 Error: 0.914969 Iteration 5 Error: 0.605791 Align patch 16 9 left Iteration 1 Error: 3.413072 Iteration 2 Error: 1.375820 Iteration 3 Error: 0.802900 Iteration 4 Error: 0.443370 Iteration 5 Error: 0.220590 Align patch 17 8 left Iteration 1 Error: 3.376416 Iteration 2 Error: 0.675470 Iteration 3 Error: 0.597568 Iteration 4 Error: 2.148482 Iteration 5 Error: 0.749231 Align patch 17 8 left Iteration 1 Error: 3.539689 Iteration 2 Error: 1.213590 Iteration 3 Error: 0.577519 Iteration 4 Error: 0.283564 Iteration 5 Error: 0.156767 Align patch 18 7 left Iteration 1 Error: 1.069152 Iteration 2 Error: 0.251212 Iteration 3 Error: 0.118022 Iteration 4 Error: 0.067954 Iteration 5 Error: 0.030090 Align patch 19 6 left Iteration 1 Error: 0.876696 Iteration 2 Error: 0.181083 Iteration 3 Error: 0.064031 Iteration 4 Error: 0.018909 Align patch 20 5 left Iteration 1 Error: 0.842984 Iteration 2 Error: 0.150361 Iteration 3 Error: 0.035118 Align patch 21 4 left Iteration 1 Error: 2.079456 Iteration 2 Error: 0.592183 Iteration 3 Error: 0.456593 Iteration 4 Error: 0.306589 Iteration 5 Error: 0.297193 Align patch 21 4 left Iteration 1 Error: 3.861509 Iteration 2 Error: 0.825190 Iteration 3 Error: 0.367121 Iteration 4 Error: 0.179312 Iteration 5 Error: 0.071630 Align patch 22 3 left Iteration 1 Error: 0.831507 Iteration 2 Error: 0.260541 Iteration 3 Error: 0.092663 Iteration 4 Error: 0.049051 Align patch 23 2 left Iteration 1 Error: 0.827045 Iteration 2 Error: 0.120346 Iteration 3 Error: 0.025009 Align patch 24 1 left Iteration 1 Error: 0.585080 Iteration 2 Error: 0.100619 Iteration 3 Error: 0.027935 Align patch 25 0 left Iteration 1 Error: 1.391618 Iteration 2 Error: 0.141556 Iteration 3 Error: 0.033557 3D Fitting completed. Patch alignment time: 16.30(sec) Local motion has been corrected. Process thread exits. Computational time: 28.750605 sec Total time: 35.776211 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00003hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00003hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.522777s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00003hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.558728s ........................................ >>>>>>TIME<<<<<< FFT: 1.315626s Defocus_U Defocus_V Angle CCC 12037.14 11275.42 82.07 0.047070 Final Values Defocus_U Defocus_V Angle CCC 12038.70 11305.13 81.76 0.088092 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00004hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00004hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 45.43 7.51 Num Hot pixels: 211 Hot pixel threshold: 90.50 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.077816 Iteration 2 Error: 0.124847 Iteration 3 Error: 0.029032 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.25 -0.12 ...... Frame ( 3) shift: -0.50 -0.24 ...... Frame ( 4) shift: -0.74 -0.36 ...... Frame ( 5) shift: -0.99 -0.48 ...... Frame ( 6) shift: -1.11 -0.47 ...... Frame ( 7) shift: -1.09 -0.34 ...... Frame ( 8) shift: -1.08 -0.21 ...... Frame ( 9) shift: -1.02 -0.10 ...... Frame ( 10) shift: -0.91 -0.01 ...... Frame ( 11) shift: -0.80 0.08 ...... Frame ( 12) shift: -0.74 0.18 ...... Frame ( 13) shift: -0.74 0.27 ...... Frame ( 14) shift: -0.74 0.36 ...... Frame ( 15) shift: -0.75 0.42 ...... Frame ( 16) shift: -0.76 0.46 ...... Frame ( 17) shift: -0.77 0.50 ...... Frame ( 18) shift: -0.76 0.57 ...... Frame ( 19) shift: -0.73 0.66 ...... Frame ( 20) shift: -0.71 0.76 ...... Frame ( 21) shift: -0.72 0.83 ...... Frame ( 22) shift: -0.78 0.87 ...... Frame ( 23) shift: -0.83 0.91 ...... Frame ( 24) shift: -0.86 0.93 ...... Frame ( 25) shift: -0.88 0.95 ...... Frame ( 26) shift: -0.89 0.97 ...... Frame ( 27) shift: -0.91 1.00 ...... Frame ( 28) shift: -0.95 1.05 ...... Frame ( 29) shift: -0.98 1.10 ...... Frame ( 30) shift: -1.00 1.13 ...... Frame ( 31) shift: -1.01 1.14 ...... Frame ( 32) shift: -1.03 1.15 ...... Frame ( 33) shift: -1.05 1.16 ...... Frame ( 34) shift: -1.08 1.17 ...... Frame ( 35) shift: -1.10 1.18 ...... Frame ( 36) shift: -1.10 1.20 ...... Frame ( 37) shift: -1.06 1.23 ...... Frame ( 38) shift: -1.03 1.25 ...... Frame ( 39) shift: -0.99 1.28 ...... Frame ( 40) shift: -0.95 1.30 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.589206 Iteration 2 Error: 0.130255 Iteration 3 Error: 0.033834 Align patch 2 23 left Iteration 1 Error: 1.272254 Iteration 2 Error: 0.141162 Iteration 3 Error: 0.025280 Align patch 3 22 left Iteration 1 Error: 1.127598 Iteration 2 Error: 0.226625 Iteration 3 Error: 0.035878 Align patch 4 21 left Iteration 1 Error: 0.909577 Iteration 2 Error: 0.128214 Iteration 3 Error: 0.045402 Align patch 5 20 left Iteration 1 Error: 0.602775 Iteration 2 Error: 0.064757 Iteration 3 Error: 0.008534 Align patch 6 19 left Iteration 1 Error: 3.124460 Iteration 2 Error: 0.312534 Iteration 3 Error: 0.140499 Iteration 4 Error: 0.033792 Align patch 7 18 left Iteration 1 Error: 0.950390 Iteration 2 Error: 0.142655 Iteration 3 Error: 0.029594 Align patch 8 17 left Iteration 1 Error: 0.747741 Iteration 2 Error: 0.104520 Iteration 3 Error: 0.029318 Align patch 9 16 left Iteration 1 Error: 0.736584 Iteration 2 Error: 0.073014 Iteration 3 Error: 0.015169 Align patch 10 15 left Iteration 1 Error: 0.772654 Iteration 2 Error: 0.112987 Iteration 3 Error: 0.036389 Align patch 11 14 left Iteration 1 Error: 0.684295 Iteration 2 Error: 0.098405 Iteration 3 Error: 0.034222 Align patch 12 13 left Iteration 1 Error: 0.736932 Iteration 2 Error: 0.127651 Iteration 3 Error: 0.023167 Align patch 13 12 left Iteration 1 Error: 0.748233 Iteration 2 Error: 0.143491 Iteration 3 Error: 0.064674 Iteration 4 Error: 0.027965 Align patch 14 11 left Iteration 1 Error: 0.619790 Iteration 2 Error: 0.088691 Iteration 3 Error: 0.020901 Align patch 15 10 left Iteration 1 Error: 0.537929 Iteration 2 Error: 0.080326 Iteration 3 Error: 0.010254 Align patch 16 9 left Iteration 1 Error: 1.387367 Iteration 2 Error: 0.408694 Iteration 3 Error: 0.078675 Iteration 4 Error: 0.027938 Align patch 17 8 left Iteration 1 Error: 0.654225 Iteration 2 Error: 0.180838 Iteration 3 Error: 0.054510 Iteration 4 Error: 0.020137 Align patch 18 7 left Iteration 1 Error: 0.857724 Iteration 2 Error: 0.113759 Iteration 3 Error: 0.022982 Align patch 19 6 left Iteration 1 Error: 0.360438 Iteration 2 Error: 0.045139 Align patch 20 5 left Iteration 1 Error: 0.527858 Iteration 2 Error: 0.047493 Align patch 21 4 left Iteration 1 Error: 1.816595 Iteration 2 Error: 0.176738 Iteration 3 Error: 0.031793 Align patch 22 3 left Iteration 1 Error: 0.987863 Iteration 2 Error: 0.120983 Iteration 3 Error: 0.030918 Align patch 23 2 left Iteration 1 Error: 0.800637 Iteration 2 Error: 0.111657 Iteration 3 Error: 0.031134 Align patch 24 1 left Iteration 1 Error: 0.721599 Iteration 2 Error: 0.117171 Iteration 3 Error: 0.032635 Align patch 25 0 left Iteration 1 Error: 0.638556 Iteration 2 Error: 0.096026 Iteration 3 Error: 0.023164 3D Fitting completed. Patch alignment time: 11.24(sec) Local motion has been corrected. Process thread exits. Computational time: 20.808228 sec Total time: 37.062057 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00004hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00004hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.808171s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00004hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.183167s ........................................ >>>>>>TIME<<<<<< FFT: 1.012103s Defocus_U Defocus_V Angle CCC 10521.48 11314.45 13.04 0.055488 Final Values Defocus_U Defocus_V Angle CCC 10530.89 11364.50 13.04 0.099513 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00004hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00004hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 45.87 7.55 Num Hot pixels: 214 Hot pixel threshold: 91.19 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.017918 Iteration 2 Error: 0.128561 Iteration 3 Error: 0.026766 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.30 -0.03 ...... Frame ( 3) shift: -0.59 -0.06 ...... Frame ( 4) shift: -0.89 -0.09 ...... Frame ( 5) shift: -1.19 -0.11 ...... Frame ( 6) shift: -1.31 -0.08 ...... Frame ( 7) shift: -1.25 0.02 ...... Frame ( 8) shift: -1.19 0.11 ...... Frame ( 9) shift: -1.13 0.21 ...... Frame ( 10) shift: -1.06 0.31 ...... Frame ( 11) shift: -0.99 0.40 ...... Frame ( 12) shift: -0.94 0.51 ...... Frame ( 13) shift: -0.91 0.62 ...... Frame ( 14) shift: -0.87 0.74 ...... Frame ( 15) shift: -0.85 0.84 ...... Frame ( 16) shift: -0.83 0.92 ...... Frame ( 17) shift: -0.81 1.01 ...... Frame ( 18) shift: -0.80 1.08 ...... Frame ( 19) shift: -0.80 1.13 ...... Frame ( 20) shift: -0.80 1.18 ...... Frame ( 21) shift: -0.79 1.21 ...... Frame ( 22) shift: -0.77 1.23 ...... Frame ( 23) shift: -0.75 1.26 ...... Frame ( 24) shift: -0.77 1.27 ...... Frame ( 25) shift: -0.84 1.28 ...... Frame ( 26) shift: -0.91 1.28 ...... Frame ( 27) shift: -0.98 1.28 ...... Frame ( 28) shift: -1.04 1.27 ...... Frame ( 29) shift: -1.11 1.26 ...... Frame ( 30) shift: -1.14 1.28 ...... Frame ( 31) shift: -1.14 1.32 ...... Frame ( 32) shift: -1.14 1.37 ...... Frame ( 33) shift: -1.19 1.40 ...... Frame ( 34) shift: -1.30 1.41 ...... Frame ( 35) shift: -1.40 1.42 ...... Frame ( 36) shift: -1.46 1.42 ...... Frame ( 37) shift: -1.46 1.42 ...... Frame ( 38) shift: -1.46 1.42 ...... Frame ( 39) shift: -1.46 1.41 ...... Frame ( 40) shift: -1.46 1.41 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.405082 Iteration 2 Error: 0.228730 Iteration 3 Error: 0.063533 Iteration 4 Error: 0.037152 Align patch 2 23 left Iteration 1 Error: 1.880758 Iteration 2 Error: 0.276424 Iteration 3 Error: 0.064253 Iteration 4 Error: 0.022085 Align patch 3 22 left Iteration 1 Error: 1.321731 Iteration 2 Error: 0.160169 Iteration 3 Error: 0.043921 Align patch 4 21 left Iteration 1 Error: 0.883078 Iteration 2 Error: 0.098015 Iteration 3 Error: 0.021231 Align patch 5 20 left Iteration 1 Error: 0.533160 Iteration 2 Error: 0.073023 Iteration 3 Error: 0.011351 Align patch 6 19 left Iteration 1 Error: 1.052409 Iteration 2 Error: 0.179943 Iteration 3 Error: 0.038251 Align patch 7 18 left Iteration 1 Error: 1.267850 Iteration 2 Error: 0.240180 Iteration 3 Error: 0.051876 Iteration 4 Error: 0.011416 Align patch 8 17 left Iteration 1 Error: 0.851276 Iteration 2 Error: 0.226837 Iteration 3 Error: 0.047588 Align patch 9 16 left Iteration 1 Error: 0.567591 Iteration 2 Error: 0.085126 Iteration 3 Error: 0.025439 Align patch 10 15 left Iteration 1 Error: 0.663487 Iteration 2 Error: 0.090803 Iteration 3 Error: 0.022554 Align patch 11 14 left Iteration 1 Error: 0.993987 Iteration 2 Error: 0.184473 Iteration 3 Error: 0.071098 Iteration 4 Error: 0.027285 Align patch 12 13 left Iteration 1 Error: 1.029610 Iteration 2 Error: 0.107699 Iteration 3 Error: 0.033608 Align patch 13 12 left Iteration 1 Error: 0.680756 Iteration 2 Error: 0.122532 Iteration 3 Error: 0.019947 Align patch 14 11 left Iteration 1 Error: 1.026488 Iteration 2 Error: 0.133546 Iteration 3 Error: 0.030056 Align patch 15 10 left Iteration 1 Error: 0.452833 Iteration 2 Error: 0.060806 Iteration 3 Error: 0.015031 Align patch 16 9 left Iteration 1 Error: 1.055245 Iteration 2 Error: 0.210244 Iteration 3 Error: 0.059130 Iteration 4 Error: 0.018733 Align patch 17 8 left Iteration 1 Error: 0.892394 Iteration 2 Error: 0.151557 Iteration 3 Error: 0.048603 Align patch 18 7 left Iteration 1 Error: 0.959219 Iteration 2 Error: 0.077285 Iteration 3 Error: 0.020793 Align patch 19 6 left Iteration 1 Error: 0.611852 Iteration 2 Error: 0.086983 Iteration 3 Error: 0.024113 Align patch 20 5 left Iteration 1 Error: 0.365192 Iteration 2 Error: 0.053664 Iteration 3 Error: 0.013509 Align patch 21 4 left Iteration 1 Error: 1.305608 Iteration 2 Error: 0.200026 Iteration 3 Error: 0.040491 Align patch 22 3 left Iteration 1 Error: 1.210339 Iteration 2 Error: 0.145248 Iteration 3 Error: 0.039651 Align patch 23 2 left Iteration 1 Error: 0.563859 Iteration 2 Error: 0.119163 Iteration 3 Error: 0.031657 Align patch 24 1 left Iteration 1 Error: 0.984767 Iteration 2 Error: 0.123848 Iteration 3 Error: 0.023642 Align patch 25 0 left Iteration 1 Error: 0.694599 Iteration 2 Error: 0.116592 Iteration 3 Error: 0.020301 3D Fitting completed. Patch alignment time: 11.94(sec) Local motion has been corrected. Process thread exits. Computational time: 23.016613 sec Total time: 44.922077 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00004hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00004hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.062074s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00004hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.737763s ........................................ >>>>>>TIME<<<<<< FFT: 0.990469s Defocus_U Defocus_V Angle CCC 11636.72 11144.53 88.06 0.056777 Final Values Defocus_U Defocus_V Angle CCC 11646.10 11153.92 88.38 0.103373 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00004hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00004hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 46.39 7.53 Num Hot pixels: 234 Hot pixel threshold: 91.59 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.019310 Iteration 2 Error: 0.197298 Iteration 3 Error: 0.034424 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.27 -0.08 ...... Frame ( 3) shift: -0.55 -0.17 ...... Frame ( 4) shift: -0.82 -0.25 ...... Frame ( 5) shift: -1.09 -0.34 ...... Frame ( 6) shift: -1.24 -0.33 ...... Frame ( 7) shift: -1.25 -0.22 ...... Frame ( 8) shift: -1.26 -0.11 ...... Frame ( 9) shift: -1.30 -0.03 ...... Frame ( 10) shift: -1.35 0.03 ...... Frame ( 11) shift: -1.41 0.09 ...... Frame ( 12) shift: -1.43 0.18 ...... Frame ( 13) shift: -1.42 0.30 ...... Frame ( 14) shift: -1.41 0.42 ...... Frame ( 15) shift: -1.38 0.51 ...... Frame ( 16) shift: -1.34 0.58 ...... Frame ( 17) shift: -1.29 0.65 ...... Frame ( 18) shift: -1.29 0.73 ...... Frame ( 19) shift: -1.34 0.82 ...... Frame ( 20) shift: -1.39 0.91 ...... Frame ( 21) shift: -1.38 0.97 ...... Frame ( 22) shift: -1.32 1.00 ...... Frame ( 23) shift: -1.27 1.02 ...... Frame ( 24) shift: -1.23 1.07 ...... Frame ( 25) shift: -1.23 1.12 ...... Frame ( 26) shift: -1.23 1.18 ...... Frame ( 27) shift: -1.21 1.22 ...... Frame ( 28) shift: -1.17 1.25 ...... Frame ( 29) shift: -1.14 1.28 ...... Frame ( 30) shift: -1.16 1.31 ...... Frame ( 31) shift: -1.24 1.34 ...... Frame ( 32) shift: -1.32 1.37 ...... Frame ( 33) shift: -1.34 1.39 ...... Frame ( 34) shift: -1.32 1.39 ...... Frame ( 35) shift: -1.30 1.39 ...... Frame ( 36) shift: -1.32 1.41 ...... Frame ( 37) shift: -1.38 1.43 ...... Frame ( 38) shift: -1.45 1.45 ...... Frame ( 39) shift: -1.51 1.47 ...... Frame ( 40) shift: -1.58 1.49 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.259302 Iteration 2 Error: 0.168576 Iteration 3 Error: 0.072731 Iteration 4 Error: 0.039921 Align patch 2 23 left Iteration 1 Error: 1.778193 Iteration 2 Error: 0.324222 Iteration 3 Error: 0.067735 Iteration 4 Error: 0.027978 Align patch 3 22 left Iteration 1 Error: 1.467541 Iteration 2 Error: 0.186746 Iteration 3 Error: 0.082282 Iteration 4 Error: 0.028557 Align patch 4 21 left Iteration 1 Error: 1.200770 Iteration 2 Error: 0.188915 Iteration 3 Error: 0.043308 Align patch 5 20 left Iteration 1 Error: 0.771688 Iteration 2 Error: 0.112172 Iteration 3 Error: 0.025270 Align patch 6 19 left Iteration 1 Error: 1.725158 Iteration 2 Error: 0.268618 Iteration 3 Error: 0.072590 Iteration 4 Error: 0.019963 Align patch 7 18 left Iteration 1 Error: 1.723345 Iteration 2 Error: 0.220690 Iteration 3 Error: 0.094626 Iteration 4 Error: 0.058625 Iteration 5 Error: 0.023633 Align patch 8 17 left Iteration 1 Error: 0.721275 Iteration 2 Error: 0.182078 Iteration 3 Error: 0.068876 Iteration 4 Error: 0.026647 Align patch 9 16 left Iteration 1 Error: 0.652801 Iteration 2 Error: 0.127892 Iteration 3 Error: 0.032173 Align patch 10 15 left Iteration 1 Error: 0.501862 Iteration 2 Error: 0.067253 Iteration 3 Error: 0.010861 Align patch 11 14 left Iteration 1 Error: 0.779241 Iteration 2 Error: 0.199923 Iteration 3 Error: 0.041928 Align patch 12 13 left Iteration 1 Error: 0.900466 Iteration 2 Error: 0.259454 Iteration 3 Error: 0.050779 Iteration 4 Error: 0.015685 Align patch 13 12 left Iteration 1 Error: 0.687921 Iteration 2 Error: 0.229145 Iteration 3 Error: 0.078398 Iteration 4 Error: 0.039597 Align patch 14 11 left Iteration 1 Error: 0.703968 Iteration 2 Error: 0.166430 Iteration 3 Error: 0.038078 Align patch 15 10 left Iteration 1 Error: 0.677696 Iteration 2 Error: 0.090389 Iteration 3 Error: 0.023250 Align patch 16 9 left Iteration 1 Error: 1.492840 Iteration 2 Error: 0.346132 Iteration 3 Error: 0.102679 Iteration 4 Error: 0.034890 Align patch 17 8 left Iteration 1 Error: 0.958421 Iteration 2 Error: 0.146568 Iteration 3 Error: 0.056063 Iteration 4 Error: 0.021071 Align patch 18 7 left Iteration 1 Error: 1.332851 Iteration 2 Error: 0.198425 Iteration 3 Error: 0.032689 Align patch 19 6 left Iteration 1 Error: 0.546145 Iteration 2 Error: 0.063524 Iteration 3 Error: 0.029253 Align patch 20 5 left Iteration 1 Error: 0.870403 Iteration 2 Error: 0.074120 Iteration 3 Error: 0.013204 Align patch 21 4 left Iteration 1 Error: 1.532512 Iteration 2 Error: 0.287698 Iteration 3 Error: 0.055516 Iteration 4 Error: 0.020591 Align patch 22 3 left Iteration 1 Error: 1.241179 Iteration 2 Error: 0.191519 Iteration 3 Error: 0.039659 Align patch 23 2 left Iteration 1 Error: 0.601364 Iteration 2 Error: 0.091818 Iteration 3 Error: 0.021779 Align patch 24 1 left Iteration 1 Error: 0.637660 Iteration 2 Error: 0.053277 Iteration 3 Error: 0.015327 Align patch 25 0 left Iteration 1 Error: 1.051628 Iteration 2 Error: 0.132243 Iteration 3 Error: 0.029232 3D Fitting completed. Patch alignment time: 12.55(sec) Local motion has been corrected. Process thread exits. Computational time: 24.524216 sec Total time: 45.796890 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00004hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00004hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.046786s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00004hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.332977s ........................................ >>>>>>TIME<<<<<< FFT: 0.906755s Defocus_U Defocus_V Angle CCC 10673.83 11548.83 7.05 0.054076 Final Values Defocus_U Defocus_V Angle CCC 10681.65 11581.65 8.33 0.099348 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00004hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00004hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.001e-01 CC threshold: 0.735 Mean Std: 46.07 7.52 Num Hot pixels: 223 Hot pixel threshold: 91.16 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.905098 Iteration 2 Error: 0.071762 Iteration 3 Error: 0.018049 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.29 -0.11 ...... Frame ( 3) shift: -0.59 -0.22 ...... Frame ( 4) shift: -0.88 -0.33 ...... Frame ( 5) shift: -1.18 -0.45 ...... Frame ( 6) shift: -1.31 -0.42 ...... Frame ( 7) shift: -1.29 -0.26 ...... Frame ( 8) shift: -1.27 -0.09 ...... Frame ( 9) shift: -1.21 0.03 ...... Frame ( 10) shift: -1.12 0.11 ...... Frame ( 11) shift: -1.03 0.20 ...... Frame ( 12) shift: -0.97 0.28 ...... Frame ( 13) shift: -0.95 0.35 ...... Frame ( 14) shift: -0.92 0.42 ...... Frame ( 15) shift: -0.93 0.48 ...... Frame ( 16) shift: -0.97 0.52 ...... Frame ( 17) shift: -1.00 0.57 ...... Frame ( 18) shift: -0.99 0.59 ...... Frame ( 19) shift: -0.92 0.58 ...... Frame ( 20) shift: -0.85 0.58 ...... Frame ( 21) shift: -0.81 0.57 ...... Frame ( 22) shift: -0.79 0.55 ...... Frame ( 23) shift: -0.78 0.53 ...... Frame ( 24) shift: -0.77 0.52 ...... Frame ( 25) shift: -0.76 0.50 ...... Frame ( 26) shift: -0.75 0.49 ...... Frame ( 27) shift: -0.73 0.48 ...... Frame ( 28) shift: -0.69 0.47 ...... Frame ( 29) shift: -0.65 0.47 ...... Frame ( 30) shift: -0.64 0.46 ...... Frame ( 31) shift: -0.67 0.44 ...... Frame ( 32) shift: -0.70 0.42 ...... Frame ( 33) shift: -0.74 0.40 ...... Frame ( 34) shift: -0.78 0.37 ...... Frame ( 35) shift: -0.83 0.34 ...... Frame ( 36) shift: -0.85 0.37 ...... Frame ( 37) shift: -0.85 0.46 ...... Frame ( 38) shift: -0.84 0.55 ...... Frame ( 39) shift: -0.84 0.64 ...... Frame ( 40) shift: -0.84 0.74 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.552973 Iteration 2 Error: 0.190697 Iteration 3 Error: 0.058684 Iteration 4 Error: 0.017048 Align patch 2 23 left Iteration 1 Error: 1.177466 Iteration 2 Error: 0.105034 Iteration 3 Error: 0.034690 Align patch 3 22 left Iteration 1 Error: 1.196571 Iteration 2 Error: 0.088340 Iteration 3 Error: 0.019818 Align patch 4 21 left Iteration 1 Error: 0.650643 Iteration 2 Error: 0.119037 Iteration 3 Error: 0.031952 Align patch 5 20 left Iteration 1 Error: 0.715081 Iteration 2 Error: 0.133661 Iteration 3 Error: 0.028854 Align patch 6 19 left Iteration 1 Error: 0.874432 Iteration 2 Error: 0.235050 Iteration 3 Error: 0.040528 Align patch 7 18 left Iteration 1 Error: 0.624078 Iteration 2 Error: 0.173356 Iteration 3 Error: 0.052838 Iteration 4 Error: 0.018288 Align patch 8 17 left Iteration 1 Error: 0.591188 Iteration 2 Error: 0.086060 Iteration 3 Error: 0.022110 Align patch 9 16 left Iteration 1 Error: 0.587915 Iteration 2 Error: 0.098498 Iteration 3 Error: 0.032903 Align patch 10 15 left Iteration 1 Error: 0.727410 Iteration 2 Error: 0.085735 Iteration 3 Error: 0.014799 Align patch 11 14 left Iteration 1 Error: 1.028887 Iteration 2 Error: 0.213802 Iteration 3 Error: 0.045857 Align patch 12 13 left Iteration 1 Error: 1.404696 Iteration 2 Error: 0.135939 Iteration 3 Error: 0.031369 Align patch 13 12 left Iteration 1 Error: 1.043198 Iteration 2 Error: 0.123204 Iteration 3 Error: 0.017239 Align patch 14 11 left Iteration 1 Error: 0.691810 Iteration 2 Error: 0.081093 Iteration 3 Error: 0.012185 Align patch 15 10 left Iteration 1 Error: 0.625988 Iteration 2 Error: 0.065667 Iteration 3 Error: 0.012268 Align patch 16 9 left Iteration 1 Error: 1.154013 Iteration 2 Error: 0.172209 Iteration 3 Error: 0.030602 Align patch 17 8 left Iteration 1 Error: 0.622392 Iteration 2 Error: 0.101852 Iteration 3 Error: 0.029838 Align patch 18 7 left Iteration 1 Error: 0.504746 Iteration 2 Error: 0.056561 Iteration 3 Error: 0.011888 Align patch 19 6 left Iteration 1 Error: 0.902564 Iteration 2 Error: 0.121062 Iteration 3 Error: 0.032931 Align patch 20 5 left Iteration 1 Error: 0.661894 Iteration 2 Error: 0.064057 Iteration 3 Error: 0.017638 Align patch 21 4 left Iteration 1 Error: 1.146284 Iteration 2 Error: 0.177177 Iteration 3 Error: 0.034416 Align patch 22 3 left Iteration 1 Error: 0.863432 Iteration 2 Error: 0.108049 Iteration 3 Error: 0.028032 Align patch 23 2 left Iteration 1 Error: 0.986640 Iteration 2 Error: 0.146868 Iteration 3 Error: 0.019124 Align patch 24 1 left Iteration 1 Error: 0.810894 Iteration 2 Error: 0.071961 Iteration 3 Error: 0.014114 Align patch 25 0 left Iteration 1 Error: 0.641300 Iteration 2 Error: 0.067473 Iteration 3 Error: 0.017011 3D Fitting completed. Patch alignment time: 12.99(sec) Local motion has been corrected. Process thread exits. Computational time: 24.874971 sec Total time: 46.425713 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00004hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00004hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.817242s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00004hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 4.389769s ........................................ >>>>>>TIME<<<<<< FFT: 1.115160s Defocus_U Defocus_V Angle CCC 12863.29 12164.05 84.15 0.053720 Final Values Defocus_U Defocus_V Angle CCC 12863.30 12167.18 83.84 0.096471 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00005hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00005hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 42.74 7.23 Num Hot pixels: 202 Hot pixel threshold: 86.13 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.673995 Iteration 2 Error: 0.254356 Iteration 3 Error: 0.076336 Iteration 4 Error: 0.021948 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.16 0.10 ...... Frame ( 3) shift: -0.33 0.20 ...... Frame ( 4) shift: -0.49 0.30 ...... Frame ( 5) shift: -0.66 0.40 ...... Frame ( 6) shift: -0.69 0.53 ...... Frame ( 7) shift: -0.59 0.70 ...... Frame ( 8) shift: -0.49 0.86 ...... Frame ( 9) shift: -0.42 0.99 ...... Frame ( 10) shift: -0.37 1.10 ...... Frame ( 11) shift: -0.32 1.21 ...... Frame ( 12) shift: -0.28 1.33 ...... Frame ( 13) shift: -0.25 1.46 ...... Frame ( 14) shift: -0.22 1.60 ...... Frame ( 15) shift: -0.23 1.71 ...... Frame ( 16) shift: -0.28 1.81 ...... Frame ( 17) shift: -0.33 1.90 ...... Frame ( 18) shift: -0.34 1.98 ...... Frame ( 19) shift: -0.30 2.05 ...... Frame ( 20) shift: -0.27 2.12 ...... Frame ( 21) shift: -0.21 2.19 ...... Frame ( 22) shift: -0.15 2.24 ...... Frame ( 23) shift: -0.08 2.30 ...... Frame ( 24) shift: -0.05 2.37 ...... Frame ( 25) shift: -0.05 2.46 ...... Frame ( 26) shift: -0.04 2.54 ...... Frame ( 27) shift: -0.04 2.64 ...... Frame ( 28) shift: -0.03 2.76 ...... Frame ( 29) shift: -0.02 2.88 ...... Frame ( 30) shift: 0.01 2.98 ...... Frame ( 31) shift: 0.06 3.05 ...... Frame ( 32) shift: 0.11 3.12 ...... Frame ( 33) shift: 0.13 3.22 ...... Frame ( 34) shift: 0.13 3.33 ...... Frame ( 35) shift: 0.13 3.44 ...... Frame ( 36) shift: 0.13 3.52 ...... Frame ( 37) shift: 0.13 3.58 ...... Frame ( 38) shift: 0.12 3.65 ...... Frame ( 39) shift: 0.12 3.71 ...... Frame ( 40) shift: 0.11 3.77 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.865874 Iteration 2 Error: 0.256155 Iteration 3 Error: 0.169083 Iteration 4 Error: 0.053462 Iteration 5 Error: 0.051724 Align patch 1 24 left Iteration 1 Error: 1.361961 Iteration 2 Error: 0.192563 Iteration 3 Error: 0.062855 Iteration 4 Error: 0.025701 Align patch 2 23 left Iteration 1 Error: 0.798343 Iteration 2 Error: 0.157858 Iteration 3 Error: 0.076933 Iteration 4 Error: 0.055592 Iteration 5 Error: 0.022909 Align patch 3 22 left Iteration 1 Error: 1.200061 Iteration 2 Error: 0.136160 Iteration 3 Error: 0.056870 Iteration 4 Error: 0.016282 Align patch 4 21 left Iteration 1 Error: 0.931269 Iteration 2 Error: 0.167119 Iteration 3 Error: 0.028092 Align patch 5 20 left Iteration 1 Error: 0.686553 Iteration 2 Error: 0.156441 Iteration 3 Error: 0.041126 Align patch 6 19 left Iteration 1 Error: 1.121460 Iteration 2 Error: 0.177484 Iteration 3 Error: 0.033919 Align patch 7 18 left Iteration 1 Error: 1.008087 Iteration 2 Error: 0.318405 Iteration 3 Error: 0.138482 Iteration 4 Error: 0.062683 Iteration 5 Error: 0.033410 Align patch 8 17 left Iteration 1 Error: 0.909497 Iteration 2 Error: 0.087207 Iteration 3 Error: 0.030027 Align patch 9 16 left Iteration 1 Error: 0.957270 Iteration 2 Error: 0.147031 Iteration 3 Error: 0.034312 Align patch 10 15 left Iteration 1 Error: 0.550665 Iteration 2 Error: 0.172084 Iteration 3 Error: 0.049646 Align patch 11 14 left Iteration 1 Error: 0.812397 Iteration 2 Error: 0.232548 Iteration 3 Error: 0.063065 Iteration 4 Error: 0.021599 Align patch 12 13 left Iteration 1 Error: 0.621407 Iteration 2 Error: 0.096702 Iteration 3 Error: 0.041896 Align patch 13 12 left Iteration 1 Error: 0.655455 Iteration 2 Error: 0.110621 Iteration 3 Error: 0.033643 Align patch 14 11 left Iteration 1 Error: 0.901385 Iteration 2 Error: 0.200628 Iteration 3 Error: 0.040247 Align patch 15 10 left Iteration 1 Error: 0.581050 Iteration 2 Error: 0.087922 Iteration 3 Error: 0.028809 Align patch 16 9 left Iteration 1 Error: 0.639994 Iteration 2 Error: 0.168190 Iteration 3 Error: 0.047597 Align patch 17 8 left Iteration 1 Error: 0.561449 Iteration 2 Error: 0.098082 Iteration 3 Error: 0.022593 Align patch 18 7 left Iteration 1 Error: 0.523110 Iteration 2 Error: 0.187818 Iteration 3 Error: 0.051409 Iteration 4 Error: 0.019197 Align patch 19 6 left Iteration 1 Error: 0.687042 Iteration 2 Error: 0.105550 Iteration 3 Error: 0.036433 Align patch 20 5 left Iteration 1 Error: 0.620169 Iteration 2 Error: 0.073819 Iteration 3 Error: 0.016624 Align patch 21 4 left Iteration 1 Error: 0.610750 Iteration 2 Error: 0.186124 Iteration 3 Error: 0.087720 Iteration 4 Error: 0.017261 Align patch 22 3 left Iteration 1 Error: 0.727739 Iteration 2 Error: 0.144930 Iteration 3 Error: 0.035561 Align patch 23 2 left Iteration 1 Error: 0.644316 Iteration 2 Error: 0.142591 Iteration 3 Error: 0.041432 Align patch 24 1 left Iteration 1 Error: 0.585269 Iteration 2 Error: 0.126117 Iteration 3 Error: 0.031449 Align patch 25 0 left Iteration 1 Error: 0.797750 Iteration 2 Error: 0.156621 Iteration 3 Error: 0.038339 3D Fitting completed. Patch alignment time: 14.11(sec) Local motion has been corrected. Process thread exits. Computational time: 27.528299 sec Total time: 47.040882 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00005hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00005hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.666042s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00005hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 4.186841s ........................................ >>>>>>TIME<<<<<< FFT: 1.051289s Defocus_U Defocus_V Angle CCC 12914.06 13796.88 11.55 0.053222 Final Values Defocus_U Defocus_V Angle CCC 12939.07 13796.88 11.87 0.088980 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00005hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00005hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 44.00 7.39 Num Hot pixels: 226 Hot pixel threshold: 88.34 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.544353 Iteration 2 Error: 0.265016 Iteration 3 Error: 0.074837 Iteration 4 Error: 0.036549 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.26 0.05 ...... Frame ( 3) shift: -0.52 0.10 ...... Frame ( 4) shift: -0.78 0.15 ...... Frame ( 5) shift: -1.04 0.20 ...... Frame ( 6) shift: -1.17 0.29 ...... Frame ( 7) shift: -1.17 0.40 ...... Frame ( 8) shift: -1.17 0.51 ...... Frame ( 9) shift: -1.17 0.63 ...... Frame ( 10) shift: -1.19 0.73 ...... Frame ( 11) shift: -1.20 0.84 ...... Frame ( 12) shift: -1.20 0.98 ...... Frame ( 13) shift: -1.19 1.15 ...... Frame ( 14) shift: -1.17 1.32 ...... Frame ( 15) shift: -1.18 1.47 ...... Frame ( 16) shift: -1.21 1.59 ...... Frame ( 17) shift: -1.24 1.71 ...... Frame ( 18) shift: -1.21 1.83 ...... Frame ( 19) shift: -1.14 1.95 ...... Frame ( 20) shift: -1.07 2.06 ...... Frame ( 21) shift: -1.07 2.17 ...... Frame ( 22) shift: -1.14 2.28 ...... Frame ( 23) shift: -1.21 2.39 ...... Frame ( 24) shift: -1.25 2.43 ...... Frame ( 25) shift: -1.27 2.41 ...... Frame ( 26) shift: -1.29 2.39 ...... Frame ( 27) shift: -1.31 2.38 ...... Frame ( 28) shift: -1.33 2.39 ...... Frame ( 29) shift: -1.36 2.40 ...... Frame ( 30) shift: -1.37 2.46 ...... Frame ( 31) shift: -1.38 2.58 ...... Frame ( 32) shift: -1.39 2.69 ...... Frame ( 33) shift: -1.40 2.75 ...... Frame ( 34) shift: -1.41 2.75 ...... Frame ( 35) shift: -1.42 2.75 ...... Frame ( 36) shift: -1.44 2.77 ...... Frame ( 37) shift: -1.47 2.81 ...... Frame ( 38) shift: -1.50 2.85 ...... Frame ( 39) shift: -1.53 2.89 ...... Frame ( 40) shift: -1.56 2.92 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.381420 Iteration 2 Error: 0.197886 Iteration 3 Error: 0.047465 Align patch 2 23 left Iteration 1 Error: 1.535511 Iteration 2 Error: 0.213062 Iteration 3 Error: 0.066673 Iteration 4 Error: 0.024031 Align patch 3 22 left Iteration 1 Error: 0.810095 Iteration 2 Error: 0.224926 Iteration 3 Error: 0.036070 Align patch 4 21 left Iteration 1 Error: 0.601570 Iteration 2 Error: 0.091833 Iteration 3 Error: 0.017468 Align patch 5 20 left Iteration 1 Error: 0.808727 Iteration 2 Error: 0.104629 Iteration 3 Error: 0.018107 Align patch 6 19 left Iteration 1 Error: 0.648280 Iteration 2 Error: 0.111341 Iteration 3 Error: 0.050159 Iteration 4 Error: 0.015909 Align patch 7 18 left Iteration 1 Error: 0.829103 Iteration 2 Error: 0.184223 Iteration 3 Error: 0.039129 Align patch 8 17 left Iteration 1 Error: 0.650214 Iteration 2 Error: 0.152247 Iteration 3 Error: 0.046030 Align patch 9 16 left Iteration 1 Error: 0.764565 Iteration 2 Error: 0.162026 Iteration 3 Error: 0.070168 Iteration 4 Error: 0.030636 Align patch 10 15 left Iteration 1 Error: 0.568814 Iteration 2 Error: 0.103503 Iteration 3 Error: 0.027052 Align patch 11 14 left Iteration 1 Error: 1.758718 Iteration 2 Error: 0.408035 Iteration 3 Error: 0.253912 Iteration 4 Error: 0.118783 Iteration 5 Error: 0.109595 Align patch 11 14 left Iteration 1 Error: 1.257904 Iteration 2 Error: 0.176187 Iteration 3 Error: 0.072280 Iteration 4 Error: 0.029824 Align patch 12 13 left Iteration 1 Error: 1.676116 Iteration 2 Error: 0.307375 Iteration 3 Error: 0.093244 Iteration 4 Error: 0.027597 Align patch 13 12 left Iteration 1 Error: 0.714295 Iteration 2 Error: 0.095381 Iteration 3 Error: 0.022843 Align patch 14 11 left Iteration 1 Error: 0.507422 Iteration 2 Error: 0.084523 Iteration 3 Error: 0.023295 Align patch 15 10 left Iteration 1 Error: 0.615566 Iteration 2 Error: 0.120862 Iteration 3 Error: 0.044983 Align patch 16 9 left Iteration 1 Error: 0.945705 Iteration 2 Error: 0.341329 Iteration 3 Error: 0.110744 Iteration 4 Error: 0.049443 Align patch 17 8 left Iteration 1 Error: 0.716296 Iteration 2 Error: 0.103817 Iteration 3 Error: 0.033381 Align patch 18 7 left Iteration 1 Error: 1.198727 Iteration 2 Error: 0.165969 Iteration 3 Error: 0.053785 Iteration 4 Error: 0.011938 Align patch 19 6 left Iteration 1 Error: 1.057690 Iteration 2 Error: 0.163378 Iteration 3 Error: 0.037161 Align patch 20 5 left Iteration 1 Error: 0.632864 Iteration 2 Error: 0.125555 Iteration 3 Error: 0.025239 Align patch 21 4 left Iteration 1 Error: 1.184143 Iteration 2 Error: 0.192309 Iteration 3 Error: 0.061601 Iteration 4 Error: 0.022284 Align patch 22 3 left Iteration 1 Error: 1.147120 Iteration 2 Error: 0.238694 Iteration 3 Error: 0.077014 Iteration 4 Error: 0.021523 Align patch 23 2 left Iteration 1 Error: 1.121695 Iteration 2 Error: 0.146363 Iteration 3 Error: 0.032025 Align patch 24 1 left Iteration 1 Error: 0.673700 Iteration 2 Error: 0.088985 Iteration 3 Error: 0.019273 Align patch 25 0 left Iteration 1 Error: 0.694474 Iteration 2 Error: 0.090884 Iteration 3 Error: 0.018320 3D Fitting completed. Patch alignment time: 14.45(sec) Local motion has been corrected. Process thread exits. Computational time: 28.680553 sec Total time: 52.494598 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00005hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00005hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.781217s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00005hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.615548s ........................................ >>>>>>TIME<<<<<< FFT: 1.001894s Defocus_U Defocus_V Angle CCC 10447.30 9970.70 89.85 0.050796 Final Values Defocus_U Defocus_V Angle CCC 9986.33 10453.55 0.17 0.092699 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00005hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00005hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 44.73 7.37 Num Hot pixels: 227 Hot pixel threshold: 88.94 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.041446 Iteration 2 Error: 0.080502 Iteration 3 Error: 0.014405 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.26 0.06 ...... Frame ( 3) shift: -0.53 0.11 ...... Frame ( 4) shift: -0.79 0.17 ...... Frame ( 5) shift: -1.06 0.22 ...... Frame ( 6) shift: -1.18 0.28 ...... Frame ( 7) shift: -1.16 0.34 ...... Frame ( 8) shift: -1.13 0.40 ...... Frame ( 9) shift: -1.12 0.43 ...... Frame ( 10) shift: -1.12 0.40 ...... Frame ( 11) shift: -1.11 0.38 ...... Frame ( 12) shift: -1.10 0.42 ...... Frame ( 13) shift: -1.08 0.52 ...... Frame ( 14) shift: -1.05 0.62 ...... Frame ( 15) shift: -1.10 0.68 ...... Frame ( 16) shift: -1.22 0.69 ...... Frame ( 17) shift: -1.35 0.71 ...... Frame ( 18) shift: -1.41 0.73 ...... Frame ( 19) shift: -1.41 0.76 ...... Frame ( 20) shift: -1.40 0.78 ...... Frame ( 21) shift: -1.38 0.78 ...... Frame ( 22) shift: -1.35 0.77 ...... Frame ( 23) shift: -1.31 0.76 ...... Frame ( 24) shift: -1.31 0.74 ...... Frame ( 25) shift: -1.36 0.71 ...... Frame ( 26) shift: -1.41 0.68 ...... Frame ( 27) shift: -1.45 0.66 ...... Frame ( 28) shift: -1.48 0.63 ...... Frame ( 29) shift: -1.52 0.61 ...... Frame ( 30) shift: -1.52 0.63 ...... Frame ( 31) shift: -1.49 0.69 ...... Frame ( 32) shift: -1.47 0.75 ...... Frame ( 33) shift: -1.46 0.79 ...... Frame ( 34) shift: -1.48 0.80 ...... Frame ( 35) shift: -1.50 0.81 ...... Frame ( 36) shift: -1.53 0.85 ...... Frame ( 37) shift: -1.55 0.90 ...... Frame ( 38) shift: -1.58 0.95 ...... Frame ( 39) shift: -1.60 1.00 ...... Frame ( 40) shift: -1.63 1.05 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.532818 Iteration 2 Error: 0.164652 Iteration 3 Error: 0.031140 Align patch 2 23 left Iteration 1 Error: 1.796797 Iteration 2 Error: 0.221836 Iteration 3 Error: 0.039068 Align patch 3 22 left Iteration 1 Error: 0.909254 Iteration 2 Error: 0.128732 Iteration 3 Error: 0.032815 Align patch 4 21 left Iteration 1 Error: 0.604980 Iteration 2 Error: 0.151128 Iteration 3 Error: 0.037085 Align patch 5 20 left Iteration 1 Error: 0.862618 Iteration 2 Error: 0.141219 Iteration 3 Error: 0.025451 Align patch 6 19 left Iteration 1 Error: 0.897207 Iteration 2 Error: 0.262536 Iteration 3 Error: 0.036078 Align patch 7 18 left Iteration 1 Error: 0.556500 Iteration 2 Error: 0.098934 Iteration 3 Error: 0.019657 Align patch 8 17 left Iteration 1 Error: 1.289745 Iteration 2 Error: 0.149847 Iteration 3 Error: 0.040614 Align patch 9 16 left Iteration 1 Error: 0.922759 Iteration 2 Error: 0.215695 Iteration 3 Error: 0.050510 Iteration 4 Error: 0.037248 Align patch 10 15 left Iteration 1 Error: 0.791991 Iteration 2 Error: 0.079309 Iteration 3 Error: 0.020893 Align patch 11 14 left Iteration 1 Error: 0.831757 Iteration 2 Error: 0.141456 Iteration 3 Error: 0.046733 Align patch 12 13 left Iteration 1 Error: 0.753678 Iteration 2 Error: 0.080191 Iteration 3 Error: 0.019092 Align patch 13 12 left Iteration 1 Error: 0.599940 Iteration 2 Error: 0.145385 Iteration 3 Error: 0.028776 Align patch 14 11 left Iteration 1 Error: 0.692213 Iteration 2 Error: 0.123414 Iteration 3 Error: 0.017229 Align patch 15 10 left Iteration 1 Error: 0.865216 Iteration 2 Error: 0.114179 Iteration 3 Error: 0.027964 Align patch 16 9 left Iteration 1 Error: 0.930627 Iteration 2 Error: 0.154129 Iteration 3 Error: 0.030959 Align patch 17 8 left Iteration 1 Error: 0.696109 Iteration 2 Error: 0.098411 Iteration 3 Error: 0.019068 Align patch 18 7 left Iteration 1 Error: 0.832648 Iteration 2 Error: 0.150476 Iteration 3 Error: 0.032557 Align patch 19 6 left Iteration 1 Error: 0.734981 Iteration 2 Error: 0.106685 Iteration 3 Error: 0.030769 Align patch 20 5 left Iteration 1 Error: 0.957884 Iteration 2 Error: 0.146462 Iteration 3 Error: 0.017485 Align patch 21 4 left Iteration 1 Error: 0.852269 Iteration 2 Error: 0.149815 Iteration 3 Error: 0.023598 Align patch 22 3 left Iteration 1 Error: 0.885485 Iteration 2 Error: 0.125229 Iteration 3 Error: 0.019159 Align patch 23 2 left Iteration 1 Error: 0.727212 Iteration 2 Error: 0.072027 Iteration 3 Error: 0.012153 Align patch 24 1 left Iteration 1 Error: 0.997421 Iteration 2 Error: 0.136367 Iteration 3 Error: 0.032491 Align patch 25 0 left Iteration 1 Error: 0.873144 Iteration 2 Error: 0.062575 Iteration 3 Error: 0.014633 3D Fitting completed. Patch alignment time: 12.18(sec) Local motion has been corrected. Process thread exits. Computational time: 29.756636 sec Total time: 50.810947 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00005hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00005hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.893241s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00005hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.942608s ........................................ >>>>>>TIME<<<<<< FFT: 1.202999s Defocus_U Defocus_V Angle CCC 13595.70 14544.92 4.35 0.050774 Final Values Defocus_U Defocus_V Angle CCC 13609.77 14546.48 4.04 0.088146 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00005hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00005hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 44.71 7.43 Num Hot pixels: 209 Hot pixel threshold: 89.32 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.420650 Iteration 2 Error: 0.133556 Iteration 3 Error: 0.027010 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.30 0.06 ...... Frame ( 3) shift: -0.60 0.12 ...... Frame ( 4) shift: -0.91 0.18 ...... Frame ( 5) shift: -1.21 0.23 ...... Frame ( 6) shift: -1.37 0.31 ...... Frame ( 7) shift: -1.37 0.41 ...... Frame ( 8) shift: -1.38 0.51 ...... Frame ( 9) shift: -1.37 0.62 ...... Frame ( 10) shift: -1.35 0.73 ...... Frame ( 11) shift: -1.33 0.85 ...... Frame ( 12) shift: -1.31 0.91 ...... Frame ( 13) shift: -1.32 0.91 ...... Frame ( 14) shift: -1.32 0.92 ...... Frame ( 15) shift: -1.35 0.95 ...... Frame ( 16) shift: -1.40 1.02 ...... Frame ( 17) shift: -1.46 1.08 ...... Frame ( 18) shift: -1.52 1.12 ...... Frame ( 19) shift: -1.59 1.14 ...... Frame ( 20) shift: -1.66 1.17 ...... Frame ( 21) shift: -1.70 1.20 ...... Frame ( 22) shift: -1.70 1.24 ...... Frame ( 23) shift: -1.70 1.27 ...... Frame ( 24) shift: -1.74 1.29 ...... Frame ( 25) shift: -1.81 1.28 ...... Frame ( 26) shift: -1.88 1.27 ...... Frame ( 27) shift: -1.93 1.27 ...... Frame ( 28) shift: -1.96 1.29 ...... Frame ( 29) shift: -1.99 1.31 ...... Frame ( 30) shift: -2.01 1.32 ...... Frame ( 31) shift: -2.02 1.34 ...... Frame ( 32) shift: -2.02 1.36 ...... Frame ( 33) shift: -2.04 1.37 ...... Frame ( 34) shift: -2.08 1.38 ...... Frame ( 35) shift: -2.13 1.39 ...... Frame ( 36) shift: -2.15 1.39 ...... Frame ( 37) shift: -2.15 1.38 ...... Frame ( 38) shift: -2.16 1.38 ...... Frame ( 39) shift: -2.16 1.38 ...... Frame ( 40) shift: -2.17 1.37 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.529800 Iteration 2 Error: 0.445079 Iteration 3 Error: 0.185579 Iteration 4 Error: 0.054234 Iteration 5 Error: 0.020460 Align patch 2 23 left Iteration 1 Error: 1.285715 Iteration 2 Error: 0.178431 Iteration 3 Error: 0.040811 Align patch 3 22 left Iteration 1 Error: 0.925350 Iteration 2 Error: 0.141212 Iteration 3 Error: 0.031197 Align patch 4 21 left Iteration 1 Error: 0.409120 Iteration 2 Error: 0.052725 Iteration 3 Error: 0.011362 Align patch 5 20 left Iteration 1 Error: 1.146488 Iteration 2 Error: 0.072460 Iteration 3 Error: 0.009602 Align patch 6 19 left Iteration 1 Error: 0.747793 Iteration 2 Error: 0.092783 Iteration 3 Error: 0.023371 Align patch 7 18 left Iteration 1 Error: 0.944496 Iteration 2 Error: 0.181101 Iteration 3 Error: 0.039564 Align patch 8 17 left Iteration 1 Error: 0.572723 Iteration 2 Error: 0.145635 Iteration 3 Error: 0.025996 Align patch 9 16 left Iteration 1 Error: 0.620545 Iteration 2 Error: 0.105064 Iteration 3 Error: 0.017744 Align patch 10 15 left Iteration 1 Error: 0.745404 Iteration 2 Error: 0.128699 Iteration 3 Error: 0.029942 Align patch 11 14 left Iteration 1 Error: 0.650813 Iteration 2 Error: 0.204684 Iteration 3 Error: 0.064484 Iteration 4 Error: 0.028757 Align patch 12 13 left Iteration 1 Error: 1.016481 Iteration 2 Error: 0.229106 Iteration 3 Error: 0.086064 Iteration 4 Error: 0.040081 Align patch 13 12 left Iteration 1 Error: 0.589903 Iteration 2 Error: 0.139065 Iteration 3 Error: 0.041772 Align patch 14 11 left Iteration 1 Error: 0.517585 Iteration 2 Error: 0.084702 Iteration 3 Error: 0.029074 Align patch 15 10 left Iteration 1 Error: 0.501801 Iteration 2 Error: 0.097128 Iteration 3 Error: 0.023177 Align patch 16 9 left Iteration 1 Error: 0.962680 Iteration 2 Error: 0.247012 Iteration 3 Error: 0.089771 Iteration 4 Error: 0.026101 Align patch 17 8 left Iteration 1 Error: 0.826087 Iteration 2 Error: 0.144828 Iteration 3 Error: 0.037519 Align patch 18 7 left Iteration 1 Error: 0.502265 Iteration 2 Error: 0.110378 Iteration 3 Error: 0.022655 Align patch 19 6 left Iteration 1 Error: 0.659119 Iteration 2 Error: 0.079709 Iteration 3 Error: 0.017618 Align patch 20 5 left Iteration 1 Error: 0.382784 Iteration 2 Error: 0.046818 Align patch 21 4 left Iteration 1 Error: 1.078542 Iteration 2 Error: 0.192255 Iteration 3 Error: 0.030722 Align patch 22 3 left Iteration 1 Error: 1.384514 Iteration 2 Error: 0.157315 Iteration 3 Error: 0.036036 Align patch 23 2 left Iteration 1 Error: 0.609740 Iteration 2 Error: 0.070184 Iteration 3 Error: 0.018632 Align patch 24 1 left Iteration 1 Error: 0.668324 Iteration 2 Error: 0.105703 Iteration 3 Error: 0.018973 Align patch 25 0 left Iteration 1 Error: 0.486134 Iteration 2 Error: 0.053038 Iteration 3 Error: 0.009944 3D Fitting completed. Patch alignment time: 12.18(sec) Local motion has been corrected. Process thread exits. Computational time: 27.834126 sec Total time: 51.230392 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00005hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00005hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.820005s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00005hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 6.113819s ........................................ >>>>>>TIME<<<<<< FFT: 1.217095s Defocus_U Defocus_V Angle CCC 15242.63 14534.71 81.43 0.054849 Final Values Defocus_U Defocus_V Angle CCC 15252.01 14531.59 82.38 0.094742 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00006hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00006hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.994e-02 CC threshold: 0.734 Mean Std: 39.04 6.65 Num Hot pixels: 222 Hot pixel threshold: 78.92 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.146847 Iteration 2 Error: 0.271482 Iteration 3 Error: 0.085245 Iteration 4 Error: 0.029725 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.14 -0.12 ...... Frame ( 3) shift: -0.29 -0.25 ...... Frame ( 4) shift: -0.43 -0.37 ...... Frame ( 5) shift: -0.57 -0.49 ...... Frame ( 6) shift: -0.63 -0.58 ...... Frame ( 7) shift: -0.60 -0.63 ...... Frame ( 8) shift: -0.58 -0.69 ...... Frame ( 9) shift: -0.51 -0.73 ...... Frame ( 10) shift: -0.42 -0.76 ...... Frame ( 11) shift: -0.32 -0.79 ...... Frame ( 12) shift: -0.21 -0.79 ...... Frame ( 13) shift: -0.07 -0.77 ...... Frame ( 14) shift: 0.06 -0.74 ...... Frame ( 15) shift: 0.13 -0.69 ...... Frame ( 16) shift: 0.12 -0.61 ...... Frame ( 17) shift: 0.12 -0.53 ...... Frame ( 18) shift: 0.17 -0.46 ...... Frame ( 19) shift: 0.28 -0.40 ...... Frame ( 20) shift: 0.38 -0.34 ...... Frame ( 21) shift: 0.44 -0.28 ...... Frame ( 22) shift: 0.46 -0.21 ...... Frame ( 23) shift: 0.48 -0.15 ...... Frame ( 24) shift: 0.49 -0.09 ...... Frame ( 25) shift: 0.51 -0.02 ...... Frame ( 26) shift: 0.52 0.05 ...... Frame ( 27) shift: 0.57 0.11 ...... Frame ( 28) shift: 0.65 0.15 ...... Frame ( 29) shift: 0.73 0.19 ...... Frame ( 30) shift: 0.87 0.29 ...... Frame ( 31) shift: 1.05 0.43 ...... Frame ( 32) shift: 1.24 0.58 ...... Frame ( 33) shift: 1.34 0.66 ...... Frame ( 34) shift: 1.35 0.67 ...... Frame ( 35) shift: 1.37 0.67 ...... Frame ( 36) shift: 1.39 0.69 ...... Frame ( 37) shift: 1.41 0.72 ...... Frame ( 38) shift: 1.43 0.74 ...... Frame ( 39) shift: 1.45 0.76 ...... Frame ( 40) shift: 1.47 0.79 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.818013 Iteration 2 Error: 0.160185 Iteration 3 Error: 0.041271 Align patch 2 23 left Iteration 1 Error: 1.223207 Iteration 2 Error: 0.204549 Iteration 3 Error: 0.091617 Iteration 4 Error: 0.031968 Align patch 3 22 left Iteration 1 Error: 1.465158 Iteration 2 Error: 0.170186 Iteration 3 Error: 0.075631 Iteration 4 Error: 0.016837 Align patch 4 21 left Iteration 1 Error: 1.049271 Iteration 2 Error: 0.175232 Iteration 3 Error: 0.049286 Align patch 5 20 left Iteration 1 Error: 0.865254 Iteration 2 Error: 0.126513 Iteration 3 Error: 0.040871 Align patch 6 19 left Iteration 1 Error: 1.050121 Iteration 2 Error: 0.192991 Iteration 3 Error: 0.086728 Iteration 4 Error: 0.032809 Align patch 7 18 left Iteration 1 Error: 0.843464 Iteration 2 Error: 0.131401 Iteration 3 Error: 0.043569 Align patch 8 17 left Iteration 1 Error: 1.133748 Iteration 2 Error: 0.218325 Iteration 3 Error: 0.068496 Iteration 4 Error: 0.016582 Align patch 9 16 left Iteration 1 Error: 0.800628 Iteration 2 Error: 0.110544 Iteration 3 Error: 0.041723 Align patch 10 15 left Iteration 1 Error: 0.882200 Iteration 2 Error: 0.260104 Iteration 3 Error: 0.087989 Iteration 4 Error: 0.027957 Align patch 11 14 left Iteration 1 Error: 1.273986 Iteration 2 Error: 0.226408 Iteration 3 Error: 0.052089 Iteration 4 Error: 0.022435 Align patch 12 13 left Iteration 1 Error: 1.511559 Iteration 2 Error: 0.515202 Iteration 3 Error: 0.208962 Iteration 4 Error: 0.178194 Iteration 5 Error: 0.078204 Align patch 12 13 left Iteration 1 Error: 1.574204 Iteration 2 Error: 0.213406 Iteration 3 Error: 0.039077 Align patch 13 12 left Iteration 1 Error: 0.683708 Iteration 2 Error: 0.089069 Iteration 3 Error: 0.018245 Align patch 14 11 left Iteration 1 Error: 0.901969 Iteration 2 Error: 0.149256 Iteration 3 Error: 0.036527 Align patch 15 10 left Iteration 1 Error: 0.993446 Iteration 2 Error: 0.162322 Iteration 3 Error: 0.059483 Iteration 4 Error: 0.011021 Align patch 16 9 left Iteration 1 Error: 0.650988 Iteration 2 Error: 0.115398 Iteration 3 Error: 0.036092 Align patch 17 8 left Iteration 1 Error: 1.217546 Iteration 2 Error: 0.160365 Iteration 3 Error: 0.078386 Iteration 4 Error: 0.011817 Align patch 18 7 left Iteration 1 Error: 0.514316 Iteration 2 Error: 0.120931 Iteration 3 Error: 0.040231 Align patch 19 6 left Iteration 1 Error: 1.025875 Iteration 2 Error: 0.202807 Iteration 3 Error: 0.087389 Iteration 4 Error: 0.026534 Align patch 20 5 left Iteration 1 Error: 1.029298 Iteration 2 Error: 0.159870 Iteration 3 Error: 0.052056 Iteration 4 Error: 0.019653 Align patch 21 4 left Iteration 1 Error: 0.877134 Iteration 2 Error: 0.197241 Iteration 3 Error: 0.068071 Iteration 4 Error: 0.014137 Align patch 22 3 left Iteration 1 Error: 0.707412 Iteration 2 Error: 0.153661 Iteration 3 Error: 0.025457 Align patch 23 2 left Iteration 1 Error: 0.682680 Iteration 2 Error: 0.123325 Iteration 3 Error: 0.054364 Iteration 4 Error: 0.012914 Align patch 24 1 left Iteration 1 Error: 0.852550 Iteration 2 Error: 0.270253 Iteration 3 Error: 0.066355 Iteration 4 Error: 0.034830 Align patch 25 0 left Iteration 1 Error: 1.156513 Iteration 2 Error: 0.167198 Iteration 3 Error: 0.053347 Iteration 4 Error: 0.026415 3D Fitting completed. Patch alignment time: 14.23(sec) Local motion has been corrected. Process thread exits. Computational time: 33.399239 sec Total time: 53.616703 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00006hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00006hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.962896s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00006hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 5.030011s ........................................ >>>>>>TIME<<<<<< FFT: 1.226323s Defocus_U Defocus_V Angle CCC 9253.93 10031.29 4.50 0.026105 Final Values Defocus_U Defocus_V Angle CCC 9250.83 10053.17 6.39 0.044617 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00006hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00006hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.995e-02 CC threshold: 0.734 Mean Std: 42.43 7.21 Num Hot pixels: 234 Hot pixel threshold: 85.67 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.864248 Iteration 2 Error: 0.167905 Iteration 3 Error: 0.048108 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.17 -0.03 ...... Frame ( 3) shift: -0.34 -0.05 ...... Frame ( 4) shift: -0.50 -0.08 ...... Frame ( 5) shift: -0.67 -0.10 ...... Frame ( 6) shift: -0.74 -0.11 ...... Frame ( 7) shift: -0.71 -0.11 ...... Frame ( 8) shift: -0.68 -0.11 ...... Frame ( 9) shift: -0.61 -0.07 ...... Frame ( 10) shift: -0.50 -0.01 ...... Frame ( 11) shift: -0.40 0.06 ...... Frame ( 12) shift: -0.30 0.13 ...... Frame ( 13) shift: -0.21 0.21 ...... Frame ( 14) shift: -0.12 0.30 ...... Frame ( 15) shift: -0.07 0.38 ...... Frame ( 16) shift: -0.05 0.46 ...... Frame ( 17) shift: -0.03 0.54 ...... Frame ( 18) shift: -0.01 0.62 ...... Frame ( 19) shift: 0.01 0.70 ...... Frame ( 20) shift: 0.04 0.78 ...... Frame ( 21) shift: 0.05 0.85 ...... Frame ( 22) shift: 0.05 0.91 ...... Frame ( 23) shift: 0.05 0.96 ...... Frame ( 24) shift: 0.06 1.03 ...... Frame ( 25) shift: 0.07 1.11 ...... Frame ( 26) shift: 0.09 1.18 ...... Frame ( 27) shift: 0.10 1.21 ...... Frame ( 28) shift: 0.10 1.20 ...... Frame ( 29) shift: 0.11 1.19 ...... Frame ( 30) shift: 0.12 1.18 ...... Frame ( 31) shift: 0.14 1.17 ...... Frame ( 32) shift: 0.17 1.17 ...... Frame ( 33) shift: 0.20 1.18 ...... Frame ( 34) shift: 0.25 1.21 ...... Frame ( 35) shift: 0.29 1.24 ...... Frame ( 36) shift: 0.32 1.28 ...... Frame ( 37) shift: 0.35 1.34 ...... Frame ( 38) shift: 0.38 1.40 ...... Frame ( 39) shift: 0.40 1.45 ...... Frame ( 40) shift: 0.43 1.51 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.750857 Iteration 2 Error: 0.370763 Iteration 3 Error: 0.122398 Iteration 4 Error: 0.031365 Align patch 2 23 left Iteration 1 Error: 0.694349 Iteration 2 Error: 0.357629 Iteration 3 Error: 0.129954 Iteration 4 Error: 0.059961 Iteration 5 Error: 0.027124 Align patch 3 22 left Iteration 1 Error: 0.658288 Iteration 2 Error: 0.218272 Iteration 3 Error: 0.050149 Iteration 4 Error: 0.015335 Align patch 4 21 left Iteration 1 Error: 0.981597 Iteration 2 Error: 0.185526 Iteration 3 Error: 0.036211 Align patch 5 20 left Iteration 1 Error: 0.788111 Iteration 2 Error: 0.146543 Iteration 3 Error: 0.050952 Iteration 4 Error: 0.022340 Align patch 6 19 left Iteration 1 Error: 1.475857 Iteration 2 Error: 0.278518 Iteration 3 Error: 0.100523 Iteration 4 Error: 0.031526 Align patch 7 18 left Iteration 1 Error: 1.249270 Iteration 2 Error: 0.207482 Iteration 3 Error: 0.043565 Align patch 8 17 left Iteration 1 Error: 1.229774 Iteration 2 Error: 0.348608 Iteration 3 Error: 0.116402 Iteration 4 Error: 0.045428 Align patch 9 16 left Iteration 1 Error: 0.777279 Iteration 2 Error: 0.153424 Iteration 3 Error: 0.053642 Iteration 4 Error: 0.016260 Align patch 10 15 left Iteration 1 Error: 0.651646 Iteration 2 Error: 0.118391 Iteration 3 Error: 0.027511 Align patch 11 14 left Iteration 1 Error: 0.689456 Iteration 2 Error: 0.169599 Iteration 3 Error: 0.046707 Align patch 12 13 left Iteration 1 Error: 0.649152 Iteration 2 Error: 0.168947 Iteration 3 Error: 0.027388 Align patch 13 12 left Iteration 1 Error: 1.223986 Iteration 2 Error: 0.182317 Iteration 3 Error: 0.061502 Iteration 4 Error: 0.022283 Align patch 14 11 left Iteration 1 Error: 0.768327 Iteration 2 Error: 0.116073 Iteration 3 Error: 0.034403 Align patch 15 10 left Iteration 1 Error: 2.598622 Iteration 2 Error: 0.757823 Iteration 3 Error: 0.463494 Iteration 4 Error: 0.185695 Iteration 5 Error: 0.088518 Align patch 15 10 left Iteration 1 Error: 3.163711 Iteration 2 Error: 0.624168 Iteration 3 Error: 0.289360 Iteration 4 Error: 0.101513 Iteration 5 Error: 0.046398 Align patch 16 9 left Iteration 1 Error: 0.985052 Iteration 2 Error: 0.279635 Iteration 3 Error: 0.054051 Iteration 4 Error: 0.017898 Align patch 17 8 left Iteration 1 Error: 0.766507 Iteration 2 Error: 0.153110 Iteration 3 Error: 0.037706 Align patch 18 7 left Iteration 1 Error: 0.834113 Iteration 2 Error: 0.171030 Iteration 3 Error: 0.045044 Align patch 19 6 left Iteration 1 Error: 0.933065 Iteration 2 Error: 0.127287 Iteration 3 Error: 0.039379 Align patch 20 5 left Iteration 1 Error: 1.159039 Iteration 2 Error: 0.202720 Iteration 3 Error: 0.081493 Iteration 4 Error: 0.027000 Align patch 21 4 left Iteration 1 Error: 0.815914 Iteration 2 Error: 0.204337 Iteration 3 Error: 0.086328 Iteration 4 Error: 0.055151 Iteration 5 Error: 0.016136 Align patch 22 3 left Iteration 1 Error: 0.799647 Iteration 2 Error: 0.255942 Iteration 3 Error: 0.105873 Iteration 4 Error: 0.051929 Iteration 5 Error: 0.019405 Align patch 23 2 left Iteration 1 Error: 1.303999 Iteration 2 Error: 0.165621 Iteration 3 Error: 0.052770 Iteration 4 Error: 0.019182 Align patch 24 1 left Iteration 1 Error: 0.701133 Iteration 2 Error: 0.314834 Iteration 3 Error: 0.096601 Iteration 4 Error: 0.047025 Align patch 25 0 left Iteration 1 Error: 0.953465 Iteration 2 Error: 0.159662 Iteration 3 Error: 0.044606 3D Fitting completed. Patch alignment time: 12.76(sec) Local motion has been corrected. Process thread exits. Computational time: 30.389999 sec Total time: 48.289333 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00006hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00006hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.707598s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00006hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.622410s ........................................ >>>>>>TIME<<<<<< FFT: 1.045918s Defocus_U Defocus_V Angle CCC 11275.40 11822.28 2.86 0.036260 Final Values Defocus_U Defocus_V Angle CCC 11292.57 11826.99 2.54 0.068967 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00006hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00006hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.997e-02 CC threshold: 0.734 Mean Std: 41.33 6.89 Num Hot pixels: 248 Hot pixel threshold: 82.64 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.738342 Iteration 2 Error: 0.137674 Iteration 3 Error: 0.041126 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.13 -0.10 ...... Frame ( 3) shift: -0.26 -0.20 ...... Frame ( 4) shift: -0.40 -0.29 ...... Frame ( 5) shift: -0.53 -0.39 ...... Frame ( 6) shift: -0.61 -0.44 ...... Frame ( 7) shift: -0.63 -0.43 ...... Frame ( 8) shift: -0.65 -0.42 ...... Frame ( 9) shift: -0.64 -0.41 ...... Frame ( 10) shift: -0.59 -0.40 ...... Frame ( 11) shift: -0.54 -0.38 ...... Frame ( 12) shift: -0.51 -0.35 ...... Frame ( 13) shift: -0.48 -0.30 ...... Frame ( 14) shift: -0.46 -0.26 ...... Frame ( 15) shift: -0.42 -0.20 ...... Frame ( 16) shift: -0.36 -0.13 ...... Frame ( 17) shift: -0.30 -0.06 ...... Frame ( 18) shift: -0.24 -0.01 ...... Frame ( 19) shift: -0.17 0.00 ...... Frame ( 20) shift: -0.09 0.02 ...... Frame ( 21) shift: -0.04 0.02 ...... Frame ( 22) shift: -0.01 -0.00 ...... Frame ( 23) shift: 0.03 -0.02 ...... Frame ( 24) shift: 0.06 0.00 ...... Frame ( 25) shift: 0.10 0.07 ...... Frame ( 26) shift: 0.13 0.14 ...... Frame ( 27) shift: 0.17 0.16 ...... Frame ( 28) shift: 0.22 0.12 ...... Frame ( 29) shift: 0.27 0.08 ...... Frame ( 30) shift: 0.33 0.07 ...... Frame ( 31) shift: 0.40 0.09 ...... Frame ( 32) shift: 0.47 0.11 ...... Frame ( 33) shift: 0.49 0.18 ...... Frame ( 34) shift: 0.47 0.30 ...... Frame ( 35) shift: 0.44 0.42 ...... Frame ( 36) shift: 0.44 0.50 ...... Frame ( 37) shift: 0.46 0.54 ...... Frame ( 38) shift: 0.49 0.57 ...... Frame ( 39) shift: 0.51 0.61 ...... Frame ( 40) shift: 0.54 0.64 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.659969 Iteration 2 Error: 0.157458 Iteration 3 Error: 0.037611 Align patch 2 23 left Iteration 1 Error: 1.134289 Iteration 2 Error: 0.185966 Iteration 3 Error: 0.039824 Align patch 3 22 left Iteration 1 Error: 0.970589 Iteration 2 Error: 0.131413 Iteration 3 Error: 0.036522 Align patch 4 21 left Iteration 1 Error: 0.926797 Iteration 2 Error: 0.230528 Iteration 3 Error: 0.104857 Iteration 4 Error: 0.036698 Align patch 5 20 left Iteration 1 Error: 0.824492 Iteration 2 Error: 0.268464 Iteration 3 Error: 0.070081 Iteration 4 Error: 0.027815 Align patch 6 19 left Iteration 1 Error: 0.722013 Iteration 2 Error: 0.160862 Iteration 3 Error: 0.036851 Align patch 7 18 left Iteration 1 Error: 0.711529 Iteration 2 Error: 0.110054 Iteration 3 Error: 0.038474 Align patch 8 17 left Iteration 1 Error: 0.583968 Iteration 2 Error: 0.092648 Iteration 3 Error: 0.017343 Align patch 9 16 left Iteration 1 Error: 0.590261 Iteration 2 Error: 0.135001 Iteration 3 Error: 0.037786 Align patch 10 15 left Iteration 1 Error: 0.823824 Iteration 2 Error: 0.121884 Iteration 3 Error: 0.046615 Align patch 11 14 left Iteration 1 Error: 0.695615 Iteration 2 Error: 0.203051 Iteration 3 Error: 0.055619 Iteration 4 Error: 0.030044 Align patch 12 13 left Iteration 1 Error: 0.935052 Iteration 2 Error: 0.111278 Iteration 3 Error: 0.032925 Align patch 13 12 left Iteration 1 Error: 0.793168 Iteration 2 Error: 0.308589 Iteration 3 Error: 0.110500 Iteration 4 Error: 0.041220 Align patch 14 11 left Iteration 1 Error: 0.943788 Iteration 2 Error: 0.375456 Iteration 3 Error: 0.092404 Iteration 4 Error: 0.080933 Iteration 5 Error: 0.021318 Align patch 15 10 left Iteration 1 Error: 1.207070 Iteration 2 Error: 0.197160 Iteration 3 Error: 0.059853 Iteration 4 Error: 0.038609 Align patch 16 9 left Iteration 1 Error: 0.743225 Iteration 2 Error: 0.185530 Iteration 3 Error: 0.050403 Iteration 4 Error: 0.021088 Align patch 17 8 left Iteration 1 Error: 0.840479 Iteration 2 Error: 0.147819 Iteration 3 Error: 0.037483 Align patch 18 7 left Iteration 1 Error: 0.892757 Iteration 2 Error: 0.192142 Iteration 3 Error: 0.057147 Iteration 4 Error: 0.025965 Align patch 19 6 left Iteration 1 Error: 1.054757 Iteration 2 Error: 0.214375 Iteration 3 Error: 0.047259 Align patch 20 5 left Iteration 1 Error: 1.052080 Iteration 2 Error: 0.243264 Iteration 3 Error: 0.099186 Iteration 4 Error: 0.027114 Align patch 21 4 left Iteration 1 Error: 0.777197 Iteration 2 Error: 0.160613 Iteration 3 Error: 0.055860 Iteration 4 Error: 0.016792 Align patch 22 3 left Iteration 1 Error: 1.034531 Iteration 2 Error: 0.171569 Iteration 3 Error: 0.035482 Align patch 23 2 left Iteration 1 Error: 0.894109 Iteration 2 Error: 0.151396 Iteration 3 Error: 0.033912 Align patch 24 1 left Iteration 1 Error: 0.726908 Iteration 2 Error: 0.264704 Iteration 3 Error: 0.066479 Iteration 4 Error: 0.051372 Iteration 5 Error: 0.013964 Align patch 25 0 left Iteration 1 Error: 1.226932 Iteration 2 Error: 0.143362 Iteration 3 Error: 0.042479 3D Fitting completed. Patch alignment time: 11.49(sec) Local motion has been corrected. Process thread exits. Computational time: 24.082827 sec Total time: 42.229183 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00006hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00006hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.819056s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00006hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.296263s ........................................ >>>>>>TIME<<<<<< FFT: 1.306660s Defocus_U Defocus_V Angle CCC 13085.94 14023.44 3.56 0.035794 Final Values Defocus_U Defocus_V Angle CCC 13084.40 14015.65 3.56 0.059173 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00006hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00006hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 43.18 7.17 Num Hot pixels: 222 Hot pixel threshold: 86.18 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.400000 Iteration 2 Error: 0.063014 Iteration 3 Error: 0.014094 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.11 -0.03 ...... Frame ( 3) shift: -0.23 -0.05 ...... Frame ( 4) shift: -0.34 -0.08 ...... Frame ( 5) shift: -0.45 -0.11 ...... Frame ( 6) shift: -0.49 -0.12 ...... Frame ( 7) shift: -0.45 -0.11 ...... Frame ( 8) shift: -0.41 -0.10 ...... Frame ( 9) shift: -0.37 -0.08 ...... Frame ( 10) shift: -0.34 -0.05 ...... Frame ( 11) shift: -0.30 -0.02 ...... Frame ( 12) shift: -0.28 -0.02 ...... Frame ( 13) shift: -0.28 -0.04 ...... Frame ( 14) shift: -0.27 -0.06 ...... Frame ( 15) shift: -0.28 -0.05 ...... Frame ( 16) shift: -0.32 -0.01 ...... Frame ( 17) shift: -0.35 0.04 ...... Frame ( 18) shift: -0.33 0.09 ...... Frame ( 19) shift: -0.24 0.16 ...... Frame ( 20) shift: -0.16 0.22 ...... Frame ( 21) shift: -0.12 0.29 ...... Frame ( 22) shift: -0.13 0.36 ...... Frame ( 23) shift: -0.13 0.44 ...... Frame ( 24) shift: -0.11 0.44 ...... Frame ( 25) shift: -0.07 0.38 ...... Frame ( 26) shift: -0.03 0.32 ...... Frame ( 27) shift: -0.01 0.30 ...... Frame ( 28) shift: -0.00 0.33 ...... Frame ( 29) shift: 0.00 0.36 ...... Frame ( 30) shift: -0.01 0.39 ...... Frame ( 31) shift: -0.04 0.43 ...... Frame ( 32) shift: -0.07 0.46 ...... Frame ( 33) shift: -0.10 0.49 ...... Frame ( 34) shift: -0.13 0.50 ...... Frame ( 35) shift: -0.15 0.52 ...... Frame ( 36) shift: -0.18 0.53 ...... Frame ( 37) shift: -0.21 0.55 ...... Frame ( 38) shift: -0.23 0.57 ...... Frame ( 39) shift: -0.26 0.59 ...... Frame ( 40) shift: -0.28 0.61 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.348870 Iteration 2 Error: 0.164834 Iteration 3 Error: 0.028962 Align patch 2 23 left Iteration 1 Error: 0.707747 Iteration 2 Error: 0.135412 Iteration 3 Error: 0.046124 Align patch 3 22 left Iteration 1 Error: 0.905316 Iteration 2 Error: 0.207004 Iteration 3 Error: 0.061962 Iteration 4 Error: 0.018887 Align patch 4 21 left Iteration 1 Error: 0.641144 Iteration 2 Error: 0.086003 Iteration 3 Error: 0.029704 Align patch 5 20 left Iteration 1 Error: 0.634202 Iteration 2 Error: 0.109854 Iteration 3 Error: 0.015255 Align patch 6 19 left Iteration 1 Error: 0.810743 Iteration 2 Error: 0.144196 Iteration 3 Error: 0.057865 Iteration 4 Error: 0.014190 Align patch 7 18 left Iteration 1 Error: 0.634724 Iteration 2 Error: 0.171441 Iteration 3 Error: 0.051109 Iteration 4 Error: 0.011194 Align patch 8 17 left Iteration 1 Error: 1.140558 Iteration 2 Error: 0.136045 Iteration 3 Error: 0.048172 Align patch 9 16 left Iteration 1 Error: 0.780232 Iteration 2 Error: 0.167229 Iteration 3 Error: 0.045357 Align patch 10 15 left Iteration 1 Error: 0.588168 Iteration 2 Error: 0.134661 Iteration 3 Error: 0.042306 Align patch 11 14 left Iteration 1 Error: 0.892020 Iteration 2 Error: 0.151192 Iteration 3 Error: 0.050232 Iteration 4 Error: 0.022614 Align patch 12 13 left Iteration 1 Error: 0.787075 Iteration 2 Error: 0.184496 Iteration 3 Error: 0.028376 Align patch 13 12 left Iteration 1 Error: 0.530503 Iteration 2 Error: 0.089606 Iteration 3 Error: 0.023047 Align patch 14 11 left Iteration 1 Error: 0.604560 Iteration 2 Error: 0.124531 Iteration 3 Error: 0.023634 Align patch 15 10 left Iteration 1 Error: 1.260438 Iteration 2 Error: 0.157724 Iteration 3 Error: 0.026520 Align patch 16 9 left Iteration 1 Error: 0.917512 Iteration 2 Error: 0.220985 Iteration 3 Error: 0.070785 Iteration 4 Error: 0.048140 Align patch 17 8 left Iteration 1 Error: 0.817178 Iteration 2 Error: 0.124934 Iteration 3 Error: 0.035082 Align patch 18 7 left Iteration 1 Error: 0.546830 Iteration 2 Error: 0.086336 Iteration 3 Error: 0.030167 Align patch 19 6 left Iteration 1 Error: 1.161051 Iteration 2 Error: 0.220975 Iteration 3 Error: 0.040288 Align patch 20 5 left Iteration 1 Error: 0.717675 Iteration 2 Error: 0.095834 Iteration 3 Error: 0.017977 Align patch 21 4 left Iteration 1 Error: 0.892425 Iteration 2 Error: 0.262646 Iteration 3 Error: 0.088018 Iteration 4 Error: 0.035597 Align patch 22 3 left Iteration 1 Error: 0.664974 Iteration 2 Error: 0.112374 Iteration 3 Error: 0.032405 Align patch 23 2 left Iteration 1 Error: 0.770048 Iteration 2 Error: 0.143144 Iteration 3 Error: 0.026577 Align patch 24 1 left Iteration 1 Error: 0.654239 Iteration 2 Error: 0.084708 Iteration 3 Error: 0.025210 Align patch 25 0 left Iteration 1 Error: 0.618755 Iteration 2 Error: 0.141383 Iteration 3 Error: 0.038469 3D Fitting completed. Patch alignment time: 11.90(sec) Local motion has been corrected. Process thread exits. Computational time: 29.276560 sec Total time: 46.304832 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00006hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00006hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.827669s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00006hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 4.201993s ........................................ >>>>>>TIME<<<<<< FFT: 1.211096s Defocus_U Defocus_V Angle CCC 10027.75 9343.43 83.30 0.033840 Final Values Defocus_U Defocus_V Angle CCC 10030.88 9359.06 83.62 0.068582 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00007hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00007hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 45.43 7.63 Num Hot pixels: 204 Hot pixel threshold: 91.19 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.016196 Iteration 2 Error: 0.184358 Iteration 3 Error: 0.044873 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.24 0.10 ...... Frame ( 3) shift: -0.48 0.19 ...... Frame ( 4) shift: -0.72 0.29 ...... Frame ( 5) shift: -0.95 0.38 ...... Frame ( 6) shift: -1.03 0.48 ...... Frame ( 7) shift: -0.95 0.58 ...... Frame ( 8) shift: -0.86 0.68 ...... Frame ( 9) shift: -0.78 0.75 ...... Frame ( 10) shift: -0.70 0.80 ...... Frame ( 11) shift: -0.62 0.86 ...... Frame ( 12) shift: -0.55 0.93 ...... Frame ( 13) shift: -0.48 1.03 ...... Frame ( 14) shift: -0.41 1.13 ...... Frame ( 15) shift: -0.35 1.17 ...... Frame ( 16) shift: -0.30 1.15 ...... Frame ( 17) shift: -0.25 1.14 ...... Frame ( 18) shift: -0.21 1.18 ...... Frame ( 19) shift: -0.18 1.27 ...... Frame ( 20) shift: -0.16 1.37 ...... Frame ( 21) shift: -0.14 1.42 ...... Frame ( 22) shift: -0.12 1.41 ...... Frame ( 23) shift: -0.11 1.40 ...... Frame ( 24) shift: -0.08 1.42 ...... Frame ( 25) shift: -0.03 1.45 ...... Frame ( 26) shift: 0.02 1.49 ...... Frame ( 27) shift: 0.01 1.53 ...... Frame ( 28) shift: -0.04 1.59 ...... Frame ( 29) shift: -0.10 1.65 ...... Frame ( 30) shift: -0.12 1.71 ...... Frame ( 31) shift: -0.12 1.76 ...... Frame ( 32) shift: -0.12 1.82 ...... Frame ( 33) shift: -0.10 1.85 ...... Frame ( 34) shift: -0.05 1.85 ...... Frame ( 35) shift: 0.00 1.86 ...... Frame ( 36) shift: 0.04 1.87 ...... Frame ( 37) shift: 0.07 1.88 ...... Frame ( 38) shift: 0.11 1.90 ...... Frame ( 39) shift: 0.14 1.92 ...... Frame ( 40) shift: 0.17 1.94 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.901335 Iteration 2 Error: 0.171583 Iteration 3 Error: 0.102946 Iteration 4 Error: 0.023296 Align patch 2 23 left Iteration 1 Error: 1.371063 Iteration 2 Error: 0.297934 Iteration 3 Error: 0.054653 Iteration 4 Error: 0.024759 Align patch 3 22 left Iteration 1 Error: 1.631040 Iteration 2 Error: 0.193128 Iteration 3 Error: 0.029443 Align patch 4 21 left Iteration 1 Error: 0.817670 Iteration 2 Error: 0.092262 Iteration 3 Error: 0.022350 Align patch 5 20 left Iteration 1 Error: 0.791579 Iteration 2 Error: 0.093174 Iteration 3 Error: 0.026327 Align patch 6 19 left Iteration 1 Error: 1.469789 Iteration 2 Error: 0.266355 Iteration 3 Error: 0.054332 Iteration 4 Error: 0.021548 Align patch 7 18 left Iteration 1 Error: 0.754239 Iteration 2 Error: 0.271796 Iteration 3 Error: 0.068583 Iteration 4 Error: 0.028884 Align patch 8 17 left Iteration 1 Error: 0.843826 Iteration 2 Error: 0.171500 Iteration 3 Error: 0.044947 Align patch 9 16 left Iteration 1 Error: 0.744609 Iteration 2 Error: 0.122318 Iteration 3 Error: 0.028997 Align patch 10 15 left Iteration 1 Error: 1.219513 Iteration 2 Error: 0.146955 Iteration 3 Error: 0.035339 Align patch 11 14 left Iteration 1 Error: 0.960193 Iteration 2 Error: 0.086567 Iteration 3 Error: 0.022295 Align patch 12 13 left Iteration 1 Error: 0.637320 Iteration 2 Error: 0.092462 Iteration 3 Error: 0.030925 Align patch 13 12 left Iteration 1 Error: 1.076008 Iteration 2 Error: 0.144559 Iteration 3 Error: 0.050950 Iteration 4 Error: 0.020721 Align patch 14 11 left Iteration 1 Error: 0.514378 Iteration 2 Error: 0.065124 Iteration 3 Error: 0.012912 Align patch 15 10 left Iteration 1 Error: 0.834043 Iteration 2 Error: 0.104541 Iteration 3 Error: 0.025348 Align patch 16 9 left Iteration 1 Error: 1.097435 Iteration 2 Error: 0.294982 Iteration 3 Error: 0.078556 Iteration 4 Error: 0.029947 Align patch 17 8 left Iteration 1 Error: 0.999696 Iteration 2 Error: 0.177748 Iteration 3 Error: 0.050273 Iteration 4 Error: 0.015851 Align patch 18 7 left Iteration 1 Error: 1.452126 Iteration 2 Error: 0.144199 Iteration 3 Error: 0.021715 Align patch 19 6 left Iteration 1 Error: 0.669447 Iteration 2 Error: 0.082576 Iteration 3 Error: 0.016018 Align patch 20 5 left Iteration 1 Error: 0.655650 Iteration 2 Error: 0.111027 Iteration 3 Error: 0.028298 Align patch 21 4 left Iteration 1 Error: 1.099837 Iteration 2 Error: 0.129953 Iteration 3 Error: 0.029853 Align patch 22 3 left Iteration 1 Error: 1.163700 Iteration 2 Error: 0.187959 Iteration 3 Error: 0.034745 Align patch 23 2 left Iteration 1 Error: 1.257391 Iteration 2 Error: 0.108602 Iteration 3 Error: 0.015170 Align patch 24 1 left Iteration 1 Error: 0.751753 Iteration 2 Error: 0.112409 Iteration 3 Error: 0.022538 Align patch 25 0 left Iteration 1 Error: 0.835194 Iteration 2 Error: 0.118475 Iteration 3 Error: 0.031832 3D Fitting completed. Patch alignment time: 11.49(sec) Local motion has been corrected. Process thread exits. Computational time: 21.937778 sec Total time: 39.975147 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00007hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00007hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.610016s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00007hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.940116s ........................................ >>>>>>TIME<<<<<< FFT: 1.051182s Defocus_U Defocus_V Angle CCC 9947.25 10771.50 14.13 0.051051 Final Values Defocus_U Defocus_V Angle CCC 9983.21 10779.33 14.45 0.093850 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00007hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00007hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 44.67 7.62 Num Hot pixels: 191 Hot pixel threshold: 90.39 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.112620 Iteration 2 Error: 0.069857 Iteration 3 Error: 0.015178 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.20 0.16 ...... Frame ( 3) shift: -0.39 0.32 ...... Frame ( 4) shift: -0.59 0.48 ...... Frame ( 5) shift: -0.79 0.64 ...... Frame ( 6) shift: -0.88 0.75 ...... Frame ( 7) shift: -0.88 0.80 ...... Frame ( 8) shift: -0.87 0.84 ...... Frame ( 9) shift: -0.86 0.92 ...... Frame ( 10) shift: -0.83 1.04 ...... Frame ( 11) shift: -0.81 1.15 ...... Frame ( 12) shift: -0.81 1.24 ...... Frame ( 13) shift: -0.84 1.30 ...... Frame ( 14) shift: -0.87 1.36 ...... Frame ( 15) shift: -0.87 1.38 ...... Frame ( 16) shift: -0.84 1.37 ...... Frame ( 17) shift: -0.81 1.36 ...... Frame ( 18) shift: -0.83 1.32 ...... Frame ( 19) shift: -0.88 1.26 ...... Frame ( 20) shift: -0.94 1.20 ...... Frame ( 21) shift: -0.98 1.18 ...... Frame ( 22) shift: -1.00 1.22 ...... Frame ( 23) shift: -1.01 1.26 ...... Frame ( 24) shift: -1.01 1.30 ...... Frame ( 25) shift: -0.99 1.33 ...... Frame ( 26) shift: -0.97 1.36 ...... Frame ( 27) shift: -0.94 1.38 ...... Frame ( 28) shift: -0.88 1.39 ...... Frame ( 29) shift: -0.83 1.40 ...... Frame ( 30) shift: -0.78 1.44 ...... Frame ( 31) shift: -0.74 1.53 ...... Frame ( 32) shift: -0.69 1.61 ...... Frame ( 33) shift: -0.67 1.66 ...... Frame ( 34) shift: -0.66 1.68 ...... Frame ( 35) shift: -0.66 1.71 ...... Frame ( 36) shift: -0.65 1.73 ...... Frame ( 37) shift: -0.64 1.76 ...... Frame ( 38) shift: -0.64 1.78 ...... Frame ( 39) shift: -0.63 1.80 ...... Frame ( 40) shift: -0.62 1.83 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.815070 Iteration 2 Error: 0.105925 Iteration 3 Error: 0.016493 Align patch 2 23 left Iteration 1 Error: 1.279724 Iteration 2 Error: 0.130417 Iteration 3 Error: 0.031558 Align patch 3 22 left Iteration 1 Error: 0.707833 Iteration 2 Error: 0.142847 Iteration 3 Error: 0.035362 Align patch 4 21 left Iteration 1 Error: 0.986753 Iteration 2 Error: 0.110144 Iteration 3 Error: 0.028786 Align patch 5 20 left Iteration 1 Error: 0.915718 Iteration 2 Error: 0.064998 Iteration 3 Error: 0.012777 Align patch 6 19 left Iteration 1 Error: 0.882913 Iteration 2 Error: 0.154599 Iteration 3 Error: 0.040058 Align patch 7 18 left Iteration 1 Error: 0.681093 Iteration 2 Error: 0.129295 Iteration 3 Error: 0.054626 Iteration 4 Error: 0.019297 Align patch 8 17 left Iteration 1 Error: 0.688733 Iteration 2 Error: 0.158573 Iteration 3 Error: 0.037678 Align patch 9 16 left Iteration 1 Error: 0.829000 Iteration 2 Error: 0.083510 Iteration 3 Error: 0.018325 Align patch 10 15 left Iteration 1 Error: 0.668307 Iteration 2 Error: 0.084471 Iteration 3 Error: 0.023335 Align patch 11 14 left Iteration 1 Error: 1.098541 Iteration 2 Error: 0.176945 Iteration 3 Error: 0.039686 Align patch 12 13 left Iteration 1 Error: 0.780158 Iteration 2 Error: 0.160039 Iteration 3 Error: 0.035695 Align patch 13 12 left Iteration 1 Error: 0.783531 Iteration 2 Error: 0.104494 Iteration 3 Error: 0.020963 Align patch 14 11 left Iteration 1 Error: 0.479467 Iteration 2 Error: 0.101384 Iteration 3 Error: 0.021522 Align patch 15 10 left Iteration 1 Error: 0.763771 Iteration 2 Error: 0.121570 Iteration 3 Error: 0.012812 Align patch 16 9 left Iteration 1 Error: 1.342596 Iteration 2 Error: 0.204182 Iteration 3 Error: 0.052882 Iteration 4 Error: 0.017047 Align patch 17 8 left Iteration 1 Error: 0.982956 Iteration 2 Error: 0.246311 Iteration 3 Error: 0.052903 Iteration 4 Error: 0.021623 Align patch 18 7 left Iteration 1 Error: 0.687664 Iteration 2 Error: 0.125968 Iteration 3 Error: 0.024788 Align patch 19 6 left Iteration 1 Error: 0.521936 Iteration 2 Error: 0.079502 Iteration 3 Error: 0.019631 Align patch 20 5 left Iteration 1 Error: 0.805474 Iteration 2 Error: 0.105107 Iteration 3 Error: 0.022969 Align patch 21 4 left Iteration 1 Error: 1.638339 Iteration 2 Error: 0.281786 Iteration 3 Error: 0.044069 Align patch 22 3 left Iteration 1 Error: 1.530450 Iteration 2 Error: 0.184229 Iteration 3 Error: 0.046675 Align patch 23 2 left Iteration 1 Error: 0.586138 Iteration 2 Error: 0.191837 Iteration 3 Error: 0.046298 Align patch 24 1 left Iteration 1 Error: 0.788348 Iteration 2 Error: 0.107066 Iteration 3 Error: 0.025965 Align patch 25 0 left Iteration 1 Error: 1.164973 Iteration 2 Error: 0.147029 Iteration 3 Error: 0.031200 3D Fitting completed. Patch alignment time: 11.61(sec) Local motion has been corrected. Process thread exits. Computational time: 22.760757 sec Total time: 31.657778 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00007hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00007hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.514218s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00007hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.303698s ........................................ >>>>>>TIME<<<<<< FFT: 1.300185s Defocus_U Defocus_V Angle CCC 12677.74 12232.43 85.13 0.051316 Final Values Defocus_U Defocus_V Angle CCC 12690.25 12238.68 85.13 0.090372 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00007hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00007hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 45.99 7.61 Num Hot pixels: 212 Hot pixel threshold: 91.62 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.160093 Iteration 2 Error: 0.167927 Iteration 3 Error: 0.023334 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.35 -0.01 ...... Frame ( 3) shift: -0.69 -0.02 ...... Frame ( 4) shift: -1.04 -0.04 ...... Frame ( 5) shift: -1.38 -0.05 ...... Frame ( 6) shift: -1.55 0.04 ...... Frame ( 7) shift: -1.53 0.23 ...... Frame ( 8) shift: -1.51 0.43 ...... Frame ( 9) shift: -1.46 0.57 ...... Frame ( 10) shift: -1.38 0.67 ...... Frame ( 11) shift: -1.30 0.76 ...... Frame ( 12) shift: -1.26 0.84 ...... Frame ( 13) shift: -1.25 0.90 ...... Frame ( 14) shift: -1.24 0.97 ...... Frame ( 15) shift: -1.23 1.04 ...... Frame ( 16) shift: -1.22 1.13 ...... Frame ( 17) shift: -1.21 1.23 ...... Frame ( 18) shift: -1.21 1.28 ...... Frame ( 19) shift: -1.23 1.31 ...... Frame ( 20) shift: -1.24 1.34 ...... Frame ( 21) shift: -1.22 1.35 ...... Frame ( 22) shift: -1.16 1.34 ...... Frame ( 23) shift: -1.11 1.33 ...... Frame ( 24) shift: -1.07 1.34 ...... Frame ( 25) shift: -1.06 1.38 ...... Frame ( 26) shift: -1.05 1.42 ...... Frame ( 27) shift: -1.00 1.46 ...... Frame ( 28) shift: -0.92 1.49 ...... Frame ( 29) shift: -0.84 1.52 ...... Frame ( 30) shift: -0.84 1.53 ...... Frame ( 31) shift: -0.91 1.52 ...... Frame ( 32) shift: -0.98 1.51 ...... Frame ( 33) shift: -1.01 1.53 ...... Frame ( 34) shift: -0.99 1.58 ...... Frame ( 35) shift: -0.97 1.62 ...... Frame ( 36) shift: -0.95 1.63 ...... Frame ( 37) shift: -0.94 1.59 ...... Frame ( 38) shift: -0.93 1.55 ...... Frame ( 39) shift: -0.92 1.51 ...... Frame ( 40) shift: -0.90 1.48 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.461925 Iteration 2 Error: 0.191297 Iteration 3 Error: 0.049678 Align patch 2 23 left Iteration 1 Error: 1.197799 Iteration 2 Error: 0.127623 Iteration 3 Error: 0.029720 Align patch 3 22 left Iteration 1 Error: 1.049523 Iteration 2 Error: 0.211546 Iteration 3 Error: 0.051929 Iteration 4 Error: 0.015902 Align patch 4 21 left Iteration 1 Error: 0.760869 Iteration 2 Error: 0.109225 Iteration 3 Error: 0.031366 Align patch 5 20 left Iteration 1 Error: 0.506831 Iteration 2 Error: 0.068174 Iteration 3 Error: 0.027098 Align patch 6 19 left Iteration 1 Error: 1.252829 Iteration 2 Error: 0.249733 Iteration 3 Error: 0.095808 Iteration 4 Error: 0.045132 Align patch 7 18 left Iteration 1 Error: 0.651408 Iteration 2 Error: 0.146446 Iteration 3 Error: 0.031061 Align patch 8 17 left Iteration 1 Error: 1.162736 Iteration 2 Error: 0.193077 Iteration 3 Error: 0.032925 Align patch 9 16 left Iteration 1 Error: 1.143655 Iteration 2 Error: 0.111864 Iteration 3 Error: 0.050147 Iteration 4 Error: 0.016284 Align patch 10 15 left Iteration 1 Error: 0.739482 Iteration 2 Error: 0.087186 Iteration 3 Error: 0.019340 Align patch 11 14 left Iteration 1 Error: 0.840475 Iteration 2 Error: 0.234610 Iteration 3 Error: 0.037489 Align patch 12 13 left Iteration 1 Error: 0.752989 Iteration 2 Error: 0.150509 Iteration 3 Error: 0.031726 Align patch 13 12 left Iteration 1 Error: 0.863021 Iteration 2 Error: 0.170062 Iteration 3 Error: 0.040390 Align patch 14 11 left Iteration 1 Error: 0.900745 Iteration 2 Error: 0.121544 Iteration 3 Error: 0.041277 Align patch 15 10 left Iteration 1 Error: 0.675354 Iteration 2 Error: 0.098735 Iteration 3 Error: 0.029363 Align patch 16 9 left Iteration 1 Error: 0.975368 Iteration 2 Error: 0.162047 Iteration 3 Error: 0.052863 Iteration 4 Error: 0.012163 Align patch 17 8 left Iteration 1 Error: 0.987362 Iteration 2 Error: 0.138431 Iteration 3 Error: 0.039159 Align patch 18 7 left Iteration 1 Error: 0.684981 Iteration 2 Error: 0.214881 Iteration 3 Error: 0.078634 Iteration 4 Error: 0.032446 Align patch 19 6 left Iteration 1 Error: 0.727903 Iteration 2 Error: 0.075800 Iteration 3 Error: 0.025362 Align patch 20 5 left Iteration 1 Error: 0.758152 Iteration 2 Error: 0.104265 Iteration 3 Error: 0.018334 Align patch 21 4 left Iteration 1 Error: 1.392978 Iteration 2 Error: 0.276474 Iteration 3 Error: 0.066612 Iteration 4 Error: 0.026154 Align patch 22 3 left Iteration 1 Error: 1.169933 Iteration 2 Error: 0.157717 Iteration 3 Error: 0.075374 Iteration 4 Error: 0.017713 Align patch 23 2 left Iteration 1 Error: 0.831891 Iteration 2 Error: 0.202673 Iteration 3 Error: 0.063034 Iteration 4 Error: 0.015811 Align patch 24 1 left Iteration 1 Error: 1.160861 Iteration 2 Error: 0.174555 Iteration 3 Error: 0.018810 Align patch 25 0 left Iteration 1 Error: 0.510560 Iteration 2 Error: 0.072275 Iteration 3 Error: 0.015112 3D Fitting completed. Patch alignment time: 11.47(sec) Local motion has been corrected. Process thread exits. Computational time: 24.160917 sec Total time: 33.536549 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00007hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00007hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.575078s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00007hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.422090s ........................................ >>>>>>TIME<<<<<< FFT: 0.885008s Defocus_U Defocus_V Angle CCC 12564.45 13419.92 4.82 0.052853 Final Values Defocus_U Defocus_V Angle CCC 12567.58 13416.80 4.82 0.089831 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00007hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00007hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 45.73 7.56 Num Hot pixels: 220 Hot pixel threshold: 91.10 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.001900 Iteration 2 Error: 0.092045 Iteration 3 Error: 0.021114 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.25 0.11 ...... Frame ( 3) shift: -0.50 0.21 ...... Frame ( 4) shift: -0.75 0.32 ...... Frame ( 5) shift: -1.00 0.43 ...... Frame ( 6) shift: -1.10 0.55 ...... Frame ( 7) shift: -1.05 0.68 ...... Frame ( 8) shift: -1.01 0.81 ...... Frame ( 9) shift: -0.96 0.91 ...... Frame ( 10) shift: -0.92 0.99 ...... Frame ( 11) shift: -0.88 1.06 ...... Frame ( 12) shift: -0.82 1.11 ...... Frame ( 13) shift: -0.73 1.12 ...... Frame ( 14) shift: -0.64 1.14 ...... Frame ( 15) shift: -0.61 1.19 ...... Frame ( 16) shift: -0.64 1.26 ...... Frame ( 17) shift: -0.66 1.33 ...... Frame ( 18) shift: -0.66 1.37 ...... Frame ( 19) shift: -0.64 1.38 ...... Frame ( 20) shift: -0.62 1.38 ...... Frame ( 21) shift: -0.59 1.35 ...... Frame ( 22) shift: -0.57 1.28 ...... Frame ( 23) shift: -0.54 1.20 ...... Frame ( 24) shift: -0.53 1.21 ...... Frame ( 25) shift: -0.53 1.30 ...... Frame ( 26) shift: -0.54 1.39 ...... Frame ( 27) shift: -0.52 1.45 ...... Frame ( 28) shift: -0.49 1.48 ...... Frame ( 29) shift: -0.46 1.50 ...... Frame ( 30) shift: -0.45 1.52 ...... Frame ( 31) shift: -0.47 1.52 ...... Frame ( 32) shift: -0.49 1.53 ...... Frame ( 33) shift: -0.48 1.51 ...... Frame ( 34) shift: -0.44 1.47 ...... Frame ( 35) shift: -0.41 1.43 ...... Frame ( 36) shift: -0.38 1.42 ...... Frame ( 37) shift: -0.36 1.45 ...... Frame ( 38) shift: -0.35 1.48 ...... Frame ( 39) shift: -0.33 1.51 ...... Frame ( 40) shift: -0.31 1.54 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.930906 Iteration 2 Error: 0.162683 Iteration 3 Error: 0.049247 Align patch 2 23 left Iteration 1 Error: 0.735001 Iteration 2 Error: 0.120678 Iteration 3 Error: 0.028752 Align patch 3 22 left Iteration 1 Error: 0.792534 Iteration 2 Error: 0.088335 Iteration 3 Error: 0.019823 Align patch 4 21 left Iteration 1 Error: 0.625876 Iteration 2 Error: 0.099363 Iteration 3 Error: 0.015828 Align patch 5 20 left Iteration 1 Error: 1.137177 Iteration 2 Error: 0.167582 Iteration 3 Error: 0.046747 Align patch 6 19 left Iteration 1 Error: 0.703078 Iteration 2 Error: 0.149317 Iteration 3 Error: 0.030372 Align patch 7 18 left Iteration 1 Error: 0.820416 Iteration 2 Error: 0.108578 Iteration 3 Error: 0.034834 Align patch 8 17 left Iteration 1 Error: 0.787794 Iteration 2 Error: 0.158942 Iteration 3 Error: 0.051071 Iteration 4 Error: 0.009012 Align patch 9 16 left Iteration 1 Error: 0.426537 Iteration 2 Error: 0.069861 Iteration 3 Error: 0.017858 Align patch 10 15 left Iteration 1 Error: 0.487835 Iteration 2 Error: 0.083856 Iteration 3 Error: 0.020052 Align patch 11 14 left Iteration 1 Error: 0.768408 Iteration 2 Error: 0.135527 Iteration 3 Error: 0.043772 Align patch 12 13 left Iteration 1 Error: 1.068297 Iteration 2 Error: 0.149188 Iteration 3 Error: 0.038556 Align patch 13 12 left Iteration 1 Error: 0.713475 Iteration 2 Error: 0.207217 Iteration 3 Error: 0.058820 Iteration 4 Error: 0.015689 Align patch 14 11 left Iteration 1 Error: 0.726450 Iteration 2 Error: 0.102775 Iteration 3 Error: 0.014571 Align patch 15 10 left Iteration 1 Error: 0.527580 Iteration 2 Error: 0.074033 Iteration 3 Error: 0.019465 Align patch 16 9 left Iteration 1 Error: 0.728391 Iteration 2 Error: 0.125966 Iteration 3 Error: 0.030769 Align patch 17 8 left Iteration 1 Error: 0.805660 Iteration 2 Error: 0.095824 Iteration 3 Error: 0.024112 Align patch 18 7 left Iteration 1 Error: 0.702658 Iteration 2 Error: 0.125070 Iteration 3 Error: 0.040867 Align patch 19 6 left Iteration 1 Error: 0.685872 Iteration 2 Error: 0.116049 Iteration 3 Error: 0.015327 Align patch 20 5 left Iteration 1 Error: 0.683130 Iteration 2 Error: 0.097888 Iteration 3 Error: 0.017317 Align patch 21 4 left Iteration 1 Error: 1.211745 Iteration 2 Error: 0.199610 Iteration 3 Error: 0.061644 Iteration 4 Error: 0.029694 Align patch 22 3 left Iteration 1 Error: 1.155469 Iteration 2 Error: 0.160796 Iteration 3 Error: 0.032829 Align patch 23 2 left Iteration 1 Error: 0.728666 Iteration 2 Error: 0.097784 Iteration 3 Error: 0.032895 Align patch 24 1 left Iteration 1 Error: 0.646667 Iteration 2 Error: 0.097201 Iteration 3 Error: 0.025611 Align patch 25 0 left Iteration 1 Error: 0.725679 Iteration 2 Error: 0.114337 Iteration 3 Error: 0.027669 3D Fitting completed. Patch alignment time: 11.99(sec) Local motion has been corrected. Process thread exits. Computational time: 22.797165 sec Total time: 31.805347 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00007hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00007hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.594252s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00007hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 5.053336s ........................................ >>>>>>TIME<<<<<< FFT: 1.049576s Defocus_U Defocus_V Angle CCC 11697.27 11181.64 86.70 0.048033 Final Values Defocus_U Defocus_V Angle CCC 11717.59 11198.83 87.97 0.087225 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00008hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00008hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 44.26 7.49 Num Hot pixels: 198 Hot pixel threshold: 89.20 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.479660 Iteration 2 Error: 0.323329 Iteration 3 Error: 0.069567 Iteration 4 Error: 0.023934 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.30 -0.03 ...... Frame ( 3) shift: -0.60 -0.06 ...... Frame ( 4) shift: -0.89 -0.09 ...... Frame ( 5) shift: -1.19 -0.12 ...... Frame ( 6) shift: -1.34 -0.07 ...... Frame ( 7) shift: -1.34 0.06 ...... Frame ( 8) shift: -1.34 0.20 ...... Frame ( 9) shift: -1.28 0.34 ...... Frame ( 10) shift: -1.18 0.49 ...... Frame ( 11) shift: -1.08 0.65 ...... Frame ( 12) shift: -1.01 0.77 ...... Frame ( 13) shift: -0.95 0.86 ...... Frame ( 14) shift: -0.90 0.95 ...... Frame ( 15) shift: -0.85 1.04 ...... Frame ( 16) shift: -0.81 1.13 ...... Frame ( 17) shift: -0.77 1.23 ...... Frame ( 18) shift: -0.71 1.33 ...... Frame ( 19) shift: -0.65 1.43 ...... Frame ( 20) shift: -0.58 1.53 ...... Frame ( 21) shift: -0.48 1.61 ...... Frame ( 22) shift: -0.35 1.66 ...... Frame ( 23) shift: -0.22 1.71 ...... Frame ( 24) shift: -0.16 1.78 ...... Frame ( 25) shift: -0.17 1.88 ...... Frame ( 26) shift: -0.19 1.98 ...... Frame ( 27) shift: -0.16 2.07 ...... Frame ( 28) shift: -0.11 2.15 ...... Frame ( 29) shift: -0.05 2.22 ...... Frame ( 30) shift: -0.02 2.31 ...... Frame ( 31) shift: -0.01 2.40 ...... Frame ( 32) shift: -0.00 2.50 ...... Frame ( 33) shift: 0.06 2.55 ...... Frame ( 34) shift: 0.18 2.55 ...... Frame ( 35) shift: 0.31 2.55 ...... Frame ( 36) shift: 0.38 2.57 ...... Frame ( 37) shift: 0.40 2.59 ...... Frame ( 38) shift: 0.43 2.62 ...... Frame ( 39) shift: 0.45 2.65 ...... Frame ( 40) shift: 0.48 2.68 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.322549 Iteration 2 Error: 0.457608 Iteration 3 Error: 0.179364 Iteration 4 Error: 0.085092 Iteration 5 Error: 0.042570 Align patch 2 23 left Iteration 1 Error: 1.604083 Iteration 2 Error: 0.208503 Iteration 3 Error: 0.066586 Iteration 4 Error: 0.018471 Align patch 3 22 left Iteration 1 Error: 1.329610 Iteration 2 Error: 0.227299 Iteration 3 Error: 0.064399 Iteration 4 Error: 0.023578 Align patch 4 21 left Iteration 1 Error: 0.909915 Iteration 2 Error: 0.083741 Iteration 3 Error: 0.018602 Align patch 5 20 left Iteration 1 Error: 0.697607 Iteration 2 Error: 0.064014 Iteration 3 Error: 0.015574 Align patch 6 19 left Iteration 1 Error: 0.950304 Iteration 2 Error: 0.415377 Iteration 3 Error: 0.151041 Iteration 4 Error: 0.060689 Iteration 5 Error: 0.036406 Align patch 7 18 left Iteration 1 Error: 1.220595 Iteration 2 Error: 0.160122 Iteration 3 Error: 0.046207 Align patch 8 17 left Iteration 1 Error: 1.058910 Iteration 2 Error: 0.128958 Iteration 3 Error: 0.024888 Align patch 9 16 left Iteration 1 Error: 0.541327 Iteration 2 Error: 0.072006 Iteration 3 Error: 0.022768 Align patch 10 15 left Iteration 1 Error: 0.785917 Iteration 2 Error: 0.160510 Iteration 3 Error: 0.044551 Align patch 11 14 left Iteration 1 Error: 1.121156 Iteration 2 Error: 0.244235 Iteration 3 Error: 0.068204 Iteration 4 Error: 0.030822 Align patch 12 13 left Iteration 1 Error: 0.667375 Iteration 2 Error: 0.137489 Iteration 3 Error: 0.034850 Align patch 13 12 left Iteration 1 Error: 0.534857 Iteration 2 Error: 0.131261 Iteration 3 Error: 0.033338 Align patch 14 11 left Iteration 1 Error: 0.429706 Iteration 2 Error: 0.083370 Iteration 3 Error: 0.026167 Align patch 15 10 left Iteration 1 Error: 1.022126 Iteration 2 Error: 0.162776 Iteration 3 Error: 0.032870 Align patch 16 9 left Iteration 1 Error: 1.131487 Iteration 2 Error: 0.230419 Iteration 3 Error: 0.040508 Align patch 17 8 left Iteration 1 Error: 1.191254 Iteration 2 Error: 0.163253 Iteration 3 Error: 0.051353 Iteration 4 Error: 0.018011 Align patch 18 7 left Iteration 1 Error: 0.946105 Iteration 2 Error: 0.120525 Iteration 3 Error: 0.027025 Align patch 19 6 left Iteration 1 Error: 0.785769 Iteration 2 Error: 0.108459 Iteration 3 Error: 0.031665 Align patch 20 5 left Iteration 1 Error: 0.541832 Iteration 2 Error: 0.093796 Iteration 3 Error: 0.023310 Align patch 21 4 left Iteration 1 Error: 1.082308 Iteration 2 Error: 0.235810 Iteration 3 Error: 0.047775 Align patch 22 3 left Iteration 1 Error: 1.404132 Iteration 2 Error: 0.198064 Iteration 3 Error: 0.030450 Align patch 23 2 left Iteration 1 Error: 0.868183 Iteration 2 Error: 0.126197 Iteration 3 Error: 0.039263 Align patch 24 1 left Iteration 1 Error: 0.540565 Iteration 2 Error: 0.075732 Iteration 3 Error: 0.021566 Align patch 25 0 left Iteration 1 Error: 1.057921 Iteration 2 Error: 0.185686 Iteration 3 Error: 0.042579 3D Fitting completed. Patch alignment time: 11.44(sec) Local motion has been corrected. Process thread exits. Computational time: 22.669535 sec Total time: 34.457378 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00008hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00008hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.608639s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00008hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.366486s ........................................ >>>>>>TIME<<<<<< FFT: 0.974029s Defocus_U Defocus_V Angle CCC 11814.46 12638.68 10.83 0.062039 Final Values Defocus_U Defocus_V Angle CCC 11828.53 12649.62 11.14 0.108087 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00008hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00008hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 44.37 7.60 Num Hot pixels: 216 Hot pixel threshold: 89.95 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.557911 Iteration 2 Error: 0.277321 Iteration 3 Error: 0.063909 Iteration 4 Error: 0.023424 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.26 0.06 ...... Frame ( 3) shift: -0.52 0.12 ...... Frame ( 4) shift: -0.78 0.18 ...... Frame ( 5) shift: -1.03 0.23 ...... Frame ( 6) shift: -1.12 0.35 ...... Frame ( 7) shift: -1.03 0.51 ...... Frame ( 8) shift: -0.94 0.68 ...... Frame ( 9) shift: -0.86 0.81 ...... Frame ( 10) shift: -0.81 0.93 ...... Frame ( 11) shift: -0.75 1.05 ...... Frame ( 12) shift: -0.67 1.16 ...... Frame ( 13) shift: -0.56 1.27 ...... Frame ( 14) shift: -0.45 1.38 ...... Frame ( 15) shift: -0.36 1.45 ...... Frame ( 16) shift: -0.30 1.49 ...... Frame ( 17) shift: -0.24 1.54 ...... Frame ( 18) shift: -0.21 1.58 ...... Frame ( 19) shift: -0.22 1.64 ...... Frame ( 20) shift: -0.22 1.70 ...... Frame ( 21) shift: -0.15 1.76 ...... Frame ( 22) shift: -0.00 1.82 ...... Frame ( 23) shift: 0.14 1.87 ...... Frame ( 24) shift: 0.23 1.94 ...... Frame ( 25) shift: 0.28 2.01 ...... Frame ( 26) shift: 0.33 2.08 ...... Frame ( 27) shift: 0.36 2.12 ...... Frame ( 28) shift: 0.37 2.15 ...... Frame ( 29) shift: 0.39 2.17 ...... Frame ( 30) shift: 0.43 2.24 ...... Frame ( 31) shift: 0.48 2.35 ...... Frame ( 32) shift: 0.54 2.47 ...... Frame ( 33) shift: 0.56 2.53 ...... Frame ( 34) shift: 0.55 2.54 ...... Frame ( 35) shift: 0.55 2.55 ...... Frame ( 36) shift: 0.54 2.59 ...... Frame ( 37) shift: 0.54 2.65 ...... Frame ( 38) shift: 0.53 2.72 ...... Frame ( 39) shift: 0.53 2.78 ...... Frame ( 40) shift: 0.53 2.85 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.970773 Iteration 2 Error: 0.383247 Iteration 3 Error: 0.292826 Iteration 4 Error: 0.078371 Iteration 5 Error: 0.030578 Align patch 2 23 left Iteration 1 Error: 1.950975 Iteration 2 Error: 0.385567 Iteration 3 Error: 0.138768 Iteration 4 Error: 0.049611 Align patch 3 22 left Iteration 1 Error: 0.898586 Iteration 2 Error: 0.235258 Iteration 3 Error: 0.054227 Iteration 4 Error: 0.023347 Align patch 4 21 left Iteration 1 Error: 0.572214 Iteration 2 Error: 0.070068 Iteration 3 Error: 0.014439 Align patch 5 20 left Iteration 1 Error: 0.569549 Iteration 2 Error: 0.089727 Iteration 3 Error: 0.019304 Align patch 6 19 left Iteration 1 Error: 1.516404 Iteration 2 Error: 0.392400 Iteration 3 Error: 0.195182 Iteration 4 Error: 0.118046 Iteration 5 Error: 0.077135 Align patch 6 19 left Iteration 1 Error: 2.631183 Iteration 2 Error: 0.345207 Iteration 3 Error: 0.109438 Iteration 4 Error: 0.041418 Align patch 7 18 left Iteration 1 Error: 1.610728 Iteration 2 Error: 0.273042 Iteration 3 Error: 0.127724 Iteration 4 Error: 0.058866 Iteration 5 Error: 0.024427 Align patch 8 17 left Iteration 1 Error: 0.638965 Iteration 2 Error: 0.104278 Iteration 3 Error: 0.022541 Align patch 9 16 left Iteration 1 Error: 0.666930 Iteration 2 Error: 0.092584 Iteration 3 Error: 0.035058 Align patch 10 15 left Iteration 1 Error: 0.721267 Iteration 2 Error: 0.095675 Iteration 3 Error: 0.020776 Align patch 11 14 left Iteration 1 Error: 1.455887 Iteration 2 Error: 0.350344 Iteration 3 Error: 0.089035 Iteration 4 Error: 0.025079 Align patch 12 13 left Iteration 1 Error: 1.302688 Iteration 2 Error: 0.310183 Iteration 3 Error: 0.046538 Align patch 13 12 left Iteration 1 Error: 0.715681 Iteration 2 Error: 0.128866 Iteration 3 Error: 0.026588 Align patch 14 11 left Iteration 1 Error: 0.612379 Iteration 2 Error: 0.080136 Iteration 3 Error: 0.018542 Align patch 15 10 left Iteration 1 Error: 0.506948 Iteration 2 Error: 0.078410 Iteration 3 Error: 0.013166 Align patch 16 9 left Iteration 1 Error: 1.144871 Iteration 2 Error: 0.183302 Iteration 3 Error: 0.048585 Align patch 17 8 left Iteration 1 Error: 1.639203 Iteration 2 Error: 0.433993 Iteration 3 Error: 0.086225 Iteration 4 Error: 0.056714 Iteration 5 Error: 0.013459 Align patch 18 7 left Iteration 1 Error: 0.673391 Iteration 2 Error: 0.102722 Iteration 3 Error: 0.039891 Align patch 19 6 left Iteration 1 Error: 0.755633 Iteration 2 Error: 0.130290 Iteration 3 Error: 0.028865 Align patch 20 5 left Iteration 1 Error: 0.828716 Iteration 2 Error: 0.080822 Iteration 3 Error: 0.017054 Align patch 21 4 left Iteration 1 Error: 1.024739 Iteration 2 Error: 0.282041 Iteration 3 Error: 0.088123 Iteration 4 Error: 0.029342 Align patch 22 3 left Iteration 1 Error: 0.902798 Iteration 2 Error: 0.229341 Iteration 3 Error: 0.059394 Iteration 4 Error: 0.020115 Align patch 23 2 left Iteration 1 Error: 1.071161 Iteration 2 Error: 0.145086 Iteration 3 Error: 0.028292 Align patch 24 1 left Iteration 1 Error: 0.738753 Iteration 2 Error: 0.112788 Iteration 3 Error: 0.030063 Align patch 25 0 left Iteration 1 Error: 1.090187 Iteration 2 Error: 0.088519 Iteration 3 Error: 0.019257 3D Fitting completed. Patch alignment time: 12.88(sec) Local motion has been corrected. Process thread exits. Computational time: 24.794495 sec Total time: 32.808338 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00008hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00008hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.565729s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00008hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.947582s ........................................ >>>>>>TIME<<<<<< FFT: 0.946433s Defocus_U Defocus_V Angle CCC 10539.06 10035.16 88.12 0.050121 Final Values Defocus_U Defocus_V Angle CCC 10554.69 10028.91 87.18 0.091977 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00008hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00008hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 9.999e-02 CC threshold: 0.734 Mean Std: 44.69 7.77 Num Hot pixels: 186 Hot pixel threshold: 91.31 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.564097 Iteration 2 Error: 0.700322 Iteration 3 Error: 0.472397 Iteration 4 Error: 0.331619 Iteration 5 Error: 0.199180 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.49 -0.09 ...... Frame ( 3) shift: -0.97 -0.18 ...... Frame ( 4) shift: -1.46 -0.27 ...... Frame ( 5) shift: -1.94 -0.37 ...... Frame ( 6) shift: -2.26 -0.41 ...... Frame ( 7) shift: -2.42 -0.39 ...... Frame ( 8) shift: -2.57 -0.38 ...... Frame ( 9) shift: -2.70 -0.38 ...... Frame ( 10) shift: -2.82 -0.40 ...... Frame ( 11) shift: -2.93 -0.41 ...... Frame ( 12) shift: -3.05 -0.46 ...... Frame ( 13) shift: -3.19 -0.54 ...... Frame ( 14) shift: -3.33 -0.61 ...... Frame ( 15) shift: -3.45 -0.69 ...... Frame ( 16) shift: -3.55 -0.76 ...... Frame ( 17) shift: -3.66 -0.83 ...... Frame ( 18) shift: -3.81 -0.95 ...... Frame ( 19) shift: -4.00 -1.13 ...... Frame ( 20) shift: -4.20 -1.30 ...... Frame ( 21) shift: -4.36 -1.43 ...... Frame ( 22) shift: -4.49 -1.52 ...... Frame ( 23) shift: -4.61 -1.62 ...... Frame ( 24) shift: -4.79 -1.73 ...... Frame ( 25) shift: -5.02 -1.86 ...... Frame ( 26) shift: -5.25 -1.99 ...... Frame ( 27) shift: -5.45 -2.08 ...... Frame ( 28) shift: -5.61 -2.13 ...... Frame ( 29) shift: -5.77 -2.18 ...... Frame ( 30) shift: -5.91 -2.25 ...... Frame ( 31) shift: -6.04 -2.35 ...... Frame ( 32) shift: -6.16 -2.45 ...... Frame ( 33) shift: -6.30 -2.55 ...... Frame ( 34) shift: -6.45 -2.64 ...... Frame ( 35) shift: -6.60 -2.74 ...... Frame ( 36) shift: -6.81 -2.82 ...... Frame ( 37) shift: -7.10 -2.86 ...... Frame ( 38) shift: -7.38 -2.91 ...... Frame ( 39) shift: -7.66 -2.96 ...... Frame ( 40) shift: -7.94 -3.00 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.924388 Iteration 2 Error: 0.326804 Iteration 3 Error: 0.145234 Iteration 4 Error: 0.062306 Iteration 5 Error: 0.057864 Align patch 1 24 left Iteration 1 Error: 2.175731 Iteration 2 Error: 0.421518 Iteration 3 Error: 0.140815 Iteration 4 Error: 0.046662 Align patch 2 23 left Iteration 1 Error: 1.595432 Iteration 2 Error: 0.950545 Iteration 3 Error: 0.275631 Iteration 4 Error: 0.127667 Iteration 5 Error: 0.068702 Align patch 2 23 left Iteration 1 Error: 2.374876 Iteration 2 Error: 0.591163 Iteration 3 Error: 0.148832 Iteration 4 Error: 0.065340 Iteration 5 Error: 0.033000 Align patch 3 22 left Iteration 1 Error: 2.305420 Iteration 2 Error: 0.878653 Iteration 3 Error: 0.370542 Iteration 4 Error: 0.177535 Iteration 5 Error: 0.086306 Align patch 3 22 left Iteration 1 Error: 3.806423 Iteration 2 Error: 0.900311 Iteration 3 Error: 0.259945 Iteration 4 Error: 0.088586 Iteration 5 Error: 0.030328 Align patch 4 21 left Iteration 1 Error: 3.781976 Iteration 2 Error: 1.257600 Iteration 3 Error: 0.346482 Iteration 4 Error: 0.144198 Iteration 5 Error: 0.048150 Align patch 5 20 left Iteration 1 Error: 1.971924 Iteration 2 Error: 0.801328 Iteration 3 Error: 0.240361 Iteration 4 Error: 0.145734 Iteration 5 Error: 0.068415 Align patch 5 20 left Iteration 1 Error: 3.206979 Iteration 2 Error: 1.021760 Iteration 3 Error: 0.366661 Iteration 4 Error: 0.183163 Iteration 5 Error: 0.076429 Align patch 6 19 left Iteration 1 Error: 1.789355 Iteration 2 Error: 0.293723 Iteration 3 Error: 0.093949 Iteration 4 Error: 0.038451 Align patch 7 18 left Iteration 1 Error: 2.850665 Iteration 2 Error: 0.802127 Iteration 3 Error: 0.457560 Iteration 4 Error: 0.246221 Iteration 5 Error: 0.143474 Align patch 7 18 left Iteration 1 Error: 2.757658 Iteration 2 Error: 0.546069 Iteration 3 Error: 0.193732 Iteration 4 Error: 0.055845 Iteration 5 Error: 0.039075 Align patch 8 17 left Iteration 1 Error: 6.054782 Iteration 2 Error: 2.580735 Iteration 3 Error: 0.617237 Iteration 4 Error: 0.178438 Iteration 5 Error: 0.065753 Align patch 8 17 left Iteration 1 Error: 5.155116 Iteration 2 Error: 1.065087 Iteration 3 Error: 0.287149 Iteration 4 Error: 0.089528 Iteration 5 Error: 0.033807 Align patch 9 16 left Iteration 1 Error: 6.341394 Iteration 2 Error: 2.047893 Iteration 3 Error: 0.655000 Iteration 4 Error: 0.366244 Iteration 5 Error: 0.183450 Align patch 9 16 left Iteration 1 Error: 6.126744 Iteration 2 Error: 1.381780 Iteration 3 Error: 0.355987 Iteration 4 Error: 0.127678 Iteration 5 Error: 0.041251 Align patch 10 15 left Iteration 1 Error: 4.972090 Iteration 2 Error: 2.857096 Iteration 3 Error: 0.794500 Iteration 4 Error: 0.487268 Iteration 5 Error: 0.375523 Align patch 10 15 left Iteration 1 Error: 4.875911 Iteration 2 Error: 1.282826 Iteration 3 Error: 0.577294 Iteration 4 Error: 0.292697 Iteration 5 Error: 0.140436 Align patch 11 14 left Iteration 1 Error: 3.265679 Iteration 2 Error: 0.600357 Iteration 3 Error: 0.185754 Iteration 4 Error: 0.072022 Iteration 5 Error: 0.048338 Align patch 12 13 left Iteration 1 Error: 3.613414 Iteration 2 Error: 0.548283 Iteration 3 Error: 0.234904 Iteration 4 Error: 0.092008 Iteration 5 Error: 0.032826 Align patch 13 12 left Iteration 1 Error: 3.080036 Iteration 2 Error: 1.619256 Iteration 3 Error: 0.617721 Iteration 4 Error: 0.266086 Iteration 5 Error: 0.122070 Align patch 13 12 left Iteration 1 Error: 3.306330 Iteration 2 Error: 0.839081 Iteration 3 Error: 0.225390 Iteration 4 Error: 0.088755 Iteration 5 Error: 0.033484 Align patch 14 11 left Iteration 1 Error: 4.081692 Iteration 2 Error: 1.234682 Iteration 3 Error: 0.444798 Iteration 4 Error: 0.200852 Iteration 5 Error: 0.093215 Align patch 14 11 left Iteration 1 Error: 5.296307 Iteration 2 Error: 1.156248 Iteration 3 Error: 0.304149 Iteration 4 Error: 0.106037 Iteration 5 Error: 0.056764 Align patch 15 10 left Iteration 1 Error: 5.648219 Iteration 2 Error: 2.764791 Iteration 3 Error: 0.985694 Iteration 4 Error: 0.656268 Iteration 5 Error: 0.495853 Align patch 15 10 left Iteration 1 Error: 6.066436 Iteration 2 Error: 1.828627 Iteration 3 Error: 0.587155 Iteration 4 Error: 0.336087 Iteration 5 Error: 0.149769 Align patch 16 9 left Iteration 1 Error: 1.943219 Iteration 2 Error: 0.441567 Iteration 3 Error: 0.188623 Iteration 4 Error: 0.048973 Align patch 17 8 left Iteration 1 Error: 1.450903 Iteration 2 Error: 0.386410 Iteration 3 Error: 0.115766 Iteration 4 Error: 0.054581 Iteration 5 Error: 0.025934 Align patch 18 7 left Iteration 1 Error: 1.441328 Iteration 2 Error: 0.508226 Iteration 3 Error: 0.175945 Iteration 4 Error: 0.066112 Iteration 5 Error: 0.031909 Align patch 19 6 left Iteration 1 Error: 2.745899 Iteration 2 Error: 0.829271 Iteration 3 Error: 0.304187 Iteration 4 Error: 0.114847 Iteration 5 Error: 0.061285 Align patch 19 6 left Iteration 1 Error: 2.450607 Iteration 2 Error: 0.525313 Iteration 3 Error: 0.133768 Iteration 4 Error: 0.037236 Align patch 20 5 left Iteration 1 Error: 3.946706 Iteration 2 Error: 2.287802 Iteration 3 Error: 1.862811 Iteration 4 Error: 1.897282 Iteration 5 Error: 1.847214 Align patch 20 5 left Iteration 1 Error: 3.334497 Iteration 2 Error: 0.930449 Iteration 3 Error: 0.290421 Iteration 4 Error: 0.121886 Iteration 5 Error: 0.049423 Align patch 21 4 left Iteration 1 Error: 2.143465 Iteration 2 Error: 0.409974 Iteration 3 Error: 0.147359 Iteration 4 Error: 0.047191 Align patch 22 3 left Iteration 1 Error: 1.540892 Iteration 2 Error: 0.814671 Iteration 3 Error: 0.261693 Iteration 4 Error: 0.101946 Iteration 5 Error: 0.026983 Align patch 23 2 left Iteration 1 Error: 1.598908 Iteration 2 Error: 0.273785 Iteration 3 Error: 0.062720 Iteration 4 Error: 0.024776 Align patch 24 1 left Iteration 1 Error: 0.865562 Iteration 2 Error: 0.181030 Iteration 3 Error: 0.132700 Iteration 4 Error: 0.049303 Align patch 25 0 left Iteration 1 Error: 1.093076 Iteration 2 Error: 0.267883 Iteration 3 Error: 0.074526 Iteration 4 Error: 0.044195 3D Fitting completed. Patch alignment time: 22.42(sec) Local motion has been corrected. Process thread exits. Computational time: 33.823891 sec Total time: 43.785099 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00008hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00008hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.594276s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00008hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.049523s ........................................ >>>>>>TIME<<<<<< FFT: 0.946502s Defocus_U Defocus_V Angle CCC 11894.56 12648.46 6.20 0.061447 Final Values Defocus_U Defocus_V Angle CCC 11889.86 12659.41 6.51 0.118075 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00008hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00008hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 44.12 7.45 Num Hot pixels: 210 Hot pixel threshold: 88.83 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.675924 Iteration 2 Error: 0.180463 Iteration 3 Error: 0.039617 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.44 0.08 ...... Frame ( 3) shift: -0.87 0.16 ...... Frame ( 4) shift: -1.31 0.25 ...... Frame ( 5) shift: -1.75 0.33 ...... Frame ( 6) shift: -1.93 0.43 ...... Frame ( 7) shift: -1.87 0.56 ...... Frame ( 8) shift: -1.80 0.68 ...... Frame ( 9) shift: -1.76 0.81 ...... Frame ( 10) shift: -1.74 0.93 ...... Frame ( 11) shift: -1.73 1.05 ...... Frame ( 12) shift: -1.70 1.18 ...... Frame ( 13) shift: -1.67 1.32 ...... Frame ( 14) shift: -1.64 1.47 ...... Frame ( 15) shift: -1.61 1.59 ...... Frame ( 16) shift: -1.59 1.71 ...... Frame ( 17) shift: -1.57 1.82 ...... Frame ( 18) shift: -1.56 1.89 ...... Frame ( 19) shift: -1.54 1.93 ...... Frame ( 20) shift: -1.53 1.98 ...... Frame ( 21) shift: -1.52 2.00 ...... Frame ( 22) shift: -1.50 2.00 ...... Frame ( 23) shift: -1.49 2.00 ...... Frame ( 24) shift: -1.49 2.06 ...... Frame ( 25) shift: -1.50 2.19 ...... Frame ( 26) shift: -1.51 2.31 ...... Frame ( 27) shift: -1.48 2.36 ...... Frame ( 28) shift: -1.42 2.33 ...... Frame ( 29) shift: -1.35 2.30 ...... Frame ( 30) shift: -1.31 2.31 ...... Frame ( 31) shift: -1.29 2.34 ...... Frame ( 32) shift: -1.27 2.38 ...... Frame ( 33) shift: -1.26 2.44 ...... Frame ( 34) shift: -1.27 2.52 ...... Frame ( 35) shift: -1.28 2.59 ...... Frame ( 36) shift: -1.25 2.65 ...... Frame ( 37) shift: -1.20 2.68 ...... Frame ( 38) shift: -1.15 2.71 ...... Frame ( 39) shift: -1.10 2.74 ...... Frame ( 40) shift: -1.05 2.78 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.602786 Iteration 2 Error: 0.258829 Iteration 3 Error: 0.110069 Iteration 4 Error: 0.059449 Iteration 5 Error: 0.025788 Align patch 2 23 left Iteration 1 Error: 0.898406 Iteration 2 Error: 0.147432 Iteration 3 Error: 0.034307 Align patch 3 22 left Iteration 1 Error: 0.593732 Iteration 2 Error: 0.090745 Iteration 3 Error: 0.032682 Align patch 4 21 left Iteration 1 Error: 0.574383 Iteration 2 Error: 0.100679 Iteration 3 Error: 0.024351 Align patch 5 20 left Iteration 1 Error: 1.006037 Iteration 2 Error: 0.137207 Iteration 3 Error: 0.031346 Align patch 6 19 left Iteration 1 Error: 0.722786 Iteration 2 Error: 0.183554 Iteration 3 Error: 0.045589 Align patch 7 18 left Iteration 1 Error: 1.147160 Iteration 2 Error: 0.209760 Iteration 3 Error: 0.037212 Align patch 8 17 left Iteration 1 Error: 0.770263 Iteration 2 Error: 0.193017 Iteration 3 Error: 0.044592 Align patch 9 16 left Iteration 1 Error: 0.544215 Iteration 2 Error: 0.089750 Iteration 3 Error: 0.024915 Align patch 10 15 left Iteration 1 Error: 0.521530 Iteration 2 Error: 0.089799 Iteration 3 Error: 0.029994 Align patch 11 14 left Iteration 1 Error: 1.185278 Iteration 2 Error: 0.133171 Iteration 3 Error: 0.027854 Align patch 12 13 left Iteration 1 Error: 0.938485 Iteration 2 Error: 0.156507 Iteration 3 Error: 0.041868 Align patch 13 12 left Iteration 1 Error: 0.609673 Iteration 2 Error: 0.174371 Iteration 3 Error: 0.047682 Align patch 14 11 left Iteration 1 Error: 0.811720 Iteration 2 Error: 0.138009 Iteration 3 Error: 0.033406 Align patch 15 10 left Iteration 1 Error: 0.679583 Iteration 2 Error: 0.117099 Iteration 3 Error: 0.018730 Align patch 16 9 left Iteration 1 Error: 1.067533 Iteration 2 Error: 0.243470 Iteration 3 Error: 0.044466 Align patch 17 8 left Iteration 1 Error: 1.059265 Iteration 2 Error: 0.194721 Iteration 3 Error: 0.044688 Align patch 18 7 left Iteration 1 Error: 0.545817 Iteration 2 Error: 0.056390 Iteration 3 Error: 0.012481 Align patch 19 6 left Iteration 1 Error: 0.534089 Iteration 2 Error: 0.069833 Iteration 3 Error: 0.014647 Align patch 20 5 left Iteration 1 Error: 0.677975 Iteration 2 Error: 0.074730 Iteration 3 Error: 0.021139 Align patch 21 4 left Iteration 1 Error: 0.787008 Iteration 2 Error: 0.159933 Iteration 3 Error: 0.046589 Align patch 22 3 left Iteration 1 Error: 0.465493 Iteration 2 Error: 0.090103 Iteration 3 Error: 0.022497 Align patch 23 2 left Iteration 1 Error: 0.711065 Iteration 2 Error: 0.135709 Iteration 3 Error: 0.038764 Align patch 24 1 left Iteration 1 Error: 0.745900 Iteration 2 Error: 0.089269 Iteration 3 Error: 0.023106 Align patch 25 0 left Iteration 1 Error: 1.129064 Iteration 2 Error: 0.164784 Iteration 3 Error: 0.036246 3D Fitting completed. Patch alignment time: 11.02(sec) Local motion has been corrected. Process thread exits. Computational time: 26.165339 sec Total time: 35.665596 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00008hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00008hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.774381s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00008hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 5.396287s ........................................ >>>>>>TIME<<<<<< FFT: 0.834405s Defocus_U Defocus_V Angle CCC 13796.87 13031.25 81.37 0.055010 Final Values Defocus_U Defocus_V Angle CCC 13804.68 13032.82 81.68 0.095419 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00009hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00009hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.001e-01 CC threshold: 0.735 Mean Std: 44.51 7.46 Num Hot pixels: 210 Hot pixel threshold: 89.26 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.315166 Iteration 2 Error: 0.209253 Iteration 3 Error: 0.051065 Iteration 4 Error: 0.013864 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.21 0.08 ...... Frame ( 3) shift: -0.41 0.16 ...... Frame ( 4) shift: -0.62 0.24 ...... Frame ( 5) shift: -0.82 0.33 ...... Frame ( 6) shift: -0.95 0.40 ...... Frame ( 7) shift: -1.00 0.46 ...... Frame ( 8) shift: -1.06 0.52 ...... Frame ( 9) shift: -1.02 0.61 ...... Frame ( 10) shift: -0.91 0.71 ...... Frame ( 11) shift: -0.79 0.82 ...... Frame ( 12) shift: -0.74 0.96 ...... Frame ( 13) shift: -0.75 1.11 ...... Frame ( 14) shift: -0.76 1.27 ...... Frame ( 15) shift: -0.74 1.37 ...... Frame ( 16) shift: -0.66 1.42 ...... Frame ( 17) shift: -0.59 1.47 ...... Frame ( 18) shift: -0.52 1.55 ...... Frame ( 19) shift: -0.46 1.65 ...... Frame ( 20) shift: -0.40 1.75 ...... Frame ( 21) shift: -0.35 1.85 ...... Frame ( 22) shift: -0.33 1.93 ...... Frame ( 23) shift: -0.30 2.01 ...... Frame ( 24) shift: -0.29 2.05 ...... Frame ( 25) shift: -0.29 2.06 ...... Frame ( 26) shift: -0.29 2.06 ...... Frame ( 27) shift: -0.30 2.11 ...... Frame ( 28) shift: -0.30 2.19 ...... Frame ( 29) shift: -0.30 2.27 ...... Frame ( 30) shift: -0.29 2.33 ...... Frame ( 31) shift: -0.27 2.37 ...... Frame ( 32) shift: -0.24 2.40 ...... Frame ( 33) shift: -0.21 2.45 ...... Frame ( 34) shift: -0.15 2.51 ...... Frame ( 35) shift: -0.09 2.57 ...... Frame ( 36) shift: -0.06 2.63 ...... Frame ( 37) shift: -0.05 2.67 ...... Frame ( 38) shift: -0.04 2.72 ...... Frame ( 39) shift: -0.04 2.77 ...... Frame ( 40) shift: -0.03 2.81 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.882469 Iteration 2 Error: 0.294392 Iteration 3 Error: 0.070598 Iteration 4 Error: 0.026079 Align patch 2 23 left Iteration 1 Error: 0.646063 Iteration 2 Error: 0.244693 Iteration 3 Error: 0.067066 Iteration 4 Error: 0.029607 Align patch 3 22 left Iteration 1 Error: 0.685707 Iteration 2 Error: 0.086225 Iteration 3 Error: 0.041790 Align patch 4 21 left Iteration 1 Error: 0.565261 Iteration 2 Error: 0.103477 Iteration 3 Error: 0.029695 Align patch 5 20 left Iteration 1 Error: 0.682064 Iteration 2 Error: 0.135975 Iteration 3 Error: 0.036310 Align patch 6 19 left Iteration 1 Error: 1.690618 Iteration 2 Error: 0.341468 Iteration 3 Error: 0.042414 Align patch 7 18 left Iteration 1 Error: 0.666136 Iteration 2 Error: 0.195172 Iteration 3 Error: 0.071400 Iteration 4 Error: 0.025988 Align patch 8 17 left Iteration 1 Error: 0.767135 Iteration 2 Error: 0.153512 Iteration 3 Error: 0.050882 Iteration 4 Error: 0.014814 Align patch 9 16 left Iteration 1 Error: 1.233136 Iteration 2 Error: 0.206381 Iteration 3 Error: 0.104720 Iteration 4 Error: 0.030060 Align patch 10 15 left Iteration 1 Error: 0.515342 Iteration 2 Error: 0.084798 Iteration 3 Error: 0.034769 Align patch 11 14 left Iteration 1 Error: 1.129006 Iteration 2 Error: 0.225678 Iteration 3 Error: 0.049142 Align patch 12 13 left Iteration 1 Error: 0.563769 Iteration 2 Error: 0.125985 Iteration 3 Error: 0.035905 Align patch 13 12 left Iteration 1 Error: 0.625130 Iteration 2 Error: 0.160789 Iteration 3 Error: 0.022997 Align patch 14 11 left Iteration 1 Error: 0.890030 Iteration 2 Error: 0.099916 Iteration 3 Error: 0.024951 Align patch 15 10 left Iteration 1 Error: 0.671153 Iteration 2 Error: 0.093791 Iteration 3 Error: 0.037142 Align patch 16 9 left Iteration 1 Error: 1.449468 Iteration 2 Error: 0.201447 Iteration 3 Error: 0.035946 Align patch 17 8 left Iteration 1 Error: 1.035866 Iteration 2 Error: 0.168766 Iteration 3 Error: 0.035869 Align patch 18 7 left Iteration 1 Error: 0.912667 Iteration 2 Error: 0.212320 Iteration 3 Error: 0.054366 Iteration 4 Error: 0.013189 Align patch 19 6 left Iteration 1 Error: 0.469021 Iteration 2 Error: 0.047400 Align patch 20 5 left Iteration 1 Error: 0.869320 Iteration 2 Error: 0.127825 Iteration 3 Error: 0.028876 Align patch 21 4 left Iteration 1 Error: 0.957808 Iteration 2 Error: 0.160082 Iteration 3 Error: 0.026412 Align patch 22 3 left Iteration 1 Error: 1.585705 Iteration 2 Error: 0.154040 Iteration 3 Error: 0.027179 Align patch 23 2 left Iteration 1 Error: 0.856519 Iteration 2 Error: 0.141154 Iteration 3 Error: 0.035387 Align patch 24 1 left Iteration 1 Error: 0.488403 Iteration 2 Error: 0.074062 Iteration 3 Error: 0.018126 Align patch 25 0 left Iteration 1 Error: 1.029555 Iteration 2 Error: 0.121046 Iteration 3 Error: 0.025077 3D Fitting completed. Patch alignment time: 11.58(sec) Local motion has been corrected. Process thread exits. Computational time: 20.338120 sec Total time: 26.556641 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00009hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00009hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.555984s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00009hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.324996s ........................................ >>>>>>TIME<<<<<< FFT: 0.829307s Defocus_U Defocus_V Angle CCC 13058.59 13925.78 11.26 0.052990 Final Values Defocus_U Defocus_V Angle CCC 13055.47 13916.41 11.26 0.093254 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00009hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00009hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 44.27 7.54 Num Hot pixels: 192 Hot pixel threshold: 89.49 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.451438 Iteration 2 Error: 0.145043 Iteration 3 Error: 0.032154 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.27 -0.01 ...... Frame ( 3) shift: -0.55 -0.02 ...... Frame ( 4) shift: -0.82 -0.03 ...... Frame ( 5) shift: -1.10 -0.03 ...... Frame ( 6) shift: -1.26 -0.00 ...... Frame ( 7) shift: -1.32 0.07 ...... Frame ( 8) shift: -1.38 0.14 ...... Frame ( 9) shift: -1.44 0.24 ...... Frame ( 10) shift: -1.49 0.37 ...... Frame ( 11) shift: -1.54 0.50 ...... Frame ( 12) shift: -1.57 0.61 ...... Frame ( 13) shift: -1.56 0.71 ...... Frame ( 14) shift: -1.56 0.82 ...... Frame ( 15) shift: -1.54 0.90 ...... Frame ( 16) shift: -1.50 0.96 ...... Frame ( 17) shift: -1.47 1.02 ...... Frame ( 18) shift: -1.47 1.11 ...... Frame ( 19) shift: -1.50 1.22 ...... Frame ( 20) shift: -1.53 1.33 ...... Frame ( 21) shift: -1.53 1.41 ...... Frame ( 22) shift: -1.52 1.48 ...... Frame ( 23) shift: -1.50 1.55 ...... Frame ( 24) shift: -1.49 1.61 ...... Frame ( 25) shift: -1.50 1.67 ...... Frame ( 26) shift: -1.50 1.73 ...... Frame ( 27) shift: -1.49 1.76 ...... Frame ( 28) shift: -1.47 1.75 ...... Frame ( 29) shift: -1.44 1.74 ...... Frame ( 30) shift: -1.44 1.74 ...... Frame ( 31) shift: -1.45 1.76 ...... Frame ( 32) shift: -1.47 1.78 ...... Frame ( 33) shift: -1.45 1.77 ...... Frame ( 34) shift: -1.40 1.73 ...... Frame ( 35) shift: -1.36 1.69 ...... Frame ( 36) shift: -1.36 1.67 ...... Frame ( 37) shift: -1.40 1.67 ...... Frame ( 38) shift: -1.45 1.67 ...... Frame ( 39) shift: -1.49 1.67 ...... Frame ( 40) shift: -1.53 1.67 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.131318 Iteration 2 Error: 0.311678 Iteration 3 Error: 0.146687 Iteration 4 Error: 0.049714 Align patch 2 23 left Iteration 1 Error: 0.963306 Iteration 2 Error: 0.157354 Iteration 3 Error: 0.026537 Align patch 3 22 left Iteration 1 Error: 0.916652 Iteration 2 Error: 0.102303 Iteration 3 Error: 0.029833 Align patch 4 21 left Iteration 1 Error: 0.555865 Iteration 2 Error: 0.053293 Iteration 3 Error: 0.015351 Align patch 5 20 left Iteration 1 Error: 0.763845 Iteration 2 Error: 0.074830 Iteration 3 Error: 0.023499 Align patch 6 19 left Iteration 1 Error: 1.258494 Iteration 2 Error: 0.265784 Iteration 3 Error: 0.104288 Iteration 4 Error: 0.059522 Iteration 5 Error: 0.027867 Align patch 7 18 left Iteration 1 Error: 0.741152 Iteration 2 Error: 0.470621 Iteration 3 Error: 0.151233 Iteration 4 Error: 0.088222 Iteration 5 Error: 0.044217 Align patch 8 17 left Iteration 1 Error: 0.543505 Iteration 2 Error: 0.102228 Iteration 3 Error: 0.023434 Align patch 9 16 left Iteration 1 Error: 0.512118 Iteration 2 Error: 0.042866 Align patch 10 15 left Iteration 1 Error: 0.713726 Iteration 2 Error: 0.061839 Iteration 3 Error: 0.012605 Align patch 11 14 left Iteration 1 Error: 0.750400 Iteration 2 Error: 0.184529 Iteration 3 Error: 0.067946 Iteration 4 Error: 0.034133 Align patch 12 13 left Iteration 1 Error: 0.986669 Iteration 2 Error: 0.174370 Iteration 3 Error: 0.039899 Align patch 13 12 left Iteration 1 Error: 0.621275 Iteration 2 Error: 0.083315 Iteration 3 Error: 0.021615 Align patch 14 11 left Iteration 1 Error: 0.412306 Iteration 2 Error: 0.065609 Iteration 3 Error: 0.018157 Align patch 15 10 left Iteration 1 Error: 0.472358 Iteration 2 Error: 0.073941 Iteration 3 Error: 0.015448 Align patch 16 9 left Iteration 1 Error: 1.023448 Iteration 2 Error: 0.144710 Iteration 3 Error: 0.046062 Align patch 17 8 left Iteration 1 Error: 0.996283 Iteration 2 Error: 0.161364 Iteration 3 Error: 0.032481 Align patch 18 7 left Iteration 1 Error: 0.570424 Iteration 2 Error: 0.071443 Iteration 3 Error: 0.019777 Align patch 19 6 left Iteration 1 Error: 0.610892 Iteration 2 Error: 0.094846 Iteration 3 Error: 0.027540 Align patch 20 5 left Iteration 1 Error: 0.573730 Iteration 2 Error: 0.099864 Iteration 3 Error: 0.021865 Align patch 21 4 left Iteration 1 Error: 0.851903 Iteration 2 Error: 0.132048 Iteration 3 Error: 0.025500 Align patch 22 3 left Iteration 1 Error: 0.492995 Iteration 2 Error: 0.062251 Iteration 3 Error: 0.017807 Align patch 23 2 left Iteration 1 Error: 0.732963 Iteration 2 Error: 0.153594 Iteration 3 Error: 0.023033 Align patch 24 1 left Iteration 1 Error: 0.700624 Iteration 2 Error: 0.133713 Iteration 3 Error: 0.024332 Align patch 25 0 left Iteration 1 Error: 0.554361 Iteration 2 Error: 0.051520 Iteration 3 Error: 0.010375 3D Fitting completed. Patch alignment time: 11.31(sec) Local motion has been corrected. Process thread exits. Computational time: 21.195808 sec Total time: 26.510710 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00009hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00009hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.589527s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00009hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.677460s ........................................ >>>>>>TIME<<<<<< FFT: 0.916089s Defocus_U Defocus_V Angle CCC 11535.16 10992.19 89.27 0.050548 Final Values Defocus_U Defocus_V Angle CCC 11546.15 11021.94 88.95 0.092987 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00009hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00009hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 44.55 7.39 Num Hot pixels: 212 Hot pixel threshold: 88.91 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.328085 Iteration 2 Error: 0.106644 Iteration 3 Error: 0.016481 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.36 0.01 ...... Frame ( 3) shift: -0.72 0.02 ...... Frame ( 4) shift: -1.08 0.03 ...... Frame ( 5) shift: -1.44 0.04 ...... Frame ( 6) shift: -1.61 0.08 ...... Frame ( 7) shift: -1.61 0.14 ...... Frame ( 8) shift: -1.61 0.21 ...... Frame ( 9) shift: -1.61 0.28 ...... Frame ( 10) shift: -1.61 0.36 ...... Frame ( 11) shift: -1.61 0.43 ...... Frame ( 12) shift: -1.60 0.48 ...... Frame ( 13) shift: -1.58 0.52 ...... Frame ( 14) shift: -1.56 0.56 ...... Frame ( 15) shift: -1.56 0.60 ...... Frame ( 16) shift: -1.57 0.64 ...... Frame ( 17) shift: -1.58 0.68 ...... Frame ( 18) shift: -1.62 0.73 ...... Frame ( 19) shift: -1.70 0.78 ...... Frame ( 20) shift: -1.77 0.83 ...... Frame ( 21) shift: -1.79 0.87 ...... Frame ( 22) shift: -1.76 0.90 ...... Frame ( 23) shift: -1.72 0.93 ...... Frame ( 24) shift: -1.74 0.96 ...... Frame ( 25) shift: -1.82 0.99 ...... Frame ( 26) shift: -1.89 1.01 ...... Frame ( 27) shift: -1.94 1.02 ...... Frame ( 28) shift: -1.96 1.00 ...... Frame ( 29) shift: -1.98 0.99 ...... Frame ( 30) shift: -1.97 0.98 ...... Frame ( 31) shift: -1.94 0.98 ...... Frame ( 32) shift: -1.91 0.99 ...... Frame ( 33) shift: -1.89 1.00 ...... Frame ( 34) shift: -1.88 1.02 ...... Frame ( 35) shift: -1.87 1.04 ...... Frame ( 36) shift: -1.85 1.06 ...... Frame ( 37) shift: -1.83 1.08 ...... Frame ( 38) shift: -1.81 1.10 ...... Frame ( 39) shift: -1.78 1.13 ...... Frame ( 40) shift: -1.76 1.15 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.485509 Iteration 2 Error: 0.373567 Iteration 3 Error: 0.030637 Align patch 2 23 left Iteration 1 Error: 1.637639 Iteration 2 Error: 0.182320 Iteration 3 Error: 0.039355 Align patch 3 22 left Iteration 1 Error: 0.762312 Iteration 2 Error: 0.094759 Iteration 3 Error: 0.020545 Align patch 4 21 left Iteration 1 Error: 0.803418 Iteration 2 Error: 0.191696 Iteration 3 Error: 0.049811 Align patch 5 20 left Iteration 1 Error: 0.721743 Iteration 2 Error: 0.135689 Iteration 3 Error: 0.029671 Align patch 6 19 left Iteration 1 Error: 1.193518 Iteration 2 Error: 0.180873 Iteration 3 Error: 0.034646 Align patch 7 18 left Iteration 1 Error: 0.729638 Iteration 2 Error: 0.220387 Iteration 3 Error: 0.068091 Iteration 4 Error: 0.025310 Align patch 8 17 left Iteration 1 Error: 0.817934 Iteration 2 Error: 0.091812 Iteration 3 Error: 0.024808 Align patch 9 16 left Iteration 1 Error: 0.734162 Iteration 2 Error: 0.149199 Iteration 3 Error: 0.032167 Align patch 10 15 left Iteration 1 Error: 0.859136 Iteration 2 Error: 0.133135 Iteration 3 Error: 0.030427 Align patch 11 14 left Iteration 1 Error: 1.043065 Iteration 2 Error: 0.175065 Iteration 3 Error: 0.034532 Align patch 12 13 left Iteration 1 Error: 1.382821 Iteration 2 Error: 0.184853 Iteration 3 Error: 0.057491 Iteration 4 Error: 0.022904 Align patch 13 12 left Iteration 1 Error: 1.073091 Iteration 2 Error: 0.170540 Iteration 3 Error: 0.048076 Align patch 14 11 left Iteration 1 Error: 1.061476 Iteration 2 Error: 0.131420 Iteration 3 Error: 0.040148 Align patch 15 10 left Iteration 1 Error: 0.586801 Iteration 2 Error: 0.087911 Iteration 3 Error: 0.020289 Align patch 16 9 left Iteration 1 Error: 1.166926 Iteration 2 Error: 0.180072 Iteration 3 Error: 0.031790 Align patch 17 8 left Iteration 1 Error: 0.812294 Iteration 2 Error: 0.159837 Iteration 3 Error: 0.050669 Iteration 4 Error: 0.022511 Align patch 18 7 left Iteration 1 Error: 0.816681 Iteration 2 Error: 0.146860 Iteration 3 Error: 0.044365 Align patch 19 6 left Iteration 1 Error: 0.852631 Iteration 2 Error: 0.211793 Iteration 3 Error: 0.036901 Align patch 20 5 left Iteration 1 Error: 0.981664 Iteration 2 Error: 0.158303 Iteration 3 Error: 0.028312 Align patch 21 4 left Iteration 1 Error: 1.310166 Iteration 2 Error: 0.203683 Iteration 3 Error: 0.037558 Align patch 22 3 left Iteration 1 Error: 1.452487 Iteration 2 Error: 0.140123 Iteration 3 Error: 0.023191 Align patch 23 2 left Iteration 1 Error: 1.264316 Iteration 2 Error: 0.155848 Iteration 3 Error: 0.037651 Align patch 24 1 left Iteration 1 Error: 0.685074 Iteration 2 Error: 0.156509 Iteration 3 Error: 0.029584 Align patch 25 0 left Iteration 1 Error: 0.420140 Iteration 2 Error: 0.055594 Iteration 3 Error: 0.015825 3D Fitting completed. Patch alignment time: 11.98(sec) Local motion has been corrected. Process thread exits. Computational time: 21.467911 sec Total time: 26.870630 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00009hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00009hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.527928s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00009hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.847618s ........................................ >>>>>>TIME<<<<<< FFT: 0.870314s Defocus_U Defocus_V Angle CCC 13173.83 14072.27 5.91 0.049770 Final Values Defocus_U Defocus_V Angle CCC 13180.08 14066.02 4.97 0.084539 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00009hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00009hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 43.41 7.50 Num Hot pixels: 207 Hot pixel threshold: 88.38 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.872181 Iteration 2 Error: 0.125984 Iteration 3 Error: 0.037621 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.31 -0.02 ...... Frame ( 3) shift: -0.61 -0.04 ...... Frame ( 4) shift: -0.92 -0.06 ...... Frame ( 5) shift: -1.22 -0.08 ...... Frame ( 6) shift: -1.37 -0.06 ...... Frame ( 7) shift: -1.37 -0.02 ...... Frame ( 8) shift: -1.37 0.03 ...... Frame ( 9) shift: -1.39 0.06 ...... Frame ( 10) shift: -1.42 0.09 ...... Frame ( 11) shift: -1.44 0.11 ...... Frame ( 12) shift: -1.41 0.14 ...... Frame ( 13) shift: -1.30 0.16 ...... Frame ( 14) shift: -1.20 0.19 ...... Frame ( 15) shift: -1.13 0.28 ...... Frame ( 16) shift: -1.11 0.41 ...... Frame ( 17) shift: -1.09 0.55 ...... Frame ( 18) shift: -1.10 0.65 ...... Frame ( 19) shift: -1.12 0.70 ...... Frame ( 20) shift: -1.15 0.75 ...... Frame ( 21) shift: -1.17 0.77 ...... Frame ( 22) shift: -1.17 0.75 ...... Frame ( 23) shift: -1.16 0.73 ...... Frame ( 24) shift: -1.19 0.71 ...... Frame ( 25) shift: -1.23 0.69 ...... Frame ( 26) shift: -1.27 0.67 ...... Frame ( 27) shift: -1.27 0.70 ...... Frame ( 28) shift: -1.21 0.77 ...... Frame ( 29) shift: -1.15 0.83 ...... Frame ( 30) shift: -1.14 0.88 ...... Frame ( 31) shift: -1.19 0.90 ...... Frame ( 32) shift: -1.23 0.91 ...... Frame ( 33) shift: -1.25 0.95 ...... Frame ( 34) shift: -1.26 1.00 ...... Frame ( 35) shift: -1.27 1.06 ...... Frame ( 36) shift: -1.26 1.09 ...... Frame ( 37) shift: -1.24 1.09 ...... Frame ( 38) shift: -1.21 1.09 ...... Frame ( 39) shift: -1.19 1.10 ...... Frame ( 40) shift: -1.17 1.10 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.553060 Iteration 2 Error: 0.224777 Iteration 3 Error: 0.061500 Iteration 4 Error: 0.022631 Align patch 2 23 left Iteration 1 Error: 0.925908 Iteration 2 Error: 0.180051 Iteration 3 Error: 0.053602 Iteration 4 Error: 0.019477 Align patch 3 22 left Iteration 1 Error: 1.162540 Iteration 2 Error: 0.254021 Iteration 3 Error: 0.081220 Iteration 4 Error: 0.020072 Align patch 4 21 left Iteration 1 Error: 1.620418 Iteration 2 Error: 0.325201 Iteration 3 Error: 0.084374 Iteration 4 Error: 0.022965 Align patch 5 20 left Iteration 1 Error: 1.882196 Iteration 2 Error: 0.240086 Iteration 3 Error: 0.067139 Iteration 4 Error: 0.015353 Align patch 6 19 left Iteration 1 Error: 1.040335 Iteration 2 Error: 0.291312 Iteration 3 Error: 0.074116 Iteration 4 Error: 0.020676 Align patch 7 18 left Iteration 1 Error: 1.002134 Iteration 2 Error: 0.220220 Iteration 3 Error: 0.052140 Iteration 4 Error: 0.023411 Align patch 8 17 left Iteration 1 Error: 1.334856 Iteration 2 Error: 0.267618 Iteration 3 Error: 0.043804 Align patch 9 16 left Iteration 1 Error: 1.386833 Iteration 2 Error: 0.284942 Iteration 3 Error: 0.079914 Iteration 4 Error: 0.014062 Align patch 10 15 left Iteration 1 Error: 1.182674 Iteration 2 Error: 0.245626 Iteration 3 Error: 0.048831 Align patch 11 14 left Iteration 1 Error: 0.969487 Iteration 2 Error: 0.306997 Iteration 3 Error: 0.069459 Iteration 4 Error: 0.021715 Align patch 12 13 left Iteration 1 Error: 0.938380 Iteration 2 Error: 0.186707 Iteration 3 Error: 0.044527 Align patch 13 12 left Iteration 1 Error: 0.886656 Iteration 2 Error: 0.153135 Iteration 3 Error: 0.032481 Align patch 14 11 left Iteration 1 Error: 0.758387 Iteration 2 Error: 0.099602 Iteration 3 Error: 0.024449 Align patch 15 10 left Iteration 1 Error: 1.232502 Iteration 2 Error: 0.235545 Iteration 3 Error: 0.041598 Align patch 16 9 left Iteration 1 Error: 2.109582 Iteration 2 Error: 0.768502 Iteration 3 Error: 0.654452 Iteration 4 Error: 0.584763 Iteration 5 Error: 0.465086 Align patch 16 9 left Iteration 1 Error: 2.704685 Iteration 2 Error: 0.676675 Iteration 3 Error: 0.260551 Iteration 4 Error: 0.118484 Iteration 5 Error: 0.061917 Align patch 17 8 left Iteration 1 Error: 0.993247 Iteration 2 Error: 0.170843 Iteration 3 Error: 0.045794 Align patch 18 7 left Iteration 1 Error: 1.444814 Iteration 2 Error: 0.366874 Iteration 3 Error: 0.221447 Iteration 4 Error: 0.122018 Iteration 5 Error: 0.063757 Align patch 18 7 left Iteration 1 Error: 2.051857 Iteration 2 Error: 0.404770 Iteration 3 Error: 0.145623 Iteration 4 Error: 0.056542 Iteration 5 Error: 0.021006 Align patch 19 6 left Iteration 1 Error: 0.837738 Iteration 2 Error: 0.263888 Iteration 3 Error: 0.109020 Iteration 4 Error: 0.037296 Align patch 20 5 left Iteration 1 Error: 0.698688 Iteration 2 Error: 0.167227 Iteration 3 Error: 0.033506 Align patch 21 4 left Iteration 1 Error: 3.068095 Iteration 2 Error: 0.877341 Iteration 3 Error: 0.819171 Iteration 4 Error: 0.695404 Iteration 5 Error: 0.532949 Align patch 21 4 left Iteration 1 Error: 3.077947 Iteration 2 Error: 0.887589 Iteration 3 Error: 0.509996 Iteration 4 Error: 0.326616 Iteration 5 Error: 0.199501 Align patch 22 3 left Iteration 1 Error: 1.729556 Iteration 2 Error: 0.465193 Iteration 3 Error: 0.202635 Iteration 4 Error: 0.103716 Iteration 5 Error: 0.045454 Align patch 23 2 left Iteration 1 Error: 2.306757 Iteration 2 Error: 0.839972 Iteration 3 Error: 0.554781 Iteration 4 Error: 0.353924 Iteration 5 Error: 0.230076 Align patch 23 2 left Iteration 1 Error: 2.116435 Iteration 2 Error: 0.503719 Iteration 3 Error: 0.168569 Iteration 4 Error: 0.071981 Iteration 5 Error: 0.033968 Align patch 24 1 left Iteration 1 Error: 0.594576 Iteration 2 Error: 0.112838 Iteration 3 Error: 0.037980 Align patch 25 0 left Iteration 1 Error: 0.598103 Iteration 2 Error: 0.096095 Iteration 3 Error: 0.015519 3D Fitting completed. Patch alignment time: 15.03(sec) Local motion has been corrected. Process thread exits. Computational time: 24.418056 sec Total time: 30.425659 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00009hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00009hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.568206s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00009hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.601500s ........................................ >>>>>>TIME<<<<<< FFT: 0.938296s Defocus_U Defocus_V Angle CCC 10892.60 10228.54 84.46 0.037935 Final Values Defocus_U Defocus_V Angle CCC 10901.98 10241.04 84.78 0.072342 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00010hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00010hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.997e-02 CC threshold: 0.734 Mean Std: 41.68 7.09 Num Hot pixels: 202 Hot pixel threshold: 84.23 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.081618 Iteration 2 Error: 0.191828 Iteration 3 Error: 0.053848 Iteration 4 Error: 0.017596 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.14 0.07 ...... Frame ( 3) shift: -0.29 0.15 ...... Frame ( 4) shift: -0.43 0.22 ...... Frame ( 5) shift: -0.58 0.30 ...... Frame ( 6) shift: -0.64 0.36 ...... Frame ( 7) shift: -0.63 0.40 ...... Frame ( 8) shift: -0.61 0.45 ...... Frame ( 9) shift: -0.61 0.53 ...... Frame ( 10) shift: -0.64 0.65 ...... Frame ( 11) shift: -0.67 0.77 ...... Frame ( 12) shift: -0.66 0.85 ...... Frame ( 13) shift: -0.59 0.90 ...... Frame ( 14) shift: -0.52 0.95 ...... Frame ( 15) shift: -0.50 0.98 ...... Frame ( 16) shift: -0.52 1.01 ...... Frame ( 17) shift: -0.55 1.04 ...... Frame ( 18) shift: -0.56 1.10 ...... Frame ( 19) shift: -0.56 1.19 ...... Frame ( 20) shift: -0.56 1.29 ...... Frame ( 21) shift: -0.53 1.39 ...... Frame ( 22) shift: -0.46 1.48 ...... Frame ( 23) shift: -0.39 1.58 ...... Frame ( 24) shift: -0.36 1.64 ...... Frame ( 25) shift: -0.35 1.67 ...... Frame ( 26) shift: -0.34 1.69 ...... Frame ( 27) shift: -0.34 1.76 ...... Frame ( 28) shift: -0.35 1.87 ...... Frame ( 29) shift: -0.36 1.99 ...... Frame ( 30) shift: -0.35 2.04 ...... Frame ( 31) shift: -0.32 2.04 ...... Frame ( 32) shift: -0.29 2.05 ...... Frame ( 33) shift: -0.26 2.04 ...... Frame ( 34) shift: -0.24 2.03 ...... Frame ( 35) shift: -0.23 2.02 ...... Frame ( 36) shift: -0.23 2.05 ...... Frame ( 37) shift: -0.25 2.13 ...... Frame ( 38) shift: -0.27 2.21 ...... Frame ( 39) shift: -0.29 2.29 ...... Frame ( 40) shift: -0.31 2.38 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.765628 Iteration 2 Error: 0.201578 Iteration 3 Error: 0.080694 Iteration 4 Error: 0.041922 Align patch 2 23 left Iteration 1 Error: 0.854900 Iteration 2 Error: 0.110207 Iteration 3 Error: 0.040619 Align patch 3 22 left Iteration 1 Error: 1.008280 Iteration 2 Error: 0.178089 Iteration 3 Error: 0.084532 Iteration 4 Error: 0.030345 Align patch 4 21 left Iteration 1 Error: 0.790582 Iteration 2 Error: 0.265481 Iteration 3 Error: 0.090037 Iteration 4 Error: 0.040351 Align patch 5 20 left Iteration 1 Error: 0.901608 Iteration 2 Error: 0.180055 Iteration 3 Error: 0.045251 Align patch 6 19 left Iteration 1 Error: 0.701124 Iteration 2 Error: 0.138979 Iteration 3 Error: 0.036436 Align patch 7 18 left Iteration 1 Error: 0.980438 Iteration 2 Error: 0.163916 Iteration 3 Error: 0.039966 Align patch 8 17 left Iteration 1 Error: 1.085153 Iteration 2 Error: 0.139980 Iteration 3 Error: 0.032205 Align patch 9 16 left Iteration 1 Error: 0.702224 Iteration 2 Error: 0.122137 Iteration 3 Error: 0.039179 Align patch 10 15 left Iteration 1 Error: 0.746262 Iteration 2 Error: 0.110523 Iteration 3 Error: 0.036820 Align patch 11 14 left Iteration 1 Error: 0.849869 Iteration 2 Error: 0.229759 Iteration 3 Error: 0.057930 Iteration 4 Error: 0.025727 Align patch 12 13 left Iteration 1 Error: 0.792470 Iteration 2 Error: 0.094930 Iteration 3 Error: 0.033808 Align patch 13 12 left Iteration 1 Error: 0.678254 Iteration 2 Error: 0.128232 Iteration 3 Error: 0.031910 Align patch 14 11 left Iteration 1 Error: 1.139474 Iteration 2 Error: 0.238317 Iteration 3 Error: 0.062525 Iteration 4 Error: 0.025711 Align patch 15 10 left Iteration 1 Error: 0.657941 Iteration 2 Error: 0.123244 Iteration 3 Error: 0.047354 Align patch 16 9 left Iteration 1 Error: 1.203877 Iteration 2 Error: 0.224910 Iteration 3 Error: 0.062813 Iteration 4 Error: 0.033665 Align patch 17 8 left Iteration 1 Error: 0.887144 Iteration 2 Error: 0.193885 Iteration 3 Error: 0.039231 Align patch 18 7 left Iteration 1 Error: 0.750143 Iteration 2 Error: 0.145951 Iteration 3 Error: 0.065794 Iteration 4 Error: 0.013198 Align patch 19 6 left Iteration 1 Error: 0.746814 Iteration 2 Error: 0.164187 Iteration 3 Error: 0.035916 Align patch 20 5 left Iteration 1 Error: 0.591396 Iteration 2 Error: 0.098212 Iteration 3 Error: 0.033018 Align patch 21 4 left Iteration 1 Error: 0.895169 Iteration 2 Error: 0.174840 Iteration 3 Error: 0.060468 Iteration 4 Error: 0.026964 Align patch 22 3 left Iteration 1 Error: 0.798650 Iteration 2 Error: 0.222438 Iteration 3 Error: 0.036571 Align patch 23 2 left Iteration 1 Error: 1.000058 Iteration 2 Error: 0.140392 Iteration 3 Error: 0.040078 Align patch 24 1 left Iteration 1 Error: 0.825979 Iteration 2 Error: 0.127438 Iteration 3 Error: 0.024248 Align patch 25 0 left Iteration 1 Error: 1.016479 Iteration 2 Error: 0.102432 Iteration 3 Error: 0.030079 3D Fitting completed. Patch alignment time: 12.13(sec) Local motion has been corrected. Process thread exits. Computational time: 21.764523 sec Total time: 27.378487 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00010hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00010hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.665491s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00010hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.501120s ........................................ >>>>>>TIME<<<<<< FFT: 0.887635s Defocus_U Defocus_V Angle CCC 10488.29 11293.11 13.50 0.034045 Final Values Defocus_U Defocus_V Angle CCC 10530.51 11329.08 13.20 0.061296 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00010hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00010hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.001e-01 CC threshold: 0.735 Mean Std: 42.93 7.31 Num Hot pixels: 214 Hot pixel threshold: 86.77 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.577902 Iteration 2 Error: 0.062560 Iteration 3 Error: 0.017387 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.21 0.02 ...... Frame ( 3) shift: -0.42 0.03 ...... Frame ( 4) shift: -0.63 0.05 ...... Frame ( 5) shift: -0.84 0.07 ...... Frame ( 6) shift: -0.94 0.10 ...... Frame ( 7) shift: -0.93 0.16 ...... Frame ( 8) shift: -0.92 0.21 ...... Frame ( 9) shift: -0.90 0.28 ...... Frame ( 10) shift: -0.88 0.36 ...... Frame ( 11) shift: -0.86 0.44 ...... Frame ( 12) shift: -0.83 0.47 ...... Frame ( 13) shift: -0.79 0.47 ...... Frame ( 14) shift: -0.75 0.46 ...... Frame ( 15) shift: -0.75 0.47 ...... Frame ( 16) shift: -0.77 0.51 ...... Frame ( 17) shift: -0.80 0.54 ...... Frame ( 18) shift: -0.83 0.59 ...... Frame ( 19) shift: -0.85 0.63 ...... Frame ( 20) shift: -0.87 0.68 ...... Frame ( 21) shift: -0.84 0.70 ...... Frame ( 22) shift: -0.77 0.68 ...... Frame ( 23) shift: -0.70 0.67 ...... Frame ( 24) shift: -0.64 0.65 ...... Frame ( 25) shift: -0.58 0.64 ...... Frame ( 26) shift: -0.52 0.63 ...... Frame ( 27) shift: -0.50 0.64 ...... Frame ( 28) shift: -0.53 0.66 ...... Frame ( 29) shift: -0.55 0.68 ...... Frame ( 30) shift: -0.56 0.68 ...... Frame ( 31) shift: -0.55 0.68 ...... Frame ( 32) shift: -0.54 0.67 ...... Frame ( 33) shift: -0.51 0.67 ...... Frame ( 34) shift: -0.47 0.68 ...... Frame ( 35) shift: -0.42 0.69 ...... Frame ( 36) shift: -0.36 0.70 ...... Frame ( 37) shift: -0.30 0.70 ...... Frame ( 38) shift: -0.24 0.69 ...... Frame ( 39) shift: -0.18 0.69 ...... Frame ( 40) shift: -0.12 0.69 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.015728 Iteration 2 Error: 0.141338 Iteration 3 Error: 0.034591 Align patch 2 23 left Iteration 1 Error: 0.602962 Iteration 2 Error: 0.141190 Iteration 3 Error: 0.038594 Align patch 3 22 left Iteration 1 Error: 0.541302 Iteration 2 Error: 0.105136 Iteration 3 Error: 0.021315 Align patch 4 21 left Iteration 1 Error: 0.682172 Iteration 2 Error: 0.084577 Iteration 3 Error: 0.021493 Align patch 5 20 left Iteration 1 Error: 0.422707 Iteration 2 Error: 0.097025 Iteration 3 Error: 0.022051 Align patch 6 19 left Iteration 1 Error: 0.772688 Iteration 2 Error: 0.109173 Iteration 3 Error: 0.030379 Align patch 7 18 left Iteration 1 Error: 0.832407 Iteration 2 Error: 0.169418 Iteration 3 Error: 0.041323 Align patch 8 17 left Iteration 1 Error: 0.859920 Iteration 2 Error: 0.110402 Iteration 3 Error: 0.028075 Align patch 9 16 left Iteration 1 Error: 0.825888 Iteration 2 Error: 0.132346 Iteration 3 Error: 0.028889 Align patch 10 15 left Iteration 1 Error: 0.526331 Iteration 2 Error: 0.079724 Iteration 3 Error: 0.013569 Align patch 11 14 left Iteration 1 Error: 0.811751 Iteration 2 Error: 0.143662 Iteration 3 Error: 0.034028 Align patch 12 13 left Iteration 1 Error: 0.794231 Iteration 2 Error: 0.149751 Iteration 3 Error: 0.041781 Align patch 13 12 left Iteration 1 Error: 0.570916 Iteration 2 Error: 0.094356 Iteration 3 Error: 0.017383 Align patch 14 11 left Iteration 1 Error: 0.600560 Iteration 2 Error: 0.104680 Iteration 3 Error: 0.039450 Align patch 15 10 left Iteration 1 Error: 0.530471 Iteration 2 Error: 0.072224 Iteration 3 Error: 0.018616 Align patch 16 9 left Iteration 1 Error: 0.686769 Iteration 2 Error: 0.113251 Iteration 3 Error: 0.029097 Align patch 17 8 left Iteration 1 Error: 0.739707 Iteration 2 Error: 0.171152 Iteration 3 Error: 0.038043 Align patch 18 7 left Iteration 1 Error: 0.785866 Iteration 2 Error: 0.102241 Iteration 3 Error: 0.028003 Align patch 19 6 left Iteration 1 Error: 0.599785 Iteration 2 Error: 0.098608 Iteration 3 Error: 0.019935 Align patch 20 5 left Iteration 1 Error: 0.631223 Iteration 2 Error: 0.097035 Iteration 3 Error: 0.025578 Align patch 21 4 left Iteration 1 Error: 0.596035 Iteration 2 Error: 0.095326 Iteration 3 Error: 0.019262 Align patch 22 3 left Iteration 1 Error: 0.504474 Iteration 2 Error: 0.106225 Iteration 3 Error: 0.037171 Align patch 23 2 left Iteration 1 Error: 0.679776 Iteration 2 Error: 0.097929 Iteration 3 Error: 0.025086 Align patch 24 1 left Iteration 1 Error: 0.562287 Iteration 2 Error: 0.175465 Iteration 3 Error: 0.055679 Iteration 4 Error: 0.019907 Align patch 25 0 left Iteration 1 Error: 0.768768 Iteration 2 Error: 0.179053 Iteration 3 Error: 0.044539 3D Fitting completed. Patch alignment time: 11.65(sec) Local motion has been corrected. Process thread exits. Computational time: 21.127552 sec Total time: 27.525089 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00010hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00010hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.649065s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00010hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.802553s ........................................ >>>>>>TIME<<<<<< FFT: 0.942205s Defocus_U Defocus_V Angle CCC 10376.97 10818.37 3.68 0.040877 Final Values Defocus_U Defocus_V Angle CCC 10392.60 10824.63 2.12 0.075150 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00010hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00010hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 40.42 7.01 Num Hot pixels: 179 Hot pixel threshold: 82.49 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.810107 Iteration 2 Error: 0.114163 Iteration 3 Error: 0.030594 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.12 0.00 ...... Frame ( 3) shift: -0.24 0.01 ...... Frame ( 4) shift: -0.35 0.01 ...... Frame ( 5) shift: -0.47 0.01 ...... Frame ( 6) shift: -0.52 0.07 ...... Frame ( 7) shift: -0.51 0.17 ...... Frame ( 8) shift: -0.50 0.27 ...... Frame ( 9) shift: -0.46 0.38 ...... Frame ( 10) shift: -0.40 0.50 ...... Frame ( 11) shift: -0.33 0.62 ...... Frame ( 12) shift: -0.28 0.68 ...... Frame ( 13) shift: -0.25 0.69 ...... Frame ( 14) shift: -0.22 0.70 ...... Frame ( 15) shift: -0.20 0.74 ...... Frame ( 16) shift: -0.20 0.82 ...... Frame ( 17) shift: -0.20 0.90 ...... Frame ( 18) shift: -0.22 0.94 ...... Frame ( 19) shift: -0.27 0.95 ...... Frame ( 20) shift: -0.32 0.95 ...... Frame ( 21) shift: -0.33 0.98 ...... Frame ( 22) shift: -0.29 1.03 ...... Frame ( 23) shift: -0.25 1.08 ...... Frame ( 24) shift: -0.20 1.13 ...... Frame ( 25) shift: -0.15 1.17 ...... Frame ( 26) shift: -0.11 1.22 ...... Frame ( 27) shift: -0.10 1.25 ...... Frame ( 28) shift: -0.13 1.29 ...... Frame ( 29) shift: -0.16 1.32 ...... Frame ( 30) shift: -0.14 1.37 ...... Frame ( 31) shift: -0.08 1.43 ...... Frame ( 32) shift: -0.02 1.50 ...... Frame ( 33) shift: 0.01 1.52 ...... Frame ( 34) shift: 0.01 1.48 ...... Frame ( 35) shift: 0.01 1.45 ...... Frame ( 36) shift: 0.02 1.43 ...... Frame ( 37) shift: 0.04 1.44 ...... Frame ( 38) shift: 0.07 1.45 ...... Frame ( 39) shift: 0.10 1.45 ...... Frame ( 40) shift: 0.13 1.46 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.510389 Iteration 2 Error: 0.251832 Iteration 3 Error: 0.098979 Iteration 4 Error: 0.032511 Align patch 2 23 left Iteration 1 Error: 0.735663 Iteration 2 Error: 0.166089 Iteration 3 Error: 0.045644 Align patch 3 22 left Iteration 1 Error: 0.539215 Iteration 2 Error: 0.099083 Iteration 3 Error: 0.025444 Align patch 4 21 left Iteration 1 Error: 0.812898 Iteration 2 Error: 0.126960 Iteration 3 Error: 0.032031 Align patch 5 20 left Iteration 1 Error: 0.855742 Iteration 2 Error: 0.148022 Iteration 3 Error: 0.062060 Iteration 4 Error: 0.010209 Align patch 6 19 left Iteration 1 Error: 0.992507 Iteration 2 Error: 0.151185 Iteration 3 Error: 0.032822 Align patch 7 18 left Iteration 1 Error: 0.609269 Iteration 2 Error: 0.142675 Iteration 3 Error: 0.049564 Align patch 8 17 left Iteration 1 Error: 0.758380 Iteration 2 Error: 0.119102 Iteration 3 Error: 0.029145 Align patch 9 16 left Iteration 1 Error: 0.554205 Iteration 2 Error: 0.073296 Iteration 3 Error: 0.015064 Align patch 10 15 left Iteration 1 Error: 0.817416 Iteration 2 Error: 0.114504 Iteration 3 Error: 0.023242 Align patch 11 14 left Iteration 1 Error: 0.885637 Iteration 2 Error: 0.199914 Iteration 3 Error: 0.059487 Iteration 4 Error: 0.026311 Align patch 12 13 left Iteration 1 Error: 0.745371 Iteration 2 Error: 0.145390 Iteration 3 Error: 0.033381 Align patch 13 12 left Iteration 1 Error: 0.750255 Iteration 2 Error: 0.142203 Iteration 3 Error: 0.034978 Align patch 14 11 left Iteration 1 Error: 0.937305 Iteration 2 Error: 0.129222 Iteration 3 Error: 0.031939 Align patch 15 10 left Iteration 1 Error: 0.558357 Iteration 2 Error: 0.083088 Iteration 3 Error: 0.013490 Align patch 16 9 left Iteration 1 Error: 0.786551 Iteration 2 Error: 0.154901 Iteration 3 Error: 0.033904 Align patch 17 8 left Iteration 1 Error: 1.026459 Iteration 2 Error: 0.200540 Iteration 3 Error: 0.038333 Align patch 18 7 left Iteration 1 Error: 0.869670 Iteration 2 Error: 0.150843 Iteration 3 Error: 0.044756 Align patch 19 6 left Iteration 1 Error: 0.861733 Iteration 2 Error: 0.112367 Iteration 3 Error: 0.028519 Align patch 20 5 left Iteration 1 Error: 0.544086 Iteration 2 Error: 0.109469 Iteration 3 Error: 0.030106 Align patch 21 4 left Iteration 1 Error: 1.106094 Iteration 2 Error: 0.134754 Iteration 3 Error: 0.034316 Align patch 22 3 left Iteration 1 Error: 0.857425 Iteration 2 Error: 0.208172 Iteration 3 Error: 0.053461 Iteration 4 Error: 0.017606 Align patch 23 2 left Iteration 1 Error: 0.754638 Iteration 2 Error: 0.148298 Iteration 3 Error: 0.029920 Align patch 24 1 left Iteration 1 Error: 1.037394 Iteration 2 Error: 0.154625 Iteration 3 Error: 0.023129 Align patch 25 0 left Iteration 1 Error: 1.418850 Iteration 2 Error: 0.116978 Iteration 3 Error: 0.016262 3D Fitting completed. Patch alignment time: 12.45(sec) Local motion has been corrected. Process thread exits. Computational time: 23.149502 sec Total time: 30.035395 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00010hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00010hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.669561s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00010hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.999401s ........................................ >>>>>>TIME<<<<<< FFT: 1.096662s Defocus_U Defocus_V Angle CCC 13912.11 14724.61 6.53 0.042583 Final Values Defocus_U Defocus_V Angle CCC 13918.36 14721.49 5.91 0.065801 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00010hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00010hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.001e-01 CC threshold: 0.735 Mean Std: 42.10 7.15 Num Hot pixels: 214 Hot pixel threshold: 84.98 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.466628 Iteration 2 Error: 0.049304 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.19 -0.03 ...... Frame ( 3) shift: -0.38 -0.06 ...... Frame ( 4) shift: -0.57 -0.09 ...... Frame ( 5) shift: -0.76 -0.12 ...... Frame ( 6) shift: -0.82 -0.08 ...... Frame ( 7) shift: -0.74 0.04 ...... Frame ( 8) shift: -0.67 0.16 ...... Frame ( 9) shift: -0.63 0.20 ...... Frame ( 10) shift: -0.62 0.16 ...... Frame ( 11) shift: -0.60 0.13 ...... Frame ( 12) shift: -0.62 0.10 ...... Frame ( 13) shift: -0.68 0.07 ...... Frame ( 14) shift: -0.73 0.05 ...... Frame ( 15) shift: -0.76 0.02 ...... Frame ( 16) shift: -0.77 -0.01 ...... Frame ( 17) shift: -0.78 -0.03 ...... Frame ( 18) shift: -0.78 -0.02 ...... Frame ( 19) shift: -0.76 0.05 ...... Frame ( 20) shift: -0.74 0.11 ...... Frame ( 21) shift: -0.72 0.16 ...... Frame ( 22) shift: -0.70 0.18 ...... Frame ( 23) shift: -0.68 0.21 ...... Frame ( 24) shift: -0.66 0.22 ...... Frame ( 25) shift: -0.63 0.20 ...... Frame ( 26) shift: -0.61 0.18 ...... Frame ( 27) shift: -0.61 0.19 ...... Frame ( 28) shift: -0.63 0.25 ...... Frame ( 29) shift: -0.64 0.30 ...... Frame ( 30) shift: -0.65 0.33 ...... Frame ( 31) shift: -0.64 0.32 ...... Frame ( 32) shift: -0.64 0.31 ...... Frame ( 33) shift: -0.62 0.37 ...... Frame ( 34) shift: -0.58 0.50 ...... Frame ( 35) shift: -0.55 0.62 ...... Frame ( 36) shift: -0.55 0.65 ...... Frame ( 37) shift: -0.60 0.59 ...... Frame ( 38) shift: -0.65 0.54 ...... Frame ( 39) shift: -0.70 0.48 ...... Frame ( 40) shift: -0.75 0.42 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.112999 Iteration 2 Error: 0.138604 Iteration 3 Error: 0.031077 Align patch 2 23 left Iteration 1 Error: 0.893644 Iteration 2 Error: 0.147710 Iteration 3 Error: 0.058126 Iteration 4 Error: 0.018692 Align patch 3 22 left Iteration 1 Error: 0.784866 Iteration 2 Error: 0.077741 Iteration 3 Error: 0.023045 Align patch 4 21 left Iteration 1 Error: 0.945618 Iteration 2 Error: 0.114163 Iteration 3 Error: 0.046056 Align patch 5 20 left Iteration 1 Error: 0.510071 Iteration 2 Error: 0.074144 Iteration 3 Error: 0.012354 Align patch 6 19 left Iteration 1 Error: 0.709229 Iteration 2 Error: 0.085820 Iteration 3 Error: 0.025855 Align patch 7 18 left Iteration 1 Error: 0.734961 Iteration 2 Error: 0.118492 Iteration 3 Error: 0.026538 Align patch 8 17 left Iteration 1 Error: 0.663241 Iteration 2 Error: 0.150496 Iteration 3 Error: 0.025288 Align patch 9 16 left Iteration 1 Error: 0.563444 Iteration 2 Error: 0.080247 Iteration 3 Error: 0.017493 Align patch 10 15 left Iteration 1 Error: 0.882260 Iteration 2 Error: 0.112036 Iteration 3 Error: 0.021600 Align patch 11 14 left Iteration 1 Error: 0.804743 Iteration 2 Error: 0.114852 Iteration 3 Error: 0.029373 Align patch 12 13 left Iteration 1 Error: 0.835083 Iteration 2 Error: 0.133727 Iteration 3 Error: 0.032676 Align patch 13 12 left Iteration 1 Error: 0.730433 Iteration 2 Error: 0.096435 Iteration 3 Error: 0.024493 Align patch 14 11 left Iteration 1 Error: 0.771754 Iteration 2 Error: 0.077390 Iteration 3 Error: 0.025122 Align patch 15 10 left Iteration 1 Error: 0.752713 Iteration 2 Error: 0.095630 Iteration 3 Error: 0.020692 Align patch 16 9 left Iteration 1 Error: 0.744174 Iteration 2 Error: 0.114821 Iteration 3 Error: 0.021603 Align patch 17 8 left Iteration 1 Error: 0.509764 Iteration 2 Error: 0.058929 Iteration 3 Error: 0.018564 Align patch 18 7 left Iteration 1 Error: 1.043929 Iteration 2 Error: 0.156899 Iteration 3 Error: 0.040386 Align patch 19 6 left Iteration 1 Error: 0.714319 Iteration 2 Error: 0.138197 Iteration 3 Error: 0.030007 Align patch 20 5 left Iteration 1 Error: 0.815152 Iteration 2 Error: 0.126437 Iteration 3 Error: 0.039949 Align patch 21 4 left Iteration 1 Error: 0.702004 Iteration 2 Error: 0.076706 Iteration 3 Error: 0.022675 Align patch 22 3 left Iteration 1 Error: 0.639818 Iteration 2 Error: 0.099043 Iteration 3 Error: 0.027172 Align patch 23 2 left Iteration 1 Error: 0.824861 Iteration 2 Error: 0.141674 Iteration 3 Error: 0.043180 Align patch 24 1 left Iteration 1 Error: 0.747464 Iteration 2 Error: 0.176814 Iteration 3 Error: 0.067581 Iteration 4 Error: 0.024152 Align patch 25 0 left Iteration 1 Error: 0.850522 Iteration 2 Error: 0.103981 Iteration 3 Error: 0.029361 3D Fitting completed. Patch alignment time: 13.67(sec) Local motion has been corrected. Process thread exits. Computational time: 22.791210 sec Total time: 32.163273 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00010hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00010hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.728508s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00010hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.379956s ........................................ >>>>>>TIME<<<<<< FFT: 1.146391s Defocus_U Defocus_V Angle CCC 14681.67 14095.68 84.39 0.046569 Final Values Defocus_U Defocus_V Angle CCC 14706.67 14098.81 85.02 0.075293 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00011hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00011hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 43.73 7.45 Num Hot pixels: 216 Hot pixel threshold: 88.43 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.117762 Iteration 2 Error: 0.164349 Iteration 3 Error: 0.041169 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.33 -0.09 ...... Frame ( 3) shift: -0.67 -0.19 ...... Frame ( 4) shift: -1.00 -0.28 ...... Frame ( 5) shift: -1.33 -0.37 ...... Frame ( 6) shift: -1.46 -0.36 ...... Frame ( 7) shift: -1.38 -0.25 ...... Frame ( 8) shift: -1.30 -0.13 ...... Frame ( 9) shift: -1.22 -0.01 ...... Frame ( 10) shift: -1.15 0.11 ...... Frame ( 11) shift: -1.07 0.24 ...... Frame ( 12) shift: -1.01 0.33 ...... Frame ( 13) shift: -0.94 0.38 ...... Frame ( 14) shift: -0.88 0.43 ...... Frame ( 15) shift: -0.86 0.48 ...... Frame ( 16) shift: -0.88 0.53 ...... Frame ( 17) shift: -0.89 0.57 ...... Frame ( 18) shift: -0.89 0.61 ...... Frame ( 19) shift: -0.87 0.65 ...... Frame ( 20) shift: -0.86 0.69 ...... Frame ( 21) shift: -0.81 0.74 ...... Frame ( 22) shift: -0.72 0.80 ...... Frame ( 23) shift: -0.64 0.87 ...... Frame ( 24) shift: -0.59 0.89 ...... Frame ( 25) shift: -0.56 0.88 ...... Frame ( 26) shift: -0.53 0.87 ...... Frame ( 27) shift: -0.52 0.90 ...... Frame ( 28) shift: -0.52 0.95 ...... Frame ( 29) shift: -0.52 1.00 ...... Frame ( 30) shift: -0.53 1.03 ...... Frame ( 31) shift: -0.54 1.06 ...... Frame ( 32) shift: -0.56 1.08 ...... Frame ( 33) shift: -0.55 1.13 ...... Frame ( 34) shift: -0.52 1.22 ...... Frame ( 35) shift: -0.49 1.31 ...... Frame ( 36) shift: -0.44 1.37 ...... Frame ( 37) shift: -0.38 1.40 ...... Frame ( 38) shift: -0.32 1.43 ...... Frame ( 39) shift: -0.26 1.47 ...... Frame ( 40) shift: -0.20 1.50 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.206768 Iteration 2 Error: 0.166447 Iteration 3 Error: 0.043775 Align patch 2 23 left Iteration 1 Error: 1.070741 Iteration 2 Error: 0.133711 Iteration 3 Error: 0.038910 Align patch 3 22 left Iteration 1 Error: 0.759309 Iteration 2 Error: 0.094305 Iteration 3 Error: 0.042196 Align patch 4 21 left Iteration 1 Error: 0.766375 Iteration 2 Error: 0.116065 Iteration 3 Error: 0.037468 Align patch 5 20 left Iteration 1 Error: 0.537025 Iteration 2 Error: 0.119559 Iteration 3 Error: 0.025864 Align patch 6 19 left Iteration 1 Error: 1.920244 Iteration 2 Error: 0.298570 Iteration 3 Error: 0.070190 Iteration 4 Error: 0.024433 Align patch 7 18 left Iteration 1 Error: 0.723971 Iteration 2 Error: 0.118549 Iteration 3 Error: 0.033557 Align patch 8 17 left Iteration 1 Error: 1.000642 Iteration 2 Error: 0.170465 Iteration 3 Error: 0.031085 Align patch 9 16 left Iteration 1 Error: 0.812845 Iteration 2 Error: 0.109896 Iteration 3 Error: 0.021523 Align patch 10 15 left Iteration 1 Error: 0.689444 Iteration 2 Error: 0.112496 Iteration 3 Error: 0.029147 Align patch 11 14 left Iteration 1 Error: 1.400144 Iteration 2 Error: 0.118265 Iteration 3 Error: 0.028943 Align patch 12 13 left Iteration 1 Error: 0.807612 Iteration 2 Error: 0.105723 Iteration 3 Error: 0.024669 Align patch 13 12 left Iteration 1 Error: 0.626699 Iteration 2 Error: 0.117901 Iteration 3 Error: 0.024753 Align patch 14 11 left Iteration 1 Error: 0.794265 Iteration 2 Error: 0.092025 Iteration 3 Error: 0.018348 Align patch 15 10 left Iteration 1 Error: 0.785191 Iteration 2 Error: 0.154857 Iteration 3 Error: 0.048846 Align patch 16 9 left Iteration 1 Error: 0.915886 Iteration 2 Error: 0.202243 Iteration 3 Error: 0.049119 Align patch 17 8 left Iteration 1 Error: 0.762605 Iteration 2 Error: 0.083925 Iteration 3 Error: 0.021455 Align patch 18 7 left Iteration 1 Error: 0.564342 Iteration 2 Error: 0.109426 Iteration 3 Error: 0.023691 Align patch 19 6 left Iteration 1 Error: 0.828820 Iteration 2 Error: 0.097250 Iteration 3 Error: 0.031522 Align patch 20 5 left Iteration 1 Error: 0.694413 Iteration 2 Error: 0.100349 Iteration 3 Error: 0.025176 Align patch 21 4 left Iteration 1 Error: 0.904675 Iteration 2 Error: 0.140254 Iteration 3 Error: 0.039659 Align patch 22 3 left Iteration 1 Error: 0.561105 Iteration 2 Error: 0.118710 Iteration 3 Error: 0.033340 Align patch 23 2 left Iteration 1 Error: 0.790281 Iteration 2 Error: 0.183463 Iteration 3 Error: 0.026812 Align patch 24 1 left Iteration 1 Error: 0.720637 Iteration 2 Error: 0.105528 Iteration 3 Error: 0.022317 Align patch 25 0 left Iteration 1 Error: 0.936640 Iteration 2 Error: 0.122158 Iteration 3 Error: 0.038052 3D Fitting completed. Patch alignment time: 12.77(sec) Local motion has been corrected. Process thread exits. Computational time: 22.390705 sec Total time: 29.129454 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00011hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00011hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.927399s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00011hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.901494s ........................................ >>>>>>TIME<<<<<< FFT: 0.941174s Defocus_U Defocus_V Angle CCC 10902.29 11796.96 12.36 0.049138 Final Values Defocus_U Defocus_V Angle CCC 10921.03 11821.97 11.75 0.086347 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00011hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00011hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.001e-01 CC threshold: 0.735 Mean Std: 43.56 7.44 Num Hot pixels: 214 Hot pixel threshold: 88.22 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.859385 Iteration 2 Error: 0.190087 Iteration 3 Error: 0.044118 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.14 0.23 ...... Frame ( 3) shift: -0.28 0.46 ...... Frame ( 4) shift: -0.42 0.69 ...... Frame ( 5) shift: -0.56 0.93 ...... Frame ( 6) shift: -0.59 1.14 ...... Frame ( 7) shift: -0.51 1.35 ...... Frame ( 8) shift: -0.42 1.55 ...... Frame ( 9) shift: -0.32 1.72 ...... Frame ( 10) shift: -0.18 1.85 ...... Frame ( 11) shift: -0.05 1.98 ...... Frame ( 12) shift: 0.03 2.11 ...... Frame ( 13) shift: 0.07 2.24 ...... Frame ( 14) shift: 0.10 2.37 ...... Frame ( 15) shift: 0.13 2.48 ...... Frame ( 16) shift: 0.15 2.58 ...... Frame ( 17) shift: 0.17 2.68 ...... Frame ( 18) shift: 0.20 2.75 ...... Frame ( 19) shift: 0.24 2.79 ...... Frame ( 20) shift: 0.27 2.82 ...... Frame ( 21) shift: 0.26 2.82 ...... Frame ( 22) shift: 0.21 2.78 ...... Frame ( 23) shift: 0.15 2.74 ...... Frame ( 24) shift: 0.13 2.72 ...... Frame ( 25) shift: 0.15 2.73 ...... Frame ( 26) shift: 0.16 2.74 ...... Frame ( 27) shift: 0.18 2.73 ...... Frame ( 28) shift: 0.20 2.70 ...... Frame ( 29) shift: 0.22 2.66 ...... Frame ( 30) shift: 0.22 2.66 ...... Frame ( 31) shift: 0.20 2.69 ...... Frame ( 32) shift: 0.18 2.71 ...... Frame ( 33) shift: 0.19 2.74 ...... Frame ( 34) shift: 0.21 2.77 ...... Frame ( 35) shift: 0.23 2.80 ...... Frame ( 36) shift: 0.26 2.84 ...... Frame ( 37) shift: 0.31 2.89 ...... Frame ( 38) shift: 0.35 2.94 ...... Frame ( 39) shift: 0.40 2.99 ...... Frame ( 40) shift: 0.44 3.05 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.862993 Iteration 2 Error: 0.144011 Iteration 3 Error: 0.049091 Align patch 2 23 left Iteration 1 Error: 1.670576 Iteration 2 Error: 0.242395 Iteration 3 Error: 0.171144 Iteration 4 Error: 0.040977 Align patch 3 22 left Iteration 1 Error: 0.542420 Iteration 2 Error: 0.114985 Iteration 3 Error: 0.046142 Align patch 4 21 left Iteration 1 Error: 0.604253 Iteration 2 Error: 0.167366 Iteration 3 Error: 0.030570 Align patch 5 20 left Iteration 1 Error: 0.861750 Iteration 2 Error: 0.173943 Iteration 3 Error: 0.026926 Align patch 6 19 left Iteration 1 Error: 0.892686 Iteration 2 Error: 0.187401 Iteration 3 Error: 0.040334 Align patch 7 18 left Iteration 1 Error: 0.618988 Iteration 2 Error: 0.073977 Iteration 3 Error: 0.017339 Align patch 8 17 left Iteration 1 Error: 0.529709 Iteration 2 Error: 0.088312 Iteration 3 Error: 0.019138 Align patch 9 16 left Iteration 1 Error: 0.450280 Iteration 2 Error: 0.080551 Iteration 3 Error: 0.029826 Align patch 10 15 left Iteration 1 Error: 0.635826 Iteration 2 Error: 0.103123 Iteration 3 Error: 0.027872 Align patch 11 14 left Iteration 1 Error: 1.356888 Iteration 2 Error: 0.173405 Iteration 3 Error: 0.026985 Align patch 12 13 left Iteration 1 Error: 0.742536 Iteration 2 Error: 0.136097 Iteration 3 Error: 0.071467 Iteration 4 Error: 0.021207 Align patch 13 12 left Iteration 1 Error: 1.046659 Iteration 2 Error: 0.146296 Iteration 3 Error: 0.026953 Align patch 14 11 left Iteration 1 Error: 0.564741 Iteration 2 Error: 0.103704 Iteration 3 Error: 0.020654 Align patch 15 10 left Iteration 1 Error: 0.747946 Iteration 2 Error: 0.118247 Iteration 3 Error: 0.030637 Align patch 16 9 left Iteration 1 Error: 1.088086 Iteration 2 Error: 0.174607 Iteration 3 Error: 0.051830 Iteration 4 Error: 0.023792 Align patch 17 8 left Iteration 1 Error: 1.215558 Iteration 2 Error: 0.196478 Iteration 3 Error: 0.073843 Iteration 4 Error: 0.014910 Align patch 18 7 left Iteration 1 Error: 0.772477 Iteration 2 Error: 0.137871 Iteration 3 Error: 0.043951 Align patch 19 6 left Iteration 1 Error: 0.636035 Iteration 2 Error: 0.097985 Iteration 3 Error: 0.021200 Align patch 20 5 left Iteration 1 Error: 1.095891 Iteration 2 Error: 0.177464 Iteration 3 Error: 0.052112 Iteration 4 Error: 0.025728 Align patch 21 4 left Iteration 1 Error: 0.995322 Iteration 2 Error: 0.206622 Iteration 3 Error: 0.062722 Iteration 4 Error: 0.017584 Align patch 22 3 left Iteration 1 Error: 0.663957 Iteration 2 Error: 0.081217 Iteration 3 Error: 0.031431 Align patch 23 2 left Iteration 1 Error: 0.874305 Iteration 2 Error: 0.078825 Iteration 3 Error: 0.015965 Align patch 24 1 left Iteration 1 Error: 0.802586 Iteration 2 Error: 0.100512 Iteration 3 Error: 0.022612 Align patch 25 0 left Iteration 1 Error: 1.212256 Iteration 2 Error: 0.173833 Iteration 3 Error: 0.047593 3D Fitting completed. Patch alignment time: 11.97(sec) Local motion has been corrected. Process thread exits. Computational time: 21.302528 sec Total time: 31.051342 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00011hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00011hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.604594s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00011hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.232098s ........................................ >>>>>>TIME<<<<<< FFT: 1.043643s Defocus_U Defocus_V Angle CCC 9800.79 10246.10 1.60 0.041141 Final Values Defocus_U Defocus_V Angle CCC 9813.29 10255.48 1.60 0.077649 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00011hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00011hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 43.62 7.28 Num Hot pixels: 240 Hot pixel threshold: 87.28 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.443207 Iteration 2 Error: 0.166654 Iteration 3 Error: 0.035414 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.28 -0.18 ...... Frame ( 3) shift: -0.56 -0.37 ...... Frame ( 4) shift: -0.85 -0.55 ...... Frame ( 5) shift: -1.13 -0.73 ...... Frame ( 6) shift: -1.23 -0.78 ...... Frame ( 7) shift: -1.16 -0.70 ...... Frame ( 8) shift: -1.09 -0.62 ...... Frame ( 9) shift: -1.07 -0.47 ...... Frame ( 10) shift: -1.09 -0.24 ...... Frame ( 11) shift: -1.11 -0.02 ...... Frame ( 12) shift: -1.09 0.19 ...... Frame ( 13) shift: -1.03 0.37 ...... Frame ( 14) shift: -0.98 0.55 ...... Frame ( 15) shift: -0.94 0.67 ...... Frame ( 16) shift: -0.91 0.72 ...... Frame ( 17) shift: -0.88 0.78 ...... Frame ( 18) shift: -0.86 0.85 ...... Frame ( 19) shift: -0.85 0.93 ...... Frame ( 20) shift: -0.84 1.02 ...... Frame ( 21) shift: -0.80 1.09 ...... Frame ( 22) shift: -0.75 1.14 ...... Frame ( 23) shift: -0.70 1.19 ...... Frame ( 24) shift: -0.66 1.21 ...... Frame ( 25) shift: -0.64 1.21 ...... Frame ( 26) shift: -0.63 1.21 ...... Frame ( 27) shift: -0.59 1.24 ...... Frame ( 28) shift: -0.52 1.30 ...... Frame ( 29) shift: -0.45 1.36 ...... Frame ( 30) shift: -0.43 1.36 ...... Frame ( 31) shift: -0.45 1.32 ...... Frame ( 32) shift: -0.48 1.27 ...... Frame ( 33) shift: -0.49 1.26 ...... Frame ( 34) shift: -0.49 1.28 ...... Frame ( 35) shift: -0.49 1.30 ...... Frame ( 36) shift: -0.49 1.31 ...... Frame ( 37) shift: -0.49 1.31 ...... Frame ( 38) shift: -0.49 1.31 ...... Frame ( 39) shift: -0.49 1.31 ...... Frame ( 40) shift: -0.49 1.31 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.623268 Iteration 2 Error: 0.252749 Iteration 3 Error: 0.074607 Iteration 4 Error: 0.026343 Align patch 2 23 left Iteration 1 Error: 1.086525 Iteration 2 Error: 0.158317 Iteration 3 Error: 0.049930 Align patch 3 22 left Iteration 1 Error: 0.700839 Iteration 2 Error: 0.091752 Iteration 3 Error: 0.020369 Align patch 4 21 left Iteration 1 Error: 0.718716 Iteration 2 Error: 0.117640 Iteration 3 Error: 0.018066 Align patch 5 20 left Iteration 1 Error: 0.708435 Iteration 2 Error: 0.098917 Iteration 3 Error: 0.020282 Align patch 6 19 left Iteration 1 Error: 2.052900 Iteration 2 Error: 0.286620 Iteration 3 Error: 0.058896 Iteration 4 Error: 0.020961 Align patch 7 18 left Iteration 1 Error: 0.973741 Iteration 2 Error: 0.121919 Iteration 3 Error: 0.045179 Align patch 8 17 left Iteration 1 Error: 0.764151 Iteration 2 Error: 0.105029 Iteration 3 Error: 0.029760 Align patch 9 16 left Iteration 1 Error: 0.746755 Iteration 2 Error: 0.087400 Iteration 3 Error: 0.018167 Align patch 10 15 left Iteration 1 Error: 0.625973 Iteration 2 Error: 0.078289 Iteration 3 Error: 0.017172 Align patch 11 14 left Iteration 1 Error: 1.236262 Iteration 2 Error: 0.125634 Iteration 3 Error: 0.031308 Align patch 12 13 left Iteration 1 Error: 1.050347 Iteration 2 Error: 0.226086 Iteration 3 Error: 0.089713 Iteration 4 Error: 0.025481 Align patch 13 12 left Iteration 1 Error: 0.510370 Iteration 2 Error: 0.068698 Iteration 3 Error: 0.022995 Align patch 14 11 left Iteration 1 Error: 0.413987 Iteration 2 Error: 0.054760 Iteration 3 Error: 0.012541 Align patch 15 10 left Iteration 1 Error: 0.518156 Iteration 2 Error: 0.061610 Iteration 3 Error: 0.017998 Align patch 16 9 left Iteration 1 Error: 1.084616 Iteration 2 Error: 0.147179 Iteration 3 Error: 0.042307 Align patch 17 8 left Iteration 1 Error: 0.969807 Iteration 2 Error: 0.059972 Iteration 3 Error: 0.018236 Align patch 18 7 left Iteration 1 Error: 0.875818 Iteration 2 Error: 0.136811 Iteration 3 Error: 0.055376 Iteration 4 Error: 0.017569 Align patch 19 6 left Iteration 1 Error: 0.590071 Iteration 2 Error: 0.082653 Iteration 3 Error: 0.020825 Align patch 20 5 left Iteration 1 Error: 0.442546 Iteration 2 Error: 0.057812 Iteration 3 Error: 0.031658 Align patch 21 4 left Iteration 1 Error: 0.661889 Iteration 2 Error: 0.148053 Iteration 3 Error: 0.034789 Align patch 22 3 left Iteration 1 Error: 0.920886 Iteration 2 Error: 0.138900 Iteration 3 Error: 0.024567 Align patch 23 2 left Iteration 1 Error: 0.497061 Iteration 2 Error: 0.074056 Iteration 3 Error: 0.018786 Align patch 24 1 left Iteration 1 Error: 0.891720 Iteration 2 Error: 0.170059 Iteration 3 Error: 0.046425 Align patch 25 0 left Iteration 1 Error: 0.824829 Iteration 2 Error: 0.102674 Iteration 3 Error: 0.022478 3D Fitting completed. Patch alignment time: 13.41(sec) Local motion has been corrected. Process thread exits. Computational time: 22.972811 sec Total time: 33.199963 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00011hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00011hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.817662s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00011hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.104561s ........................................ >>>>>>TIME<<<<<< FFT: 1.202649s Defocus_U Defocus_V Angle CCC 13826.17 14662.11 5.59 0.055207 Final Values Defocus_U Defocus_V Angle CCC 13805.85 14669.93 6.22 0.089798 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00011hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00011hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 44.56 7.40 Num Hot pixels: 221 Hot pixel threshold: 88.97 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.314231 Iteration 2 Error: 0.173605 Iteration 3 Error: 0.042503 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.27 0.09 ...... Frame ( 3) shift: -0.54 0.19 ...... Frame ( 4) shift: -0.81 0.28 ...... Frame ( 5) shift: -1.08 0.38 ...... Frame ( 6) shift: -1.19 0.49 ...... Frame ( 7) shift: -1.14 0.61 ...... Frame ( 8) shift: -1.09 0.74 ...... Frame ( 9) shift: -0.99 0.87 ...... Frame ( 10) shift: -0.85 1.02 ...... Frame ( 11) shift: -0.71 1.16 ...... Frame ( 12) shift: -0.61 1.28 ...... Frame ( 13) shift: -0.55 1.38 ...... Frame ( 14) shift: -0.49 1.49 ...... Frame ( 15) shift: -0.46 1.57 ...... Frame ( 16) shift: -0.46 1.62 ...... Frame ( 17) shift: -0.45 1.68 ...... Frame ( 18) shift: -0.47 1.75 ...... Frame ( 19) shift: -0.50 1.84 ...... Frame ( 20) shift: -0.53 1.94 ...... Frame ( 21) shift: -0.51 1.99 ...... Frame ( 22) shift: -0.44 2.01 ...... Frame ( 23) shift: -0.38 2.04 ...... Frame ( 24) shift: -0.32 2.06 ...... Frame ( 25) shift: -0.28 2.10 ...... Frame ( 26) shift: -0.24 2.13 ...... Frame ( 27) shift: -0.23 2.14 ...... Frame ( 28) shift: -0.24 2.13 ...... Frame ( 29) shift: -0.26 2.11 ...... Frame ( 30) shift: -0.22 2.11 ...... Frame ( 31) shift: -0.14 2.11 ...... Frame ( 32) shift: -0.05 2.12 ...... Frame ( 33) shift: -0.00 2.11 ...... Frame ( 34) shift: 0.00 2.08 ...... Frame ( 35) shift: 0.01 2.05 ...... Frame ( 36) shift: 0.01 2.05 ...... Frame ( 37) shift: -0.01 2.09 ...... Frame ( 38) shift: -0.02 2.12 ...... Frame ( 39) shift: -0.03 2.16 ...... Frame ( 40) shift: -0.05 2.19 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.240320 Iteration 2 Error: 0.302683 Iteration 3 Error: 0.124948 Iteration 4 Error: 0.031642 Align patch 2 23 left Iteration 1 Error: 0.977625 Iteration 2 Error: 0.123968 Iteration 3 Error: 0.029419 Align patch 3 22 left Iteration 1 Error: 0.544222 Iteration 2 Error: 0.105191 Iteration 3 Error: 0.036216 Align patch 4 21 left Iteration 1 Error: 0.652782 Iteration 2 Error: 0.164533 Iteration 3 Error: 0.039263 Align patch 5 20 left Iteration 1 Error: 0.531122 Iteration 2 Error: 0.105639 Iteration 3 Error: 0.012483 Align patch 6 19 left Iteration 1 Error: 0.818222 Iteration 2 Error: 0.228714 Iteration 3 Error: 0.056208 Iteration 4 Error: 0.016674 Align patch 7 18 left Iteration 1 Error: 0.714299 Iteration 2 Error: 0.144136 Iteration 3 Error: 0.044502 Align patch 8 17 left Iteration 1 Error: 0.769420 Iteration 2 Error: 0.160549 Iteration 3 Error: 0.043995 Align patch 9 16 left Iteration 1 Error: 0.722123 Iteration 2 Error: 0.080464 Iteration 3 Error: 0.019018 Align patch 10 15 left Iteration 1 Error: 0.957555 Iteration 2 Error: 0.113094 Iteration 3 Error: 0.025115 Align patch 11 14 left Iteration 1 Error: 1.576628 Iteration 2 Error: 0.274637 Iteration 3 Error: 0.123894 Iteration 4 Error: 0.025041 Align patch 12 13 left Iteration 1 Error: 1.729286 Iteration 2 Error: 0.204815 Iteration 3 Error: 0.070846 Iteration 4 Error: 0.023020 Align patch 13 12 left Iteration 1 Error: 0.600433 Iteration 2 Error: 0.209489 Iteration 3 Error: 0.051550 Iteration 4 Error: 0.027609 Align patch 14 11 left Iteration 1 Error: 0.929611 Iteration 2 Error: 0.164265 Iteration 3 Error: 0.032847 Align patch 15 10 left Iteration 1 Error: 0.881229 Iteration 2 Error: 0.113938 Iteration 3 Error: 0.019703 Align patch 16 9 left Iteration 1 Error: 1.032729 Iteration 2 Error: 0.218009 Iteration 3 Error: 0.057745 Iteration 4 Error: 0.020844 Align patch 17 8 left Iteration 1 Error: 0.744389 Iteration 2 Error: 0.165966 Iteration 3 Error: 0.028669 Align patch 18 7 left Iteration 1 Error: 0.553193 Iteration 2 Error: 0.119006 Iteration 3 Error: 0.036774 Align patch 19 6 left Iteration 1 Error: 0.690299 Iteration 2 Error: 0.100329 Iteration 3 Error: 0.027217 Align patch 20 5 left Iteration 1 Error: 1.066014 Iteration 2 Error: 0.104737 Iteration 3 Error: 0.024217 Align patch 21 4 left Iteration 1 Error: 0.954621 Iteration 2 Error: 0.181137 Iteration 3 Error: 0.050958 Iteration 4 Error: 0.022184 Align patch 22 3 left Iteration 1 Error: 0.791249 Iteration 2 Error: 0.096122 Iteration 3 Error: 0.031865 Align patch 23 2 left Iteration 1 Error: 1.630898 Iteration 2 Error: 0.167575 Iteration 3 Error: 0.031983 Align patch 24 1 left Iteration 1 Error: 1.135427 Iteration 2 Error: 0.123801 Iteration 3 Error: 0.029346 Align patch 25 0 left Iteration 1 Error: 1.178871 Iteration 2 Error: 0.207081 Iteration 3 Error: 0.050928 Iteration 4 Error: 0.012106 3D Fitting completed. Patch alignment time: 12.73(sec) Local motion has been corrected. Process thread exits. Computational time: 22.715960 sec Total time: 34.100033 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00011hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00011hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.523290s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00011hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.182572s ........................................ >>>>>>TIME<<<<<< FFT: 0.940281s Defocus_U Defocus_V Angle CCC 14679.67 14722.69 39.37 0.045165 Final Values Defocus_U Defocus_V Angle CCC 15038.35 14366.60 84.48 0.085264 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00012hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00012hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 43.23 7.55 Num Hot pixels: 204 Hot pixel threshold: 88.51 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.987626 Iteration 2 Error: 0.468827 Iteration 3 Error: 0.130077 Iteration 4 Error: 0.042328 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.32 -0.22 ...... Frame ( 3) shift: -0.65 -0.44 ...... Frame ( 4) shift: -0.97 -0.66 ...... Frame ( 5) shift: -1.30 -0.88 ...... Frame ( 6) shift: -1.43 -0.94 ...... Frame ( 7) shift: -1.36 -0.86 ...... Frame ( 8) shift: -1.30 -0.78 ...... Frame ( 9) shift: -1.21 -0.69 ...... Frame ( 10) shift: -1.11 -0.60 ...... Frame ( 11) shift: -1.01 -0.51 ...... Frame ( 12) shift: -0.89 -0.44 ...... Frame ( 13) shift: -0.75 -0.39 ...... Frame ( 14) shift: -0.62 -0.34 ...... Frame ( 15) shift: -0.53 -0.26 ...... Frame ( 16) shift: -0.47 -0.17 ...... Frame ( 17) shift: -0.42 -0.08 ...... Frame ( 18) shift: -0.33 0.02 ...... Frame ( 19) shift: -0.22 0.12 ...... Frame ( 20) shift: -0.10 0.22 ...... Frame ( 21) shift: 0.00 0.30 ...... Frame ( 22) shift: 0.09 0.36 ...... Frame ( 23) shift: 0.17 0.42 ...... Frame ( 24) shift: 0.30 0.49 ...... Frame ( 25) shift: 0.46 0.58 ...... Frame ( 26) shift: 0.63 0.67 ...... Frame ( 27) shift: 0.74 0.75 ...... Frame ( 28) shift: 0.79 0.83 ...... Frame ( 29) shift: 0.84 0.90 ...... Frame ( 30) shift: 0.90 0.97 ...... Frame ( 31) shift: 0.98 1.02 ...... Frame ( 32) shift: 1.06 1.08 ...... Frame ( 33) shift: 1.13 1.15 ...... Frame ( 34) shift: 1.17 1.26 ...... Frame ( 35) shift: 1.22 1.36 ...... Frame ( 36) shift: 1.32 1.44 ...... Frame ( 37) shift: 1.48 1.50 ...... Frame ( 38) shift: 1.64 1.55 ...... Frame ( 39) shift: 1.80 1.60 ...... Frame ( 40) shift: 1.96 1.65 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.454040 Iteration 2 Error: 0.553497 Iteration 3 Error: 0.298977 Iteration 4 Error: 0.147028 Iteration 5 Error: 0.106033 Align patch 1 24 left Iteration 1 Error: 1.952209 Iteration 2 Error: 0.479028 Iteration 3 Error: 0.127790 Iteration 4 Error: 0.048485 Align patch 2 23 left Iteration 1 Error: 2.075103 Iteration 2 Error: 0.372674 Iteration 3 Error: 0.158373 Iteration 4 Error: 0.094800 Iteration 5 Error: 0.053207 Align patch 2 23 left Iteration 1 Error: 2.076755 Iteration 2 Error: 0.346168 Iteration 3 Error: 0.069657 Iteration 4 Error: 0.016552 Align patch 3 22 left Iteration 1 Error: 0.922174 Iteration 2 Error: 0.150015 Iteration 3 Error: 0.054868 Iteration 4 Error: 0.028351 Align patch 4 21 left Iteration 1 Error: 0.874963 Iteration 2 Error: 0.156586 Iteration 3 Error: 0.035678 Align patch 5 20 left Iteration 1 Error: 0.769094 Iteration 2 Error: 0.227544 Iteration 3 Error: 0.079628 Iteration 4 Error: 0.036157 Align patch 6 19 left Iteration 1 Error: 2.535598 Iteration 2 Error: 0.806884 Iteration 3 Error: 0.494948 Iteration 4 Error: 0.328936 Iteration 5 Error: 0.192646 Align patch 6 19 left Iteration 1 Error: 2.044499 Iteration 2 Error: 0.555750 Iteration 3 Error: 0.177940 Iteration 4 Error: 0.090907 Iteration 5 Error: 0.049479 Align patch 7 18 left Iteration 1 Error: 1.706796 Iteration 2 Error: 0.647836 Iteration 3 Error: 0.322717 Iteration 4 Error: 0.157455 Iteration 5 Error: 0.058347 Align patch 7 18 left Iteration 1 Error: 2.059629 Iteration 2 Error: 0.402730 Iteration 3 Error: 0.094483 Iteration 4 Error: 0.031520 Align patch 8 17 left Iteration 1 Error: 0.964111 Iteration 2 Error: 0.249093 Iteration 3 Error: 0.070547 Iteration 4 Error: 0.031551 Align patch 9 16 left Iteration 1 Error: 0.828766 Iteration 2 Error: 0.186137 Iteration 3 Error: 0.048329 Align patch 10 15 left Iteration 1 Error: 0.742272 Iteration 2 Error: 0.195036 Iteration 3 Error: 0.072555 Iteration 4 Error: 0.023386 Align patch 11 14 left Iteration 1 Error: 2.066576 Iteration 2 Error: 1.154016 Iteration 3 Error: 0.536313 Iteration 4 Error: 0.362849 Iteration 5 Error: 0.239822 Align patch 11 14 left Iteration 1 Error: 1.969169 Iteration 2 Error: 0.480968 Iteration 3 Error: 0.188575 Iteration 4 Error: 0.050294 Iteration 5 Error: 0.034895 Align patch 12 13 left Iteration 1 Error: 1.134842 Iteration 2 Error: 0.477067 Iteration 3 Error: 0.337791 Iteration 4 Error: 0.164163 Iteration 5 Error: 0.103721 Align patch 12 13 left Iteration 1 Error: 1.907381 Iteration 2 Error: 0.345351 Iteration 3 Error: 0.097354 Iteration 4 Error: 0.033097 Align patch 13 12 left Iteration 1 Error: 0.884222 Iteration 2 Error: 0.244518 Iteration 3 Error: 0.085879 Iteration 4 Error: 0.026912 Align patch 14 11 left Iteration 1 Error: 0.851127 Iteration 2 Error: 0.125902 Iteration 3 Error: 0.028346 Align patch 15 10 left Iteration 1 Error: 0.961432 Iteration 2 Error: 0.220550 Iteration 3 Error: 0.070107 Iteration 4 Error: 0.022226 Align patch 16 9 left Iteration 1 Error: 2.280865 Iteration 2 Error: 1.002353 Iteration 3 Error: 0.536882 Iteration 4 Error: 0.263116 Iteration 5 Error: 0.134049 Align patch 16 9 left Iteration 1 Error: 2.090839 Iteration 2 Error: 0.365131 Iteration 3 Error: 0.094360 Iteration 4 Error: 0.035943 Align patch 17 8 left Iteration 1 Error: 1.460358 Iteration 2 Error: 0.356709 Iteration 3 Error: 0.192963 Iteration 4 Error: 0.108909 Iteration 5 Error: 0.051947 Align patch 17 8 left Iteration 1 Error: 2.081040 Iteration 2 Error: 0.303937 Iteration 3 Error: 0.064367 Iteration 4 Error: 0.022919 Align patch 18 7 left Iteration 1 Error: 1.032528 Iteration 2 Error: 0.333335 Iteration 3 Error: 0.112705 Iteration 4 Error: 0.059880 Iteration 5 Error: 0.022245 Align patch 19 6 left Iteration 1 Error: 0.771062 Iteration 2 Error: 0.151876 Iteration 3 Error: 0.034333 Align patch 20 5 left Iteration 1 Error: 0.977937 Iteration 2 Error: 0.093890 Iteration 3 Error: 0.022812 Align patch 21 4 left Iteration 1 Error: 2.282055 Iteration 2 Error: 0.571586 Iteration 3 Error: 0.195174 Iteration 4 Error: 0.108738 Iteration 5 Error: 0.076199 Align patch 21 4 left Iteration 1 Error: 2.074185 Iteration 2 Error: 0.281583 Iteration 3 Error: 0.062211 Iteration 4 Error: 0.021865 Align patch 22 3 left Iteration 1 Error: 2.100722 Iteration 2 Error: 0.301250 Iteration 3 Error: 0.109248 Iteration 4 Error: 0.057758 Iteration 5 Error: 0.019653 Align patch 23 2 left Iteration 1 Error: 0.681857 Iteration 2 Error: 0.194744 Iteration 3 Error: 0.059996 Iteration 4 Error: 0.031272 Align patch 24 1 left Iteration 1 Error: 0.781868 Iteration 2 Error: 0.091664 Iteration 3 Error: 0.024653 Align patch 25 0 left Iteration 1 Error: 0.871403 Iteration 2 Error: 0.062848 Iteration 3 Error: 0.008580 3D Fitting completed. Patch alignment time: 22.94(sec) Local motion has been corrected. Process thread exits. Computational time: 33.149479 sec Total time: 44.930939 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00012hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00012hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.755382s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00012hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.084173s ........................................ >>>>>>TIME<<<<<< FFT: 0.916386s Defocus_U Defocus_V Angle CCC 10705.08 11560.57 10.24 0.049244 Final Values Defocus_U Defocus_V Angle CCC 10725.39 11568.39 10.56 0.092861 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00012hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00012hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 43.70 7.48 Num Hot pixels: 207 Hot pixel threshold: 88.60 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.529155 Iteration 2 Error: 0.259192 Iteration 3 Error: 0.060898 Iteration 4 Error: 0.021813 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.30 -0.12 ...... Frame ( 3) shift: -0.60 -0.24 ...... Frame ( 4) shift: -0.90 -0.36 ...... Frame ( 5) shift: -1.20 -0.47 ...... Frame ( 6) shift: -1.29 -0.42 ...... Frame ( 7) shift: -1.18 -0.18 ...... Frame ( 8) shift: -1.06 0.06 ...... Frame ( 9) shift: -0.98 0.23 ...... Frame ( 10) shift: -0.94 0.35 ...... Frame ( 11) shift: -0.90 0.47 ...... Frame ( 12) shift: -0.90 0.58 ...... Frame ( 13) shift: -0.93 0.68 ...... Frame ( 14) shift: -0.97 0.78 ...... Frame ( 15) shift: -1.02 0.83 ...... Frame ( 16) shift: -1.09 0.83 ...... Frame ( 17) shift: -1.17 0.83 ...... Frame ( 18) shift: -1.19 0.89 ...... Frame ( 19) shift: -1.15 0.99 ...... Frame ( 20) shift: -1.12 1.10 ...... Frame ( 21) shift: -1.05 1.18 ...... Frame ( 22) shift: -0.93 1.23 ...... Frame ( 23) shift: -0.82 1.27 ...... Frame ( 24) shift: -0.75 1.34 ...... Frame ( 25) shift: -0.73 1.42 ...... Frame ( 26) shift: -0.70 1.51 ...... Frame ( 27) shift: -0.67 1.57 ...... Frame ( 28) shift: -0.63 1.61 ...... Frame ( 29) shift: -0.59 1.65 ...... Frame ( 30) shift: -0.56 1.71 ...... Frame ( 31) shift: -0.54 1.79 ...... Frame ( 32) shift: -0.52 1.88 ...... Frame ( 33) shift: -0.50 2.00 ...... Frame ( 34) shift: -0.49 2.16 ...... Frame ( 35) shift: -0.48 2.32 ...... Frame ( 36) shift: -0.43 2.42 ...... Frame ( 37) shift: -0.34 2.46 ...... Frame ( 38) shift: -0.26 2.51 ...... Frame ( 39) shift: -0.17 2.56 ...... Frame ( 40) shift: -0.09 2.60 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.445374 Iteration 2 Error: 0.295069 Iteration 3 Error: 0.148998 Iteration 4 Error: 0.033944 Align patch 2 23 left Iteration 1 Error: 2.375118 Iteration 2 Error: 0.438395 Iteration 3 Error: 0.128132 Iteration 4 Error: 0.052732 Iteration 5 Error: 0.039921 Align patch 3 22 left Iteration 1 Error: 0.786379 Iteration 2 Error: 0.098573 Iteration 3 Error: 0.022025 Align patch 4 21 left Iteration 1 Error: 0.750798 Iteration 2 Error: 0.121470 Iteration 3 Error: 0.023772 Align patch 5 20 left Iteration 1 Error: 0.810973 Iteration 2 Error: 0.186912 Iteration 3 Error: 0.080464 Iteration 4 Error: 0.026186 Align patch 6 19 left Iteration 1 Error: 1.966245 Iteration 2 Error: 0.713915 Iteration 3 Error: 0.214297 Iteration 4 Error: 0.154414 Iteration 5 Error: 0.062203 Align patch 6 19 left Iteration 1 Error: 3.384086 Iteration 2 Error: 0.977865 Iteration 3 Error: 0.440961 Iteration 4 Error: 0.276297 Iteration 5 Error: 0.189178 Align patch 7 18 left Iteration 1 Error: 1.360471 Iteration 2 Error: 0.231426 Iteration 3 Error: 0.049322 Align patch 8 17 left Iteration 1 Error: 0.846786 Iteration 2 Error: 0.275298 Iteration 3 Error: 0.072498 Iteration 4 Error: 0.040278 Align patch 9 16 left Iteration 1 Error: 0.714304 Iteration 2 Error: 0.130703 Iteration 3 Error: 0.021242 Align patch 10 15 left Iteration 1 Error: 0.659644 Iteration 2 Error: 0.163540 Iteration 3 Error: 0.032889 Align patch 11 14 left Iteration 1 Error: 12.359900 Iteration 2 Error: 5.030910 Iteration 3 Error: 7.390804 Iteration 4 Error: 2.449324 Iteration 5 Error: 0.850216 Align patch 11 14 left Iteration 1 Error: 7.584220 Iteration 2 Error: 2.746973 Iteration 3 Error: 3.245043 Iteration 4 Error: 1.050054 Iteration 5 Error: 0.537594 Align patch 12 13 left Iteration 1 Error: 0.962343 Iteration 2 Error: 0.296594 Iteration 3 Error: 0.074508 Iteration 4 Error: 0.025225 Align patch 13 12 left Iteration 1 Error: 0.919924 Iteration 2 Error: 0.132780 Iteration 3 Error: 0.023154 Align patch 14 11 left Iteration 1 Error: 0.580378 Iteration 2 Error: 0.078629 Iteration 3 Error: 0.015765 Align patch 15 10 left Iteration 1 Error: 0.776011 Iteration 2 Error: 0.083345 Iteration 3 Error: 0.014405 Align patch 16 9 left Iteration 1 Error: 1.158903 Iteration 2 Error: 0.300732 Iteration 3 Error: 0.050761 Iteration 4 Error: 0.033667 Align patch 17 8 left Iteration 1 Error: 1.033913 Iteration 2 Error: 0.176294 Iteration 3 Error: 0.032431 Align patch 18 7 left Iteration 1 Error: 0.824179 Iteration 2 Error: 0.115427 Iteration 3 Error: 0.028815 Align patch 19 6 left Iteration 1 Error: 0.574495 Iteration 2 Error: 0.200490 Iteration 3 Error: 0.067380 Iteration 4 Error: 0.021701 Align patch 20 5 left Iteration 1 Error: 0.775760 Iteration 2 Error: 0.205085 Iteration 3 Error: 0.068378 Iteration 4 Error: 0.024039 Align patch 21 4 left Iteration 1 Error: 0.998817 Iteration 2 Error: 0.115857 Iteration 3 Error: 0.051631 Iteration 4 Error: 0.024632 Align patch 22 3 left Iteration 1 Error: 1.000933 Iteration 2 Error: 0.143713 Iteration 3 Error: 0.041625 Align patch 23 2 left Iteration 1 Error: 0.781355 Iteration 2 Error: 0.125087 Iteration 3 Error: 0.026260 Align patch 24 1 left Iteration 1 Error: 1.017643 Iteration 2 Error: 0.153910 Iteration 3 Error: 0.045788 Align patch 25 0 left Iteration 1 Error: 1.105750 Iteration 2 Error: 0.147816 Iteration 3 Error: 0.035750 3D Fitting completed. Patch alignment time: 13.98(sec) Local motion has been corrected. Process thread exits. Computational time: 22.240339 sec Total time: 31.415092 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00012hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00012hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.705504s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00012hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.803884s ........................................ >>>>>>TIME<<<<<< FFT: 1.082064s Defocus_U Defocus_V Angle CCC 13367.21 12820.32 88.13 0.049086 Final Values Defocus_U Defocus_V Angle CCC 13360.96 12820.32 89.07 0.088628 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00012hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00012hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 43.02 7.39 Num Hot pixels: 190 Hot pixel threshold: 87.35 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 3.757567 Iteration 2 Error: 1.362582 Iteration 3 Error: 0.639409 Iteration 4 Error: 0.348366 Iteration 5 Error: 0.184266 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.05 -0.10 ...... Frame ( 3) shift: -0.09 -0.20 ...... Frame ( 4) shift: -0.14 -0.30 ...... Frame ( 5) shift: -0.19 -0.40 ...... Frame ( 6) shift: -0.10 -0.40 ...... Frame ( 7) shift: 0.12 -0.28 ...... Frame ( 8) shift: 0.33 -0.17 ...... Frame ( 9) shift: 0.60 -0.08 ...... Frame ( 10) shift: 0.91 -0.02 ...... Frame ( 11) shift: 1.22 0.05 ...... Frame ( 12) shift: 1.51 0.06 ...... Frame ( 13) shift: 1.77 0.03 ...... Frame ( 14) shift: 2.03 -0.01 ...... Frame ( 15) shift: 2.33 -0.07 ...... Frame ( 16) shift: 2.66 -0.15 ...... Frame ( 17) shift: 2.99 -0.24 ...... Frame ( 18) shift: 3.34 -0.29 ...... Frame ( 19) shift: 3.72 -0.32 ...... Frame ( 20) shift: 4.09 -0.35 ...... Frame ( 21) shift: 4.46 -0.36 ...... Frame ( 22) shift: 4.80 -0.35 ...... Frame ( 23) shift: 5.15 -0.33 ...... Frame ( 24) shift: 5.49 -0.37 ...... Frame ( 25) shift: 5.82 -0.46 ...... Frame ( 26) shift: 6.15 -0.54 ...... Frame ( 27) shift: 6.48 -0.59 ...... Frame ( 28) shift: 6.80 -0.61 ...... Frame ( 29) shift: 7.12 -0.62 ...... Frame ( 30) shift: 7.45 -0.65 ...... Frame ( 31) shift: 7.79 -0.68 ...... Frame ( 32) shift: 8.13 -0.72 ...... Frame ( 33) shift: 8.43 -0.76 ...... Frame ( 34) shift: 8.67 -0.80 ...... Frame ( 35) shift: 8.92 -0.84 ...... Frame ( 36) shift: 9.20 -0.87 ...... Frame ( 37) shift: 9.51 -0.90 ...... Frame ( 38) shift: 9.83 -0.93 ...... Frame ( 39) shift: 10.14 -0.95 ...... Frame ( 40) shift: 10.45 -0.98 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.584769 Iteration 2 Error: 0.972141 Iteration 3 Error: 0.270791 Iteration 4 Error: 0.126809 Iteration 5 Error: 0.065153 Align patch 1 24 left Iteration 1 Error: 2.920511 Iteration 2 Error: 0.696904 Iteration 3 Error: 0.205803 Iteration 4 Error: 0.089347 Iteration 5 Error: 0.024286 Align patch 2 23 left Iteration 1 Error: 3.372318 Iteration 2 Error: 1.177561 Iteration 3 Error: 0.372239 Iteration 4 Error: 0.191085 Iteration 5 Error: 0.073066 Align patch 2 23 left Iteration 1 Error: 3.530029 Iteration 2 Error: 0.877358 Iteration 3 Error: 0.246928 Iteration 4 Error: 0.097789 Iteration 5 Error: 0.033540 Align patch 3 22 left Iteration 1 Error: 3.883424 Iteration 2 Error: 2.226301 Iteration 3 Error: 0.598152 Iteration 4 Error: 0.245856 Iteration 5 Error: 0.115537 Align patch 3 22 left Iteration 1 Error: 4.573558 Iteration 2 Error: 1.481592 Iteration 3 Error: 0.381724 Iteration 4 Error: 0.122212 Iteration 5 Error: 0.049736 Align patch 4 21 left Iteration 1 Error: 5.662058 Iteration 2 Error: 4.451268 Iteration 3 Error: 2.129678 Iteration 4 Error: 0.872814 Iteration 5 Error: 0.487078 Align patch 4 21 left Iteration 1 Error: 5.719542 Iteration 2 Error: 3.433485 Iteration 3 Error: 1.029672 Iteration 4 Error: 0.357216 Iteration 5 Error: 0.174307 Align patch 5 20 left Iteration 1 Error: 5.624996 Iteration 2 Error: 2.880596 Iteration 3 Error: 2.546471 Iteration 4 Error: 1.797648 Iteration 5 Error: 0.854918 Align patch 5 20 left Iteration 1 Error: 6.092501 Iteration 2 Error: 2.695639 Iteration 3 Error: 1.410573 Iteration 4 Error: 0.971169 Iteration 5 Error: 0.723099 Align patch 6 19 left Iteration 1 Error: 1.393820 Iteration 2 Error: 0.561581 Iteration 3 Error: 0.209476 Iteration 4 Error: 0.101262 Iteration 5 Error: 0.039041 Align patch 7 18 left Iteration 1 Error: 2.678044 Iteration 2 Error: 0.866842 Iteration 3 Error: 0.457283 Iteration 4 Error: 0.247363 Iteration 5 Error: 0.157991 Align patch 7 18 left Iteration 1 Error: 3.161667 Iteration 2 Error: 0.869914 Iteration 3 Error: 0.362695 Iteration 4 Error: 0.175619 Iteration 5 Error: 0.070802 Align patch 8 17 left Iteration 1 Error: 2.863828 Iteration 2 Error: 2.100327 Iteration 3 Error: 2.010207 Iteration 4 Error: 0.668935 Iteration 5 Error: 0.444655 Align patch 8 17 left Iteration 1 Error: 3.959958 Iteration 2 Error: 1.484096 Iteration 3 Error: 0.601184 Iteration 4 Error: 0.262573 Iteration 5 Error: 0.125160 Align patch 9 16 left Iteration 1 Error: 4.683454 Iteration 2 Error: 2.686296 Iteration 3 Error: 2.186652 Iteration 4 Error: 2.774183 Iteration 5 Error: 1.627751 Align patch 9 16 left Iteration 1 Error: 5.811293 Iteration 2 Error: 3.007131 Iteration 3 Error: 1.722266 Iteration 4 Error: 0.797596 Iteration 5 Error: 0.384127 Align patch 10 15 left Iteration 1 Error: 11.098663 Iteration 2 Error: 24.506325 Iteration 3 Error: 25.966482 Iteration 4 Error: 29.554592 Iteration 5 Error: 29.590208 Align patch 10 15 left Iteration 1 Error: 6.061693 Iteration 2 Error: 10.673646 Iteration 3 Error: 16.860783 Iteration 4 Error: 18.259935 Iteration 5 Error: 20.553854 Align patch 11 14 left Iteration 1 Error: 1.278295 Iteration 2 Error: 0.253789 Iteration 3 Error: 0.050841 Iteration 4 Error: 0.030611 Align patch 12 13 left Iteration 1 Error: 2.615590 Iteration 2 Error: 0.624734 Iteration 3 Error: 0.306093 Iteration 4 Error: 0.107945 Iteration 5 Error: 0.058312 Align patch 12 13 left Iteration 1 Error: 2.008043 Iteration 2 Error: 0.486549 Iteration 3 Error: 0.155269 Iteration 4 Error: 0.058138 Iteration 5 Error: 0.029978 Align patch 13 12 left Iteration 1 Error: 3.333468 Iteration 2 Error: 1.733236 Iteration 3 Error: 0.775092 Iteration 4 Error: 0.840657 Iteration 5 Error: 0.431032 Align patch 13 12 left Iteration 1 Error: 2.821452 Iteration 2 Error: 1.140960 Iteration 3 Error: 0.378673 Iteration 4 Error: 0.176706 Iteration 5 Error: 0.082461 Align patch 14 11 left Iteration 1 Error: 10.308667 Iteration 2 Error: 4.290591 Iteration 3 Error: 1.225663 Iteration 4 Error: 0.478417 Iteration 5 Error: 0.164667 Align patch 14 11 left Iteration 1 Error: 5.762331 Iteration 2 Error: 1.621196 Iteration 3 Error: 0.664816 Iteration 4 Error: 0.229855 Iteration 5 Error: 0.094031 Align patch 15 10 left Iteration 1 Error: 6.325620 Iteration 2 Error: 8.820810 Iteration 3 Error: 5.730949 Iteration 4 Error: 2.127538 Iteration 5 Error: 0.851307 Align patch 15 10 left Iteration 1 Error: 5.642519 Iteration 2 Error: 2.160433 Iteration 3 Error: 1.214509 Iteration 4 Error: 0.596760 Iteration 5 Error: 0.319577 Align patch 16 9 left Iteration 1 Error: 0.899195 Iteration 2 Error: 0.212322 Iteration 3 Error: 0.080088 Iteration 4 Error: 0.028609 Align patch 17 8 left Iteration 1 Error: 1.584953 Iteration 2 Error: 0.555639 Iteration 3 Error: 0.171199 Iteration 4 Error: 0.084716 Iteration 5 Error: 0.037918 Align patch 18 7 left Iteration 1 Error: 1.914917 Iteration 2 Error: 0.853828 Iteration 3 Error: 0.307106 Iteration 4 Error: 0.131001 Iteration 5 Error: 0.055396 Align patch 18 7 left Iteration 1 Error: 0.851292 Iteration 2 Error: 0.209742 Iteration 3 Error: 0.054573 Iteration 4 Error: 0.015518 Align patch 19 6 left Iteration 1 Error: 3.099167 Iteration 2 Error: 0.744676 Iteration 3 Error: 0.218444 Iteration 4 Error: 0.086922 Iteration 5 Error: 0.033477 Align patch 20 5 left Iteration 1 Error: 3.724043 Iteration 2 Error: 1.180133 Iteration 3 Error: 0.527859 Iteration 4 Error: 0.289536 Iteration 5 Error: 0.156756 Align patch 20 5 left Iteration 1 Error: 3.230092 Iteration 2 Error: 0.800816 Iteration 3 Error: 0.317502 Iteration 4 Error: 0.138355 Iteration 5 Error: 0.062526 Align patch 21 4 left Iteration 1 Error: 2.925030 Iteration 2 Error: 1.055571 Iteration 3 Error: 0.385473 Iteration 4 Error: 0.152486 Iteration 5 Error: 0.080026 Align patch 21 4 left Iteration 1 Error: 2.026835 Iteration 2 Error: 0.445268 Iteration 3 Error: 0.143881 Iteration 4 Error: 0.029972 Align patch 22 3 left Iteration 1 Error: 2.279461 Iteration 2 Error: 0.684434 Iteration 3 Error: 0.363156 Iteration 4 Error: 0.209904 Iteration 5 Error: 0.093391 Align patch 22 3 left Iteration 1 Error: 0.942408 Iteration 2 Error: 0.169333 Iteration 3 Error: 0.046106 Align patch 23 2 left Iteration 1 Error: 2.307687 Iteration 2 Error: 0.409744 Iteration 3 Error: 0.131287 Iteration 4 Error: 0.046666 Align patch 24 1 left Iteration 1 Error: 1.834131 Iteration 2 Error: 0.165215 Iteration 3 Error: 0.021699 Align patch 25 0 left Iteration 1 Error: 1.381507 Iteration 2 Error: 0.236116 Iteration 3 Error: 0.045367 3D Fitting completed. Patch alignment time: 26.89(sec) Local motion has been corrected. Process thread exits. Computational time: 35.458897 sec Total time: 41.742432 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00012hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00012hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.621705s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00012hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.038778s ........................................ >>>>>>TIME<<<<<< FFT: 0.965755s Defocus_U Defocus_V Angle CCC 13072.25 13935.57 6.72 0.082568 Final Values Defocus_U Defocus_V Angle CCC 13075.37 13932.44 6.40 0.149984 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00012hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00012hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.736 Mean Std: 43.71 7.36 Num Hot pixels: 213 Hot pixel threshold: 87.87 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.289990 Iteration 2 Error: 0.153466 Iteration 3 Error: 0.024190 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.33 -0.19 ...... Frame ( 3) shift: -0.66 -0.38 ...... Frame ( 4) shift: -0.99 -0.57 ...... Frame ( 5) shift: -1.32 -0.77 ...... Frame ( 6) shift: -1.50 -0.82 ...... Frame ( 7) shift: -1.55 -0.73 ...... Frame ( 8) shift: -1.59 -0.65 ...... Frame ( 9) shift: -1.63 -0.54 ...... Frame ( 10) shift: -1.67 -0.41 ...... Frame ( 11) shift: -1.70 -0.28 ...... Frame ( 12) shift: -1.72 -0.18 ...... Frame ( 13) shift: -1.72 -0.09 ...... Frame ( 14) shift: -1.72 -0.01 ...... Frame ( 15) shift: -1.73 0.05 ...... Frame ( 16) shift: -1.75 0.10 ...... Frame ( 17) shift: -1.76 0.14 ...... Frame ( 18) shift: -1.77 0.18 ...... Frame ( 19) shift: -1.77 0.23 ...... Frame ( 20) shift: -1.76 0.27 ...... Frame ( 21) shift: -1.79 0.32 ...... Frame ( 22) shift: -1.84 0.39 ...... Frame ( 23) shift: -1.90 0.46 ...... Frame ( 24) shift: -1.92 0.50 ...... Frame ( 25) shift: -1.91 0.50 ...... Frame ( 26) shift: -1.89 0.51 ...... Frame ( 27) shift: -1.89 0.55 ...... Frame ( 28) shift: -1.90 0.62 ...... Frame ( 29) shift: -1.92 0.68 ...... Frame ( 30) shift: -1.93 0.72 ...... Frame ( 31) shift: -1.95 0.71 ...... Frame ( 32) shift: -1.97 0.71 ...... Frame ( 33) shift: -1.99 0.74 ...... Frame ( 34) shift: -2.01 0.79 ...... Frame ( 35) shift: -2.03 0.84 ...... Frame ( 36) shift: -2.02 0.87 ...... Frame ( 37) shift: -1.98 0.90 ...... Frame ( 38) shift: -1.94 0.92 ...... Frame ( 39) shift: -1.89 0.95 ...... Frame ( 40) shift: -1.85 0.97 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.678111 Iteration 2 Error: 0.163457 Iteration 3 Error: 0.068254 Iteration 4 Error: 0.014857 Align patch 2 23 left Iteration 1 Error: 1.792451 Iteration 2 Error: 0.257342 Iteration 3 Error: 0.067656 Iteration 4 Error: 0.020141 Align patch 3 22 left Iteration 1 Error: 0.988289 Iteration 2 Error: 0.084352 Iteration 3 Error: 0.027772 Align patch 4 21 left Iteration 1 Error: 0.935820 Iteration 2 Error: 0.105018 Iteration 3 Error: 0.025504 Align patch 5 20 left Iteration 1 Error: 0.748145 Iteration 2 Error: 0.085134 Iteration 3 Error: 0.018053 Align patch 6 19 left Iteration 1 Error: 2.147166 Iteration 2 Error: 0.232924 Iteration 3 Error: 0.096002 Iteration 4 Error: 0.040371 Align patch 7 18 left Iteration 1 Error: 1.443645 Iteration 2 Error: 0.150903 Iteration 3 Error: 0.033040 Align patch 8 17 left Iteration 1 Error: 0.684604 Iteration 2 Error: 0.072000 Iteration 3 Error: 0.022297 Align patch 9 16 left Iteration 1 Error: 0.520930 Iteration 2 Error: 0.059783 Iteration 3 Error: 0.011713 Align patch 10 15 left Iteration 1 Error: 0.522106 Iteration 2 Error: 0.088764 Iteration 3 Error: 0.016079 Align patch 11 14 left Iteration 1 Error: 0.655994 Iteration 2 Error: 0.087584 Iteration 3 Error: 0.025758 Align patch 12 13 left Iteration 1 Error: 0.512109 Iteration 2 Error: 0.094109 Iteration 3 Error: 0.019765 Align patch 13 12 left Iteration 1 Error: 0.685483 Iteration 2 Error: 0.098429 Iteration 3 Error: 0.025790 Align patch 14 11 left Iteration 1 Error: 0.632475 Iteration 2 Error: 0.151354 Iteration 3 Error: 0.051451 Iteration 4 Error: 0.021227 Align patch 15 10 left Iteration 1 Error: 0.665329 Iteration 2 Error: 0.117990 Iteration 3 Error: 0.032629 Align patch 16 9 left Iteration 1 Error: 0.892258 Iteration 2 Error: 0.161366 Iteration 3 Error: 0.059197 Iteration 4 Error: 0.013182 Align patch 17 8 left Iteration 1 Error: 0.813546 Iteration 2 Error: 0.149674 Iteration 3 Error: 0.038520 Align patch 18 7 left Iteration 1 Error: 0.651093 Iteration 2 Error: 0.157212 Iteration 3 Error: 0.041441 Align patch 19 6 left Iteration 1 Error: 1.040573 Iteration 2 Error: 0.129646 Iteration 3 Error: 0.038004 Align patch 20 5 left Iteration 1 Error: 0.715810 Iteration 2 Error: 0.097787 Iteration 3 Error: 0.028278 Align patch 21 4 left Iteration 1 Error: 1.050763 Iteration 2 Error: 0.099400 Iteration 3 Error: 0.021161 Align patch 22 3 left Iteration 1 Error: 0.814993 Iteration 2 Error: 0.167590 Iteration 3 Error: 0.038540 Align patch 23 2 left Iteration 1 Error: 0.672512 Iteration 2 Error: 0.076058 Iteration 3 Error: 0.019119 Align patch 24 1 left Iteration 1 Error: 0.822771 Iteration 2 Error: 0.095482 Iteration 3 Error: 0.015615 Align patch 25 0 left Iteration 1 Error: 0.664937 Iteration 2 Error: 0.107076 Iteration 3 Error: 0.017548 3D Fitting completed. Patch alignment time: 11.87(sec) Local motion has been corrected. Process thread exits. Computational time: 20.816479 sec Total time: 26.221590 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00012hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00012hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.864892s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00012hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.220875s ........................................ >>>>>>TIME<<<<<< FFT: 1.146270s Defocus_U Defocus_V Angle CCC 12503.96 11871.10 84.75 0.050919 Final Values Defocus_U Defocus_V Angle CCC 12496.14 11878.91 84.75 0.092458 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00013hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00013hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 43.09 7.40 Num Hot pixels: 208 Hot pixel threshold: 87.49 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.054172 Iteration 2 Error: 0.181615 Iteration 3 Error: 0.039996 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.19 -0.07 ...... Frame ( 3) shift: -0.37 -0.13 ...... Frame ( 4) shift: -0.56 -0.20 ...... Frame ( 5) shift: -0.75 -0.26 ...... Frame ( 6) shift: -0.81 -0.24 ...... Frame ( 7) shift: -0.76 -0.14 ...... Frame ( 8) shift: -0.70 -0.04 ...... Frame ( 9) shift: -0.67 0.02 ...... Frame ( 10) shift: -0.65 0.04 ...... Frame ( 11) shift: -0.63 0.05 ...... Frame ( 12) shift: -0.59 0.11 ...... Frame ( 13) shift: -0.54 0.21 ...... Frame ( 14) shift: -0.48 0.32 ...... Frame ( 15) shift: -0.45 0.37 ...... Frame ( 16) shift: -0.43 0.37 ...... Frame ( 17) shift: -0.40 0.36 ...... Frame ( 18) shift: -0.38 0.36 ...... Frame ( 19) shift: -0.36 0.37 ...... Frame ( 20) shift: -0.33 0.38 ...... Frame ( 21) shift: -0.29 0.38 ...... Frame ( 22) shift: -0.23 0.37 ...... Frame ( 23) shift: -0.16 0.36 ...... Frame ( 24) shift: -0.10 0.39 ...... Frame ( 25) shift: -0.03 0.45 ...... Frame ( 26) shift: 0.03 0.52 ...... Frame ( 27) shift: 0.02 0.57 ...... Frame ( 28) shift: -0.05 0.62 ...... Frame ( 29) shift: -0.13 0.67 ...... Frame ( 30) shift: -0.16 0.72 ...... Frame ( 31) shift: -0.15 0.79 ...... Frame ( 32) shift: -0.13 0.86 ...... Frame ( 33) shift: -0.05 0.94 ...... Frame ( 34) shift: 0.10 1.05 ...... Frame ( 35) shift: 0.25 1.16 ...... Frame ( 36) shift: 0.34 1.24 ...... Frame ( 37) shift: 0.38 1.30 ...... Frame ( 38) shift: 0.42 1.35 ...... Frame ( 39) shift: 0.46 1.41 ...... Frame ( 40) shift: 0.50 1.46 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.883005 Iteration 2 Error: 0.171554 Iteration 3 Error: 0.062738 Iteration 4 Error: 0.029133 Align patch 2 23 left Iteration 1 Error: 0.605321 Iteration 2 Error: 0.169193 Iteration 3 Error: 0.049785 Align patch 3 22 left Iteration 1 Error: 0.961876 Iteration 2 Error: 0.175515 Iteration 3 Error: 0.057499 Iteration 4 Error: 0.021835 Align patch 4 21 left Iteration 1 Error: 1.071503 Iteration 2 Error: 0.186434 Iteration 3 Error: 0.036312 Align patch 5 20 left Iteration 1 Error: 0.891796 Iteration 2 Error: 0.152553 Iteration 3 Error: 0.030134 Align patch 6 19 left Iteration 1 Error: 0.666097 Iteration 2 Error: 0.076564 Iteration 3 Error: 0.021298 Align patch 7 18 left Iteration 1 Error: 1.006377 Iteration 2 Error: 0.229498 Iteration 3 Error: 0.051495 Iteration 4 Error: 0.015664 Align patch 8 17 left Iteration 1 Error: 0.591397 Iteration 2 Error: 0.117675 Iteration 3 Error: 0.038168 Align patch 9 16 left Iteration 1 Error: 0.760617 Iteration 2 Error: 0.147490 Iteration 3 Error: 0.055990 Iteration 4 Error: 0.029514 Align patch 10 15 left Iteration 1 Error: 0.931132 Iteration 2 Error: 0.104035 Iteration 3 Error: 0.035426 Align patch 11 14 left Iteration 1 Error: 0.719796 Iteration 2 Error: 0.233578 Iteration 3 Error: 0.112528 Iteration 4 Error: 0.048070 Align patch 12 13 left Iteration 1 Error: 0.932861 Iteration 2 Error: 0.206574 Iteration 3 Error: 0.065737 Iteration 4 Error: 0.031752 Align patch 13 12 left Iteration 1 Error: 0.638725 Iteration 2 Error: 0.133658 Iteration 3 Error: 0.036088 Align patch 14 11 left Iteration 1 Error: 0.597008 Iteration 2 Error: 0.091748 Iteration 3 Error: 0.029136 Align patch 15 10 left Iteration 1 Error: 0.915700 Iteration 2 Error: 0.161477 Iteration 3 Error: 0.027756 Align patch 16 9 left Iteration 1 Error: 0.662121 Iteration 2 Error: 0.157570 Iteration 3 Error: 0.044893 Align patch 17 8 left Iteration 1 Error: 0.723405 Iteration 2 Error: 0.108373 Iteration 3 Error: 0.031846 Align patch 18 7 left Iteration 1 Error: 0.869160 Iteration 2 Error: 0.153812 Iteration 3 Error: 0.027780 Align patch 19 6 left Iteration 1 Error: 0.874289 Iteration 2 Error: 0.098230 Iteration 3 Error: 0.030447 Align patch 20 5 left Iteration 1 Error: 0.800907 Iteration 2 Error: 0.099104 Iteration 3 Error: 0.021996 Align patch 21 4 left Iteration 1 Error: 1.222211 Iteration 2 Error: 0.184248 Iteration 3 Error: 0.035840 Align patch 22 3 left Iteration 1 Error: 0.556409 Iteration 2 Error: 0.111394 Iteration 3 Error: 0.027091 Align patch 23 2 left Iteration 1 Error: 0.700645 Iteration 2 Error: 0.110067 Iteration 3 Error: 0.023509 Align patch 24 1 left Iteration 1 Error: 0.857692 Iteration 2 Error: 0.108284 Iteration 3 Error: 0.023064 Align patch 25 0 left Iteration 1 Error: 0.635903 Iteration 2 Error: 0.117984 Iteration 3 Error: 0.037926 3D Fitting completed. Patch alignment time: 12.72(sec) Local motion has been corrected. Process thread exits. Computational time: 22.740726 sec Total time: 28.219139 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00013hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00013hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.628264s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00013hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.546642s ........................................ >>>>>>TIME<<<<<< FFT: 1.073588s Defocus_U Defocus_V Angle CCC 10517.58 11353.52 13.96 0.043581 Final Values Defocus_U Defocus_V Angle CCC 10530.07 11362.90 13.96 0.080048 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00013hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00013hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 43.30 7.45 Num Hot pixels: 210 Hot pixel threshold: 88.00 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.800045 Iteration 2 Error: 0.162302 Iteration 3 Error: 0.042510 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.25 0.03 ...... Frame ( 3) shift: -0.50 0.07 ...... Frame ( 4) shift: -0.75 0.10 ...... Frame ( 5) shift: -1.00 0.14 ...... Frame ( 6) shift: -1.10 0.16 ...... Frame ( 7) shift: -1.05 0.18 ...... Frame ( 8) shift: -0.99 0.19 ...... Frame ( 9) shift: -0.94 0.18 ...... Frame ( 10) shift: -0.90 0.15 ...... Frame ( 11) shift: -0.85 0.11 ...... Frame ( 12) shift: -0.80 0.14 ...... Frame ( 13) shift: -0.74 0.23 ...... Frame ( 14) shift: -0.68 0.32 ...... Frame ( 15) shift: -0.63 0.38 ...... Frame ( 16) shift: -0.60 0.42 ...... Frame ( 17) shift: -0.58 0.47 ...... Frame ( 18) shift: -0.50 0.57 ...... Frame ( 19) shift: -0.37 0.73 ...... Frame ( 20) shift: -0.24 0.89 ...... Frame ( 21) shift: -0.13 1.00 ...... Frame ( 22) shift: -0.03 1.06 ...... Frame ( 23) shift: 0.06 1.12 ...... Frame ( 24) shift: 0.06 1.16 ...... Frame ( 25) shift: -0.04 1.19 ...... Frame ( 26) shift: -0.15 1.22 ...... Frame ( 27) shift: -0.19 1.28 ...... Frame ( 28) shift: -0.18 1.36 ...... Frame ( 29) shift: -0.17 1.44 ...... Frame ( 30) shift: -0.16 1.50 ...... Frame ( 31) shift: -0.16 1.54 ...... Frame ( 32) shift: -0.15 1.58 ...... Frame ( 33) shift: -0.12 1.57 ...... Frame ( 34) shift: -0.07 1.52 ...... Frame ( 35) shift: -0.02 1.46 ...... Frame ( 36) shift: 0.01 1.42 ...... Frame ( 37) shift: 0.00 1.41 ...... Frame ( 38) shift: -0.01 1.39 ...... Frame ( 39) shift: -0.01 1.38 ...... Frame ( 40) shift: -0.02 1.37 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.856148 Iteration 2 Error: 0.112375 Iteration 3 Error: 0.037090 Align patch 2 23 left Iteration 1 Error: 0.802908 Iteration 2 Error: 0.114479 Iteration 3 Error: 0.052936 Iteration 4 Error: 0.017441 Align patch 3 22 left Iteration 1 Error: 0.640194 Iteration 2 Error: 0.140123 Iteration 3 Error: 0.053156 Iteration 4 Error: 0.018252 Align patch 4 21 left Iteration 1 Error: 0.699867 Iteration 2 Error: 0.213885 Iteration 3 Error: 0.059738 Iteration 4 Error: 0.017089 Align patch 5 20 left Iteration 1 Error: 0.653548 Iteration 2 Error: 0.109017 Iteration 3 Error: 0.027443 Align patch 6 19 left Iteration 1 Error: 1.091282 Iteration 2 Error: 0.144314 Iteration 3 Error: 0.029050 Align patch 7 18 left Iteration 1 Error: 0.615975 Iteration 2 Error: 0.118183 Iteration 3 Error: 0.024223 Align patch 8 17 left Iteration 1 Error: 0.840267 Iteration 2 Error: 0.111351 Iteration 3 Error: 0.026074 Align patch 9 16 left Iteration 1 Error: 0.643949 Iteration 2 Error: 0.121656 Iteration 3 Error: 0.023906 Align patch 10 15 left Iteration 1 Error: 0.670383 Iteration 2 Error: 0.086214 Iteration 3 Error: 0.016417 Align patch 11 14 left Iteration 1 Error: 0.808944 Iteration 2 Error: 0.152958 Iteration 3 Error: 0.031031 Align patch 12 13 left Iteration 1 Error: 0.623580 Iteration 2 Error: 0.084444 Iteration 3 Error: 0.017847 Align patch 13 12 left Iteration 1 Error: 0.628637 Iteration 2 Error: 0.103947 Iteration 3 Error: 0.025134 Align patch 14 11 left Iteration 1 Error: 0.629392 Iteration 2 Error: 0.184596 Iteration 3 Error: 0.042185 Align patch 15 10 left Iteration 1 Error: 0.675952 Iteration 2 Error: 0.121167 Iteration 3 Error: 0.025938 Align patch 16 9 left Iteration 1 Error: 0.952485 Iteration 2 Error: 0.158015 Iteration 3 Error: 0.029015 Align patch 17 8 left Iteration 1 Error: 0.786510 Iteration 2 Error: 0.110936 Iteration 3 Error: 0.032922 Align patch 18 7 left Iteration 1 Error: 0.684297 Iteration 2 Error: 0.123103 Iteration 3 Error: 0.035924 Align patch 19 6 left Iteration 1 Error: 1.334274 Iteration 2 Error: 0.146971 Iteration 3 Error: 0.047502 Align patch 20 5 left Iteration 1 Error: 0.823219 Iteration 2 Error: 0.126927 Iteration 3 Error: 0.031030 Align patch 21 4 left Iteration 1 Error: 0.630017 Iteration 2 Error: 0.126731 Iteration 3 Error: 0.032460 Align patch 22 3 left Iteration 1 Error: 0.891718 Iteration 2 Error: 0.148536 Iteration 3 Error: 0.038684 Align patch 23 2 left Iteration 1 Error: 0.752662 Iteration 2 Error: 0.109160 Iteration 3 Error: 0.025510 Align patch 24 1 left Iteration 1 Error: 0.532826 Iteration 2 Error: 0.077813 Iteration 3 Error: 0.022983 Align patch 25 0 left Iteration 1 Error: 0.846261 Iteration 2 Error: 0.092716 Iteration 3 Error: 0.014061 3D Fitting completed. Patch alignment time: 11.66(sec) Local motion has been corrected. Process thread exits. Computational time: 21.464056 sec Total time: 27.377382 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00013hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00013hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.003584s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00013hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.570712s ........................................ >>>>>>TIME<<<<<< FFT: 1.166303s Defocus_U Defocus_V Angle CCC 11955.09 12466.81 0.84 0.049867 Final Values Defocus_U Defocus_V Angle CCC 11969.15 12462.12 0.84 0.088059 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00013hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00013hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 41.12 6.97 Num Hot pixels: 217 Hot pixel threshold: 82.96 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 3.223795 Iteration 2 Error: 0.528117 Iteration 3 Error: 0.156391 Iteration 4 Error: 0.047200 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.04 0.54 ...... Frame ( 3) shift: 0.08 1.08 ...... Frame ( 4) shift: 0.11 1.61 ...... Frame ( 5) shift: 0.15 2.15 ...... Frame ( 6) shift: 0.26 2.59 ...... Frame ( 7) shift: 0.45 2.91 ...... Frame ( 8) shift: 0.63 3.24 ...... Frame ( 9) shift: 0.74 3.53 ...... Frame ( 10) shift: 0.78 3.77 ...... Frame ( 11) shift: 0.82 4.02 ...... Frame ( 12) shift: 0.86 4.19 ...... Frame ( 13) shift: 0.89 4.30 ...... Frame ( 14) shift: 0.93 4.41 ...... Frame ( 15) shift: 0.95 4.47 ...... Frame ( 16) shift: 0.94 4.48 ...... Frame ( 17) shift: 0.94 4.49 ...... Frame ( 18) shift: 0.96 4.53 ...... Frame ( 19) shift: 0.99 4.60 ...... Frame ( 20) shift: 1.02 4.67 ...... Frame ( 21) shift: 1.03 4.71 ...... Frame ( 22) shift: 1.00 4.72 ...... Frame ( 23) shift: 0.98 4.74 ...... Frame ( 24) shift: 1.01 4.78 ...... Frame ( 25) shift: 1.11 4.85 ...... Frame ( 26) shift: 1.20 4.92 ...... Frame ( 27) shift: 1.25 5.01 ...... Frame ( 28) shift: 1.27 5.10 ...... Frame ( 29) shift: 1.28 5.20 ...... Frame ( 30) shift: 1.31 5.29 ...... Frame ( 31) shift: 1.35 5.36 ...... Frame ( 32) shift: 1.39 5.44 ...... Frame ( 33) shift: 1.42 5.50 ...... Frame ( 34) shift: 1.45 5.55 ...... Frame ( 35) shift: 1.47 5.59 ...... Frame ( 36) shift: 1.47 5.67 ...... Frame ( 37) shift: 1.46 5.78 ...... Frame ( 38) shift: 1.45 5.90 ...... Frame ( 39) shift: 1.43 6.01 ...... Frame ( 40) shift: 1.42 6.12 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 4.910258 Iteration 2 Error: 0.713851 Iteration 3 Error: 0.167579 Iteration 4 Error: 0.062310 Iteration 5 Error: 0.026241 Align patch 2 23 left Iteration 1 Error: 2.799043 Iteration 2 Error: 0.362611 Iteration 3 Error: 0.089480 Iteration 4 Error: 0.038560 Align patch 3 22 left Iteration 1 Error: 1.207808 Iteration 2 Error: 0.262392 Iteration 3 Error: 0.061187 Iteration 4 Error: 0.023963 Align patch 4 21 left Iteration 1 Error: 2.336102 Iteration 2 Error: 0.218920 Iteration 3 Error: 0.050937 Iteration 4 Error: 0.016270 Align patch 5 20 left Iteration 1 Error: 2.164626 Iteration 2 Error: 0.202377 Iteration 3 Error: 0.093709 Iteration 4 Error: 0.035863 Align patch 6 19 left Iteration 1 Error: 3.373211 Iteration 2 Error: 0.263532 Iteration 3 Error: 0.113017 Iteration 4 Error: 0.019259 Align patch 7 18 left Iteration 1 Error: 1.855120 Iteration 2 Error: 0.427247 Iteration 3 Error: 0.323245 Iteration 4 Error: 0.215765 Iteration 5 Error: 0.123908 Align patch 7 18 left Iteration 1 Error: 0.719737 Iteration 2 Error: 0.197193 Iteration 3 Error: 0.035978 Align patch 8 17 left Iteration 1 Error: 1.779869 Iteration 2 Error: 0.194329 Iteration 3 Error: 0.090033 Iteration 4 Error: 0.051118 Iteration 5 Error: 0.021251 Align patch 9 16 left Iteration 1 Error: 2.507616 Iteration 2 Error: 0.388949 Iteration 3 Error: 0.135665 Iteration 4 Error: 0.060462 Iteration 5 Error: 0.029768 Align patch 10 15 left Iteration 1 Error: 2.982443 Iteration 2 Error: 0.388918 Iteration 3 Error: 0.101268 Iteration 4 Error: 0.039617 Align patch 11 14 left Iteration 1 Error: 2.247111 Iteration 2 Error: 0.301086 Iteration 3 Error: 0.061777 Iteration 4 Error: 0.021718 Align patch 12 13 left Iteration 1 Error: 1.618711 Iteration 2 Error: 0.207988 Iteration 3 Error: 0.144469 Iteration 4 Error: 0.041082 Align patch 13 12 left Iteration 1 Error: 1.516058 Iteration 2 Error: 0.254803 Iteration 3 Error: 0.043550 Align patch 14 11 left Iteration 1 Error: 2.445054 Iteration 2 Error: 0.324115 Iteration 3 Error: 0.080613 Iteration 4 Error: 0.018698 Align patch 15 10 left Iteration 1 Error: 2.675198 Iteration 2 Error: 0.153405 Iteration 3 Error: 0.030509 Align patch 16 9 left Iteration 1 Error: 2.657772 Iteration 2 Error: 0.446682 Iteration 3 Error: 0.076799 Iteration 4 Error: 0.036002 Align patch 17 8 left Iteration 1 Error: 3.409941 Iteration 2 Error: 0.642933 Iteration 3 Error: 0.141453 Iteration 4 Error: 0.057256 Iteration 5 Error: 0.013519 Align patch 18 7 left Iteration 1 Error: 2.281011 Iteration 2 Error: 0.405854 Iteration 3 Error: 0.116889 Iteration 4 Error: 0.034370 Align patch 19 6 left Iteration 1 Error: 2.059331 Iteration 2 Error: 0.240270 Iteration 3 Error: 0.130333 Iteration 4 Error: 0.051250 Iteration 5 Error: 0.024698 Align patch 20 5 left Iteration 1 Error: 1.259514 Iteration 2 Error: 0.183567 Iteration 3 Error: 0.087761 Iteration 4 Error: 0.037176 Align patch 21 4 left Iteration 1 Error: 3.780880 Iteration 2 Error: 0.965546 Iteration 3 Error: 0.262948 Iteration 4 Error: 0.117349 Iteration 5 Error: 0.039590 Align patch 22 3 left Iteration 1 Error: 3.734343 Iteration 2 Error: 0.363840 Iteration 3 Error: 0.139109 Iteration 4 Error: 0.043465 Align patch 23 2 left Iteration 1 Error: 3.632664 Iteration 2 Error: 0.318305 Iteration 3 Error: 0.074491 Iteration 4 Error: 0.025644 Align patch 24 1 left Iteration 1 Error: 3.232698 Iteration 2 Error: 0.742990 Iteration 3 Error: 0.300400 Iteration 4 Error: 0.095979 Iteration 5 Error: 0.055376 Align patch 24 1 left Iteration 1 Error: 2.483340 Iteration 2 Error: 0.253844 Iteration 3 Error: 0.067610 Iteration 4 Error: 0.024878 Align patch 25 0 left Iteration 1 Error: 1.358546 Iteration 2 Error: 0.271667 Iteration 3 Error: 0.117599 Iteration 4 Error: 0.054818 Iteration 5 Error: 0.036410 3D Fitting completed. Patch alignment time: 15.71(sec) Local motion has been corrected. Process thread exits. Computational time: 25.814629 sec Total time: 31.302101 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00013hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00013hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.652072s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00013hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.087369s ........................................ >>>>>>TIME<<<<<< FFT: 1.017687s Defocus_U Defocus_V Angle CCC 11845.72 12650.41 3.67 0.057204 Final Values Defocus_U Defocus_V Angle CCC 11859.78 12617.60 3.35 0.109696 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00013hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00013hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.996e-02 CC threshold: 0.734 Mean Std: 42.26 7.02 Num Hot pixels: 241 Hot pixel threshold: 84.36 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.079720 Iteration 2 Error: 0.043693 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.27 0.30 ...... Frame ( 3) shift: 0.54 0.60 ...... Frame ( 4) shift: 0.81 0.89 ...... Frame ( 5) shift: 1.08 1.19 ...... Frame ( 6) shift: 1.27 1.41 ...... Frame ( 7) shift: 1.40 1.53 ...... Frame ( 8) shift: 1.53 1.66 ...... Frame ( 9) shift: 1.56 1.71 ...... Frame ( 10) shift: 1.51 1.68 ...... Frame ( 11) shift: 1.45 1.65 ...... Frame ( 12) shift: 1.39 1.60 ...... Frame ( 13) shift: 1.33 1.54 ...... Frame ( 14) shift: 1.27 1.47 ...... Frame ( 15) shift: 1.21 1.40 ...... Frame ( 16) shift: 1.16 1.33 ...... Frame ( 17) shift: 1.10 1.26 ...... Frame ( 18) shift: 1.04 1.26 ...... Frame ( 19) shift: 0.99 1.31 ...... Frame ( 20) shift: 0.94 1.36 ...... Frame ( 21) shift: 0.88 1.38 ...... Frame ( 22) shift: 0.81 1.37 ...... Frame ( 23) shift: 0.74 1.36 ...... Frame ( 24) shift: 0.72 1.35 ...... Frame ( 25) shift: 0.73 1.35 ...... Frame ( 26) shift: 0.74 1.35 ...... Frame ( 27) shift: 0.74 1.33 ...... Frame ( 28) shift: 0.72 1.30 ...... Frame ( 29) shift: 0.70 1.28 ...... Frame ( 30) shift: 0.73 1.27 ...... Frame ( 31) shift: 0.79 1.30 ...... Frame ( 32) shift: 0.85 1.33 ...... Frame ( 33) shift: 0.90 1.31 ...... Frame ( 34) shift: 0.93 1.25 ...... Frame ( 35) shift: 0.96 1.20 ...... Frame ( 36) shift: 0.99 1.18 ...... Frame ( 37) shift: 1.02 1.20 ...... Frame ( 38) shift: 1.06 1.22 ...... Frame ( 39) shift: 1.10 1.24 ...... Frame ( 40) shift: 1.13 1.26 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.124955 Iteration 2 Error: 0.235290 Iteration 3 Error: 0.061002 Iteration 4 Error: 0.021634 Align patch 2 23 left Iteration 1 Error: 0.748857 Iteration 2 Error: 0.214786 Iteration 3 Error: 0.041870 Align patch 3 22 left Iteration 1 Error: 1.186101 Iteration 2 Error: 0.150542 Iteration 3 Error: 0.034116 Align patch 4 21 left Iteration 1 Error: 0.945775 Iteration 2 Error: 0.227813 Iteration 3 Error: 0.063579 Iteration 4 Error: 0.017048 Align patch 5 20 left Iteration 1 Error: 0.926536 Iteration 2 Error: 0.163911 Iteration 3 Error: 0.033253 Align patch 6 19 left Iteration 1 Error: 1.176868 Iteration 2 Error: 0.169127 Iteration 3 Error: 0.055982 Iteration 4 Error: 0.019729 Align patch 7 18 left Iteration 1 Error: 0.669169 Iteration 2 Error: 0.085431 Iteration 3 Error: 0.014648 Align patch 8 17 left Iteration 1 Error: 0.472815 Iteration 2 Error: 0.084283 Iteration 3 Error: 0.039178 Align patch 9 16 left Iteration 1 Error: 1.123590 Iteration 2 Error: 0.207481 Iteration 3 Error: 0.042765 Align patch 10 15 left Iteration 1 Error: 0.912398 Iteration 2 Error: 0.117585 Iteration 3 Error: 0.030649 Align patch 11 14 left Iteration 1 Error: 1.066558 Iteration 2 Error: 0.193951 Iteration 3 Error: 0.064735 Iteration 4 Error: 0.027157 Align patch 12 13 left Iteration 1 Error: 0.756160 Iteration 2 Error: 0.132170 Iteration 3 Error: 0.037521 Align patch 13 12 left Iteration 1 Error: 1.464113 Iteration 2 Error: 0.272819 Iteration 3 Error: 0.112860 Iteration 4 Error: 0.034859 Align patch 14 11 left Iteration 1 Error: 0.696931 Iteration 2 Error: 0.096204 Iteration 3 Error: 0.025423 Align patch 15 10 left Iteration 1 Error: 0.871430 Iteration 2 Error: 0.096037 Iteration 3 Error: 0.014460 Align patch 16 9 left Iteration 1 Error: 1.555362 Iteration 2 Error: 0.402903 Iteration 3 Error: 0.119219 Iteration 4 Error: 0.048364 Align patch 17 8 left Iteration 1 Error: 0.886331 Iteration 2 Error: 0.300458 Iteration 3 Error: 0.050772 Iteration 4 Error: 0.031026 Align patch 18 7 left Iteration 1 Error: 1.219472 Iteration 2 Error: 0.192441 Iteration 3 Error: 0.052930 Iteration 4 Error: 0.016863 Align patch 19 6 left Iteration 1 Error: 0.757887 Iteration 2 Error: 0.124965 Iteration 3 Error: 0.030209 Align patch 20 5 left Iteration 1 Error: 0.866431 Iteration 2 Error: 0.168573 Iteration 3 Error: 0.033855 Align patch 21 4 left Iteration 1 Error: 0.797692 Iteration 2 Error: 0.173442 Iteration 3 Error: 0.069288 Iteration 4 Error: 0.042330 Align patch 22 3 left Iteration 1 Error: 0.636689 Iteration 2 Error: 0.179325 Iteration 3 Error: 0.041563 Align patch 23 2 left Iteration 1 Error: 0.717252 Iteration 2 Error: 0.118509 Iteration 3 Error: 0.036054 Align patch 24 1 left Iteration 1 Error: 0.780255 Iteration 2 Error: 0.110122 Iteration 3 Error: 0.024268 Align patch 25 0 left Iteration 1 Error: 0.805852 Iteration 2 Error: 0.153726 Iteration 3 Error: 0.030858 3D Fitting completed. Patch alignment time: 13.01(sec) Local motion has been corrected. Process thread exits. Computational time: 23.172588 sec Total time: 29.027765 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00013hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00013hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.007884s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00013hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.026858s ........................................ >>>>>>TIME<<<<<< FFT: 1.184949s Defocus_U Defocus_V Angle CCC 13288.10 12629.87 79.86 0.039080 Final Values Defocus_U Defocus_V Angle CCC 13316.23 12670.51 79.24 0.067142 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00014hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00014hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.999e-02 CC threshold: 0.734 Mean Std: 39.86 6.85 Num Hot pixels: 232 Hot pixel threshold: 80.99 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.945519 Iteration 2 Error: 0.231432 Iteration 3 Error: 0.062455 Iteration 4 Error: 0.022201 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.15 -0.07 ...... Frame ( 3) shift: -0.30 -0.14 ...... Frame ( 4) shift: -0.46 -0.21 ...... Frame ( 5) shift: -0.61 -0.28 ...... Frame ( 6) shift: -0.66 -0.28 ...... Frame ( 7) shift: -0.60 -0.20 ...... Frame ( 8) shift: -0.55 -0.12 ...... Frame ( 9) shift: -0.50 -0.04 ...... Frame ( 10) shift: -0.46 0.04 ...... Frame ( 11) shift: -0.41 0.12 ...... Frame ( 12) shift: -0.38 0.21 ...... Frame ( 13) shift: -0.36 0.31 ...... Frame ( 14) shift: -0.35 0.41 ...... Frame ( 15) shift: -0.30 0.50 ...... Frame ( 16) shift: -0.21 0.58 ...... Frame ( 17) shift: -0.12 0.66 ...... Frame ( 18) shift: -0.09 0.73 ...... Frame ( 19) shift: -0.09 0.78 ...... Frame ( 20) shift: -0.10 0.83 ...... Frame ( 21) shift: -0.06 0.87 ...... Frame ( 22) shift: 0.04 0.90 ...... Frame ( 23) shift: 0.14 0.94 ...... Frame ( 24) shift: 0.22 0.94 ...... Frame ( 25) shift: 0.26 0.92 ...... Frame ( 26) shift: 0.30 0.91 ...... Frame ( 27) shift: 0.32 0.94 ...... Frame ( 28) shift: 0.30 1.03 ...... Frame ( 29) shift: 0.29 1.11 ...... Frame ( 30) shift: 0.33 1.19 ...... Frame ( 31) shift: 0.40 1.25 ...... Frame ( 32) shift: 0.48 1.32 ...... Frame ( 33) shift: 0.56 1.37 ...... Frame ( 34) shift: 0.64 1.39 ...... Frame ( 35) shift: 0.72 1.41 ...... Frame ( 36) shift: 0.72 1.43 ...... Frame ( 37) shift: 0.66 1.46 ...... Frame ( 38) shift: 0.60 1.50 ...... Frame ( 39) shift: 0.54 1.53 ...... Frame ( 40) shift: 0.48 1.56 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.907183 Iteration 2 Error: 0.217271 Iteration 3 Error: 0.069978 Iteration 4 Error: 0.036824 Align patch 2 23 left Iteration 1 Error: 1.070300 Iteration 2 Error: 0.250635 Iteration 3 Error: 0.094825 Iteration 4 Error: 0.040837 Align patch 3 22 left Iteration 1 Error: 0.709661 Iteration 2 Error: 0.220844 Iteration 3 Error: 0.098106 Iteration 4 Error: 0.035540 Align patch 4 21 left Iteration 1 Error: 0.783092 Iteration 2 Error: 0.159295 Iteration 3 Error: 0.037302 Align patch 5 20 left Iteration 1 Error: 0.744641 Iteration 2 Error: 0.144319 Iteration 3 Error: 0.037396 Align patch 6 19 left Iteration 1 Error: 1.899860 Iteration 2 Error: 0.506379 Iteration 3 Error: 0.154209 Iteration 4 Error: 0.061117 Iteration 5 Error: 0.025525 Align patch 7 18 left Iteration 1 Error: 0.938650 Iteration 2 Error: 0.170792 Iteration 3 Error: 0.040395 Align patch 8 17 left Iteration 1 Error: 0.918970 Iteration 2 Error: 0.181599 Iteration 3 Error: 0.022117 Align patch 9 16 left Iteration 1 Error: 1.109992 Iteration 2 Error: 0.218819 Iteration 3 Error: 0.078909 Iteration 4 Error: 0.024554 Align patch 10 15 left Iteration 1 Error: 1.032362 Iteration 2 Error: 0.091247 Iteration 3 Error: 0.017965 Align patch 11 14 left Iteration 1 Error: 1.484864 Iteration 2 Error: 0.256321 Iteration 3 Error: 0.106325 Iteration 4 Error: 0.031041 Align patch 12 13 left Iteration 1 Error: 0.843646 Iteration 2 Error: 0.156999 Iteration 3 Error: 0.059454 Iteration 4 Error: 0.023433 Align patch 13 12 left Iteration 1 Error: 0.636812 Iteration 2 Error: 0.145371 Iteration 3 Error: 0.053461 Iteration 4 Error: 0.026164 Align patch 14 11 left Iteration 1 Error: 0.750881 Iteration 2 Error: 0.145889 Iteration 3 Error: 0.044099 Align patch 15 10 left Iteration 1 Error: 0.982496 Iteration 2 Error: 0.226052 Iteration 3 Error: 0.045925 Align patch 16 9 left Iteration 1 Error: 0.974276 Iteration 2 Error: 0.290233 Iteration 3 Error: 0.069227 Iteration 4 Error: 0.028734 Align patch 17 8 left Iteration 1 Error: 1.124632 Iteration 2 Error: 0.261472 Iteration 3 Error: 0.041994 Align patch 18 7 left Iteration 1 Error: 0.894572 Iteration 2 Error: 0.173860 Iteration 3 Error: 0.039287 Align patch 19 6 left Iteration 1 Error: 0.680521 Iteration 2 Error: 0.222829 Iteration 3 Error: 0.062101 Iteration 4 Error: 0.031661 Align patch 20 5 left Iteration 1 Error: 1.345579 Iteration 2 Error: 0.121932 Iteration 3 Error: 0.027593 Align patch 21 4 left Iteration 1 Error: 0.860197 Iteration 2 Error: 0.277921 Iteration 3 Error: 0.096791 Iteration 4 Error: 0.050777 Iteration 5 Error: 0.025543 Align patch 22 3 left Iteration 1 Error: 0.605788 Iteration 2 Error: 0.107025 Iteration 3 Error: 0.027962 Align patch 23 2 left Iteration 1 Error: 0.814236 Iteration 2 Error: 0.140789 Iteration 3 Error: 0.043508 Align patch 24 1 left Iteration 1 Error: 1.323983 Iteration 2 Error: 0.235521 Iteration 3 Error: 0.089557 Iteration 4 Error: 0.031822 Align patch 25 0 left Iteration 1 Error: 1.058107 Iteration 2 Error: 0.219945 Iteration 3 Error: 0.050572 Iteration 4 Error: 0.027194 3D Fitting completed. Patch alignment time: 12.55(sec) Local motion has been corrected. Process thread exits. Computational time: 22.492208 sec Total time: 28.952656 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00014hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00014hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.727035s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00014hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.759160s ........................................ >>>>>>TIME<<<<<< FFT: 1.037322s Defocus_U Defocus_V Angle CCC 12968.77 13820.33 13.27 0.036156 Final Values Defocus_U Defocus_V Angle CCC 12992.21 13843.78 12.65 0.057586 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00014hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00014hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 39.51 6.98 Num Hot pixels: 225 Hot pixel threshold: 81.42 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.803089 Iteration 2 Error: 0.078062 Iteration 3 Error: 0.020898 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.26 0.05 ...... Frame ( 3) shift: -0.53 0.09 ...... Frame ( 4) shift: -0.79 0.14 ...... Frame ( 5) shift: -1.06 0.18 ...... Frame ( 6) shift: -1.18 0.22 ...... Frame ( 7) shift: -1.17 0.24 ...... Frame ( 8) shift: -1.16 0.27 ...... Frame ( 9) shift: -1.15 0.34 ...... Frame ( 10) shift: -1.15 0.45 ...... Frame ( 11) shift: -1.15 0.57 ...... Frame ( 12) shift: -1.15 0.66 ...... Frame ( 13) shift: -1.14 0.71 ...... Frame ( 14) shift: -1.13 0.76 ...... Frame ( 15) shift: -1.14 0.79 ...... Frame ( 16) shift: -1.17 0.80 ...... Frame ( 17) shift: -1.19 0.81 ...... Frame ( 18) shift: -1.16 0.81 ...... Frame ( 19) shift: -1.06 0.81 ...... Frame ( 20) shift: -0.96 0.81 ...... Frame ( 21) shift: -0.91 0.81 ...... Frame ( 22) shift: -0.92 0.80 ...... Frame ( 23) shift: -0.92 0.79 ...... Frame ( 24) shift: -0.95 0.77 ...... Frame ( 25) shift: -1.01 0.75 ...... Frame ( 26) shift: -1.06 0.72 ...... Frame ( 27) shift: -1.06 0.70 ...... Frame ( 28) shift: -1.02 0.69 ...... Frame ( 29) shift: -0.97 0.68 ...... Frame ( 30) shift: -0.93 0.70 ...... Frame ( 31) shift: -0.89 0.74 ...... Frame ( 32) shift: -0.86 0.79 ...... Frame ( 33) shift: -0.86 0.81 ...... Frame ( 34) shift: -0.89 0.82 ...... Frame ( 35) shift: -0.92 0.83 ...... Frame ( 36) shift: -0.89 0.82 ...... Frame ( 37) shift: -0.81 0.80 ...... Frame ( 38) shift: -0.72 0.78 ...... Frame ( 39) shift: -0.64 0.76 ...... Frame ( 40) shift: -0.55 0.74 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.425006 Iteration 2 Error: 0.230188 Iteration 3 Error: 0.078040 Iteration 4 Error: 0.019968 Align patch 2 23 left Iteration 1 Error: 1.789288 Iteration 2 Error: 0.377866 Iteration 3 Error: 0.162668 Iteration 4 Error: 0.083474 Iteration 5 Error: 0.040980 Align patch 3 22 left Iteration 1 Error: 0.810071 Iteration 2 Error: 0.223736 Iteration 3 Error: 0.061481 Iteration 4 Error: 0.026642 Align patch 4 21 left Iteration 1 Error: 0.807943 Iteration 2 Error: 0.147484 Iteration 3 Error: 0.038512 Align patch 5 20 left Iteration 1 Error: 1.562352 Iteration 2 Error: 0.277398 Iteration 3 Error: 0.082953 Iteration 4 Error: 0.025563 Align patch 6 19 left Iteration 1 Error: 9.245613 Iteration 2 Error: 7.977227 Iteration 3 Error: 8.989872 Iteration 4 Error: 2.806591 Iteration 5 Error: 0.741066 Align patch 6 19 left Iteration 1 Error: 3.857672 Iteration 2 Error: 1.229093 Iteration 3 Error: 0.474968 Iteration 4 Error: 0.328892 Iteration 5 Error: 0.204391 Align patch 7 18 left Iteration 1 Error: 0.775556 Iteration 2 Error: 0.155007 Iteration 3 Error: 0.046752 Align patch 8 17 left Iteration 1 Error: 0.850435 Iteration 2 Error: 0.172311 Iteration 3 Error: 0.033781 Align patch 9 16 left Iteration 1 Error: 0.833412 Iteration 2 Error: 0.168841 Iteration 3 Error: 0.052311 Iteration 4 Error: 0.018276 Align patch 10 15 left Iteration 1 Error: 0.647462 Iteration 2 Error: 0.086257 Iteration 3 Error: 0.020497 Align patch 11 14 left Iteration 1 Error: 0.905264 Iteration 2 Error: 0.162279 Iteration 3 Error: 0.041937 Align patch 12 13 left Iteration 1 Error: 0.863205 Iteration 2 Error: 0.134427 Iteration 3 Error: 0.037577 Align patch 13 12 left Iteration 1 Error: 0.914828 Iteration 2 Error: 0.104108 Iteration 3 Error: 0.030652 Align patch 14 11 left Iteration 1 Error: 0.635978 Iteration 2 Error: 0.260420 Iteration 3 Error: 0.074766 Iteration 4 Error: 0.035257 Align patch 15 10 left Iteration 1 Error: 0.674548 Iteration 2 Error: 0.124992 Iteration 3 Error: 0.047576 Align patch 16 9 left Iteration 1 Error: 1.050901 Iteration 2 Error: 0.134487 Iteration 3 Error: 0.027503 Align patch 17 8 left Iteration 1 Error: 0.912427 Iteration 2 Error: 0.152589 Iteration 3 Error: 0.044751 Align patch 18 7 left Iteration 1 Error: 1.088987 Iteration 2 Error: 0.154468 Iteration 3 Error: 0.052112 Iteration 4 Error: 0.009034 Align patch 19 6 left Iteration 1 Error: 0.648567 Iteration 2 Error: 0.160428 Iteration 3 Error: 0.041347 Align patch 20 5 left Iteration 1 Error: 1.026391 Iteration 2 Error: 0.161242 Iteration 3 Error: 0.046852 Align patch 21 4 left Iteration 1 Error: 0.911635 Iteration 2 Error: 0.150824 Iteration 3 Error: 0.050241 Iteration 4 Error: 0.018220 Align patch 22 3 left Iteration 1 Error: 0.574333 Iteration 2 Error: 0.129935 Iteration 3 Error: 0.028031 Align patch 23 2 left Iteration 1 Error: 0.651655 Iteration 2 Error: 0.099936 Iteration 3 Error: 0.021970 Align patch 24 1 left Iteration 1 Error: 0.492053 Iteration 2 Error: 0.114702 Iteration 3 Error: 0.022707 Align patch 25 0 left Iteration 1 Error: 0.661237 Iteration 2 Error: 0.128584 Iteration 3 Error: 0.037066 3D Fitting completed. Patch alignment time: 13.12(sec) Local motion has been corrected. Process thread exits. Computational time: 23.453310 sec Total time: 29.122536 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00014hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00014hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.699738s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00014hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.836130s ........................................ >>>>>>TIME<<<<<< FFT: 1.007071s Defocus_U Defocus_V Angle CCC 11914.73 11394.30 84.71 0.028453 Final Values Defocus_U Defocus_V Angle CCC 11961.62 11422.44 84.40 0.049927 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00014hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00014hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.994e-02 CC threshold: 0.734 Mean Std: 39.02 6.62 Num Hot pixels: 246 Hot pixel threshold: 78.73 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.246644 Iteration 2 Error: 0.248352 Iteration 3 Error: 0.065105 Iteration 4 Error: 0.027945 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.00 0.11 ...... Frame ( 3) shift: -0.01 0.21 ...... Frame ( 4) shift: -0.01 0.32 ...... Frame ( 5) shift: -0.02 0.43 ...... Frame ( 6) shift: 0.02 0.52 ...... Frame ( 7) shift: 0.09 0.58 ...... Frame ( 8) shift: 0.17 0.65 ...... Frame ( 9) shift: 0.24 0.75 ...... Frame ( 10) shift: 0.31 0.89 ...... Frame ( 11) shift: 0.38 1.03 ...... Frame ( 12) shift: 0.43 1.12 ...... Frame ( 13) shift: 0.44 1.15 ...... Frame ( 14) shift: 0.46 1.19 ...... Frame ( 15) shift: 0.48 1.23 ...... Frame ( 16) shift: 0.51 1.29 ...... Frame ( 17) shift: 0.54 1.34 ...... Frame ( 18) shift: 0.58 1.42 ...... Frame ( 19) shift: 0.61 1.53 ...... Frame ( 20) shift: 0.64 1.63 ...... Frame ( 21) shift: 0.63 1.69 ...... Frame ( 22) shift: 0.59 1.71 ...... Frame ( 23) shift: 0.55 1.72 ...... Frame ( 24) shift: 0.55 1.75 ...... Frame ( 25) shift: 0.60 1.79 ...... Frame ( 26) shift: 0.64 1.84 ...... Frame ( 27) shift: 0.66 1.92 ...... Frame ( 28) shift: 0.65 2.06 ...... Frame ( 29) shift: 0.63 2.19 ...... Frame ( 30) shift: 0.63 2.29 ...... Frame ( 31) shift: 0.64 2.36 ...... Frame ( 32) shift: 0.64 2.42 ...... Frame ( 33) shift: 0.66 2.48 ...... Frame ( 34) shift: 0.69 2.54 ...... Frame ( 35) shift: 0.71 2.60 ...... Frame ( 36) shift: 0.70 2.63 ...... Frame ( 37) shift: 0.64 2.64 ...... Frame ( 38) shift: 0.58 2.64 ...... Frame ( 39) shift: 0.52 2.65 ...... Frame ( 40) shift: 0.46 2.65 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.820675 Iteration 2 Error: 0.285245 Iteration 3 Error: 0.103669 Iteration 4 Error: 0.048369 Align patch 2 23 left Iteration 1 Error: 0.970839 Iteration 2 Error: 0.116225 Iteration 3 Error: 0.047432 Align patch 3 22 left Iteration 1 Error: 1.018234 Iteration 2 Error: 0.332703 Iteration 3 Error: 0.100228 Iteration 4 Error: 0.063067 Iteration 5 Error: 0.023141 Align patch 4 21 left Iteration 1 Error: 0.773114 Iteration 2 Error: 0.221806 Iteration 3 Error: 0.047402 Align patch 5 20 left Iteration 1 Error: 0.803904 Iteration 2 Error: 0.134711 Iteration 3 Error: 0.035165 Align patch 6 19 left Iteration 1 Error: 0.749397 Iteration 2 Error: 0.185058 Iteration 3 Error: 0.044929 Align patch 7 18 left Iteration 1 Error: 1.426829 Iteration 2 Error: 0.301314 Iteration 3 Error: 0.144609 Iteration 4 Error: 0.053596 Iteration 5 Error: 0.024838 Align patch 8 17 left Iteration 1 Error: 1.546466 Iteration 2 Error: 0.299111 Iteration 3 Error: 0.094970 Iteration 4 Error: 0.038821 Align patch 9 16 left Iteration 1 Error: 0.683577 Iteration 2 Error: 0.171691 Iteration 3 Error: 0.047724 Align patch 10 15 left Iteration 1 Error: 1.145640 Iteration 2 Error: 0.240658 Iteration 3 Error: 0.104776 Iteration 4 Error: 0.036809 Align patch 11 14 left Iteration 1 Error: 0.746748 Iteration 2 Error: 0.229004 Iteration 3 Error: 0.099488 Iteration 4 Error: 0.050574 Iteration 5 Error: 0.036256 Align patch 12 13 left Iteration 1 Error: 1.239741 Iteration 2 Error: 0.371768 Iteration 3 Error: 0.077705 Iteration 4 Error: 0.044269 Align patch 13 12 left Iteration 1 Error: 0.588684 Iteration 2 Error: 0.145069 Iteration 3 Error: 0.049078 Align patch 14 11 left Iteration 1 Error: 1.077632 Iteration 2 Error: 0.170069 Iteration 3 Error: 0.044481 Align patch 15 10 left Iteration 1 Error: 0.976241 Iteration 2 Error: 0.190851 Iteration 3 Error: 0.062896 Iteration 4 Error: 0.016481 Align patch 16 9 left Iteration 1 Error: 1.299384 Iteration 2 Error: 0.200482 Iteration 3 Error: 0.036874 Align patch 17 8 left Iteration 1 Error: 0.671984 Iteration 2 Error: 0.149117 Iteration 3 Error: 0.049825 Align patch 18 7 left Iteration 1 Error: 0.965026 Iteration 2 Error: 0.153770 Iteration 3 Error: 0.052075 Iteration 4 Error: 0.018066 Align patch 19 6 left Iteration 1 Error: 0.724616 Iteration 2 Error: 0.140305 Iteration 3 Error: 0.034670 Align patch 20 5 left Iteration 1 Error: 1.020433 Iteration 2 Error: 0.230690 Iteration 3 Error: 0.073841 Iteration 4 Error: 0.023517 Align patch 21 4 left Iteration 1 Error: 1.117575 Iteration 2 Error: 0.185981 Iteration 3 Error: 0.041884 Align patch 22 3 left Iteration 1 Error: 0.924383 Iteration 2 Error: 0.193157 Iteration 3 Error: 0.049678 Align patch 23 2 left Iteration 1 Error: 0.858672 Iteration 2 Error: 0.110504 Iteration 3 Error: 0.024671 Align patch 24 1 left Iteration 1 Error: 0.974219 Iteration 2 Error: 0.238504 Iteration 3 Error: 0.048863 Align patch 25 0 left Iteration 1 Error: 0.939907 Iteration 2 Error: 0.232193 Iteration 3 Error: 0.052562 Iteration 4 Error: 0.016828 3D Fitting completed. Patch alignment time: 11.96(sec) Local motion has been corrected. Process thread exits. Computational time: 22.007469 sec Total time: 27.928476 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00014hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00014hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.885018s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00014hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.798574s ........................................ >>>>>>TIME<<<<<< FFT: 1.439056s Defocus_U Defocus_V Angle CCC 11976.57 12789.07 7.67 0.028668 Final Values Defocus_U Defocus_V Angle CCC 12010.95 12792.22 7.04 0.046220 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00014hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00014hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.995e-02 CC threshold: 0.734 Mean Std: 39.76 6.82 Num Hot pixels: 229 Hot pixel threshold: 80.70 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.989626 Iteration 2 Error: 0.156676 Iteration 3 Error: 0.040565 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.20 -0.10 ...... Frame ( 3) shift: -0.41 -0.20 ...... Frame ( 4) shift: -0.61 -0.30 ...... Frame ( 5) shift: -0.82 -0.40 ...... Frame ( 6) shift: -0.91 -0.42 ...... Frame ( 7) shift: -0.88 -0.36 ...... Frame ( 8) shift: -0.85 -0.30 ...... Frame ( 9) shift: -0.80 -0.21 ...... Frame ( 10) shift: -0.73 -0.08 ...... Frame ( 11) shift: -0.65 0.05 ...... Frame ( 12) shift: -0.58 0.13 ...... Frame ( 13) shift: -0.51 0.16 ...... Frame ( 14) shift: -0.44 0.19 ...... Frame ( 15) shift: -0.40 0.25 ...... Frame ( 16) shift: -0.38 0.34 ...... Frame ( 17) shift: -0.37 0.43 ...... Frame ( 18) shift: -0.35 0.51 ...... Frame ( 19) shift: -0.32 0.57 ...... Frame ( 20) shift: -0.30 0.64 ...... Frame ( 21) shift: -0.30 0.71 ...... Frame ( 22) shift: -0.33 0.79 ...... Frame ( 23) shift: -0.35 0.88 ...... Frame ( 24) shift: -0.35 0.91 ...... Frame ( 25) shift: -0.32 0.90 ...... Frame ( 26) shift: -0.29 0.88 ...... Frame ( 27) shift: -0.24 0.91 ...... Frame ( 28) shift: -0.17 0.98 ...... Frame ( 29) shift: -0.10 1.05 ...... Frame ( 30) shift: -0.10 1.10 ...... Frame ( 31) shift: -0.17 1.12 ...... Frame ( 32) shift: -0.23 1.15 ...... Frame ( 33) shift: -0.23 1.19 ...... Frame ( 34) shift: -0.16 1.23 ...... Frame ( 35) shift: -0.09 1.27 ...... Frame ( 36) shift: -0.05 1.28 ...... Frame ( 37) shift: -0.05 1.24 ...... Frame ( 38) shift: -0.05 1.21 ...... Frame ( 39) shift: -0.05 1.17 ...... Frame ( 40) shift: -0.05 1.14 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.526533 Iteration 2 Error: 0.398583 Iteration 3 Error: 0.126638 Iteration 4 Error: 0.056296 Iteration 5 Error: 0.022830 Align patch 2 23 left Iteration 1 Error: 3.290966 Iteration 2 Error: 0.847922 Iteration 3 Error: 0.248303 Iteration 4 Error: 0.130002 Iteration 5 Error: 0.042752 Align patch 3 22 left Iteration 1 Error: 1.272269 Iteration 2 Error: 0.222562 Iteration 3 Error: 0.134321 Iteration 4 Error: 0.049529 Align patch 4 21 left Iteration 1 Error: 0.925563 Iteration 2 Error: 0.174107 Iteration 3 Error: 0.034273 Align patch 5 20 left Iteration 1 Error: 1.182950 Iteration 2 Error: 0.155801 Iteration 3 Error: 0.040376 Align patch 6 19 left Iteration 1 Error: 1.405019 Iteration 2 Error: 0.370492 Iteration 3 Error: 0.107262 Iteration 4 Error: 0.051132 Iteration 5 Error: 0.030215 Align patch 7 18 left Iteration 1 Error: 1.736900 Iteration 2 Error: 0.386976 Iteration 3 Error: 0.122736 Iteration 4 Error: 0.052781 Iteration 5 Error: 0.026099 Align patch 8 17 left Iteration 1 Error: 0.779004 Iteration 2 Error: 0.114766 Iteration 3 Error: 0.035608 Align patch 9 16 left Iteration 1 Error: 1.007721 Iteration 2 Error: 0.174172 Iteration 3 Error: 0.060210 Iteration 4 Error: 0.016131 Align patch 10 15 left Iteration 1 Error: 1.133255 Iteration 2 Error: 0.352990 Iteration 3 Error: 0.146034 Iteration 4 Error: 0.069066 Iteration 5 Error: 0.024001 Align patch 11 14 left Iteration 1 Error: 1.059480 Iteration 2 Error: 0.226613 Iteration 3 Error: 0.097585 Iteration 4 Error: 0.033893 Align patch 12 13 left Iteration 1 Error: 0.899883 Iteration 2 Error: 0.329280 Iteration 3 Error: 0.147347 Iteration 4 Error: 0.061785 Iteration 5 Error: 0.030728 Align patch 13 12 left Iteration 1 Error: 0.614529 Iteration 2 Error: 0.101903 Iteration 3 Error: 0.025194 Align patch 14 11 left Iteration 1 Error: 1.086630 Iteration 2 Error: 0.216830 Iteration 3 Error: 0.052958 Iteration 4 Error: 0.023820 Align patch 15 10 left Iteration 1 Error: 0.830300 Iteration 2 Error: 0.188854 Iteration 3 Error: 0.049117 Align patch 16 9 left Iteration 1 Error: 1.039598 Iteration 2 Error: 0.187576 Iteration 3 Error: 0.045111 Align patch 17 8 left Iteration 1 Error: 0.722033 Iteration 2 Error: 0.139074 Iteration 3 Error: 0.054455 Iteration 4 Error: 0.014712 Align patch 18 7 left Iteration 1 Error: 0.973238 Iteration 2 Error: 0.187845 Iteration 3 Error: 0.057890 Iteration 4 Error: 0.021231 Align patch 19 6 left Iteration 1 Error: 1.042816 Iteration 2 Error: 0.469414 Iteration 3 Error: 0.172299 Iteration 4 Error: 0.057200 Iteration 5 Error: 0.021232 Align patch 20 5 left Iteration 1 Error: 0.784510 Iteration 2 Error: 0.202294 Iteration 3 Error: 0.076429 Iteration 4 Error: 0.020908 Align patch 21 4 left Iteration 1 Error: 0.980267 Iteration 2 Error: 0.203428 Iteration 3 Error: 0.071725 Iteration 4 Error: 0.020541 Align patch 22 3 left Iteration 1 Error: 0.745544 Iteration 2 Error: 0.135774 Iteration 3 Error: 0.039222 Align patch 23 2 left Iteration 1 Error: 0.769297 Iteration 2 Error: 0.150900 Iteration 3 Error: 0.037580 Align patch 24 1 left Iteration 1 Error: 0.899167 Iteration 2 Error: 0.094109 Iteration 3 Error: 0.026817 Align patch 25 0 left Iteration 1 Error: 1.366896 Iteration 2 Error: 0.261639 Iteration 3 Error: 0.066613 Iteration 4 Error: 0.018178 3D Fitting completed. Patch alignment time: 12.74(sec) Local motion has been corrected. Process thread exits. Computational time: 22.250715 sec Total time: 27.918886 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00014hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00014hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.829373s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00014hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.042168s ........................................ >>>>>>TIME<<<<<< FFT: 1.042291s Defocus_U Defocus_V Angle CCC 15142.60 14486.35 86.99 0.034900 Final Values Defocus_U Defocus_V Angle CCC 15186.36 14476.99 88.25 0.053708 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00015hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00015hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.998e-02 CC threshold: 0.734 Mean Std: 44.07 7.32 Num Hot pixels: 238 Hot pixel threshold: 87.96 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.873230 Iteration 2 Error: 0.352321 Iteration 3 Error: 0.138462 Iteration 4 Error: 0.050380 Iteration 5 Error: 0.025541 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.20 -0.02 ...... Frame ( 3) shift: -0.41 -0.04 ...... Frame ( 4) shift: -0.61 -0.06 ...... Frame ( 5) shift: -0.82 -0.08 ...... Frame ( 6) shift: -0.89 -0.03 ...... Frame ( 7) shift: -0.82 0.08 ...... Frame ( 8) shift: -0.76 0.20 ...... Frame ( 9) shift: -0.64 0.36 ...... Frame ( 10) shift: -0.48 0.58 ...... Frame ( 11) shift: -0.32 0.79 ...... Frame ( 12) shift: -0.20 0.96 ...... Frame ( 13) shift: -0.14 1.09 ...... Frame ( 14) shift: -0.07 1.22 ...... Frame ( 15) shift: -0.01 1.34 ...... Frame ( 16) shift: 0.05 1.44 ...... Frame ( 17) shift: 0.10 1.55 ...... Frame ( 18) shift: 0.17 1.68 ...... Frame ( 19) shift: 0.24 1.84 ...... Frame ( 20) shift: 0.31 2.00 ...... Frame ( 21) shift: 0.38 2.07 ...... Frame ( 22) shift: 0.45 2.05 ...... Frame ( 23) shift: 0.52 2.03 ...... Frame ( 24) shift: 0.65 2.10 ...... Frame ( 25) shift: 0.84 2.26 ...... Frame ( 26) shift: 1.04 2.42 ...... Frame ( 27) shift: 1.16 2.56 ...... Frame ( 28) shift: 1.22 2.68 ...... Frame ( 29) shift: 1.27 2.81 ...... Frame ( 30) shift: 1.31 2.85 ...... Frame ( 31) shift: 1.32 2.83 ...... Frame ( 32) shift: 1.33 2.80 ...... Frame ( 33) shift: 1.34 2.79 ...... Frame ( 34) shift: 1.35 2.79 ...... Frame ( 35) shift: 1.36 2.78 ...... Frame ( 36) shift: 1.40 2.78 ...... Frame ( 37) shift: 1.47 2.76 ...... Frame ( 38) shift: 1.54 2.75 ...... Frame ( 39) shift: 1.60 2.74 ...... Frame ( 40) shift: 1.67 2.72 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.869082 Iteration 2 Error: 0.385235 Iteration 3 Error: 0.126377 Iteration 4 Error: 0.061151 Iteration 5 Error: 0.022110 Align patch 2 23 left Iteration 1 Error: 0.869888 Iteration 2 Error: 0.316419 Iteration 3 Error: 0.128895 Iteration 4 Error: 0.055199 Iteration 5 Error: 0.024797 Align patch 3 22 left Iteration 1 Error: 1.249962 Iteration 2 Error: 0.254860 Iteration 3 Error: 0.118819 Iteration 4 Error: 0.050814 Iteration 5 Error: 0.024323 Align patch 4 21 left Iteration 1 Error: 1.104876 Iteration 2 Error: 0.389467 Iteration 3 Error: 0.072248 Iteration 4 Error: 0.037427 Align patch 5 20 left Iteration 1 Error: 0.583556 Iteration 2 Error: 0.201472 Iteration 3 Error: 0.047726 Align patch 6 19 left Iteration 1 Error: 2.517762 Iteration 2 Error: 0.590283 Iteration 3 Error: 0.155489 Iteration 4 Error: 0.068800 Iteration 5 Error: 0.034159 Align patch 7 18 left Iteration 1 Error: 0.971286 Iteration 2 Error: 0.278043 Iteration 3 Error: 0.126063 Iteration 4 Error: 0.042579 Align patch 8 17 left Iteration 1 Error: 0.763759 Iteration 2 Error: 0.145382 Iteration 3 Error: 0.043770 Align patch 9 16 left Iteration 1 Error: 0.735108 Iteration 2 Error: 0.122790 Iteration 3 Error: 0.029007 Align patch 10 15 left Iteration 1 Error: 1.000423 Iteration 2 Error: 0.230278 Iteration 3 Error: 0.041550 Align patch 11 14 left Iteration 1 Error: 0.874820 Iteration 2 Error: 0.335347 Iteration 3 Error: 0.101769 Iteration 4 Error: 0.043435 Align patch 12 13 left Iteration 1 Error: 0.814264 Iteration 2 Error: 0.242903 Iteration 3 Error: 0.077470 Iteration 4 Error: 0.031444 Align patch 13 12 left Iteration 1 Error: 1.282782 Iteration 2 Error: 0.357086 Iteration 3 Error: 0.071990 Iteration 4 Error: 0.037727 Align patch 14 11 left Iteration 1 Error: 1.050218 Iteration 2 Error: 0.251308 Iteration 3 Error: 0.089492 Iteration 4 Error: 0.038486 Align patch 15 10 left Iteration 1 Error: 0.681786 Iteration 2 Error: 0.138924 Iteration 3 Error: 0.033190 Align patch 16 9 left Iteration 1 Error: 0.800605 Iteration 2 Error: 0.213549 Iteration 3 Error: 0.079025 Iteration 4 Error: 0.024182 Align patch 17 8 left Iteration 1 Error: 0.634226 Iteration 2 Error: 0.141975 Iteration 3 Error: 0.043628 Align patch 18 7 left Iteration 1 Error: 0.822588 Iteration 2 Error: 0.252144 Iteration 3 Error: 0.058442 Iteration 4 Error: 0.025440 Align patch 19 6 left Iteration 1 Error: 0.665711 Iteration 2 Error: 0.168843 Iteration 3 Error: 0.052537 Iteration 4 Error: 0.024006 Align patch 20 5 left Iteration 1 Error: 0.863971 Iteration 2 Error: 0.162595 Iteration 3 Error: 0.055733 Iteration 4 Error: 0.015957 Align patch 21 4 left Iteration 1 Error: 0.669489 Iteration 2 Error: 0.183976 Iteration 3 Error: 0.062186 Iteration 4 Error: 0.028558 Align patch 22 3 left Iteration 1 Error: 0.867586 Iteration 2 Error: 0.197474 Iteration 3 Error: 0.065858 Iteration 4 Error: 0.018913 Align patch 23 2 left Iteration 1 Error: 1.208146 Iteration 2 Error: 0.320242 Iteration 3 Error: 0.083686 Iteration 4 Error: 0.035883 Align patch 24 1 left Iteration 1 Error: 0.833476 Iteration 2 Error: 0.222872 Iteration 3 Error: 0.069709 Iteration 4 Error: 0.025029 Align patch 25 0 left Iteration 1 Error: 0.860147 Iteration 2 Error: 0.131042 Iteration 3 Error: 0.018813 3D Fitting completed. Patch alignment time: 12.97(sec) Local motion has been corrected. Process thread exits. Computational time: 23.886234 sec Total time: 29.957836 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00015hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00015hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.567295s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00015hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.561835s ........................................ >>>>>>TIME<<<<<< FFT: 1.100515s Defocus_U Defocus_V Angle CCC 12751.96 13619.15 15.76 0.046984 Final Values Defocus_U Defocus_V Angle CCC 12756.65 13623.84 15.13 0.079489 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00015hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00015hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.996e-02 CC threshold: 0.734 Mean Std: 42.80 7.21 Num Hot pixels: 231 Hot pixel threshold: 86.05 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.429140 Iteration 2 Error: 0.322579 Iteration 3 Error: 0.128006 Iteration 4 Error: 0.048208 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.22 -0.05 ...... Frame ( 3) shift: -0.44 -0.09 ...... Frame ( 4) shift: -0.67 -0.14 ...... Frame ( 5) shift: -0.89 -0.19 ...... Frame ( 6) shift: -1.01 -0.13 ...... Frame ( 7) shift: -1.03 0.04 ...... Frame ( 8) shift: -1.06 0.20 ...... Frame ( 9) shift: -1.03 0.34 ...... Frame ( 10) shift: -0.95 0.45 ...... Frame ( 11) shift: -0.87 0.57 ...... Frame ( 12) shift: -0.81 0.72 ...... Frame ( 13) shift: -0.75 0.91 ...... Frame ( 14) shift: -0.69 1.10 ...... Frame ( 15) shift: -0.59 1.22 ...... Frame ( 16) shift: -0.45 1.27 ...... Frame ( 17) shift: -0.31 1.33 ...... Frame ( 18) shift: -0.24 1.43 ...... Frame ( 19) shift: -0.25 1.60 ...... Frame ( 20) shift: -0.25 1.77 ...... Frame ( 21) shift: -0.25 1.87 ...... Frame ( 22) shift: -0.24 1.90 ...... Frame ( 23) shift: -0.24 1.93 ...... Frame ( 24) shift: -0.24 2.01 ...... Frame ( 25) shift: -0.25 2.14 ...... Frame ( 26) shift: -0.26 2.27 ...... Frame ( 27) shift: -0.22 2.34 ...... Frame ( 28) shift: -0.12 2.36 ...... Frame ( 29) shift: -0.02 2.38 ...... Frame ( 30) shift: 0.04 2.44 ...... Frame ( 31) shift: 0.06 2.53 ...... Frame ( 32) shift: 0.08 2.63 ...... Frame ( 33) shift: 0.13 2.68 ...... Frame ( 34) shift: 0.20 2.66 ...... Frame ( 35) shift: 0.27 2.65 ...... Frame ( 36) shift: 0.31 2.65 ...... Frame ( 37) shift: 0.32 2.64 ...... Frame ( 38) shift: 0.33 2.64 ...... Frame ( 39) shift: 0.34 2.64 ...... Frame ( 40) shift: 0.35 2.64 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.825432 Iteration 2 Error: 0.243895 Iteration 3 Error: 0.154218 Iteration 4 Error: 0.053946 Iteration 5 Error: 0.033872 Align patch 2 23 left Iteration 1 Error: 1.261924 Iteration 2 Error: 0.470693 Iteration 3 Error: 0.205592 Iteration 4 Error: 0.083711 Iteration 5 Error: 0.057623 Align patch 2 23 left Iteration 1 Error: 1.714741 Iteration 2 Error: 0.194161 Iteration 3 Error: 0.057557 Iteration 4 Error: 0.020092 Align patch 3 22 left Iteration 1 Error: 1.163889 Iteration 2 Error: 0.328744 Iteration 3 Error: 0.088861 Iteration 4 Error: 0.041174 Align patch 4 21 left Iteration 1 Error: 0.953492 Iteration 2 Error: 0.239487 Iteration 3 Error: 0.074648 Iteration 4 Error: 0.033503 Align patch 5 20 left Iteration 1 Error: 0.808234 Iteration 2 Error: 0.209616 Iteration 3 Error: 0.052020 Iteration 4 Error: 0.031730 Align patch 6 19 left Iteration 1 Error: 1.753688 Iteration 2 Error: 0.193729 Iteration 3 Error: 0.121809 Iteration 4 Error: 0.039743 Align patch 7 18 left Iteration 1 Error: 2.717850 Iteration 2 Error: 0.287609 Iteration 3 Error: 0.151841 Iteration 4 Error: 0.050999 Iteration 5 Error: 0.043517 Align patch 8 17 left Iteration 1 Error: 0.604646 Iteration 2 Error: 0.110153 Iteration 3 Error: 0.039184 Align patch 9 16 left Iteration 1 Error: 0.993240 Iteration 2 Error: 0.243336 Iteration 3 Error: 0.094542 Iteration 4 Error: 0.026295 Align patch 10 15 left Iteration 1 Error: 0.755515 Iteration 2 Error: 0.133564 Iteration 3 Error: 0.037858 Align patch 11 14 left Iteration 1 Error: 1.490318 Iteration 2 Error: 0.408494 Iteration 3 Error: 0.113944 Iteration 4 Error: 0.114704 Iteration 5 Error: 0.037530 Align patch 12 13 left Iteration 1 Error: 0.795403 Iteration 2 Error: 0.139975 Iteration 3 Error: 0.074654 Iteration 4 Error: 0.028637 Align patch 13 12 left Iteration 1 Error: 1.942796 Iteration 2 Error: 0.279954 Iteration 3 Error: 0.107170 Iteration 4 Error: 0.041330 Align patch 14 11 left Iteration 1 Error: 0.548866 Iteration 2 Error: 0.114062 Iteration 3 Error: 0.038858 Align patch 15 10 left Iteration 1 Error: 0.810214 Iteration 2 Error: 0.144559 Iteration 3 Error: 0.032872 Align patch 16 9 left Iteration 1 Error: 1.026542 Iteration 2 Error: 0.251104 Iteration 3 Error: 0.090766 Iteration 4 Error: 0.030933 Align patch 17 8 left Iteration 1 Error: 1.068875 Iteration 2 Error: 0.219060 Iteration 3 Error: 0.048776 Align patch 18 7 left Iteration 1 Error: 0.863128 Iteration 2 Error: 0.144180 Iteration 3 Error: 0.080287 Iteration 4 Error: 0.023217 Align patch 19 6 left Iteration 1 Error: 0.644963 Iteration 2 Error: 0.113022 Iteration 3 Error: 0.034833 Align patch 20 5 left Iteration 1 Error: 0.835023 Iteration 2 Error: 0.142962 Iteration 3 Error: 0.032788 Align patch 21 4 left Iteration 1 Error: 1.675372 Iteration 2 Error: 10.880289 Iteration 3 Error: 1.823442 Iteration 4 Error: 0.368374 Iteration 5 Error: 0.122356 Align patch 21 4 left Iteration 1 Error: 2.060803 Iteration 2 Error: 0.383767 Iteration 3 Error: 0.074269 Iteration 4 Error: 0.021323 Align patch 22 3 left Iteration 1 Error: 1.005126 Iteration 2 Error: 0.459387 Iteration 3 Error: 0.103587 Iteration 4 Error: 0.036658 Align patch 23 2 left Iteration 1 Error: 1.180709 Iteration 2 Error: 0.405634 Iteration 3 Error: 0.151649 Iteration 4 Error: 0.033028 Align patch 24 1 left Iteration 1 Error: 0.808406 Iteration 2 Error: 0.120524 Iteration 3 Error: 0.031430 Align patch 25 0 left Iteration 1 Error: 0.909726 Iteration 2 Error: 0.146353 Iteration 3 Error: 0.032734 3D Fitting completed. Patch alignment time: 13.13(sec) Local motion has been corrected. Process thread exits. Computational time: 20.695557 sec Total time: 26.191259 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00015hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00015hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.648556s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00015hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.368659s ........................................ >>>>>>TIME<<<<<< FFT: 0.972663s Defocus_U Defocus_V Angle CCC 10771.49 11603.52 7.88 0.041546 Final Values Defocus_U Defocus_V Angle CCC 10776.12 11636.38 7.88 0.076662 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00015hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00015hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.995e-02 CC threshold: 0.734 Mean Std: 41.52 6.90 Num Hot pixels: 237 Hot pixel threshold: 82.92 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.964783 Iteration 2 Error: 0.209707 Iteration 3 Error: 0.066462 Iteration 4 Error: 0.027936 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.02 0.07 ...... Frame ( 3) shift: -0.04 0.14 ...... Frame ( 4) shift: -0.05 0.21 ...... Frame ( 5) shift: -0.07 0.27 ...... Frame ( 6) shift: -0.08 0.34 ...... Frame ( 7) shift: -0.07 0.40 ...... Frame ( 8) shift: -0.06 0.46 ...... Frame ( 9) shift: 0.03 0.55 ...... Frame ( 10) shift: 0.18 0.67 ...... Frame ( 11) shift: 0.33 0.78 ...... Frame ( 12) shift: 0.41 0.87 ...... Frame ( 13) shift: 0.40 0.92 ...... Frame ( 14) shift: 0.40 0.97 ...... Frame ( 15) shift: 0.40 1.02 ...... Frame ( 16) shift: 0.40 1.06 ...... Frame ( 17) shift: 0.40 1.10 ...... Frame ( 18) shift: 0.44 1.17 ...... Frame ( 19) shift: 0.53 1.28 ...... Frame ( 20) shift: 0.61 1.40 ...... Frame ( 21) shift: 0.66 1.43 ...... Frame ( 22) shift: 0.69 1.39 ...... Frame ( 23) shift: 0.71 1.35 ...... Frame ( 24) shift: 0.73 1.36 ...... Frame ( 25) shift: 0.73 1.42 ...... Frame ( 26) shift: 0.74 1.48 ...... Frame ( 27) shift: 0.78 1.56 ...... Frame ( 28) shift: 0.86 1.66 ...... Frame ( 29) shift: 0.94 1.75 ...... Frame ( 30) shift: 1.00 1.81 ...... Frame ( 31) shift: 1.03 1.82 ...... Frame ( 32) shift: 1.05 1.83 ...... Frame ( 33) shift: 1.07 1.84 ...... Frame ( 34) shift: 1.09 1.83 ...... Frame ( 35) shift: 1.11 1.82 ...... Frame ( 36) shift: 1.11 1.82 ...... Frame ( 37) shift: 1.10 1.85 ...... Frame ( 38) shift: 1.09 1.87 ...... Frame ( 39) shift: 1.08 1.90 ...... Frame ( 40) shift: 1.07 1.92 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.649796 Iteration 2 Error: 0.289448 Iteration 3 Error: 0.232627 Iteration 4 Error: 0.097074 Iteration 5 Error: 0.061762 Align patch 1 24 left Iteration 1 Error: 1.264968 Iteration 2 Error: 0.201867 Iteration 3 Error: 0.065464 Iteration 4 Error: 0.015755 Align patch 2 23 left Iteration 1 Error: 0.829721 Iteration 2 Error: 0.173126 Iteration 3 Error: 0.054780 Iteration 4 Error: 0.024156 Align patch 3 22 left Iteration 1 Error: 0.602698 Iteration 2 Error: 0.133154 Iteration 3 Error: 0.036258 Align patch 4 21 left Iteration 1 Error: 0.830081 Iteration 2 Error: 0.210475 Iteration 3 Error: 0.085009 Iteration 4 Error: 0.036820 Align patch 5 20 left Iteration 1 Error: 0.559705 Iteration 2 Error: 0.132757 Iteration 3 Error: 0.033938 Align patch 6 19 left Iteration 1 Error: 1.178581 Iteration 2 Error: 0.311320 Iteration 3 Error: 0.092101 Iteration 4 Error: 0.027651 Align patch 7 18 left Iteration 1 Error: 0.742849 Iteration 2 Error: 0.166745 Iteration 3 Error: 0.052261 Iteration 4 Error: 0.030379 Align patch 8 17 left Iteration 1 Error: 0.782274 Iteration 2 Error: 0.244729 Iteration 3 Error: 0.063262 Iteration 4 Error: 0.027424 Align patch 9 16 left Iteration 1 Error: 1.362100 Iteration 2 Error: 0.147533 Iteration 3 Error: 0.028794 Align patch 10 15 left Iteration 1 Error: 0.435100 Iteration 2 Error: 0.135908 Iteration 3 Error: 0.068715 Iteration 4 Error: 0.033180 Align patch 11 14 left Iteration 1 Error: 1.190012 Iteration 2 Error: 0.193263 Iteration 3 Error: 0.048633 Align patch 12 13 left Iteration 1 Error: 1.139455 Iteration 2 Error: 0.351127 Iteration 3 Error: 0.168754 Iteration 4 Error: 0.059012 Iteration 5 Error: 0.035027 Align patch 13 12 left Iteration 1 Error: 0.879676 Iteration 2 Error: 0.201814 Iteration 3 Error: 0.045312 Align patch 14 11 left Iteration 1 Error: 0.672997 Iteration 2 Error: 0.153554 Iteration 3 Error: 0.030733 Align patch 15 10 left Iteration 1 Error: 1.067076 Iteration 2 Error: 0.128737 Iteration 3 Error: 0.030506 Align patch 16 9 left Iteration 1 Error: 0.910030 Iteration 2 Error: 0.111434 Iteration 3 Error: 0.054373 Iteration 4 Error: 0.018861 Align patch 17 8 left Iteration 1 Error: 0.968286 Iteration 2 Error: 0.194700 Iteration 3 Error: 0.042961 Align patch 18 7 left Iteration 1 Error: 0.816596 Iteration 2 Error: 0.237536 Iteration 3 Error: 0.102818 Iteration 4 Error: 0.042044 Align patch 19 6 left Iteration 1 Error: 0.580873 Iteration 2 Error: 0.118526 Iteration 3 Error: 0.042533 Align patch 20 5 left Iteration 1 Error: 0.612768 Iteration 2 Error: 0.146322 Iteration 3 Error: 0.030318 Align patch 21 4 left Iteration 1 Error: 0.729834 Iteration 2 Error: 0.165939 Iteration 3 Error: 0.050517 Iteration 4 Error: 0.034747 Align patch 22 3 left Iteration 1 Error: 0.916531 Iteration 2 Error: 0.108754 Iteration 3 Error: 0.026247 Align patch 23 2 left Iteration 1 Error: 0.860177 Iteration 2 Error: 0.159174 Iteration 3 Error: 0.068443 Iteration 4 Error: 0.042726 Align patch 24 1 left Iteration 1 Error: 0.830852 Iteration 2 Error: 0.109263 Iteration 3 Error: 0.040695 Align patch 25 0 left Iteration 1 Error: 0.841170 Iteration 2 Error: 0.181432 Iteration 3 Error: 0.046191 3D Fitting completed. Patch alignment time: 14.07(sec) Local motion has been corrected. Process thread exits. Computational time: 23.635164 sec Total time: 28.968678 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00015hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00015hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.082649s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00015hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.889993s ........................................ >>>>>>TIME<<<<<< FFT: 0.920133s Defocus_U Defocus_V Angle CCC 10183.65 9570.20 89.27 0.031263 Final Values Defocus_U Defocus_V Angle CCC 10202.41 9563.95 88.33 0.057103 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00016hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00016hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 44.27 7.33 Num Hot pixels: 195 Hot pixel threshold: 88.27 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.640660 Iteration 2 Error: 0.170244 Iteration 3 Error: 0.042489 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.20 0.17 ...... Frame ( 3) shift: -0.41 0.34 ...... Frame ( 4) shift: -0.61 0.52 ...... Frame ( 5) shift: -0.81 0.69 ...... Frame ( 6) shift: -0.91 0.83 ...... Frame ( 7) shift: -0.90 0.94 ...... Frame ( 8) shift: -0.89 1.05 ...... Frame ( 9) shift: -0.92 1.18 ...... Frame ( 10) shift: -0.99 1.31 ...... Frame ( 11) shift: -1.07 1.44 ...... Frame ( 12) shift: -1.11 1.55 ...... Frame ( 13) shift: -1.11 1.65 ...... Frame ( 14) shift: -1.12 1.76 ...... Frame ( 15) shift: -1.10 1.84 ...... Frame ( 16) shift: -1.07 1.90 ...... Frame ( 17) shift: -1.03 1.96 ...... Frame ( 18) shift: -1.02 2.05 ...... Frame ( 19) shift: -1.03 2.15 ...... Frame ( 20) shift: -1.04 2.26 ...... Frame ( 21) shift: -1.03 2.33 ...... Frame ( 22) shift: -1.00 2.37 ...... Frame ( 23) shift: -0.96 2.41 ...... Frame ( 24) shift: -0.92 2.44 ...... Frame ( 25) shift: -0.88 2.45 ...... Frame ( 26) shift: -0.83 2.47 ...... Frame ( 27) shift: -0.81 2.50 ...... Frame ( 28) shift: -0.79 2.54 ...... Frame ( 29) shift: -0.78 2.59 ...... Frame ( 30) shift: -0.75 2.61 ...... Frame ( 31) shift: -0.69 2.61 ...... Frame ( 32) shift: -0.64 2.60 ...... Frame ( 33) shift: -0.58 2.61 ...... Frame ( 34) shift: -0.51 2.63 ...... Frame ( 35) shift: -0.45 2.65 ...... Frame ( 36) shift: -0.38 2.68 ...... Frame ( 37) shift: -0.30 2.73 ...... Frame ( 38) shift: -0.23 2.78 ...... Frame ( 39) shift: -0.15 2.83 ...... Frame ( 40) shift: -0.08 2.88 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.445512 Iteration 2 Error: 0.224836 Iteration 3 Error: 0.047664 Align patch 2 23 left Iteration 1 Error: 0.795646 Iteration 2 Error: 0.087639 Iteration 3 Error: 0.030452 Align patch 3 22 left Iteration 1 Error: 0.752298 Iteration 2 Error: 0.173375 Iteration 3 Error: 0.035626 Align patch 4 21 left Iteration 1 Error: 1.104655 Iteration 2 Error: 0.160636 Iteration 3 Error: 0.025416 Align patch 5 20 left Iteration 1 Error: 0.721095 Iteration 2 Error: 0.190050 Iteration 3 Error: 0.034124 Align patch 6 19 left Iteration 1 Error: 1.183947 Iteration 2 Error: 0.202822 Iteration 3 Error: 0.069176 Iteration 4 Error: 0.031099 Align patch 7 18 left Iteration 1 Error: 0.803777 Iteration 2 Error: 0.120669 Iteration 3 Error: 0.041190 Align patch 8 17 left Iteration 1 Error: 0.906268 Iteration 2 Error: 0.216430 Iteration 3 Error: 0.083485 Iteration 4 Error: 0.035605 Align patch 9 16 left Iteration 1 Error: 0.794297 Iteration 2 Error: 0.159487 Iteration 3 Error: 0.036470 Align patch 10 15 left Iteration 1 Error: 0.837372 Iteration 2 Error: 0.088892 Iteration 3 Error: 0.024089 Align patch 11 14 left Iteration 1 Error: 1.190915 Iteration 2 Error: 0.163916 Iteration 3 Error: 0.039703 Align patch 12 13 left Iteration 1 Error: 0.615583 Iteration 2 Error: 0.134532 Iteration 3 Error: 0.041233 Align patch 13 12 left Iteration 1 Error: 0.510271 Iteration 2 Error: 0.084466 Iteration 3 Error: 0.027136 Align patch 14 11 left Iteration 1 Error: 0.784148 Iteration 2 Error: 0.075681 Iteration 3 Error: 0.023193 Align patch 15 10 left Iteration 1 Error: 0.766580 Iteration 2 Error: 0.082189 Iteration 3 Error: 0.012139 Align patch 16 9 left Iteration 1 Error: 1.043099 Iteration 2 Error: 0.201989 Iteration 3 Error: 0.062181 Iteration 4 Error: 0.030668 Align patch 17 8 left Iteration 1 Error: 0.758507 Iteration 2 Error: 0.172591 Iteration 3 Error: 0.081944 Iteration 4 Error: 0.025307 Align patch 18 7 left Iteration 1 Error: 0.718929 Iteration 2 Error: 0.248936 Iteration 3 Error: 0.069286 Iteration 4 Error: 0.018516 Align patch 19 6 left Iteration 1 Error: 0.537723 Iteration 2 Error: 0.071021 Iteration 3 Error: 0.016850 Align patch 20 5 left Iteration 1 Error: 0.625315 Iteration 2 Error: 0.128602 Iteration 3 Error: 0.026335 Align patch 21 4 left Iteration 1 Error: 1.053267 Iteration 2 Error: 0.174522 Iteration 3 Error: 0.063652 Iteration 4 Error: 0.022137 Align patch 22 3 left Iteration 1 Error: 0.796375 Iteration 2 Error: 0.103304 Iteration 3 Error: 0.038089 Align patch 23 2 left Iteration 1 Error: 0.628525 Iteration 2 Error: 0.204120 Iteration 3 Error: 0.060742 Iteration 4 Error: 0.023049 Align patch 24 1 left Iteration 1 Error: 0.712332 Iteration 2 Error: 0.076498 Iteration 3 Error: 0.019938 Align patch 25 0 left Iteration 1 Error: 1.045240 Iteration 2 Error: 0.127400 Iteration 3 Error: 0.025107 3D Fitting completed. Patch alignment time: 13.99(sec) Local motion has been corrected. Process thread exits. Computational time: 23.658440 sec Total time: 30.081312 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00016hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00016hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.541897s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00016hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.843510s ........................................ >>>>>>TIME<<<<<< FFT: 0.970339s Defocus_U Defocus_V Angle CCC 11718.75 12617.19 9.58 0.050830 Final Values Defocus_U Defocus_V Angle CCC 11726.56 12615.63 10.52 0.093464 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00016hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00016hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 43.84 7.30 Num Hot pixels: 227 Hot pixel threshold: 87.64 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.936541 Iteration 2 Error: 0.201095 Iteration 3 Error: 0.048084 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.22 -0.05 ...... Frame ( 3) shift: -0.43 -0.10 ...... Frame ( 4) shift: -0.65 -0.15 ...... Frame ( 5) shift: -0.86 -0.20 ...... Frame ( 6) shift: -1.01 -0.21 ...... Frame ( 7) shift: -1.08 -0.19 ...... Frame ( 8) shift: -1.15 -0.17 ...... Frame ( 9) shift: -1.18 -0.10 ...... Frame ( 10) shift: -1.17 0.02 ...... Frame ( 11) shift: -1.15 0.14 ...... Frame ( 12) shift: -1.17 0.24 ...... Frame ( 13) shift: -1.20 0.32 ...... Frame ( 14) shift: -1.24 0.41 ...... Frame ( 15) shift: -1.25 0.47 ...... Frame ( 16) shift: -1.21 0.53 ...... Frame ( 17) shift: -1.18 0.58 ...... Frame ( 18) shift: -1.17 0.65 ...... Frame ( 19) shift: -1.18 0.75 ...... Frame ( 20) shift: -1.20 0.85 ...... Frame ( 21) shift: -1.15 0.95 ...... Frame ( 22) shift: -1.05 1.06 ...... Frame ( 23) shift: -0.95 1.17 ...... Frame ( 24) shift: -0.88 1.25 ...... Frame ( 25) shift: -0.83 1.30 ...... Frame ( 26) shift: -0.77 1.35 ...... Frame ( 27) shift: -0.74 1.38 ...... Frame ( 28) shift: -0.73 1.39 ...... Frame ( 29) shift: -0.72 1.40 ...... Frame ( 30) shift: -0.70 1.42 ...... Frame ( 31) shift: -0.66 1.46 ...... Frame ( 32) shift: -0.63 1.49 ...... Frame ( 33) shift: -0.53 1.54 ...... Frame ( 34) shift: -0.35 1.61 ...... Frame ( 35) shift: -0.18 1.67 ...... Frame ( 36) shift: -0.10 1.70 ...... Frame ( 37) shift: -0.13 1.69 ...... Frame ( 38) shift: -0.15 1.68 ...... Frame ( 39) shift: -0.17 1.67 ...... Frame ( 40) shift: -0.20 1.66 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.096820 Iteration 2 Error: 0.346612 Iteration 3 Error: 0.104387 Iteration 4 Error: 0.033423 Align patch 2 23 left Iteration 1 Error: 0.706244 Iteration 2 Error: 0.129176 Iteration 3 Error: 0.036683 Align patch 3 22 left Iteration 1 Error: 0.958242 Iteration 2 Error: 0.258196 Iteration 3 Error: 0.086725 Iteration 4 Error: 0.039613 Align patch 4 21 left Iteration 1 Error: 0.858630 Iteration 2 Error: 0.206524 Iteration 3 Error: 0.046538 Align patch 5 20 left Iteration 1 Error: 0.801984 Iteration 2 Error: 0.132449 Iteration 3 Error: 0.030275 Align patch 6 19 left Iteration 1 Error: 1.691507 Iteration 2 Error: 0.286096 Iteration 3 Error: 0.067825 Iteration 4 Error: 0.019328 Align patch 7 18 left Iteration 1 Error: 0.583164 Iteration 2 Error: 0.084713 Iteration 3 Error: 0.023888 Align patch 8 17 left Iteration 1 Error: 1.173719 Iteration 2 Error: 0.212670 Iteration 3 Error: 0.056969 Iteration 4 Error: 0.022201 Align patch 9 16 left Iteration 1 Error: 1.089655 Iteration 2 Error: 0.154610 Iteration 3 Error: 0.078051 Iteration 4 Error: 0.018260 Align patch 10 15 left Iteration 1 Error: 0.625043 Iteration 2 Error: 0.118393 Iteration 3 Error: 0.028624 Align patch 11 14 left Iteration 1 Error: 0.811713 Iteration 2 Error: 0.241651 Iteration 3 Error: 0.093091 Iteration 4 Error: 0.033464 Align patch 12 13 left Iteration 1 Error: 1.382490 Iteration 2 Error: 0.137170 Iteration 3 Error: 0.040368 Align patch 13 12 left Iteration 1 Error: 0.541530 Iteration 2 Error: 0.082626 Iteration 3 Error: 0.016667 Align patch 14 11 left Iteration 1 Error: 0.666693 Iteration 2 Error: 0.142317 Iteration 3 Error: 0.047176 Align patch 15 10 left Iteration 1 Error: 0.607696 Iteration 2 Error: 0.099565 Iteration 3 Error: 0.033382 Align patch 16 9 left Iteration 1 Error: 1.098667 Iteration 2 Error: 0.181509 Iteration 3 Error: 0.045753 Align patch 17 8 left Iteration 1 Error: 0.672282 Iteration 2 Error: 0.127416 Iteration 3 Error: 0.035856 Align patch 18 7 left Iteration 1 Error: 0.718502 Iteration 2 Error: 0.140078 Iteration 3 Error: 0.040611 Align patch 19 6 left Iteration 1 Error: 1.266747 Iteration 2 Error: 0.203057 Iteration 3 Error: 0.056398 Iteration 4 Error: 0.015332 Align patch 20 5 left Iteration 1 Error: 0.658090 Iteration 2 Error: 0.135407 Iteration 3 Error: 0.035730 Align patch 21 4 left Iteration 1 Error: 0.796253 Iteration 2 Error: 0.200456 Iteration 3 Error: 0.050218 Iteration 4 Error: 0.016100 Align patch 22 3 left Iteration 1 Error: 0.601515 Iteration 2 Error: 0.072394 Iteration 3 Error: 0.011483 Align patch 23 2 left Iteration 1 Error: 0.890364 Iteration 2 Error: 0.207091 Iteration 3 Error: 0.075894 Iteration 4 Error: 0.039651 Align patch 24 1 left Iteration 1 Error: 0.645867 Iteration 2 Error: 0.159677 Iteration 3 Error: 0.030370 Align patch 25 0 left Iteration 1 Error: 0.674701 Iteration 2 Error: 0.164198 Iteration 3 Error: 0.035127 3D Fitting completed. Patch alignment time: 12.93(sec) Local motion has been corrected. Process thread exits. Computational time: 23.907597 sec Total time: 30.935837 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00016hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00016hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.780057s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00016hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.059551s ........................................ >>>>>>TIME<<<<<< FFT: 1.200283s Defocus_U Defocus_V Angle CCC 10638.52 11158.36 0.38 0.048529 Final Values Defocus_U Defocus_V Angle CCC 10630.70 11166.17 1.01 0.089114 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00016hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00016hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 1.000e-01 CC threshold: 0.735 Mean Std: 42.95 7.20 Num Hot pixels: 210 Hot pixel threshold: 86.12 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.014523 Iteration 2 Error: 0.093495 Iteration 3 Error: 0.016574 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.24 0.10 ...... Frame ( 3) shift: -0.48 0.21 ...... Frame ( 4) shift: -0.72 0.31 ...... Frame ( 5) shift: -0.96 0.41 ...... Frame ( 6) shift: -1.09 0.50 ...... Frame ( 7) shift: -1.10 0.58 ...... Frame ( 8) shift: -1.11 0.66 ...... Frame ( 9) shift: -1.09 0.71 ...... Frame ( 10) shift: -1.03 0.73 ...... Frame ( 11) shift: -0.98 0.75 ...... Frame ( 12) shift: -1.00 0.76 ...... Frame ( 13) shift: -1.09 0.77 ...... Frame ( 14) shift: -1.17 0.78 ...... Frame ( 15) shift: -1.18 0.80 ...... Frame ( 16) shift: -1.11 0.84 ...... Frame ( 17) shift: -1.05 0.88 ...... Frame ( 18) shift: -1.02 0.94 ...... Frame ( 19) shift: -1.05 1.02 ...... Frame ( 20) shift: -1.07 1.09 ...... Frame ( 21) shift: -1.07 1.16 ...... Frame ( 22) shift: -1.05 1.21 ...... Frame ( 23) shift: -1.02 1.25 ...... Frame ( 24) shift: -1.00 1.25 ...... Frame ( 25) shift: -0.99 1.18 ...... Frame ( 26) shift: -0.97 1.11 ...... Frame ( 27) shift: -0.95 1.10 ...... Frame ( 28) shift: -0.92 1.14 ...... Frame ( 29) shift: -0.89 1.18 ...... Frame ( 30) shift: -0.91 1.21 ...... Frame ( 31) shift: -1.00 1.21 ...... Frame ( 32) shift: -1.09 1.22 ...... Frame ( 33) shift: -1.11 1.22 ...... Frame ( 34) shift: -1.07 1.21 ...... Frame ( 35) shift: -1.03 1.20 ...... Frame ( 36) shift: -1.04 1.23 ...... Frame ( 37) shift: -1.09 1.31 ...... Frame ( 38) shift: -1.15 1.38 ...... Frame ( 39) shift: -1.21 1.45 ...... Frame ( 40) shift: -1.27 1.53 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.764230 Iteration 2 Error: 0.148291 Iteration 3 Error: 0.045010 Align patch 2 23 left Iteration 1 Error: 0.724496 Iteration 2 Error: 0.111759 Iteration 3 Error: 0.031149 Align patch 3 22 left Iteration 1 Error: 0.526065 Iteration 2 Error: 0.072886 Iteration 3 Error: 0.023848 Align patch 4 21 left Iteration 1 Error: 0.616728 Iteration 2 Error: 0.153267 Iteration 3 Error: 0.044443 Align patch 5 20 left Iteration 1 Error: 0.757411 Iteration 2 Error: 0.124785 Iteration 3 Error: 0.030979 Align patch 6 19 left Iteration 1 Error: 0.596378 Iteration 2 Error: 0.112805 Iteration 3 Error: 0.027525 Align patch 7 18 left Iteration 1 Error: 0.482042 Iteration 2 Error: 0.066197 Iteration 3 Error: 0.020482 Align patch 8 17 left Iteration 1 Error: 1.046914 Iteration 2 Error: 0.145548 Iteration 3 Error: 0.035102 Align patch 9 16 left Iteration 1 Error: 0.630734 Iteration 2 Error: 0.079324 Iteration 3 Error: 0.028267 Align patch 10 15 left Iteration 1 Error: 0.511918 Iteration 2 Error: 0.093267 Iteration 3 Error: 0.023601 Align patch 11 14 left Iteration 1 Error: 0.845489 Iteration 2 Error: 0.144636 Iteration 3 Error: 0.043103 Align patch 12 13 left Iteration 1 Error: 0.579072 Iteration 2 Error: 0.082350 Iteration 3 Error: 0.023626 Align patch 13 12 left Iteration 1 Error: 0.781229 Iteration 2 Error: 0.112858 Iteration 3 Error: 0.029318 Align patch 14 11 left Iteration 1 Error: 0.791805 Iteration 2 Error: 0.129479 Iteration 3 Error: 0.029957 Align patch 15 10 left Iteration 1 Error: 0.468063 Iteration 2 Error: 0.103294 Iteration 3 Error: 0.024694 Align patch 16 9 left Iteration 1 Error: 0.904125 Iteration 2 Error: 0.172596 Iteration 3 Error: 0.048659 Align patch 17 8 left Iteration 1 Error: 0.641065 Iteration 2 Error: 0.101697 Iteration 3 Error: 0.023919 Align patch 18 7 left Iteration 1 Error: 0.533622 Iteration 2 Error: 0.086404 Iteration 3 Error: 0.024556 Align patch 19 6 left Iteration 1 Error: 0.633365 Iteration 2 Error: 0.107459 Iteration 3 Error: 0.043085 Align patch 20 5 left Iteration 1 Error: 0.716919 Iteration 2 Error: 0.095280 Iteration 3 Error: 0.018346 Align patch 21 4 left Iteration 1 Error: 1.093429 Iteration 2 Error: 0.187509 Iteration 3 Error: 0.034815 Align patch 22 3 left Iteration 1 Error: 1.007426 Iteration 2 Error: 0.117540 Iteration 3 Error: 0.038011 Align patch 23 2 left Iteration 1 Error: 1.094052 Iteration 2 Error: 0.173464 Iteration 3 Error: 0.037982 Align patch 24 1 left Iteration 1 Error: 0.586353 Iteration 2 Error: 0.083742 Iteration 3 Error: 0.023800 Align patch 25 0 left Iteration 1 Error: 0.538824 Iteration 2 Error: 0.080733 Iteration 3 Error: 0.012769 3D Fitting completed. Patch alignment time: 11.35(sec) Local motion has been corrected. Process thread exits. Computational time: 21.479410 sec Total time: 27.621485 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00016hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00016hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.738311s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00016hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.682396s ........................................ >>>>>>TIME<<<<<< FFT: 1.038242s Defocus_U Defocus_V Angle CCC 10541.02 11404.30 4.93 0.043138 Final Values Defocus_U Defocus_V Angle CCC 10547.28 11435.57 4.62 0.079052 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00016hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00016hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 43.20 7.17 Num Hot pixels: 248 Hot pixel threshold: 86.20 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.960040 Iteration 2 Error: 0.084586 Iteration 3 Error: 0.018543 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.16 0.07 ...... Frame ( 3) shift: -0.31 0.15 ...... Frame ( 4) shift: -0.47 0.22 ...... Frame ( 5) shift: -0.62 0.29 ...... Frame ( 6) shift: -0.70 0.36 ...... Frame ( 7) shift: -0.70 0.43 ...... Frame ( 8) shift: -0.70 0.49 ...... Frame ( 9) shift: -0.73 0.56 ...... Frame ( 10) shift: -0.79 0.65 ...... Frame ( 11) shift: -0.85 0.74 ...... Frame ( 12) shift: -0.86 0.82 ...... Frame ( 13) shift: -0.83 0.90 ...... Frame ( 14) shift: -0.79 0.97 ...... Frame ( 15) shift: -0.79 1.02 ...... Frame ( 16) shift: -0.81 1.04 ...... Frame ( 17) shift: -0.84 1.06 ...... Frame ( 18) shift: -0.84 1.08 ...... Frame ( 19) shift: -0.83 1.09 ...... Frame ( 20) shift: -0.81 1.10 ...... Frame ( 21) shift: -0.80 1.12 ...... Frame ( 22) shift: -0.80 1.14 ...... Frame ( 23) shift: -0.80 1.16 ...... Frame ( 24) shift: -0.80 1.16 ...... Frame ( 25) shift: -0.80 1.16 ...... Frame ( 26) shift: -0.80 1.15 ...... Frame ( 27) shift: -0.80 1.18 ...... Frame ( 28) shift: -0.80 1.25 ...... Frame ( 29) shift: -0.80 1.31 ...... Frame ( 30) shift: -0.80 1.36 ...... Frame ( 31) shift: -0.81 1.39 ...... Frame ( 32) shift: -0.81 1.42 ...... Frame ( 33) shift: -0.81 1.44 ...... Frame ( 34) shift: -0.81 1.45 ...... Frame ( 35) shift: -0.80 1.47 ...... Frame ( 36) shift: -0.82 1.46 ...... Frame ( 37) shift: -0.87 1.42 ...... Frame ( 38) shift: -0.92 1.39 ...... Frame ( 39) shift: -0.97 1.35 ...... Frame ( 40) shift: -1.01 1.31 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.739920 Iteration 2 Error: 0.129635 Iteration 3 Error: 0.031416 Align patch 2 23 left Iteration 1 Error: 0.717714 Iteration 2 Error: 0.111719 Iteration 3 Error: 0.020124 Align patch 3 22 left Iteration 1 Error: 0.861355 Iteration 2 Error: 0.092624 Iteration 3 Error: 0.022585 Align patch 4 21 left Iteration 1 Error: 0.553070 Iteration 2 Error: 0.109496 Iteration 3 Error: 0.023607 Align patch 5 20 left Iteration 1 Error: 0.875712 Iteration 2 Error: 0.104425 Iteration 3 Error: 0.030096 Align patch 6 19 left Iteration 1 Error: 1.388463 Iteration 2 Error: 0.147877 Iteration 3 Error: 0.058296 Iteration 4 Error: 0.018111 Align patch 7 18 left Iteration 1 Error: 0.774737 Iteration 2 Error: 0.095563 Iteration 3 Error: 0.031752 Align patch 8 17 left Iteration 1 Error: 0.805951 Iteration 2 Error: 0.113615 Iteration 3 Error: 0.036254 Align patch 9 16 left Iteration 1 Error: 0.446750 Iteration 2 Error: 0.111746 Iteration 3 Error: 0.029618 Align patch 10 15 left Iteration 1 Error: 0.546813 Iteration 2 Error: 0.082264 Iteration 3 Error: 0.014371 Align patch 11 14 left Iteration 1 Error: 0.686470 Iteration 2 Error: 0.143364 Iteration 3 Error: 0.028066 Align patch 12 13 left Iteration 1 Error: 0.578119 Iteration 2 Error: 0.081753 Iteration 3 Error: 0.025043 Align patch 13 12 left Iteration 1 Error: 0.636217 Iteration 2 Error: 0.120009 Iteration 3 Error: 0.026254 Align patch 14 11 left Iteration 1 Error: 0.506692 Iteration 2 Error: 0.083762 Iteration 3 Error: 0.016785 Align patch 15 10 left Iteration 1 Error: 1.031261 Iteration 2 Error: 0.136591 Iteration 3 Error: 0.035872 Align patch 16 9 left Iteration 1 Error: 0.873961 Iteration 2 Error: 0.188006 Iteration 3 Error: 0.048184 Align patch 17 8 left Iteration 1 Error: 0.819258 Iteration 2 Error: 0.104893 Iteration 3 Error: 0.040365 Align patch 18 7 left Iteration 1 Error: 0.656728 Iteration 2 Error: 0.105163 Iteration 3 Error: 0.030029 Align patch 19 6 left Iteration 1 Error: 0.900171 Iteration 2 Error: 0.101147 Iteration 3 Error: 0.023554 Align patch 20 5 left Iteration 1 Error: 0.766754 Iteration 2 Error: 0.118616 Iteration 3 Error: 0.032677 Align patch 21 4 left Iteration 1 Error: 1.115525 Iteration 2 Error: 0.098316 Iteration 3 Error: 0.020318 Align patch 22 3 left Iteration 1 Error: 0.510043 Iteration 2 Error: 0.119199 Iteration 3 Error: 0.026502 Align patch 23 2 left Iteration 1 Error: 0.768311 Iteration 2 Error: 0.141874 Iteration 3 Error: 0.035684 Align patch 24 1 left Iteration 1 Error: 0.533941 Iteration 2 Error: 0.109664 Iteration 3 Error: 0.037453 Align patch 25 0 left Iteration 1 Error: 0.646804 Iteration 2 Error: 0.193973 Iteration 3 Error: 0.052937 Iteration 4 Error: 0.017441 3D Fitting completed. Patch alignment time: 11.43(sec) Local motion has been corrected. Process thread exits. Computational time: 21.280859 sec Total time: 27.824970 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00016hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00016hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.722287s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00016hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.606845s ........................................ >>>>>>TIME<<<<<< FFT: 1.086739s Defocus_U Defocus_V Angle CCC 12411.33 11748.84 82.64 0.045756 Final Values Defocus_U Defocus_V Angle CCC 12422.26 11775.42 82.95 0.083424 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00017hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00017hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.734 Mean Std: 42.40 7.13 Num Hot pixels: 229 Hot pixel threshold: 85.16 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.365782 Iteration 2 Error: 0.198001 Iteration 3 Error: 0.047987 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.12 0.14 ...... Frame ( 3) shift: -0.24 0.28 ...... Frame ( 4) shift: -0.37 0.41 ...... Frame ( 5) shift: -0.49 0.55 ...... Frame ( 6) shift: -0.58 0.67 ...... Frame ( 7) shift: -0.64 0.78 ...... Frame ( 8) shift: -0.70 0.88 ...... Frame ( 9) shift: -0.69 0.96 ...... Frame ( 10) shift: -0.62 1.01 ...... Frame ( 11) shift: -0.55 1.07 ...... Frame ( 12) shift: -0.51 1.13 ...... Frame ( 13) shift: -0.48 1.22 ...... Frame ( 14) shift: -0.45 1.30 ...... Frame ( 15) shift: -0.43 1.34 ...... Frame ( 16) shift: -0.43 1.35 ...... Frame ( 17) shift: -0.42 1.36 ...... Frame ( 18) shift: -0.38 1.40 ...... Frame ( 19) shift: -0.29 1.47 ...... Frame ( 20) shift: -0.20 1.54 ...... Frame ( 21) shift: -0.12 1.60 ...... Frame ( 22) shift: -0.05 1.65 ...... Frame ( 23) shift: 0.01 1.70 ...... Frame ( 24) shift: 0.07 1.74 ...... Frame ( 25) shift: 0.13 1.77 ...... Frame ( 26) shift: 0.19 1.80 ...... Frame ( 27) shift: 0.23 1.76 ...... Frame ( 28) shift: 0.26 1.65 ...... Frame ( 29) shift: 0.29 1.55 ...... Frame ( 30) shift: 0.33 1.48 ...... Frame ( 31) shift: 0.37 1.44 ...... Frame ( 32) shift: 0.41 1.39 ...... Frame ( 33) shift: 0.51 1.37 ...... Frame ( 34) shift: 0.69 1.36 ...... Frame ( 35) shift: 0.87 1.36 ...... Frame ( 36) shift: 1.03 1.36 ...... Frame ( 37) shift: 1.17 1.38 ...... Frame ( 38) shift: 1.31 1.40 ...... Frame ( 39) shift: 1.45 1.41 ...... Frame ( 40) shift: 1.59 1.43 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.063916 Iteration 2 Error: 0.177542 Iteration 3 Error: 0.027886 Align patch 2 23 left Iteration 1 Error: 0.786071 Iteration 2 Error: 0.163625 Iteration 3 Error: 0.042071 Align patch 3 22 left Iteration 1 Error: 0.645054 Iteration 2 Error: 0.094649 Iteration 3 Error: 0.030545 Align patch 4 21 left Iteration 1 Error: 0.705797 Iteration 2 Error: 0.206948 Iteration 3 Error: 0.079156 Iteration 4 Error: 0.029207 Align patch 5 20 left Iteration 1 Error: 0.972802 Iteration 2 Error: 0.131840 Iteration 3 Error: 0.042342 Align patch 6 19 left Iteration 1 Error: 0.842256 Iteration 2 Error: 0.138210 Iteration 3 Error: 0.055257 Iteration 4 Error: 0.020999 Align patch 7 18 left Iteration 1 Error: 0.762275 Iteration 2 Error: 0.151639 Iteration 3 Error: 0.040290 Align patch 8 17 left Iteration 1 Error: 0.972526 Iteration 2 Error: 0.187592 Iteration 3 Error: 0.056832 Iteration 4 Error: 0.017199 Align patch 9 16 left Iteration 1 Error: 1.092974 Iteration 2 Error: 0.170240 Iteration 3 Error: 0.049597 Align patch 10 15 left Iteration 1 Error: 1.148765 Iteration 2 Error: 0.322253 Iteration 3 Error: 0.077565 Iteration 4 Error: 0.020819 Align patch 11 14 left Iteration 1 Error: 0.580962 Iteration 2 Error: 0.091934 Iteration 3 Error: 0.032079 Align patch 12 13 left Iteration 1 Error: 0.904932 Iteration 2 Error: 0.143614 Iteration 3 Error: 0.038583 Align patch 13 12 left Iteration 1 Error: 0.907077 Iteration 2 Error: 0.259208 Iteration 3 Error: 0.075327 Iteration 4 Error: 0.019878 Align patch 14 11 left Iteration 1 Error: 0.630269 Iteration 2 Error: 0.074358 Iteration 3 Error: 0.018096 Align patch 15 10 left Iteration 1 Error: 0.502192 Iteration 2 Error: 0.062409 Iteration 3 Error: 0.017904 Align patch 16 9 left Iteration 1 Error: 0.991962 Iteration 2 Error: 0.199691 Iteration 3 Error: 0.069423 Iteration 4 Error: 0.018544 Align patch 17 8 left Iteration 1 Error: 0.664901 Iteration 2 Error: 0.129381 Iteration 3 Error: 0.020766 Align patch 18 7 left Iteration 1 Error: 0.849762 Iteration 2 Error: 0.226292 Iteration 3 Error: 0.061217 Iteration 4 Error: 0.013430 Align patch 19 6 left Iteration 1 Error: 1.265291 Iteration 2 Error: 0.112294 Iteration 3 Error: 0.037302 Align patch 20 5 left Iteration 1 Error: 0.596817 Iteration 2 Error: 0.077985 Iteration 3 Error: 0.012143 Align patch 21 4 left Iteration 1 Error: 0.934367 Iteration 2 Error: 0.201069 Iteration 3 Error: 0.104048 Iteration 4 Error: 0.025240 Align patch 22 3 left Iteration 1 Error: 0.736793 Iteration 2 Error: 0.111521 Iteration 3 Error: 0.024743 Align patch 23 2 left Iteration 1 Error: 0.795061 Iteration 2 Error: 0.143660 Iteration 3 Error: 0.045001 Align patch 24 1 left Iteration 1 Error: 0.543283 Iteration 2 Error: 0.077565 Iteration 3 Error: 0.017085 Align patch 25 0 left Iteration 1 Error: 0.952621 Iteration 2 Error: 0.117235 Iteration 3 Error: 0.041270 3D Fitting completed. Patch alignment time: 12.64(sec) Local motion has been corrected. Process thread exits. Computational time: 22.795479 sec Total time: 29.214981 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00017hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00017hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.597471s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00017hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.976328s ........................................ >>>>>>TIME<<<<<< FFT: 1.099140s Defocus_U Defocus_V Angle CCC 10302.74 11146.49 12.56 0.038786 Final Values Defocus_U Defocus_V Angle CCC 10321.49 11152.74 12.56 0.069558 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00017hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00017hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 43.37 7.14 Num Hot pixels: 203 Hot pixel threshold: 86.22 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.347778 Iteration 2 Error: 0.033009 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.11 0.08 ...... Frame ( 3) shift: -0.21 0.17 ...... Frame ( 4) shift: -0.32 0.25 ...... Frame ( 5) shift: -0.42 0.33 ...... Frame ( 6) shift: -0.47 0.41 ...... Frame ( 7) shift: -0.47 0.47 ...... Frame ( 8) shift: -0.47 0.54 ...... Frame ( 9) shift: -0.48 0.56 ...... Frame ( 10) shift: -0.52 0.53 ...... Frame ( 11) shift: -0.56 0.50 ...... Frame ( 12) shift: -0.57 0.45 ...... Frame ( 13) shift: -0.55 0.40 ...... Frame ( 14) shift: -0.53 0.34 ...... Frame ( 15) shift: -0.51 0.31 ...... Frame ( 16) shift: -0.50 0.31 ...... Frame ( 17) shift: -0.49 0.31 ...... Frame ( 18) shift: -0.45 0.29 ...... Frame ( 19) shift: -0.40 0.25 ...... Frame ( 20) shift: -0.34 0.22 ...... Frame ( 21) shift: -0.35 0.23 ...... Frame ( 22) shift: -0.40 0.28 ...... Frame ( 23) shift: -0.46 0.34 ...... Frame ( 24) shift: -0.48 0.32 ...... Frame ( 25) shift: -0.47 0.23 ...... Frame ( 26) shift: -0.45 0.13 ...... Frame ( 27) shift: -0.43 0.13 ...... Frame ( 28) shift: -0.41 0.21 ...... Frame ( 29) shift: -0.39 0.29 ...... Frame ( 30) shift: -0.38 0.34 ...... Frame ( 31) shift: -0.39 0.35 ...... Frame ( 32) shift: -0.39 0.36 ...... Frame ( 33) shift: -0.37 0.33 ...... Frame ( 34) shift: -0.31 0.26 ...... Frame ( 35) shift: -0.24 0.19 ...... Frame ( 36) shift: -0.25 0.19 ...... Frame ( 37) shift: -0.32 0.25 ...... Frame ( 38) shift: -0.39 0.31 ...... Frame ( 39) shift: -0.45 0.37 ...... Frame ( 40) shift: -0.52 0.43 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.779210 Iteration 2 Error: 0.132923 Iteration 3 Error: 0.030783 Align patch 2 23 left Iteration 1 Error: 0.867165 Iteration 2 Error: 0.131958 Iteration 3 Error: 0.053837 Iteration 4 Error: 0.011899 Align patch 3 22 left Iteration 1 Error: 0.717684 Iteration 2 Error: 0.133787 Iteration 3 Error: 0.036930 Align patch 4 21 left Iteration 1 Error: 1.006011 Iteration 2 Error: 0.171924 Iteration 3 Error: 0.030626 Align patch 5 20 left Iteration 1 Error: 0.891638 Iteration 2 Error: 0.129135 Iteration 3 Error: 0.035145 Align patch 6 19 left Iteration 1 Error: 0.795082 Iteration 2 Error: 0.109409 Iteration 3 Error: 0.024034 Align patch 7 18 left Iteration 1 Error: 0.882642 Iteration 2 Error: 0.093500 Iteration 3 Error: 0.025655 Align patch 8 17 left Iteration 1 Error: 0.758172 Iteration 2 Error: 0.088806 Iteration 3 Error: 0.027312 Align patch 9 16 left Iteration 1 Error: 1.252759 Iteration 2 Error: 0.140738 Iteration 3 Error: 0.027290 Align patch 10 15 left Iteration 1 Error: 0.862688 Iteration 2 Error: 0.143348 Iteration 3 Error: 0.024846 Align patch 11 14 left Iteration 1 Error: 1.096774 Iteration 2 Error: 0.196681 Iteration 3 Error: 0.044217 Align patch 12 13 left Iteration 1 Error: 1.107702 Iteration 2 Error: 0.159600 Iteration 3 Error: 0.027871 Align patch 13 12 left Iteration 1 Error: 0.754461 Iteration 2 Error: 0.096676 Iteration 3 Error: 0.023767 Align patch 14 11 left Iteration 1 Error: 0.909171 Iteration 2 Error: 0.118000 Iteration 3 Error: 0.038192 Align patch 15 10 left Iteration 1 Error: 0.618840 Iteration 2 Error: 0.154377 Iteration 3 Error: 0.030215 Align patch 16 9 left Iteration 1 Error: 0.939220 Iteration 2 Error: 0.112157 Iteration 3 Error: 0.022370 Align patch 17 8 left Iteration 1 Error: 0.681654 Iteration 2 Error: 0.113291 Iteration 3 Error: 0.033819 Align patch 18 7 left Iteration 1 Error: 0.674737 Iteration 2 Error: 0.133504 Iteration 3 Error: 0.023982 Align patch 19 6 left Iteration 1 Error: 0.814039 Iteration 2 Error: 0.102518 Iteration 3 Error: 0.030139 Align patch 20 5 left Iteration 1 Error: 0.823929 Iteration 2 Error: 0.154999 Iteration 3 Error: 0.046921 Align patch 21 4 left Iteration 1 Error: 0.726050 Iteration 2 Error: 0.244795 Iteration 3 Error: 0.102552 Iteration 4 Error: 0.043739 Align patch 22 3 left Iteration 1 Error: 0.637267 Iteration 2 Error: 0.106142 Iteration 3 Error: 0.018733 Align patch 23 2 left Iteration 1 Error: 0.922044 Iteration 2 Error: 0.121532 Iteration 3 Error: 0.028744 Align patch 24 1 left Iteration 1 Error: 0.622143 Iteration 2 Error: 0.086531 Iteration 3 Error: 0.026032 Align patch 25 0 left Iteration 1 Error: 0.674780 Iteration 2 Error: 0.093450 Iteration 3 Error: 0.016767 3D Fitting completed. Patch alignment time: 12.17(sec) Local motion has been corrected. Process thread exits. Computational time: 22.425072 sec Total time: 28.382910 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00017hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00017hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.715713s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00017hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.999028s ........................................ >>>>>>TIME<<<<<< FFT: 1.035407s Defocus_U Defocus_V Angle CCC 9523.45 9015.62 89.58 0.032618 Final Values Defocus_U Defocus_V Angle CCC 9540.63 9001.55 89.58 0.065619 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00017hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00017hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.999e-02 CC threshold: 0.734 Mean Std: 41.65 6.91 Num Hot pixels: 227 Hot pixel threshold: 83.13 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.807221 Iteration 2 Error: 0.458339 Iteration 3 Error: 0.193166 Iteration 4 Error: 0.098721 Iteration 5 Error: 0.052256 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.03 0.04 ...... Frame ( 3) shift: 0.05 0.09 ...... Frame ( 4) shift: 0.08 0.13 ...... Frame ( 5) shift: 0.11 0.18 ...... Frame ( 6) shift: 0.16 0.31 ...... Frame ( 7) shift: 0.23 0.54 ...... Frame ( 8) shift: 0.30 0.76 ...... Frame ( 9) shift: 0.37 0.96 ...... Frame ( 10) shift: 0.42 1.14 ...... Frame ( 11) shift: 0.48 1.31 ...... Frame ( 12) shift: 0.54 1.46 ...... Frame ( 13) shift: 0.59 1.59 ...... Frame ( 14) shift: 0.64 1.71 ...... Frame ( 15) shift: 0.68 1.86 ...... Frame ( 16) shift: 0.69 2.04 ...... Frame ( 17) shift: 0.71 2.22 ...... Frame ( 18) shift: 0.75 2.34 ...... Frame ( 19) shift: 0.82 2.40 ...... Frame ( 20) shift: 0.89 2.46 ...... Frame ( 21) shift: 0.96 2.53 ...... Frame ( 22) shift: 1.03 2.62 ...... Frame ( 23) shift: 1.11 2.71 ...... Frame ( 24) shift: 1.16 2.84 ...... Frame ( 25) shift: 1.20 3.00 ...... Frame ( 26) shift: 1.24 3.17 ...... Frame ( 27) shift: 1.28 3.32 ...... Frame ( 28) shift: 1.31 3.47 ...... Frame ( 29) shift: 1.35 3.62 ...... Frame ( 30) shift: 1.43 3.72 ...... Frame ( 31) shift: 1.55 3.77 ...... Frame ( 32) shift: 1.67 3.83 ...... Frame ( 33) shift: 1.72 3.87 ...... Frame ( 34) shift: 1.69 3.90 ...... Frame ( 35) shift: 1.66 3.93 ...... Frame ( 36) shift: 1.69 3.98 ...... Frame ( 37) shift: 1.78 4.05 ...... Frame ( 38) shift: 1.88 4.11 ...... Frame ( 39) shift: 1.97 4.18 ...... Frame ( 40) shift: 2.06 4.24 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 3.193013 Iteration 2 Error: 0.662376 Iteration 3 Error: 0.348940 Iteration 4 Error: 0.184638 Iteration 5 Error: 0.072922 Align patch 1 24 left Iteration 1 Error: 3.518170 Iteration 2 Error: 1.000885 Iteration 3 Error: 0.252426 Iteration 4 Error: 0.071209 Iteration 5 Error: 0.039619 Align patch 2 23 left Iteration 1 Error: 1.758779 Iteration 2 Error: 0.634478 Iteration 3 Error: 0.308725 Iteration 4 Error: 0.215635 Iteration 5 Error: 0.128128 Align patch 2 23 left Iteration 1 Error: 2.672778 Iteration 2 Error: 0.580947 Iteration 3 Error: 0.148803 Iteration 4 Error: 0.050437 Iteration 5 Error: 0.021364 Align patch 3 22 left Iteration 1 Error: 1.639117 Iteration 2 Error: 0.224395 Iteration 3 Error: 0.087632 Iteration 4 Error: 0.026705 Align patch 4 21 left Iteration 1 Error: 0.853213 Iteration 2 Error: 0.300958 Iteration 3 Error: 0.061354 Iteration 4 Error: 0.020200 Align patch 5 20 left Iteration 1 Error: 1.057980 Iteration 2 Error: 0.385407 Iteration 3 Error: 0.161996 Iteration 4 Error: 0.084344 Iteration 5 Error: 0.041265 Align patch 6 19 left Iteration 1 Error: 3.804909 Iteration 2 Error: 1.768798 Iteration 3 Error: 0.693551 Iteration 4 Error: 0.254169 Iteration 5 Error: 0.177480 Align patch 6 19 left Iteration 1 Error: 3.949528 Iteration 2 Error: 0.978225 Iteration 3 Error: 0.200289 Iteration 4 Error: 0.047833 Align patch 7 18 left Iteration 1 Error: 3.008777 Iteration 2 Error: 2.228976 Iteration 3 Error: 0.685442 Iteration 4 Error: 0.299608 Iteration 5 Error: 0.126778 Align patch 7 18 left Iteration 1 Error: 2.988855 Iteration 2 Error: 0.617851 Iteration 3 Error: 0.118670 Iteration 4 Error: 0.032677 Align patch 8 17 left Iteration 1 Error: 0.959967 Iteration 2 Error: 0.365517 Iteration 3 Error: 0.165410 Iteration 4 Error: 0.085230 Iteration 5 Error: 0.037042 Align patch 9 16 left Iteration 1 Error: 0.755308 Iteration 2 Error: 0.175801 Iteration 3 Error: 0.080931 Iteration 4 Error: 0.035620 Align patch 10 15 left Iteration 1 Error: 1.574540 Iteration 2 Error: 0.295817 Iteration 3 Error: 0.102052 Iteration 4 Error: 0.049756 Align patch 11 14 left Iteration 1 Error: 3.038977 Iteration 2 Error: 1.814324 Iteration 3 Error: 0.425709 Iteration 4 Error: 0.219587 Iteration 5 Error: 0.061938 Align patch 11 14 left Iteration 1 Error: 3.314544 Iteration 2 Error: 0.725032 Iteration 3 Error: 0.155213 Iteration 4 Error: 0.068624 Iteration 5 Error: 0.023694 Align patch 12 13 left Iteration 1 Error: 2.243353 Iteration 2 Error: 0.661203 Iteration 3 Error: 0.330543 Iteration 4 Error: 0.138702 Iteration 5 Error: 0.092570 Align patch 12 13 left Iteration 1 Error: 2.160779 Iteration 2 Error: 0.552631 Iteration 3 Error: 0.138438 Iteration 4 Error: 0.037470 Align patch 13 12 left Iteration 1 Error: 0.864805 Iteration 2 Error: 0.204703 Iteration 3 Error: 0.111966 Iteration 4 Error: 0.060015 Iteration 5 Error: 0.032439 Align patch 14 11 left Iteration 1 Error: 1.515332 Iteration 2 Error: 0.273465 Iteration 3 Error: 0.133685 Iteration 4 Error: 0.065854 Iteration 5 Error: 0.028705 Align patch 15 10 left Iteration 1 Error: 1.466892 Iteration 2 Error: 0.195252 Iteration 3 Error: 0.064185 Iteration 4 Error: 0.023187 Align patch 16 9 left Iteration 1 Error: 1.844925 Iteration 2 Error: 0.553471 Iteration 3 Error: 0.339478 Iteration 4 Error: 0.220916 Iteration 5 Error: 0.122505 Align patch 16 9 left Iteration 1 Error: 1.927515 Iteration 2 Error: 0.467910 Iteration 3 Error: 0.095067 Iteration 4 Error: 0.042682 Align patch 17 8 left Iteration 1 Error: 1.778673 Iteration 2 Error: 0.446257 Iteration 3 Error: 0.219792 Iteration 4 Error: 0.132182 Iteration 5 Error: 0.075345 Align patch 17 8 left Iteration 1 Error: 1.232193 Iteration 2 Error: 0.323292 Iteration 3 Error: 0.087072 Iteration 4 Error: 0.050850 Iteration 5 Error: 0.017140 Align patch 18 7 left Iteration 1 Error: 1.026605 Iteration 2 Error: 0.228323 Iteration 3 Error: 0.049250 Align patch 19 6 left Iteration 1 Error: 0.774013 Iteration 2 Error: 0.148825 Iteration 3 Error: 0.056026 Iteration 4 Error: 0.021679 Align patch 20 5 left Iteration 1 Error: 0.943016 Iteration 2 Error: 0.186689 Iteration 3 Error: 0.070227 Iteration 4 Error: 0.026709 Align patch 21 4 left Iteration 1 Error: 1.104552 Iteration 2 Error: 0.256922 Iteration 3 Error: 0.140360 Iteration 4 Error: 0.075569 Iteration 5 Error: 0.047440 Align patch 22 3 left Iteration 1 Error: 1.071620 Iteration 2 Error: 0.407687 Iteration 3 Error: 0.078387 Iteration 4 Error: 0.050395 Iteration 5 Error: 0.020282 Align patch 23 2 left Iteration 1 Error: 1.243134 Iteration 2 Error: 0.346226 Iteration 3 Error: 0.092425 Iteration 4 Error: 0.047066 Align patch 24 1 left Iteration 1 Error: 0.979325 Iteration 2 Error: 0.243222 Iteration 3 Error: 0.058564 Iteration 4 Error: 0.024173 Align patch 25 0 left Iteration 1 Error: 0.910505 Iteration 2 Error: 0.270441 Iteration 3 Error: 0.096283 Iteration 4 Error: 0.034795 3D Fitting completed. Patch alignment time: 20.42(sec) Local motion has been corrected. Process thread exits. Computational time: 33.054989 sec Total time: 39.489288 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00017hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00017hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.772311s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00017hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 4.285995s ........................................ >>>>>>TIME<<<<<< FFT: 1.325067s Defocus_U Defocus_V Angle CCC 10865.23 11767.69 8.33 0.039583 Final Values Defocus_U Defocus_V Angle CCC 10869.92 11788.02 8.33 0.069857 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00003sq_v01_00017hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00017hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.992e-02 CC threshold: 0.734 Mean Std: 42.33 6.96 Num Hot pixels: 253 Hot pixel threshold: 84.10 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.242864 Iteration 2 Error: 1.070696 Iteration 3 Error: 1.125370 Iteration 4 Error: 1.008240 Iteration 5 Error: 0.874023 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.02 0.36 ...... Frame ( 3) shift: -0.04 0.72 ...... Frame ( 4) shift: -0.06 1.08 ...... Frame ( 5) shift: -0.08 1.44 ...... Frame ( 6) shift: -0.04 1.82 ...... Frame ( 7) shift: 0.08 2.21 ...... Frame ( 8) shift: 0.20 2.61 ...... Frame ( 9) shift: 0.29 2.95 ...... Frame ( 10) shift: 0.35 3.23 ...... Frame ( 11) shift: 0.41 3.51 ...... Frame ( 12) shift: 0.45 3.83 ...... Frame ( 13) shift: 0.46 4.19 ...... Frame ( 14) shift: 0.47 4.54 ...... Frame ( 15) shift: 0.50 4.91 ...... Frame ( 16) shift: 0.56 5.30 ...... Frame ( 17) shift: 0.62 5.70 ...... Frame ( 18) shift: 0.70 6.00 ...... Frame ( 19) shift: 0.80 6.21 ...... Frame ( 20) shift: 0.91 6.42 ...... Frame ( 21) shift: 0.99 6.65 ...... Frame ( 22) shift: 1.04 6.89 ...... Frame ( 23) shift: 1.09 7.13 ...... Frame ( 24) shift: 1.16 7.43 ...... Frame ( 25) shift: 1.25 7.80 ...... Frame ( 26) shift: 1.33 8.17 ...... Frame ( 27) shift: 1.36 8.45 ...... Frame ( 28) shift: 1.33 8.64 ...... Frame ( 29) shift: 1.31 8.83 ...... Frame ( 30) shift: 1.32 9.10 ...... Frame ( 31) shift: 1.37 9.43 ...... Frame ( 32) shift: 1.43 9.77 ...... Frame ( 33) shift: 1.43 10.11 ...... Frame ( 34) shift: 1.38 10.46 ...... Frame ( 35) shift: 1.32 10.80 ...... Frame ( 36) shift: 1.33 11.12 ...... Frame ( 37) shift: 1.41 11.42 ...... Frame ( 38) shift: 1.49 11.71 ...... Frame ( 39) shift: 1.57 12.01 ...... Frame ( 40) shift: 1.65 12.30 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 11.816931 Iteration 2 Error: 8.318520 Iteration 3 Error: 5.623399 Iteration 4 Error: 5.386572 Iteration 5 Error: 3.925783 Align patch 1 24 left Iteration 1 Error: 10.915351 Iteration 2 Error: 4.454234 Iteration 3 Error: 1.434985 Iteration 4 Error: 0.377592 Iteration 5 Error: 0.134976 Align patch 2 23 left Iteration 1 Error: 10.689651 Iteration 2 Error: 6.392311 Iteration 3 Error: 1.394247 Iteration 4 Error: 0.683476 Iteration 5 Error: 0.228478 Align patch 2 23 left Iteration 1 Error: 9.830709 Iteration 2 Error: 5.612289 Iteration 3 Error: 0.648760 Iteration 4 Error: 0.174980 Iteration 5 Error: 0.057412 Align patch 3 22 left Iteration 1 Error: 9.739365 Iteration 2 Error: 7.004968 Iteration 3 Error: 1.846676 Iteration 4 Error: 0.874493 Iteration 5 Error: 0.329262 Align patch 3 22 left Iteration 1 Error: 6.474998 Iteration 2 Error: 2.181192 Iteration 3 Error: 0.966309 Iteration 4 Error: 0.219086 Iteration 5 Error: 0.081340 Align patch 4 21 left Iteration 1 Error: 3.448079 Iteration 2 Error: 1.497476 Iteration 3 Error: 0.774127 Iteration 4 Error: 0.525079 Iteration 5 Error: 0.223945 Align patch 4 21 left Iteration 1 Error: 3.131008 Iteration 2 Error: 1.145629 Iteration 3 Error: 0.324939 Iteration 4 Error: 0.155242 Iteration 5 Error: 0.059048 Align patch 5 20 left Iteration 1 Error: 1.650077 Iteration 2 Error: 0.857333 Iteration 3 Error: 0.711789 Iteration 4 Error: 0.458979 Iteration 5 Error: 0.424130 Align patch 5 20 left Iteration 1 Error: 1.846232 Iteration 2 Error: 0.438750 Iteration 3 Error: 0.141679 Iteration 4 Error: 0.056336 Iteration 5 Error: 0.031293 Align patch 6 19 left Iteration 1 Error: 12.252596 Iteration 2 Error: 12.516489 Iteration 3 Error: 4.240868 Iteration 4 Error: 1.065129 Iteration 5 Error: 0.241380 Align patch 6 19 left Iteration 1 Error: 9.440446 Iteration 2 Error: 5.905556 Iteration 3 Error: 1.284536 Iteration 4 Error: 0.305413 Iteration 5 Error: 0.072893 Align patch 7 18 left Iteration 1 Error: 8.547904 Iteration 2 Error: 6.898727 Iteration 3 Error: 2.267669 Iteration 4 Error: 0.779513 Iteration 5 Error: 0.356041 Align patch 7 18 left Iteration 1 Error: 9.200476 Iteration 2 Error: 4.511753 Iteration 3 Error: 0.792603 Iteration 4 Error: 0.184370 Iteration 5 Error: 0.085806 Align patch 8 17 left Iteration 1 Error: 8.035191 Iteration 2 Error: 2.722090 Iteration 3 Error: 0.991680 Iteration 4 Error: 0.413042 Iteration 5 Error: 0.204356 Align patch 8 17 left Iteration 1 Error: 5.668472 Iteration 2 Error: 2.051496 Iteration 3 Error: 0.548137 Iteration 4 Error: 0.183809 Iteration 5 Error: 0.070919 Align patch 9 16 left Iteration 1 Error: 2.848262 Iteration 2 Error: 1.379793 Iteration 3 Error: 0.550261 Iteration 4 Error: 0.238870 Iteration 5 Error: 0.117131 Align patch 9 16 left Iteration 1 Error: 2.405558 Iteration 2 Error: 0.811165 Iteration 3 Error: 0.371104 Iteration 4 Error: 0.120366 Iteration 5 Error: 0.063023 Align patch 10 15 left Iteration 1 Error: 1.519836 Iteration 2 Error: 0.326035 Iteration 3 Error: 0.186117 Iteration 4 Error: 0.086156 Iteration 5 Error: 0.062484 Align patch 10 15 left Iteration 1 Error: 1.247280 Iteration 2 Error: 0.314706 Iteration 3 Error: 0.162434 Iteration 4 Error: 0.080073 Iteration 5 Error: 0.041299 Align patch 11 14 left Iteration 1 Error: 8.210485 Iteration 2 Error: 8.975493 Iteration 3 Error: 3.559944 Iteration 4 Error: 1.130484 Iteration 5 Error: 0.631064 Align patch 11 14 left Iteration 1 Error: 7.900645 Iteration 2 Error: 2.689329 Iteration 3 Error: 0.983439 Iteration 4 Error: 0.496155 Iteration 5 Error: 0.225492 Align patch 12 13 left Iteration 1 Error: 8.122346 Iteration 2 Error: 1.843236 Iteration 3 Error: 0.630359 Iteration 4 Error: 0.343143 Iteration 5 Error: 0.226688 Align patch 12 13 left Iteration 1 Error: 6.083564 Iteration 2 Error: 2.262881 Iteration 3 Error: 0.802197 Iteration 4 Error: 0.283135 Iteration 5 Error: 0.130275 Align patch 13 12 left Iteration 1 Error: 2.579442 Iteration 2 Error: 1.376319 Iteration 3 Error: 0.709220 Iteration 4 Error: 0.406555 Iteration 5 Error: 0.267015 Align patch 13 12 left Iteration 1 Error: 2.759256 Iteration 2 Error: 0.994281 Iteration 3 Error: 0.365137 Iteration 4 Error: 0.145195 Iteration 5 Error: 0.064178 Align patch 14 11 left Iteration 1 Error: 2.476605 Iteration 2 Error: 0.740343 Iteration 3 Error: 0.363030 Iteration 4 Error: 0.394373 Iteration 5 Error: 0.222644 Align patch 14 11 left Iteration 1 Error: 1.249561 Iteration 2 Error: 0.551130 Iteration 3 Error: 0.229009 Iteration 4 Error: 0.079432 Iteration 5 Error: 0.048391 Align patch 15 10 left Iteration 1 Error: 1.429415 Iteration 2 Error: 0.463100 Iteration 3 Error: 0.289857 Iteration 4 Error: 0.160026 Iteration 5 Error: 0.102808 Align patch 15 10 left Iteration 1 Error: 0.877991 Iteration 2 Error: 0.165492 Iteration 3 Error: 0.079153 Iteration 4 Error: 0.050020 Iteration 5 Error: 0.024298 Align patch 16 9 left Iteration 1 Error: 9.018235 Iteration 2 Error: 4.116495 Iteration 3 Error: 0.895731 Iteration 4 Error: 0.315006 Iteration 5 Error: 0.164876 Align patch 16 9 left Iteration 1 Error: 4.205118 Iteration 2 Error: 1.130628 Iteration 3 Error: 0.388481 Iteration 4 Error: 0.108817 Iteration 5 Error: 0.047289 Align patch 17 8 left Iteration 1 Error: 4.882567 Iteration 2 Error: 3.119948 Iteration 3 Error: 0.729540 Iteration 4 Error: 0.411814 Iteration 5 Error: 0.273289 Align patch 17 8 left Iteration 1 Error: 3.363546 Iteration 2 Error: 1.043655 Iteration 3 Error: 0.282976 Iteration 4 Error: 0.129370 Iteration 5 Error: 0.064980 Align patch 18 7 left Iteration 1 Error: 1.447069 Iteration 2 Error: 0.949699 Iteration 3 Error: 0.299064 Iteration 4 Error: 0.333156 Iteration 5 Error: 0.105501 Align patch 18 7 left Iteration 1 Error: 1.814620 Iteration 2 Error: 0.459953 Iteration 3 Error: 0.125037 Iteration 4 Error: 0.078046 Iteration 5 Error: 0.032519 Align patch 19 6 left Iteration 1 Error: 1.267395 Iteration 2 Error: 0.288450 Iteration 3 Error: 0.162409 Iteration 4 Error: 0.046716 Align patch 20 5 left Iteration 1 Error: 2.395141 Iteration 2 Error: 0.719499 Iteration 3 Error: 0.298211 Iteration 4 Error: 0.195513 Iteration 5 Error: 0.099176 Align patch 20 5 left Iteration 1 Error: 1.551004 Iteration 2 Error: 0.307609 Iteration 3 Error: 0.104134 Iteration 4 Error: 0.045340 Align patch 21 4 left Iteration 1 Error: 1.718288 Iteration 2 Error: 0.768334 Iteration 3 Error: 0.400924 Iteration 4 Error: 0.225536 Iteration 5 Error: 0.112305 Align patch 21 4 left Iteration 1 Error: 2.444615 Iteration 2 Error: 0.824169 Iteration 3 Error: 0.294387 Iteration 4 Error: 0.099095 Iteration 5 Error: 0.051149 Align patch 22 3 left Iteration 1 Error: 1.359063 Iteration 2 Error: 0.617738 Iteration 3 Error: 0.260122 Iteration 4 Error: 0.179215 Iteration 5 Error: 0.101506 Align patch 22 3 left Iteration 1 Error: 1.866168 Iteration 2 Error: 0.546857 Iteration 3 Error: 0.202439 Iteration 4 Error: 0.091148 Iteration 5 Error: 0.038342 Align patch 23 2 left Iteration 1 Error: 1.145907 Iteration 2 Error: 0.394547 Iteration 3 Error: 0.158813 Iteration 4 Error: 0.085054 Iteration 5 Error: 0.063664 Align patch 23 2 left Iteration 1 Error: 1.018892 Iteration 2 Error: 0.259989 Iteration 3 Error: 0.114536 Iteration 4 Error: 0.049650 Align patch 24 1 left Iteration 1 Error: 2.003018 Iteration 2 Error: 0.792694 Iteration 3 Error: 0.316913 Iteration 4 Error: 0.125337 Iteration 5 Error: 0.071990 Align patch 24 1 left Iteration 1 Error: 1.022332 Iteration 2 Error: 0.205759 Iteration 3 Error: 0.072409 Iteration 4 Error: 0.023342 Align patch 25 0 left Iteration 1 Error: 2.562286 Iteration 2 Error: 1.074863 Iteration 3 Error: 0.640335 Iteration 4 Error: 0.301856 Iteration 5 Error: 0.181267 Align patch 25 0 left Iteration 1 Error: 2.167850 Iteration 2 Error: 0.371457 Iteration 3 Error: 0.087538 Iteration 4 Error: 0.037757 3D Fitting completed. Patch alignment time: 32.14(sec) Local motion has been corrected. Process thread exits. Computational time: 43.525768 sec Total time: 50.919884 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00017hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00017hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.660663s Reading file: gc_18feb27f_CTD_g1_00012gr_00003sq_v01_00017hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.862230s ........................................ >>>>>>TIME<<<<<< FFT: 1.046818s Defocus_U Defocus_V Angle CCC 12999.51 12332.58 84.47 0.056107 Final Values Defocus_U Defocus_V Angle CCC 12980.75 12332.60 85.41 0.104896 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00002hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00002hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.003e-01 CC threshold: 0.736 Mean Std: 40.16 6.91 Num Hot pixels: 225 Hot pixel threshold: 81.60 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.475000 Iteration 2 Error: 0.546334 Iteration 3 Error: 0.147402 Iteration 4 Error: 0.044398 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.24 0.20 ...... Frame ( 3) shift: -0.49 0.41 ...... Frame ( 4) shift: -0.73 0.61 ...... Frame ( 5) shift: -0.97 0.82 ...... Frame ( 6) shift: -1.07 0.99 ...... Frame ( 7) shift: -1.02 1.14 ...... Frame ( 8) shift: -0.98 1.28 ...... Frame ( 9) shift: -0.91 1.45 ...... Frame ( 10) shift: -0.84 1.65 ...... Frame ( 11) shift: -0.76 1.85 ...... Frame ( 12) shift: -0.68 2.02 ...... Frame ( 13) shift: -0.57 2.17 ...... Frame ( 14) shift: -0.47 2.33 ...... Frame ( 15) shift: -0.38 2.48 ...... Frame ( 16) shift: -0.32 2.64 ...... Frame ( 17) shift: -0.26 2.80 ...... Frame ( 18) shift: -0.24 2.99 ...... Frame ( 19) shift: -0.26 3.20 ...... Frame ( 20) shift: -0.28 3.41 ...... Frame ( 21) shift: -0.24 3.61 ...... Frame ( 22) shift: -0.16 3.78 ...... Frame ( 23) shift: -0.07 3.96 ...... Frame ( 24) shift: 0.01 4.12 ...... Frame ( 25) shift: 0.09 4.25 ...... Frame ( 26) shift: 0.17 4.39 ...... Frame ( 27) shift: 0.23 4.54 ...... Frame ( 28) shift: 0.29 4.71 ...... Frame ( 29) shift: 0.35 4.88 ...... Frame ( 30) shift: 0.41 5.04 ...... Frame ( 31) shift: 0.46 5.19 ...... Frame ( 32) shift: 0.51 5.34 ...... Frame ( 33) shift: 0.57 5.46 ...... Frame ( 34) shift: 0.65 5.56 ...... Frame ( 35) shift: 0.72 5.65 ...... Frame ( 36) shift: 0.75 5.76 ...... Frame ( 37) shift: 0.73 5.89 ...... Frame ( 38) shift: 0.70 6.02 ...... Frame ( 39) shift: 0.68 6.15 ...... Frame ( 40) shift: 0.66 6.28 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.833565 Iteration 2 Error: 0.404279 Iteration 3 Error: 0.107984 Iteration 4 Error: 0.038853 Align patch 2 23 left Iteration 1 Error: 1.200079 Iteration 2 Error: 0.240512 Iteration 3 Error: 0.108212 Iteration 4 Error: 0.036501 Align patch 3 22 left Iteration 1 Error: 0.767141 Iteration 2 Error: 0.124374 Iteration 3 Error: 0.035711 Align patch 4 21 left Iteration 1 Error: 0.670408 Iteration 2 Error: 0.168886 Iteration 3 Error: 0.043027 Align patch 5 20 left Iteration 1 Error: 0.568684 Iteration 2 Error: 0.101282 Iteration 3 Error: 0.034359 Align patch 6 19 left Iteration 1 Error: 0.903137 Iteration 2 Error: 0.326712 Iteration 3 Error: 0.132583 Iteration 4 Error: 0.043955 Align patch 7 18 left Iteration 1 Error: 1.317117 Iteration 2 Error: 0.338506 Iteration 3 Error: 0.116732 Iteration 4 Error: 0.043327 Align patch 8 17 left Iteration 1 Error: 0.731026 Iteration 2 Error: 0.132032 Iteration 3 Error: 0.052026 Iteration 4 Error: 0.017202 Align patch 9 16 left Iteration 1 Error: 0.672790 Iteration 2 Error: 0.095827 Iteration 3 Error: 0.027541 Align patch 10 15 left Iteration 1 Error: 0.690431 Iteration 2 Error: 0.071541 Iteration 3 Error: 0.017980 Align patch 11 14 left Iteration 1 Error: 0.704214 Iteration 2 Error: 0.119186 Iteration 3 Error: 0.037091 Align patch 12 13 left Iteration 1 Error: 0.868926 Iteration 2 Error: 0.174098 Iteration 3 Error: 0.056485 Iteration 4 Error: 0.020041 Align patch 13 12 left Iteration 1 Error: 0.578944 Iteration 2 Error: 0.113845 Iteration 3 Error: 0.032784 Align patch 14 11 left Iteration 1 Error: 0.618928 Iteration 2 Error: 0.080162 Iteration 3 Error: 0.015761 Align patch 15 10 left Iteration 1 Error: 0.694332 Iteration 2 Error: 0.109276 Iteration 3 Error: 0.026607 Align patch 16 9 left Iteration 1 Error: 0.497102 Iteration 2 Error: 0.093089 Iteration 3 Error: 0.015906 Align patch 17 8 left Iteration 1 Error: 1.082138 Iteration 2 Error: 0.253551 Iteration 3 Error: 0.063937 Iteration 4 Error: 0.019829 Align patch 18 7 left Iteration 1 Error: 0.454965 Iteration 2 Error: 0.090962 Iteration 3 Error: 0.022092 Align patch 19 6 left Iteration 1 Error: 0.963359 Iteration 2 Error: 0.235430 Iteration 3 Error: 0.050943 Iteration 4 Error: 0.016553 Align patch 20 5 left Iteration 1 Error: 1.019203 Iteration 2 Error: 0.146577 Iteration 3 Error: 0.034542 Align patch 21 4 left Iteration 1 Error: 1.291387 Iteration 2 Error: 0.149987 Iteration 3 Error: 0.037927 Align patch 22 3 left Iteration 1 Error: 0.922509 Iteration 2 Error: 0.096896 Iteration 3 Error: 0.031439 Align patch 23 2 left Iteration 1 Error: 0.715382 Iteration 2 Error: 0.142434 Iteration 3 Error: 0.026431 Align patch 24 1 left Iteration 1 Error: 0.796202 Iteration 2 Error: 0.244925 Iteration 3 Error: 0.068519 Iteration 4 Error: 0.025440 Align patch 25 0 left Iteration 1 Error: 0.581257 Iteration 2 Error: 0.109863 Iteration 3 Error: 0.020122 3D Fitting completed. Patch alignment time: 12.85(sec) Local motion has been corrected. Process thread exits. Computational time: 22.732250 sec Total time: 31.591587 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00002hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00002hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.715130s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00002hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.614049s ........................................ >>>>>>TIME<<<<<< FFT: 1.030486s Defocus_U Defocus_V Angle CCC 10978.52 11783.20 11.76 0.072321 Final Values Defocus_U Defocus_V Angle CCC 11000.40 11801.97 11.76 0.121755 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00002hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00002hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 39.65 6.84 Num Hot pixels: 217 Hot pixel threshold: 80.67 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.119038 Iteration 2 Error: 0.429029 Iteration 3 Error: 0.122204 Iteration 4 Error: 0.037953 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.12 0.15 ...... Frame ( 3) shift: -0.23 0.29 ...... Frame ( 4) shift: -0.35 0.44 ...... Frame ( 5) shift: -0.46 0.59 ...... Frame ( 6) shift: -0.50 0.68 ...... Frame ( 7) shift: -0.46 0.71 ...... Frame ( 8) shift: -0.42 0.74 ...... Frame ( 9) shift: -0.38 0.81 ...... Frame ( 10) shift: -0.34 0.93 ...... Frame ( 11) shift: -0.31 1.05 ...... Frame ( 12) shift: -0.27 1.15 ...... Frame ( 13) shift: -0.24 1.25 ...... Frame ( 14) shift: -0.22 1.34 ...... Frame ( 15) shift: -0.15 1.45 ...... Frame ( 16) shift: -0.05 1.58 ...... Frame ( 17) shift: 0.05 1.71 ...... Frame ( 18) shift: 0.14 1.83 ...... Frame ( 19) shift: 0.22 1.95 ...... Frame ( 20) shift: 0.31 2.07 ...... Frame ( 21) shift: 0.37 2.18 ...... Frame ( 22) shift: 0.40 2.28 ...... Frame ( 23) shift: 0.44 2.39 ...... Frame ( 24) shift: 0.45 2.52 ...... Frame ( 25) shift: 0.45 2.68 ...... Frame ( 26) shift: 0.45 2.84 ...... Frame ( 27) shift: 0.47 2.98 ...... Frame ( 28) shift: 0.52 3.09 ...... Frame ( 29) shift: 0.57 3.21 ...... Frame ( 30) shift: 0.63 3.33 ...... Frame ( 31) shift: 0.70 3.45 ...... Frame ( 32) shift: 0.76 3.58 ...... Frame ( 33) shift: 0.86 3.69 ...... Frame ( 34) shift: 0.99 3.81 ...... Frame ( 35) shift: 1.12 3.92 ...... Frame ( 36) shift: 1.20 4.04 ...... Frame ( 37) shift: 1.22 4.16 ...... Frame ( 38) shift: 1.25 4.29 ...... Frame ( 39) shift: 1.27 4.41 ...... Frame ( 40) shift: 1.29 4.53 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.952414 Iteration 2 Error: 0.235534 Iteration 3 Error: 0.080653 Iteration 4 Error: 0.026104 Align patch 2 23 left Iteration 1 Error: 0.619131 Iteration 2 Error: 0.163687 Iteration 3 Error: 0.059357 Iteration 4 Error: 0.019628 Align patch 3 22 left Iteration 1 Error: 0.656030 Iteration 2 Error: 0.129887 Iteration 3 Error: 0.029339 Align patch 4 21 left Iteration 1 Error: 0.723337 Iteration 2 Error: 0.138850 Iteration 3 Error: 0.031999 Align patch 5 20 left Iteration 1 Error: 0.614704 Iteration 2 Error: 0.116558 Iteration 3 Error: 0.032517 Align patch 6 19 left Iteration 1 Error: 0.888097 Iteration 2 Error: 0.182774 Iteration 3 Error: 0.051656 Iteration 4 Error: 0.011824 Align patch 7 18 left Iteration 1 Error: 0.716650 Iteration 2 Error: 0.090171 Iteration 3 Error: 0.017948 Align patch 8 17 left Iteration 1 Error: 0.455690 Iteration 2 Error: 0.117283 Iteration 3 Error: 0.042794 Align patch 9 16 left Iteration 1 Error: 0.623542 Iteration 2 Error: 0.045405 Align patch 10 15 left Iteration 1 Error: 0.624238 Iteration 2 Error: 0.134903 Iteration 3 Error: 0.027900 Align patch 11 14 left Iteration 1 Error: 0.502612 Iteration 2 Error: 0.155340 Iteration 3 Error: 0.034258 Align patch 12 13 left Iteration 1 Error: 0.475917 Iteration 2 Error: 0.051800 Iteration 3 Error: 0.017304 Align patch 13 12 left Iteration 1 Error: 0.640912 Iteration 2 Error: 0.133177 Iteration 3 Error: 0.044165 Align patch 14 11 left Iteration 1 Error: 0.412374 Iteration 2 Error: 0.033615 Align patch 15 10 left Iteration 1 Error: 0.395947 Iteration 2 Error: 0.099836 Iteration 3 Error: 0.028748 Align patch 16 9 left Iteration 1 Error: 0.693559 Iteration 2 Error: 0.137262 Iteration 3 Error: 0.034110 Align patch 17 8 left Iteration 1 Error: 0.479503 Iteration 2 Error: 0.085620 Iteration 3 Error: 0.020751 Align patch 18 7 left Iteration 1 Error: 0.605799 Iteration 2 Error: 0.114073 Iteration 3 Error: 0.024156 Align patch 19 6 left Iteration 1 Error: 0.564943 Iteration 2 Error: 0.098833 Iteration 3 Error: 0.019811 Align patch 20 5 left Iteration 1 Error: 0.538412 Iteration 2 Error: 0.102254 Iteration 3 Error: 0.027093 Align patch 21 4 left Iteration 1 Error: 0.849990 Iteration 2 Error: 0.193368 Iteration 3 Error: 0.088471 Iteration 4 Error: 0.029939 Align patch 22 3 left Iteration 1 Error: 0.782978 Iteration 2 Error: 0.160177 Iteration 3 Error: 0.054320 Iteration 4 Error: 0.019566 Align patch 23 2 left Iteration 1 Error: 0.401122 Iteration 2 Error: 0.038490 Align patch 24 1 left Iteration 1 Error: 0.547640 Iteration 2 Error: 0.128328 Iteration 3 Error: 0.018706 Align patch 25 0 left Iteration 1 Error: 0.444547 Iteration 2 Error: 0.100065 Iteration 3 Error: 0.015423 3D Fitting completed. Patch alignment time: 12.97(sec) Local motion has been corrected. Process thread exits. Computational time: 23.574268 sec Total time: 31.067554 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00002hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00002hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.700160s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00002hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.646541s ........................................ >>>>>>TIME<<<<<< FFT: 0.999722s Defocus_U Defocus_V Angle CCC 11173.83 11732.42 2.07 0.061295 Final Values Defocus_U Defocus_V Angle CCC 11217.59 11741.81 0.83 0.103108 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00002hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00002hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.350e-01 1.004e-01 CC threshold: 0.737 Mean Std: 41.20 7.03 Num Hot pixels: 218 Hot pixel threshold: 83.37 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.836655 Iteration 2 Error: 0.300377 Iteration 3 Error: 0.068954 Iteration 4 Error: 0.018845 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.35 -0.08 ...... Frame ( 3) shift: -0.70 -0.16 ...... Frame ( 4) shift: -1.05 -0.24 ...... Frame ( 5) shift: -1.40 -0.33 ...... Frame ( 6) shift: -1.57 -0.37 ...... Frame ( 7) shift: -1.55 -0.36 ...... Frame ( 8) shift: -1.53 -0.36 ...... Frame ( 9) shift: -1.48 -0.34 ...... Frame ( 10) shift: -1.41 -0.30 ...... Frame ( 11) shift: -1.34 -0.26 ...... Frame ( 12) shift: -1.27 -0.19 ...... Frame ( 13) shift: -1.20 -0.09 ...... Frame ( 14) shift: -1.13 0.02 ...... Frame ( 15) shift: -1.12 0.09 ...... Frame ( 16) shift: -1.16 0.13 ...... Frame ( 17) shift: -1.20 0.17 ...... Frame ( 18) shift: -1.15 0.25 ...... Frame ( 19) shift: -1.01 0.39 ...... Frame ( 20) shift: -0.87 0.52 ...... Frame ( 21) shift: -0.80 0.62 ...... Frame ( 22) shift: -0.79 0.70 ...... Frame ( 23) shift: -0.78 0.78 ...... Frame ( 24) shift: -0.77 0.87 ...... Frame ( 25) shift: -0.75 0.95 ...... Frame ( 26) shift: -0.73 1.04 ...... Frame ( 27) shift: -0.67 1.15 ...... Frame ( 28) shift: -0.57 1.29 ...... Frame ( 29) shift: -0.46 1.43 ...... Frame ( 30) shift: -0.37 1.54 ...... Frame ( 31) shift: -0.28 1.63 ...... Frame ( 32) shift: -0.19 1.71 ...... Frame ( 33) shift: -0.14 1.83 ...... Frame ( 34) shift: -0.12 1.98 ...... Frame ( 35) shift: -0.11 2.14 ...... Frame ( 36) shift: -0.10 2.27 ...... Frame ( 37) shift: -0.10 2.39 ...... Frame ( 38) shift: -0.10 2.50 ...... Frame ( 39) shift: -0.10 2.62 ...... Frame ( 40) shift: -0.10 2.73 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.438497 Iteration 2 Error: 0.221130 Iteration 3 Error: 0.042536 Align patch 2 23 left Iteration 1 Error: 1.096568 Iteration 2 Error: 0.160465 Iteration 3 Error: 0.043586 Align patch 3 22 left Iteration 1 Error: 0.672173 Iteration 2 Error: 0.162707 Iteration 3 Error: 0.056558 Iteration 4 Error: 0.017032 Align patch 4 21 left Iteration 1 Error: 0.835305 Iteration 2 Error: 0.133678 Iteration 3 Error: 0.031771 Align patch 5 20 left Iteration 1 Error: 0.619789 Iteration 2 Error: 0.064259 Iteration 3 Error: 0.014707 Align patch 6 19 left Iteration 1 Error: 1.437185 Iteration 2 Error: 0.241166 Iteration 3 Error: 0.073134 Iteration 4 Error: 0.026397 Align patch 7 18 left Iteration 1 Error: 0.711859 Iteration 2 Error: 0.140550 Iteration 3 Error: 0.066568 Iteration 4 Error: 0.023640 Align patch 8 17 left Iteration 1 Error: 0.602236 Iteration 2 Error: 0.131002 Iteration 3 Error: 0.049684 Align patch 9 16 left Iteration 1 Error: 0.821601 Iteration 2 Error: 0.101669 Iteration 3 Error: 0.022072 Align patch 10 15 left Iteration 1 Error: 0.559222 Iteration 2 Error: 0.059869 Iteration 3 Error: 0.019481 Align patch 11 14 left Iteration 1 Error: 0.827395 Iteration 2 Error: 0.159688 Iteration 3 Error: 0.050913 Iteration 4 Error: 0.016783 Align patch 12 13 left Iteration 1 Error: 0.563385 Iteration 2 Error: 0.066354 Iteration 3 Error: 0.019101 Align patch 13 12 left Iteration 1 Error: 0.443519 Iteration 2 Error: 0.060545 Iteration 3 Error: 0.013472 Align patch 14 11 left Iteration 1 Error: 0.756391 Iteration 2 Error: 0.088965 Iteration 3 Error: 0.014419 Align patch 15 10 left Iteration 1 Error: 0.499669 Iteration 2 Error: 0.054013 Iteration 3 Error: 0.016718 Align patch 16 9 left Iteration 1 Error: 0.605974 Iteration 2 Error: 0.097050 Iteration 3 Error: 0.018429 Align patch 17 8 left Iteration 1 Error: 0.562904 Iteration 2 Error: 0.073961 Iteration 3 Error: 0.011958 Align patch 18 7 left Iteration 1 Error: 0.446378 Iteration 2 Error: 0.100231 Iteration 3 Error: 0.020570 Align patch 19 6 left Iteration 1 Error: 0.445998 Iteration 2 Error: 0.048718 Align patch 20 5 left Iteration 1 Error: 0.568624 Iteration 2 Error: 0.085333 Iteration 3 Error: 0.017076 Align patch 21 4 left Iteration 1 Error: 1.163257 Iteration 2 Error: 0.119649 Iteration 3 Error: 0.029310 Align patch 22 3 left Iteration 1 Error: 0.906949 Iteration 2 Error: 0.089601 Iteration 3 Error: 0.020493 Align patch 23 2 left Iteration 1 Error: 0.724411 Iteration 2 Error: 0.103095 Iteration 3 Error: 0.024498 Align patch 24 1 left Iteration 1 Error: 0.581458 Iteration 2 Error: 0.073454 Iteration 3 Error: 0.015609 Align patch 25 0 left Iteration 1 Error: 0.530691 Iteration 2 Error: 0.081564 Iteration 3 Error: 0.014737 3D Fitting completed. Patch alignment time: 12.60(sec) Local motion has been corrected. Process thread exits. Computational time: 22.554518 sec Total time: 29.024042 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00002hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00002hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.674460s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00002hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.697701s ........................................ >>>>>>TIME<<<<<< FFT: 1.004951s Defocus_U Defocus_V Angle CCC 12804.73 13671.92 7.17 0.071058 Final Values Defocus_U Defocus_V Angle CCC 12807.86 13671.92 7.17 0.114512 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00002hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00002hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.350e-01 1.004e-01 CC threshold: 0.737 Mean Std: 40.83 7.04 Num Hot pixels: 206 Hot pixel threshold: 83.06 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.986652 Iteration 2 Error: 0.142337 Iteration 3 Error: 0.031429 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.20 0.03 ...... Frame ( 3) shift: -0.40 0.05 ...... Frame ( 4) shift: -0.60 0.08 ...... Frame ( 5) shift: -0.79 0.11 ...... Frame ( 6) shift: -0.92 0.16 ...... Frame ( 7) shift: -0.97 0.23 ...... Frame ( 8) shift: -1.01 0.30 ...... Frame ( 9) shift: -1.05 0.35 ...... Frame ( 10) shift: -1.07 0.35 ...... Frame ( 11) shift: -1.09 0.36 ...... Frame ( 12) shift: -1.07 0.42 ...... Frame ( 13) shift: -1.01 0.54 ...... Frame ( 14) shift: -0.95 0.65 ...... Frame ( 15) shift: -0.92 0.75 ...... Frame ( 16) shift: -0.94 0.83 ...... Frame ( 17) shift: -0.95 0.90 ...... Frame ( 18) shift: -0.91 0.95 ...... Frame ( 19) shift: -0.82 0.97 ...... Frame ( 20) shift: -0.73 1.00 ...... Frame ( 21) shift: -0.70 1.04 ...... Frame ( 22) shift: -0.72 1.12 ...... Frame ( 23) shift: -0.75 1.19 ...... Frame ( 24) shift: -0.76 1.28 ...... Frame ( 25) shift: -0.75 1.38 ...... Frame ( 26) shift: -0.74 1.49 ...... Frame ( 27) shift: -0.71 1.53 ...... Frame ( 28) shift: -0.68 1.52 ...... Frame ( 29) shift: -0.64 1.51 ...... Frame ( 30) shift: -0.60 1.51 ...... Frame ( 31) shift: -0.57 1.54 ...... Frame ( 32) shift: -0.53 1.56 ...... Frame ( 33) shift: -0.51 1.62 ...... Frame ( 34) shift: -0.52 1.72 ...... Frame ( 35) shift: -0.52 1.82 ...... Frame ( 36) shift: -0.52 1.87 ...... Frame ( 37) shift: -0.51 1.88 ...... Frame ( 38) shift: -0.51 1.88 ...... Frame ( 39) shift: -0.50 1.89 ...... Frame ( 40) shift: -0.49 1.89 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.841421 Iteration 2 Error: 0.222886 Iteration 3 Error: 0.063449 Iteration 4 Error: 0.021932 Align patch 2 23 left Iteration 1 Error: 0.676412 Iteration 2 Error: 0.190425 Iteration 3 Error: 0.059449 Iteration 4 Error: 0.021878 Align patch 3 22 left Iteration 1 Error: 0.642409 Iteration 2 Error: 0.098709 Iteration 3 Error: 0.017661 Align patch 4 21 left Iteration 1 Error: 0.737914 Iteration 2 Error: 0.089756 Iteration 3 Error: 0.013077 Align patch 5 20 left Iteration 1 Error: 0.692106 Iteration 2 Error: 0.099765 Iteration 3 Error: 0.018913 Align patch 6 19 left Iteration 1 Error: 1.658604 Iteration 2 Error: 0.202758 Iteration 3 Error: 0.075749 Iteration 4 Error: 0.023094 Align patch 7 18 left Iteration 1 Error: 0.777232 Iteration 2 Error: 0.204855 Iteration 3 Error: 0.052974 Iteration 4 Error: 0.018880 Align patch 8 17 left Iteration 1 Error: 0.805266 Iteration 2 Error: 0.115431 Iteration 3 Error: 0.023611 Align patch 9 16 left Iteration 1 Error: 0.670408 Iteration 2 Error: 0.131333 Iteration 3 Error: 0.028706 Align patch 10 15 left Iteration 1 Error: 0.376193 Iteration 2 Error: 0.056968 Iteration 3 Error: 0.009655 Align patch 11 14 left Iteration 1 Error: 0.709784 Iteration 2 Error: 0.147451 Iteration 3 Error: 0.039213 Align patch 12 13 left Iteration 1 Error: 0.617552 Iteration 2 Error: 0.139551 Iteration 3 Error: 0.031907 Align patch 13 12 left Iteration 1 Error: 0.625005 Iteration 2 Error: 0.129533 Iteration 3 Error: 0.034139 Align patch 14 11 left Iteration 1 Error: 0.389268 Iteration 2 Error: 0.060510 Iteration 3 Error: 0.013080 Align patch 15 10 left Iteration 1 Error: 0.531027 Iteration 2 Error: 0.073781 Iteration 3 Error: 0.017511 Align patch 16 9 left Iteration 1 Error: 0.658167 Iteration 2 Error: 0.081989 Iteration 3 Error: 0.016318 Align patch 17 8 left Iteration 1 Error: 0.736217 Iteration 2 Error: 0.085399 Iteration 3 Error: 0.016677 Align patch 18 7 left Iteration 1 Error: 0.538939 Iteration 2 Error: 0.068675 Iteration 3 Error: 0.014181 Align patch 19 6 left Iteration 1 Error: 0.514584 Iteration 2 Error: 0.049782 Align patch 20 5 left Iteration 1 Error: 0.379533 Iteration 2 Error: 0.055787 Iteration 3 Error: 0.012370 Align patch 21 4 left Iteration 1 Error: 1.328402 Iteration 2 Error: 0.159885 Iteration 3 Error: 0.038016 Align patch 22 3 left Iteration 1 Error: 0.803264 Iteration 2 Error: 0.101197 Iteration 3 Error: 0.024038 Align patch 23 2 left Iteration 1 Error: 0.819210 Iteration 2 Error: 0.102677 Iteration 3 Error: 0.015760 Align patch 24 1 left Iteration 1 Error: 0.881981 Iteration 2 Error: 0.100186 Iteration 3 Error: 0.017126 Align patch 25 0 left Iteration 1 Error: 0.534220 Iteration 2 Error: 0.075163 Iteration 3 Error: 0.015938 3D Fitting completed. Patch alignment time: 13.13(sec) Local motion has been corrected. Process thread exits. Computational time: 24.433449 sec Total time: 30.755737 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00002hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00002hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.657747s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00002hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.716175s ........................................ >>>>>>TIME<<<<<< FFT: 1.037260s Defocus_U Defocus_V Angle CCC 11705.08 11021.48 87.52 0.061952 Final Values Defocus_U Defocus_V Angle CCC 11706.67 11051.21 87.21 0.101052 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00003hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00003hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.331e-01 9.905e-02 CC threshold: 0.727 Mean Std: 37.90 6.63 Num Hot pixels: 232 Hot pixel threshold: 77.67 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.572402 Iteration 2 Error: 0.196946 Iteration 3 Error: 0.046065 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.25 -0.11 ...... Frame ( 3) shift: -0.50 -0.22 ...... Frame ( 4) shift: -0.75 -0.33 ...... Frame ( 5) shift: -0.99 -0.44 ...... Frame ( 6) shift: -1.17 -0.61 ...... Frame ( 7) shift: -1.28 -0.84 ...... Frame ( 8) shift: -1.38 -1.08 ...... Frame ( 9) shift: -1.47 -1.29 ...... Frame ( 10) shift: -1.54 -1.48 ...... Frame ( 11) shift: -1.60 -1.68 ...... Frame ( 12) shift: -1.65 -1.81 ...... Frame ( 13) shift: -1.67 -1.88 ...... Frame ( 14) shift: -1.68 -1.95 ...... Frame ( 15) shift: -1.63 -1.99 ...... Frame ( 16) shift: -1.52 -2.01 ...... Frame ( 17) shift: -1.40 -2.02 ...... Frame ( 18) shift: -1.35 -2.03 ...... Frame ( 19) shift: -1.35 -2.05 ...... Frame ( 20) shift: -1.35 -2.07 ...... Frame ( 21) shift: -1.31 -2.07 ...... Frame ( 22) shift: -1.24 -2.06 ...... Frame ( 23) shift: -1.17 -2.05 ...... Frame ( 24) shift: -1.11 -2.05 ...... Frame ( 25) shift: -1.06 -2.07 ...... Frame ( 26) shift: -1.00 -2.09 ...... Frame ( 27) shift: -0.94 -2.09 ...... Frame ( 28) shift: -0.85 -2.07 ...... Frame ( 29) shift: -0.77 -2.06 ...... Frame ( 30) shift: -0.69 -2.03 ...... Frame ( 31) shift: -0.61 -2.01 ...... Frame ( 32) shift: -0.54 -1.98 ...... Frame ( 33) shift: -0.48 -1.97 ...... Frame ( 34) shift: -0.46 -1.98 ...... Frame ( 35) shift: -0.43 -1.99 ...... Frame ( 36) shift: -0.39 -1.98 ...... Frame ( 37) shift: -0.31 -1.97 ...... Frame ( 38) shift: -0.24 -1.97 ...... Frame ( 39) shift: -0.17 -1.96 ...... Frame ( 40) shift: -0.09 -1.95 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.919131 Iteration 2 Error: 0.597575 Iteration 3 Error: 0.179773 Iteration 4 Error: 0.088638 Iteration 5 Error: 0.038980 Align patch 2 23 left Iteration 1 Error: 0.961105 Iteration 2 Error: 0.218438 Iteration 3 Error: 0.088018 Iteration 4 Error: 0.023525 Align patch 3 22 left Iteration 1 Error: 0.921375 Iteration 2 Error: 0.242703 Iteration 3 Error: 0.037312 Align patch 4 21 left Iteration 1 Error: 1.382932 Iteration 2 Error: 0.283853 Iteration 3 Error: 0.056175 Iteration 4 Error: 0.022634 Align patch 5 20 left Iteration 1 Error: 1.936818 Iteration 2 Error: 0.355431 Iteration 3 Error: 0.107302 Iteration 4 Error: 0.026998 Align patch 6 19 left Iteration 1 Error: 1.799904 Iteration 2 Error: 0.385065 Iteration 3 Error: 0.149118 Iteration 4 Error: 0.040319 Align patch 7 18 left Iteration 1 Error: 1.120964 Iteration 2 Error: 0.186227 Iteration 3 Error: 0.069944 Iteration 4 Error: 0.022399 Align patch 8 17 left Iteration 1 Error: 0.818876 Iteration 2 Error: 0.146464 Iteration 3 Error: 0.030404 Align patch 9 16 left Iteration 1 Error: 1.315772 Iteration 2 Error: 0.300650 Iteration 3 Error: 0.066941 Iteration 4 Error: 0.014494 Align patch 10 15 left Iteration 1 Error: 1.368212 Iteration 2 Error: 0.292503 Iteration 3 Error: 0.062087 Iteration 4 Error: 0.012220 Align patch 11 14 left Iteration 1 Error: 3.716146 Iteration 2 Error: 0.474367 Iteration 3 Error: 0.226134 Iteration 4 Error: 0.107433 Iteration 5 Error: 0.074012 Align patch 11 14 left Iteration 1 Error: 3.032186 Iteration 2 Error: 0.332720 Iteration 3 Error: 0.101705 Iteration 4 Error: 0.033560 Align patch 12 13 left Iteration 1 Error: 1.913230 Iteration 2 Error: 0.228135 Iteration 3 Error: 0.112305 Iteration 4 Error: 0.034469 Align patch 13 12 left Iteration 1 Error: 1.107279 Iteration 2 Error: 0.147637 Iteration 3 Error: 0.058432 Iteration 4 Error: 0.015896 Align patch 14 11 left Iteration 1 Error: 0.791594 Iteration 2 Error: 0.231801 Iteration 3 Error: 0.079017 Iteration 4 Error: 0.018154 Align patch 15 10 left Iteration 1 Error: 1.647511 Iteration 2 Error: 0.290234 Iteration 3 Error: 0.055247 Iteration 4 Error: 0.014708 Align patch 16 9 left Iteration 1 Error: 3.343092 Iteration 2 Error: 0.854508 Iteration 3 Error: 0.370170 Iteration 4 Error: 0.181841 Iteration 5 Error: 0.082623 Align patch 16 9 left Iteration 1 Error: 3.370727 Iteration 2 Error: 0.461818 Iteration 3 Error: 0.125895 Iteration 4 Error: 0.037783 Align patch 17 8 left Iteration 1 Error: 1.999731 Iteration 2 Error: 0.286172 Iteration 3 Error: 0.109777 Iteration 4 Error: 0.033520 Align patch 18 7 left Iteration 1 Error: 0.606369 Iteration 2 Error: 0.171491 Iteration 3 Error: 0.046594 Align patch 19 6 left Iteration 1 Error: 1.493438 Iteration 2 Error: 0.198333 Iteration 3 Error: 0.071871 Iteration 4 Error: 0.015038 Align patch 20 5 left Iteration 1 Error: 1.916513 Iteration 2 Error: 0.240501 Iteration 3 Error: 0.039285 Align patch 21 4 left Iteration 1 Error: 3.532543 Iteration 2 Error: 0.452814 Iteration 3 Error: 0.187652 Iteration 4 Error: 0.070472 Iteration 5 Error: 0.022213 Align patch 22 3 left Iteration 1 Error: 2.570751 Iteration 2 Error: 0.481155 Iteration 3 Error: 0.146227 Iteration 4 Error: 0.051940 Iteration 5 Error: 0.020316 Align patch 23 2 left Iteration 1 Error: 1.154398 Iteration 2 Error: 0.141187 Iteration 3 Error: 0.044862 Align patch 24 1 left Iteration 1 Error: 1.318278 Iteration 2 Error: 0.181898 Iteration 3 Error: 0.063032 Iteration 4 Error: 0.019730 Align patch 25 0 left Iteration 1 Error: 2.385748 Iteration 2 Error: 0.328176 Iteration 3 Error: 0.061366 Iteration 4 Error: 0.017040 3D Fitting completed. Patch alignment time: 14.90(sec) Local motion has been corrected. Process thread exits. Computational time: 26.150118 sec Total time: 33.158222 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00003hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00003hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.619926s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00003hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.018197s ........................................ >>>>>>TIME<<<<<< FFT: 1.029730s Defocus_U Defocus_V Angle CCC 7992.19 8816.41 14.56 -0.015022 Final Values Defocus_U Defocus_V Angle CCC 7985.92 8847.67 16.75 -0.093729 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00003hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00003hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.326e-01 9.880e-02 CC threshold: 0.725 Mean Std: 33.05 6.27 Num Hot pixels: 166 Hot pixel threshold: 70.65 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 3.074822 Iteration 2 Error: 0.310243 Iteration 3 Error: 0.093668 Iteration 4 Error: 0.039305 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.42 -0.41 ...... Frame ( 3) shift: -0.84 -0.82 ...... Frame ( 4) shift: -1.25 -1.23 ...... Frame ( 5) shift: -1.67 -1.64 ...... Frame ( 6) shift: -1.97 -2.00 ...... Frame ( 7) shift: -2.14 -2.30 ...... Frame ( 8) shift: -2.31 -2.60 ...... Frame ( 9) shift: -2.48 -2.80 ...... Frame ( 10) shift: -2.64 -2.89 ...... Frame ( 11) shift: -2.80 -2.99 ...... Frame ( 12) shift: -2.89 -3.08 ...... Frame ( 13) shift: -2.92 -3.16 ...... Frame ( 14) shift: -2.95 -3.23 ...... Frame ( 15) shift: -2.98 -3.32 ...... Frame ( 16) shift: -3.02 -3.41 ...... Frame ( 17) shift: -3.05 -3.50 ...... Frame ( 18) shift: -3.07 -3.57 ...... Frame ( 19) shift: -3.07 -3.60 ...... Frame ( 20) shift: -3.07 -3.62 ...... Frame ( 21) shift: -3.05 -3.68 ...... Frame ( 22) shift: -3.02 -3.77 ...... Frame ( 23) shift: -2.98 -3.86 ...... Frame ( 24) shift: -2.97 -3.90 ...... Frame ( 25) shift: -2.97 -3.89 ...... Frame ( 26) shift: -2.97 -3.87 ...... Frame ( 27) shift: -2.97 -3.84 ...... Frame ( 28) shift: -2.95 -3.80 ...... Frame ( 29) shift: -2.93 -3.75 ...... Frame ( 30) shift: -2.86 -3.81 ...... Frame ( 31) shift: -2.74 -3.99 ...... Frame ( 32) shift: -2.63 -4.17 ...... Frame ( 33) shift: -2.56 -4.21 ...... Frame ( 34) shift: -2.54 -4.12 ...... Frame ( 35) shift: -2.52 -4.02 ...... Frame ( 36) shift: -2.50 -3.98 ...... Frame ( 37) shift: -2.49 -4.00 ...... Frame ( 38) shift: -2.48 -4.02 ...... Frame ( 39) shift: -2.46 -4.04 ...... Frame ( 40) shift: -2.45 -4.06 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.371852 Iteration 2 Error: 0.206447 Iteration 3 Error: 0.071638 Iteration 4 Error: 0.029085 Align patch 2 23 left Iteration 1 Error: 1.056600 Iteration 2 Error: 0.177320 Iteration 3 Error: 0.045353 Align patch 3 22 left Iteration 1 Error: 1.406269 Iteration 2 Error: 0.346067 Iteration 3 Error: 0.125890 Iteration 4 Error: 0.074111 Iteration 5 Error: 0.027934 Align patch 4 21 left Iteration 1 Error: 1.504185 Iteration 2 Error: 0.303739 Iteration 3 Error: 0.107357 Iteration 4 Error: 0.040080 Align patch 5 20 left Iteration 1 Error: 3.139056 Iteration 2 Error: 0.316748 Iteration 3 Error: 0.094379 Iteration 4 Error: 0.028621 Align patch 6 19 left Iteration 1 Error: 2.496980 Iteration 2 Error: 0.294528 Iteration 3 Error: 0.092581 Iteration 4 Error: 0.029814 Align patch 7 18 left Iteration 1 Error: 1.800365 Iteration 2 Error: 0.222107 Iteration 3 Error: 0.067978 Iteration 4 Error: 0.030806 Align patch 8 17 left Iteration 1 Error: 1.183643 Iteration 2 Error: 0.191259 Iteration 3 Error: 0.134332 Iteration 4 Error: 0.045987 Align patch 9 16 left Iteration 1 Error: 0.902542 Iteration 2 Error: 0.263818 Iteration 3 Error: 0.184373 Iteration 4 Error: 0.066770 Iteration 5 Error: 0.048425 Align patch 10 15 left Iteration 1 Error: 2.402894 Iteration 2 Error: 0.303736 Iteration 3 Error: 0.093072 Iteration 4 Error: 0.053099 Iteration 5 Error: 0.023372 Align patch 11 14 left Iteration 1 Error: 2.601839 Iteration 2 Error: 0.653325 Iteration 3 Error: 0.284985 Iteration 4 Error: 0.106603 Iteration 5 Error: 0.041097 Align patch 12 13 left Iteration 1 Error: 3.739897 Iteration 2 Error: 0.393771 Iteration 3 Error: 0.121592 Iteration 4 Error: 0.047844 Align patch 13 12 left Iteration 1 Error: 2.180158 Iteration 2 Error: 0.233591 Iteration 3 Error: 0.066531 Iteration 4 Error: 0.015084 Align patch 14 11 left Iteration 1 Error: 2.007178 Iteration 2 Error: 0.242878 Iteration 3 Error: 0.097714 Iteration 4 Error: 0.027736 Align patch 15 10 left Iteration 1 Error: 2.489151 Iteration 2 Error: 0.314615 Iteration 3 Error: 0.071638 Iteration 4 Error: 0.014284 Align patch 16 9 left Iteration 1 Error: 4.681991 Iteration 2 Error: 0.757119 Iteration 3 Error: 0.238303 Iteration 4 Error: 0.084278 Iteration 5 Error: 0.035661 Align patch 17 8 left Iteration 1 Error: 2.803283 Iteration 2 Error: 0.671622 Iteration 3 Error: 0.152547 Iteration 4 Error: 0.073003 Iteration 5 Error: 0.024582 Align patch 18 7 left Iteration 1 Error: 2.457004 Iteration 2 Error: 0.380923 Iteration 3 Error: 0.239634 Iteration 4 Error: 0.068069 Iteration 5 Error: 0.034631 Align patch 19 6 left Iteration 1 Error: 1.350820 Iteration 2 Error: 0.393760 Iteration 3 Error: 0.107891 Iteration 4 Error: 0.042518 Align patch 20 5 left Iteration 1 Error: 2.112249 Iteration 2 Error: 0.406752 Iteration 3 Error: 0.104489 Iteration 4 Error: 0.036346 Align patch 21 4 left Iteration 1 Error: 3.205323 Iteration 2 Error: 0.599111 Iteration 3 Error: 0.200832 Iteration 4 Error: 0.078691 Iteration 5 Error: 0.042013 Align patch 22 3 left Iteration 1 Error: 2.090547 Iteration 2 Error: 0.434300 Iteration 3 Error: 0.129509 Iteration 4 Error: 0.070760 Iteration 5 Error: 0.015782 Align patch 23 2 left Iteration 1 Error: 0.976639 Iteration 2 Error: 0.288912 Iteration 3 Error: 0.121975 Iteration 4 Error: 0.039946 Align patch 24 1 left Iteration 1 Error: 1.728288 Iteration 2 Error: 0.274570 Iteration 3 Error: 0.084507 Iteration 4 Error: 0.028197 Align patch 25 0 left Iteration 1 Error: 2.619911 Iteration 2 Error: 0.343041 Iteration 3 Error: 0.073646 Iteration 4 Error: 0.018462 3D Fitting completed. Patch alignment time: 14.07(sec) Local motion has been corrected. Process thread exits. Computational time: 24.720812 sec Total time: 31.777193 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00003hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00003hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.865925s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00003hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.189451s ........................................ >>>>>>TIME<<<<<< FFT: 1.048328s Defocus_U Defocus_V Angle CCC 11187.53 10078.13 74.21 -0.012179 Final Values Defocus_U Defocus_V Angle CCC 11282.83 10010.97 71.09 -0.085193 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00003hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00003hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.003e-01 CC threshold: 0.736 Mean Std: 39.43 6.75 Num Hot pixels: 211 Hot pixel threshold: 79.90 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.562163 Iteration 2 Error: 0.271623 Iteration 3 Error: 0.059147 Iteration 4 Error: 0.014562 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.04 0.07 ...... Frame ( 3) shift: -0.08 0.15 ...... Frame ( 4) shift: -0.12 0.22 ...... Frame ( 5) shift: -0.16 0.30 ...... Frame ( 6) shift: -0.20 0.35 ...... Frame ( 7) shift: -0.26 0.40 ...... Frame ( 8) shift: -0.32 0.44 ...... Frame ( 9) shift: -0.33 0.48 ...... Frame ( 10) shift: -0.30 0.54 ...... Frame ( 11) shift: -0.27 0.60 ...... Frame ( 12) shift: -0.24 0.69 ...... Frame ( 13) shift: -0.21 0.81 ...... Frame ( 14) shift: -0.19 0.93 ...... Frame ( 15) shift: -0.18 1.01 ...... Frame ( 16) shift: -0.20 1.04 ...... Frame ( 17) shift: -0.21 1.08 ...... Frame ( 18) shift: -0.19 1.15 ...... Frame ( 19) shift: -0.11 1.26 ...... Frame ( 20) shift: -0.04 1.37 ...... Frame ( 21) shift: 0.01 1.46 ...... Frame ( 22) shift: 0.05 1.53 ...... Frame ( 23) shift: 0.09 1.60 ...... Frame ( 24) shift: 0.13 1.70 ...... Frame ( 25) shift: 0.17 1.85 ...... Frame ( 26) shift: 0.20 1.99 ...... Frame ( 27) shift: 0.26 2.09 ...... Frame ( 28) shift: 0.34 2.14 ...... Frame ( 29) shift: 0.42 2.20 ...... Frame ( 30) shift: 0.48 2.24 ...... Frame ( 31) shift: 0.52 2.26 ...... Frame ( 32) shift: 0.57 2.28 ...... Frame ( 33) shift: 0.65 2.33 ...... Frame ( 34) shift: 0.78 2.40 ...... Frame ( 35) shift: 0.90 2.48 ...... Frame ( 36) shift: 0.98 2.56 ...... Frame ( 37) shift: 1.01 2.64 ...... Frame ( 38) shift: 1.05 2.73 ...... Frame ( 39) shift: 1.09 2.81 ...... Frame ( 40) shift: 1.12 2.90 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.821567 Iteration 2 Error: 0.177685 Iteration 3 Error: 0.028189 Align patch 2 23 left Iteration 1 Error: 0.868607 Iteration 2 Error: 0.088680 Iteration 3 Error: 0.022210 Align patch 3 22 left Iteration 1 Error: 0.571437 Iteration 2 Error: 0.078858 Iteration 3 Error: 0.014323 Align patch 4 21 left Iteration 1 Error: 0.837902 Iteration 2 Error: 0.118742 Iteration 3 Error: 0.030208 Align patch 5 20 left Iteration 1 Error: 0.968166 Iteration 2 Error: 0.073965 Iteration 3 Error: 0.019604 Align patch 6 19 left Iteration 1 Error: 0.413628 Iteration 2 Error: 0.097903 Iteration 3 Error: 0.022209 Align patch 7 18 left Iteration 1 Error: 0.596435 Iteration 2 Error: 0.143162 Iteration 3 Error: 0.047429 Align patch 8 17 left Iteration 1 Error: 0.768107 Iteration 2 Error: 0.179015 Iteration 3 Error: 0.044152 Align patch 9 16 left Iteration 1 Error: 0.496893 Iteration 2 Error: 0.096689 Iteration 3 Error: 0.025460 Align patch 10 15 left Iteration 1 Error: 0.855243 Iteration 2 Error: 0.118425 Iteration 3 Error: 0.027126 Align patch 11 14 left Iteration 1 Error: 0.797768 Iteration 2 Error: 0.115346 Iteration 3 Error: 0.041914 Align patch 12 13 left Iteration 1 Error: 0.519811 Iteration 2 Error: 0.088115 Iteration 3 Error: 0.027034 Align patch 13 12 left Iteration 1 Error: 0.627183 Iteration 2 Error: 0.071806 Iteration 3 Error: 0.009704 Align patch 14 11 left Iteration 1 Error: 0.402347 Iteration 2 Error: 0.062805 Iteration 3 Error: 0.016590 Align patch 15 10 left Iteration 1 Error: 0.435400 Iteration 2 Error: 0.071422 Iteration 3 Error: 0.016367 Align patch 16 9 left Iteration 1 Error: 0.795879 Iteration 2 Error: 0.118834 Iteration 3 Error: 0.032476 Align patch 17 8 left Iteration 1 Error: 1.206055 Iteration 2 Error: 0.166469 Iteration 3 Error: 0.031959 Align patch 18 7 left Iteration 1 Error: 0.475969 Iteration 2 Error: 0.048964 Align patch 19 6 left Iteration 1 Error: 0.628715 Iteration 2 Error: 0.095637 Iteration 3 Error: 0.018353 Align patch 20 5 left Iteration 1 Error: 0.557794 Iteration 2 Error: 0.068845 Iteration 3 Error: 0.014941 Align patch 21 4 left Iteration 1 Error: 0.992278 Iteration 2 Error: 0.127219 Iteration 3 Error: 0.030726 Align patch 22 3 left Iteration 1 Error: 0.807614 Iteration 2 Error: 0.153109 Iteration 3 Error: 0.030953 Align patch 23 2 left Iteration 1 Error: 0.883440 Iteration 2 Error: 0.154195 Iteration 3 Error: 0.034654 Align patch 24 1 left Iteration 1 Error: 0.865370 Iteration 2 Error: 0.152395 Iteration 3 Error: 0.026475 Align patch 25 0 left Iteration 1 Error: 0.662098 Iteration 2 Error: 0.102620 Iteration 3 Error: 0.018836 3D Fitting completed. Patch alignment time: 12.95(sec) Local motion has been corrected. Process thread exits. Computational time: 24.046082 sec Total time: 31.012472 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00003hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00003hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.557926s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00003hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.540736s ........................................ >>>>>>TIME<<<<<< FFT: 1.057739s Defocus_U Defocus_V Angle CCC 10607.42 11412.11 7.65 0.054211 Final Values Defocus_U Defocus_V Angle CCC 10618.37 11454.33 7.96 0.085818 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00003hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00003hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 38.33 6.69 Num Hot pixels: 222 Hot pixel threshold: 78.46 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.092128 Iteration 2 Error: 0.268179 Iteration 3 Error: 0.063020 Iteration 4 Error: 0.017089 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.23 0.04 ...... Frame ( 3) shift: -0.46 0.09 ...... Frame ( 4) shift: -0.69 0.13 ...... Frame ( 5) shift: -0.92 0.17 ...... Frame ( 6) shift: -1.01 0.21 ...... Frame ( 7) shift: -0.95 0.24 ...... Frame ( 8) shift: -0.89 0.27 ...... Frame ( 9) shift: -0.83 0.30 ...... Frame ( 10) shift: -0.75 0.34 ...... Frame ( 11) shift: -0.68 0.37 ...... Frame ( 12) shift: -0.62 0.42 ...... Frame ( 13) shift: -0.57 0.50 ...... Frame ( 14) shift: -0.51 0.58 ...... Frame ( 15) shift: -0.46 0.67 ...... Frame ( 16) shift: -0.42 0.77 ...... Frame ( 17) shift: -0.37 0.87 ...... Frame ( 18) shift: -0.31 0.95 ...... Frame ( 19) shift: -0.22 1.01 ...... Frame ( 20) shift: -0.13 1.07 ...... Frame ( 21) shift: -0.02 1.16 ...... Frame ( 22) shift: 0.13 1.30 ...... Frame ( 23) shift: 0.27 1.44 ...... Frame ( 24) shift: 0.37 1.54 ...... Frame ( 25) shift: 0.42 1.62 ...... Frame ( 26) shift: 0.47 1.69 ...... Frame ( 27) shift: 0.51 1.76 ...... Frame ( 28) shift: 0.54 1.83 ...... Frame ( 29) shift: 0.57 1.89 ...... Frame ( 30) shift: 0.58 1.93 ...... Frame ( 31) shift: 0.56 1.96 ...... Frame ( 32) shift: 0.54 1.99 ...... Frame ( 33) shift: 0.53 2.02 ...... Frame ( 34) shift: 0.52 2.04 ...... Frame ( 35) shift: 0.51 2.06 ...... Frame ( 36) shift: 0.54 2.07 ...... Frame ( 37) shift: 0.60 2.07 ...... Frame ( 38) shift: 0.65 2.07 ...... Frame ( 39) shift: 0.71 2.07 ...... Frame ( 40) shift: 0.77 2.07 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.697971 Iteration 2 Error: 0.108242 Iteration 3 Error: 0.027552 Align patch 2 23 left Iteration 1 Error: 0.547383 Iteration 2 Error: 0.061150 Iteration 3 Error: 0.011364 Align patch 3 22 left Iteration 1 Error: 0.675079 Iteration 2 Error: 0.065245 Iteration 3 Error: 0.010886 Align patch 4 21 left Iteration 1 Error: 0.721185 Iteration 2 Error: 0.094669 Iteration 3 Error: 0.016813 Align patch 5 20 left Iteration 1 Error: 1.298716 Iteration 2 Error: 0.174185 Iteration 3 Error: 0.046739 Align patch 6 19 left Iteration 1 Error: 0.796596 Iteration 2 Error: 0.139849 Iteration 3 Error: 0.037966 Align patch 7 18 left Iteration 1 Error: 0.532783 Iteration 2 Error: 0.062616 Iteration 3 Error: 0.014272 Align patch 8 17 left Iteration 1 Error: 0.649828 Iteration 2 Error: 0.076672 Iteration 3 Error: 0.023740 Align patch 9 16 left Iteration 1 Error: 0.592218 Iteration 2 Error: 0.089273 Iteration 3 Error: 0.018373 Align patch 10 15 left Iteration 1 Error: 0.970756 Iteration 2 Error: 0.099469 Iteration 3 Error: 0.027467 Align patch 11 14 left Iteration 1 Error: 0.583133 Iteration 2 Error: 0.100922 Iteration 3 Error: 0.019050 Align patch 12 13 left Iteration 1 Error: 0.628659 Iteration 2 Error: 0.096082 Iteration 3 Error: 0.025751 Align patch 13 12 left Iteration 1 Error: 0.596058 Iteration 2 Error: 0.133759 Iteration 3 Error: 0.030631 Align patch 14 11 left Iteration 1 Error: 0.772873 Iteration 2 Error: 0.106797 Iteration 3 Error: 0.021417 Align patch 15 10 left Iteration 1 Error: 0.557653 Iteration 2 Error: 0.075617 Iteration 3 Error: 0.013000 Align patch 16 9 left Iteration 1 Error: 0.747549 Iteration 2 Error: 0.141097 Iteration 3 Error: 0.027517 Align patch 17 8 left Iteration 1 Error: 0.510546 Iteration 2 Error: 0.071376 Iteration 3 Error: 0.013353 Align patch 18 7 left Iteration 1 Error: 0.522329 Iteration 2 Error: 0.092083 Iteration 3 Error: 0.021035 Align patch 19 6 left Iteration 1 Error: 0.483628 Iteration 2 Error: 0.046317 Align patch 20 5 left Iteration 1 Error: 0.561314 Iteration 2 Error: 0.131978 Iteration 3 Error: 0.028783 Align patch 21 4 left Iteration 1 Error: 1.074722 Iteration 2 Error: 0.213810 Iteration 3 Error: 0.047569 Align patch 22 3 left Iteration 1 Error: 0.510918 Iteration 2 Error: 0.081002 Iteration 3 Error: 0.019319 Align patch 23 2 left Iteration 1 Error: 0.609822 Iteration 2 Error: 0.051861 Iteration 3 Error: 0.011471 Align patch 24 1 left Iteration 1 Error: 0.532273 Iteration 2 Error: 0.084511 Iteration 3 Error: 0.015220 Align patch 25 0 left Iteration 1 Error: 0.490533 Iteration 2 Error: 0.090731 Iteration 3 Error: 0.012775 3D Fitting completed. Patch alignment time: 12.55(sec) Local motion has been corrected. Process thread exits. Computational time: 26.992331 sec Total time: 34.339062 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00003hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00003hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.576086s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00003hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.526224s ........................................ >>>>>>TIME<<<<<< FFT: 1.221813s Defocus_U Defocus_V Angle CCC 13277.36 12617.20 83.95 0.059619 Final Values Defocus_U Defocus_V Angle CCC 13297.66 12621.91 85.52 0.089069 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00004hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00004hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.303e-01 9.730e-02 CC threshold: 0.714 Mean Std: 36.83 6.70 Num Hot pixels: 216 Hot pixel threshold: 77.04 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.709894 Iteration 2 Error: 0.254712 Iteration 3 Error: 0.053105 Iteration 4 Error: 0.016382 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.15 0.09 ...... Frame ( 3) shift: 0.30 0.18 ...... Frame ( 4) shift: 0.45 0.27 ...... Frame ( 5) shift: 0.59 0.35 ...... Frame ( 6) shift: 0.72 0.48 ...... Frame ( 7) shift: 0.81 0.63 ...... Frame ( 8) shift: 0.91 0.79 ...... Frame ( 9) shift: 1.00 0.87 ...... Frame ( 10) shift: 1.08 0.89 ...... Frame ( 11) shift: 1.16 0.92 ...... Frame ( 12) shift: 1.26 0.94 ...... Frame ( 13) shift: 1.36 0.96 ...... Frame ( 14) shift: 1.47 0.98 ...... Frame ( 15) shift: 1.53 1.04 ...... Frame ( 16) shift: 1.57 1.12 ...... Frame ( 17) shift: 1.60 1.21 ...... Frame ( 18) shift: 1.59 1.28 ...... Frame ( 19) shift: 1.55 1.33 ...... Frame ( 20) shift: 1.52 1.38 ...... Frame ( 21) shift: 1.53 1.43 ...... Frame ( 22) shift: 1.60 1.47 ...... Frame ( 23) shift: 1.66 1.51 ...... Frame ( 24) shift: 1.73 1.51 ...... Frame ( 25) shift: 1.79 1.47 ...... Frame ( 26) shift: 1.85 1.43 ...... Frame ( 27) shift: 1.92 1.47 ...... Frame ( 28) shift: 1.98 1.58 ...... Frame ( 29) shift: 2.05 1.70 ...... Frame ( 30) shift: 2.11 1.76 ...... Frame ( 31) shift: 2.18 1.79 ...... Frame ( 32) shift: 2.24 1.81 ...... Frame ( 33) shift: 2.30 1.85 ...... Frame ( 34) shift: 2.35 1.90 ...... Frame ( 35) shift: 2.40 1.96 ...... Frame ( 36) shift: 2.46 1.99 ...... Frame ( 37) shift: 2.52 2.01 ...... Frame ( 38) shift: 2.59 2.03 ...... Frame ( 39) shift: 2.65 2.04 ...... Frame ( 40) shift: 2.71 2.06 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.927774 Iteration 2 Error: 0.324588 Iteration 3 Error: 0.073280 Iteration 4 Error: 0.035010 Align patch 2 23 left Iteration 1 Error: 0.793788 Iteration 2 Error: 0.231087 Iteration 3 Error: 0.049090 Align patch 3 22 left Iteration 1 Error: 0.627556 Iteration 2 Error: 0.111765 Iteration 3 Error: 0.031856 Align patch 4 21 left Iteration 1 Error: 0.711779 Iteration 2 Error: 0.082213 Iteration 3 Error: 0.014724 Align patch 5 20 left Iteration 1 Error: 1.137455 Iteration 2 Error: 0.206619 Iteration 3 Error: 0.037325 Align patch 6 19 left Iteration 1 Error: 0.908305 Iteration 2 Error: 0.226042 Iteration 3 Error: 0.049225 Align patch 7 18 left Iteration 1 Error: 0.711259 Iteration 2 Error: 0.093952 Iteration 3 Error: 0.023263 Align patch 8 17 left Iteration 1 Error: 0.567599 Iteration 2 Error: 0.085094 Iteration 3 Error: 0.028881 Align patch 9 16 left Iteration 1 Error: 1.078019 Iteration 2 Error: 0.117934 Iteration 3 Error: 0.026541 Align patch 10 15 left Iteration 1 Error: 1.103347 Iteration 2 Error: 0.298466 Iteration 3 Error: 0.098688 Iteration 4 Error: 0.040350 Align patch 11 14 left Iteration 1 Error: 1.081043 Iteration 2 Error: 0.241851 Iteration 3 Error: 0.064942 Iteration 4 Error: 0.030794 Align patch 12 13 left Iteration 1 Error: 0.582734 Iteration 2 Error: 0.124273 Iteration 3 Error: 0.030544 Align patch 13 12 left Iteration 1 Error: 0.737984 Iteration 2 Error: 0.125235 Iteration 3 Error: 0.019537 Align patch 14 11 left Iteration 1 Error: 0.598336 Iteration 2 Error: 0.113258 Iteration 3 Error: 0.020207 Align patch 15 10 left Iteration 1 Error: 0.728951 Iteration 2 Error: 0.162954 Iteration 3 Error: 0.038919 Align patch 16 9 left Iteration 1 Error: 1.045231 Iteration 2 Error: 0.230649 Iteration 3 Error: 0.094347 Iteration 4 Error: 0.038584 Align patch 17 8 left Iteration 1 Error: 0.794564 Iteration 2 Error: 0.200639 Iteration 3 Error: 0.054870 Iteration 4 Error: 0.020371 Align patch 18 7 left Iteration 1 Error: 0.489415 Iteration 2 Error: 0.085420 Iteration 3 Error: 0.015824 Align patch 19 6 left Iteration 1 Error: 0.795234 Iteration 2 Error: 0.162872 Iteration 3 Error: 0.052626 Iteration 4 Error: 0.021367 Align patch 20 5 left Iteration 1 Error: 0.572546 Iteration 2 Error: 0.126967 Iteration 3 Error: 0.026963 Align patch 21 4 left Iteration 1 Error: 0.805395 Iteration 2 Error: 0.136490 Iteration 3 Error: 0.034210 Align patch 22 3 left Iteration 1 Error: 0.497283 Iteration 2 Error: 0.194595 Iteration 3 Error: 0.058127 Iteration 4 Error: 0.022764 Align patch 23 2 left Iteration 1 Error: 0.718344 Iteration 2 Error: 0.097093 Iteration 3 Error: 0.019191 Align patch 24 1 left Iteration 1 Error: 0.911942 Iteration 2 Error: 0.150226 Iteration 3 Error: 0.031023 Align patch 25 0 left Iteration 1 Error: 0.906140 Iteration 2 Error: 0.145172 Iteration 3 Error: 0.035766 3D Fitting completed. Patch alignment time: 12.38(sec) Local motion has been corrected. Process thread exits. Computational time: 22.483852 sec Total time: 29.677139 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00004hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00004hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.669303s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00004hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.532262s ........................................ >>>>>>TIME<<<<<< FFT: 1.062943s Defocus_U Defocus_V Angle CCC 9499.96 10558.64 10.87 -0.061205 Final Values Defocus_U Defocus_V Angle CCC 9431.17 10514.95 10.89 -0.285793 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00004hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00004hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.276e-01 9.545e-02 CC threshold: 0.700 Mean Std: 39.13 7.22 Num Hot pixels: 184 Hot pixel threshold: 82.45 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.548910 Iteration 2 Error: 0.055205 Iteration 3 Error: 0.010813 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.05 0.08 ...... Frame ( 3) shift: 0.10 0.16 ...... Frame ( 4) shift: 0.15 0.25 ...... Frame ( 5) shift: 0.21 0.33 ...... Frame ( 6) shift: 0.21 0.40 ...... Frame ( 7) shift: 0.16 0.45 ...... Frame ( 8) shift: 0.12 0.51 ...... Frame ( 9) shift: 0.11 0.56 ...... Frame ( 10) shift: 0.15 0.59 ...... Frame ( 11) shift: 0.19 0.63 ...... Frame ( 12) shift: 0.19 0.66 ...... Frame ( 13) shift: 0.15 0.68 ...... Frame ( 14) shift: 0.12 0.70 ...... Frame ( 15) shift: 0.10 0.70 ...... Frame ( 16) shift: 0.12 0.68 ...... Frame ( 17) shift: 0.13 0.66 ...... Frame ( 18) shift: 0.18 0.64 ...... Frame ( 19) shift: 0.27 0.62 ...... Frame ( 20) shift: 0.36 0.59 ...... Frame ( 21) shift: 0.42 0.60 ...... Frame ( 22) shift: 0.45 0.65 ...... Frame ( 23) shift: 0.48 0.69 ...... Frame ( 24) shift: 0.49 0.71 ...... Frame ( 25) shift: 0.48 0.71 ...... Frame ( 26) shift: 0.47 0.70 ...... Frame ( 27) shift: 0.49 0.66 ...... Frame ( 28) shift: 0.52 0.58 ...... Frame ( 29) shift: 0.55 0.51 ...... Frame ( 30) shift: 0.58 0.47 ...... Frame ( 31) shift: 0.61 0.49 ...... Frame ( 32) shift: 0.64 0.50 ...... Frame ( 33) shift: 0.68 0.51 ...... Frame ( 34) shift: 0.74 0.49 ...... Frame ( 35) shift: 0.79 0.48 ...... Frame ( 36) shift: 0.84 0.48 ...... Frame ( 37) shift: 0.88 0.49 ...... Frame ( 38) shift: 0.92 0.49 ...... Frame ( 39) shift: 0.96 0.50 ...... Frame ( 40) shift: 1.00 0.51 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.660173 Iteration 2 Error: 0.082060 Iteration 3 Error: 0.025050 Align patch 2 23 left Iteration 1 Error: 0.567378 Iteration 2 Error: 0.081757 Iteration 3 Error: 0.012246 Align patch 3 22 left Iteration 1 Error: 0.451407 Iteration 2 Error: 0.048598 Align patch 4 21 left Iteration 1 Error: 0.706024 Iteration 2 Error: 0.072507 Iteration 3 Error: 0.008961 Align patch 5 20 left Iteration 1 Error: 0.741828 Iteration 2 Error: 0.124666 Iteration 3 Error: 0.020821 Align patch 6 19 left Iteration 1 Error: 0.687862 Iteration 2 Error: 0.067655 Iteration 3 Error: 0.012974 Align patch 7 18 left Iteration 1 Error: 0.557073 Iteration 2 Error: 0.086352 Iteration 3 Error: 0.013727 Align patch 8 17 left Iteration 1 Error: 0.508449 Iteration 2 Error: 0.029594 Align patch 9 16 left Iteration 1 Error: 0.516842 Iteration 2 Error: 0.083075 Iteration 3 Error: 0.014797 Align patch 10 15 left Iteration 1 Error: 0.682600 Iteration 2 Error: 0.067001 Iteration 3 Error: 0.014484 Align patch 11 14 left Iteration 1 Error: 0.817984 Iteration 2 Error: 0.154065 Iteration 3 Error: 0.027776 Align patch 12 13 left Iteration 1 Error: 0.523446 Iteration 2 Error: 0.043914 Align patch 13 12 left Iteration 1 Error: 0.432971 Iteration 2 Error: 0.034074 Align patch 14 11 left Iteration 1 Error: 0.581892 Iteration 2 Error: 0.111494 Iteration 3 Error: 0.016905 Align patch 15 10 left Iteration 1 Error: 0.568929 Iteration 2 Error: 0.076294 Iteration 3 Error: 0.020723 Align patch 16 9 left Iteration 1 Error: 0.599050 Iteration 2 Error: 0.077618 Iteration 3 Error: 0.016188 Align patch 17 8 left Iteration 1 Error: 0.599552 Iteration 2 Error: 0.099139 Iteration 3 Error: 0.019850 Align patch 18 7 left Iteration 1 Error: 0.340415 Iteration 2 Error: 0.047555 Align patch 19 6 left Iteration 1 Error: 0.556405 Iteration 2 Error: 0.060942 Iteration 3 Error: 0.017912 Align patch 20 5 left Iteration 1 Error: 0.626314 Iteration 2 Error: 0.111796 Iteration 3 Error: 0.020714 Align patch 21 4 left Iteration 1 Error: 0.786476 Iteration 2 Error: 0.078784 Iteration 3 Error: 0.014715 Align patch 22 3 left Iteration 1 Error: 0.609537 Iteration 2 Error: 0.074815 Iteration 3 Error: 0.017601 Align patch 23 2 left Iteration 1 Error: 0.537643 Iteration 2 Error: 0.060148 Iteration 3 Error: 0.012475 Align patch 24 1 left Iteration 1 Error: 0.612759 Iteration 2 Error: 0.064237 Iteration 3 Error: 0.013957 Align patch 25 0 left Iteration 1 Error: 0.640306 Iteration 2 Error: 0.062547 Iteration 3 Error: 0.011432 3D Fitting completed. Patch alignment time: 12.10(sec) Local motion has been corrected. Process thread exits. Computational time: 23.862928 sec Total time: 31.071251 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00004hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00004hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.602754s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00004hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.511917s ........................................ >>>>>>TIME<<<<<< FFT: 1.085380s Defocus_U Defocus_V Angle CCC 10910.17 10945.33 39.43 -0.039889 Final Values Defocus_U Defocus_V Angle CCC 11189.44 10825.55 88.65 -0.230602 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00004hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00004hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.268e-01 9.486e-02 CC threshold: 0.696 Mean Std: 38.36 7.15 Num Hot pixels: 182 Hot pixel threshold: 81.28 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.676415 Iteration 2 Error: 0.086277 Iteration 3 Error: 0.017757 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.05 0.05 ...... Frame ( 3) shift: 0.09 0.10 ...... Frame ( 4) shift: 0.14 0.14 ...... Frame ( 5) shift: 0.18 0.19 ...... Frame ( 6) shift: 0.23 0.25 ...... Frame ( 7) shift: 0.27 0.32 ...... Frame ( 8) shift: 0.31 0.39 ...... Frame ( 9) shift: 0.36 0.39 ...... Frame ( 10) shift: 0.43 0.34 ...... Frame ( 11) shift: 0.49 0.28 ...... Frame ( 12) shift: 0.54 0.26 ...... Frame ( 13) shift: 0.56 0.27 ...... Frame ( 14) shift: 0.59 0.29 ...... Frame ( 15) shift: 0.61 0.32 ...... Frame ( 16) shift: 0.64 0.38 ...... Frame ( 17) shift: 0.66 0.44 ...... Frame ( 18) shift: 0.73 0.48 ...... Frame ( 19) shift: 0.83 0.52 ...... Frame ( 20) shift: 0.93 0.55 ...... Frame ( 21) shift: 0.99 0.56 ...... Frame ( 22) shift: 1.00 0.53 ...... Frame ( 23) shift: 1.02 0.51 ...... Frame ( 24) shift: 1.04 0.52 ...... Frame ( 25) shift: 1.08 0.57 ...... Frame ( 26) shift: 1.12 0.61 ...... Frame ( 27) shift: 1.11 0.65 ...... Frame ( 28) shift: 1.04 0.68 ...... Frame ( 29) shift: 0.97 0.71 ...... Frame ( 30) shift: 0.95 0.71 ...... Frame ( 31) shift: 0.97 0.67 ...... Frame ( 32) shift: 0.99 0.63 ...... Frame ( 33) shift: 1.04 0.59 ...... Frame ( 34) shift: 1.10 0.55 ...... Frame ( 35) shift: 1.17 0.51 ...... Frame ( 36) shift: 1.19 0.48 ...... Frame ( 37) shift: 1.18 0.47 ...... Frame ( 38) shift: 1.16 0.46 ...... Frame ( 39) shift: 1.15 0.45 ...... Frame ( 40) shift: 1.14 0.44 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.914716 Iteration 2 Error: 0.154393 Iteration 3 Error: 0.052964 Iteration 4 Error: 0.017980 Align patch 2 23 left Iteration 1 Error: 0.699827 Iteration 2 Error: 0.085389 Iteration 3 Error: 0.012893 Align patch 3 22 left Iteration 1 Error: 0.626972 Iteration 2 Error: 0.089533 Iteration 3 Error: 0.023767 Align patch 4 21 left Iteration 1 Error: 0.651543 Iteration 2 Error: 0.060649 Iteration 3 Error: 0.010252 Align patch 5 20 left Iteration 1 Error: 0.847889 Iteration 2 Error: 0.111766 Iteration 3 Error: 0.018513 Align patch 6 19 left Iteration 1 Error: 0.615960 Iteration 2 Error: 0.136521 Iteration 3 Error: 0.023703 Align patch 7 18 left Iteration 1 Error: 0.732322 Iteration 2 Error: 0.122755 Iteration 3 Error: 0.025526 Align patch 8 17 left Iteration 1 Error: 0.836871 Iteration 2 Error: 0.124398 Iteration 3 Error: 0.018844 Align patch 9 16 left Iteration 1 Error: 0.508202 Iteration 2 Error: 0.066993 Iteration 3 Error: 0.018243 Align patch 10 15 left Iteration 1 Error: 0.566172 Iteration 2 Error: 0.074675 Iteration 3 Error: 0.023567 Align patch 11 14 left Iteration 1 Error: 0.524308 Iteration 2 Error: 0.075450 Iteration 3 Error: 0.014229 Align patch 12 13 left Iteration 1 Error: 0.515687 Iteration 2 Error: 0.097138 Iteration 3 Error: 0.016357 Align patch 13 12 left Iteration 1 Error: 0.783579 Iteration 2 Error: 0.083502 Iteration 3 Error: 0.023879 Align patch 14 11 left Iteration 1 Error: 0.785006 Iteration 2 Error: 0.076152 Iteration 3 Error: 0.018120 Align patch 15 10 left Iteration 1 Error: 0.724836 Iteration 2 Error: 0.091232 Iteration 3 Error: 0.012195 Align patch 16 9 left Iteration 1 Error: 0.729699 Iteration 2 Error: 0.098580 Iteration 3 Error: 0.021870 Align patch 17 8 left Iteration 1 Error: 0.515700 Iteration 2 Error: 0.080000 Iteration 3 Error: 0.016139 Align patch 18 7 left Iteration 1 Error: 0.648352 Iteration 2 Error: 0.062141 Iteration 3 Error: 0.013887 Align patch 19 6 left Iteration 1 Error: 0.820566 Iteration 2 Error: 0.112933 Iteration 3 Error: 0.025040 Align patch 20 5 left Iteration 1 Error: 0.734696 Iteration 2 Error: 0.160753 Iteration 3 Error: 0.042674 Align patch 21 4 left Iteration 1 Error: 0.579013 Iteration 2 Error: 0.083351 Iteration 3 Error: 0.022133 Align patch 22 3 left Iteration 1 Error: 0.544751 Iteration 2 Error: 0.078405 Iteration 3 Error: 0.016850 Align patch 23 2 left Iteration 1 Error: 0.687515 Iteration 2 Error: 0.083336 Iteration 3 Error: 0.024794 Align patch 24 1 left Iteration 1 Error: 0.911123 Iteration 2 Error: 0.139940 Iteration 3 Error: 0.025979 Align patch 25 0 left Iteration 1 Error: 0.744633 Iteration 2 Error: 0.140861 Iteration 3 Error: 0.032540 3D Fitting completed. Patch alignment time: 12.41(sec) Local motion has been corrected. Process thread exits. Computational time: 24.016537 sec Total time: 30.728571 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00004hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00004hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.685639s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00004hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.673361s ........................................ >>>>>>TIME<<<<<< FFT: 1.219688s Defocus_U Defocus_V Angle CCC 13297.82 13995.22 7.09 -0.049221 Final Values Defocus_U Defocus_V Angle CCC 13447.82 13929.68 8.35 -0.263600 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00004hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00004hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.328e-01 9.890e-02 CC threshold: 0.726 Mean Std: 38.87 6.85 Num Hot pixels: 212 Hot pixel threshold: 79.99 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.534738 Iteration 2 Error: 0.447435 Iteration 3 Error: 0.101494 Iteration 4 Error: 0.037663 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.20 -0.08 ...... Frame ( 3) shift: 0.39 -0.15 ...... Frame ( 4) shift: 0.59 -0.23 ...... Frame ( 5) shift: 0.79 -0.31 ...... Frame ( 6) shift: 0.96 -0.45 ...... Frame ( 7) shift: 1.11 -0.66 ...... Frame ( 8) shift: 1.26 -0.87 ...... Frame ( 9) shift: 1.36 -1.03 ...... Frame ( 10) shift: 1.42 -1.13 ...... Frame ( 11) shift: 1.47 -1.23 ...... Frame ( 12) shift: 1.55 -1.35 ...... Frame ( 13) shift: 1.65 -1.47 ...... Frame ( 14) shift: 1.74 -1.60 ...... Frame ( 15) shift: 1.85 -1.75 ...... Frame ( 16) shift: 1.97 -1.92 ...... Frame ( 17) shift: 2.08 -2.10 ...... Frame ( 18) shift: 2.20 -2.24 ...... Frame ( 19) shift: 2.33 -2.36 ...... Frame ( 20) shift: 2.46 -2.47 ...... Frame ( 21) shift: 2.58 -2.51 ...... Frame ( 22) shift: 2.72 -2.49 ...... Frame ( 23) shift: 2.85 -2.47 ...... Frame ( 24) shift: 2.94 -2.51 ...... Frame ( 25) shift: 3.00 -2.62 ...... Frame ( 26) shift: 3.05 -2.73 ...... Frame ( 27) shift: 3.15 -2.84 ...... Frame ( 28) shift: 3.28 -2.94 ...... Frame ( 29) shift: 3.42 -3.04 ...... Frame ( 30) shift: 3.55 -3.09 ...... Frame ( 31) shift: 3.69 -3.10 ...... Frame ( 32) shift: 3.82 -3.11 ...... Frame ( 33) shift: 3.93 -3.14 ...... Frame ( 34) shift: 4.02 -3.19 ...... Frame ( 35) shift: 4.11 -3.24 ...... Frame ( 36) shift: 4.16 -3.27 ...... Frame ( 37) shift: 4.16 -3.28 ...... Frame ( 38) shift: 4.16 -3.28 ...... Frame ( 39) shift: 4.15 -3.29 ...... Frame ( 40) shift: 4.15 -3.30 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.426774 Iteration 2 Error: 0.359058 Iteration 3 Error: 0.110008 Iteration 4 Error: 0.046057 Align patch 2 23 left Iteration 1 Error: 0.529657 Iteration 2 Error: 0.079480 Iteration 3 Error: 0.022522 Align patch 3 22 left Iteration 1 Error: 0.899208 Iteration 2 Error: 0.194301 Iteration 3 Error: 0.054254 Iteration 4 Error: 0.019938 Align patch 4 21 left Iteration 1 Error: 0.634292 Iteration 2 Error: 0.121818 Iteration 3 Error: 0.036895 Align patch 5 20 left Iteration 1 Error: 0.438465 Iteration 2 Error: 0.110548 Iteration 3 Error: 0.028683 Align patch 6 19 left Iteration 1 Error: 1.430717 Iteration 2 Error: 0.397099 Iteration 3 Error: 0.153980 Iteration 4 Error: 0.048765 Align patch 7 18 left Iteration 1 Error: 1.302328 Iteration 2 Error: 0.340774 Iteration 3 Error: 0.093147 Iteration 4 Error: 0.036338 Align patch 8 17 left Iteration 1 Error: 1.066235 Iteration 2 Error: 0.102606 Iteration 3 Error: 0.029465 Align patch 9 16 left Iteration 1 Error: 0.705017 Iteration 2 Error: 0.066034 Iteration 3 Error: 0.014614 Align patch 10 15 left Iteration 1 Error: 0.717604 Iteration 2 Error: 0.129823 Iteration 3 Error: 0.020464 Align patch 11 14 left Iteration 1 Error: 1.164152 Iteration 2 Error: 0.330364 Iteration 3 Error: 0.104916 Iteration 4 Error: 0.038581 Align patch 12 13 left Iteration 1 Error: 0.594507 Iteration 2 Error: 0.131886 Iteration 3 Error: 0.037246 Align patch 13 12 left Iteration 1 Error: 0.636294 Iteration 2 Error: 0.080685 Iteration 3 Error: 0.018369 Align patch 14 11 left Iteration 1 Error: 0.761120 Iteration 2 Error: 0.103851 Iteration 3 Error: 0.019999 Align patch 15 10 left Iteration 1 Error: 0.671679 Iteration 2 Error: 0.109898 Iteration 3 Error: 0.030332 Align patch 16 9 left Iteration 1 Error: 0.734567 Iteration 2 Error: 0.082035 Iteration 3 Error: 0.019667 Align patch 17 8 left Iteration 1 Error: 0.420532 Iteration 2 Error: 0.093720 Iteration 3 Error: 0.010627 Align patch 18 7 left Iteration 1 Error: 0.756046 Iteration 2 Error: 0.102844 Iteration 3 Error: 0.024151 Align patch 19 6 left Iteration 1 Error: 0.792112 Iteration 2 Error: 0.130590 Iteration 3 Error: 0.031674 Align patch 20 5 left Iteration 1 Error: 1.347956 Iteration 2 Error: 0.200018 Iteration 3 Error: 0.042612 Align patch 21 4 left Iteration 1 Error: 0.744292 Iteration 2 Error: 0.120944 Iteration 3 Error: 0.037005 Align patch 22 3 left Iteration 1 Error: 0.787345 Iteration 2 Error: 0.107955 Iteration 3 Error: 0.027801 Align patch 23 2 left Iteration 1 Error: 1.170156 Iteration 2 Error: 0.126272 Iteration 3 Error: 0.025444 Align patch 24 1 left Iteration 1 Error: 0.985401 Iteration 2 Error: 0.145910 Iteration 3 Error: 0.034646 Align patch 25 0 left Iteration 1 Error: 1.712994 Iteration 2 Error: 0.357050 Iteration 3 Error: 0.056997 Iteration 4 Error: 0.011540 3D Fitting completed. Patch alignment time: 11.80(sec) Local motion has been corrected. Process thread exits. Computational time: 23.692495 sec Total time: 31.834661 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00004hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00004hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.563567s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00004hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.889732s ........................................ >>>>>>TIME<<<<<< FFT: 1.025289s Defocus_U Defocus_V Angle CCC 12460.94 11796.88 81.13 -0.015117 Final Values Defocus_U Defocus_V Angle CCC 12471.88 11820.32 81.44 -0.176134 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00005hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00005hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.994e-02 CC threshold: 0.734 Mean Std: 39.87 6.83 Num Hot pixels: 214 Hot pixel threshold: 80.85 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 6.166075 Iteration 2 Error: 0.736769 Iteration 3 Error: 0.329563 Iteration 4 Error: 0.129495 Iteration 5 Error: 0.058592 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.22 -0.74 ...... Frame ( 3) shift: 0.45 -1.48 ...... Frame ( 4) shift: 0.67 -2.21 ...... Frame ( 5) shift: 0.89 -2.95 ...... Frame ( 6) shift: 1.14 -3.65 ...... Frame ( 7) shift: 1.41 -4.31 ...... Frame ( 8) shift: 1.67 -4.97 ...... Frame ( 9) shift: 1.85 -5.54 ...... Frame ( 10) shift: 1.95 -6.01 ...... Frame ( 11) shift: 2.04 -6.48 ...... Frame ( 12) shift: 2.16 -6.86 ...... Frame ( 13) shift: 2.30 -7.15 ...... Frame ( 14) shift: 2.45 -7.45 ...... Frame ( 15) shift: 2.58 -7.66 ...... Frame ( 16) shift: 2.69 -7.79 ...... Frame ( 17) shift: 2.81 -7.92 ...... Frame ( 18) shift: 2.91 -8.07 ...... Frame ( 19) shift: 2.99 -8.25 ...... Frame ( 20) shift: 3.07 -8.43 ...... Frame ( 21) shift: 3.12 -8.61 ...... Frame ( 22) shift: 3.14 -8.78 ...... Frame ( 23) shift: 3.16 -8.95 ...... Frame ( 24) shift: 3.17 -9.08 ...... Frame ( 25) shift: 3.16 -9.17 ...... Frame ( 26) shift: 3.15 -9.25 ...... Frame ( 27) shift: 3.19 -9.33 ...... Frame ( 28) shift: 3.29 -9.39 ...... Frame ( 29) shift: 3.39 -9.45 ...... Frame ( 30) shift: 3.45 -9.49 ...... Frame ( 31) shift: 3.48 -9.51 ...... Frame ( 32) shift: 3.50 -9.53 ...... Frame ( 33) shift: 3.57 -9.54 ...... Frame ( 34) shift: 3.67 -9.54 ...... Frame ( 35) shift: 3.76 -9.53 ...... Frame ( 36) shift: 3.81 -9.55 ...... Frame ( 37) shift: 3.80 -9.59 ...... Frame ( 38) shift: 3.79 -9.63 ...... Frame ( 39) shift: 3.78 -9.67 ...... Frame ( 40) shift: 3.77 -9.72 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.135449 Iteration 2 Error: 0.192967 Iteration 3 Error: 0.048940 Align patch 2 23 left Iteration 1 Error: 0.813432 Iteration 2 Error: 0.161658 Iteration 3 Error: 0.040189 Align patch 3 22 left Iteration 1 Error: 1.780909 Iteration 2 Error: 0.257539 Iteration 3 Error: 0.081737 Iteration 4 Error: 0.036108 Align patch 4 21 left Iteration 1 Error: 2.961217 Iteration 2 Error: 0.391932 Iteration 3 Error: 0.088010 Iteration 4 Error: 0.021817 Align patch 5 20 left Iteration 1 Error: 5.374196 Iteration 2 Error: 0.433641 Iteration 3 Error: 0.102954 Iteration 4 Error: 0.020029 Align patch 6 19 left Iteration 1 Error: 2.650419 Iteration 2 Error: 0.380608 Iteration 3 Error: 0.120889 Iteration 4 Error: 0.046824 Align patch 7 18 left Iteration 1 Error: 1.361223 Iteration 2 Error: 0.260833 Iteration 3 Error: 0.065776 Iteration 4 Error: 0.025833 Align patch 8 17 left Iteration 1 Error: 0.586632 Iteration 2 Error: 0.119094 Iteration 3 Error: 0.023313 Align patch 9 16 left Iteration 1 Error: 2.324275 Iteration 2 Error: 0.323907 Iteration 3 Error: 0.079121 Iteration 4 Error: 0.014793 Align patch 10 15 left Iteration 1 Error: 3.630701 Iteration 2 Error: 0.446794 Iteration 3 Error: 0.092671 Iteration 4 Error: 0.024484 Align patch 11 14 left Iteration 1 Error: 3.839115 Iteration 2 Error: 0.662250 Iteration 3 Error: 0.158008 Iteration 4 Error: 0.073479 Iteration 5 Error: 0.022317 Align patch 12 13 left Iteration 1 Error: 3.055125 Iteration 2 Error: 0.520797 Iteration 3 Error: 0.152766 Iteration 4 Error: 0.052555 Iteration 5 Error: 0.016433 Align patch 13 12 left Iteration 1 Error: 1.583276 Iteration 2 Error: 0.291468 Iteration 3 Error: 0.060707 Iteration 4 Error: 0.020973 Align patch 14 11 left Iteration 1 Error: 1.233611 Iteration 2 Error: 0.193812 Iteration 3 Error: 0.047046 Align patch 15 10 left Iteration 1 Error: 2.542446 Iteration 2 Error: 0.613516 Iteration 3 Error: 0.216271 Iteration 4 Error: 0.061384 Iteration 5 Error: 0.019950 Align patch 16 9 left Iteration 1 Error: 3.979676 Iteration 2 Error: 0.689267 Iteration 3 Error: 0.269279 Iteration 4 Error: 0.124310 Iteration 5 Error: 0.059350 Align patch 16 9 left Iteration 1 Error: 3.927348 Iteration 2 Error: 0.392579 Iteration 3 Error: 0.052366 Iteration 4 Error: 0.017365 Align patch 17 8 left Iteration 1 Error: 3.673515 Iteration 2 Error: 0.598774 Iteration 3 Error: 0.150404 Iteration 4 Error: 0.045881 Align patch 18 7 left Iteration 1 Error: 2.283826 Iteration 2 Error: 0.375814 Iteration 3 Error: 0.109965 Iteration 4 Error: 0.033983 Align patch 19 6 left Iteration 1 Error: 0.740857 Iteration 2 Error: 0.093444 Iteration 3 Error: 0.016734 Align patch 20 5 left Iteration 1 Error: 2.696122 Iteration 2 Error: 0.456643 Iteration 3 Error: 0.102111 Iteration 4 Error: 0.035904 Align patch 21 4 left Iteration 1 Error: 3.855631 Iteration 2 Error: 0.565179 Iteration 3 Error: 0.205753 Iteration 4 Error: 0.080183 Iteration 5 Error: 0.030692 Align patch 22 3 left Iteration 1 Error: 3.006479 Iteration 2 Error: 0.437046 Iteration 3 Error: 0.090352 Iteration 4 Error: 0.032083 Align patch 23 2 left Iteration 1 Error: 1.900400 Iteration 2 Error: 0.345673 Iteration 3 Error: 0.120662 Iteration 4 Error: 0.047660 Align patch 24 1 left Iteration 1 Error: 1.113546 Iteration 2 Error: 0.164298 Iteration 3 Error: 0.028503 Align patch 25 0 left Iteration 1 Error: 2.863396 Iteration 2 Error: 0.381780 Iteration 3 Error: 0.106789 Iteration 4 Error: 0.036475 3D Fitting completed. Patch alignment time: 12.99(sec) Local motion has been corrected. Process thread exits. Computational time: 24.064499 sec Total time: 29.814562 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00005hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00005hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.735311s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00005hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.949222s ........................................ >>>>>>TIME<<<<<< FFT: 0.923321s Defocus_U Defocus_V Angle CCC 8632.81 9421.88 12.17 0.037135 Final Values Defocus_U Defocus_V Angle CCC 8637.50 9439.07 12.48 0.037830 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00005hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00005hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.351e-01 1.004e-01 CC threshold: 0.738 Mean Std: 40.34 6.91 Num Hot pixels: 236 Hot pixel threshold: 81.77 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.916645 Iteration 2 Error: 0.124760 Iteration 3 Error: 0.021705 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.24 -0.03 ...... Frame ( 3) shift: -0.47 -0.05 ...... Frame ( 4) shift: -0.71 -0.08 ...... Frame ( 5) shift: -0.95 -0.10 ...... Frame ( 6) shift: -1.09 -0.09 ...... Frame ( 7) shift: -1.13 -0.04 ...... Frame ( 8) shift: -1.17 0.01 ...... Frame ( 9) shift: -1.20 0.06 ...... Frame ( 10) shift: -1.22 0.11 ...... Frame ( 11) shift: -1.24 0.16 ...... Frame ( 12) shift: -1.24 0.22 ...... Frame ( 13) shift: -1.23 0.29 ...... Frame ( 14) shift: -1.22 0.36 ...... Frame ( 15) shift: -1.21 0.41 ...... Frame ( 16) shift: -1.21 0.45 ...... Frame ( 17) shift: -1.21 0.49 ...... Frame ( 18) shift: -1.19 0.53 ...... Frame ( 19) shift: -1.15 0.58 ...... Frame ( 20) shift: -1.12 0.63 ...... Frame ( 21) shift: -1.09 0.69 ...... Frame ( 22) shift: -1.06 0.75 ...... Frame ( 23) shift: -1.04 0.82 ...... Frame ( 24) shift: -1.02 0.88 ...... Frame ( 25) shift: -1.01 0.94 ...... Frame ( 26) shift: -0.99 0.99 ...... Frame ( 27) shift: -0.99 1.03 ...... Frame ( 28) shift: -0.99 1.04 ...... Frame ( 29) shift: -1.00 1.05 ...... Frame ( 30) shift: -0.99 1.07 ...... Frame ( 31) shift: -0.96 1.07 ...... Frame ( 32) shift: -0.94 1.08 ...... Frame ( 33) shift: -0.92 1.13 ...... Frame ( 34) shift: -0.92 1.23 ...... Frame ( 35) shift: -0.92 1.33 ...... Frame ( 36) shift: -0.90 1.39 ...... Frame ( 37) shift: -0.86 1.42 ...... Frame ( 38) shift: -0.83 1.45 ...... Frame ( 39) shift: -0.79 1.48 ...... Frame ( 40) shift: -0.76 1.51 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.607800 Iteration 2 Error: 0.230819 Iteration 3 Error: 0.064047 Iteration 4 Error: 0.019370 Align patch 2 23 left Iteration 1 Error: 0.889502 Iteration 2 Error: 0.116009 Iteration 3 Error: 0.029067 Align patch 3 22 left Iteration 1 Error: 0.456178 Iteration 2 Error: 0.077226 Iteration 3 Error: 0.015588 Align patch 4 21 left Iteration 1 Error: 0.574093 Iteration 2 Error: 0.051169 Iteration 3 Error: 0.008666 Align patch 5 20 left Iteration 1 Error: 0.544396 Iteration 2 Error: 0.070932 Iteration 3 Error: 0.009481 Align patch 6 19 left Iteration 1 Error: 1.626043 Iteration 2 Error: 0.205701 Iteration 3 Error: 0.071737 Iteration 4 Error: 0.018811 Align patch 7 18 left Iteration 1 Error: 0.614903 Iteration 2 Error: 0.152651 Iteration 3 Error: 0.042548 Align patch 8 17 left Iteration 1 Error: 0.517519 Iteration 2 Error: 0.089673 Iteration 3 Error: 0.022985 Align patch 9 16 left Iteration 1 Error: 0.508831 Iteration 2 Error: 0.071495 Iteration 3 Error: 0.017927 Align patch 10 15 left Iteration 1 Error: 0.624412 Iteration 2 Error: 0.129958 Iteration 3 Error: 0.017151 Align patch 11 14 left Iteration 1 Error: 0.764140 Iteration 2 Error: 0.143507 Iteration 3 Error: 0.039254 Align patch 12 13 left Iteration 1 Error: 0.630141 Iteration 2 Error: 0.099884 Iteration 3 Error: 0.033655 Align patch 13 12 left Iteration 1 Error: 0.437478 Iteration 2 Error: 0.081411 Iteration 3 Error: 0.011440 Align patch 14 11 left Iteration 1 Error: 0.499551 Iteration 2 Error: 0.087977 Iteration 3 Error: 0.018810 Align patch 15 10 left Iteration 1 Error: 0.715232 Iteration 2 Error: 0.114292 Iteration 3 Error: 0.012567 Align patch 16 9 left Iteration 1 Error: 0.741588 Iteration 2 Error: 0.148673 Iteration 3 Error: 0.032572 Align patch 17 8 left Iteration 1 Error: 0.425759 Iteration 2 Error: 0.046560 Align patch 18 7 left Iteration 1 Error: 0.599236 Iteration 2 Error: 0.100139 Iteration 3 Error: 0.018971 Align patch 19 6 left Iteration 1 Error: 0.533412 Iteration 2 Error: 0.084644 Iteration 3 Error: 0.018315 Align patch 20 5 left Iteration 1 Error: 0.623776 Iteration 2 Error: 0.077472 Iteration 3 Error: 0.023377 Align patch 21 4 left Iteration 1 Error: 0.956393 Iteration 2 Error: 0.117829 Iteration 3 Error: 0.027601 Align patch 22 3 left Iteration 1 Error: 0.568477 Iteration 2 Error: 0.075006 Iteration 3 Error: 0.011815 Align patch 23 2 left Iteration 1 Error: 0.727458 Iteration 2 Error: 0.070508 Iteration 3 Error: 0.014896 Align patch 24 1 left Iteration 1 Error: 0.502624 Iteration 2 Error: 0.090457 Iteration 3 Error: 0.015386 Align patch 25 0 left Iteration 1 Error: 0.504232 Iteration 2 Error: 0.066410 Iteration 3 Error: 0.014210 3D Fitting completed. Patch alignment time: 12.53(sec) Local motion has been corrected. Process thread exits. Computational time: 23.412079 sec Total time: 31.346987 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00005hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00005hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.600634s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00005hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.727157s ........................................ >>>>>>TIME<<<<<< FFT: 0.998015s Defocus_U Defocus_V Angle CCC 9455.10 9939.48 0.10 0.053682 Final Values Defocus_U Defocus_V Angle CCC 9466.04 9941.04 0.42 0.096248 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00005hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00005hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.350e-01 1.004e-01 CC threshold: 0.738 Mean Std: 40.28 6.86 Num Hot pixels: 223 Hot pixel threshold: 81.42 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.046236 Iteration 2 Error: 0.146797 Iteration 3 Error: 0.016781 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.36 -0.18 ...... Frame ( 3) shift: -0.72 -0.37 ...... Frame ( 4) shift: -1.08 -0.55 ...... Frame ( 5) shift: -1.44 -0.74 ...... Frame ( 6) shift: -1.65 -0.82 ...... Frame ( 7) shift: -1.72 -0.81 ...... Frame ( 8) shift: -1.78 -0.81 ...... Frame ( 9) shift: -1.79 -0.79 ...... Frame ( 10) shift: -1.73 -0.77 ...... Frame ( 11) shift: -1.66 -0.74 ...... Frame ( 12) shift: -1.66 -0.70 ...... Frame ( 13) shift: -1.71 -0.65 ...... Frame ( 14) shift: -1.76 -0.59 ...... Frame ( 15) shift: -1.75 -0.55 ...... Frame ( 16) shift: -1.67 -0.52 ...... Frame ( 17) shift: -1.59 -0.49 ...... Frame ( 18) shift: -1.55 -0.46 ...... Frame ( 19) shift: -1.55 -0.44 ...... Frame ( 20) shift: -1.55 -0.41 ...... Frame ( 21) shift: -1.54 -0.36 ...... Frame ( 22) shift: -1.51 -0.30 ...... Frame ( 23) shift: -1.48 -0.24 ...... Frame ( 24) shift: -1.48 -0.17 ...... Frame ( 25) shift: -1.51 -0.11 ...... Frame ( 26) shift: -1.55 -0.04 ...... Frame ( 27) shift: -1.55 0.00 ...... Frame ( 28) shift: -1.51 0.03 ...... Frame ( 29) shift: -1.48 0.05 ...... Frame ( 30) shift: -1.45 0.09 ...... Frame ( 31) shift: -1.44 0.14 ...... Frame ( 32) shift: -1.43 0.18 ...... Frame ( 33) shift: -1.39 0.20 ...... Frame ( 34) shift: -1.33 0.19 ...... Frame ( 35) shift: -1.27 0.18 ...... Frame ( 36) shift: -1.25 0.19 ...... Frame ( 37) shift: -1.26 0.22 ...... Frame ( 38) shift: -1.28 0.26 ...... Frame ( 39) shift: -1.30 0.30 ...... Frame ( 40) shift: -1.31 0.33 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.868111 Iteration 2 Error: 0.216665 Iteration 3 Error: 0.053062 Iteration 4 Error: 0.021104 Align patch 2 23 left Iteration 1 Error: 1.115999 Iteration 2 Error: 0.200959 Iteration 3 Error: 0.068045 Iteration 4 Error: 0.017194 Align patch 3 22 left Iteration 1 Error: 0.891198 Iteration 2 Error: 0.130688 Iteration 3 Error: 0.028897 Align patch 4 21 left Iteration 1 Error: 0.851551 Iteration 2 Error: 0.068790 Iteration 3 Error: 0.017652 Align patch 5 20 left Iteration 1 Error: 0.749186 Iteration 2 Error: 0.086024 Iteration 3 Error: 0.022183 Align patch 6 19 left Iteration 1 Error: 1.304448 Iteration 2 Error: 0.208349 Iteration 3 Error: 0.050740 Iteration 4 Error: 0.014935 Align patch 7 18 left Iteration 1 Error: 0.650487 Iteration 2 Error: 0.161044 Iteration 3 Error: 0.048167 Align patch 8 17 left Iteration 1 Error: 1.024211 Iteration 2 Error: 0.110251 Iteration 3 Error: 0.021019 Align patch 9 16 left Iteration 1 Error: 0.775871 Iteration 2 Error: 0.049872 Align patch 10 15 left Iteration 1 Error: 0.805061 Iteration 2 Error: 0.081727 Iteration 3 Error: 0.019563 Align patch 11 14 left Iteration 1 Error: 0.860265 Iteration 2 Error: 0.083234 Iteration 3 Error: 0.020154 Align patch 12 13 left Iteration 1 Error: 0.588663 Iteration 2 Error: 0.095416 Iteration 3 Error: 0.021608 Align patch 13 12 left Iteration 1 Error: 0.561430 Iteration 2 Error: 0.062492 Iteration 3 Error: 0.015967 Align patch 14 11 left Iteration 1 Error: 0.402732 Iteration 2 Error: 0.071382 Iteration 3 Error: 0.015432 Align patch 15 10 left Iteration 1 Error: 0.536725 Iteration 2 Error: 0.087022 Iteration 3 Error: 0.015196 Align patch 16 9 left Iteration 1 Error: 0.538069 Iteration 2 Error: 0.078275 Iteration 3 Error: 0.013814 Align patch 17 8 left Iteration 1 Error: 0.674477 Iteration 2 Error: 0.085115 Iteration 3 Error: 0.016858 Align patch 18 7 left Iteration 1 Error: 0.567945 Iteration 2 Error: 0.087736 Iteration 3 Error: 0.022753 Align patch 19 6 left Iteration 1 Error: 0.478769 Iteration 2 Error: 0.087249 Iteration 3 Error: 0.025537 Align patch 20 5 left Iteration 1 Error: 0.605877 Iteration 2 Error: 0.116399 Iteration 3 Error: 0.030506 Align patch 21 4 left Iteration 1 Error: 0.964836 Iteration 2 Error: 0.118094 Iteration 3 Error: 0.021591 Align patch 22 3 left Iteration 1 Error: 1.135346 Iteration 2 Error: 0.124673 Iteration 3 Error: 0.019621 Align patch 23 2 left Iteration 1 Error: 0.877955 Iteration 2 Error: 0.100633 Iteration 3 Error: 0.020116 Align patch 24 1 left Iteration 1 Error: 0.861147 Iteration 2 Error: 0.072052 Iteration 3 Error: 0.014801 Align patch 25 0 left Iteration 1 Error: 0.635490 Iteration 2 Error: 0.071645 Iteration 3 Error: 0.013905 3D Fitting completed. Patch alignment time: 11.85(sec) Local motion has been corrected. Process thread exits. Computational time: 23.384914 sec Total time: 29.816523 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00005hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00005hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.654797s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00005hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.730573s ........................................ >>>>>>TIME<<<<<< FFT: 1.290889s Defocus_U Defocus_V Angle CCC 12744.14 13615.24 3.83 0.063909 Final Values Defocus_U Defocus_V Angle CCC 12758.21 13588.69 3.83 0.099343 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00005hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00005hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.350e-01 1.004e-01 CC threshold: 0.738 Mean Std: 41.26 7.06 Num Hot pixels: 204 Hot pixel threshold: 83.60 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.279736 Iteration 2 Error: 0.140971 Iteration 3 Error: 0.016021 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.50 -0.15 ...... Frame ( 3) shift: -0.99 -0.30 ...... Frame ( 4) shift: -1.49 -0.45 ...... Frame ( 5) shift: -1.98 -0.60 ...... Frame ( 6) shift: -2.23 -0.65 ...... Frame ( 7) shift: -2.22 -0.60 ...... Frame ( 8) shift: -2.22 -0.56 ...... Frame ( 9) shift: -2.18 -0.51 ...... Frame ( 10) shift: -2.10 -0.48 ...... Frame ( 11) shift: -2.02 -0.45 ...... Frame ( 12) shift: -2.00 -0.39 ...... Frame ( 13) shift: -2.03 -0.32 ...... Frame ( 14) shift: -2.05 -0.24 ...... Frame ( 15) shift: -2.08 -0.18 ...... Frame ( 16) shift: -2.09 -0.13 ...... Frame ( 17) shift: -2.11 -0.08 ...... Frame ( 18) shift: -2.11 -0.04 ...... Frame ( 19) shift: -2.10 0.01 ...... Frame ( 20) shift: -2.10 0.05 ...... Frame ( 21) shift: -2.07 0.09 ...... Frame ( 22) shift: -2.01 0.12 ...... Frame ( 23) shift: -1.95 0.15 ...... Frame ( 24) shift: -1.90 0.17 ...... Frame ( 25) shift: -1.86 0.16 ...... Frame ( 26) shift: -1.82 0.16 ...... Frame ( 27) shift: -1.79 0.17 ...... Frame ( 28) shift: -1.77 0.18 ...... Frame ( 29) shift: -1.75 0.20 ...... Frame ( 30) shift: -1.76 0.23 ...... Frame ( 31) shift: -1.79 0.27 ...... Frame ( 32) shift: -1.81 0.31 ...... Frame ( 33) shift: -1.83 0.33 ...... Frame ( 34) shift: -1.83 0.32 ...... Frame ( 35) shift: -1.83 0.32 ...... Frame ( 36) shift: -1.85 0.34 ...... Frame ( 37) shift: -1.88 0.40 ...... Frame ( 38) shift: -1.91 0.45 ...... Frame ( 39) shift: -1.94 0.51 ...... Frame ( 40) shift: -1.97 0.56 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.099884 Iteration 2 Error: 0.302091 Iteration 3 Error: 0.050776 Iteration 4 Error: 0.013270 Align patch 2 23 left Iteration 1 Error: 1.376170 Iteration 2 Error: 0.180741 Iteration 3 Error: 0.032834 Align patch 3 22 left Iteration 1 Error: 0.663612 Iteration 2 Error: 0.126299 Iteration 3 Error: 0.026836 Align patch 4 21 left Iteration 1 Error: 0.410145 Iteration 2 Error: 0.065429 Iteration 3 Error: 0.008761 Align patch 5 20 left Iteration 1 Error: 0.646812 Iteration 2 Error: 0.063423 Iteration 3 Error: 0.012158 Align patch 6 19 left Iteration 1 Error: 1.950844 Iteration 2 Error: 0.213921 Iteration 3 Error: 0.051746 Iteration 4 Error: 0.018954 Align patch 7 18 left Iteration 1 Error: 1.542704 Iteration 2 Error: 0.172674 Iteration 3 Error: 0.030052 Align patch 8 17 left Iteration 1 Error: 0.622030 Iteration 2 Error: 0.104354 Iteration 3 Error: 0.016361 Align patch 9 16 left Iteration 1 Error: 0.588368 Iteration 2 Error: 0.098990 Iteration 3 Error: 0.021191 Align patch 10 15 left Iteration 1 Error: 0.563730 Iteration 2 Error: 0.063565 Iteration 3 Error: 0.012671 Align patch 11 14 left Iteration 1 Error: 1.012361 Iteration 2 Error: 0.126686 Iteration 3 Error: 0.030602 Align patch 12 13 left Iteration 1 Error: 0.855377 Iteration 2 Error: 0.117893 Iteration 3 Error: 0.034275 Align patch 13 12 left Iteration 1 Error: 0.731864 Iteration 2 Error: 0.097563 Iteration 3 Error: 0.015688 Align patch 14 11 left Iteration 1 Error: 0.582789 Iteration 2 Error: 0.095782 Iteration 3 Error: 0.025161 Align patch 15 10 left Iteration 1 Error: 0.475823 Iteration 2 Error: 0.080221 Iteration 3 Error: 0.012223 Align patch 16 9 left Iteration 1 Error: 1.258597 Iteration 2 Error: 0.145908 Iteration 3 Error: 0.031863 Align patch 17 8 left Iteration 1 Error: 0.908394 Iteration 2 Error: 0.132952 Iteration 3 Error: 0.016194 Align patch 18 7 left Iteration 1 Error: 0.646932 Iteration 2 Error: 0.133881 Iteration 3 Error: 0.028644 Align patch 19 6 left Iteration 1 Error: 0.867161 Iteration 2 Error: 0.117347 Iteration 3 Error: 0.017356 Align patch 20 5 left Iteration 1 Error: 0.791712 Iteration 2 Error: 0.054149 Iteration 3 Error: 0.007327 Align patch 21 4 left Iteration 1 Error: 1.025985 Iteration 2 Error: 0.077576 Iteration 3 Error: 0.018768 Align patch 22 3 left Iteration 1 Error: 0.646050 Iteration 2 Error: 0.070174 Iteration 3 Error: 0.012888 Align patch 23 2 left Iteration 1 Error: 0.987718 Iteration 2 Error: 0.099290 Iteration 3 Error: 0.014938 Align patch 24 1 left Iteration 1 Error: 0.847104 Iteration 2 Error: 0.096922 Iteration 3 Error: 0.022884 Align patch 25 0 left Iteration 1 Error: 0.677611 Iteration 2 Error: 0.062418 Iteration 3 Error: 0.013067 3D Fitting completed. Patch alignment time: 12.00(sec) Local motion has been corrected. Process thread exits. Computational time: 24.016697 sec Total time: 30.708067 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00005hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00005hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.462954s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00005hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.096873s ........................................ >>>>>>TIME<<<<<< FFT: 0.939344s Defocus_U Defocus_V Angle CCC 12798.83 12150.39 80.44 0.069166 Final Values Defocus_U Defocus_V Angle CCC 12803.48 12164.49 80.13 0.113519 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00006hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00006hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.313e-01 9.786e-02 CC threshold: 0.718 Mean Std: 36.95 6.68 Num Hot pixels: 185 Hot pixel threshold: 77.00 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.493477 Iteration 2 Error: 0.350989 Iteration 3 Error: 0.099930 Iteration 4 Error: 0.039158 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.20 0.18 ...... Frame ( 3) shift: 0.39 0.36 ...... Frame ( 4) shift: 0.59 0.55 ...... Frame ( 5) shift: 0.78 0.73 ...... Frame ( 6) shift: 0.96 0.88 ...... Frame ( 7) shift: 1.12 1.00 ...... Frame ( 8) shift: 1.28 1.12 ...... Frame ( 9) shift: 1.44 1.23 ...... Frame ( 10) shift: 1.59 1.30 ...... Frame ( 11) shift: 1.75 1.38 ...... Frame ( 12) shift: 1.87 1.48 ...... Frame ( 13) shift: 1.94 1.59 ...... Frame ( 14) shift: 2.01 1.70 ...... Frame ( 15) shift: 2.07 1.80 ...... Frame ( 16) shift: 2.13 1.90 ...... Frame ( 17) shift: 2.19 1.99 ...... Frame ( 18) shift: 2.29 2.06 ...... Frame ( 19) shift: 2.42 2.11 ...... Frame ( 20) shift: 2.56 2.15 ...... Frame ( 21) shift: 2.70 2.16 ...... Frame ( 22) shift: 2.84 2.13 ...... Frame ( 23) shift: 2.99 2.09 ...... Frame ( 24) shift: 3.09 2.12 ...... Frame ( 25) shift: 3.14 2.21 ...... Frame ( 26) shift: 3.19 2.29 ...... Frame ( 27) shift: 3.24 2.33 ...... Frame ( 28) shift: 3.28 2.31 ...... Frame ( 29) shift: 3.32 2.29 ...... Frame ( 30) shift: 3.41 2.31 ...... Frame ( 31) shift: 3.53 2.38 ...... Frame ( 32) shift: 3.65 2.44 ...... Frame ( 33) shift: 3.76 2.51 ...... Frame ( 34) shift: 3.85 2.61 ...... Frame ( 35) shift: 3.95 2.70 ...... Frame ( 36) shift: 4.08 2.74 ...... Frame ( 37) shift: 4.25 2.73 ...... Frame ( 38) shift: 4.41 2.72 ...... Frame ( 39) shift: 4.58 2.71 ...... Frame ( 40) shift: 4.75 2.71 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.032592 Iteration 2 Error: 0.233752 Iteration 3 Error: 0.056856 Iteration 4 Error: 0.025300 Align patch 2 23 left Iteration 1 Error: 0.727886 Iteration 2 Error: 0.170647 Iteration 3 Error: 0.043767 Align patch 3 22 left Iteration 1 Error: 0.506311 Iteration 2 Error: 0.068191 Iteration 3 Error: 0.015366 Align patch 4 21 left Iteration 1 Error: 0.756546 Iteration 2 Error: 0.178567 Iteration 3 Error: 0.057680 Iteration 4 Error: 0.020494 Align patch 5 20 left Iteration 1 Error: 1.282679 Iteration 2 Error: 0.175247 Iteration 3 Error: 0.040685 Align patch 6 19 left Iteration 1 Error: 0.796436 Iteration 2 Error: 0.111860 Iteration 3 Error: 0.025225 Align patch 7 18 left Iteration 1 Error: 0.474406 Iteration 2 Error: 0.099311 Iteration 3 Error: 0.021276 Align patch 8 17 left Iteration 1 Error: 0.741942 Iteration 2 Error: 0.179393 Iteration 3 Error: 0.043248 Align patch 9 16 left Iteration 1 Error: 0.498207 Iteration 2 Error: 0.070466 Iteration 3 Error: 0.015249 Align patch 10 15 left Iteration 1 Error: 0.583709 Iteration 2 Error: 0.152073 Iteration 3 Error: 0.028803 Align patch 11 14 left Iteration 1 Error: 0.794436 Iteration 2 Error: 0.124026 Iteration 3 Error: 0.032199 Align patch 12 13 left Iteration 1 Error: 0.784538 Iteration 2 Error: 0.080674 Iteration 3 Error: 0.027912 Align patch 13 12 left Iteration 1 Error: 0.545136 Iteration 2 Error: 0.070183 Iteration 3 Error: 0.017039 Align patch 14 11 left Iteration 1 Error: 0.750029 Iteration 2 Error: 0.168010 Iteration 3 Error: 0.065919 Iteration 4 Error: 0.025158 Align patch 15 10 left Iteration 1 Error: 0.834431 Iteration 2 Error: 0.155507 Iteration 3 Error: 0.032737 Align patch 16 9 left Iteration 1 Error: 1.014284 Iteration 2 Error: 0.123885 Iteration 3 Error: 0.039084 Align patch 17 8 left Iteration 1 Error: 0.948155 Iteration 2 Error: 0.246150 Iteration 3 Error: 0.076619 Iteration 4 Error: 0.029256 Align patch 18 7 left Iteration 1 Error: 0.498007 Iteration 2 Error: 0.085995 Iteration 3 Error: 0.023025 Align patch 19 6 left Iteration 1 Error: 0.819556 Iteration 2 Error: 0.099674 Iteration 3 Error: 0.017034 Align patch 20 5 left Iteration 1 Error: 0.743024 Iteration 2 Error: 0.164954 Iteration 3 Error: 0.048240 Align patch 21 4 left Iteration 1 Error: 1.220849 Iteration 2 Error: 0.150702 Iteration 3 Error: 0.044248 Align patch 22 3 left Iteration 1 Error: 0.766393 Iteration 2 Error: 0.099171 Iteration 3 Error: 0.026366 Align patch 23 2 left Iteration 1 Error: 0.829344 Iteration 2 Error: 0.106523 Iteration 3 Error: 0.024077 Align patch 24 1 left Iteration 1 Error: 0.926159 Iteration 2 Error: 0.133307 Iteration 3 Error: 0.029628 Align patch 25 0 left Iteration 1 Error: 1.071869 Iteration 2 Error: 0.225916 Iteration 3 Error: 0.052351 Iteration 4 Error: 0.015898 3D Fitting completed. Patch alignment time: 11.82(sec) Local motion has been corrected. Process thread exits. Computational time: 22.090887 sec Total time: 29.481236 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00006hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00006hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.563968s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00006hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.064897s ........................................ >>>>>>TIME<<<<<< FFT: 1.009521s Defocus_U Defocus_V Angle CCC 12105.47 12148.47 7.12 -0.061695 Final Values Defocus_U Defocus_V Angle CCC 12095.35 12064.84 83.81 -0.293083 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00006hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00006hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.303e-01 9.729e-02 CC threshold: 0.714 Mean Std: 36.82 6.86 Num Hot pixels: 189 Hot pixel threshold: 77.99 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.314580 Iteration 2 Error: 0.126391 Iteration 3 Error: 0.029926 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.11 0.10 ...... Frame ( 3) shift: 0.22 0.19 ...... Frame ( 4) shift: 0.33 0.29 ...... Frame ( 5) shift: 0.44 0.38 ...... Frame ( 6) shift: 0.56 0.47 ...... Frame ( 7) shift: 0.70 0.56 ...... Frame ( 8) shift: 0.84 0.65 ...... Frame ( 9) shift: 0.90 0.68 ...... Frame ( 10) shift: 0.90 0.67 ...... Frame ( 11) shift: 0.89 0.66 ...... Frame ( 12) shift: 0.94 0.66 ...... Frame ( 13) shift: 1.06 0.69 ...... Frame ( 14) shift: 1.17 0.71 ...... Frame ( 15) shift: 1.27 0.74 ...... Frame ( 16) shift: 1.34 0.75 ...... Frame ( 17) shift: 1.42 0.77 ...... Frame ( 18) shift: 1.49 0.78 ...... Frame ( 19) shift: 1.56 0.77 ...... Frame ( 20) shift: 1.63 0.76 ...... Frame ( 21) shift: 1.70 0.77 ...... Frame ( 22) shift: 1.77 0.80 ...... Frame ( 23) shift: 1.84 0.84 ...... Frame ( 24) shift: 1.92 0.85 ...... Frame ( 25) shift: 2.00 0.84 ...... Frame ( 26) shift: 2.09 0.83 ...... Frame ( 27) shift: 2.10 0.79 ...... Frame ( 28) shift: 2.05 0.73 ...... Frame ( 29) shift: 2.00 0.66 ...... Frame ( 30) shift: 1.99 0.57 ...... Frame ( 31) shift: 2.03 0.46 ...... Frame ( 32) shift: 2.08 0.36 ...... Frame ( 33) shift: 2.15 0.29 ...... Frame ( 34) shift: 2.25 0.28 ...... Frame ( 35) shift: 2.35 0.26 ...... Frame ( 36) shift: 2.41 0.25 ...... Frame ( 37) shift: 2.44 0.27 ...... Frame ( 38) shift: 2.46 0.28 ...... Frame ( 39) shift: 2.48 0.30 ...... Frame ( 40) shift: 2.50 0.31 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.080476 Iteration 2 Error: 0.190150 Iteration 3 Error: 0.072438 Iteration 4 Error: 0.030692 Align patch 2 23 left Iteration 1 Error: 0.830838 Iteration 2 Error: 0.148653 Iteration 3 Error: 0.037994 Align patch 3 22 left Iteration 1 Error: 0.666050 Iteration 2 Error: 0.154744 Iteration 3 Error: 0.053137 Iteration 4 Error: 0.011680 Align patch 4 21 left Iteration 1 Error: 0.586887 Iteration 2 Error: 0.134211 Iteration 3 Error: 0.031989 Align patch 5 20 left Iteration 1 Error: 1.249329 Iteration 2 Error: 0.139766 Iteration 3 Error: 0.026618 Align patch 6 19 left Iteration 1 Error: 1.299822 Iteration 2 Error: 0.141517 Iteration 3 Error: 0.030127 Align patch 7 18 left Iteration 1 Error: 0.768068 Iteration 2 Error: 0.190563 Iteration 3 Error: 0.067680 Iteration 4 Error: 0.027253 Align patch 8 17 left Iteration 1 Error: 0.772715 Iteration 2 Error: 0.110504 Iteration 3 Error: 0.025777 Align patch 9 16 left Iteration 1 Error: 0.758174 Iteration 2 Error: 0.196429 Iteration 3 Error: 0.038795 Align patch 10 15 left Iteration 1 Error: 0.741477 Iteration 2 Error: 0.117547 Iteration 3 Error: 0.035858 Align patch 11 14 left Iteration 1 Error: 0.960883 Iteration 2 Error: 0.137633 Iteration 3 Error: 0.026979 Align patch 12 13 left Iteration 1 Error: 1.094234 Iteration 2 Error: 0.135843 Iteration 3 Error: 0.031379 Align patch 13 12 left Iteration 1 Error: 0.992909 Iteration 2 Error: 0.139735 Iteration 3 Error: 0.034302 Align patch 14 11 left Iteration 1 Error: 0.565817 Iteration 2 Error: 0.103797 Iteration 3 Error: 0.034628 Align patch 15 10 left Iteration 1 Error: 0.590985 Iteration 2 Error: 0.092623 Iteration 3 Error: 0.027455 Align patch 16 9 left Iteration 1 Error: 0.677519 Iteration 2 Error: 0.128883 Iteration 3 Error: 0.048047 Align patch 17 8 left Iteration 1 Error: 0.864861 Iteration 2 Error: 0.173112 Iteration 3 Error: 0.068814 Iteration 4 Error: 0.023380 Align patch 18 7 left Iteration 1 Error: 0.777334 Iteration 2 Error: 0.140862 Iteration 3 Error: 0.029560 Align patch 19 6 left Iteration 1 Error: 0.617363 Iteration 2 Error: 0.089923 Iteration 3 Error: 0.026706 Align patch 20 5 left Iteration 1 Error: 0.574244 Iteration 2 Error: 0.084972 Iteration 3 Error: 0.018250 Align patch 21 4 left Iteration 1 Error: 1.560848 Iteration 2 Error: 0.294095 Iteration 3 Error: 0.071956 Iteration 4 Error: 0.021719 Align patch 22 3 left Iteration 1 Error: 0.663729 Iteration 2 Error: 0.167031 Iteration 3 Error: 0.048030 Align patch 23 2 left Iteration 1 Error: 0.794672 Iteration 2 Error: 0.095557 Iteration 3 Error: 0.026909 Align patch 24 1 left Iteration 1 Error: 0.557166 Iteration 2 Error: 0.177001 Iteration 3 Error: 0.040153 Align patch 25 0 left Iteration 1 Error: 0.443536 Iteration 2 Error: 0.095425 Iteration 3 Error: 0.018885 3D Fitting completed. Patch alignment time: 12.28(sec) Local motion has been corrected. Process thread exits. Computational time: 22.690557 sec Total time: 30.205507 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00006hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00006hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.143913s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00006hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.678321s ........................................ >>>>>>TIME<<<<<< FFT: 1.141566s Defocus_U Defocus_V Angle CCC 9384.74 9630.88 9.65 -0.071607 Final Values Defocus_U Defocus_V Angle CCC 9455.08 9607.47 10.61 -0.304591 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00007hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00007hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.264e-01 9.457e-02 CC threshold: 0.694 Mean Std: 36.63 7.14 Num Hot pixels: 190 Hot pixel threshold: 79.50 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.543383 Iteration 2 Error: 0.086112 Iteration 3 Error: 0.014716 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.09 0.07 ...... Frame ( 3) shift: 0.19 0.15 ...... Frame ( 4) shift: 0.28 0.22 ...... Frame ( 5) shift: 0.37 0.30 ...... Frame ( 6) shift: 0.42 0.34 ...... Frame ( 7) shift: 0.41 0.34 ...... Frame ( 8) shift: 0.41 0.35 ...... Frame ( 9) shift: 0.42 0.37 ...... Frame ( 10) shift: 0.43 0.40 ...... Frame ( 11) shift: 0.45 0.43 ...... Frame ( 12) shift: 0.45 0.45 ...... Frame ( 13) shift: 0.44 0.47 ...... Frame ( 14) shift: 0.43 0.48 ...... Frame ( 15) shift: 0.42 0.49 ...... Frame ( 16) shift: 0.40 0.48 ...... Frame ( 17) shift: 0.39 0.48 ...... Frame ( 18) shift: 0.43 0.47 ...... Frame ( 19) shift: 0.53 0.45 ...... Frame ( 20) shift: 0.63 0.43 ...... Frame ( 21) shift: 0.69 0.41 ...... Frame ( 22) shift: 0.73 0.39 ...... Frame ( 23) shift: 0.77 0.37 ...... Frame ( 24) shift: 0.77 0.33 ...... Frame ( 25) shift: 0.75 0.25 ...... Frame ( 26) shift: 0.73 0.18 ...... Frame ( 27) shift: 0.73 0.13 ...... Frame ( 28) shift: 0.78 0.11 ...... Frame ( 29) shift: 0.82 0.08 ...... Frame ( 30) shift: 0.88 0.08 ...... Frame ( 31) shift: 0.94 0.10 ...... Frame ( 32) shift: 1.01 0.13 ...... Frame ( 33) shift: 1.04 0.12 ...... Frame ( 34) shift: 1.03 0.07 ...... Frame ( 35) shift: 1.03 0.03 ...... Frame ( 36) shift: 1.06 0.03 ...... Frame ( 37) shift: 1.11 0.06 ...... Frame ( 38) shift: 1.17 0.10 ...... Frame ( 39) shift: 1.22 0.14 ...... Frame ( 40) shift: 1.28 0.17 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.616174 Iteration 2 Error: 0.078871 Iteration 3 Error: 0.021410 Align patch 2 23 left Iteration 1 Error: 0.410095 Iteration 2 Error: 0.117641 Iteration 3 Error: 0.018096 Align patch 3 22 left Iteration 1 Error: 0.705840 Iteration 2 Error: 0.141980 Iteration 3 Error: 0.044967 Align patch 4 21 left Iteration 1 Error: 0.545801 Iteration 2 Error: 0.083836 Iteration 3 Error: 0.013232 Align patch 5 20 left Iteration 1 Error: 0.686919 Iteration 2 Error: 0.140007 Iteration 3 Error: 0.044264 Align patch 6 19 left Iteration 1 Error: 0.585208 Iteration 2 Error: 0.059936 Iteration 3 Error: 0.012146 Align patch 7 18 left Iteration 1 Error: 0.744964 Iteration 2 Error: 0.112061 Iteration 3 Error: 0.022278 Align patch 8 17 left Iteration 1 Error: 0.358733 Iteration 2 Error: 0.050947 Iteration 3 Error: 0.009312 Align patch 9 16 left Iteration 1 Error: 0.681062 Iteration 2 Error: 0.061061 Iteration 3 Error: 0.012722 Align patch 10 15 left Iteration 1 Error: 0.571678 Iteration 2 Error: 0.122208 Iteration 3 Error: 0.026140 Align patch 11 14 left Iteration 1 Error: 0.668579 Iteration 2 Error: 0.114104 Iteration 3 Error: 0.032019 Align patch 12 13 left Iteration 1 Error: 0.728931 Iteration 2 Error: 0.097095 Iteration 3 Error: 0.028042 Align patch 13 12 left Iteration 1 Error: 0.594979 Iteration 2 Error: 0.095814 Iteration 3 Error: 0.015316 Align patch 14 11 left Iteration 1 Error: 0.618091 Iteration 2 Error: 0.067468 Iteration 3 Error: 0.015848 Align patch 15 10 left Iteration 1 Error: 0.484599 Iteration 2 Error: 0.070053 Iteration 3 Error: 0.008197 Align patch 16 9 left Iteration 1 Error: 0.697201 Iteration 2 Error: 0.137311 Iteration 3 Error: 0.020991 Align patch 17 8 left Iteration 1 Error: 0.497090 Iteration 2 Error: 0.085425 Iteration 3 Error: 0.018651 Align patch 18 7 left Iteration 1 Error: 0.671711 Iteration 2 Error: 0.103453 Iteration 3 Error: 0.031829 Align patch 19 6 left Iteration 1 Error: 0.475020 Iteration 2 Error: 0.046957 Align patch 20 5 left Iteration 1 Error: 0.657499 Iteration 2 Error: 0.086671 Iteration 3 Error: 0.015425 Align patch 21 4 left Iteration 1 Error: 0.417897 Iteration 2 Error: 0.055922 Iteration 3 Error: 0.014753 Align patch 22 3 left Iteration 1 Error: 0.634572 Iteration 2 Error: 0.084591 Iteration 3 Error: 0.010804 Align patch 23 2 left Iteration 1 Error: 0.472693 Iteration 2 Error: 0.066964 Iteration 3 Error: 0.015870 Align patch 24 1 left Iteration 1 Error: 0.475796 Iteration 2 Error: 0.057264 Iteration 3 Error: 0.015284 Align patch 25 0 left Iteration 1 Error: 0.460560 Iteration 2 Error: 0.075803 Iteration 3 Error: 0.011954 3D Fitting completed. Patch alignment time: 11.63(sec) Local motion has been corrected. Process thread exits. Computational time: 21.756477 sec Total time: 30.181108 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00007hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00007hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.467321s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00007hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.321301s ........................................ >>>>>>TIME<<<<<< FFT: 1.030691s Defocus_U Defocus_V Angle CCC 10998.07 11486.35 8.11 -0.050646 Final Values Defocus_U Defocus_V Angle CCC 11291.23 11090.05 78.26 -0.269848 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00007hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00007hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 38.94 6.73 Num Hot pixels: 228 Hot pixel threshold: 79.32 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 4.316915 Iteration 2 Error: 0.534761 Iteration 3 Error: 0.276938 Iteration 4 Error: 0.106534 Iteration 5 Error: 0.043423 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.25 -0.64 ...... Frame ( 3) shift: 0.50 -1.28 ...... Frame ( 4) shift: 0.74 -1.92 ...... Frame ( 5) shift: 0.99 -2.56 ...... Frame ( 6) shift: 1.25 -3.10 ...... Frame ( 7) shift: 1.51 -3.53 ...... Frame ( 8) shift: 1.78 -3.95 ...... Frame ( 9) shift: 2.00 -4.25 ...... Frame ( 10) shift: 2.17 -4.43 ...... Frame ( 11) shift: 2.35 -4.61 ...... Frame ( 12) shift: 2.52 -4.79 ...... Frame ( 13) shift: 2.69 -4.99 ...... Frame ( 14) shift: 2.86 -5.19 ...... Frame ( 15) shift: 2.97 -5.32 ...... Frame ( 16) shift: 3.03 -5.38 ...... Frame ( 17) shift: 3.08 -5.44 ...... Frame ( 18) shift: 3.17 -5.50 ...... Frame ( 19) shift: 3.30 -5.58 ...... Frame ( 20) shift: 3.43 -5.65 ...... Frame ( 21) shift: 3.58 -5.72 ...... Frame ( 22) shift: 3.75 -5.77 ...... Frame ( 23) shift: 3.91 -5.83 ...... Frame ( 24) shift: 4.02 -5.88 ...... Frame ( 25) shift: 4.07 -5.93 ...... Frame ( 26) shift: 4.13 -5.98 ...... Frame ( 27) shift: 4.18 -6.06 ...... Frame ( 28) shift: 4.25 -6.18 ...... Frame ( 29) shift: 4.31 -6.29 ...... Frame ( 30) shift: 4.37 -6.37 ...... Frame ( 31) shift: 4.42 -6.41 ...... Frame ( 32) shift: 4.48 -6.46 ...... Frame ( 33) shift: 4.55 -6.48 ...... Frame ( 34) shift: 4.62 -6.47 ...... Frame ( 35) shift: 4.70 -6.46 ...... Frame ( 36) shift: 4.81 -6.46 ...... Frame ( 37) shift: 4.95 -6.49 ...... Frame ( 38) shift: 5.08 -6.51 ...... Frame ( 39) shift: 5.22 -6.53 ...... Frame ( 40) shift: 5.36 -6.56 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.566188 Iteration 2 Error: 0.281445 Iteration 3 Error: 0.050144 Iteration 4 Error: 0.015782 Align patch 2 23 left Iteration 1 Error: 0.869699 Iteration 2 Error: 0.157499 Iteration 3 Error: 0.043264 Align patch 3 22 left Iteration 1 Error: 2.171312 Iteration 2 Error: 0.295004 Iteration 3 Error: 0.062600 Iteration 4 Error: 0.018028 Align patch 4 21 left Iteration 1 Error: 2.747483 Iteration 2 Error: 0.356842 Iteration 3 Error: 0.102751 Iteration 4 Error: 0.026847 Align patch 5 20 left Iteration 1 Error: 4.629502 Iteration 2 Error: 0.530432 Iteration 3 Error: 0.100964 Iteration 4 Error: 0.025226 Align patch 6 19 left Iteration 1 Error: 2.388930 Iteration 2 Error: 0.518704 Iteration 3 Error: 0.182011 Iteration 4 Error: 0.065164 Iteration 5 Error: 0.021689 Align patch 7 18 left Iteration 1 Error: 0.770167 Iteration 2 Error: 0.169960 Iteration 3 Error: 0.032648 Align patch 8 17 left Iteration 1 Error: 0.990277 Iteration 2 Error: 0.194735 Iteration 3 Error: 0.045173 Align patch 9 16 left Iteration 1 Error: 2.446618 Iteration 2 Error: 0.272607 Iteration 3 Error: 0.079811 Iteration 4 Error: 0.015943 Align patch 10 15 left Iteration 1 Error: 3.827898 Iteration 2 Error: 0.561735 Iteration 3 Error: 0.151888 Iteration 4 Error: 0.045820 Align patch 11 14 left Iteration 1 Error: 3.530183 Iteration 2 Error: 0.409587 Iteration 3 Error: 0.088138 Iteration 4 Error: 0.025282 Align patch 12 13 left Iteration 1 Error: 2.055534 Iteration 2 Error: 0.233698 Iteration 3 Error: 0.048771 Align patch 13 12 left Iteration 1 Error: 0.789673 Iteration 2 Error: 0.121612 Iteration 3 Error: 0.029575 Align patch 14 11 left Iteration 1 Error: 1.183440 Iteration 2 Error: 0.178943 Iteration 3 Error: 0.040561 Align patch 15 10 left Iteration 1 Error: 4.278819 Iteration 2 Error: 0.468785 Iteration 3 Error: 0.102150 Iteration 4 Error: 0.031349 Align patch 16 9 left Iteration 1 Error: 5.120412 Iteration 2 Error: 0.757723 Iteration 3 Error: 0.149755 Iteration 4 Error: 0.052021 Iteration 5 Error: 0.021813 Align patch 17 8 left Iteration 1 Error: 3.515302 Iteration 2 Error: 0.464026 Iteration 3 Error: 0.105692 Iteration 4 Error: 0.041764 Align patch 18 7 left Iteration 1 Error: 2.087177 Iteration 2 Error: 0.281172 Iteration 3 Error: 0.047047 Align patch 19 6 left Iteration 1 Error: 1.008569 Iteration 2 Error: 0.187151 Iteration 3 Error: 0.048235 Align patch 20 5 left Iteration 1 Error: 3.419576 Iteration 2 Error: 0.430600 Iteration 3 Error: 0.074045 Iteration 4 Error: 0.020538 Align patch 21 4 left Iteration 1 Error: 6.174379 Iteration 2 Error: 0.791032 Iteration 3 Error: 0.198814 Iteration 4 Error: 0.071444 Iteration 5 Error: 0.022637 Align patch 22 3 left Iteration 1 Error: 4.786703 Iteration 2 Error: 0.588870 Iteration 3 Error: 0.174769 Iteration 4 Error: 0.078557 Iteration 5 Error: 0.031803 Align patch 23 2 left Iteration 1 Error: 2.786259 Iteration 2 Error: 0.316076 Iteration 3 Error: 0.085787 Iteration 4 Error: 0.031639 Align patch 24 1 left Iteration 1 Error: 0.425449 Iteration 2 Error: 0.098493 Iteration 3 Error: 0.023517 Align patch 25 0 left Iteration 1 Error: 2.386657 Iteration 2 Error: 0.420473 Iteration 3 Error: 0.105752 Iteration 4 Error: 0.034905 3D Fitting completed. Patch alignment time: 12.39(sec) Local motion has been corrected. Process thread exits. Computational time: 23.183062 sec Total time: 30.155716 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00007hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00007hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.502491s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00007hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.252194s ........................................ >>>>>>TIME<<<<<< FFT: 1.060282s Defocus_U Defocus_V Angle CCC 13603.52 14072.27 2.80 0.061977 Final Values Defocus_U Defocus_V Angle CCC 13612.90 14081.65 2.49 0.089258 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00007hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00007hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.301e-01 9.709e-02 CC threshold: 0.713 Mean Std: 38.94 7.11 Num Hot pixels: 189 Hot pixel threshold: 81.61 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.981944 Iteration 2 Error: 0.100320 Iteration 3 Error: 0.021500 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.11 0.08 ...... Frame ( 3) shift: 0.23 0.16 ...... Frame ( 4) shift: 0.34 0.25 ...... Frame ( 5) shift: 0.45 0.33 ...... Frame ( 6) shift: 0.55 0.36 ...... Frame ( 7) shift: 0.62 0.34 ...... Frame ( 8) shift: 0.70 0.32 ...... Frame ( 9) shift: 0.79 0.30 ...... Frame ( 10) shift: 0.89 0.29 ...... Frame ( 11) shift: 1.00 0.28 ...... Frame ( 12) shift: 1.03 0.25 ...... Frame ( 13) shift: 0.98 0.20 ...... Frame ( 14) shift: 0.94 0.15 ...... Frame ( 15) shift: 0.94 0.10 ...... Frame ( 16) shift: 0.98 0.04 ...... Frame ( 17) shift: 1.03 -0.01 ...... Frame ( 18) shift: 1.07 0.01 ...... Frame ( 19) shift: 1.11 0.08 ...... Frame ( 20) shift: 1.15 0.15 ...... Frame ( 21) shift: 1.17 0.19 ...... Frame ( 22) shift: 1.19 0.20 ...... Frame ( 23) shift: 1.21 0.21 ...... Frame ( 24) shift: 1.27 0.18 ...... Frame ( 25) shift: 1.36 0.11 ...... Frame ( 26) shift: 1.45 0.05 ...... Frame ( 27) shift: 1.54 0.00 ...... Frame ( 28) shift: 1.62 -0.02 ...... Frame ( 29) shift: 1.71 -0.04 ...... Frame ( 30) shift: 1.79 -0.05 ...... Frame ( 31) shift: 1.87 -0.05 ...... Frame ( 32) shift: 1.95 -0.06 ...... Frame ( 33) shift: 1.99 -0.04 ...... Frame ( 34) shift: 1.97 0.02 ...... Frame ( 35) shift: 1.95 0.07 ...... Frame ( 36) shift: 1.95 0.07 ...... Frame ( 37) shift: 1.97 0.02 ...... Frame ( 38) shift: 1.99 -0.03 ...... Frame ( 39) shift: 2.00 -0.07 ...... Frame ( 40) shift: 2.02 -0.12 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.583756 Iteration 2 Error: 0.123612 Iteration 3 Error: 0.028915 Align patch 2 23 left Iteration 1 Error: 0.803135 Iteration 2 Error: 0.131502 Iteration 3 Error: 0.028407 Align patch 3 22 left Iteration 1 Error: 0.437783 Iteration 2 Error: 0.073494 Iteration 3 Error: 0.019194 Align patch 4 21 left Iteration 1 Error: 0.583751 Iteration 2 Error: 0.077440 Iteration 3 Error: 0.013209 Align patch 5 20 left Iteration 1 Error: 0.578291 Iteration 2 Error: 0.079176 Iteration 3 Error: 0.013466 Align patch 6 19 left Iteration 1 Error: 0.845368 Iteration 2 Error: 0.196467 Iteration 3 Error: 0.033524 Align patch 7 18 left Iteration 1 Error: 0.456290 Iteration 2 Error: 0.084596 Iteration 3 Error: 0.015935 Align patch 8 17 left Iteration 1 Error: 0.614032 Iteration 2 Error: 0.090561 Iteration 3 Error: 0.012321 Align patch 9 16 left Iteration 1 Error: 0.622274 Iteration 2 Error: 0.058593 Iteration 3 Error: 0.012897 Align patch 10 15 left Iteration 1 Error: 0.568161 Iteration 2 Error: 0.052396 Iteration 3 Error: 0.017768 Align patch 11 14 left Iteration 1 Error: 0.941175 Iteration 2 Error: 0.105894 Iteration 3 Error: 0.028166 Align patch 12 13 left Iteration 1 Error: 0.648237 Iteration 2 Error: 0.091023 Iteration 3 Error: 0.015643 Align patch 13 12 left Iteration 1 Error: 0.506192 Iteration 2 Error: 0.052116 Iteration 3 Error: 0.009833 Align patch 14 11 left Iteration 1 Error: 0.542610 Iteration 2 Error: 0.063361 Iteration 3 Error: 0.014944 Align patch 15 10 left Iteration 1 Error: 0.454656 Iteration 2 Error: 0.065494 Iteration 3 Error: 0.013571 Align patch 16 9 left Iteration 1 Error: 0.792201 Iteration 2 Error: 0.094652 Iteration 3 Error: 0.020714 Align patch 17 8 left Iteration 1 Error: 0.522029 Iteration 2 Error: 0.061089 Iteration 3 Error: 0.011390 Align patch 18 7 left Iteration 1 Error: 0.658591 Iteration 2 Error: 0.123103 Iteration 3 Error: 0.028584 Align patch 19 6 left Iteration 1 Error: 0.549053 Iteration 2 Error: 0.054886 Iteration 3 Error: 0.009489 Align patch 20 5 left Iteration 1 Error: 0.612164 Iteration 2 Error: 0.104434 Iteration 3 Error: 0.018373 Align patch 21 4 left Iteration 1 Error: 0.661224 Iteration 2 Error: 0.094913 Iteration 3 Error: 0.010132 Align patch 22 3 left Iteration 1 Error: 1.121119 Iteration 2 Error: 0.226972 Iteration 3 Error: 0.038296 Align patch 23 2 left Iteration 1 Error: 0.670542 Iteration 2 Error: 0.051174 Iteration 3 Error: 0.013089 Align patch 24 1 left Iteration 1 Error: 0.583245 Iteration 2 Error: 0.080449 Iteration 3 Error: 0.018388 Align patch 25 0 left Iteration 1 Error: 0.852177 Iteration 2 Error: 0.078248 Iteration 3 Error: 0.013070 3D Fitting completed. Patch alignment time: 11.31(sec) Local motion has been corrected. Process thread exits. Computational time: 23.174704 sec Total time: 30.405907 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00007hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00007hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.581379s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00007hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.232070s ........................................ >>>>>>TIME<<<<<< FFT: 0.959025s Defocus_U Defocus_V Angle CCC 13646.50 14486.34 6.33 -0.023218 Final Values Defocus_U Defocus_V Angle CCC 13643.38 14498.86 6.33 -0.204601 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00007hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00007hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.350e-01 1.004e-01 CC threshold: 0.737 Mean Std: 40.26 6.85 Num Hot pixels: 222 Hot pixel threshold: 81.38 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.834067 Iteration 2 Error: 0.126703 Iteration 3 Error: 0.026364 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.09 -0.16 ...... Frame ( 3) shift: -0.18 -0.32 ...... Frame ( 4) shift: -0.27 -0.48 ...... Frame ( 5) shift: -0.36 -0.65 ...... Frame ( 6) shift: -0.38 -0.75 ...... Frame ( 7) shift: -0.33 -0.79 ...... Frame ( 8) shift: -0.29 -0.84 ...... Frame ( 9) shift: -0.24 -0.87 ...... Frame ( 10) shift: -0.18 -0.89 ...... Frame ( 11) shift: -0.12 -0.90 ...... Frame ( 12) shift: -0.07 -0.90 ...... Frame ( 13) shift: -0.01 -0.87 ...... Frame ( 14) shift: 0.05 -0.85 ...... Frame ( 15) shift: 0.12 -0.82 ...... Frame ( 16) shift: 0.21 -0.80 ...... Frame ( 17) shift: 0.30 -0.77 ...... Frame ( 18) shift: 0.37 -0.74 ...... Frame ( 19) shift: 0.43 -0.69 ...... Frame ( 20) shift: 0.49 -0.64 ...... Frame ( 21) shift: 0.54 -0.60 ...... Frame ( 22) shift: 0.58 -0.55 ...... Frame ( 23) shift: 0.62 -0.50 ...... Frame ( 24) shift: 0.67 -0.49 ...... Frame ( 25) shift: 0.73 -0.51 ...... Frame ( 26) shift: 0.79 -0.54 ...... Frame ( 27) shift: 0.82 -0.55 ...... Frame ( 28) shift: 0.84 -0.54 ...... Frame ( 29) shift: 0.87 -0.53 ...... Frame ( 30) shift: 0.92 -0.53 ...... Frame ( 31) shift: 1.02 -0.52 ...... Frame ( 32) shift: 1.12 -0.52 ...... Frame ( 33) shift: 1.19 -0.52 ...... Frame ( 34) shift: 1.24 -0.53 ...... Frame ( 35) shift: 1.28 -0.55 ...... Frame ( 36) shift: 1.32 -0.56 ...... Frame ( 37) shift: 1.34 -0.58 ...... Frame ( 38) shift: 1.36 -0.60 ...... Frame ( 39) shift: 1.39 -0.62 ...... Frame ( 40) shift: 1.41 -0.64 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.659857 Iteration 2 Error: 0.101990 Iteration 3 Error: 0.025102 Align patch 2 23 left Iteration 1 Error: 0.524115 Iteration 2 Error: 0.065018 Iteration 3 Error: 0.012394 Align patch 3 22 left Iteration 1 Error: 0.973999 Iteration 2 Error: 0.096643 Iteration 3 Error: 0.016631 Align patch 4 21 left Iteration 1 Error: 1.119203 Iteration 2 Error: 0.097246 Iteration 3 Error: 0.024933 Align patch 5 20 left Iteration 1 Error: 1.397329 Iteration 2 Error: 0.098802 Iteration 3 Error: 0.016364 Align patch 6 19 left Iteration 1 Error: 1.367998 Iteration 2 Error: 0.191004 Iteration 3 Error: 0.043711 Align patch 7 18 left Iteration 1 Error: 0.590563 Iteration 2 Error: 0.105875 Iteration 3 Error: 0.016112 Align patch 8 17 left Iteration 1 Error: 0.841745 Iteration 2 Error: 0.097127 Iteration 3 Error: 0.017467 Align patch 9 16 left Iteration 1 Error: 1.003114 Iteration 2 Error: 0.126256 Iteration 3 Error: 0.030525 Align patch 10 15 left Iteration 1 Error: 1.181928 Iteration 2 Error: 0.104861 Iteration 3 Error: 0.019105 Align patch 11 14 left Iteration 1 Error: 2.042746 Iteration 2 Error: 0.376771 Iteration 3 Error: 0.121751 Iteration 4 Error: 0.039845 Align patch 12 13 left Iteration 1 Error: 1.136363 Iteration 2 Error: 0.130215 Iteration 3 Error: 0.041482 Align patch 13 12 left Iteration 1 Error: 0.491119 Iteration 2 Error: 0.073313 Iteration 3 Error: 0.024566 Align patch 14 11 left Iteration 1 Error: 1.022810 Iteration 2 Error: 0.095490 Iteration 3 Error: 0.014119 Align patch 15 10 left Iteration 1 Error: 0.946113 Iteration 2 Error: 0.073894 Iteration 3 Error: 0.013178 Align patch 16 9 left Iteration 1 Error: 1.041949 Iteration 2 Error: 0.140806 Iteration 3 Error: 0.032975 Align patch 17 8 left Iteration 1 Error: 1.179249 Iteration 2 Error: 0.164589 Iteration 3 Error: 0.025454 Align patch 18 7 left Iteration 1 Error: 0.561314 Iteration 2 Error: 0.066343 Iteration 3 Error: 0.009518 Align patch 19 6 left Iteration 1 Error: 0.786486 Iteration 2 Error: 0.092688 Iteration 3 Error: 0.021757 Align patch 20 5 left Iteration 1 Error: 0.761215 Iteration 2 Error: 0.127326 Iteration 3 Error: 0.029881 Align patch 21 4 left Iteration 1 Error: 1.886554 Iteration 2 Error: 0.155045 Iteration 3 Error: 0.036321 Align patch 22 3 left Iteration 1 Error: 1.295958 Iteration 2 Error: 0.244190 Iteration 3 Error: 0.033669 Align patch 23 2 left Iteration 1 Error: 0.851482 Iteration 2 Error: 0.142911 Iteration 3 Error: 0.033722 Align patch 24 1 left Iteration 1 Error: 0.597807 Iteration 2 Error: 0.097782 Iteration 3 Error: 0.012582 Align patch 25 0 left Iteration 1 Error: 0.585950 Iteration 2 Error: 0.078706 Iteration 3 Error: 0.017995 3D Fitting completed. Patch alignment time: 11.76(sec) Local motion has been corrected. Process thread exits. Computational time: 21.877306 sec Total time: 29.660299 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00007hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00007hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.639046s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00007hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.621123s ........................................ >>>>>>TIME<<<<<< FFT: 0.927112s Defocus_U Defocus_V Angle CCC 11812.62 11199.16 83.04 0.057096 Final Values Defocus_U Defocus_V Angle CCC 11854.84 11213.25 83.35 0.092602 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00008hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00008hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.350e-01 1.004e-01 CC threshold: 0.737 Mean Std: 38.96 6.71 Num Hot pixels: 209 Hot pixel threshold: 79.22 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.950193 Iteration 2 Error: 0.387884 Iteration 3 Error: 0.098879 Iteration 4 Error: 0.030386 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.04 0.16 ...... Frame ( 3) shift: -0.08 0.32 ...... Frame ( 4) shift: -0.12 0.48 ...... Frame ( 5) shift: -0.17 0.64 ...... Frame ( 6) shift: -0.15 0.75 ...... Frame ( 7) shift: -0.09 0.81 ...... Frame ( 8) shift: -0.02 0.87 ...... Frame ( 9) shift: 0.09 0.93 ...... Frame ( 10) shift: 0.25 1.01 ...... Frame ( 11) shift: 0.41 1.08 ...... Frame ( 12) shift: 0.54 1.11 ...... Frame ( 13) shift: 0.64 1.11 ...... Frame ( 14) shift: 0.74 1.10 ...... Frame ( 15) shift: 0.86 1.14 ...... Frame ( 16) shift: 1.00 1.21 ...... Frame ( 17) shift: 1.14 1.28 ...... Frame ( 18) shift: 1.28 1.35 ...... Frame ( 19) shift: 1.42 1.41 ...... Frame ( 20) shift: 1.56 1.48 ...... Frame ( 21) shift: 1.67 1.54 ...... Frame ( 22) shift: 1.76 1.59 ...... Frame ( 23) shift: 1.86 1.65 ...... Frame ( 24) shift: 1.97 1.72 ...... Frame ( 25) shift: 2.12 1.79 ...... Frame ( 26) shift: 2.26 1.87 ...... Frame ( 27) shift: 2.36 1.95 ...... Frame ( 28) shift: 2.41 2.03 ...... Frame ( 29) shift: 2.47 2.12 ...... Frame ( 30) shift: 2.55 2.16 ...... Frame ( 31) shift: 2.65 2.14 ...... Frame ( 32) shift: 2.76 2.13 ...... Frame ( 33) shift: 2.88 2.13 ...... Frame ( 34) shift: 3.00 2.16 ...... Frame ( 35) shift: 3.13 2.18 ...... Frame ( 36) shift: 3.25 2.21 ...... Frame ( 37) shift: 3.38 2.24 ...... Frame ( 38) shift: 3.50 2.28 ...... Frame ( 39) shift: 3.62 2.31 ...... Frame ( 40) shift: 3.74 2.35 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.953990 Iteration 2 Error: 0.147376 Iteration 3 Error: 0.043089 Align patch 2 23 left Iteration 1 Error: 1.035575 Iteration 2 Error: 0.184172 Iteration 3 Error: 0.062034 Iteration 4 Error: 0.032780 Align patch 3 22 left Iteration 1 Error: 0.410348 Iteration 2 Error: 0.084512 Iteration 3 Error: 0.023697 Align patch 4 21 left Iteration 1 Error: 0.487556 Iteration 2 Error: 0.071316 Iteration 3 Error: 0.020975 Align patch 5 20 left Iteration 1 Error: 0.604461 Iteration 2 Error: 0.058375 Iteration 3 Error: 0.016445 Align patch 6 19 left Iteration 1 Error: 1.231283 Iteration 2 Error: 0.161564 Iteration 3 Error: 0.051942 Iteration 4 Error: 0.017983 Align patch 7 18 left Iteration 1 Error: 0.568679 Iteration 2 Error: 0.116522 Iteration 3 Error: 0.027568 Align patch 8 17 left Iteration 1 Error: 0.555554 Iteration 2 Error: 0.079094 Iteration 3 Error: 0.017566 Align patch 9 16 left Iteration 1 Error: 0.721991 Iteration 2 Error: 0.083479 Iteration 3 Error: 0.022936 Align patch 10 15 left Iteration 1 Error: 0.591304 Iteration 2 Error: 0.133734 Iteration 3 Error: 0.019844 Align patch 11 14 left Iteration 1 Error: 0.613172 Iteration 2 Error: 0.129827 Iteration 3 Error: 0.034530 Align patch 12 13 left Iteration 1 Error: 0.760136 Iteration 2 Error: 0.138211 Iteration 3 Error: 0.029839 Align patch 13 12 left Iteration 1 Error: 0.426346 Iteration 2 Error: 0.130027 Iteration 3 Error: 0.038499 Align patch 14 11 left Iteration 1 Error: 0.800594 Iteration 2 Error: 0.187085 Iteration 3 Error: 0.063786 Iteration 4 Error: 0.022371 Align patch 15 10 left Iteration 1 Error: 0.694829 Iteration 2 Error: 0.093889 Iteration 3 Error: 0.026140 Align patch 16 9 left Iteration 1 Error: 0.641473 Iteration 2 Error: 0.068298 Iteration 3 Error: 0.019780 Align patch 17 8 left Iteration 1 Error: 0.605954 Iteration 2 Error: 0.073769 Iteration 3 Error: 0.014444 Align patch 18 7 left Iteration 1 Error: 0.491983 Iteration 2 Error: 0.056594 Iteration 3 Error: 0.015550 Align patch 19 6 left Iteration 1 Error: 0.555073 Iteration 2 Error: 0.117605 Iteration 3 Error: 0.044171 Align patch 20 5 left Iteration 1 Error: 0.829866 Iteration 2 Error: 0.128019 Iteration 3 Error: 0.032464 Align patch 21 4 left Iteration 1 Error: 0.794005 Iteration 2 Error: 0.094087 Iteration 3 Error: 0.029462 Align patch 22 3 left Iteration 1 Error: 0.527490 Iteration 2 Error: 0.130377 Iteration 3 Error: 0.025603 Align patch 23 2 left Iteration 1 Error: 0.602434 Iteration 2 Error: 0.144742 Iteration 3 Error: 0.040252 Align patch 24 1 left Iteration 1 Error: 0.487652 Iteration 2 Error: 0.104371 Iteration 3 Error: 0.021999 Align patch 25 0 left Iteration 1 Error: 0.558452 Iteration 2 Error: 0.109252 Iteration 3 Error: 0.024357 3D Fitting completed. Patch alignment time: 11.68(sec) Local motion has been corrected. Process thread exits. Computational time: 23.789965 sec Total time: 30.798506 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00008hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00008hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.583803s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00008hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.200542s ........................................ >>>>>>TIME<<<<<< FFT: 0.935065s Defocus_U Defocus_V Angle CCC 10931.67 11752.03 12.13 0.061132 Final Values Defocus_U Defocus_V Angle CCC 10955.13 11750.49 11.50 0.098155 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00008hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00008hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.003e-01 CC threshold: 0.737 Mean Std: 38.41 6.90 Num Hot pixels: 201 Hot pixel threshold: 79.82 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.305462 Iteration 2 Error: 0.252157 Iteration 3 Error: 0.063646 Iteration 4 Error: 0.019643 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.05 0.02 ...... Frame ( 3) shift: -0.11 0.04 ...... Frame ( 4) shift: -0.16 0.06 ...... Frame ( 5) shift: -0.21 0.08 ...... Frame ( 6) shift: -0.21 0.08 ...... Frame ( 7) shift: -0.16 0.06 ...... Frame ( 8) shift: -0.11 0.05 ...... Frame ( 9) shift: -0.07 0.06 ...... Frame ( 10) shift: -0.03 0.11 ...... Frame ( 11) shift: -0.00 0.16 ...... Frame ( 12) shift: 0.07 0.20 ...... Frame ( 13) shift: 0.18 0.22 ...... Frame ( 14) shift: 0.29 0.24 ...... Frame ( 15) shift: 0.36 0.29 ...... Frame ( 16) shift: 0.39 0.37 ...... Frame ( 17) shift: 0.43 0.46 ...... Frame ( 18) shift: 0.46 0.51 ...... Frame ( 19) shift: 0.48 0.55 ...... Frame ( 20) shift: 0.50 0.59 ...... Frame ( 21) shift: 0.57 0.62 ...... Frame ( 22) shift: 0.67 0.66 ...... Frame ( 23) shift: 0.78 0.69 ...... Frame ( 24) shift: 0.87 0.71 ...... Frame ( 25) shift: 0.95 0.70 ...... Frame ( 26) shift: 1.04 0.70 ...... Frame ( 27) shift: 1.13 0.75 ...... Frame ( 28) shift: 1.23 0.85 ...... Frame ( 29) shift: 1.33 0.95 ...... Frame ( 30) shift: 1.41 1.03 ...... Frame ( 31) shift: 1.46 1.08 ...... Frame ( 32) shift: 1.51 1.13 ...... Frame ( 33) shift: 1.53 1.17 ...... Frame ( 34) shift: 1.52 1.20 ...... Frame ( 35) shift: 1.51 1.23 ...... Frame ( 36) shift: 1.55 1.27 ...... Frame ( 37) shift: 1.65 1.33 ...... Frame ( 38) shift: 1.75 1.38 ...... Frame ( 39) shift: 1.85 1.43 ...... Frame ( 40) shift: 1.94 1.48 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.678201 Iteration 2 Error: 0.121194 Iteration 3 Error: 0.035104 Align patch 2 23 left Iteration 1 Error: 0.639492 Iteration 2 Error: 0.102230 Iteration 3 Error: 0.030816 Align patch 3 22 left Iteration 1 Error: 0.754342 Iteration 2 Error: 0.132136 Iteration 3 Error: 0.050694 Iteration 4 Error: 0.013346 Align patch 4 21 left Iteration 1 Error: 0.631522 Iteration 2 Error: 0.133021 Iteration 3 Error: 0.032705 Align patch 5 20 left Iteration 1 Error: 0.542129 Iteration 2 Error: 0.214412 Iteration 3 Error: 0.071867 Iteration 4 Error: 0.025594 Align patch 6 19 left Iteration 1 Error: 0.842709 Iteration 2 Error: 0.221390 Iteration 3 Error: 0.051690 Iteration 4 Error: 0.019405 Align patch 7 18 left Iteration 1 Error: 0.602088 Iteration 2 Error: 0.113091 Iteration 3 Error: 0.029006 Align patch 8 17 left Iteration 1 Error: 0.721672 Iteration 2 Error: 0.146577 Iteration 3 Error: 0.048229 Align patch 9 16 left Iteration 1 Error: 0.913174 Iteration 2 Error: 0.159355 Iteration 3 Error: 0.048383 Align patch 10 15 left Iteration 1 Error: 0.660998 Iteration 2 Error: 0.119624 Iteration 3 Error: 0.034759 Align patch 11 14 left Iteration 1 Error: 0.577154 Iteration 2 Error: 0.160654 Iteration 3 Error: 0.044231 Align patch 12 13 left Iteration 1 Error: 0.896984 Iteration 2 Error: 0.231006 Iteration 3 Error: 0.067980 Iteration 4 Error: 0.022790 Align patch 13 12 left Iteration 1 Error: 0.750820 Iteration 2 Error: 0.165963 Iteration 3 Error: 0.055232 Iteration 4 Error: 0.022139 Align patch 14 11 left Iteration 1 Error: 0.624293 Iteration 2 Error: 0.112601 Iteration 3 Error: 0.017665 Align patch 15 10 left Iteration 1 Error: 0.865062 Iteration 2 Error: 0.104616 Iteration 3 Error: 0.021734 Align patch 16 9 left Iteration 1 Error: 1.093723 Iteration 2 Error: 0.123991 Iteration 3 Error: 0.040916 Align patch 17 8 left Iteration 1 Error: 1.022890 Iteration 2 Error: 0.127809 Iteration 3 Error: 0.036792 Align patch 18 7 left Iteration 1 Error: 0.539114 Iteration 2 Error: 0.075379 Iteration 3 Error: 0.022143 Align patch 19 6 left Iteration 1 Error: 0.811087 Iteration 2 Error: 0.147609 Iteration 3 Error: 0.029477 Align patch 20 5 left Iteration 1 Error: 0.551305 Iteration 2 Error: 0.112742 Iteration 3 Error: 0.021663 Align patch 21 4 left Iteration 1 Error: 1.058610 Iteration 2 Error: 0.132967 Iteration 3 Error: 0.033531 Align patch 22 3 left Iteration 1 Error: 0.995945 Iteration 2 Error: 0.157461 Iteration 3 Error: 0.046629 Align patch 23 2 left Iteration 1 Error: 0.453232 Iteration 2 Error: 0.097449 Iteration 3 Error: 0.027724 Align patch 24 1 left Iteration 1 Error: 0.723207 Iteration 2 Error: 0.100266 Iteration 3 Error: 0.022087 Align patch 25 0 left Iteration 1 Error: 0.503624 Iteration 2 Error: 0.108990 Iteration 3 Error: 0.015708 3D Fitting completed. Patch alignment time: 11.41(sec) Local motion has been corrected. Process thread exits. Computational time: 24.020187 sec Total time: 33.818382 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00008hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00008hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.472545s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00008hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.535325s ........................................ >>>>>>TIME<<<<<< FFT: 1.042377s Defocus_U Defocus_V Angle CCC 11027.36 11496.11 0.09 0.046043 Final Values Defocus_U Defocus_V Angle CCC 11516.42 11047.67 89.78 0.075157 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00008hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00008hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.003e-01 CC threshold: 0.737 Mean Std: 41.46 6.94 Num Hot pixels: 251 Hot pixel threshold: 83.08 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.567904 Iteration 2 Error: 0.259869 Iteration 3 Error: 0.062532 Iteration 4 Error: 0.019775 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.01 0.12 ...... Frame ( 3) shift: -0.01 0.23 ...... Frame ( 4) shift: -0.02 0.35 ...... Frame ( 5) shift: -0.02 0.46 ...... Frame ( 6) shift: 0.02 0.54 ...... Frame ( 7) shift: 0.10 0.57 ...... Frame ( 8) shift: 0.19 0.60 ...... Frame ( 9) shift: 0.30 0.67 ...... Frame ( 10) shift: 0.44 0.76 ...... Frame ( 11) shift: 0.57 0.84 ...... Frame ( 12) shift: 0.68 0.93 ...... Frame ( 13) shift: 0.76 1.01 ...... Frame ( 14) shift: 0.84 1.09 ...... Frame ( 15) shift: 0.93 1.16 ...... Frame ( 16) shift: 1.03 1.21 ...... Frame ( 17) shift: 1.12 1.27 ...... Frame ( 18) shift: 1.18 1.32 ...... Frame ( 19) shift: 1.21 1.37 ...... Frame ( 20) shift: 1.24 1.41 ...... Frame ( 21) shift: 1.31 1.45 ...... Frame ( 22) shift: 1.42 1.48 ...... Frame ( 23) shift: 1.53 1.50 ...... Frame ( 24) shift: 1.65 1.56 ...... Frame ( 25) shift: 1.77 1.65 ...... Frame ( 26) shift: 1.89 1.75 ...... Frame ( 27) shift: 1.97 1.80 ...... Frame ( 28) shift: 2.00 1.81 ...... Frame ( 29) shift: 2.02 1.83 ...... Frame ( 30) shift: 2.06 1.85 ...... Frame ( 31) shift: 2.10 1.89 ...... Frame ( 32) shift: 2.15 1.92 ...... Frame ( 33) shift: 2.18 1.94 ...... Frame ( 34) shift: 2.21 1.94 ...... Frame ( 35) shift: 2.24 1.94 ...... Frame ( 36) shift: 2.29 1.89 ...... Frame ( 37) shift: 2.37 1.80 ...... Frame ( 38) shift: 2.44 1.70 ...... Frame ( 39) shift: 2.52 1.61 ...... Frame ( 40) shift: 2.59 1.52 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.135829 Iteration 2 Error: 0.384022 Iteration 3 Error: 0.155233 Iteration 4 Error: 0.056144 Iteration 5 Error: 0.028177 Align patch 2 23 left Iteration 1 Error: 0.806248 Iteration 2 Error: 0.229902 Iteration 3 Error: 0.087195 Iteration 4 Error: 0.033144 Align patch 3 22 left Iteration 1 Error: 0.996651 Iteration 2 Error: 0.276304 Iteration 3 Error: 0.092394 Iteration 4 Error: 0.036229 Align patch 4 21 left Iteration 1 Error: 0.377760 Iteration 2 Error: 0.048048 Align patch 5 20 left Iteration 1 Error: 0.790412 Iteration 2 Error: 0.049462 Align patch 6 19 left Iteration 1 Error: 0.837769 Iteration 2 Error: 0.386311 Iteration 3 Error: 0.150377 Iteration 4 Error: 0.078358 Iteration 5 Error: 0.036963 Align patch 7 18 left Iteration 1 Error: 0.612554 Iteration 2 Error: 0.131096 Iteration 3 Error: 0.048516 Align patch 8 17 left Iteration 1 Error: 0.768710 Iteration 2 Error: 0.150005 Iteration 3 Error: 0.053265 Iteration 4 Error: 0.016165 Align patch 9 16 left Iteration 1 Error: 0.693451 Iteration 2 Error: 0.088428 Iteration 3 Error: 0.029344 Align patch 10 15 left Iteration 1 Error: 0.771265 Iteration 2 Error: 0.096453 Iteration 3 Error: 0.023932 Align patch 11 14 left Iteration 1 Error: 1.664589 Iteration 2 Error: 0.230199 Iteration 3 Error: 0.089476 Iteration 4 Error: 0.028982 Align patch 12 13 left Iteration 1 Error: 0.666282 Iteration 2 Error: 0.150218 Iteration 3 Error: 0.053791 Iteration 4 Error: 0.025197 Align patch 13 12 left Iteration 1 Error: 0.633721 Iteration 2 Error: 0.066112 Iteration 3 Error: 0.013406 Align patch 14 11 left Iteration 1 Error: 0.736577 Iteration 2 Error: 0.087057 Iteration 3 Error: 0.018689 Align patch 15 10 left Iteration 1 Error: 0.623982 Iteration 2 Error: 0.101552 Iteration 3 Error: 0.023356 Align patch 16 9 left Iteration 1 Error: 0.979170 Iteration 2 Error: 0.136447 Iteration 3 Error: 0.029739 Align patch 17 8 left Iteration 1 Error: 0.542132 Iteration 2 Error: 0.051459 Iteration 3 Error: 0.012668 Align patch 18 7 left Iteration 1 Error: 0.441500 Iteration 2 Error: 0.047417 Align patch 19 6 left Iteration 1 Error: 0.687601 Iteration 2 Error: 0.078927 Iteration 3 Error: 0.017157 Align patch 20 5 left Iteration 1 Error: 0.804061 Iteration 2 Error: 0.095969 Iteration 3 Error: 0.016719 Align patch 21 4 left Iteration 1 Error: 0.633450 Iteration 2 Error: 0.116298 Iteration 3 Error: 0.026993 Align patch 22 3 left Iteration 1 Error: 1.066168 Iteration 2 Error: 0.168796 Iteration 3 Error: 0.026409 Align patch 23 2 left Iteration 1 Error: 0.984529 Iteration 2 Error: 0.179724 Iteration 3 Error: 0.033412 Align patch 24 1 left Iteration 1 Error: 0.756408 Iteration 2 Error: 0.092322 Iteration 3 Error: 0.018480 Align patch 25 0 left Iteration 1 Error: 0.694524 Iteration 2 Error: 0.147067 Iteration 3 Error: 0.037252 3D Fitting completed. Patch alignment time: 11.42(sec) Local motion has been corrected. Process thread exits. Computational time: 23.018532 sec Total time: 33.824242 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00008hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00008hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.495446s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00008hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.274503s ........................................ >>>>>>TIME<<<<<< FFT: 0.965281s Defocus_U Defocus_V Angle CCC 9904.30 10783.20 5.51 0.057130 Final Values Defocus_U Defocus_V Angle CCC 9919.93 10798.84 4.89 0.101472 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00008hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00008hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 40.17 6.83 Num Hot pixels: 198 Hot pixel threshold: 81.14 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.162649 Iteration 2 Error: 0.164772 Iteration 3 Error: 0.045242 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.10 0.11 ...... Frame ( 3) shift: -0.20 0.23 ...... Frame ( 4) shift: -0.30 0.34 ...... Frame ( 5) shift: -0.40 0.46 ...... Frame ( 6) shift: -0.45 0.58 ...... Frame ( 7) shift: -0.43 0.71 ...... Frame ( 8) shift: -0.42 0.85 ...... Frame ( 9) shift: -0.40 0.94 ...... Frame ( 10) shift: -0.38 1.01 ...... Frame ( 11) shift: -0.35 1.07 ...... Frame ( 12) shift: -0.31 1.12 ...... Frame ( 13) shift: -0.26 1.16 ...... Frame ( 14) shift: -0.21 1.20 ...... Frame ( 15) shift: -0.19 1.25 ...... Frame ( 16) shift: -0.20 1.31 ...... Frame ( 17) shift: -0.21 1.37 ...... Frame ( 18) shift: -0.19 1.43 ...... Frame ( 19) shift: -0.13 1.50 ...... Frame ( 20) shift: -0.07 1.57 ...... Frame ( 21) shift: -0.01 1.63 ...... Frame ( 22) shift: 0.06 1.69 ...... Frame ( 23) shift: 0.13 1.74 ...... Frame ( 24) shift: 0.16 1.78 ...... Frame ( 25) shift: 0.16 1.80 ...... Frame ( 26) shift: 0.15 1.82 ...... Frame ( 27) shift: 0.17 1.84 ...... Frame ( 28) shift: 0.21 1.88 ...... Frame ( 29) shift: 0.25 1.92 ...... Frame ( 30) shift: 0.26 1.97 ...... Frame ( 31) shift: 0.24 2.03 ...... Frame ( 32) shift: 0.22 2.08 ...... Frame ( 33) shift: 0.23 2.12 ...... Frame ( 34) shift: 0.26 2.13 ...... Frame ( 35) shift: 0.30 2.15 ...... Frame ( 36) shift: 0.34 2.16 ...... Frame ( 37) shift: 0.39 2.18 ...... Frame ( 38) shift: 0.44 2.19 ...... Frame ( 39) shift: 0.49 2.20 ...... Frame ( 40) shift: 0.55 2.22 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.202122 Iteration 2 Error: 0.254078 Iteration 3 Error: 0.065383 Iteration 4 Error: 0.023580 Align patch 2 23 left Iteration 1 Error: 1.074484 Iteration 2 Error: 0.242403 Iteration 3 Error: 0.056588 Iteration 4 Error: 0.016358 Align patch 3 22 left Iteration 1 Error: 0.615624 Iteration 2 Error: 0.074028 Iteration 3 Error: 0.017035 Align patch 4 21 left Iteration 1 Error: 0.594851 Iteration 2 Error: 0.157238 Iteration 3 Error: 0.025514 Align patch 5 20 left Iteration 1 Error: 0.495871 Iteration 2 Error: 0.109204 Iteration 3 Error: 0.018131 Align patch 6 19 left Iteration 1 Error: 1.103145 Iteration 2 Error: 0.153750 Iteration 3 Error: 0.048647 Align patch 7 18 left Iteration 1 Error: 0.770906 Iteration 2 Error: 0.226619 Iteration 3 Error: 0.058119 Iteration 4 Error: 0.025135 Align patch 8 17 left Iteration 1 Error: 0.466393 Iteration 2 Error: 0.159562 Iteration 3 Error: 0.040341 Align patch 9 16 left Iteration 1 Error: 0.844938 Iteration 2 Error: 0.075082 Iteration 3 Error: 0.017139 Align patch 10 15 left Iteration 1 Error: 0.640030 Iteration 2 Error: 0.083517 Iteration 3 Error: 0.021486 Align patch 11 14 left Iteration 1 Error: 1.020921 Iteration 2 Error: 0.185579 Iteration 3 Error: 0.045564 Align patch 12 13 left Iteration 1 Error: 0.666710 Iteration 2 Error: 0.086255 Iteration 3 Error: 0.035063 Align patch 13 12 left Iteration 1 Error: 0.417673 Iteration 2 Error: 0.104017 Iteration 3 Error: 0.023970 Align patch 14 11 left Iteration 1 Error: 1.006554 Iteration 2 Error: 0.110133 Iteration 3 Error: 0.027437 Align patch 15 10 left Iteration 1 Error: 0.870422 Iteration 2 Error: 0.096631 Iteration 3 Error: 0.013484 Align patch 16 9 left Iteration 1 Error: 0.856154 Iteration 2 Error: 0.072969 Iteration 3 Error: 0.016871 Align patch 17 8 left Iteration 1 Error: 0.416726 Iteration 2 Error: 0.060430 Iteration 3 Error: 0.022617 Align patch 18 7 left Iteration 1 Error: 0.435898 Iteration 2 Error: 0.071076 Iteration 3 Error: 0.014262 Align patch 19 6 left Iteration 1 Error: 0.650894 Iteration 2 Error: 0.160014 Iteration 3 Error: 0.034897 Align patch 20 5 left Iteration 1 Error: 0.582162 Iteration 2 Error: 0.078236 Iteration 3 Error: 0.028158 Align patch 21 4 left Iteration 1 Error: 0.531450 Iteration 2 Error: 0.056494 Iteration 3 Error: 0.019936 Align patch 22 3 left Iteration 1 Error: 0.545533 Iteration 2 Error: 0.083887 Iteration 3 Error: 0.018373 Align patch 23 2 left Iteration 1 Error: 0.768069 Iteration 2 Error: 0.133956 Iteration 3 Error: 0.034123 Align patch 24 1 left Iteration 1 Error: 0.588969 Iteration 2 Error: 0.086739 Iteration 3 Error: 0.015331 Align patch 25 0 left Iteration 1 Error: 0.439740 Iteration 2 Error: 0.091909 Iteration 3 Error: 0.030078 3D Fitting completed. Patch alignment time: 11.77(sec) Local motion has been corrected. Process thread exits. Computational time: 24.480402 sec Total time: 32.182343 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00008hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00008hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.598957s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00008hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.769705s ........................................ >>>>>>TIME<<<<<< FFT: 0.920364s Defocus_U Defocus_V Angle CCC 10441.43 9839.87 85.38 0.050890 Final Values Defocus_U Defocus_V Angle CCC 10438.31 9858.62 85.70 0.090539 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00009hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00009hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.002e-01 CC threshold: 0.736 Mean Std: 39.23 6.95 Num Hot pixels: 220 Hot pixel threshold: 80.92 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.727580 Iteration 2 Error: 0.335955 Iteration 3 Error: 0.070606 Iteration 4 Error: 0.023637 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.50 -0.15 ...... Frame ( 3) shift: -0.99 -0.29 ...... Frame ( 4) shift: -1.49 -0.44 ...... Frame ( 5) shift: -1.99 -0.59 ...... Frame ( 6) shift: -2.26 -0.65 ...... Frame ( 7) shift: -2.30 -0.64 ...... Frame ( 8) shift: -2.34 -0.62 ...... Frame ( 9) shift: -2.31 -0.55 ...... Frame ( 10) shift: -2.21 -0.44 ...... Frame ( 11) shift: -2.10 -0.33 ...... Frame ( 12) shift: -1.98 -0.23 ...... Frame ( 13) shift: -1.85 -0.14 ...... Frame ( 14) shift: -1.72 -0.05 ...... Frame ( 15) shift: -1.58 0.07 ...... Frame ( 16) shift: -1.42 0.21 ...... Frame ( 17) shift: -1.26 0.35 ...... Frame ( 18) shift: -1.08 0.46 ...... Frame ( 19) shift: -0.87 0.53 ...... Frame ( 20) shift: -0.67 0.60 ...... Frame ( 21) shift: -0.55 0.70 ...... Frame ( 22) shift: -0.51 0.82 ...... Frame ( 23) shift: -0.48 0.94 ...... Frame ( 24) shift: -0.44 1.04 ...... Frame ( 25) shift: -0.41 1.11 ...... Frame ( 26) shift: -0.37 1.18 ...... Frame ( 27) shift: -0.32 1.24 ...... Frame ( 28) shift: -0.25 1.29 ...... Frame ( 29) shift: -0.18 1.34 ...... Frame ( 30) shift: -0.10 1.40 ...... Frame ( 31) shift: -0.01 1.46 ...... Frame ( 32) shift: 0.08 1.52 ...... Frame ( 33) shift: 0.14 1.55 ...... Frame ( 34) shift: 0.16 1.56 ...... Frame ( 35) shift: 0.18 1.57 ...... Frame ( 36) shift: 0.22 1.60 ...... Frame ( 37) shift: 0.29 1.66 ...... Frame ( 38) shift: 0.35 1.72 ...... Frame ( 39) shift: 0.41 1.77 ...... Frame ( 40) shift: 0.47 1.83 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.368775 Iteration 2 Error: 0.238297 Iteration 3 Error: 0.116942 Iteration 4 Error: 0.046357 Align patch 2 23 left Iteration 1 Error: 0.874651 Iteration 2 Error: 0.217779 Iteration 3 Error: 0.065717 Iteration 4 Error: 0.031817 Align patch 3 22 left Iteration 1 Error: 0.545497 Iteration 2 Error: 0.108872 Iteration 3 Error: 0.030390 Align patch 4 21 left Iteration 1 Error: 0.505447 Iteration 2 Error: 0.103852 Iteration 3 Error: 0.023216 Align patch 5 20 left Iteration 1 Error: 0.415071 Iteration 2 Error: 0.055629 Iteration 3 Error: 0.017057 Align patch 6 19 left Iteration 1 Error: 1.883932 Iteration 2 Error: 0.332125 Iteration 3 Error: 0.092407 Iteration 4 Error: 0.037193 Align patch 7 18 left Iteration 1 Error: 0.757269 Iteration 2 Error: 0.186313 Iteration 3 Error: 0.037798 Align patch 8 17 left Iteration 1 Error: 0.395943 Iteration 2 Error: 0.089904 Iteration 3 Error: 0.013671 Align patch 9 16 left Iteration 1 Error: 0.434470 Iteration 2 Error: 0.121411 Iteration 3 Error: 0.038358 Align patch 10 15 left Iteration 1 Error: 0.699149 Iteration 2 Error: 0.124074 Iteration 3 Error: 0.027701 Align patch 11 14 left Iteration 1 Error: 1.312814 Iteration 2 Error: 0.130098 Iteration 3 Error: 0.046492 Align patch 12 13 left Iteration 1 Error: 0.561491 Iteration 2 Error: 0.131762 Iteration 3 Error: 0.027202 Align patch 13 12 left Iteration 1 Error: 0.398321 Iteration 2 Error: 0.071475 Iteration 3 Error: 0.017840 Align patch 14 11 left Iteration 1 Error: 0.489147 Iteration 2 Error: 0.062578 Iteration 3 Error: 0.010178 Align patch 15 10 left Iteration 1 Error: 0.611369 Iteration 2 Error: 0.056145 Iteration 3 Error: 0.016140 Align patch 16 9 left Iteration 1 Error: 0.629675 Iteration 2 Error: 0.101994 Iteration 3 Error: 0.034948 Align patch 17 8 left Iteration 1 Error: 0.926247 Iteration 2 Error: 0.077401 Iteration 3 Error: 0.018327 Align patch 18 7 left Iteration 1 Error: 0.565266 Iteration 2 Error: 0.077193 Iteration 3 Error: 0.020059 Align patch 19 6 left Iteration 1 Error: 0.550478 Iteration 2 Error: 0.042219 Align patch 20 5 left Iteration 1 Error: 0.608099 Iteration 2 Error: 0.053262 Iteration 3 Error: 0.010092 Align patch 21 4 left Iteration 1 Error: 2.417428 Iteration 2 Error: 0.488757 Iteration 3 Error: 0.173042 Iteration 4 Error: 0.067330 Iteration 5 Error: 0.027875 Align patch 22 3 left Iteration 1 Error: 1.212509 Iteration 2 Error: 0.215571 Iteration 3 Error: 0.065477 Iteration 4 Error: 0.011321 Align patch 23 2 left Iteration 1 Error: 0.677643 Iteration 2 Error: 0.056844 Iteration 3 Error: 0.020280 Align patch 24 1 left Iteration 1 Error: 0.464476 Iteration 2 Error: 0.069511 Iteration 3 Error: 0.020522 Align patch 25 0 left Iteration 1 Error: 0.747961 Iteration 2 Error: 0.131996 Iteration 3 Error: 0.028928 3D Fitting completed. Patch alignment time: 11.64(sec) Local motion has been corrected. Process thread exits. Computational time: 22.760368 sec Total time: 30.613798 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00009hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00009hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.521072s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00009hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.868171s ........................................ >>>>>>TIME<<<<<< FFT: 1.180551s Defocus_U Defocus_V Angle CCC 12570.31 13394.53 13.35 0.065114 Final Values Defocus_U Defocus_V Angle CCC 12575.00 13408.60 13.67 0.101694 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00009hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00009hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.353e-01 1.006e-01 CC threshold: 0.739 Mean Std: 39.52 7.10 Num Hot pixels: 214 Hot pixel threshold: 82.13 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.567456 Iteration 2 Error: 0.189957 Iteration 3 Error: 0.018942 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.31 -0.20 ...... Frame ( 3) shift: -0.62 -0.40 ...... Frame ( 4) shift: -0.93 -0.60 ...... Frame ( 5) shift: -1.24 -0.80 ...... Frame ( 6) shift: -1.40 -0.88 ...... Frame ( 7) shift: -1.42 -0.84 ...... Frame ( 8) shift: -1.43 -0.80 ...... Frame ( 9) shift: -1.40 -0.74 ...... Frame ( 10) shift: -1.30 -0.67 ...... Frame ( 11) shift: -1.21 -0.59 ...... Frame ( 12) shift: -1.11 -0.52 ...... Frame ( 13) shift: -0.99 -0.44 ...... Frame ( 14) shift: -0.88 -0.36 ...... Frame ( 15) shift: -0.80 -0.27 ...... Frame ( 16) shift: -0.76 -0.17 ...... Frame ( 17) shift: -0.73 -0.07 ...... Frame ( 18) shift: -0.67 0.01 ...... Frame ( 19) shift: -0.59 0.06 ...... Frame ( 20) shift: -0.51 0.12 ...... Frame ( 21) shift: -0.44 0.18 ...... Frame ( 22) shift: -0.38 0.23 ...... Frame ( 23) shift: -0.32 0.29 ...... Frame ( 24) shift: -0.24 0.30 ...... Frame ( 25) shift: -0.15 0.28 ...... Frame ( 26) shift: -0.06 0.26 ...... Frame ( 27) shift: 0.02 0.29 ...... Frame ( 28) shift: 0.07 0.36 ...... Frame ( 29) shift: 0.12 0.44 ...... Frame ( 30) shift: 0.18 0.50 ...... Frame ( 31) shift: 0.23 0.56 ...... Frame ( 32) shift: 0.29 0.61 ...... Frame ( 33) shift: 0.34 0.67 ...... Frame ( 34) shift: 0.39 0.72 ...... Frame ( 35) shift: 0.44 0.77 ...... Frame ( 36) shift: 0.50 0.84 ...... Frame ( 37) shift: 0.57 0.91 ...... Frame ( 38) shift: 0.64 0.97 ...... Frame ( 39) shift: 0.71 1.04 ...... Frame ( 40) shift: 0.78 1.11 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.832951 Iteration 2 Error: 0.171533 Iteration 3 Error: 0.032022 Align patch 2 23 left Iteration 1 Error: 0.624106 Iteration 2 Error: 0.072168 Iteration 3 Error: 0.019729 Align patch 3 22 left Iteration 1 Error: 0.629817 Iteration 2 Error: 0.081559 Iteration 3 Error: 0.020815 Align patch 4 21 left Iteration 1 Error: 0.419746 Iteration 2 Error: 0.040951 Align patch 5 20 left Iteration 1 Error: 0.583314 Iteration 2 Error: 0.098237 Iteration 3 Error: 0.023755 Align patch 6 19 left Iteration 1 Error: 1.040565 Iteration 2 Error: 0.139900 Iteration 3 Error: 0.025718 Align patch 7 18 left Iteration 1 Error: 0.550952 Iteration 2 Error: 0.099496 Iteration 3 Error: 0.029141 Align patch 8 17 left Iteration 1 Error: 0.513878 Iteration 2 Error: 0.069596 Iteration 3 Error: 0.012511 Align patch 9 16 left Iteration 1 Error: 0.581680 Iteration 2 Error: 0.053062 Iteration 3 Error: 0.013764 Align patch 10 15 left Iteration 1 Error: 0.500737 Iteration 2 Error: 0.042511 Align patch 11 14 left Iteration 1 Error: 0.729686 Iteration 2 Error: 0.146175 Iteration 3 Error: 0.021944 Align patch 12 13 left Iteration 1 Error: 0.572701 Iteration 2 Error: 0.063046 Iteration 3 Error: 0.015796 Align patch 13 12 left Iteration 1 Error: 0.546359 Iteration 2 Error: 0.058225 Iteration 3 Error: 0.011289 Align patch 14 11 left Iteration 1 Error: 0.878665 Iteration 2 Error: 0.068257 Iteration 3 Error: 0.018108 Align patch 15 10 left Iteration 1 Error: 1.029474 Iteration 2 Error: 0.043979 Align patch 16 9 left Iteration 1 Error: 0.792642 Iteration 2 Error: 0.190914 Iteration 3 Error: 0.058331 Iteration 4 Error: 0.018764 Align patch 17 8 left Iteration 1 Error: 0.469551 Iteration 2 Error: 0.075360 Iteration 3 Error: 0.017241 Align patch 18 7 left Iteration 1 Error: 0.519788 Iteration 2 Error: 0.111137 Iteration 3 Error: 0.028110 Align patch 19 6 left Iteration 1 Error: 0.314282 Iteration 2 Error: 0.036125 Align patch 20 5 left Iteration 1 Error: 0.643478 Iteration 2 Error: 0.034786 Align patch 21 4 left Iteration 1 Error: 0.852926 Iteration 2 Error: 0.088709 Iteration 3 Error: 0.015497 Align patch 22 3 left Iteration 1 Error: 0.685086 Iteration 2 Error: 0.070077 Iteration 3 Error: 0.017567 Align patch 23 2 left Iteration 1 Error: 0.608102 Iteration 2 Error: 0.104931 Iteration 3 Error: 0.018259 Align patch 24 1 left Iteration 1 Error: 0.808702 Iteration 2 Error: 0.074216 Iteration 3 Error: 0.012941 Align patch 25 0 left Iteration 1 Error: 0.574886 Iteration 2 Error: 0.026445 3D Fitting completed. Patch alignment time: 11.39(sec) Local motion has been corrected. Process thread exits. Computational time: 21.407742 sec Total time: 29.290127 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00009hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00009hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.519405s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00009hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.502768s ........................................ >>>>>>TIME<<<<<< FFT: 0.946842s Defocus_U Defocus_V Angle CCC 13373.07 12857.43 89.05 0.082926 Final Values Defocus_U Defocus_V Angle CCC 13366.82 12869.93 88.42 0.131024 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00009hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00009hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.736 Mean Std: 41.64 7.05 Num Hot pixels: 212 Hot pixel threshold: 83.95 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.039409 Iteration 2 Error: 0.167248 Iteration 3 Error: 0.032893 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.26 -0.20 ...... Frame ( 3) shift: -0.52 -0.41 ...... Frame ( 4) shift: -0.78 -0.61 ...... Frame ( 5) shift: -1.04 -0.82 ...... Frame ( 6) shift: -1.16 -0.92 ...... Frame ( 7) shift: -1.13 -0.93 ...... Frame ( 8) shift: -1.11 -0.93 ...... Frame ( 9) shift: -1.06 -0.89 ...... Frame ( 10) shift: -0.99 -0.81 ...... Frame ( 11) shift: -0.93 -0.72 ...... Frame ( 12) shift: -0.87 -0.64 ...... Frame ( 13) shift: -0.83 -0.56 ...... Frame ( 14) shift: -0.79 -0.48 ...... Frame ( 15) shift: -0.70 -0.39 ...... Frame ( 16) shift: -0.56 -0.30 ...... Frame ( 17) shift: -0.43 -0.21 ...... Frame ( 18) shift: -0.34 -0.16 ...... Frame ( 19) shift: -0.29 -0.17 ...... Frame ( 20) shift: -0.24 -0.17 ...... Frame ( 21) shift: -0.16 -0.13 ...... Frame ( 22) shift: -0.07 -0.05 ...... Frame ( 23) shift: 0.02 0.02 ...... Frame ( 24) shift: 0.09 0.13 ...... Frame ( 25) shift: 0.14 0.27 ...... Frame ( 26) shift: 0.19 0.41 ...... Frame ( 27) shift: 0.22 0.49 ...... Frame ( 28) shift: 0.22 0.54 ...... Frame ( 29) shift: 0.23 0.58 ...... Frame ( 30) shift: 0.20 0.61 ...... Frame ( 31) shift: 0.15 0.64 ...... Frame ( 32) shift: 0.09 0.67 ...... Frame ( 33) shift: 0.06 0.69 ...... Frame ( 34) shift: 0.04 0.69 ...... Frame ( 35) shift: 0.03 0.70 ...... Frame ( 36) shift: 0.00 0.71 ...... Frame ( 37) shift: -0.03 0.71 ...... Frame ( 38) shift: -0.06 0.72 ...... Frame ( 39) shift: -0.10 0.72 ...... Frame ( 40) shift: -0.13 0.73 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.625861 Iteration 2 Error: 0.234958 Iteration 3 Error: 0.068148 Iteration 4 Error: 0.034936 Align patch 2 23 left Iteration 1 Error: 1.333665 Iteration 2 Error: 0.146332 Iteration 3 Error: 0.042757 Align patch 3 22 left Iteration 1 Error: 0.942628 Iteration 2 Error: 0.109962 Iteration 3 Error: 0.027812 Align patch 4 21 left Iteration 1 Error: 0.758054 Iteration 2 Error: 0.083320 Iteration 3 Error: 0.016810 Align patch 5 20 left Iteration 1 Error: 0.490543 Iteration 2 Error: 0.058273 Iteration 3 Error: 0.009297 Align patch 6 19 left Iteration 1 Error: 0.887452 Iteration 2 Error: 0.135883 Iteration 3 Error: 0.025122 Align patch 7 18 left Iteration 1 Error: 0.756588 Iteration 2 Error: 0.166216 Iteration 3 Error: 0.045828 Align patch 8 17 left Iteration 1 Error: 0.756725 Iteration 2 Error: 0.109961 Iteration 3 Error: 0.016093 Align patch 9 16 left Iteration 1 Error: 0.613585 Iteration 2 Error: 0.088928 Iteration 3 Error: 0.020651 Align patch 10 15 left Iteration 1 Error: 0.435061 Iteration 2 Error: 0.065993 Iteration 3 Error: 0.011699 Align patch 11 14 left Iteration 1 Error: 0.599022 Iteration 2 Error: 0.138484 Iteration 3 Error: 0.038546 Align patch 12 13 left Iteration 1 Error: 0.777629 Iteration 2 Error: 0.215560 Iteration 3 Error: 0.056596 Iteration 4 Error: 0.020232 Align patch 13 12 left Iteration 1 Error: 0.663437 Iteration 2 Error: 0.109821 Iteration 3 Error: 0.034266 Align patch 14 11 left Iteration 1 Error: 0.540452 Iteration 2 Error: 0.078251 Iteration 3 Error: 0.017318 Align patch 15 10 left Iteration 1 Error: 0.552158 Iteration 2 Error: 0.074018 Iteration 3 Error: 0.016532 Align patch 16 9 left Iteration 1 Error: 0.665997 Iteration 2 Error: 0.173309 Iteration 3 Error: 0.036188 Align patch 17 8 left Iteration 1 Error: 0.735586 Iteration 2 Error: 0.146242 Iteration 3 Error: 0.026674 Align patch 18 7 left Iteration 1 Error: 0.467126 Iteration 2 Error: 0.066124 Iteration 3 Error: 0.011835 Align patch 19 6 left Iteration 1 Error: 0.647375 Iteration 2 Error: 0.098453 Iteration 3 Error: 0.015179 Align patch 20 5 left Iteration 1 Error: 0.528154 Iteration 2 Error: 0.074130 Iteration 3 Error: 0.010730 Align patch 21 4 left Iteration 1 Error: 1.027774 Iteration 2 Error: 0.204448 Iteration 3 Error: 0.024243 Align patch 22 3 left Iteration 1 Error: 0.618919 Iteration 2 Error: 0.071812 Iteration 3 Error: 0.011319 Align patch 23 2 left Iteration 1 Error: 0.532901 Iteration 2 Error: 0.104364 Iteration 3 Error: 0.018385 Align patch 24 1 left Iteration 1 Error: 0.638673 Iteration 2 Error: 0.100438 Iteration 3 Error: 0.017294 Align patch 25 0 left Iteration 1 Error: 0.607861 Iteration 2 Error: 0.047786 3D Fitting completed. Patch alignment time: 11.30(sec) Local motion has been corrected. Process thread exits. Computational time: 25.278423 sec Total time: 33.740822 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00009hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00009hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.641473s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00009hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.630821s ........................................ >>>>>>TIME<<<<<< FFT: 0.919247s Defocus_U Defocus_V Angle CCC 11554.69 12414.06 6.45 0.061568 Final Values Defocus_U Defocus_V Angle CCC 11571.89 12437.52 6.14 0.105418 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00009hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00009hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 38.61 6.95 Num Hot pixels: 200 Hot pixel threshold: 80.34 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.947484 Iteration 2 Error: 0.392342 Iteration 3 Error: 0.108754 Iteration 4 Error: 0.043082 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.25 -0.25 ...... Frame ( 3) shift: -0.51 -0.49 ...... Frame ( 4) shift: -0.76 -0.74 ...... Frame ( 5) shift: -1.01 -0.98 ...... Frame ( 6) shift: -1.14 -1.12 ...... Frame ( 7) shift: -1.14 -1.15 ...... Frame ( 8) shift: -1.14 -1.18 ...... Frame ( 9) shift: -1.13 -1.16 ...... Frame ( 10) shift: -1.11 -1.09 ...... Frame ( 11) shift: -1.10 -1.02 ...... Frame ( 12) shift: -1.09 -0.95 ...... Frame ( 13) shift: -1.07 -0.87 ...... Frame ( 14) shift: -1.06 -0.80 ...... Frame ( 15) shift: -1.06 -0.71 ...... Frame ( 16) shift: -1.08 -0.62 ...... Frame ( 17) shift: -1.09 -0.52 ...... Frame ( 18) shift: -1.08 -0.43 ...... Frame ( 19) shift: -1.04 -0.33 ...... Frame ( 20) shift: -1.00 -0.24 ...... Frame ( 21) shift: -1.00 -0.13 ...... Frame ( 22) shift: -1.03 0.01 ...... Frame ( 23) shift: -1.06 0.15 ...... Frame ( 24) shift: -1.07 0.32 ...... Frame ( 25) shift: -1.05 0.53 ...... Frame ( 26) shift: -1.03 0.73 ...... Frame ( 27) shift: -1.04 0.93 ...... Frame ( 28) shift: -1.06 1.13 ...... Frame ( 29) shift: -1.09 1.34 ...... Frame ( 30) shift: -1.04 1.49 ...... Frame ( 31) shift: -0.91 1.60 ...... Frame ( 32) shift: -0.79 1.71 ...... Frame ( 33) shift: -0.74 1.79 ...... Frame ( 34) shift: -0.77 1.84 ...... Frame ( 35) shift: -0.79 1.90 ...... Frame ( 36) shift: -0.77 2.00 ...... Frame ( 37) shift: -0.70 2.15 ...... Frame ( 38) shift: -0.63 2.31 ...... Frame ( 39) shift: -0.56 2.47 ...... Frame ( 40) shift: -0.49 2.62 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 3.654797 Iteration 2 Error: 1.156525 Iteration 3 Error: 0.260710 Iteration 4 Error: 0.099097 Iteration 5 Error: 0.041906 Align patch 2 23 left Iteration 1 Error: 2.544777 Iteration 2 Error: 1.160101 Iteration 3 Error: 0.325671 Iteration 4 Error: 0.134923 Iteration 5 Error: 0.049502 Align patch 3 22 left Iteration 1 Error: 2.590882 Iteration 2 Error: 0.980368 Iteration 3 Error: 0.300342 Iteration 4 Error: 0.128529 Iteration 5 Error: 0.051402 Align patch 3 22 left Iteration 1 Error: 2.579633 Iteration 2 Error: 0.520471 Iteration 3 Error: 0.103165 Iteration 4 Error: 0.026301 Align patch 4 21 left Iteration 1 Error: 0.527132 Iteration 2 Error: 0.099974 Iteration 3 Error: 0.038027 Align patch 5 20 left Iteration 1 Error: 2.940941 Iteration 2 Error: 0.469097 Iteration 3 Error: 0.070214 Iteration 4 Error: 0.015903 Align patch 6 19 left Iteration 1 Error: 2.321882 Iteration 2 Error: 0.707416 Iteration 3 Error: 0.207355 Iteration 4 Error: 0.078081 Iteration 5 Error: 0.031466 Align patch 7 18 left Iteration 1 Error: 2.481305 Iteration 2 Error: 0.645570 Iteration 3 Error: 0.232022 Iteration 4 Error: 0.070612 Iteration 5 Error: 0.026861 Align patch 8 17 left Iteration 1 Error: 1.212573 Iteration 2 Error: 0.207173 Iteration 3 Error: 0.045620 Align patch 9 16 left Iteration 1 Error: 0.870362 Iteration 2 Error: 0.086251 Iteration 3 Error: 0.013654 Align patch 10 15 left Iteration 1 Error: 2.493072 Iteration 2 Error: 0.334519 Iteration 3 Error: 0.046198 Align patch 11 14 left Iteration 1 Error: 3.843210 Iteration 2 Error: 0.991994 Iteration 3 Error: 0.494069 Iteration 4 Error: 0.289427 Iteration 5 Error: 0.167297 Align patch 11 14 left Iteration 1 Error: 3.623974 Iteration 2 Error: 0.642175 Iteration 3 Error: 0.171689 Iteration 4 Error: 0.063972 Iteration 5 Error: 0.020450 Align patch 12 13 left Iteration 1 Error: 1.790418 Iteration 2 Error: 0.352106 Iteration 3 Error: 0.052355 Iteration 4 Error: 0.017527 Align patch 13 12 left Iteration 1 Error: 0.509849 Iteration 2 Error: 0.042679 Align patch 14 11 left Iteration 1 Error: 1.053227 Iteration 2 Error: 0.131164 Iteration 3 Error: 0.020808 Align patch 15 10 left Iteration 1 Error: 1.671557 Iteration 2 Error: 0.210506 Iteration 3 Error: 0.047607 Align patch 16 9 left Iteration 1 Error: 1.031495 Iteration 2 Error: 0.277280 Iteration 3 Error: 0.065511 Iteration 4 Error: 0.027679 Align patch 17 8 left Iteration 1 Error: 1.036897 Iteration 2 Error: 0.114236 Iteration 3 Error: 0.036226 Align patch 18 7 left Iteration 1 Error: 0.644724 Iteration 2 Error: 0.085589 Iteration 3 Error: 0.015962 Align patch 19 6 left Iteration 1 Error: 1.312298 Iteration 2 Error: 0.218302 Iteration 3 Error: 0.053685 Iteration 4 Error: 0.012731 Align patch 20 5 left Iteration 1 Error: 1.346973 Iteration 2 Error: 0.249117 Iteration 3 Error: 0.051683 Iteration 4 Error: 0.013035 Align patch 21 4 left Iteration 1 Error: 1.021824 Iteration 2 Error: 0.233473 Iteration 3 Error: 0.057965 Iteration 4 Error: 0.017273 Align patch 22 3 left Iteration 1 Error: 0.869962 Iteration 2 Error: 0.232240 Iteration 3 Error: 0.039369 Align patch 23 2 left Iteration 1 Error: 0.760941 Iteration 2 Error: 0.169810 Iteration 3 Error: 0.027743 Align patch 24 1 left Iteration 1 Error: 1.554469 Iteration 2 Error: 0.163339 Iteration 3 Error: 0.030570 Align patch 25 0 left Iteration 1 Error: 1.154670 Iteration 2 Error: 0.261738 Iteration 3 Error: 0.037958 3D Fitting completed. Patch alignment time: 14.03(sec) Local motion has been corrected. Process thread exits. Computational time: 24.980852 sec Total time: 31.550060 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00009hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00009hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.457768s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00009hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.291308s ........................................ >>>>>>TIME<<<<<< FFT: 1.197553s Defocus_U Defocus_V Angle CCC 13201.18 12521.48 82.78 0.064992 Final Values Defocus_U Defocus_V Angle CCC 13204.31 12537.12 83.41 0.103385 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00010hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00010hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 40.89 7.04 Num Hot pixels: 222 Hot pixel threshold: 83.12 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.161292 Iteration 2 Error: 0.182195 Iteration 3 Error: 0.040537 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.34 -0.16 ...... Frame ( 3) shift: -0.69 -0.31 ...... Frame ( 4) shift: -1.03 -0.47 ...... Frame ( 5) shift: -1.37 -0.63 ...... Frame ( 6) shift: -1.56 -0.67 ...... Frame ( 7) shift: -1.58 -0.58 ...... Frame ( 8) shift: -1.60 -0.50 ...... Frame ( 9) shift: -1.61 -0.41 ...... Frame ( 10) shift: -1.59 -0.31 ...... Frame ( 11) shift: -1.58 -0.20 ...... Frame ( 12) shift: -1.52 -0.08 ...... Frame ( 13) shift: -1.43 0.06 ...... Frame ( 14) shift: -1.34 0.19 ...... Frame ( 15) shift: -1.28 0.26 ...... Frame ( 16) shift: -1.26 0.26 ...... Frame ( 17) shift: -1.24 0.27 ...... Frame ( 18) shift: -1.22 0.33 ...... Frame ( 19) shift: -1.19 0.46 ...... Frame ( 20) shift: -1.16 0.59 ...... Frame ( 21) shift: -1.10 0.66 ...... Frame ( 22) shift: -1.00 0.68 ...... Frame ( 23) shift: -0.89 0.69 ...... Frame ( 24) shift: -0.85 0.73 ...... Frame ( 25) shift: -0.86 0.80 ...... Frame ( 26) shift: -0.87 0.86 ...... Frame ( 27) shift: -0.86 0.95 ...... Frame ( 28) shift: -0.82 1.06 ...... Frame ( 29) shift: -0.77 1.17 ...... Frame ( 30) shift: -0.78 1.26 ...... Frame ( 31) shift: -0.85 1.33 ...... Frame ( 32) shift: -0.92 1.40 ...... Frame ( 33) shift: -0.92 1.46 ...... Frame ( 34) shift: -0.86 1.49 ...... Frame ( 35) shift: -0.80 1.53 ...... Frame ( 36) shift: -0.75 1.55 ...... Frame ( 37) shift: -0.71 1.57 ...... Frame ( 38) shift: -0.66 1.59 ...... Frame ( 39) shift: -0.62 1.60 ...... Frame ( 40) shift: -0.58 1.62 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.176516 Iteration 2 Error: 0.192009 Iteration 3 Error: 0.054895 Iteration 4 Error: 0.026705 Align patch 2 23 left Iteration 1 Error: 1.127136 Iteration 2 Error: 0.176888 Iteration 3 Error: 0.059717 Iteration 4 Error: 0.016561 Align patch 3 22 left Iteration 1 Error: 0.483278 Iteration 2 Error: 0.087034 Iteration 3 Error: 0.028228 Align patch 4 21 left Iteration 1 Error: 0.644341 Iteration 2 Error: 0.093858 Iteration 3 Error: 0.017144 Align patch 5 20 left Iteration 1 Error: 0.544268 Iteration 2 Error: 0.090580 Iteration 3 Error: 0.017046 Align patch 6 19 left Iteration 1 Error: 0.601454 Iteration 2 Error: 0.093739 Iteration 3 Error: 0.024813 Align patch 7 18 left Iteration 1 Error: 0.758998 Iteration 2 Error: 0.162566 Iteration 3 Error: 0.039321 Align patch 8 17 left Iteration 1 Error: 0.714343 Iteration 2 Error: 0.106897 Iteration 3 Error: 0.024353 Align patch 9 16 left Iteration 1 Error: 0.699829 Iteration 2 Error: 0.084024 Iteration 3 Error: 0.021401 Align patch 10 15 left Iteration 1 Error: 0.473593 Iteration 2 Error: 0.043554 Align patch 11 14 left Iteration 1 Error: 0.584828 Iteration 2 Error: 0.122726 Iteration 3 Error: 0.019631 Align patch 12 13 left Iteration 1 Error: 0.624840 Iteration 2 Error: 0.083706 Iteration 3 Error: 0.018972 Align patch 13 12 left Iteration 1 Error: 0.509425 Iteration 2 Error: 0.102217 Iteration 3 Error: 0.020546 Align patch 14 11 left Iteration 1 Error: 0.491906 Iteration 2 Error: 0.079014 Iteration 3 Error: 0.016860 Align patch 15 10 left Iteration 1 Error: 0.528141 Iteration 2 Error: 0.054447 Iteration 3 Error: 0.016161 Align patch 16 9 left Iteration 1 Error: 0.627715 Iteration 2 Error: 0.175904 Iteration 3 Error: 0.034549 Align patch 17 8 left Iteration 1 Error: 1.093555 Iteration 2 Error: 0.133977 Iteration 3 Error: 0.020964 Align patch 18 7 left Iteration 1 Error: 0.588409 Iteration 2 Error: 0.079316 Iteration 3 Error: 0.016485 Align patch 19 6 left Iteration 1 Error: 0.787365 Iteration 2 Error: 0.107675 Iteration 3 Error: 0.018550 Align patch 20 5 left Iteration 1 Error: 0.458403 Iteration 2 Error: 0.079048 Iteration 3 Error: 0.015132 Align patch 21 4 left Iteration 1 Error: 0.864654 Iteration 2 Error: 0.166478 Iteration 3 Error: 0.049456 Align patch 22 3 left Iteration 1 Error: 0.739868 Iteration 2 Error: 0.077088 Iteration 3 Error: 0.014767 Align patch 23 2 left Iteration 1 Error: 0.821663 Iteration 2 Error: 0.066751 Iteration 3 Error: 0.015114 Align patch 24 1 left Iteration 1 Error: 0.554227 Iteration 2 Error: 0.090063 Iteration 3 Error: 0.010458 Align patch 25 0 left Iteration 1 Error: 0.510131 Iteration 2 Error: 0.143776 Iteration 3 Error: 0.019712 3D Fitting completed. Patch alignment time: 11.30(sec) Local motion has been corrected. Process thread exits. Computational time: 22.041920 sec Total time: 29.847544 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00010hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00010hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.696821s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00010hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.196164s ........................................ >>>>>>TIME<<<<<< FFT: 0.960728s Defocus_U Defocus_V Angle CCC 9011.72 9828.12 12.26 0.050819 Final Values Defocus_U Defocus_V Angle CCC 9003.90 9848.45 12.57 0.095059 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00010hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00010hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.352e-01 1.005e-01 CC threshold: 0.738 Mean Std: 39.72 7.11 Num Hot pixels: 205 Hot pixel threshold: 82.36 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.745334 Iteration 2 Error: 0.112375 Iteration 3 Error: 0.022387 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.21 -0.12 ...... Frame ( 3) shift: -0.42 -0.24 ...... Frame ( 4) shift: -0.63 -0.36 ...... Frame ( 5) shift: -0.84 -0.48 ...... Frame ( 6) shift: -0.93 -0.53 ...... Frame ( 7) shift: -0.91 -0.52 ...... Frame ( 8) shift: -0.89 -0.52 ...... Frame ( 9) shift: -0.86 -0.48 ...... Frame ( 10) shift: -0.82 -0.43 ...... Frame ( 11) shift: -0.78 -0.37 ...... Frame ( 12) shift: -0.73 -0.29 ...... Frame ( 13) shift: -0.68 -0.20 ...... Frame ( 14) shift: -0.64 -0.12 ...... Frame ( 15) shift: -0.59 -0.10 ...... Frame ( 16) shift: -0.56 -0.16 ...... Frame ( 17) shift: -0.53 -0.22 ...... Frame ( 18) shift: -0.52 -0.24 ...... Frame ( 19) shift: -0.52 -0.22 ...... Frame ( 20) shift: -0.53 -0.21 ...... Frame ( 21) shift: -0.51 -0.17 ...... Frame ( 22) shift: -0.45 -0.12 ...... Frame ( 23) shift: -0.40 -0.07 ...... Frame ( 24) shift: -0.38 0.01 ...... Frame ( 25) shift: -0.39 0.10 ...... Frame ( 26) shift: -0.40 0.20 ...... Frame ( 27) shift: -0.38 0.28 ...... Frame ( 28) shift: -0.31 0.36 ...... Frame ( 29) shift: -0.24 0.44 ...... Frame ( 30) shift: -0.24 0.48 ...... Frame ( 31) shift: -0.31 0.49 ...... Frame ( 32) shift: -0.38 0.50 ...... Frame ( 33) shift: -0.41 0.53 ...... Frame ( 34) shift: -0.40 0.58 ...... Frame ( 35) shift: -0.38 0.63 ...... Frame ( 36) shift: -0.36 0.68 ...... Frame ( 37) shift: -0.33 0.72 ...... Frame ( 38) shift: -0.30 0.77 ...... Frame ( 39) shift: -0.26 0.81 ...... Frame ( 40) shift: -0.23 0.85 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.923069 Iteration 2 Error: 0.149440 Iteration 3 Error: 0.026346 Align patch 2 23 left Iteration 1 Error: 0.619457 Iteration 2 Error: 0.077159 Iteration 3 Error: 0.015033 Align patch 3 22 left Iteration 1 Error: 0.575504 Iteration 2 Error: 0.082925 Iteration 3 Error: 0.010631 Align patch 4 21 left Iteration 1 Error: 0.456717 Iteration 2 Error: 0.053322 Iteration 3 Error: 0.007195 Align patch 5 20 left Iteration 1 Error: 0.350868 Iteration 2 Error: 0.045297 Align patch 6 19 left Iteration 1 Error: 0.721616 Iteration 2 Error: 0.184331 Iteration 3 Error: 0.029858 Align patch 7 18 left Iteration 1 Error: 0.733567 Iteration 2 Error: 0.153209 Iteration 3 Error: 0.041285 Align patch 8 17 left Iteration 1 Error: 0.607155 Iteration 2 Error: 0.150888 Iteration 3 Error: 0.021725 Align patch 9 16 left Iteration 1 Error: 0.483930 Iteration 2 Error: 0.068526 Iteration 3 Error: 0.013634 Align patch 10 15 left Iteration 1 Error: 0.635636 Iteration 2 Error: 0.112168 Iteration 3 Error: 0.020187 Align patch 11 14 left Iteration 1 Error: 0.978181 Iteration 2 Error: 0.119242 Iteration 3 Error: 0.029663 Align patch 12 13 left Iteration 1 Error: 0.709568 Iteration 2 Error: 0.085568 Iteration 3 Error: 0.023441 Align patch 13 12 left Iteration 1 Error: 0.472821 Iteration 2 Error: 0.054589 Iteration 3 Error: 0.011099 Align patch 14 11 left Iteration 1 Error: 0.580540 Iteration 2 Error: 0.086157 Iteration 3 Error: 0.026043 Align patch 15 10 left Iteration 1 Error: 1.103676 Iteration 2 Error: 0.182244 Iteration 3 Error: 0.027169 Align patch 16 9 left Iteration 1 Error: 0.697141 Iteration 2 Error: 0.112994 Iteration 3 Error: 0.020786 Align patch 17 8 left Iteration 1 Error: 0.726893 Iteration 2 Error: 0.118893 Iteration 3 Error: 0.037650 Align patch 18 7 left Iteration 1 Error: 0.668337 Iteration 2 Error: 0.103842 Iteration 3 Error: 0.013567 Align patch 19 6 left Iteration 1 Error: 0.445122 Iteration 2 Error: 0.064327 Iteration 3 Error: 0.011798 Align patch 20 5 left Iteration 1 Error: 0.696169 Iteration 2 Error: 0.102169 Iteration 3 Error: 0.011325 Align patch 21 4 left Iteration 1 Error: 0.647447 Iteration 2 Error: 0.097801 Iteration 3 Error: 0.024740 Align patch 22 3 left Iteration 1 Error: 0.420669 Iteration 2 Error: 0.047292 Align patch 23 2 left Iteration 1 Error: 0.555609 Iteration 2 Error: 0.070590 Iteration 3 Error: 0.015319 Align patch 24 1 left Iteration 1 Error: 0.543322 Iteration 2 Error: 0.130859 Iteration 3 Error: 0.023471 Align patch 25 0 left Iteration 1 Error: 0.582182 Iteration 2 Error: 0.086908 Iteration 3 Error: 0.020827 3D Fitting completed. Patch alignment time: 11.10(sec) Local motion has been corrected. Process thread exits. Computational time: 22.358927 sec Total time: 29.790234 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00010hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00010hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.641298s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00010hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.063967s ........................................ >>>>>>TIME<<<<<< FFT: 1.042115s Defocus_U Defocus_V Angle CCC 11503.95 12015.68 1.97 0.051582 Final Values Defocus_U Defocus_V Angle CCC 11510.20 12037.57 2.29 0.085505 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00010hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00010hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 41.16 7.06 Num Hot pixels: 234 Hot pixel threshold: 83.54 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.081198 Iteration 2 Error: 0.160189 Iteration 3 Error: 0.031354 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.34 -0.11 ...... Frame ( 3) shift: -0.68 -0.21 ...... Frame ( 4) shift: -1.01 -0.32 ...... Frame ( 5) shift: -1.35 -0.43 ...... Frame ( 6) shift: -1.51 -0.44 ...... Frame ( 7) shift: -1.50 -0.36 ...... Frame ( 8) shift: -1.48 -0.29 ...... Frame ( 9) shift: -1.43 -0.18 ...... Frame ( 10) shift: -1.33 -0.03 ...... Frame ( 11) shift: -1.24 0.11 ...... Frame ( 12) shift: -1.15 0.23 ...... Frame ( 13) shift: -1.09 0.34 ...... Frame ( 14) shift: -1.02 0.44 ...... Frame ( 15) shift: -0.97 0.51 ...... Frame ( 16) shift: -0.94 0.54 ...... Frame ( 17) shift: -0.90 0.58 ...... Frame ( 18) shift: -0.89 0.63 ...... Frame ( 19) shift: -0.89 0.71 ...... Frame ( 20) shift: -0.90 0.78 ...... Frame ( 21) shift: -0.90 0.79 ...... Frame ( 22) shift: -0.89 0.74 ...... Frame ( 23) shift: -0.89 0.68 ...... Frame ( 24) shift: -0.87 0.66 ...... Frame ( 25) shift: -0.84 0.69 ...... Frame ( 26) shift: -0.82 0.71 ...... Frame ( 27) shift: -0.75 0.72 ...... Frame ( 28) shift: -0.65 0.73 ...... Frame ( 29) shift: -0.54 0.75 ...... Frame ( 30) shift: -0.44 0.81 ...... Frame ( 31) shift: -0.35 0.91 ...... Frame ( 32) shift: -0.26 1.02 ...... Frame ( 33) shift: -0.23 1.05 ...... Frame ( 34) shift: -0.25 0.99 ...... Frame ( 35) shift: -0.28 0.93 ...... Frame ( 36) shift: -0.26 0.89 ...... Frame ( 37) shift: -0.20 0.88 ...... Frame ( 38) shift: -0.14 0.86 ...... Frame ( 39) shift: -0.08 0.85 ...... Frame ( 40) shift: -0.01 0.83 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.941588 Iteration 2 Error: 0.123414 Iteration 3 Error: 0.032514 Align patch 2 23 left Iteration 1 Error: 1.102094 Iteration 2 Error: 0.128228 Iteration 3 Error: 0.017785 Align patch 3 22 left Iteration 1 Error: 0.887074 Iteration 2 Error: 0.106944 Iteration 3 Error: 0.033557 Align patch 4 21 left Iteration 1 Error: 0.817583 Iteration 2 Error: 0.128996 Iteration 3 Error: 0.030405 Align patch 5 20 left Iteration 1 Error: 0.908974 Iteration 2 Error: 0.244607 Iteration 3 Error: 0.035246 Align patch 6 19 left Iteration 1 Error: 1.314892 Iteration 2 Error: 0.160971 Iteration 3 Error: 0.047226 Align patch 7 18 left Iteration 1 Error: 1.135460 Iteration 2 Error: 0.142447 Iteration 3 Error: 0.033004 Align patch 8 17 left Iteration 1 Error: 0.721198 Iteration 2 Error: 0.182041 Iteration 3 Error: 0.033654 Align patch 9 16 left Iteration 1 Error: 0.623912 Iteration 2 Error: 0.066382 Iteration 3 Error: 0.011593 Align patch 10 15 left Iteration 1 Error: 0.658614 Iteration 2 Error: 0.142071 Iteration 3 Error: 0.030409 Align patch 11 14 left Iteration 1 Error: 0.718682 Iteration 2 Error: 0.103352 Iteration 3 Error: 0.026773 Align patch 12 13 left Iteration 1 Error: 0.570705 Iteration 2 Error: 0.165410 Iteration 3 Error: 0.048089 Align patch 13 12 left Iteration 1 Error: 0.594117 Iteration 2 Error: 0.092078 Iteration 3 Error: 0.020689 Align patch 14 11 left Iteration 1 Error: 0.559474 Iteration 2 Error: 0.061820 Iteration 3 Error: 0.019194 Align patch 15 10 left Iteration 1 Error: 0.715948 Iteration 2 Error: 0.144051 Iteration 3 Error: 0.024396 Align patch 16 9 left Iteration 1 Error: 1.062049 Iteration 2 Error: 0.145597 Iteration 3 Error: 0.052006 Iteration 4 Error: 0.020224 Align patch 17 8 left Iteration 1 Error: 0.938931 Iteration 2 Error: 0.166829 Iteration 3 Error: 0.041974 Align patch 18 7 left Iteration 1 Error: 0.524451 Iteration 2 Error: 0.068751 Iteration 3 Error: 0.011118 Align patch 19 6 left Iteration 1 Error: 0.758738 Iteration 2 Error: 0.110005 Iteration 3 Error: 0.014998 Align patch 20 5 left Iteration 1 Error: 0.674363 Iteration 2 Error: 0.119705 Iteration 3 Error: 0.022537 Align patch 21 4 left Iteration 1 Error: 0.776034 Iteration 2 Error: 0.136717 Iteration 3 Error: 0.033031 Align patch 22 3 left Iteration 1 Error: 0.440323 Iteration 2 Error: 0.055011 Iteration 3 Error: 0.022725 Align patch 23 2 left Iteration 1 Error: 0.857081 Iteration 2 Error: 0.075968 Iteration 3 Error: 0.015621 Align patch 24 1 left Iteration 1 Error: 0.413852 Iteration 2 Error: 0.062506 Iteration 3 Error: 0.016243 Align patch 25 0 left Iteration 1 Error: 0.591191 Iteration 2 Error: 0.086310 Iteration 3 Error: 0.021249 3D Fitting completed. Patch alignment time: 11.46(sec) Local motion has been corrected. Process thread exits. Computational time: 22.522181 sec Total time: 29.548679 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00010hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00010hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.648036s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00010hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 5.387755s ........................................ >>>>>>TIME<<<<<< FFT: 1.156385s Defocus_U Defocus_V Angle CCC 10640.63 11488.29 3.91 0.056475 Final Values Defocus_U Defocus_V Angle CCC 10645.33 11505.49 3.91 0.098355 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00010hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00010hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.350e-01 1.003e-01 CC threshold: 0.737 Mean Std: 40.44 6.97 Num Hot pixels: 228 Hot pixel threshold: 82.24 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.186946 Iteration 2 Error: 0.120490 Iteration 3 Error: 0.027269 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.23 0.09 ...... Frame ( 3) shift: -0.46 0.18 ...... Frame ( 4) shift: -0.68 0.27 ...... Frame ( 5) shift: -0.91 0.35 ...... Frame ( 6) shift: -1.00 0.47 ...... Frame ( 7) shift: -0.94 0.62 ...... Frame ( 8) shift: -0.88 0.77 ...... Frame ( 9) shift: -0.83 0.88 ...... Frame ( 10) shift: -0.80 0.95 ...... Frame ( 11) shift: -0.77 1.03 ...... Frame ( 12) shift: -0.74 1.10 ...... Frame ( 13) shift: -0.73 1.16 ...... Frame ( 14) shift: -0.71 1.22 ...... Frame ( 15) shift: -0.69 1.30 ...... Frame ( 16) shift: -0.66 1.40 ...... Frame ( 17) shift: -0.63 1.50 ...... Frame ( 18) shift: -0.58 1.55 ...... Frame ( 19) shift: -0.49 1.56 ...... Frame ( 20) shift: -0.41 1.57 ...... Frame ( 21) shift: -0.36 1.59 ...... Frame ( 22) shift: -0.34 1.63 ...... Frame ( 23) shift: -0.33 1.67 ...... Frame ( 24) shift: -0.30 1.71 ...... Frame ( 25) shift: -0.26 1.76 ...... Frame ( 26) shift: -0.23 1.81 ...... Frame ( 27) shift: -0.19 1.83 ...... Frame ( 28) shift: -0.15 1.81 ...... Frame ( 29) shift: -0.12 1.79 ...... Frame ( 30) shift: -0.06 1.79 ...... Frame ( 31) shift: 0.01 1.80 ...... Frame ( 32) shift: 0.09 1.82 ...... Frame ( 33) shift: 0.09 1.81 ...... Frame ( 34) shift: 0.03 1.76 ...... Frame ( 35) shift: -0.03 1.72 ...... Frame ( 36) shift: -0.06 1.71 ...... Frame ( 37) shift: -0.04 1.73 ...... Frame ( 38) shift: -0.02 1.75 ...... Frame ( 39) shift: 0.00 1.78 ...... Frame ( 40) shift: 0.02 1.80 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.687962 Iteration 2 Error: 0.097736 Iteration 3 Error: 0.026902 Align patch 2 23 left Iteration 1 Error: 0.642064 Iteration 2 Error: 0.087267 Iteration 3 Error: 0.019141 Align patch 3 22 left Iteration 1 Error: 0.800711 Iteration 2 Error: 0.124085 Iteration 3 Error: 0.021096 Align patch 4 21 left Iteration 1 Error: 0.849730 Iteration 2 Error: 0.138353 Iteration 3 Error: 0.024941 Align patch 5 20 left Iteration 1 Error: 0.534410 Iteration 2 Error: 0.050112 Iteration 3 Error: 0.012113 Align patch 6 19 left Iteration 1 Error: 1.083259 Iteration 2 Error: 0.127278 Iteration 3 Error: 0.035294 Align patch 7 18 left Iteration 1 Error: 0.492129 Iteration 2 Error: 0.124766 Iteration 3 Error: 0.032231 Align patch 8 17 left Iteration 1 Error: 0.621464 Iteration 2 Error: 0.060774 Iteration 3 Error: 0.011782 Align patch 9 16 left Iteration 1 Error: 0.352719 Iteration 2 Error: 0.037399 Align patch 10 15 left Iteration 1 Error: 0.554625 Iteration 2 Error: 0.072271 Iteration 3 Error: 0.019254 Align patch 11 14 left Iteration 1 Error: 0.706951 Iteration 2 Error: 0.070418 Iteration 3 Error: 0.013189 Align patch 12 13 left Iteration 1 Error: 0.376795 Iteration 2 Error: 0.062290 Iteration 3 Error: 0.012619 Align patch 13 12 left Iteration 1 Error: 0.788325 Iteration 2 Error: 0.088532 Iteration 3 Error: 0.018362 Align patch 14 11 left Iteration 1 Error: 0.327886 Iteration 2 Error: 0.065940 Iteration 3 Error: 0.013270 Align patch 15 10 left Iteration 1 Error: 0.903029 Iteration 2 Error: 0.100488 Iteration 3 Error: 0.021890 Align patch 16 9 left Iteration 1 Error: 0.780488 Iteration 2 Error: 0.078519 Iteration 3 Error: 0.016957 Align patch 17 8 left Iteration 1 Error: 0.808163 Iteration 2 Error: 0.102374 Iteration 3 Error: 0.014725 Align patch 18 7 left Iteration 1 Error: 0.630958 Iteration 2 Error: 0.084206 Iteration 3 Error: 0.017979 Align patch 19 6 left Iteration 1 Error: 0.552624 Iteration 2 Error: 0.046600 Align patch 20 5 left Iteration 1 Error: 0.439085 Iteration 2 Error: 0.056639 Iteration 3 Error: 0.008913 Align patch 21 4 left Iteration 1 Error: 0.556190 Iteration 2 Error: 0.104054 Iteration 3 Error: 0.024901 Align patch 22 3 left Iteration 1 Error: 0.585697 Iteration 2 Error: 0.138157 Iteration 3 Error: 0.019454 Align patch 23 2 left Iteration 1 Error: 0.694823 Iteration 2 Error: 0.077051 Iteration 3 Error: 0.016177 Align patch 24 1 left Iteration 1 Error: 0.597034 Iteration 2 Error: 0.070684 Iteration 3 Error: 0.012403 Align patch 25 0 left Iteration 1 Error: 0.570468 Iteration 2 Error: 0.085002 Iteration 3 Error: 0.014546 3D Fitting completed. Patch alignment time: 10.65(sec) Local motion has been corrected. Process thread exits. Computational time: 21.894129 sec Total time: 30.182947 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00010hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00010hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.690864s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00010hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.897944s ........................................ >>>>>>TIME<<<<<< FFT: 1.037180s Defocus_U Defocus_V Angle CCC 11863.28 11140.62 83.59 0.062063 Final Values Defocus_U Defocus_V Angle CCC 11882.04 11159.38 84.53 0.104449 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00011hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00011hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.320e-01 9.834e-02 CC threshold: 0.722 Mean Std: 39.29 6.94 Num Hot pixels: 222 Hot pixel threshold: 80.91 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.724001 Iteration 2 Error: 0.316575 Iteration 3 Error: 0.063690 Iteration 4 Error: 0.016062 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.15 0.16 ...... Frame ( 3) shift: 0.30 0.31 ...... Frame ( 4) shift: 0.45 0.47 ...... Frame ( 5) shift: 0.60 0.63 ...... Frame ( 6) shift: 0.71 0.72 ...... Frame ( 7) shift: 0.77 0.74 ...... Frame ( 8) shift: 0.84 0.76 ...... Frame ( 9) shift: 0.92 0.79 ...... Frame ( 10) shift: 1.03 0.81 ...... Frame ( 11) shift: 1.13 0.84 ...... Frame ( 12) shift: 1.20 0.89 ...... Frame ( 13) shift: 1.23 0.97 ...... Frame ( 14) shift: 1.27 1.05 ...... Frame ( 15) shift: 1.33 1.10 ...... Frame ( 16) shift: 1.43 1.12 ...... Frame ( 17) shift: 1.53 1.13 ...... Frame ( 18) shift: 1.65 1.12 ...... Frame ( 19) shift: 1.77 1.07 ...... Frame ( 20) shift: 1.90 1.02 ...... Frame ( 21) shift: 2.03 1.00 ...... Frame ( 22) shift: 2.17 1.02 ...... Frame ( 23) shift: 2.31 1.03 ...... Frame ( 24) shift: 2.40 1.05 ...... Frame ( 25) shift: 2.46 1.08 ...... Frame ( 26) shift: 2.51 1.11 ...... Frame ( 27) shift: 2.60 1.17 ...... Frame ( 28) shift: 2.72 1.24 ...... Frame ( 29) shift: 2.84 1.32 ...... Frame ( 30) shift: 2.92 1.39 ...... Frame ( 31) shift: 2.96 1.46 ...... Frame ( 32) shift: 3.00 1.52 ...... Frame ( 33) shift: 3.09 1.59 ...... Frame ( 34) shift: 3.23 1.66 ...... Frame ( 35) shift: 3.38 1.73 ...... Frame ( 36) shift: 3.47 1.79 ...... Frame ( 37) shift: 3.51 1.83 ...... Frame ( 38) shift: 3.55 1.87 ...... Frame ( 39) shift: 3.59 1.91 ...... Frame ( 40) shift: 3.63 1.94 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.548190 Iteration 2 Error: 0.100596 Iteration 3 Error: 0.031007 Align patch 2 23 left Iteration 1 Error: 0.516332 Iteration 2 Error: 0.092700 Iteration 3 Error: 0.019654 Align patch 3 22 left Iteration 1 Error: 0.690091 Iteration 2 Error: 0.078976 Iteration 3 Error: 0.021935 Align patch 4 21 left Iteration 1 Error: 0.727172 Iteration 2 Error: 0.136182 Iteration 3 Error: 0.045399 Align patch 5 20 left Iteration 1 Error: 0.576929 Iteration 2 Error: 0.081693 Iteration 3 Error: 0.014914 Align patch 6 19 left Iteration 1 Error: 0.522650 Iteration 2 Error: 0.103719 Iteration 3 Error: 0.036283 Align patch 7 18 left Iteration 1 Error: 0.475502 Iteration 2 Error: 0.137941 Iteration 3 Error: 0.040681 Align patch 8 17 left Iteration 1 Error: 0.519632 Iteration 2 Error: 0.088451 Iteration 3 Error: 0.016634 Align patch 9 16 left Iteration 1 Error: 0.677316 Iteration 2 Error: 0.062082 Iteration 3 Error: 0.009998 Align patch 10 15 left Iteration 1 Error: 0.580648 Iteration 2 Error: 0.071959 Iteration 3 Error: 0.014348 Align patch 11 14 left Iteration 1 Error: 0.816661 Iteration 2 Error: 0.117782 Iteration 3 Error: 0.053105 Iteration 4 Error: 0.015569 Align patch 12 13 left Iteration 1 Error: 0.862568 Iteration 2 Error: 0.111394 Iteration 3 Error: 0.022066 Align patch 13 12 left Iteration 1 Error: 0.580001 Iteration 2 Error: 0.124221 Iteration 3 Error: 0.022490 Align patch 14 11 left Iteration 1 Error: 0.492700 Iteration 2 Error: 0.063956 Iteration 3 Error: 0.008853 Align patch 15 10 left Iteration 1 Error: 0.727873 Iteration 2 Error: 0.093751 Iteration 3 Error: 0.018576 Align patch 16 9 left Iteration 1 Error: 0.645830 Iteration 2 Error: 0.134764 Iteration 3 Error: 0.042215 Align patch 17 8 left Iteration 1 Error: 0.583117 Iteration 2 Error: 0.073971 Iteration 3 Error: 0.014415 Align patch 18 7 left Iteration 1 Error: 0.568524 Iteration 2 Error: 0.071814 Iteration 3 Error: 0.012324 Align patch 19 6 left Iteration 1 Error: 0.738135 Iteration 2 Error: 0.116836 Iteration 3 Error: 0.027863 Align patch 20 5 left Iteration 1 Error: 0.941847 Iteration 2 Error: 0.202878 Iteration 3 Error: 0.034456 Align patch 21 4 left Iteration 1 Error: 0.617529 Iteration 2 Error: 0.163745 Iteration 3 Error: 0.028101 Align patch 22 3 left Iteration 1 Error: 0.768092 Iteration 2 Error: 0.137876 Iteration 3 Error: 0.025212 Align patch 23 2 left Iteration 1 Error: 0.942386 Iteration 2 Error: 0.131565 Iteration 3 Error: 0.041402 Align patch 24 1 left Iteration 1 Error: 0.530293 Iteration 2 Error: 0.084484 Iteration 3 Error: 0.020002 Align patch 25 0 left Iteration 1 Error: 0.917298 Iteration 2 Error: 0.181685 Iteration 3 Error: 0.030616 3D Fitting completed. Patch alignment time: 11.06(sec) Local motion has been corrected. Process thread exits. Computational time: 24.702974 sec Total time: 31.543545 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00011hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00011hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.627527s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00011hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.969975s ........................................ >>>>>>TIME<<<<<< FFT: 0.948132s Defocus_U Defocus_V Angle CCC 12779.34 13693.41 13.42 -0.022033 Final Values Defocus_U Defocus_V Angle CCC 12798.10 13696.54 11.56 -0.191948 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00011hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00011hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.350e-01 1.004e-01 CC threshold: 0.737 Mean Std: 39.77 7.05 Num Hot pixels: 218 Hot pixel threshold: 82.08 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.248054 Iteration 2 Error: 0.249319 Iteration 3 Error: 0.053707 Iteration 4 Error: 0.016593 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.17 -0.05 ...... Frame ( 3) shift: -0.33 -0.10 ...... Frame ( 4) shift: -0.50 -0.15 ...... Frame ( 5) shift: -0.66 -0.20 ...... Frame ( 6) shift: -0.71 -0.17 ...... Frame ( 7) shift: -0.64 -0.06 ...... Frame ( 8) shift: -0.57 0.05 ...... Frame ( 9) shift: -0.53 0.16 ...... Frame ( 10) shift: -0.50 0.29 ...... Frame ( 11) shift: -0.48 0.42 ...... Frame ( 12) shift: -0.42 0.48 ...... Frame ( 13) shift: -0.31 0.47 ...... Frame ( 14) shift: -0.20 0.46 ...... Frame ( 15) shift: -0.11 0.50 ...... Frame ( 16) shift: -0.04 0.58 ...... Frame ( 17) shift: 0.04 0.66 ...... Frame ( 18) shift: 0.10 0.72 ...... Frame ( 19) shift: 0.13 0.75 ...... Frame ( 20) shift: 0.17 0.79 ...... Frame ( 21) shift: 0.23 0.84 ...... Frame ( 22) shift: 0.31 0.90 ...... Frame ( 23) shift: 0.38 0.96 ...... Frame ( 24) shift: 0.47 1.03 ...... Frame ( 25) shift: 0.55 1.11 ...... Frame ( 26) shift: 0.63 1.18 ...... Frame ( 27) shift: 0.70 1.24 ...... Frame ( 28) shift: 0.76 1.28 ...... Frame ( 29) shift: 0.81 1.31 ...... Frame ( 30) shift: 0.87 1.36 ...... Frame ( 31) shift: 0.93 1.43 ...... Frame ( 32) shift: 0.99 1.49 ...... Frame ( 33) shift: 1.04 1.53 ...... Frame ( 34) shift: 1.08 1.55 ...... Frame ( 35) shift: 1.12 1.57 ...... Frame ( 36) shift: 1.15 1.62 ...... Frame ( 37) shift: 1.18 1.70 ...... Frame ( 38) shift: 1.21 1.79 ...... Frame ( 39) shift: 1.24 1.88 ...... Frame ( 40) shift: 1.27 1.96 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.370198 Iteration 2 Error: 0.070223 Iteration 3 Error: 0.017019 Align patch 2 23 left Iteration 1 Error: 0.708562 Iteration 2 Error: 0.159852 Iteration 3 Error: 0.041187 Align patch 3 22 left Iteration 1 Error: 0.825413 Iteration 2 Error: 0.125855 Iteration 3 Error: 0.020912 Align patch 4 21 left Iteration 1 Error: 0.685960 Iteration 2 Error: 0.091534 Iteration 3 Error: 0.011867 Align patch 5 20 left Iteration 1 Error: 1.055281 Iteration 2 Error: 0.167840 Iteration 3 Error: 0.047239 Align patch 6 19 left Iteration 1 Error: 0.661362 Iteration 2 Error: 0.099869 Iteration 3 Error: 0.016434 Align patch 7 18 left Iteration 1 Error: 0.500257 Iteration 2 Error: 0.112131 Iteration 3 Error: 0.022952 Align patch 8 17 left Iteration 1 Error: 0.715114 Iteration 2 Error: 0.076802 Iteration 3 Error: 0.018397 Align patch 9 16 left Iteration 1 Error: 0.950625 Iteration 2 Error: 0.242746 Iteration 3 Error: 0.079998 Iteration 4 Error: 0.029111 Align patch 10 15 left Iteration 1 Error: 0.712089 Iteration 2 Error: 0.261035 Iteration 3 Error: 0.094067 Iteration 4 Error: 0.033495 Align patch 11 14 left Iteration 1 Error: 0.997222 Iteration 2 Error: 0.109126 Iteration 3 Error: 0.030917 Align patch 12 13 left Iteration 1 Error: 0.748769 Iteration 2 Error: 0.136473 Iteration 3 Error: 0.027562 Align patch 13 12 left Iteration 1 Error: 0.801375 Iteration 2 Error: 0.083399 Iteration 3 Error: 0.015916 Align patch 14 11 left Iteration 1 Error: 1.279373 Iteration 2 Error: 0.229477 Iteration 3 Error: 0.066051 Iteration 4 Error: 0.025707 Align patch 15 10 left Iteration 1 Error: 0.729246 Iteration 2 Error: 0.115560 Iteration 3 Error: 0.021290 Align patch 16 9 left Iteration 1 Error: 1.210317 Iteration 2 Error: 0.108428 Iteration 3 Error: 0.027490 Align patch 17 8 left Iteration 1 Error: 1.133627 Iteration 2 Error: 0.187132 Iteration 3 Error: 0.037135 Align patch 18 7 left Iteration 1 Error: 0.574476 Iteration 2 Error: 0.094742 Iteration 3 Error: 0.015574 Align patch 19 6 left Iteration 1 Error: 0.595260 Iteration 2 Error: 0.079258 Iteration 3 Error: 0.010946 Align patch 20 5 left Iteration 1 Error: 0.472546 Iteration 2 Error: 0.084927 Iteration 3 Error: 0.024649 Align patch 21 4 left Iteration 1 Error: 1.337273 Iteration 2 Error: 0.220501 Iteration 3 Error: 0.038183 Align patch 22 3 left Iteration 1 Error: 0.885907 Iteration 2 Error: 0.163695 Iteration 3 Error: 0.043124 Align patch 23 2 left Iteration 1 Error: 0.815974 Iteration 2 Error: 0.159794 Iteration 3 Error: 0.052009 Iteration 4 Error: 0.012655 Align patch 24 1 left Iteration 1 Error: 0.546337 Iteration 2 Error: 0.069586 Iteration 3 Error: 0.016823 Align patch 25 0 left Iteration 1 Error: 0.469025 Iteration 2 Error: 0.080943 Iteration 3 Error: 0.016941 3D Fitting completed. Patch alignment time: 11.53(sec) Local motion has been corrected. Process thread exits. Computational time: 22.024754 sec Total time: 27.865381 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00011hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00011hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.567280s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00011hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.681103s ........................................ >>>>>>TIME<<<<<< FFT: 0.870015s Defocus_U Defocus_V Angle CCC 10740.23 11240.23 1.34 0.052905 Final Values Defocus_U Defocus_V Angle CCC 10766.82 11269.95 2.93 0.086690 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00011hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00011hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.310e-01 9.770e-02 CC threshold: 0.717 Mean Std: 38.76 6.96 Num Hot pixels: 229 Hot pixel threshold: 80.51 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.414943 Iteration 2 Error: 0.257570 Iteration 3 Error: 0.068083 Iteration 4 Error: 0.017346 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.11 0.16 ...... Frame ( 3) shift: 0.23 0.32 ...... Frame ( 4) shift: 0.34 0.49 ...... Frame ( 5) shift: 0.46 0.65 ...... Frame ( 6) shift: 0.63 0.78 ...... Frame ( 7) shift: 0.85 0.88 ...... Frame ( 8) shift: 1.07 0.98 ...... Frame ( 9) shift: 1.31 1.05 ...... Frame ( 10) shift: 1.58 1.09 ...... Frame ( 11) shift: 1.85 1.14 ...... Frame ( 12) shift: 2.06 1.17 ...... Frame ( 13) shift: 2.22 1.19 ...... Frame ( 14) shift: 2.37 1.21 ...... Frame ( 15) shift: 2.50 1.26 ...... Frame ( 16) shift: 2.61 1.35 ...... Frame ( 17) shift: 2.72 1.43 ...... Frame ( 18) shift: 2.80 1.49 ...... Frame ( 19) shift: 2.84 1.53 ...... Frame ( 20) shift: 2.88 1.57 ...... Frame ( 21) shift: 2.93 1.64 ...... Frame ( 22) shift: 2.99 1.73 ...... Frame ( 23) shift: 3.05 1.82 ...... Frame ( 24) shift: 3.06 1.88 ...... Frame ( 25) shift: 3.02 1.92 ...... Frame ( 26) shift: 2.99 1.96 ...... Frame ( 27) shift: 2.99 1.96 ...... Frame ( 28) shift: 3.03 1.93 ...... Frame ( 29) shift: 3.07 1.89 ...... Frame ( 30) shift: 3.17 1.88 ...... Frame ( 31) shift: 3.33 1.89 ...... Frame ( 32) shift: 3.49 1.90 ...... Frame ( 33) shift: 3.58 1.88 ...... Frame ( 34) shift: 3.59 1.83 ...... Frame ( 35) shift: 3.60 1.78 ...... Frame ( 36) shift: 3.63 1.75 ...... Frame ( 37) shift: 3.68 1.74 ...... Frame ( 38) shift: 3.73 1.72 ...... Frame ( 39) shift: 3.78 1.71 ...... Frame ( 40) shift: 3.83 1.70 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.528629 Iteration 2 Error: 0.076601 Iteration 3 Error: 0.016333 Align patch 2 23 left Iteration 1 Error: 0.405291 Iteration 2 Error: 0.090471 Iteration 3 Error: 0.025326 Align patch 3 22 left Iteration 1 Error: 0.503801 Iteration 2 Error: 0.148180 Iteration 3 Error: 0.060266 Iteration 4 Error: 0.024665 Align patch 4 21 left Iteration 1 Error: 0.628836 Iteration 2 Error: 0.084205 Iteration 3 Error: 0.015666 Align patch 5 20 left Iteration 1 Error: 0.449002 Iteration 2 Error: 0.086698 Iteration 3 Error: 0.016588 Align patch 6 19 left Iteration 1 Error: 0.744074 Iteration 2 Error: 0.102074 Iteration 3 Error: 0.025033 Align patch 7 18 left Iteration 1 Error: 0.520984 Iteration 2 Error: 0.079773 Iteration 3 Error: 0.024012 Align patch 8 17 left Iteration 1 Error: 0.693114 Iteration 2 Error: 0.114118 Iteration 3 Error: 0.037238 Align patch 9 16 left Iteration 1 Error: 0.727125 Iteration 2 Error: 0.173309 Iteration 3 Error: 0.025003 Align patch 10 15 left Iteration 1 Error: 1.106487 Iteration 2 Error: 0.186365 Iteration 3 Error: 0.039741 Align patch 11 14 left Iteration 1 Error: 0.734650 Iteration 2 Error: 0.150265 Iteration 3 Error: 0.013235 Align patch 12 13 left Iteration 1 Error: 0.780506 Iteration 2 Error: 0.111708 Iteration 3 Error: 0.013527 Align patch 13 12 left Iteration 1 Error: 0.982433 Iteration 2 Error: 0.115175 Iteration 3 Error: 0.014592 Align patch 14 11 left Iteration 1 Error: 0.563970 Iteration 2 Error: 0.139011 Iteration 3 Error: 0.033362 Align patch 15 10 left Iteration 1 Error: 0.642317 Iteration 2 Error: 0.112703 Iteration 3 Error: 0.025986 Align patch 16 9 left Iteration 1 Error: 0.930057 Iteration 2 Error: 0.173185 Iteration 3 Error: 0.040033 Align patch 17 8 left Iteration 1 Error: 0.704333 Iteration 2 Error: 0.080945 Iteration 3 Error: 0.019931 Align patch 18 7 left Iteration 1 Error: 0.449619 Iteration 2 Error: 0.062384 Iteration 3 Error: 0.016417 Align patch 19 6 left Iteration 1 Error: 0.884287 Iteration 2 Error: 0.137321 Iteration 3 Error: 0.030629 Align patch 20 5 left Iteration 1 Error: 0.790866 Iteration 2 Error: 0.066293 Iteration 3 Error: 0.008290 Align patch 21 4 left Iteration 1 Error: 0.686120 Iteration 2 Error: 0.150592 Iteration 3 Error: 0.051526 Iteration 4 Error: 0.016323 Align patch 22 3 left Iteration 1 Error: 0.474316 Iteration 2 Error: 0.048737 Align patch 23 2 left Iteration 1 Error: 0.529279 Iteration 2 Error: 0.078505 Iteration 3 Error: 0.011586 Align patch 24 1 left Iteration 1 Error: 0.732040 Iteration 2 Error: 0.108681 Iteration 3 Error: 0.016625 Align patch 25 0 left Iteration 1 Error: 0.575675 Iteration 2 Error: 0.049586 3D Fitting completed. Patch alignment time: 11.80(sec) Local motion has been corrected. Process thread exits. Computational time: 21.414000 sec Total time: 26.947147 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00011hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00011hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.744267s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00011hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.806500s ........................................ >>>>>>TIME<<<<<< FFT: 1.058765s Defocus_U Defocus_V Angle CCC 14056.64 14884.77 3.02 -0.027313 Final Values Defocus_U Defocus_V Angle CCC 14076.94 14883.23 4.28 -0.212703 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00011hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00011hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.350e-01 1.004e-01 CC threshold: 0.737 Mean Std: 39.71 6.81 Num Hot pixels: 234 Hot pixel threshold: 80.54 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.009307 Iteration 2 Error: 0.211317 Iteration 3 Error: 0.040275 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.03 -0.02 ...... Frame ( 3) shift: 0.06 -0.04 ...... Frame ( 4) shift: 0.10 -0.06 ...... Frame ( 5) shift: 0.13 -0.08 ...... Frame ( 6) shift: 0.21 -0.07 ...... Frame ( 7) shift: 0.35 -0.03 ...... Frame ( 8) shift: 0.49 0.01 ...... Frame ( 9) shift: 0.58 0.07 ...... Frame ( 10) shift: 0.63 0.14 ...... Frame ( 11) shift: 0.67 0.22 ...... Frame ( 12) shift: 0.72 0.26 ...... Frame ( 13) shift: 0.77 0.26 ...... Frame ( 14) shift: 0.82 0.25 ...... Frame ( 15) shift: 0.87 0.26 ...... Frame ( 16) shift: 0.92 0.29 ...... Frame ( 17) shift: 0.97 0.31 ...... Frame ( 18) shift: 1.01 0.34 ...... Frame ( 19) shift: 1.04 0.37 ...... Frame ( 20) shift: 1.07 0.41 ...... Frame ( 21) shift: 1.11 0.40 ...... Frame ( 22) shift: 1.18 0.36 ...... Frame ( 23) shift: 1.24 0.31 ...... Frame ( 24) shift: 1.31 0.30 ...... Frame ( 25) shift: 1.36 0.31 ...... Frame ( 26) shift: 1.42 0.33 ...... Frame ( 27) shift: 1.47 0.39 ...... Frame ( 28) shift: 1.52 0.50 ...... Frame ( 29) shift: 1.57 0.61 ...... Frame ( 30) shift: 1.66 0.70 ...... Frame ( 31) shift: 1.79 0.76 ...... Frame ( 32) shift: 1.92 0.82 ...... Frame ( 33) shift: 1.98 0.87 ...... Frame ( 34) shift: 1.97 0.91 ...... Frame ( 35) shift: 1.96 0.95 ...... Frame ( 36) shift: 1.97 0.95 ...... Frame ( 37) shift: 2.01 0.90 ...... Frame ( 38) shift: 2.04 0.85 ...... Frame ( 39) shift: 2.08 0.80 ...... Frame ( 40) shift: 2.12 0.76 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.730287 Iteration 2 Error: 0.119895 Iteration 3 Error: 0.032574 Align patch 2 23 left Iteration 1 Error: 0.806956 Iteration 2 Error: 0.083659 Iteration 3 Error: 0.015825 Align patch 3 22 left Iteration 1 Error: 0.754684 Iteration 2 Error: 0.124276 Iteration 3 Error: 0.024997 Align patch 4 21 left Iteration 1 Error: 0.638998 Iteration 2 Error: 0.089641 Iteration 3 Error: 0.015065 Align patch 5 20 left Iteration 1 Error: 0.976801 Iteration 2 Error: 0.114266 Iteration 3 Error: 0.028822 Align patch 6 19 left Iteration 1 Error: 0.949172 Iteration 2 Error: 0.118158 Iteration 3 Error: 0.029961 Align patch 7 18 left Iteration 1 Error: 0.380065 Iteration 2 Error: 0.105023 Iteration 3 Error: 0.023317 Align patch 8 17 left Iteration 1 Error: 0.512068 Iteration 2 Error: 0.090605 Iteration 3 Error: 0.010450 Align patch 9 16 left Iteration 1 Error: 0.604380 Iteration 2 Error: 0.106953 Iteration 3 Error: 0.019156 Align patch 10 15 left Iteration 1 Error: 1.214409 Iteration 2 Error: 0.084469 Iteration 3 Error: 0.015899 Align patch 11 14 left Iteration 1 Error: 1.051806 Iteration 2 Error: 0.096994 Iteration 3 Error: 0.027020 Align patch 12 13 left Iteration 1 Error: 0.679583 Iteration 2 Error: 0.144658 Iteration 3 Error: 0.031904 Align patch 13 12 left Iteration 1 Error: 0.994156 Iteration 2 Error: 0.135262 Iteration 3 Error: 0.041598 Align patch 14 11 left Iteration 1 Error: 0.675755 Iteration 2 Error: 0.064264 Iteration 3 Error: 0.010203 Align patch 15 10 left Iteration 1 Error: 0.825160 Iteration 2 Error: 0.114814 Iteration 3 Error: 0.025309 Align patch 16 9 left Iteration 1 Error: 1.055937 Iteration 2 Error: 0.143165 Iteration 3 Error: 0.038590 Align patch 17 8 left Iteration 1 Error: 0.840866 Iteration 2 Error: 0.118705 Iteration 3 Error: 0.019875 Align patch 18 7 left Iteration 1 Error: 0.525013 Iteration 2 Error: 0.100410 Iteration 3 Error: 0.016888 Align patch 19 6 left Iteration 1 Error: 0.429810 Iteration 2 Error: 0.058422 Iteration 3 Error: 0.010342 Align patch 20 5 left Iteration 1 Error: 0.782808 Iteration 2 Error: 0.098788 Iteration 3 Error: 0.022938 Align patch 21 4 left Iteration 1 Error: 1.307279 Iteration 2 Error: 0.149802 Iteration 3 Error: 0.044196 Align patch 22 3 left Iteration 1 Error: 0.901902 Iteration 2 Error: 0.098693 Iteration 3 Error: 0.017113 Align patch 23 2 left Iteration 1 Error: 1.016809 Iteration 2 Error: 0.080846 Iteration 3 Error: 0.013957 Align patch 24 1 left Iteration 1 Error: 0.683852 Iteration 2 Error: 0.090739 Iteration 3 Error: 0.022706 Align patch 25 0 left Iteration 1 Error: 0.711341 Iteration 2 Error: 0.118766 Iteration 3 Error: 0.035651 3D Fitting completed. Patch alignment time: 11.40(sec) Local motion has been corrected. Process thread exits. Computational time: 23.914366 sec Total time: 29.973476 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00011hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00011hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.587893s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00011hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 4.447959s ........................................ >>>>>>TIME<<<<<< FFT: 1.308677s Defocus_U Defocus_V Angle CCC 11041.82 10438.76 83.51 0.055627 Final Values Defocus_U Defocus_V Angle CCC 11077.79 10471.61 81.64 0.092112 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00012hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00012hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 39.86 6.86 Num Hot pixels: 205 Hot pixel threshold: 81.04 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 4.282609 Iteration 2 Error: 1.922061 Iteration 3 Error: 1.069207 Iteration 4 Error: 0.653383 Iteration 5 Error: 0.318209 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.08 0.09 ...... Frame ( 3) shift: -0.17 0.17 ...... Frame ( 4) shift: -0.25 0.26 ...... Frame ( 5) shift: -0.34 0.34 ...... Frame ( 6) shift: -0.24 0.50 ...... Frame ( 7) shift: 0.04 0.73 ...... Frame ( 8) shift: 0.33 0.96 ...... Frame ( 9) shift: 0.66 1.19 ...... Frame ( 10) shift: 1.04 1.43 ...... Frame ( 11) shift: 1.42 1.67 ...... Frame ( 12) shift: 1.84 1.88 ...... Frame ( 13) shift: 2.28 2.05 ...... Frame ( 14) shift: 2.73 2.22 ...... Frame ( 15) shift: 3.16 2.40 ...... Frame ( 16) shift: 3.56 2.60 ...... Frame ( 17) shift: 3.96 2.80 ...... Frame ( 18) shift: 4.36 2.97 ...... Frame ( 19) shift: 4.77 3.09 ...... Frame ( 20) shift: 5.18 3.21 ...... Frame ( 21) shift: 5.56 3.35 ...... Frame ( 22) shift: 5.93 3.50 ...... Frame ( 23) shift: 6.30 3.66 ...... Frame ( 24) shift: 6.64 3.77 ...... Frame ( 25) shift: 6.96 3.84 ...... Frame ( 26) shift: 7.28 3.92 ...... Frame ( 27) shift: 7.57 3.97 ...... Frame ( 28) shift: 7.83 4.00 ...... Frame ( 29) shift: 8.09 4.03 ...... Frame ( 30) shift: 8.37 4.13 ...... Frame ( 31) shift: 8.67 4.32 ...... Frame ( 32) shift: 8.96 4.51 ...... Frame ( 33) shift: 9.31 4.69 ...... Frame ( 34) shift: 9.70 4.86 ...... Frame ( 35) shift: 10.09 5.02 ...... Frame ( 36) shift: 10.44 5.19 ...... Frame ( 37) shift: 10.74 5.37 ...... Frame ( 38) shift: 11.03 5.54 ...... Frame ( 39) shift: 11.33 5.72 ...... Frame ( 40) shift: 11.63 5.89 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 4.281722 Iteration 2 Error: 1.745021 Iteration 3 Error: 0.658788 Iteration 4 Error: 0.411764 Iteration 5 Error: 0.259956 Align patch 1 24 left Iteration 1 Error: 5.127197 Iteration 2 Error: 1.079596 Iteration 3 Error: 0.227514 Iteration 4 Error: 0.048079 Align patch 2 23 left Iteration 1 Error: 4.891320 Iteration 2 Error: 1.951303 Iteration 3 Error: 0.488313 Iteration 4 Error: 0.192268 Iteration 5 Error: 0.065961 Align patch 2 23 left Iteration 1 Error: 4.971450 Iteration 2 Error: 0.965884 Iteration 3 Error: 0.171283 Iteration 4 Error: 0.043369 Align patch 3 22 left Iteration 1 Error: 2.209156 Iteration 2 Error: 0.850123 Iteration 3 Error: 0.432193 Iteration 4 Error: 0.247936 Iteration 5 Error: 0.196392 Align patch 3 22 left Iteration 1 Error: 2.643839 Iteration 2 Error: 0.515722 Iteration 3 Error: 0.183075 Iteration 4 Error: 0.049730 Align patch 4 21 left Iteration 1 Error: 1.515306 Iteration 2 Error: 0.538579 Iteration 3 Error: 0.204130 Iteration 4 Error: 0.127669 Iteration 5 Error: 0.057691 Align patch 4 21 left Iteration 1 Error: 1.591128 Iteration 2 Error: 0.317495 Iteration 3 Error: 0.077207 Iteration 4 Error: 0.027008 Align patch 5 20 left Iteration 1 Error: 1.669380 Iteration 2 Error: 0.342659 Iteration 3 Error: 0.060864 Iteration 4 Error: 0.021138 Align patch 6 19 left Iteration 1 Error: 5.817519 Iteration 2 Error: 1.422957 Iteration 3 Error: 0.462322 Iteration 4 Error: 0.213886 Iteration 5 Error: 0.159563 Align patch 6 19 left Iteration 1 Error: 4.671384 Iteration 2 Error: 1.057157 Iteration 3 Error: 0.180156 Iteration 4 Error: 0.070989 Iteration 5 Error: 0.012836 Align patch 7 18 left Iteration 1 Error: 5.954475 Iteration 2 Error: 2.097180 Iteration 3 Error: 0.478388 Iteration 4 Error: 0.146136 Iteration 5 Error: 0.036026 Align patch 8 17 left Iteration 1 Error: 2.227729 Iteration 2 Error: 0.731892 Iteration 3 Error: 0.275140 Iteration 4 Error: 0.133810 Iteration 5 Error: 0.070699 Align patch 8 17 left Iteration 1 Error: 2.624949 Iteration 2 Error: 0.513662 Iteration 3 Error: 0.132917 Iteration 4 Error: 0.045857 Align patch 9 16 left Iteration 1 Error: 1.483656 Iteration 2 Error: 0.545646 Iteration 3 Error: 0.346147 Iteration 4 Error: 0.178950 Iteration 5 Error: 0.121039 Align patch 9 16 left Iteration 1 Error: 1.448940 Iteration 2 Error: 0.360113 Iteration 3 Error: 0.099042 Iteration 4 Error: 0.034306 Align patch 10 15 left Iteration 1 Error: 1.573323 Iteration 2 Error: 0.460962 Iteration 3 Error: 0.185252 Iteration 4 Error: 0.077002 Iteration 5 Error: 0.025144 Align patch 11 14 left Iteration 1 Error: 3.748293 Iteration 2 Error: 1.785974 Iteration 3 Error: 0.865172 Iteration 4 Error: 0.749783 Iteration 5 Error: 0.650728 Align patch 11 14 left Iteration 1 Error: 3.981081 Iteration 2 Error: 0.762217 Iteration 3 Error: 0.292479 Iteration 4 Error: 0.090938 Iteration 5 Error: 0.036798 Align patch 12 13 left Iteration 1 Error: 3.729676 Iteration 2 Error: 1.422076 Iteration 3 Error: 0.560650 Iteration 4 Error: 0.235679 Iteration 5 Error: 0.150330 Align patch 12 13 left Iteration 1 Error: 4.080470 Iteration 2 Error: 0.739997 Iteration 3 Error: 0.234340 Iteration 4 Error: 0.058452 Iteration 5 Error: 0.031449 Align patch 13 12 left Iteration 1 Error: 2.056627 Iteration 2 Error: 1.060291 Iteration 3 Error: 0.321931 Iteration 4 Error: 0.170117 Iteration 5 Error: 0.071297 Align patch 13 12 left Iteration 1 Error: 1.966031 Iteration 2 Error: 0.471166 Iteration 3 Error: 0.098420 Iteration 4 Error: 0.025314 Align patch 14 11 left Iteration 1 Error: 1.191482 Iteration 2 Error: 0.216993 Iteration 3 Error: 0.086100 Iteration 4 Error: 0.040935 Align patch 15 10 left Iteration 1 Error: 2.007732 Iteration 2 Error: 0.801901 Iteration 3 Error: 0.331395 Iteration 4 Error: 0.214215 Iteration 5 Error: 0.113825 Align patch 15 10 left Iteration 1 Error: 1.907811 Iteration 2 Error: 0.390838 Iteration 3 Error: 0.111022 Iteration 4 Error: 0.039782 Align patch 16 9 left Iteration 1 Error: 4.288913 Iteration 2 Error: 1.692123 Iteration 3 Error: 0.408090 Iteration 4 Error: 0.154244 Iteration 5 Error: 0.054907 Align patch 16 9 left Iteration 1 Error: 3.569489 Iteration 2 Error: 0.900626 Iteration 3 Error: 0.336087 Iteration 4 Error: 0.101830 Iteration 5 Error: 0.051053 Align patch 17 8 left Iteration 1 Error: 2.353485 Iteration 2 Error: 0.750697 Iteration 3 Error: 0.375400 Iteration 4 Error: 0.217833 Iteration 5 Error: 0.113576 Align patch 17 8 left Iteration 1 Error: 3.390922 Iteration 2 Error: 0.799140 Iteration 3 Error: 0.268153 Iteration 4 Error: 0.086581 Iteration 5 Error: 0.036298 Align patch 18 7 left Iteration 1 Error: 1.541276 Iteration 2 Error: 0.478420 Iteration 3 Error: 0.089055 Iteration 4 Error: 0.031479 Align patch 19 6 left Iteration 1 Error: 0.615462 Iteration 2 Error: 0.125431 Iteration 3 Error: 0.071487 Iteration 4 Error: 0.018770 Align patch 20 5 left Iteration 1 Error: 3.078174 Iteration 2 Error: 1.176704 Iteration 3 Error: 0.618618 Iteration 4 Error: 0.329164 Iteration 5 Error: 0.172600 Align patch 20 5 left Iteration 1 Error: 2.060095 Iteration 2 Error: 0.487853 Iteration 3 Error: 0.155406 Iteration 4 Error: 0.061430 Iteration 5 Error: 0.026774 Align patch 21 4 left Iteration 1 Error: 4.440987 Iteration 2 Error: 1.487218 Iteration 3 Error: 0.451281 Iteration 4 Error: 0.134961 Iteration 5 Error: 0.083433 Align patch 21 4 left Iteration 1 Error: 3.958148 Iteration 2 Error: 0.852562 Iteration 3 Error: 0.247555 Iteration 4 Error: 0.066884 Iteration 5 Error: 0.024248 Align patch 22 3 left Iteration 1 Error: 2.543035 Iteration 2 Error: 1.058857 Iteration 3 Error: 0.380919 Iteration 4 Error: 0.197997 Iteration 5 Error: 0.096038 Align patch 22 3 left Iteration 1 Error: 3.364482 Iteration 2 Error: 0.747381 Iteration 3 Error: 0.234083 Iteration 4 Error: 0.075996 Iteration 5 Error: 0.022799 Align patch 23 2 left Iteration 1 Error: 1.070873 Iteration 2 Error: 0.208455 Iteration 3 Error: 0.057990 Iteration 4 Error: 0.014672 Align patch 24 1 left Iteration 1 Error: 1.554962 Iteration 2 Error: 0.276551 Iteration 3 Error: 0.109700 Iteration 4 Error: 0.042184 Align patch 25 0 left Iteration 1 Error: 3.401196 Iteration 2 Error: 2.241634 Iteration 3 Error: 0.747045 Iteration 4 Error: 0.450779 Iteration 5 Error: 0.236264 Align patch 25 0 left Iteration 1 Error: 2.393509 Iteration 2 Error: 0.519507 Iteration 3 Error: 0.184604 Iteration 4 Error: 0.061162 Iteration 5 Error: 0.021039 3D Fitting completed. Patch alignment time: 25.00(sec) Local motion has been corrected. Process thread exits. Computational time: 35.200542 sec Total time: 41.495888 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00012hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00012hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.603949s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00012hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.069184s ........................................ >>>>>>TIME<<<<<< FFT: 0.888629s Defocus_U Defocus_V Angle CCC 12550.78 13363.28 12.55 0.068066 Final Values Defocus_U Defocus_V Angle CCC 12560.16 13347.66 11.93 0.119927 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00012hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00012hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.351e-01 1.004e-01 CC threshold: 0.738 Mean Std: 39.24 6.88 Num Hot pixels: 202 Hot pixel threshold: 80.50 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.131057 Iteration 2 Error: 0.178018 Iteration 3 Error: 0.046506 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.02 0.06 ...... Frame ( 3) shift: -0.03 0.12 ...... Frame ( 4) shift: -0.05 0.17 ...... Frame ( 5) shift: -0.06 0.23 ...... Frame ( 6) shift: -0.06 0.29 ...... Frame ( 7) shift: -0.05 0.35 ...... Frame ( 8) shift: -0.04 0.41 ...... Frame ( 9) shift: 0.00 0.49 ...... Frame ( 10) shift: 0.08 0.61 ...... Frame ( 11) shift: 0.15 0.72 ...... Frame ( 12) shift: 0.24 0.83 ...... Frame ( 13) shift: 0.34 0.95 ...... Frame ( 14) shift: 0.44 1.06 ...... Frame ( 15) shift: 0.49 1.18 ...... Frame ( 16) shift: 0.48 1.30 ...... Frame ( 17) shift: 0.47 1.42 ...... Frame ( 18) shift: 0.48 1.51 ...... Frame ( 19) shift: 0.51 1.57 ...... Frame ( 20) shift: 0.53 1.63 ...... Frame ( 21) shift: 0.57 1.66 ...... Frame ( 22) shift: 0.63 1.68 ...... Frame ( 23) shift: 0.68 1.70 ...... Frame ( 24) shift: 0.71 1.71 ...... Frame ( 25) shift: 0.73 1.72 ...... Frame ( 26) shift: 0.75 1.74 ...... Frame ( 27) shift: 0.79 1.71 ...... Frame ( 28) shift: 0.83 1.65 ...... Frame ( 29) shift: 0.88 1.59 ...... Frame ( 30) shift: 0.92 1.55 ...... Frame ( 31) shift: 0.96 1.54 ...... Frame ( 32) shift: 1.00 1.54 ...... Frame ( 33) shift: 1.06 1.56 ...... Frame ( 34) shift: 1.14 1.60 ...... Frame ( 35) shift: 1.21 1.64 ...... Frame ( 36) shift: 1.28 1.67 ...... Frame ( 37) shift: 1.35 1.68 ...... Frame ( 38) shift: 1.41 1.69 ...... Frame ( 39) shift: 1.48 1.70 ...... Frame ( 40) shift: 1.54 1.72 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.488163 Iteration 2 Error: 0.337710 Iteration 3 Error: 0.094420 Iteration 4 Error: 0.038819 Align patch 2 23 left Iteration 1 Error: 0.687798 Iteration 2 Error: 0.192926 Iteration 3 Error: 0.062465 Iteration 4 Error: 0.022492 Align patch 3 22 left Iteration 1 Error: 0.439716 Iteration 2 Error: 0.068784 Iteration 3 Error: 0.016927 Align patch 4 21 left Iteration 1 Error: 0.443053 Iteration 2 Error: 0.077035 Iteration 3 Error: 0.010364 Align patch 5 20 left Iteration 1 Error: 0.744444 Iteration 2 Error: 0.208775 Iteration 3 Error: 0.072188 Iteration 4 Error: 0.023057 Align patch 6 19 left Iteration 1 Error: 1.670734 Iteration 2 Error: 0.258168 Iteration 3 Error: 0.072120 Iteration 4 Error: 0.021460 Align patch 7 18 left Iteration 1 Error: 1.005956 Iteration 2 Error: 0.194340 Iteration 3 Error: 0.052036 Iteration 4 Error: 0.011204 Align patch 8 17 left Iteration 1 Error: 0.721982 Iteration 2 Error: 0.101652 Iteration 3 Error: 0.024555 Align patch 9 16 left Iteration 1 Error: 0.420864 Iteration 2 Error: 0.059667 Iteration 3 Error: 0.012030 Align patch 10 15 left Iteration 1 Error: 0.429755 Iteration 2 Error: 0.045493 Align patch 11 14 left Iteration 1 Error: 1.214714 Iteration 2 Error: 0.274774 Iteration 3 Error: 0.074258 Iteration 4 Error: 0.032558 Align patch 12 13 left Iteration 1 Error: 0.906787 Iteration 2 Error: 0.130854 Iteration 3 Error: 0.028380 Align patch 13 12 left Iteration 1 Error: 0.600950 Iteration 2 Error: 0.055536 Iteration 3 Error: 0.011533 Align patch 14 11 left Iteration 1 Error: 0.518854 Iteration 2 Error: 0.050624 Iteration 3 Error: 0.013430 Align patch 15 10 left Iteration 1 Error: 0.692757 Iteration 2 Error: 0.086172 Iteration 3 Error: 0.015904 Align patch 16 9 left Iteration 1 Error: 0.687506 Iteration 2 Error: 0.169625 Iteration 3 Error: 0.057486 Iteration 4 Error: 0.017635 Align patch 17 8 left Iteration 1 Error: 0.683739 Iteration 2 Error: 0.111768 Iteration 3 Error: 0.026941 Align patch 18 7 left Iteration 1 Error: 0.632609 Iteration 2 Error: 0.096858 Iteration 3 Error: 0.023458 Align patch 19 6 left Iteration 1 Error: 0.674763 Iteration 2 Error: 0.090271 Iteration 3 Error: 0.014148 Align patch 20 5 left Iteration 1 Error: 0.755132 Iteration 2 Error: 0.132457 Iteration 3 Error: 0.030961 Align patch 21 4 left Iteration 1 Error: 0.776102 Iteration 2 Error: 0.120004 Iteration 3 Error: 0.021283 Align patch 22 3 left Iteration 1 Error: 0.541855 Iteration 2 Error: 0.139465 Iteration 3 Error: 0.038163 Align patch 23 2 left Iteration 1 Error: 0.644017 Iteration 2 Error: 0.088484 Iteration 3 Error: 0.016676 Align patch 24 1 left Iteration 1 Error: 0.698944 Iteration 2 Error: 0.088929 Iteration 3 Error: 0.027558 Align patch 25 0 left Iteration 1 Error: 0.521488 Iteration 2 Error: 0.103600 Iteration 3 Error: 0.019154 3D Fitting completed. Patch alignment time: 11.67(sec) Local motion has been corrected. Process thread exits. Computational time: 20.442234 sec Total time: 26.615974 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00012hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00012hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.506596s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00012hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.429342s ........................................ >>>>>>TIME<<<<<< FFT: 0.891050s Defocus_U Defocus_V Angle CCC 8888.62 9373.11 1.68 0.044787 Final Values Defocus_U Defocus_V Angle CCC 8893.31 9380.93 1.37 0.083055 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00012hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00012hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.003e-01 CC threshold: 0.736 Mean Std: 41.82 7.00 Num Hot pixels: 227 Hot pixel threshold: 83.81 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.804067 Iteration 2 Error: 0.297092 Iteration 3 Error: 0.072783 Iteration 4 Error: 0.020637 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.11 -0.14 ...... Frame ( 3) shift: -0.23 -0.28 ...... Frame ( 4) shift: -0.34 -0.42 ...... Frame ( 5) shift: -0.45 -0.57 ...... Frame ( 6) shift: -0.49 -0.65 ...... Frame ( 7) shift: -0.45 -0.69 ...... Frame ( 8) shift: -0.41 -0.72 ...... Frame ( 9) shift: -0.27 -0.67 ...... Frame ( 10) shift: -0.02 -0.52 ...... Frame ( 11) shift: 0.23 -0.38 ...... Frame ( 12) shift: 0.45 -0.24 ...... Frame ( 13) shift: 0.67 -0.12 ...... Frame ( 14) shift: 0.88 0.01 ...... Frame ( 15) shift: 1.01 0.09 ...... Frame ( 16) shift: 1.07 0.12 ...... Frame ( 17) shift: 1.12 0.16 ...... Frame ( 18) shift: 1.21 0.23 ...... Frame ( 19) shift: 1.32 0.33 ...... Frame ( 20) shift: 1.44 0.42 ...... Frame ( 21) shift: 1.54 0.54 ...... Frame ( 22) shift: 1.65 0.68 ...... Frame ( 23) shift: 1.75 0.81 ...... Frame ( 24) shift: 1.82 0.93 ...... Frame ( 25) shift: 1.85 1.02 ...... Frame ( 26) shift: 1.89 1.12 ...... Frame ( 27) shift: 1.90 1.17 ...... Frame ( 28) shift: 1.91 1.17 ...... Frame ( 29) shift: 1.91 1.17 ...... Frame ( 30) shift: 1.99 1.20 ...... Frame ( 31) shift: 2.14 1.28 ...... Frame ( 32) shift: 2.30 1.35 ...... Frame ( 33) shift: 2.41 1.38 ...... Frame ( 34) shift: 2.46 1.37 ...... Frame ( 35) shift: 2.52 1.36 ...... Frame ( 36) shift: 2.60 1.35 ...... Frame ( 37) shift: 2.69 1.35 ...... Frame ( 38) shift: 2.79 1.35 ...... Frame ( 39) shift: 2.89 1.35 ...... Frame ( 40) shift: 2.99 1.34 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.025534 Iteration 2 Error: 0.228652 Iteration 3 Error: 0.057649 Iteration 4 Error: 0.021757 Align patch 2 23 left Iteration 1 Error: 0.753375 Iteration 2 Error: 0.081355 Iteration 3 Error: 0.021715 Align patch 3 22 left Iteration 1 Error: 0.991950 Iteration 2 Error: 0.200909 Iteration 3 Error: 0.067179 Iteration 4 Error: 0.025359 Align patch 4 21 left Iteration 1 Error: 0.690580 Iteration 2 Error: 0.093302 Iteration 3 Error: 0.020613 Align patch 5 20 left Iteration 1 Error: 0.419093 Iteration 2 Error: 0.067129 Iteration 3 Error: 0.012760 Align patch 6 19 left Iteration 1 Error: 1.207173 Iteration 2 Error: 0.200352 Iteration 3 Error: 0.058989 Iteration 4 Error: 0.021189 Align patch 7 18 left Iteration 1 Error: 1.114226 Iteration 2 Error: 0.067665 Iteration 3 Error: 0.019690 Align patch 8 17 left Iteration 1 Error: 0.700740 Iteration 2 Error: 0.104500 Iteration 3 Error: 0.036104 Align patch 9 16 left Iteration 1 Error: 0.542130 Iteration 2 Error: 0.099189 Iteration 3 Error: 0.034339 Align patch 10 15 left Iteration 1 Error: 0.644940 Iteration 2 Error: 0.093466 Iteration 3 Error: 0.017937 Align patch 11 14 left Iteration 1 Error: 0.633074 Iteration 2 Error: 0.076080 Iteration 3 Error: 0.020220 Align patch 12 13 left Iteration 1 Error: 0.537592 Iteration 2 Error: 0.083722 Iteration 3 Error: 0.027418 Align patch 13 12 left Iteration 1 Error: 0.310456 Iteration 2 Error: 0.069087 Iteration 3 Error: 0.028574 Align patch 14 11 left Iteration 1 Error: 0.523993 Iteration 2 Error: 0.049730 Align patch 15 10 left Iteration 1 Error: 1.311853 Iteration 2 Error: 0.156105 Iteration 3 Error: 0.029890 Align patch 16 9 left Iteration 1 Error: 1.076052 Iteration 2 Error: 0.132432 Iteration 3 Error: 0.028339 Align patch 17 8 left Iteration 1 Error: 0.422396 Iteration 2 Error: 0.090685 Iteration 3 Error: 0.050334 Iteration 4 Error: 0.010148 Align patch 18 7 left Iteration 1 Error: 0.480046 Iteration 2 Error: 0.090011 Iteration 3 Error: 0.025237 Align patch 19 6 left Iteration 1 Error: 0.509484 Iteration 2 Error: 0.066324 Iteration 3 Error: 0.020891 Align patch 20 5 left Iteration 1 Error: 0.747038 Iteration 2 Error: 0.099588 Iteration 3 Error: 0.023014 Align patch 21 4 left Iteration 1 Error: 0.537586 Iteration 2 Error: 0.098014 Iteration 3 Error: 0.028055 Align patch 22 3 left Iteration 1 Error: 0.665129 Iteration 2 Error: 0.092561 Iteration 3 Error: 0.017736 Align patch 23 2 left Iteration 1 Error: 0.590951 Iteration 2 Error: 0.056697 Iteration 3 Error: 0.008297 Align patch 24 1 left Iteration 1 Error: 0.452197 Iteration 2 Error: 0.043677 Align patch 25 0 left Iteration 1 Error: 0.427188 Iteration 2 Error: 0.067048 Iteration 3 Error: 0.016590 3D Fitting completed. Patch alignment time: 11.38(sec) Local motion has been corrected. Process thread exits. Computational time: 21.565765 sec Total time: 28.788366 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00012hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00012hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.649477s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00012hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.845752s ........................................ >>>>>>TIME<<<<<< FFT: 0.939753s Defocus_U Defocus_V Angle CCC 12921.88 13855.47 4.91 0.068805 Final Values Defocus_U Defocus_V Angle CCC 12931.25 13861.72 5.54 0.111718 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00012hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00012hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 40.76 6.90 Num Hot pixels: 207 Hot pixel threshold: 82.17 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.919591 Iteration 2 Error: 0.140878 Iteration 3 Error: 0.030492 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.16 0.03 ...... Frame ( 3) shift: -0.32 0.05 ...... Frame ( 4) shift: -0.48 0.08 ...... Frame ( 5) shift: -0.64 0.10 ...... Frame ( 6) shift: -0.70 0.15 ...... Frame ( 7) shift: -0.66 0.22 ...... Frame ( 8) shift: -0.61 0.29 ...... Frame ( 9) shift: -0.55 0.38 ...... Frame ( 10) shift: -0.46 0.48 ...... Frame ( 11) shift: -0.37 0.59 ...... Frame ( 12) shift: -0.32 0.67 ...... Frame ( 13) shift: -0.31 0.73 ...... Frame ( 14) shift: -0.30 0.78 ...... Frame ( 15) shift: -0.30 0.85 ...... Frame ( 16) shift: -0.32 0.93 ...... Frame ( 17) shift: -0.33 1.01 ...... Frame ( 18) shift: -0.32 1.08 ...... Frame ( 19) shift: -0.26 1.15 ...... Frame ( 20) shift: -0.21 1.21 ...... Frame ( 21) shift: -0.18 1.27 ...... Frame ( 22) shift: -0.16 1.32 ...... Frame ( 23) shift: -0.15 1.36 ...... Frame ( 24) shift: -0.12 1.41 ...... Frame ( 25) shift: -0.08 1.46 ...... Frame ( 26) shift: -0.03 1.52 ...... Frame ( 27) shift: -0.04 1.55 ...... Frame ( 28) shift: -0.09 1.56 ...... Frame ( 29) shift: -0.14 1.57 ...... Frame ( 30) shift: -0.16 1.61 ...... Frame ( 31) shift: -0.16 1.67 ...... Frame ( 32) shift: -0.16 1.74 ...... Frame ( 33) shift: -0.21 1.77 ...... Frame ( 34) shift: -0.30 1.77 ...... Frame ( 35) shift: -0.39 1.77 ...... Frame ( 36) shift: -0.40 1.77 ...... Frame ( 37) shift: -0.32 1.77 ...... Frame ( 38) shift: -0.24 1.78 ...... Frame ( 39) shift: -0.17 1.78 ...... Frame ( 40) shift: -0.09 1.78 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.713329 Iteration 2 Error: 0.297285 Iteration 3 Error: 0.070063 Iteration 4 Error: 0.024995 Align patch 2 23 left Iteration 1 Error: 1.270464 Iteration 2 Error: 0.215528 Iteration 3 Error: 0.057387 Iteration 4 Error: 0.019687 Align patch 3 22 left Iteration 1 Error: 0.505583 Iteration 2 Error: 0.062710 Iteration 3 Error: 0.008658 Align patch 4 21 left Iteration 1 Error: 0.530230 Iteration 2 Error: 0.059282 Iteration 3 Error: 0.013165 Align patch 5 20 left Iteration 1 Error: 0.606026 Iteration 2 Error: 0.082794 Iteration 3 Error: 0.017240 Align patch 6 19 left Iteration 1 Error: 1.361237 Iteration 2 Error: 0.201274 Iteration 3 Error: 0.063714 Iteration 4 Error: 0.017946 Align patch 7 18 left Iteration 1 Error: 1.003120 Iteration 2 Error: 0.190076 Iteration 3 Error: 0.041837 Align patch 8 17 left Iteration 1 Error: 0.588333 Iteration 2 Error: 0.075077 Iteration 3 Error: 0.011232 Align patch 9 16 left Iteration 1 Error: 0.657065 Iteration 2 Error: 0.108427 Iteration 3 Error: 0.029564 Align patch 10 15 left Iteration 1 Error: 0.609968 Iteration 2 Error: 0.119825 Iteration 3 Error: 0.027401 Align patch 11 14 left Iteration 1 Error: 1.572483 Iteration 2 Error: 0.178087 Iteration 3 Error: 0.059466 Iteration 4 Error: 0.021972 Align patch 12 13 left Iteration 1 Error: 0.917909 Iteration 2 Error: 0.201266 Iteration 3 Error: 0.038396 Align patch 13 12 left Iteration 1 Error: 0.368892 Iteration 2 Error: 0.054184 Iteration 3 Error: 0.010567 Align patch 14 11 left Iteration 1 Error: 0.946849 Iteration 2 Error: 0.156477 Iteration 3 Error: 0.028461 Align patch 15 10 left Iteration 1 Error: 0.787889 Iteration 2 Error: 0.161418 Iteration 3 Error: 0.025274 Align patch 16 9 left Iteration 1 Error: 0.808590 Iteration 2 Error: 0.135463 Iteration 3 Error: 0.035918 Align patch 17 8 left Iteration 1 Error: 1.308570 Iteration 2 Error: 0.178360 Iteration 3 Error: 0.038928 Align patch 18 7 left Iteration 1 Error: 0.553410 Iteration 2 Error: 0.073375 Iteration 3 Error: 0.015308 Align patch 19 6 left Iteration 1 Error: 0.645917 Iteration 2 Error: 0.089397 Iteration 3 Error: 0.020677 Align patch 20 5 left Iteration 1 Error: 0.761385 Iteration 2 Error: 0.158608 Iteration 3 Error: 0.026174 Align patch 21 4 left Iteration 1 Error: 0.779571 Iteration 2 Error: 0.084234 Iteration 3 Error: 0.021016 Align patch 22 3 left Iteration 1 Error: 0.721184 Iteration 2 Error: 0.095892 Iteration 3 Error: 0.021338 Align patch 23 2 left Iteration 1 Error: 0.543065 Iteration 2 Error: 0.067644 Iteration 3 Error: 0.013949 Align patch 24 1 left Iteration 1 Error: 0.703622 Iteration 2 Error: 0.086269 Iteration 3 Error: 0.014205 Align patch 25 0 left Iteration 1 Error: 0.906390 Iteration 2 Error: 0.129883 Iteration 3 Error: 0.028670 3D Fitting completed. Patch alignment time: 11.60(sec) Local motion has been corrected. Process thread exits. Computational time: 22.292593 sec Total time: 29.704544 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00012hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00012hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.541795s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00012hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 4.192722s ........................................ >>>>>>TIME<<<<<< FFT: 1.098470s Defocus_U Defocus_V Angle CCC 12904.33 12326.18 83.73 0.058894 Final Values Defocus_U Defocus_V Angle CCC 12948.11 12326.20 83.42 0.095230 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00013hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00013hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 39.99 6.97 Num Hot pixels: 221 Hot pixel threshold: 81.83 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.650791 Iteration 2 Error: 1.051253 Iteration 3 Error: 0.437720 Iteration 4 Error: 0.218581 Iteration 5 Error: 0.101833 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.31 0.11 ...... Frame ( 3) shift: -0.62 0.21 ...... Frame ( 4) shift: -0.93 0.32 ...... Frame ( 5) shift: -1.24 0.43 ...... Frame ( 6) shift: -1.42 0.54 ...... Frame ( 7) shift: -1.47 0.67 ...... Frame ( 8) shift: -1.52 0.80 ...... Frame ( 9) shift: -1.51 1.00 ...... Frame ( 10) shift: -1.44 1.27 ...... Frame ( 11) shift: -1.37 1.55 ...... Frame ( 12) shift: -1.27 1.84 ...... Frame ( 13) shift: -1.15 2.16 ...... Frame ( 14) shift: -1.03 2.47 ...... Frame ( 15) shift: -0.94 2.82 ...... Frame ( 16) shift: -0.89 3.21 ...... Frame ( 17) shift: -0.83 3.60 ...... Frame ( 18) shift: -0.75 3.98 ...... Frame ( 19) shift: -0.65 4.35 ...... Frame ( 20) shift: -0.55 4.71 ...... Frame ( 21) shift: -0.45 5.03 ...... Frame ( 22) shift: -0.35 5.28 ...... Frame ( 23) shift: -0.25 5.53 ...... Frame ( 24) shift: -0.20 5.80 ...... Frame ( 25) shift: -0.20 6.08 ...... Frame ( 26) shift: -0.19 6.37 ...... Frame ( 27) shift: -0.14 6.56 ...... Frame ( 28) shift: -0.03 6.67 ...... Frame ( 29) shift: 0.08 6.78 ...... Frame ( 30) shift: 0.13 6.89 ...... Frame ( 31) shift: 0.11 7.02 ...... Frame ( 32) shift: 0.10 7.14 ...... Frame ( 33) shift: 0.08 7.29 ...... Frame ( 34) shift: 0.06 7.47 ...... Frame ( 35) shift: 0.04 7.64 ...... Frame ( 36) shift: 0.08 7.80 ...... Frame ( 37) shift: 0.16 7.96 ...... Frame ( 38) shift: 0.24 8.11 ...... Frame ( 39) shift: 0.33 8.26 ...... Frame ( 40) shift: 0.41 8.41 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.605721 Iteration 2 Error: 0.373838 Iteration 3 Error: 0.097001 Iteration 4 Error: 0.035675 Align patch 2 23 left Iteration 1 Error: 1.103055 Iteration 2 Error: 0.195744 Iteration 3 Error: 0.041368 Align patch 3 22 left Iteration 1 Error: 0.931806 Iteration 2 Error: 0.203830 Iteration 3 Error: 0.045956 Align patch 4 21 left Iteration 1 Error: 1.923163 Iteration 2 Error: 0.355239 Iteration 3 Error: 0.075276 Iteration 4 Error: 0.021215 Align patch 5 20 left Iteration 1 Error: 2.575395 Iteration 2 Error: 0.426697 Iteration 3 Error: 0.078049 Iteration 4 Error: 0.014815 Align patch 6 19 left Iteration 1 Error: 2.637893 Iteration 2 Error: 0.856276 Iteration 3 Error: 0.208303 Iteration 4 Error: 0.083219 Iteration 5 Error: 0.029397 Align patch 7 18 left Iteration 1 Error: 1.260326 Iteration 2 Error: 0.316462 Iteration 3 Error: 0.063169 Iteration 4 Error: 0.024215 Align patch 8 17 left Iteration 1 Error: 0.561887 Iteration 2 Error: 0.090015 Iteration 3 Error: 0.026692 Align patch 9 16 left Iteration 1 Error: 1.413319 Iteration 2 Error: 0.278602 Iteration 3 Error: 0.072867 Iteration 4 Error: 0.020072 Align patch 10 15 left Iteration 1 Error: 2.030204 Iteration 2 Error: 0.441255 Iteration 3 Error: 0.113055 Iteration 4 Error: 0.024483 Align patch 11 14 left Iteration 1 Error: 4.180892 Iteration 2 Error: 1.047968 Iteration 3 Error: 0.186925 Iteration 4 Error: 0.073166 Iteration 5 Error: 0.019936 Align patch 12 13 left Iteration 1 Error: 2.297719 Iteration 2 Error: 0.496694 Iteration 3 Error: 0.129517 Iteration 4 Error: 0.046772 Align patch 13 12 left Iteration 1 Error: 0.705042 Iteration 2 Error: 0.179455 Iteration 3 Error: 0.069123 Iteration 4 Error: 0.019414 Align patch 14 11 left Iteration 1 Error: 1.194071 Iteration 2 Error: 0.362205 Iteration 3 Error: 0.080938 Iteration 4 Error: 0.033736 Align patch 15 10 left Iteration 1 Error: 2.204355 Iteration 2 Error: 0.486234 Iteration 3 Error: 0.090141 Iteration 4 Error: 0.023976 Align patch 16 9 left Iteration 1 Error: 5.070612 Iteration 2 Error: 1.750691 Iteration 3 Error: 0.375214 Iteration 4 Error: 0.117712 Iteration 5 Error: 0.032623 Align patch 17 8 left Iteration 1 Error: 3.252693 Iteration 2 Error: 0.932811 Iteration 3 Error: 0.208456 Iteration 4 Error: 0.072217 Iteration 5 Error: 0.026858 Align patch 18 7 left Iteration 1 Error: 1.615825 Iteration 2 Error: 0.447063 Iteration 3 Error: 0.084478 Iteration 4 Error: 0.028034 Align patch 19 6 left Iteration 1 Error: 1.178467 Iteration 2 Error: 0.195443 Iteration 3 Error: 0.059606 Iteration 4 Error: 0.028129 Align patch 20 5 left Iteration 1 Error: 1.859831 Iteration 2 Error: 0.521804 Iteration 3 Error: 0.118161 Iteration 4 Error: 0.047337 Align patch 21 4 left Iteration 1 Error: 5.675391 Iteration 2 Error: 2.354522 Iteration 3 Error: 0.680982 Iteration 4 Error: 0.171168 Iteration 5 Error: 0.055642 Align patch 21 4 left Iteration 1 Error: 4.299965 Iteration 2 Error: 0.966069 Iteration 3 Error: 0.148994 Iteration 4 Error: 0.036211 Align patch 22 3 left Iteration 1 Error: 4.590811 Iteration 2 Error: 1.156024 Iteration 3 Error: 0.480029 Iteration 4 Error: 0.101756 Iteration 5 Error: 0.042179 Align patch 23 2 left Iteration 1 Error: 2.132556 Iteration 2 Error: 0.495372 Iteration 3 Error: 0.142339 Iteration 4 Error: 0.034496 Align patch 24 1 left Iteration 1 Error: 0.997339 Iteration 2 Error: 0.125785 Iteration 3 Error: 0.042343 Align patch 25 0 left Iteration 1 Error: 1.950081 Iteration 2 Error: 0.543917 Iteration 3 Error: 0.192942 Iteration 4 Error: 0.089935 Iteration 5 Error: 0.029072 3D Fitting completed. Patch alignment time: 13.41(sec) Local motion has been corrected. Process thread exits. Computational time: 23.790415 sec Total time: 32.649075 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00013hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00013hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.464381s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00013hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.937678s ........................................ >>>>>>TIME<<<<<< FFT: 0.918332s Defocus_U Defocus_V Angle CCC 12923.83 13775.39 13.11 0.078374 Final Values Defocus_U Defocus_V Angle CCC 12922.27 13773.83 12.80 0.128102 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00013hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00013hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 40.40 6.97 Num Hot pixels: 216 Hot pixel threshold: 82.24 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.264434 Iteration 2 Error: 0.238188 Iteration 3 Error: 0.059809 Iteration 4 Error: 0.014111 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.21 -0.10 ...... Frame ( 3) shift: -0.42 -0.20 ...... Frame ( 4) shift: -0.64 -0.30 ...... Frame ( 5) shift: -0.85 -0.39 ...... Frame ( 6) shift: -0.96 -0.46 ...... Frame ( 7) shift: -0.96 -0.51 ...... Frame ( 8) shift: -0.97 -0.55 ...... Frame ( 9) shift: -0.91 -0.53 ...... Frame ( 10) shift: -0.78 -0.43 ...... Frame ( 11) shift: -0.64 -0.33 ...... Frame ( 12) shift: -0.52 -0.26 ...... Frame ( 13) shift: -0.39 -0.20 ...... Frame ( 14) shift: -0.26 -0.15 ...... Frame ( 15) shift: -0.15 -0.06 ...... Frame ( 16) shift: -0.05 0.05 ...... Frame ( 17) shift: 0.04 0.16 ...... Frame ( 18) shift: 0.10 0.29 ...... Frame ( 19) shift: 0.13 0.42 ...... Frame ( 20) shift: 0.15 0.55 ...... Frame ( 21) shift: 0.18 0.70 ...... Frame ( 22) shift: 0.21 0.87 ...... Frame ( 23) shift: 0.23 1.04 ...... Frame ( 24) shift: 0.30 1.14 ...... Frame ( 25) shift: 0.40 1.16 ...... Frame ( 26) shift: 0.51 1.19 ...... Frame ( 27) shift: 0.54 1.23 ...... Frame ( 28) shift: 0.51 1.29 ...... Frame ( 29) shift: 0.48 1.35 ...... Frame ( 30) shift: 0.48 1.36 ...... Frame ( 31) shift: 0.53 1.35 ...... Frame ( 32) shift: 0.58 1.33 ...... Frame ( 33) shift: 0.63 1.32 ...... Frame ( 34) shift: 0.67 1.32 ...... Frame ( 35) shift: 0.71 1.33 ...... Frame ( 36) shift: 0.77 1.34 ...... Frame ( 37) shift: 0.85 1.36 ...... Frame ( 38) shift: 0.93 1.37 ...... Frame ( 39) shift: 1.00 1.39 ...... Frame ( 40) shift: 1.08 1.41 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.185621 Iteration 2 Error: 0.185365 Iteration 3 Error: 0.046820 Align patch 2 23 left Iteration 1 Error: 0.517581 Iteration 2 Error: 0.087394 Iteration 3 Error: 0.036127 Align patch 3 22 left Iteration 1 Error: 0.608376 Iteration 2 Error: 0.090835 Iteration 3 Error: 0.013014 Align patch 4 21 left Iteration 1 Error: 0.543706 Iteration 2 Error: 0.049064 Align patch 5 20 left Iteration 1 Error: 0.392177 Iteration 2 Error: 0.061380 Iteration 3 Error: 0.008699 Align patch 6 19 left Iteration 1 Error: 0.704991 Iteration 2 Error: 0.061127 Iteration 3 Error: 0.012568 Align patch 7 18 left Iteration 1 Error: 0.958473 Iteration 2 Error: 0.170965 Iteration 3 Error: 0.032908 Align patch 8 17 left Iteration 1 Error: 0.817841 Iteration 2 Error: 0.080297 Iteration 3 Error: 0.018013 Align patch 9 16 left Iteration 1 Error: 0.579400 Iteration 2 Error: 0.064211 Iteration 3 Error: 0.011398 Align patch 10 15 left Iteration 1 Error: 0.311719 Iteration 2 Error: 0.030779 Align patch 11 14 left Iteration 1 Error: 0.654500 Iteration 2 Error: 0.085648 Iteration 3 Error: 0.027665 Align patch 12 13 left Iteration 1 Error: 0.474300 Iteration 2 Error: 0.059011 Iteration 3 Error: 0.016259 Align patch 13 12 left Iteration 1 Error: 0.521390 Iteration 2 Error: 0.063418 Iteration 3 Error: 0.021554 Align patch 14 11 left Iteration 1 Error: 0.647147 Iteration 2 Error: 0.056292 Iteration 3 Error: 0.010300 Align patch 15 10 left Iteration 1 Error: 0.433044 Iteration 2 Error: 0.081511 Iteration 3 Error: 0.015126 Align patch 16 9 left Iteration 1 Error: 0.565141 Iteration 2 Error: 0.105496 Iteration 3 Error: 0.021370 Align patch 17 8 left Iteration 1 Error: 0.459015 Iteration 2 Error: 0.072277 Iteration 3 Error: 0.022031 Align patch 18 7 left Iteration 1 Error: 0.449626 Iteration 2 Error: 0.060478 Iteration 3 Error: 0.012508 Align patch 19 6 left Iteration 1 Error: 0.468145 Iteration 2 Error: 0.062894 Iteration 3 Error: 0.013636 Align patch 20 5 left Iteration 1 Error: 0.585066 Iteration 2 Error: 0.075060 Iteration 3 Error: 0.019545 Align patch 21 4 left Iteration 1 Error: 0.707834 Iteration 2 Error: 0.101037 Iteration 3 Error: 0.015339 Align patch 22 3 left Iteration 1 Error: 0.698251 Iteration 2 Error: 0.095376 Iteration 3 Error: 0.011932 Align patch 23 2 left Iteration 1 Error: 0.567326 Iteration 2 Error: 0.077681 Iteration 3 Error: 0.012306 Align patch 24 1 left Iteration 1 Error: 0.641260 Iteration 2 Error: 0.108606 Iteration 3 Error: 0.025925 Align patch 25 0 left Iteration 1 Error: 0.474554 Iteration 2 Error: 0.063162 Iteration 3 Error: 0.013019 3D Fitting completed. Patch alignment time: 11.46(sec) Local motion has been corrected. Process thread exits. Computational time: 22.265869 sec Total time: 29.196291 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00013hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00013hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.561613s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00013hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.099869s ........................................ >>>>>>TIME<<<<<< FFT: 1.129302s Defocus_U Defocus_V Angle CCC 11378.93 11918.00 1.82 0.060066 Final Values Defocus_U Defocus_V Angle CCC 11418.02 11928.97 2.14 0.099136 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00013hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00013hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 41.44 6.98 Num Hot pixels: 223 Hot pixel threshold: 83.31 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.692198 Iteration 2 Error: 0.099552 Iteration 3 Error: 0.020942 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.24 -0.22 ...... Frame ( 3) shift: -0.47 -0.44 ...... Frame ( 4) shift: -0.71 -0.66 ...... Frame ( 5) shift: -0.94 -0.89 ...... Frame ( 6) shift: -1.06 -0.99 ...... Frame ( 7) shift: -1.07 -0.98 ...... Frame ( 8) shift: -1.07 -0.97 ...... Frame ( 9) shift: -1.05 -0.92 ...... Frame ( 10) shift: -1.02 -0.82 ...... Frame ( 11) shift: -0.98 -0.73 ...... Frame ( 12) shift: -0.93 -0.65 ...... Frame ( 13) shift: -0.87 -0.59 ...... Frame ( 14) shift: -0.81 -0.53 ...... Frame ( 15) shift: -0.79 -0.50 ...... Frame ( 16) shift: -0.80 -0.49 ...... Frame ( 17) shift: -0.82 -0.48 ...... Frame ( 18) shift: -0.79 -0.44 ...... Frame ( 19) shift: -0.72 -0.38 ...... Frame ( 20) shift: -0.65 -0.33 ...... Frame ( 21) shift: -0.63 -0.28 ...... Frame ( 22) shift: -0.65 -0.25 ...... Frame ( 23) shift: -0.68 -0.22 ...... Frame ( 24) shift: -0.69 -0.18 ...... Frame ( 25) shift: -0.69 -0.13 ...... Frame ( 26) shift: -0.69 -0.09 ...... Frame ( 27) shift: -0.69 -0.04 ...... Frame ( 28) shift: -0.68 -0.00 ...... Frame ( 29) shift: -0.68 0.03 ...... Frame ( 30) shift: -0.66 0.05 ...... Frame ( 31) shift: -0.62 0.04 ...... Frame ( 32) shift: -0.58 0.03 ...... Frame ( 33) shift: -0.57 0.05 ...... Frame ( 34) shift: -0.59 0.11 ...... Frame ( 35) shift: -0.60 0.16 ...... Frame ( 36) shift: -0.62 0.21 ...... Frame ( 37) shift: -0.64 0.24 ...... Frame ( 38) shift: -0.65 0.27 ...... Frame ( 39) shift: -0.67 0.29 ...... Frame ( 40) shift: -0.69 0.32 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.269258 Iteration 2 Error: 0.143368 Iteration 3 Error: 0.047004 Align patch 2 23 left Iteration 1 Error: 1.167982 Iteration 2 Error: 0.099202 Iteration 3 Error: 0.025534 Align patch 3 22 left Iteration 1 Error: 0.691580 Iteration 2 Error: 0.072126 Iteration 3 Error: 0.017916 Align patch 4 21 left Iteration 1 Error: 0.895314 Iteration 2 Error: 0.083621 Iteration 3 Error: 0.021223 Align patch 5 20 left Iteration 1 Error: 0.965046 Iteration 2 Error: 0.070607 Iteration 3 Error: 0.021250 Align patch 6 19 left Iteration 1 Error: 0.723183 Iteration 2 Error: 0.086980 Iteration 3 Error: 0.025665 Align patch 7 18 left Iteration 1 Error: 0.879107 Iteration 2 Error: 0.086466 Iteration 3 Error: 0.021092 Align patch 8 17 left Iteration 1 Error: 0.862378 Iteration 2 Error: 0.115899 Iteration 3 Error: 0.033629 Align patch 9 16 left Iteration 1 Error: 0.836552 Iteration 2 Error: 0.105939 Iteration 3 Error: 0.023411 Align patch 10 15 left Iteration 1 Error: 0.595997 Iteration 2 Error: 0.040133 Align patch 11 14 left Iteration 1 Error: 0.612375 Iteration 2 Error: 0.065804 Iteration 3 Error: 0.012513 Align patch 12 13 left Iteration 1 Error: 0.706528 Iteration 2 Error: 0.082126 Iteration 3 Error: 0.012256 Align patch 13 12 left Iteration 1 Error: 0.619063 Iteration 2 Error: 0.124028 Iteration 3 Error: 0.027099 Align patch 14 11 left Iteration 1 Error: 0.633451 Iteration 2 Error: 0.113290 Iteration 3 Error: 0.028497 Align patch 15 10 left Iteration 1 Error: 0.415790 Iteration 2 Error: 0.055562 Iteration 3 Error: 0.014319 Align patch 16 9 left Iteration 1 Error: 0.897118 Iteration 2 Error: 0.107293 Iteration 3 Error: 0.020022 Align patch 17 8 left Iteration 1 Error: 0.850966 Iteration 2 Error: 0.090723 Iteration 3 Error: 0.021876 Align patch 18 7 left Iteration 1 Error: 0.928224 Iteration 2 Error: 0.107920 Iteration 3 Error: 0.025389 Align patch 19 6 left Iteration 1 Error: 0.441556 Iteration 2 Error: 0.074199 Iteration 3 Error: 0.018496 Align patch 20 5 left Iteration 1 Error: 0.702539 Iteration 2 Error: 0.090402 Iteration 3 Error: 0.021385 Align patch 21 4 left Iteration 1 Error: 1.149203 Iteration 2 Error: 0.088776 Iteration 3 Error: 0.019374 Align patch 22 3 left Iteration 1 Error: 0.772507 Iteration 2 Error: 0.084116 Iteration 3 Error: 0.022148 Align patch 23 2 left Iteration 1 Error: 0.943233 Iteration 2 Error: 0.103272 Iteration 3 Error: 0.038151 Align patch 24 1 left Iteration 1 Error: 0.572866 Iteration 2 Error: 0.091837 Iteration 3 Error: 0.014689 Align patch 25 0 left Iteration 1 Error: 0.538087 Iteration 2 Error: 0.064430 Iteration 3 Error: 0.016710 3D Fitting completed. Patch alignment time: 11.96(sec) Local motion has been corrected. Process thread exits. Computational time: 22.226297 sec Total time: 29.841766 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00013hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00013hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.458922s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00013hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.984868s ........................................ >>>>>>TIME<<<<<< FFT: 0.902780s Defocus_U Defocus_V Angle CCC 10402.39 11238.36 5.93 0.054219 Final Values Defocus_U Defocus_V Angle CCC 10410.21 11255.57 6.87 0.094996 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00013hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00013hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.350e-01 1.004e-01 CC threshold: 0.738 Mean Std: 41.66 7.01 Num Hot pixels: 229 Hot pixel threshold: 83.75 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.686404 Iteration 2 Error: 0.098916 Iteration 3 Error: 0.021386 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.11 0.00 ...... Frame ( 3) shift: -0.22 0.00 ...... Frame ( 4) shift: -0.33 0.00 ...... Frame ( 5) shift: -0.44 0.00 ...... Frame ( 6) shift: -0.48 0.04 ...... Frame ( 7) shift: -0.45 0.10 ...... Frame ( 8) shift: -0.42 0.17 ...... Frame ( 9) shift: -0.37 0.25 ...... Frame ( 10) shift: -0.30 0.35 ...... Frame ( 11) shift: -0.24 0.45 ...... Frame ( 12) shift: -0.22 0.51 ...... Frame ( 13) shift: -0.24 0.52 ...... Frame ( 14) shift: -0.26 0.54 ...... Frame ( 15) shift: -0.26 0.54 ...... Frame ( 16) shift: -0.23 0.53 ...... Frame ( 17) shift: -0.21 0.52 ...... Frame ( 18) shift: -0.18 0.55 ...... Frame ( 19) shift: -0.17 0.60 ...... Frame ( 20) shift: -0.16 0.66 ...... Frame ( 21) shift: -0.16 0.72 ...... Frame ( 22) shift: -0.18 0.78 ...... Frame ( 23) shift: -0.20 0.83 ...... Frame ( 24) shift: -0.22 0.87 ...... Frame ( 25) shift: -0.24 0.89 ...... Frame ( 26) shift: -0.25 0.90 ...... Frame ( 27) shift: -0.26 0.95 ...... Frame ( 28) shift: -0.25 1.04 ...... Frame ( 29) shift: -0.25 1.13 ...... Frame ( 30) shift: -0.22 1.22 ...... Frame ( 31) shift: -0.17 1.31 ...... Frame ( 32) shift: -0.13 1.40 ...... Frame ( 33) shift: -0.12 1.43 ...... Frame ( 34) shift: -0.14 1.41 ...... Frame ( 35) shift: -0.17 1.39 ...... Frame ( 36) shift: -0.19 1.36 ...... Frame ( 37) shift: -0.20 1.33 ...... Frame ( 38) shift: -0.21 1.29 ...... Frame ( 39) shift: -0.21 1.25 ...... Frame ( 40) shift: -0.22 1.22 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.237284 Iteration 2 Error: 0.084776 Iteration 3 Error: 0.017710 Align patch 2 23 left Iteration 1 Error: 0.723103 Iteration 2 Error: 0.084113 Iteration 3 Error: 0.019644 Align patch 3 22 left Iteration 1 Error: 0.515440 Iteration 2 Error: 0.047263 Align patch 4 21 left Iteration 1 Error: 0.569914 Iteration 2 Error: 0.061222 Iteration 3 Error: 0.012145 Align patch 5 20 left Iteration 1 Error: 0.515948 Iteration 2 Error: 0.075678 Iteration 3 Error: 0.011325 Align patch 6 19 left Iteration 1 Error: 0.990198 Iteration 2 Error: 0.141839 Iteration 3 Error: 0.032188 Align patch 7 18 left Iteration 1 Error: 0.767843 Iteration 2 Error: 0.078111 Iteration 3 Error: 0.017767 Align patch 8 17 left Iteration 1 Error: 0.626164 Iteration 2 Error: 0.081988 Iteration 3 Error: 0.018978 Align patch 9 16 left Iteration 1 Error: 0.590866 Iteration 2 Error: 0.073929 Iteration 3 Error: 0.015969 Align patch 10 15 left Iteration 1 Error: 0.435587 Iteration 2 Error: 0.045704 Align patch 11 14 left Iteration 1 Error: 0.604965 Iteration 2 Error: 0.061869 Iteration 3 Error: 0.013025 Align patch 12 13 left Iteration 1 Error: 0.617680 Iteration 2 Error: 0.072055 Iteration 3 Error: 0.020640 Align patch 13 12 left Iteration 1 Error: 0.524753 Iteration 2 Error: 0.082479 Iteration 3 Error: 0.015909 Align patch 14 11 left Iteration 1 Error: 0.326848 Iteration 2 Error: 0.036323 Align patch 15 10 left Iteration 1 Error: 0.581694 Iteration 2 Error: 0.043144 Align patch 16 9 left Iteration 1 Error: 0.527882 Iteration 2 Error: 0.061343 Iteration 3 Error: 0.018327 Align patch 17 8 left Iteration 1 Error: 0.399831 Iteration 2 Error: 0.089477 Iteration 3 Error: 0.016113 Align patch 18 7 left Iteration 1 Error: 0.537913 Iteration 2 Error: 0.075066 Iteration 3 Error: 0.021075 Align patch 19 6 left Iteration 1 Error: 0.398829 Iteration 2 Error: 0.046672 Align patch 20 5 left Iteration 1 Error: 0.738349 Iteration 2 Error: 0.086914 Iteration 3 Error: 0.014282 Align patch 21 4 left Iteration 1 Error: 0.908701 Iteration 2 Error: 0.096309 Iteration 3 Error: 0.016504 Align patch 22 3 left Iteration 1 Error: 0.508772 Iteration 2 Error: 0.080833 Iteration 3 Error: 0.015499 Align patch 23 2 left Iteration 1 Error: 0.583594 Iteration 2 Error: 0.095024 Iteration 3 Error: 0.018288 Align patch 24 1 left Iteration 1 Error: 0.680224 Iteration 2 Error: 0.085161 Iteration 3 Error: 0.014179 Align patch 25 0 left Iteration 1 Error: 0.465666 Iteration 2 Error: 0.068669 Iteration 3 Error: 0.008747 3D Fitting completed. Patch alignment time: 10.61(sec) Local motion has been corrected. Process thread exits. Computational time: 21.218801 sec Total time: 27.923828 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00013hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00013hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.836019s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00013hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.873181s ........................................ >>>>>>TIME<<<<<< FFT: 1.104747s Defocus_U Defocus_V Angle CCC 10875.01 10261.73 86.13 0.058267 Final Values Defocus_U Defocus_V Angle CCC 10895.33 10275.80 85.19 0.101040 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00014hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00014hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.354e-01 1.007e-01 CC threshold: 0.740 Mean Std: 38.76 6.80 Num Hot pixels: 214 Hot pixel threshold: 79.58 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.055858 Iteration 2 Error: 0.145031 Iteration 3 Error: 0.020586 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.10 0.16 ...... Frame ( 3) shift: -0.21 0.33 ...... Frame ( 4) shift: -0.31 0.49 ...... Frame ( 5) shift: -0.42 0.66 ...... Frame ( 6) shift: -0.45 0.72 ...... Frame ( 7) shift: -0.40 0.70 ...... Frame ( 8) shift: -0.35 0.67 ...... Frame ( 9) shift: -0.29 0.62 ...... Frame ( 10) shift: -0.22 0.54 ...... Frame ( 11) shift: -0.15 0.46 ...... Frame ( 12) shift: -0.13 0.38 ...... Frame ( 13) shift: -0.16 0.32 ...... Frame ( 14) shift: -0.19 0.25 ...... Frame ( 15) shift: -0.16 0.20 ...... Frame ( 16) shift: -0.06 0.17 ...... Frame ( 17) shift: 0.05 0.14 ...... Frame ( 18) shift: 0.12 0.12 ...... Frame ( 19) shift: 0.15 0.09 ...... Frame ( 20) shift: 0.19 0.06 ...... Frame ( 21) shift: 0.24 0.04 ...... Frame ( 22) shift: 0.31 0.02 ...... Frame ( 23) shift: 0.38 0.00 ...... Frame ( 24) shift: 0.47 -0.01 ...... Frame ( 25) shift: 0.59 -0.00 ...... Frame ( 26) shift: 0.70 0.01 ...... Frame ( 27) shift: 0.78 0.00 ...... Frame ( 28) shift: 0.83 -0.01 ...... Frame ( 29) shift: 0.88 -0.03 ...... Frame ( 30) shift: 0.92 -0.06 ...... Frame ( 31) shift: 0.94 -0.10 ...... Frame ( 32) shift: 0.96 -0.14 ...... Frame ( 33) shift: 1.01 -0.15 ...... Frame ( 34) shift: 1.08 -0.14 ...... Frame ( 35) shift: 1.15 -0.12 ...... Frame ( 36) shift: 1.22 -0.09 ...... Frame ( 37) shift: 1.29 -0.06 ...... Frame ( 38) shift: 1.36 -0.02 ...... Frame ( 39) shift: 1.43 0.01 ...... Frame ( 40) shift: 1.50 0.05 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.387083 Iteration 2 Error: 0.401646 Iteration 3 Error: 0.054852 Iteration 4 Error: 0.015181 Align patch 2 23 left Iteration 1 Error: 1.672608 Iteration 2 Error: 0.165313 Iteration 3 Error: 0.034785 Align patch 3 22 left Iteration 1 Error: 1.015132 Iteration 2 Error: 0.112038 Iteration 3 Error: 0.027461 Align patch 4 21 left Iteration 1 Error: 2.039967 Iteration 2 Error: 0.251876 Iteration 3 Error: 0.036660 Align patch 5 20 left Iteration 1 Error: 2.345636 Iteration 2 Error: 0.196703 Iteration 3 Error: 0.031246 Align patch 6 19 left Iteration 1 Error: 2.219303 Iteration 2 Error: 0.418299 Iteration 3 Error: 0.067918 Iteration 4 Error: 0.016812 Align patch 7 18 left Iteration 1 Error: 1.800581 Iteration 2 Error: 0.191884 Iteration 3 Error: 0.037752 Align patch 8 17 left Iteration 1 Error: 0.477918 Iteration 2 Error: 0.063994 Iteration 3 Error: 0.021421 Align patch 9 16 left Iteration 1 Error: 0.843002 Iteration 2 Error: 0.110537 Iteration 3 Error: 0.034302 Align patch 10 15 left Iteration 1 Error: 1.474351 Iteration 2 Error: 0.096622 Iteration 3 Error: 0.010129 Align patch 11 14 left Iteration 1 Error: 2.205739 Iteration 2 Error: 0.274010 Iteration 3 Error: 0.059239 Iteration 4 Error: 0.016093 Align patch 12 13 left Iteration 1 Error: 0.983580 Iteration 2 Error: 0.212814 Iteration 3 Error: 0.036077 Align patch 13 12 left Iteration 1 Error: 0.454320 Iteration 2 Error: 0.076058 Iteration 3 Error: 0.020035 Align patch 14 11 left Iteration 1 Error: 0.679625 Iteration 2 Error: 0.128610 Iteration 3 Error: 0.031568 Align patch 15 10 left Iteration 1 Error: 0.802516 Iteration 2 Error: 0.081436 Iteration 3 Error: 0.011775 Align patch 16 9 left Iteration 1 Error: 1.596783 Iteration 2 Error: 0.266830 Iteration 3 Error: 0.038365 Align patch 17 8 left Iteration 1 Error: 0.703805 Iteration 2 Error: 0.155635 Iteration 3 Error: 0.023806 Align patch 18 7 left Iteration 1 Error: 0.520471 Iteration 2 Error: 0.081988 Iteration 3 Error: 0.012061 Align patch 19 6 left Iteration 1 Error: 0.753700 Iteration 2 Error: 0.093164 Iteration 3 Error: 0.021421 Align patch 20 5 left Iteration 1 Error: 0.611382 Iteration 2 Error: 0.086292 Iteration 3 Error: 0.011199 Align patch 21 4 left Iteration 1 Error: 1.256565 Iteration 2 Error: 0.224593 Iteration 3 Error: 0.062354 Iteration 4 Error: 0.017591 Align patch 22 3 left Iteration 1 Error: 0.936751 Iteration 2 Error: 0.138839 Iteration 3 Error: 0.029579 Align patch 23 2 left Iteration 1 Error: 0.760666 Iteration 2 Error: 0.124318 Iteration 3 Error: 0.023319 Align patch 24 1 left Iteration 1 Error: 0.567983 Iteration 2 Error: 0.080934 Iteration 3 Error: 0.014571 Align patch 25 0 left Iteration 1 Error: 0.817903 Iteration 2 Error: 0.152510 Iteration 3 Error: 0.022695 3D Fitting completed. Patch alignment time: 11.74(sec) Local motion has been corrected. Process thread exits. Computational time: 22.217569 sec Total time: 28.761372 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00014hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00014hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.450129s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00014hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.600231s ........................................ >>>>>>TIME<<<<<< FFT: 1.158595s Defocus_U Defocus_V Angle CCC 12156.26 13039.07 12.61 0.082298 Final Values Defocus_U Defocus_V Angle CCC 12159.36 13057.85 12.61 0.130787 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00014hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00014hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.351e-01 1.004e-01 CC threshold: 0.738 Mean Std: 42.03 7.14 Num Hot pixels: 231 Hot pixel threshold: 84.87 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.830355 Iteration 2 Error: 0.102427 Iteration 3 Error: 0.016941 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.20 0.04 ...... Frame ( 3) shift: -0.40 0.08 ...... Frame ( 4) shift: -0.60 0.11 ...... Frame ( 5) shift: -0.80 0.15 ...... Frame ( 6) shift: -0.87 0.20 ...... Frame ( 7) shift: -0.81 0.25 ...... Frame ( 8) shift: -0.75 0.30 ...... Frame ( 9) shift: -0.70 0.36 ...... Frame ( 10) shift: -0.66 0.43 ...... Frame ( 11) shift: -0.62 0.50 ...... Frame ( 12) shift: -0.57 0.59 ...... Frame ( 13) shift: -0.52 0.71 ...... Frame ( 14) shift: -0.46 0.83 ...... Frame ( 15) shift: -0.43 0.93 ...... Frame ( 16) shift: -0.43 1.02 ...... Frame ( 17) shift: -0.42 1.11 ...... Frame ( 18) shift: -0.41 1.16 ...... Frame ( 19) shift: -0.38 1.17 ...... Frame ( 20) shift: -0.34 1.18 ...... Frame ( 21) shift: -0.30 1.17 ...... Frame ( 22) shift: -0.23 1.16 ...... Frame ( 23) shift: -0.17 1.14 ...... Frame ( 24) shift: -0.14 1.15 ...... Frame ( 25) shift: -0.13 1.18 ...... Frame ( 26) shift: -0.13 1.21 ...... Frame ( 27) shift: -0.15 1.23 ...... Frame ( 28) shift: -0.19 1.24 ...... Frame ( 29) shift: -0.23 1.25 ...... Frame ( 30) shift: -0.28 1.26 ...... Frame ( 31) shift: -0.33 1.28 ...... Frame ( 32) shift: -0.38 1.30 ...... Frame ( 33) shift: -0.38 1.34 ...... Frame ( 34) shift: -0.32 1.39 ...... Frame ( 35) shift: -0.27 1.43 ...... Frame ( 36) shift: -0.24 1.50 ...... Frame ( 37) shift: -0.24 1.57 ...... Frame ( 38) shift: -0.24 1.65 ...... Frame ( 39) shift: -0.24 1.73 ...... Frame ( 40) shift: -0.24 1.80 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.200573 Iteration 2 Error: 0.191869 Iteration 3 Error: 0.047924 Align patch 2 23 left Iteration 1 Error: 0.700849 Iteration 2 Error: 0.088716 Iteration 3 Error: 0.020655 Align patch 3 22 left Iteration 1 Error: 0.288232 Iteration 2 Error: 0.038441 Align patch 4 21 left Iteration 1 Error: 0.547613 Iteration 2 Error: 0.044989 Align patch 5 20 left Iteration 1 Error: 0.703805 Iteration 2 Error: 0.119579 Iteration 3 Error: 0.024609 Align patch 6 19 left Iteration 1 Error: 0.821951 Iteration 2 Error: 0.137909 Iteration 3 Error: 0.028555 Align patch 7 18 left Iteration 1 Error: 0.608380 Iteration 2 Error: 0.063860 Iteration 3 Error: 0.012861 Align patch 8 17 left Iteration 1 Error: 0.596245 Iteration 2 Error: 0.119249 Iteration 3 Error: 0.017054 Align patch 9 16 left Iteration 1 Error: 0.712315 Iteration 2 Error: 0.100941 Iteration 3 Error: 0.025321 Align patch 10 15 left Iteration 1 Error: 0.562788 Iteration 2 Error: 0.131382 Iteration 3 Error: 0.015121 Align patch 11 14 left Iteration 1 Error: 0.659226 Iteration 2 Error: 0.127394 Iteration 3 Error: 0.036104 Align patch 12 13 left Iteration 1 Error: 0.582420 Iteration 2 Error: 0.129449 Iteration 3 Error: 0.031509 Align patch 13 12 left Iteration 1 Error: 0.502221 Iteration 2 Error: 0.057750 Iteration 3 Error: 0.009921 Align patch 14 11 left Iteration 1 Error: 0.571788 Iteration 2 Error: 0.095240 Iteration 3 Error: 0.021983 Align patch 15 10 left Iteration 1 Error: 0.919798 Iteration 2 Error: 0.057068 Iteration 3 Error: 0.005737 Align patch 16 9 left Iteration 1 Error: 0.986359 Iteration 2 Error: 0.214640 Iteration 3 Error: 0.045676 Align patch 17 8 left Iteration 1 Error: 0.922046 Iteration 2 Error: 0.092916 Iteration 3 Error: 0.019757 Align patch 18 7 left Iteration 1 Error: 0.429822 Iteration 2 Error: 0.051009 Iteration 3 Error: 0.009811 Align patch 19 6 left Iteration 1 Error: 0.714490 Iteration 2 Error: 0.098745 Iteration 3 Error: 0.016812 Align patch 20 5 left Iteration 1 Error: 0.926476 Iteration 2 Error: 0.102697 Iteration 3 Error: 0.017822 Align patch 21 4 left Iteration 1 Error: 0.823804 Iteration 2 Error: 0.289007 Iteration 3 Error: 0.073847 Iteration 4 Error: 0.017851 Align patch 22 3 left Iteration 1 Error: 0.558463 Iteration 2 Error: 0.121308 Iteration 3 Error: 0.038327 Align patch 23 2 left Iteration 1 Error: 0.491202 Iteration 2 Error: 0.055256 Iteration 3 Error: 0.015710 Align patch 24 1 left Iteration 1 Error: 0.631294 Iteration 2 Error: 0.064320 Iteration 3 Error: 0.013513 Align patch 25 0 left Iteration 1 Error: 0.893593 Iteration 2 Error: 0.202857 Iteration 3 Error: 0.028961 3D Fitting completed. Patch alignment time: 10.87(sec) Local motion has been corrected. Process thread exits. Computational time: 21.201191 sec Total time: 28.681583 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00014hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00014hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.490635s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00014hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.586446s ........................................ >>>>>>TIME<<<<<< FFT: 0.908545s Defocus_U Defocus_V Angle CCC 13457.43 12913.79 89.80 0.068500 Final Values Defocus_U Defocus_V Angle CCC 13463.68 12929.43 89.18 0.113930 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00014hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00014hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.350e-01 1.004e-01 CC threshold: 0.737 Mean Std: 36.34 6.71 Num Hot pixels: 202 Hot pixel threshold: 76.57 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.517391 Iteration 2 Error: 0.144788 Iteration 3 Error: 0.028936 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.19 -0.04 ...... Frame ( 3) shift: -0.38 -0.08 ...... Frame ( 4) shift: -0.56 -0.12 ...... Frame ( 5) shift: -0.75 -0.16 ...... Frame ( 6) shift: -0.78 -0.08 ...... Frame ( 7) shift: -0.66 0.11 ...... Frame ( 8) shift: -0.53 0.30 ...... Frame ( 9) shift: -0.42 0.49 ...... Frame ( 10) shift: -0.33 0.66 ...... Frame ( 11) shift: -0.24 0.82 ...... Frame ( 12) shift: -0.22 0.94 ...... Frame ( 13) shift: -0.27 0.99 ...... Frame ( 14) shift: -0.32 1.04 ...... Frame ( 15) shift: -0.32 1.14 ...... Frame ( 16) shift: -0.27 1.28 ...... Frame ( 17) shift: -0.21 1.43 ...... Frame ( 18) shift: -0.18 1.53 ...... Frame ( 19) shift: -0.17 1.60 ...... Frame ( 20) shift: -0.16 1.67 ...... Frame ( 21) shift: -0.20 1.76 ...... Frame ( 22) shift: -0.30 1.86 ...... Frame ( 23) shift: -0.39 1.95 ...... Frame ( 24) shift: -0.43 2.05 ...... Frame ( 25) shift: -0.42 2.13 ...... Frame ( 26) shift: -0.42 2.22 ...... Frame ( 27) shift: -0.42 2.25 ...... Frame ( 28) shift: -0.45 2.21 ...... Frame ( 29) shift: -0.47 2.18 ...... Frame ( 30) shift: -0.50 2.15 ...... Frame ( 31) shift: -0.53 2.12 ...... Frame ( 32) shift: -0.55 2.10 ...... Frame ( 33) shift: -0.56 2.08 ...... Frame ( 34) shift: -0.56 2.08 ...... Frame ( 35) shift: -0.56 2.07 ...... Frame ( 36) shift: -0.56 2.05 ...... Frame ( 37) shift: -0.57 2.03 ...... Frame ( 38) shift: -0.58 2.00 ...... Frame ( 39) shift: -0.59 1.98 ...... Frame ( 40) shift: -0.60 1.95 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.294972 Iteration 2 Error: 0.254578 Iteration 3 Error: 0.077714 Iteration 4 Error: 0.013764 Align patch 2 23 left Iteration 1 Error: 0.859126 Iteration 2 Error: 0.221448 Iteration 3 Error: 0.069227 Iteration 4 Error: 0.020221 Align patch 3 22 left Iteration 1 Error: 0.554208 Iteration 2 Error: 0.099886 Iteration 3 Error: 0.036198 Align patch 4 21 left Iteration 1 Error: 0.646400 Iteration 2 Error: 0.079705 Iteration 3 Error: 0.016238 Align patch 5 20 left Iteration 1 Error: 0.374624 Iteration 2 Error: 0.056234 Iteration 3 Error: 0.011257 Align patch 6 19 left Iteration 1 Error: 0.842914 Iteration 2 Error: 0.090654 Iteration 3 Error: 0.023637 Align patch 7 18 left Iteration 1 Error: 0.433397 Iteration 2 Error: 0.050664 Iteration 3 Error: 0.012137 Align patch 8 17 left Iteration 1 Error: 0.519314 Iteration 2 Error: 0.106738 Iteration 3 Error: 0.034045 Align patch 9 16 left Iteration 1 Error: 0.465866 Iteration 2 Error: 0.099090 Iteration 3 Error: 0.020565 Align patch 10 15 left Iteration 1 Error: 0.754176 Iteration 2 Error: 0.098166 Iteration 3 Error: 0.020218 Align patch 11 14 left Iteration 1 Error: 1.022050 Iteration 2 Error: 0.087078 Iteration 3 Error: 0.019878 Align patch 12 13 left Iteration 1 Error: 0.684301 Iteration 2 Error: 0.095499 Iteration 3 Error: 0.021481 Align patch 13 12 left Iteration 1 Error: 0.402798 Iteration 2 Error: 0.047139 Align patch 14 11 left Iteration 1 Error: 0.473178 Iteration 2 Error: 0.061453 Iteration 3 Error: 0.015584 Align patch 15 10 left Iteration 1 Error: 0.586848 Iteration 2 Error: 0.115499 Iteration 3 Error: 0.014578 Align patch 16 9 left Iteration 1 Error: 0.483999 Iteration 2 Error: 0.068397 Iteration 3 Error: 0.015321 Align patch 17 8 left Iteration 1 Error: 0.696460 Iteration 2 Error: 0.083622 Iteration 3 Error: 0.020642 Align patch 18 7 left Iteration 1 Error: 0.594404 Iteration 2 Error: 0.067612 Iteration 3 Error: 0.014850 Align patch 19 6 left Iteration 1 Error: 0.866295 Iteration 2 Error: 0.097384 Iteration 3 Error: 0.017543 Align patch 20 5 left Iteration 1 Error: 0.799719 Iteration 2 Error: 0.056325 Iteration 3 Error: 0.007890 Align patch 21 4 left Iteration 1 Error: 1.064477 Iteration 2 Error: 0.129345 Iteration 3 Error: 0.022306 Align patch 22 3 left Iteration 1 Error: 0.929810 Iteration 2 Error: 0.101775 Iteration 3 Error: 0.025415 Align patch 23 2 left Iteration 1 Error: 0.833936 Iteration 2 Error: 0.090824 Iteration 3 Error: 0.017990 Align patch 24 1 left Iteration 1 Error: 0.739706 Iteration 2 Error: 0.070547 Iteration 3 Error: 0.014625 Align patch 25 0 left Iteration 1 Error: 1.001026 Iteration 2 Error: 0.083570 Iteration 3 Error: 0.022789 3D Fitting completed. Patch alignment time: 11.17(sec) Local motion has been corrected. Process thread exits. Computational time: 20.600445 sec Total time: 29.741055 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00014hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00014hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.580820s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00014hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.280014s ........................................ >>>>>>TIME<<<<<< FFT: 1.044147s Defocus_U Defocus_V Angle CCC 11794.18 12616.11 8.27 0.050621 Final Values Defocus_U Defocus_V Angle CCC 11837.97 12772.49 8.27 0.072768 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00014hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00014hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.351e-01 1.004e-01 CC threshold: 0.737 Mean Std: 40.74 7.03 Num Hot pixels: 224 Hot pixel threshold: 82.90 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.602029 Iteration 2 Error: 0.070436 Iteration 3 Error: 0.012055 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.25 -0.12 ...... Frame ( 3) shift: -0.50 -0.25 ...... Frame ( 4) shift: -0.75 -0.37 ...... Frame ( 5) shift: -1.00 -0.50 ...... Frame ( 6) shift: -1.15 -0.53 ...... Frame ( 7) shift: -1.19 -0.48 ...... Frame ( 8) shift: -1.24 -0.43 ...... Frame ( 9) shift: -1.24 -0.38 ...... Frame ( 10) shift: -1.20 -0.33 ...... Frame ( 11) shift: -1.16 -0.28 ...... Frame ( 12) shift: -1.13 -0.26 ...... Frame ( 13) shift: -1.11 -0.27 ...... Frame ( 14) shift: -1.08 -0.28 ...... Frame ( 15) shift: -1.05 -0.27 ...... Frame ( 16) shift: -1.02 -0.25 ...... Frame ( 17) shift: -0.99 -0.22 ...... Frame ( 18) shift: -1.00 -0.20 ...... Frame ( 19) shift: -1.04 -0.17 ...... Frame ( 20) shift: -1.08 -0.14 ...... Frame ( 21) shift: -1.08 -0.07 ...... Frame ( 22) shift: -1.03 0.03 ...... Frame ( 23) shift: -0.99 0.13 ...... Frame ( 24) shift: -0.95 0.19 ...... Frame ( 25) shift: -0.93 0.21 ...... Frame ( 26) shift: -0.91 0.24 ...... Frame ( 27) shift: -0.88 0.26 ...... Frame ( 28) shift: -0.83 0.30 ...... Frame ( 29) shift: -0.79 0.33 ...... Frame ( 30) shift: -0.77 0.34 ...... Frame ( 31) shift: -0.79 0.32 ...... Frame ( 32) shift: -0.80 0.30 ...... Frame ( 33) shift: -0.78 0.27 ...... Frame ( 34) shift: -0.72 0.23 ...... Frame ( 35) shift: -0.66 0.20 ...... Frame ( 36) shift: -0.63 0.18 ...... Frame ( 37) shift: -0.63 0.19 ...... Frame ( 38) shift: -0.63 0.20 ...... Frame ( 39) shift: -0.63 0.20 ...... Frame ( 40) shift: -0.63 0.21 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.212701 Iteration 2 Error: 0.124787 Iteration 3 Error: 0.023485 Align patch 2 23 left Iteration 1 Error: 0.741764 Iteration 2 Error: 0.120982 Iteration 3 Error: 0.026012 Align patch 3 22 left Iteration 1 Error: 0.889881 Iteration 2 Error: 0.091886 Iteration 3 Error: 0.019463 Align patch 4 21 left Iteration 1 Error: 0.782149 Iteration 2 Error: 0.107859 Iteration 3 Error: 0.032361 Align patch 5 20 left Iteration 1 Error: 0.436480 Iteration 2 Error: 0.075677 Iteration 3 Error: 0.009237 Align patch 6 19 left Iteration 1 Error: 0.875378 Iteration 2 Error: 0.140572 Iteration 3 Error: 0.023881 Align patch 7 18 left Iteration 1 Error: 0.549889 Iteration 2 Error: 0.110002 Iteration 3 Error: 0.030873 Align patch 8 17 left Iteration 1 Error: 0.444687 Iteration 2 Error: 0.057918 Iteration 3 Error: 0.012898 Align patch 9 16 left Iteration 1 Error: 0.523774 Iteration 2 Error: 0.053791 Iteration 3 Error: 0.014130 Align patch 10 15 left Iteration 1 Error: 0.649052 Iteration 2 Error: 0.067042 Iteration 3 Error: 0.011670 Align patch 11 14 left Iteration 1 Error: 0.737109 Iteration 2 Error: 0.131600 Iteration 3 Error: 0.026923 Align patch 12 13 left Iteration 1 Error: 0.542272 Iteration 2 Error: 0.072107 Iteration 3 Error: 0.021211 Align patch 13 12 left Iteration 1 Error: 0.401917 Iteration 2 Error: 0.068329 Iteration 3 Error: 0.011079 Align patch 14 11 left Iteration 1 Error: 0.420415 Iteration 2 Error: 0.071427 Iteration 3 Error: 0.016287 Align patch 15 10 left Iteration 1 Error: 0.798365 Iteration 2 Error: 0.098840 Iteration 3 Error: 0.024011 Align patch 16 9 left Iteration 1 Error: 0.472094 Iteration 2 Error: 0.055009 Iteration 3 Error: 0.011585 Align patch 17 8 left Iteration 1 Error: 0.882605 Iteration 2 Error: 0.104593 Iteration 3 Error: 0.021075 Align patch 18 7 left Iteration 1 Error: 0.578254 Iteration 2 Error: 0.081116 Iteration 3 Error: 0.013244 Align patch 19 6 left Iteration 1 Error: 0.533406 Iteration 2 Error: 0.055702 Iteration 3 Error: 0.008150 Align patch 20 5 left Iteration 1 Error: 0.734660 Iteration 2 Error: 0.140973 Iteration 3 Error: 0.022825 Align patch 21 4 left Iteration 1 Error: 0.593535 Iteration 2 Error: 0.057285 Iteration 3 Error: 0.013686 Align patch 22 3 left Iteration 1 Error: 0.607946 Iteration 2 Error: 0.078500 Iteration 3 Error: 0.015870 Align patch 23 2 left Iteration 1 Error: 0.611832 Iteration 2 Error: 0.070324 Iteration 3 Error: 0.016368 Align patch 24 1 left Iteration 1 Error: 0.557202 Iteration 2 Error: 0.073565 Iteration 3 Error: 0.016241 Align patch 25 0 left Iteration 1 Error: 0.665927 Iteration 2 Error: 0.079800 Iteration 3 Error: 0.017338 3D Fitting completed. Patch alignment time: 10.97(sec) Local motion has been corrected. Process thread exits. Computational time: 22.964417 sec Total time: 32.858959 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00014hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00014hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.534333s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00014hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 4.755336s ........................................ >>>>>>TIME<<<<<< FFT: 1.047527s Defocus_U Defocus_V Angle CCC 14068.38 13404.32 81.76 0.069362 Final Values Defocus_U Defocus_V Angle CCC 14073.05 13405.90 81.76 0.109437 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00015hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00015hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.310e-01 9.773e-02 CC threshold: 0.717 Mean Std: 39.64 6.92 Num Hot pixels: 239 Hot pixel threshold: 81.14 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.688842 Iteration 2 Error: 0.281541 Iteration 3 Error: 0.067423 Iteration 4 Error: 0.022652 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.22 0.07 ...... Frame ( 3) shift: 0.45 0.13 ...... Frame ( 4) shift: 0.67 0.20 ...... Frame ( 5) shift: 0.89 0.27 ...... Frame ( 6) shift: 1.04 0.38 ...... Frame ( 7) shift: 1.12 0.53 ...... Frame ( 8) shift: 1.19 0.69 ...... Frame ( 9) shift: 1.25 0.75 ...... Frame ( 10) shift: 1.30 0.72 ...... Frame ( 11) shift: 1.34 0.69 ...... Frame ( 12) shift: 1.41 0.73 ...... Frame ( 13) shift: 1.49 0.82 ...... Frame ( 14) shift: 1.57 0.92 ...... Frame ( 15) shift: 1.63 0.97 ...... Frame ( 16) shift: 1.66 0.98 ...... Frame ( 17) shift: 1.69 0.99 ...... Frame ( 18) shift: 1.74 1.02 ...... Frame ( 19) shift: 1.81 1.07 ...... Frame ( 20) shift: 1.88 1.12 ...... Frame ( 21) shift: 1.98 1.16 ...... Frame ( 22) shift: 2.13 1.21 ...... Frame ( 23) shift: 2.27 1.26 ...... Frame ( 24) shift: 2.37 1.29 ...... Frame ( 25) shift: 2.43 1.31 ...... Frame ( 26) shift: 2.49 1.32 ...... Frame ( 27) shift: 2.54 1.32 ...... Frame ( 28) shift: 2.57 1.30 ...... Frame ( 29) shift: 2.59 1.28 ...... Frame ( 30) shift: 2.66 1.30 ...... Frame ( 31) shift: 2.75 1.35 ...... Frame ( 32) shift: 2.85 1.41 ...... Frame ( 33) shift: 2.95 1.46 ...... Frame ( 34) shift: 3.04 1.51 ...... Frame ( 35) shift: 3.13 1.56 ...... Frame ( 36) shift: 3.21 1.61 ...... Frame ( 37) shift: 3.28 1.68 ...... Frame ( 38) shift: 3.34 1.75 ...... Frame ( 39) shift: 3.41 1.82 ...... Frame ( 40) shift: 3.47 1.88 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.689593 Iteration 2 Error: 0.070871 Iteration 3 Error: 0.016941 Align patch 2 23 left Iteration 1 Error: 0.635953 Iteration 2 Error: 0.128056 Iteration 3 Error: 0.026406 Align patch 3 22 left Iteration 1 Error: 0.726943 Iteration 2 Error: 0.172193 Iteration 3 Error: 0.060011 Iteration 4 Error: 0.019733 Align patch 4 21 left Iteration 1 Error: 0.745692 Iteration 2 Error: 0.153071 Iteration 3 Error: 0.044404 Align patch 5 20 left Iteration 1 Error: 0.801135 Iteration 2 Error: 0.122141 Iteration 3 Error: 0.028437 Align patch 6 19 left Iteration 1 Error: 0.740843 Iteration 2 Error: 0.111309 Iteration 3 Error: 0.026075 Align patch 7 18 left Iteration 1 Error: 0.998385 Iteration 2 Error: 0.173940 Iteration 3 Error: 0.043205 Align patch 8 17 left Iteration 1 Error: 0.634132 Iteration 2 Error: 0.119312 Iteration 3 Error: 0.050371 Iteration 4 Error: 0.012027 Align patch 9 16 left Iteration 1 Error: 0.576443 Iteration 2 Error: 0.169390 Iteration 3 Error: 0.046529 Align patch 10 15 left Iteration 1 Error: 0.658740 Iteration 2 Error: 0.117152 Iteration 3 Error: 0.021213 Align patch 11 14 left Iteration 1 Error: 0.568980 Iteration 2 Error: 0.222552 Iteration 3 Error: 0.062678 Iteration 4 Error: 0.033726 Align patch 12 13 left Iteration 1 Error: 0.567652 Iteration 2 Error: 0.102523 Iteration 3 Error: 0.024249 Align patch 13 12 left Iteration 1 Error: 0.560351 Iteration 2 Error: 0.135187 Iteration 3 Error: 0.026436 Align patch 14 11 left Iteration 1 Error: 0.654541 Iteration 2 Error: 0.216438 Iteration 3 Error: 0.046040 Align patch 15 10 left Iteration 1 Error: 0.856003 Iteration 2 Error: 0.108678 Iteration 3 Error: 0.027908 Align patch 16 9 left Iteration 1 Error: 1.020724 Iteration 2 Error: 0.378442 Iteration 3 Error: 0.116505 Iteration 4 Error: 0.045036 Align patch 17 8 left Iteration 1 Error: 0.969408 Iteration 2 Error: 0.213018 Iteration 3 Error: 0.063258 Iteration 4 Error: 0.028453 Align patch 18 7 left Iteration 1 Error: 0.861270 Iteration 2 Error: 0.156233 Iteration 3 Error: 0.029026 Align patch 19 6 left Iteration 1 Error: 0.784179 Iteration 2 Error: 0.145971 Iteration 3 Error: 0.034778 Align patch 20 5 left Iteration 1 Error: 0.660063 Iteration 2 Error: 0.089893 Iteration 3 Error: 0.015212 Align patch 21 4 left Iteration 1 Error: 0.661894 Iteration 2 Error: 0.095755 Iteration 3 Error: 0.035933 Align patch 22 3 left Iteration 1 Error: 0.792962 Iteration 2 Error: 0.157522 Iteration 3 Error: 0.028392 Align patch 23 2 left Iteration 1 Error: 0.532336 Iteration 2 Error: 0.103125 Iteration 3 Error: 0.039716 Align patch 24 1 left Iteration 1 Error: 0.762721 Iteration 2 Error: 0.140105 Iteration 3 Error: 0.038660 Align patch 25 0 left Iteration 1 Error: 0.643945 Iteration 2 Error: 0.127832 Iteration 3 Error: 0.026854 3D Fitting completed. Patch alignment time: 12.53(sec) Local motion has been corrected. Process thread exits. Computational time: 23.317348 sec Total time: 30.196184 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00015hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00015hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.757702s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00015hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.011252s ........................................ >>>>>>TIME<<<<<< FFT: 1.005925s Defocus_U Defocus_V Angle CCC 8375.04 9132.86 12.57 -0.055532 Final Values Defocus_U Defocus_V Angle CCC 8470.32 9046.99 9.78 -0.258740 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00015hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00015hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.339e-01 9.962e-02 CC threshold: 0.732 Mean Std: 38.17 6.66 Num Hot pixels: 233 Hot pixel threshold: 78.10 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 5.120208 Iteration 2 Error: 1.310982 Iteration 3 Error: 0.390344 Iteration 4 Error: 0.157429 Iteration 5 Error: 0.058942 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.64 0.10 ...... Frame ( 3) shift: 1.28 0.19 ...... Frame ( 4) shift: 1.91 0.29 ...... Frame ( 5) shift: 2.55 0.39 ...... Frame ( 6) shift: 3.13 0.50 ...... Frame ( 7) shift: 3.65 0.62 ...... Frame ( 8) shift: 4.17 0.75 ...... Frame ( 9) shift: 4.61 0.88 ...... Frame ( 10) shift: 4.97 1.03 ...... Frame ( 11) shift: 5.34 1.18 ...... Frame ( 12) shift: 5.69 1.26 ...... Frame ( 13) shift: 6.03 1.28 ...... Frame ( 14) shift: 6.38 1.30 ...... Frame ( 15) shift: 6.64 1.32 ...... Frame ( 16) shift: 6.82 1.35 ...... Frame ( 17) shift: 7.00 1.38 ...... Frame ( 18) shift: 7.17 1.38 ...... Frame ( 19) shift: 7.33 1.37 ...... Frame ( 20) shift: 7.49 1.35 ...... Frame ( 21) shift: 7.65 1.35 ...... Frame ( 22) shift: 7.82 1.36 ...... Frame ( 23) shift: 7.99 1.36 ...... Frame ( 24) shift: 8.17 1.41 ...... Frame ( 25) shift: 8.38 1.50 ...... Frame ( 26) shift: 8.58 1.58 ...... Frame ( 27) shift: 8.71 1.61 ...... Frame ( 28) shift: 8.78 1.59 ...... Frame ( 29) shift: 8.84 1.56 ...... Frame ( 30) shift: 8.98 1.57 ...... Frame ( 31) shift: 9.19 1.60 ...... Frame ( 32) shift: 9.39 1.63 ...... Frame ( 33) shift: 9.50 1.71 ...... Frame ( 34) shift: 9.50 1.82 ...... Frame ( 35) shift: 9.51 1.94 ...... Frame ( 36) shift: 9.60 1.99 ...... Frame ( 37) shift: 9.80 1.97 ...... Frame ( 38) shift: 9.99 1.96 ...... Frame ( 39) shift: 10.19 1.95 ...... Frame ( 40) shift: 10.38 1.93 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.015378 Iteration 2 Error: 0.608792 Iteration 3 Error: 0.243974 Iteration 4 Error: 0.090201 Iteration 5 Error: 0.036643 Align patch 2 23 left Iteration 1 Error: 1.721160 Iteration 2 Error: 0.481915 Iteration 3 Error: 0.168481 Iteration 4 Error: 0.082086 Iteration 5 Error: 0.034860 Align patch 3 22 left Iteration 1 Error: 2.086019 Iteration 2 Error: 0.599559 Iteration 3 Error: 0.186037 Iteration 4 Error: 0.067443 Iteration 5 Error: 0.039997 Align patch 4 21 left Iteration 1 Error: 2.525609 Iteration 2 Error: 0.528552 Iteration 3 Error: 0.124204 Iteration 4 Error: 0.042777 Align patch 5 20 left Iteration 1 Error: 4.487881 Iteration 2 Error: 0.634434 Iteration 3 Error: 0.196591 Iteration 4 Error: 0.052610 Iteration 5 Error: 0.013824 Align patch 6 19 left Iteration 1 Error: 2.972047 Iteration 2 Error: 0.932727 Iteration 3 Error: 0.234057 Iteration 4 Error: 0.109904 Iteration 5 Error: 0.036466 Align patch 7 18 left Iteration 1 Error: 1.561160 Iteration 2 Error: 0.429395 Iteration 3 Error: 0.142012 Iteration 4 Error: 0.047234 Align patch 8 17 left Iteration 1 Error: 1.021862 Iteration 2 Error: 0.265172 Iteration 3 Error: 0.077694 Iteration 4 Error: 0.028097 Align patch 9 16 left Iteration 1 Error: 1.296923 Iteration 2 Error: 0.259529 Iteration 3 Error: 0.128791 Iteration 4 Error: 0.027255 Align patch 10 15 left Iteration 1 Error: 3.456333 Iteration 2 Error: 0.572280 Iteration 3 Error: 0.160299 Iteration 4 Error: 0.047418 Align patch 11 14 left Iteration 1 Error: 3.321856 Iteration 2 Error: 0.988751 Iteration 3 Error: 0.328949 Iteration 4 Error: 0.080771 Iteration 5 Error: 0.038872 Align patch 12 13 left Iteration 1 Error: 1.810769 Iteration 2 Error: 0.700978 Iteration 3 Error: 0.286401 Iteration 4 Error: 0.155857 Iteration 5 Error: 0.082743 Align patch 12 13 left Iteration 1 Error: 2.307025 Iteration 2 Error: 0.452626 Iteration 3 Error: 0.071420 Iteration 4 Error: 0.013494 Align patch 13 12 left Iteration 1 Error: 0.887042 Iteration 2 Error: 0.363299 Iteration 3 Error: 0.101759 Iteration 4 Error: 0.036192 Align patch 14 11 left Iteration 1 Error: 1.513729 Iteration 2 Error: 0.153775 Iteration 3 Error: 0.047363 Align patch 15 10 left Iteration 1 Error: 2.650666 Iteration 2 Error: 0.479855 Iteration 3 Error: 0.095986 Iteration 4 Error: 0.035145 Align patch 16 9 left Iteration 1 Error: 3.231119 Iteration 2 Error: 0.912661 Iteration 3 Error: 0.237158 Iteration 4 Error: 0.055667 Iteration 5 Error: 0.021394 Align patch 17 8 left Iteration 1 Error: 1.641155 Iteration 2 Error: 0.557366 Iteration 3 Error: 0.475565 Iteration 4 Error: 0.211231 Iteration 5 Error: 0.128498 Align patch 17 8 left Iteration 1 Error: 1.997187 Iteration 2 Error: 0.427019 Iteration 3 Error: 0.086707 Iteration 4 Error: 0.022303 Align patch 18 7 left Iteration 1 Error: 1.428323 Iteration 2 Error: 0.348199 Iteration 3 Error: 0.100986 Iteration 4 Error: 0.033183 Align patch 19 6 left Iteration 1 Error: 1.729210 Iteration 2 Error: 0.242818 Iteration 3 Error: 0.059436 Iteration 4 Error: 0.015928 Align patch 20 5 left Iteration 1 Error: 3.489632 Iteration 2 Error: 0.520547 Iteration 3 Error: 0.117992 Iteration 4 Error: 0.042653 Align patch 21 4 left Iteration 1 Error: 3.607160 Iteration 2 Error: 0.713203 Iteration 3 Error: 0.354265 Iteration 4 Error: 0.148036 Iteration 5 Error: 0.062114 Align patch 21 4 left Iteration 1 Error: 2.920851 Iteration 2 Error: 0.557910 Iteration 3 Error: 0.089083 Iteration 4 Error: 0.023952 Align patch 22 3 left Iteration 1 Error: 2.518316 Iteration 2 Error: 0.443633 Iteration 3 Error: 0.138521 Iteration 4 Error: 0.046308 Align patch 23 2 left Iteration 1 Error: 2.514570 Iteration 2 Error: 0.338022 Iteration 3 Error: 0.061133 Iteration 4 Error: 0.020681 Align patch 24 1 left Iteration 1 Error: 1.624164 Iteration 2 Error: 0.625602 Iteration 3 Error: 0.140318 Iteration 4 Error: 0.081650 Iteration 5 Error: 0.019084 Align patch 25 0 left Iteration 1 Error: 3.619024 Iteration 2 Error: 0.526351 Iteration 3 Error: 0.152396 Iteration 4 Error: 0.047114 3D Fitting completed. Patch alignment time: 14.62(sec) Local motion has been corrected. Process thread exits. Computational time: 27.678135 sec Total time: 36.169773 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00015hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00015hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.491331s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00015hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.930620s ........................................ >>>>>>TIME<<<<<< FFT: 1.022413s Defocus_U Defocus_V Angle CCC 10292.97 9796.88 88.39 0.010123 Final Values Defocus_U Defocus_V Angle CCC 10314.85 9790.63 88.71 -0.061512 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00015hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00015hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.309e-01 9.761e-02 CC threshold: 0.717 Mean Std: 36.87 6.64 Num Hot pixels: 220 Hot pixel threshold: 76.73 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.132892 Iteration 2 Error: 0.264023 Iteration 3 Error: 0.082809 Iteration 4 Error: 0.030463 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.17 0.19 ...... Frame ( 3) shift: 0.34 0.38 ...... Frame ( 4) shift: 0.50 0.56 ...... Frame ( 5) shift: 0.67 0.75 ...... Frame ( 6) shift: 0.85 0.89 ...... Frame ( 7) shift: 1.03 0.97 ...... Frame ( 8) shift: 1.22 1.05 ...... Frame ( 9) shift: 1.32 1.13 ...... Frame ( 10) shift: 1.34 1.21 ...... Frame ( 11) shift: 1.37 1.29 ...... Frame ( 12) shift: 1.45 1.37 ...... Frame ( 13) shift: 1.59 1.43 ...... Frame ( 14) shift: 1.73 1.50 ...... Frame ( 15) shift: 1.82 1.56 ...... Frame ( 16) shift: 1.87 1.62 ...... Frame ( 17) shift: 1.92 1.67 ...... Frame ( 18) shift: 1.99 1.69 ...... Frame ( 19) shift: 2.09 1.67 ...... Frame ( 20) shift: 2.18 1.65 ...... Frame ( 21) shift: 2.26 1.70 ...... Frame ( 22) shift: 2.32 1.84 ...... Frame ( 23) shift: 2.38 1.98 ...... Frame ( 24) shift: 2.44 2.06 ...... Frame ( 25) shift: 2.51 2.07 ...... Frame ( 26) shift: 2.59 2.09 ...... Frame ( 27) shift: 2.68 2.10 ...... Frame ( 28) shift: 2.80 2.11 ...... Frame ( 29) shift: 2.91 2.12 ...... Frame ( 30) shift: 3.02 2.14 ...... Frame ( 31) shift: 3.13 2.17 ...... Frame ( 32) shift: 3.24 2.20 ...... Frame ( 33) shift: 3.30 2.22 ...... Frame ( 34) shift: 3.32 2.22 ...... Frame ( 35) shift: 3.33 2.23 ...... Frame ( 36) shift: 3.39 2.24 ...... Frame ( 37) shift: 3.50 2.26 ...... Frame ( 38) shift: 3.60 2.28 ...... Frame ( 39) shift: 3.71 2.29 ...... Frame ( 40) shift: 3.82 2.31 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.843446 Iteration 2 Error: 0.228689 Iteration 3 Error: 0.089378 Iteration 4 Error: 0.025803 Align patch 2 23 left Iteration 1 Error: 0.905173 Iteration 2 Error: 0.158729 Iteration 3 Error: 0.033058 Align patch 3 22 left Iteration 1 Error: 0.506187 Iteration 2 Error: 0.117748 Iteration 3 Error: 0.031371 Align patch 4 21 left Iteration 1 Error: 0.582706 Iteration 2 Error: 0.078745 Iteration 3 Error: 0.016848 Align patch 5 20 left Iteration 1 Error: 0.659820 Iteration 2 Error: 0.138996 Iteration 3 Error: 0.053137 Iteration 4 Error: 0.021198 Align patch 6 19 left Iteration 1 Error: 0.860444 Iteration 2 Error: 0.129086 Iteration 3 Error: 0.054091 Iteration 4 Error: 0.015162 Align patch 7 18 left Iteration 1 Error: 1.158878 Iteration 2 Error: 0.212155 Iteration 3 Error: 0.070327 Iteration 4 Error: 0.027348 Align patch 8 17 left Iteration 1 Error: 0.664183 Iteration 2 Error: 0.122349 Iteration 3 Error: 0.027618 Align patch 9 16 left Iteration 1 Error: 0.647739 Iteration 2 Error: 0.132363 Iteration 3 Error: 0.032244 Align patch 10 15 left Iteration 1 Error: 0.772923 Iteration 2 Error: 0.195746 Iteration 3 Error: 0.057294 Iteration 4 Error: 0.019720 Align patch 11 14 left Iteration 1 Error: 0.641767 Iteration 2 Error: 0.115889 Iteration 3 Error: 0.054840 Iteration 4 Error: 0.016039 Align patch 12 13 left Iteration 1 Error: 0.507935 Iteration 2 Error: 0.102801 Iteration 3 Error: 0.026873 Align patch 13 12 left Iteration 1 Error: 1.076752 Iteration 2 Error: 0.132732 Iteration 3 Error: 0.029789 Align patch 14 11 left Iteration 1 Error: 1.600034 Iteration 2 Error: 0.230216 Iteration 3 Error: 0.036610 Align patch 15 10 left Iteration 1 Error: 0.614709 Iteration 2 Error: 0.133749 Iteration 3 Error: 0.045234 Align patch 16 9 left Iteration 1 Error: 0.672803 Iteration 2 Error: 0.161008 Iteration 3 Error: 0.048150 Align patch 17 8 left Iteration 1 Error: 0.579447 Iteration 2 Error: 0.146031 Iteration 3 Error: 0.036135 Align patch 18 7 left Iteration 1 Error: 0.655588 Iteration 2 Error: 0.145194 Iteration 3 Error: 0.061248 Iteration 4 Error: 0.013421 Align patch 19 6 left Iteration 1 Error: 1.133050 Iteration 2 Error: 0.158400 Iteration 3 Error: 0.034997 Align patch 20 5 left Iteration 1 Error: 1.092545 Iteration 2 Error: 0.117632 Iteration 3 Error: 0.025634 Align patch 21 4 left Iteration 1 Error: 0.560322 Iteration 2 Error: 0.115047 Iteration 3 Error: 0.014861 Align patch 22 3 left Iteration 1 Error: 0.669335 Iteration 2 Error: 0.063446 Iteration 3 Error: 0.011788 Align patch 23 2 left Iteration 1 Error: 0.562301 Iteration 2 Error: 0.184903 Iteration 3 Error: 0.046801 Align patch 24 1 left Iteration 1 Error: 0.760552 Iteration 2 Error: 0.108179 Iteration 3 Error: 0.024088 Align patch 25 0 left Iteration 1 Error: 0.777054 Iteration 2 Error: 0.126784 Iteration 3 Error: 0.037730 3D Fitting completed. Patch alignment time: 12.27(sec) Local motion has been corrected. Process thread exits. Computational time: 24.696526 sec Total time: 32.882828 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00015hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00015hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.835435s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00015hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.620428s ........................................ >>>>>>TIME<<<<<< FFT: 0.975191s Defocus_U Defocus_V Angle CCC 12048.90 12802.87 5.26 -0.053305 Final Values Defocus_U Defocus_V Angle CCC 11987.91 12967.02 7.80 -0.265893 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00016hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00016hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.002e-01 CC threshold: 0.736 Mean Std: 40.94 6.93 Num Hot pixels: 247 Hot pixel threshold: 82.51 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.059685 Iteration 2 Error: 0.163160 Iteration 3 Error: 0.031861 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.08 0.13 ...... Frame ( 3) shift: -0.16 0.26 ...... Frame ( 4) shift: -0.23 0.39 ...... Frame ( 5) shift: -0.31 0.53 ...... Frame ( 6) shift: -0.33 0.59 ...... Frame ( 7) shift: -0.28 0.59 ...... Frame ( 8) shift: -0.24 0.59 ...... Frame ( 9) shift: -0.22 0.63 ...... Frame ( 10) shift: -0.21 0.71 ...... Frame ( 11) shift: -0.20 0.78 ...... Frame ( 12) shift: -0.19 0.86 ...... Frame ( 13) shift: -0.17 0.93 ...... Frame ( 14) shift: -0.15 1.00 ...... Frame ( 15) shift: -0.13 1.08 ...... Frame ( 16) shift: -0.11 1.15 ...... Frame ( 17) shift: -0.09 1.22 ...... Frame ( 18) shift: -0.06 1.28 ...... Frame ( 19) shift: -0.01 1.32 ...... Frame ( 20) shift: 0.03 1.37 ...... Frame ( 21) shift: 0.08 1.45 ...... Frame ( 22) shift: 0.14 1.55 ...... Frame ( 23) shift: 0.19 1.65 ...... Frame ( 24) shift: 0.22 1.72 ...... Frame ( 25) shift: 0.23 1.74 ...... Frame ( 26) shift: 0.24 1.76 ...... Frame ( 27) shift: 0.29 1.77 ...... Frame ( 28) shift: 0.37 1.79 ...... Frame ( 29) shift: 0.45 1.81 ...... Frame ( 30) shift: 0.54 1.82 ...... Frame ( 31) shift: 0.64 1.83 ...... Frame ( 32) shift: 0.73 1.85 ...... Frame ( 33) shift: 0.79 1.89 ...... Frame ( 34) shift: 0.80 1.95 ...... Frame ( 35) shift: 0.81 2.01 ...... Frame ( 36) shift: 0.82 2.06 ...... Frame ( 37) shift: 0.82 2.10 ...... Frame ( 38) shift: 0.81 2.14 ...... Frame ( 39) shift: 0.81 2.17 ...... Frame ( 40) shift: 0.81 2.21 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.656804 Iteration 2 Error: 0.142570 Iteration 3 Error: 0.028898 Align patch 2 23 left Iteration 1 Error: 0.547445 Iteration 2 Error: 0.120719 Iteration 3 Error: 0.039514 Align patch 3 22 left Iteration 1 Error: 0.781013 Iteration 2 Error: 0.151724 Iteration 3 Error: 0.033648 Align patch 4 21 left Iteration 1 Error: 0.874298 Iteration 2 Error: 0.134414 Iteration 3 Error: 0.019917 Align patch 5 20 left Iteration 1 Error: 0.513912 Iteration 2 Error: 0.079186 Iteration 3 Error: 0.015845 Align patch 6 19 left Iteration 1 Error: 0.957884 Iteration 2 Error: 0.084949 Iteration 3 Error: 0.031558 Align patch 7 18 left Iteration 1 Error: 0.729312 Iteration 2 Error: 0.061328 Iteration 3 Error: 0.017844 Align patch 8 17 left Iteration 1 Error: 0.914952 Iteration 2 Error: 0.216176 Iteration 3 Error: 0.037270 Align patch 9 16 left Iteration 1 Error: 0.461717 Iteration 2 Error: 0.064670 Iteration 3 Error: 0.012574 Align patch 10 15 left Iteration 1 Error: 0.652225 Iteration 2 Error: 0.086234 Iteration 3 Error: 0.020457 Align patch 11 14 left Iteration 1 Error: 0.535934 Iteration 2 Error: 0.059086 Iteration 3 Error: 0.011212 Align patch 12 13 left Iteration 1 Error: 0.708145 Iteration 2 Error: 0.094243 Iteration 3 Error: 0.021490 Align patch 13 12 left Iteration 1 Error: 0.746485 Iteration 2 Error: 0.064679 Iteration 3 Error: 0.015253 Align patch 14 11 left Iteration 1 Error: 0.609857 Iteration 2 Error: 0.059191 Iteration 3 Error: 0.017527 Align patch 15 10 left Iteration 1 Error: 0.778389 Iteration 2 Error: 0.069008 Iteration 3 Error: 0.020865 Align patch 16 9 left Iteration 1 Error: 0.570283 Iteration 2 Error: 0.112322 Iteration 3 Error: 0.041666 Align patch 17 8 left Iteration 1 Error: 0.436966 Iteration 2 Error: 0.059000 Iteration 3 Error: 0.008456 Align patch 18 7 left Iteration 1 Error: 0.652129 Iteration 2 Error: 0.110129 Iteration 3 Error: 0.021102 Align patch 19 6 left Iteration 1 Error: 0.611474 Iteration 2 Error: 0.172660 Iteration 3 Error: 0.030366 Align patch 20 5 left Iteration 1 Error: 0.603184 Iteration 2 Error: 0.072146 Iteration 3 Error: 0.017201 Align patch 21 4 left Iteration 1 Error: 0.685642 Iteration 2 Error: 0.118696 Iteration 3 Error: 0.038546 Align patch 22 3 left Iteration 1 Error: 0.784938 Iteration 2 Error: 0.092866 Iteration 3 Error: 0.022103 Align patch 23 2 left Iteration 1 Error: 0.567302 Iteration 2 Error: 0.086386 Iteration 3 Error: 0.015162 Align patch 24 1 left Iteration 1 Error: 1.090214 Iteration 2 Error: 0.117710 Iteration 3 Error: 0.031040 Align patch 25 0 left Iteration 1 Error: 0.804115 Iteration 2 Error: 0.108785 Iteration 3 Error: 0.016588 3D Fitting completed. Patch alignment time: 11.59(sec) Local motion has been corrected. Process thread exits. Computational time: 23.343166 sec Total time: 31.998461 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00016hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00016hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.574002s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00016hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.589781s ........................................ >>>>>>TIME<<<<<< FFT: 0.945700s Defocus_U Defocus_V Angle CCC 11800.82 12636.76 11.95 0.056765 Final Values Defocus_U Defocus_V Angle CCC 11811.77 12650.84 11.95 0.096260 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00016hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00016hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 40.78 6.90 Num Hot pixels: 243 Hot pixel threshold: 82.16 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.978193 Iteration 2 Error: 0.152026 Iteration 3 Error: 0.026515 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.01 -0.05 ...... Frame ( 3) shift: -0.03 -0.09 ...... Frame ( 4) shift: -0.04 -0.14 ...... Frame ( 5) shift: -0.06 -0.18 ...... Frame ( 6) shift: -0.02 -0.18 ...... Frame ( 7) shift: 0.07 -0.13 ...... Frame ( 8) shift: 0.16 -0.08 ...... Frame ( 9) shift: 0.24 -0.05 ...... Frame ( 10) shift: 0.30 -0.06 ...... Frame ( 11) shift: 0.35 -0.06 ...... Frame ( 12) shift: 0.39 -0.02 ...... Frame ( 13) shift: 0.40 0.05 ...... Frame ( 14) shift: 0.41 0.12 ...... Frame ( 15) shift: 0.45 0.15 ...... Frame ( 16) shift: 0.51 0.15 ...... Frame ( 17) shift: 0.58 0.15 ...... Frame ( 18) shift: 0.62 0.17 ...... Frame ( 19) shift: 0.63 0.22 ...... Frame ( 20) shift: 0.64 0.27 ...... Frame ( 21) shift: 0.66 0.30 ...... Frame ( 22) shift: 0.68 0.30 ...... Frame ( 23) shift: 0.70 0.30 ...... Frame ( 24) shift: 0.75 0.30 ...... Frame ( 25) shift: 0.84 0.28 ...... Frame ( 26) shift: 0.93 0.27 ...... Frame ( 27) shift: 0.99 0.24 ...... Frame ( 28) shift: 1.03 0.20 ...... Frame ( 29) shift: 1.07 0.16 ...... Frame ( 30) shift: 1.11 0.17 ...... Frame ( 31) shift: 1.16 0.24 ...... Frame ( 32) shift: 1.20 0.31 ...... Frame ( 33) shift: 1.28 0.34 ...... Frame ( 34) shift: 1.39 0.34 ...... Frame ( 35) shift: 1.51 0.34 ...... Frame ( 36) shift: 1.58 0.37 ...... Frame ( 37) shift: 1.61 0.42 ...... Frame ( 38) shift: 1.64 0.48 ...... Frame ( 39) shift: 1.66 0.54 ...... Frame ( 40) shift: 1.69 0.59 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.154655 Iteration 2 Error: 0.127623 Iteration 3 Error: 0.027696 Align patch 2 23 left Iteration 1 Error: 1.061880 Iteration 2 Error: 0.116311 Iteration 3 Error: 0.023474 Align patch 3 22 left Iteration 1 Error: 0.586497 Iteration 2 Error: 0.123039 Iteration 3 Error: 0.030043 Align patch 4 21 left Iteration 1 Error: 0.548126 Iteration 2 Error: 0.093978 Iteration 3 Error: 0.029335 Align patch 5 20 left Iteration 1 Error: 0.719017 Iteration 2 Error: 0.105212 Iteration 3 Error: 0.031201 Align patch 6 19 left Iteration 1 Error: 1.073338 Iteration 2 Error: 0.174750 Iteration 3 Error: 0.046321 Align patch 7 18 left Iteration 1 Error: 0.643261 Iteration 2 Error: 0.108118 Iteration 3 Error: 0.019612 Align patch 8 17 left Iteration 1 Error: 0.540138 Iteration 2 Error: 0.094920 Iteration 3 Error: 0.026905 Align patch 9 16 left Iteration 1 Error: 0.857423 Iteration 2 Error: 0.076668 Iteration 3 Error: 0.016285 Align patch 10 15 left Iteration 1 Error: 0.639229 Iteration 2 Error: 0.107446 Iteration 3 Error: 0.022458 Align patch 11 14 left Iteration 1 Error: 0.948314 Iteration 2 Error: 0.162995 Iteration 3 Error: 0.047425 Align patch 12 13 left Iteration 1 Error: 0.482628 Iteration 2 Error: 0.085332 Iteration 3 Error: 0.012684 Align patch 13 12 left Iteration 1 Error: 0.449952 Iteration 2 Error: 0.066077 Iteration 3 Error: 0.016309 Align patch 14 11 left Iteration 1 Error: 0.452207 Iteration 2 Error: 0.038680 Align patch 15 10 left Iteration 1 Error: 0.828075 Iteration 2 Error: 0.111103 Iteration 3 Error: 0.034869 Align patch 16 9 left Iteration 1 Error: 0.820208 Iteration 2 Error: 0.099446 Iteration 3 Error: 0.023985 Align patch 17 8 left Iteration 1 Error: 0.549866 Iteration 2 Error: 0.110718 Iteration 3 Error: 0.018321 Align patch 18 7 left Iteration 1 Error: 1.085342 Iteration 2 Error: 0.188214 Iteration 3 Error: 0.049526 Align patch 19 6 left Iteration 1 Error: 0.657006 Iteration 2 Error: 0.088726 Iteration 3 Error: 0.023578 Align patch 20 5 left Iteration 1 Error: 0.592988 Iteration 2 Error: 0.074655 Iteration 3 Error: 0.014049 Align patch 21 4 left Iteration 1 Error: 0.513349 Iteration 2 Error: 0.053921 Iteration 3 Error: 0.014187 Align patch 22 3 left Iteration 1 Error: 0.702896 Iteration 2 Error: 0.134100 Iteration 3 Error: 0.032470 Align patch 23 2 left Iteration 1 Error: 0.708257 Iteration 2 Error: 0.121679 Iteration 3 Error: 0.016413 Align patch 24 1 left Iteration 1 Error: 0.809633 Iteration 2 Error: 0.124293 Iteration 3 Error: 0.017430 Align patch 25 0 left Iteration 1 Error: 0.548034 Iteration 2 Error: 0.086593 Iteration 3 Error: 0.022484 3D Fitting completed. Patch alignment time: 10.82(sec) Local motion has been corrected. Process thread exits. Computational time: 24.784386 sec Total time: 35.303890 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00016hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00016hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.604938s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00016hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.709971s ........................................ >>>>>>TIME<<<<<< FFT: 1.116262s Defocus_U Defocus_V Angle CCC 11646.48 12131.05 2.75 0.054045 Final Values Defocus_U Defocus_V Angle CCC 11673.04 12135.74 1.81 0.090237 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00016hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00016hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.002e-01 CC threshold: 0.736 Mean Std: 41.25 6.95 Num Hot pixels: 245 Hot pixel threshold: 82.93 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.089272 Iteration 2 Error: 0.208738 Iteration 3 Error: 0.042627 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.14 0.04 ...... Frame ( 3) shift: -0.27 0.08 ...... Frame ( 4) shift: -0.41 0.12 ...... Frame ( 5) shift: -0.54 0.16 ...... Frame ( 6) shift: -0.58 0.20 ...... Frame ( 7) shift: -0.53 0.25 ...... Frame ( 8) shift: -0.47 0.31 ...... Frame ( 9) shift: -0.44 0.37 ...... Frame ( 10) shift: -0.43 0.44 ...... Frame ( 11) shift: -0.42 0.52 ...... Frame ( 12) shift: -0.35 0.61 ...... Frame ( 13) shift: -0.20 0.70 ...... Frame ( 14) shift: -0.05 0.80 ...... Frame ( 15) shift: 0.08 0.88 ...... Frame ( 16) shift: 0.18 0.94 ...... Frame ( 17) shift: 0.29 1.01 ...... Frame ( 18) shift: 0.39 1.07 ...... Frame ( 19) shift: 0.49 1.14 ...... Frame ( 20) shift: 0.60 1.22 ...... Frame ( 21) shift: 0.66 1.28 ...... Frame ( 22) shift: 0.68 1.35 ...... Frame ( 23) shift: 0.70 1.42 ...... Frame ( 24) shift: 0.75 1.45 ...... Frame ( 25) shift: 0.82 1.45 ...... Frame ( 26) shift: 0.90 1.45 ...... Frame ( 27) shift: 0.96 1.45 ...... Frame ( 28) shift: 1.01 1.46 ...... Frame ( 29) shift: 1.06 1.46 ...... Frame ( 30) shift: 1.11 1.45 ...... Frame ( 31) shift: 1.16 1.42 ...... Frame ( 32) shift: 1.21 1.39 ...... Frame ( 33) shift: 1.21 1.37 ...... Frame ( 34) shift: 1.16 1.35 ...... Frame ( 35) shift: 1.11 1.33 ...... Frame ( 36) shift: 1.15 1.33 ...... Frame ( 37) shift: 1.28 1.34 ...... Frame ( 38) shift: 1.42 1.34 ...... Frame ( 39) shift: 1.55 1.35 ...... Frame ( 40) shift: 1.68 1.36 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.769468 Iteration 2 Error: 0.113514 Iteration 3 Error: 0.024003 Align patch 2 23 left Iteration 1 Error: 0.633199 Iteration 2 Error: 0.091197 Iteration 3 Error: 0.017981 Align patch 3 22 left Iteration 1 Error: 0.474600 Iteration 2 Error: 0.081165 Iteration 3 Error: 0.020812 Align patch 4 21 left Iteration 1 Error: 0.344693 Iteration 2 Error: 0.035368 Align patch 5 20 left Iteration 1 Error: 0.656371 Iteration 2 Error: 0.054015 Iteration 3 Error: 0.008664 Align patch 6 19 left Iteration 1 Error: 0.837160 Iteration 2 Error: 0.158153 Iteration 3 Error: 0.057340 Iteration 4 Error: 0.022264 Align patch 7 18 left Iteration 1 Error: 0.728696 Iteration 2 Error: 0.100268 Iteration 3 Error: 0.016953 Align patch 8 17 left Iteration 1 Error: 0.736162 Iteration 2 Error: 0.122400 Iteration 3 Error: 0.040076 Align patch 9 16 left Iteration 1 Error: 0.606987 Iteration 2 Error: 0.072608 Iteration 3 Error: 0.010850 Align patch 10 15 left Iteration 1 Error: 0.536556 Iteration 2 Error: 0.054518 Iteration 3 Error: 0.012836 Align patch 11 14 left Iteration 1 Error: 0.556811 Iteration 2 Error: 0.112742 Iteration 3 Error: 0.044222 Align patch 12 13 left Iteration 1 Error: 0.665730 Iteration 2 Error: 0.117245 Iteration 3 Error: 0.030978 Align patch 13 12 left Iteration 1 Error: 0.699466 Iteration 2 Error: 0.083080 Iteration 3 Error: 0.027153 Align patch 14 11 left Iteration 1 Error: 0.526308 Iteration 2 Error: 0.082295 Iteration 3 Error: 0.028315 Align patch 15 10 left Iteration 1 Error: 0.544323 Iteration 2 Error: 0.102922 Iteration 3 Error: 0.022499 Align patch 16 9 left Iteration 1 Error: 0.649214 Iteration 2 Error: 0.119884 Iteration 3 Error: 0.026127 Align patch 17 8 left Iteration 1 Error: 0.736968 Iteration 2 Error: 0.088836 Iteration 3 Error: 0.016021 Align patch 18 7 left Iteration 1 Error: 0.622922 Iteration 2 Error: 0.143814 Iteration 3 Error: 0.043910 Align patch 19 6 left Iteration 1 Error: 0.750120 Iteration 2 Error: 0.140697 Iteration 3 Error: 0.029606 Align patch 20 5 left Iteration 1 Error: 0.549156 Iteration 2 Error: 0.111444 Iteration 3 Error: 0.022500 Align patch 21 4 left Iteration 1 Error: 0.421526 Iteration 2 Error: 0.041415 Align patch 22 3 left Iteration 1 Error: 0.490734 Iteration 2 Error: 0.047540 Align patch 23 2 left Iteration 1 Error: 0.810397 Iteration 2 Error: 0.117925 Iteration 3 Error: 0.029254 Align patch 24 1 left Iteration 1 Error: 0.562989 Iteration 2 Error: 0.093817 Iteration 3 Error: 0.015802 Align patch 25 0 left Iteration 1 Error: 0.724252 Iteration 2 Error: 0.141430 Iteration 3 Error: 0.022645 3D Fitting completed. Patch alignment time: 11.59(sec) Local motion has been corrected. Process thread exits. Computational time: 24.138939 sec Total time: 32.734634 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00016hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00016hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.553191s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00016hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.101319s ........................................ >>>>>>TIME<<<<<< FFT: 0.967177s Defocus_U Defocus_V Angle CCC 14345.71 15197.27 6.60 0.062395 Final Values Defocus_U Defocus_V Angle CCC 14347.26 15205.08 6.60 0.098853 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00016hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00016hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.002e-01 CC threshold: 0.736 Mean Std: 39.61 6.74 Num Hot pixels: 233 Hot pixel threshold: 80.08 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.795822 Iteration 2 Error: 0.086708 Iteration 3 Error: 0.027385 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.02 0.09 ...... Frame ( 3) shift: -0.04 0.18 ...... Frame ( 4) shift: -0.06 0.27 ...... Frame ( 5) shift: -0.09 0.36 ...... Frame ( 6) shift: -0.07 0.43 ...... Frame ( 7) shift: -0.03 0.48 ...... Frame ( 8) shift: 0.02 0.53 ...... Frame ( 9) shift: 0.05 0.59 ...... Frame ( 10) shift: 0.06 0.66 ...... Frame ( 11) shift: 0.07 0.73 ...... Frame ( 12) shift: 0.08 0.80 ...... Frame ( 13) shift: 0.09 0.89 ...... Frame ( 14) shift: 0.10 0.97 ...... Frame ( 15) shift: 0.11 1.03 ...... Frame ( 16) shift: 0.14 1.04 ...... Frame ( 17) shift: 0.16 1.06 ...... Frame ( 18) shift: 0.20 1.09 ...... Frame ( 19) shift: 0.27 1.14 ...... Frame ( 20) shift: 0.34 1.19 ...... Frame ( 21) shift: 0.38 1.18 ...... Frame ( 22) shift: 0.37 1.13 ...... Frame ( 23) shift: 0.37 1.07 ...... Frame ( 24) shift: 0.36 1.09 ...... Frame ( 25) shift: 0.36 1.19 ...... Frame ( 26) shift: 0.35 1.28 ...... Frame ( 27) shift: 0.34 1.31 ...... Frame ( 28) shift: 0.34 1.29 ...... Frame ( 29) shift: 0.34 1.27 ...... Frame ( 30) shift: 0.34 1.28 ...... Frame ( 31) shift: 0.34 1.32 ...... Frame ( 32) shift: 0.34 1.36 ...... Frame ( 33) shift: 0.34 1.36 ...... Frame ( 34) shift: 0.36 1.35 ...... Frame ( 35) shift: 0.37 1.33 ...... Frame ( 36) shift: 0.39 1.30 ...... Frame ( 37) shift: 0.41 1.26 ...... Frame ( 38) shift: 0.43 1.22 ...... Frame ( 39) shift: 0.45 1.18 ...... Frame ( 40) shift: 0.46 1.14 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.060020 Iteration 2 Error: 0.186080 Iteration 3 Error: 0.048871 Align patch 2 23 left Iteration 1 Error: 0.650957 Iteration 2 Error: 0.114576 Iteration 3 Error: 0.031849 Align patch 3 22 left Iteration 1 Error: 0.681994 Iteration 2 Error: 0.080533 Iteration 3 Error: 0.025030 Align patch 4 21 left Iteration 1 Error: 0.655616 Iteration 2 Error: 0.065922 Iteration 3 Error: 0.017747 Align patch 5 20 left Iteration 1 Error: 0.853613 Iteration 2 Error: 0.146268 Iteration 3 Error: 0.041521 Align patch 6 19 left Iteration 1 Error: 0.847256 Iteration 2 Error: 0.168529 Iteration 3 Error: 0.036006 Align patch 7 18 left Iteration 1 Error: 0.568264 Iteration 2 Error: 0.091629 Iteration 3 Error: 0.021397 Align patch 8 17 left Iteration 1 Error: 0.652422 Iteration 2 Error: 0.153343 Iteration 3 Error: 0.051258 Iteration 4 Error: 0.012739 Align patch 9 16 left Iteration 1 Error: 0.641375 Iteration 2 Error: 0.106764 Iteration 3 Error: 0.021222 Align patch 10 15 left Iteration 1 Error: 0.544945 Iteration 2 Error: 0.117854 Iteration 3 Error: 0.042433 Align patch 11 14 left Iteration 1 Error: 0.889253 Iteration 2 Error: 0.151391 Iteration 3 Error: 0.036608 Align patch 12 13 left Iteration 1 Error: 0.748141 Iteration 2 Error: 0.096242 Iteration 3 Error: 0.031348 Align patch 13 12 left Iteration 1 Error: 0.690020 Iteration 2 Error: 0.086362 Iteration 3 Error: 0.020243 Align patch 14 11 left Iteration 1 Error: 0.563931 Iteration 2 Error: 0.119223 Iteration 3 Error: 0.018809 Align patch 15 10 left Iteration 1 Error: 0.902421 Iteration 2 Error: 0.101015 Iteration 3 Error: 0.020964 Align patch 16 9 left Iteration 1 Error: 0.603366 Iteration 2 Error: 0.075376 Iteration 3 Error: 0.013184 Align patch 17 8 left Iteration 1 Error: 0.533326 Iteration 2 Error: 0.116455 Iteration 3 Error: 0.034830 Align patch 18 7 left Iteration 1 Error: 0.491257 Iteration 2 Error: 0.075543 Iteration 3 Error: 0.014334 Align patch 19 6 left Iteration 1 Error: 0.468317 Iteration 2 Error: 0.076018 Iteration 3 Error: 0.014545 Align patch 20 5 left Iteration 1 Error: 0.529070 Iteration 2 Error: 0.090000 Iteration 3 Error: 0.026181 Align patch 21 4 left Iteration 1 Error: 0.498881 Iteration 2 Error: 0.104259 Iteration 3 Error: 0.021372 Align patch 22 3 left Iteration 1 Error: 0.662316 Iteration 2 Error: 0.074218 Iteration 3 Error: 0.017225 Align patch 23 2 left Iteration 1 Error: 0.645225 Iteration 2 Error: 0.091916 Iteration 3 Error: 0.026118 Align patch 24 1 left Iteration 1 Error: 0.678630 Iteration 2 Error: 0.137882 Iteration 3 Error: 0.029879 Align patch 25 0 left Iteration 1 Error: 0.586010 Iteration 2 Error: 0.147169 Iteration 3 Error: 0.017917 3D Fitting completed. Patch alignment time: 11.27(sec) Local motion has been corrected. Process thread exits. Computational time: 25.132671 sec Total time: 33.352367 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00016hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00016hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.506882s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00016hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.920092s ........................................ >>>>>>TIME<<<<<< FFT: 1.034816s Defocus_U Defocus_V Angle CCC 11257.81 10562.50 83.26 0.041494 Final Values Defocus_U Defocus_V Angle CCC 11289.07 10575.00 82.94 0.070229 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00017hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00017hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.001e-01 CC threshold: 0.736 Mean Std: 38.68 6.78 Num Hot pixels: 226 Hot pixel threshold: 79.38 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.600398 Iteration 2 Error: 0.330060 Iteration 3 Error: 0.088625 Iteration 4 Error: 0.033556 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.31 -0.08 ...... Frame ( 3) shift: -0.61 -0.16 ...... Frame ( 4) shift: -0.92 -0.23 ...... Frame ( 5) shift: -1.22 -0.31 ...... Frame ( 6) shift: -1.37 -0.34 ...... Frame ( 7) shift: -1.35 -0.30 ...... Frame ( 8) shift: -1.33 -0.27 ...... Frame ( 9) shift: -1.28 -0.22 ...... Frame ( 10) shift: -1.19 -0.16 ...... Frame ( 11) shift: -1.11 -0.09 ...... Frame ( 12) shift: -1.03 -0.03 ...... Frame ( 13) shift: -0.97 0.04 ...... Frame ( 14) shift: -0.90 0.11 ...... Frame ( 15) shift: -0.81 0.22 ...... Frame ( 16) shift: -0.70 0.37 ...... Frame ( 17) shift: -0.59 0.52 ...... Frame ( 18) shift: -0.51 0.64 ...... Frame ( 19) shift: -0.48 0.72 ...... Frame ( 20) shift: -0.44 0.80 ...... Frame ( 21) shift: -0.32 0.90 ...... Frame ( 22) shift: -0.11 1.00 ...... Frame ( 23) shift: 0.09 1.11 ...... Frame ( 24) shift: 0.24 1.22 ...... Frame ( 25) shift: 0.33 1.34 ...... Frame ( 26) shift: 0.42 1.46 ...... Frame ( 27) shift: 0.50 1.50 ...... Frame ( 28) shift: 0.56 1.46 ...... Frame ( 29) shift: 0.63 1.42 ...... Frame ( 30) shift: 0.65 1.42 ...... Frame ( 31) shift: 0.62 1.45 ...... Frame ( 32) shift: 0.60 1.48 ...... Frame ( 33) shift: 0.59 1.56 ...... Frame ( 34) shift: 0.59 1.70 ...... Frame ( 35) shift: 0.60 1.83 ...... Frame ( 36) shift: 0.63 1.95 ...... Frame ( 37) shift: 0.69 2.07 ...... Frame ( 38) shift: 0.75 2.19 ...... Frame ( 39) shift: 0.80 2.30 ...... Frame ( 40) shift: 0.86 2.42 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.784212 Iteration 2 Error: 0.080541 Iteration 3 Error: 0.029185 Align patch 2 23 left Iteration 1 Error: 0.804825 Iteration 2 Error: 0.147741 Iteration 3 Error: 0.060302 Iteration 4 Error: 0.023565 Align patch 3 22 left Iteration 1 Error: 0.567196 Iteration 2 Error: 0.134075 Iteration 3 Error: 0.052379 Iteration 4 Error: 0.020385 Align patch 4 21 left Iteration 1 Error: 0.875216 Iteration 2 Error: 0.113299 Iteration 3 Error: 0.031421 Align patch 5 20 left Iteration 1 Error: 0.455934 Iteration 2 Error: 0.064078 Iteration 3 Error: 0.011685 Align patch 6 19 left Iteration 1 Error: 0.955491 Iteration 2 Error: 0.100377 Iteration 3 Error: 0.021698 Align patch 7 18 left Iteration 1 Error: 0.830026 Iteration 2 Error: 0.125096 Iteration 3 Error: 0.054383 Iteration 4 Error: 0.023685 Align patch 8 17 left Iteration 1 Error: 0.549186 Iteration 2 Error: 0.108177 Iteration 3 Error: 0.019352 Align patch 9 16 left Iteration 1 Error: 0.966338 Iteration 2 Error: 0.170020 Iteration 3 Error: 0.050919 Iteration 4 Error: 0.014847 Align patch 10 15 left Iteration 1 Error: 0.519064 Iteration 2 Error: 0.062367 Iteration 3 Error: 0.015574 Align patch 11 14 left Iteration 1 Error: 0.498734 Iteration 2 Error: 0.119808 Iteration 3 Error: 0.022531 Align patch 12 13 left Iteration 1 Error: 0.617358 Iteration 2 Error: 0.096294 Iteration 3 Error: 0.022309 Align patch 13 12 left Iteration 1 Error: 0.768623 Iteration 2 Error: 0.185899 Iteration 3 Error: 0.038798 Align patch 14 11 left Iteration 1 Error: 0.571828 Iteration 2 Error: 0.091214 Iteration 3 Error: 0.029029 Align patch 15 10 left Iteration 1 Error: 0.655563 Iteration 2 Error: 0.114181 Iteration 3 Error: 0.018156 Align patch 16 9 left Iteration 1 Error: 0.988595 Iteration 2 Error: 0.097020 Iteration 3 Error: 0.023927 Align patch 17 8 left Iteration 1 Error: 0.819799 Iteration 2 Error: 0.111671 Iteration 3 Error: 0.031047 Align patch 18 7 left Iteration 1 Error: 0.600783 Iteration 2 Error: 0.105942 Iteration 3 Error: 0.034737 Align patch 19 6 left Iteration 1 Error: 0.501775 Iteration 2 Error: 0.112848 Iteration 3 Error: 0.018378 Align patch 20 5 left Iteration 1 Error: 0.740578 Iteration 2 Error: 0.110086 Iteration 3 Error: 0.023241 Align patch 21 4 left Iteration 1 Error: 0.656179 Iteration 2 Error: 0.132782 Iteration 3 Error: 0.026385 Align patch 22 3 left Iteration 1 Error: 0.758172 Iteration 2 Error: 0.104483 Iteration 3 Error: 0.034560 Align patch 23 2 left Iteration 1 Error: 0.634231 Iteration 2 Error: 0.098427 Iteration 3 Error: 0.022105 Align patch 24 1 left Iteration 1 Error: 0.491122 Iteration 2 Error: 0.158536 Iteration 3 Error: 0.033697 Align patch 25 0 left Iteration 1 Error: 0.853442 Iteration 2 Error: 0.145043 Iteration 3 Error: 0.044577 3D Fitting completed. Patch alignment time: 11.32(sec) Local motion has been corrected. Process thread exits. Computational time: 26.936920 sec Total time: 36.060520 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00017hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00017hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.551893s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00017hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.158674s ........................................ >>>>>>TIME<<<<<< FFT: 0.966882s Defocus_U Defocus_V Angle CCC 10689.47 11560.56 10.85 0.043610 Final Values Defocus_U Defocus_V Angle CCC 10708.23 11591.83 11.80 0.068373 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00017hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00017hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 40.03 6.90 Num Hot pixels: 222 Hot pixel threshold: 81.44 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.005592 Iteration 2 Error: 0.144831 Iteration 3 Error: 0.027215 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.10 -0.12 ...... Frame ( 3) shift: -0.20 -0.25 ...... Frame ( 4) shift: -0.31 -0.37 ...... Frame ( 5) shift: -0.41 -0.49 ...... Frame ( 6) shift: -0.46 -0.52 ...... Frame ( 7) shift: -0.47 -0.46 ...... Frame ( 8) shift: -0.48 -0.40 ...... Frame ( 9) shift: -0.50 -0.34 ...... Frame ( 10) shift: -0.52 -0.28 ...... Frame ( 11) shift: -0.55 -0.22 ...... Frame ( 12) shift: -0.55 -0.18 ...... Frame ( 13) shift: -0.52 -0.17 ...... Frame ( 14) shift: -0.49 -0.15 ...... Frame ( 15) shift: -0.45 -0.13 ...... Frame ( 16) shift: -0.41 -0.11 ...... Frame ( 17) shift: -0.36 -0.08 ...... Frame ( 18) shift: -0.32 -0.07 ...... Frame ( 19) shift: -0.28 -0.06 ...... Frame ( 20) shift: -0.25 -0.06 ...... Frame ( 21) shift: -0.21 0.01 ...... Frame ( 22) shift: -0.16 0.13 ...... Frame ( 23) shift: -0.12 0.25 ...... Frame ( 24) shift: -0.10 0.31 ...... Frame ( 25) shift: -0.10 0.32 ...... Frame ( 26) shift: -0.11 0.32 ...... Frame ( 27) shift: -0.11 0.35 ...... Frame ( 28) shift: -0.11 0.38 ...... Frame ( 29) shift: -0.11 0.42 ...... Frame ( 30) shift: -0.07 0.47 ...... Frame ( 31) shift: -0.00 0.55 ...... Frame ( 32) shift: 0.07 0.62 ...... Frame ( 33) shift: 0.10 0.68 ...... Frame ( 34) shift: 0.10 0.71 ...... Frame ( 35) shift: 0.09 0.75 ...... Frame ( 36) shift: 0.10 0.82 ...... Frame ( 37) shift: 0.11 0.93 ...... Frame ( 38) shift: 0.13 1.04 ...... Frame ( 39) shift: 0.15 1.15 ...... Frame ( 40) shift: 0.16 1.26 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.571720 Iteration 2 Error: 0.083115 Iteration 3 Error: 0.023402 Align patch 2 23 left Iteration 1 Error: 0.925904 Iteration 2 Error: 0.211942 Iteration 3 Error: 0.043552 Align patch 3 22 left Iteration 1 Error: 0.704668 Iteration 2 Error: 0.095084 Iteration 3 Error: 0.017077 Align patch 4 21 left Iteration 1 Error: 0.830657 Iteration 2 Error: 0.140814 Iteration 3 Error: 0.022856 Align patch 5 20 left Iteration 1 Error: 0.338574 Iteration 2 Error: 0.032856 Align patch 6 19 left Iteration 1 Error: 0.980576 Iteration 2 Error: 0.154163 Iteration 3 Error: 0.031757 Align patch 7 18 left Iteration 1 Error: 1.105011 Iteration 2 Error: 0.238602 Iteration 3 Error: 0.059783 Iteration 4 Error: 0.022180 Align patch 8 17 left Iteration 1 Error: 0.782848 Iteration 2 Error: 0.154641 Iteration 3 Error: 0.028654 Align patch 9 16 left Iteration 1 Error: 0.754676 Iteration 2 Error: 0.103349 Iteration 3 Error: 0.019574 Align patch 10 15 left Iteration 1 Error: 0.523329 Iteration 2 Error: 0.082593 Iteration 3 Error: 0.016889 Align patch 11 14 left Iteration 1 Error: 0.668290 Iteration 2 Error: 0.206416 Iteration 3 Error: 0.066424 Iteration 4 Error: 0.030673 Align patch 12 13 left Iteration 1 Error: 0.863025 Iteration 2 Error: 0.174897 Iteration 3 Error: 0.035915 Align patch 13 12 left Iteration 1 Error: 0.792892 Iteration 2 Error: 0.096529 Iteration 3 Error: 0.016936 Align patch 14 11 left Iteration 1 Error: 0.855759 Iteration 2 Error: 0.141227 Iteration 3 Error: 0.033812 Align patch 15 10 left Iteration 1 Error: 0.582120 Iteration 2 Error: 0.101863 Iteration 3 Error: 0.021273 Align patch 16 9 left Iteration 1 Error: 0.958930 Iteration 2 Error: 0.119177 Iteration 3 Error: 0.034418 Align patch 17 8 left Iteration 1 Error: 0.718706 Iteration 2 Error: 0.106597 Iteration 3 Error: 0.018137 Align patch 18 7 left Iteration 1 Error: 0.486508 Iteration 2 Error: 0.058097 Iteration 3 Error: 0.015683 Align patch 19 6 left Iteration 1 Error: 0.607356 Iteration 2 Error: 0.080924 Iteration 3 Error: 0.016853 Align patch 20 5 left Iteration 1 Error: 0.801552 Iteration 2 Error: 0.088011 Iteration 3 Error: 0.022301 Align patch 21 4 left Iteration 1 Error: 0.980024 Iteration 2 Error: 0.102438 Iteration 3 Error: 0.026714 Align patch 22 3 left Iteration 1 Error: 0.628263 Iteration 2 Error: 0.103572 Iteration 3 Error: 0.027681 Align patch 23 2 left Iteration 1 Error: 0.528620 Iteration 2 Error: 0.122833 Iteration 3 Error: 0.034441 Align patch 24 1 left Iteration 1 Error: 0.478129 Iteration 2 Error: 0.088998 Iteration 3 Error: 0.016370 Align patch 25 0 left Iteration 1 Error: 0.701490 Iteration 2 Error: 0.099383 Iteration 3 Error: 0.017124 3D Fitting completed. Patch alignment time: 12.59(sec) Local motion has been corrected. Process thread exits. Computational time: 24.237528 sec Total time: 30.318260 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00017hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00017hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.546623s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00017hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.013505s ........................................ >>>>>>TIME<<<<<< FFT: 0.871781s Defocus_U Defocus_V Angle CCC 9099.35 8592.06 88.07 0.034573 Final Values Defocus_U Defocus_V Angle CCC 9100.92 8599.88 87.45 0.069127 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00017hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00017hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.992e-02 CC threshold: 0.734 Mean Std: 37.75 6.56 Num Hot pixels: 257 Hot pixel threshold: 77.08 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 4.880478 Iteration 2 Error: 0.660766 Iteration 3 Error: 0.268777 Iteration 4 Error: 0.126529 Iteration 5 Error: 0.069515 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.59 0.49 ...... Frame ( 3) shift: 1.19 0.98 ...... Frame ( 4) shift: 1.78 1.48 ...... Frame ( 5) shift: 2.38 1.97 ...... Frame ( 6) shift: 2.82 2.36 ...... Frame ( 7) shift: 3.13 2.66 ...... Frame ( 8) shift: 3.43 2.96 ...... Frame ( 9) shift: 3.67 3.19 ...... Frame ( 10) shift: 3.84 3.36 ...... Frame ( 11) shift: 4.01 3.53 ...... Frame ( 12) shift: 4.17 3.66 ...... Frame ( 13) shift: 4.32 3.76 ...... Frame ( 14) shift: 4.47 3.86 ...... Frame ( 15) shift: 4.59 3.97 ...... Frame ( 16) shift: 4.68 4.10 ...... Frame ( 17) shift: 4.77 4.23 ...... Frame ( 18) shift: 4.88 4.38 ...... Frame ( 19) shift: 4.99 4.56 ...... Frame ( 20) shift: 5.10 4.74 ...... Frame ( 21) shift: 5.19 4.86 ...... Frame ( 22) shift: 5.26 4.93 ...... Frame ( 23) shift: 5.32 5.01 ...... Frame ( 24) shift: 5.43 5.08 ...... Frame ( 25) shift: 5.57 5.16 ...... Frame ( 26) shift: 5.71 5.23 ...... Frame ( 27) shift: 5.81 5.26 ...... Frame ( 28) shift: 5.85 5.22 ...... Frame ( 29) shift: 5.89 5.19 ...... Frame ( 30) shift: 5.96 5.18 ...... Frame ( 31) shift: 6.05 5.20 ...... Frame ( 32) shift: 6.14 5.22 ...... Frame ( 33) shift: 6.18 5.28 ...... Frame ( 34) shift: 6.17 5.40 ...... Frame ( 35) shift: 6.16 5.51 ...... Frame ( 36) shift: 6.21 5.60 ...... Frame ( 37) shift: 6.30 5.65 ...... Frame ( 38) shift: 6.40 5.70 ...... Frame ( 39) shift: 6.50 5.76 ...... Frame ( 40) shift: 6.59 5.81 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 4.061038 Iteration 2 Error: 1.181300 Iteration 3 Error: 0.377566 Iteration 4 Error: 0.241769 Iteration 5 Error: 0.122666 Align patch 1 24 left Iteration 1 Error: 3.656229 Iteration 2 Error: 0.439772 Iteration 3 Error: 0.081512 Iteration 4 Error: 0.024571 Align patch 2 23 left Iteration 1 Error: 3.269257 Iteration 2 Error: 0.525811 Iteration 3 Error: 0.121859 Iteration 4 Error: 0.060559 Iteration 5 Error: 0.019450 Align patch 3 22 left Iteration 1 Error: 2.387102 Iteration 2 Error: 0.490516 Iteration 3 Error: 0.155652 Iteration 4 Error: 0.065662 Iteration 5 Error: 0.030117 Align patch 4 21 left Iteration 1 Error: 1.958283 Iteration 2 Error: 0.424267 Iteration 3 Error: 0.137586 Iteration 4 Error: 0.036245 Align patch 5 20 left Iteration 1 Error: 3.901503 Iteration 2 Error: 0.443896 Iteration 3 Error: 0.148851 Iteration 4 Error: 0.058449 Iteration 5 Error: 0.027280 Align patch 6 19 left Iteration 1 Error: 2.956882 Iteration 2 Error: 0.655866 Iteration 3 Error: 0.188950 Iteration 4 Error: 0.098377 Iteration 5 Error: 0.031476 Align patch 7 18 left Iteration 1 Error: 2.861003 Iteration 2 Error: 0.671606 Iteration 3 Error: 0.276067 Iteration 4 Error: 0.108081 Iteration 5 Error: 0.035334 Align patch 8 17 left Iteration 1 Error: 1.345240 Iteration 2 Error: 0.308474 Iteration 3 Error: 0.085656 Iteration 4 Error: 0.051175 Iteration 5 Error: 0.020834 Align patch 9 16 left Iteration 1 Error: 1.626546 Iteration 2 Error: 0.210990 Iteration 3 Error: 0.064133 Iteration 4 Error: 0.015772 Align patch 10 15 left Iteration 1 Error: 2.737945 Iteration 2 Error: 0.417974 Iteration 3 Error: 0.142544 Iteration 4 Error: 0.055539 Iteration 5 Error: 0.027824 Align patch 11 14 left Iteration 1 Error: 4.334507 Iteration 2 Error: 0.683760 Iteration 3 Error: 0.195368 Iteration 4 Error: 0.079066 Iteration 5 Error: 0.020626 Align patch 12 13 left Iteration 1 Error: 2.869913 Iteration 2 Error: 0.590073 Iteration 3 Error: 0.372438 Iteration 4 Error: 0.196283 Iteration 5 Error: 0.108351 Align patch 12 13 left Iteration 1 Error: 2.668122 Iteration 2 Error: 0.339526 Iteration 3 Error: 0.067058 Iteration 4 Error: 0.025310 Align patch 13 12 left Iteration 1 Error: 1.232340 Iteration 2 Error: 0.194593 Iteration 3 Error: 0.089388 Iteration 4 Error: 0.049629 Align patch 14 11 left Iteration 1 Error: 2.198481 Iteration 2 Error: 0.346899 Iteration 3 Error: 0.086448 Iteration 4 Error: 0.040685 Align patch 15 10 left Iteration 1 Error: 3.548097 Iteration 2 Error: 0.390110 Iteration 3 Error: 0.091950 Iteration 4 Error: 0.040386 Align patch 16 9 left Iteration 1 Error: 3.091084 Iteration 2 Error: 0.528536 Iteration 3 Error: 0.129890 Iteration 4 Error: 0.083737 Iteration 5 Error: 0.048139 Align patch 17 8 left Iteration 1 Error: 1.345164 Iteration 2 Error: 0.301658 Iteration 3 Error: 0.143510 Iteration 4 Error: 0.046783 Align patch 18 7 left Iteration 1 Error: 0.821066 Iteration 2 Error: 0.135644 Iteration 3 Error: 0.043637 Align patch 19 6 left Iteration 1 Error: 1.862365 Iteration 2 Error: 0.343315 Iteration 3 Error: 0.101752 Iteration 4 Error: 0.033403 Align patch 20 5 left Iteration 1 Error: 2.987871 Iteration 2 Error: 0.517673 Iteration 3 Error: 0.169520 Iteration 4 Error: 0.095865 Iteration 5 Error: 0.046340 Align patch 21 4 left Iteration 1 Error: 2.953908 Iteration 2 Error: 0.549632 Iteration 3 Error: 0.184807 Iteration 4 Error: 0.079720 Iteration 5 Error: 0.036583 Align patch 22 3 left Iteration 1 Error: 1.346593 Iteration 2 Error: 0.459631 Iteration 3 Error: 0.101670 Iteration 4 Error: 0.060703 Iteration 5 Error: 0.016607 Align patch 23 2 left Iteration 1 Error: 0.998775 Iteration 2 Error: 0.400358 Iteration 3 Error: 0.110781 Iteration 4 Error: 0.069881 Iteration 5 Error: 0.028041 Align patch 24 1 left Iteration 1 Error: 1.741555 Iteration 2 Error: 0.480973 Iteration 3 Error: 0.103742 Iteration 4 Error: 0.040645 Align patch 25 0 left Iteration 1 Error: 2.984874 Iteration 2 Error: 0.599180 Iteration 3 Error: 0.166373 Iteration 4 Error: 0.054230 Iteration 5 Error: 0.023316 3D Fitting completed. Patch alignment time: 16.08(sec) Local motion has been corrected. Process thread exits. Computational time: 28.105227 sec Total time: 35.114323 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00017hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00017hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.573449s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00017hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.874102s ........................................ >>>>>>TIME<<<<<< FFT: 0.907305s Defocus_U Defocus_V Angle CCC 12820.33 13703.14 6.22 0.039897 Final Values Defocus_U Defocus_V Angle CCC 12867.21 13668.77 4.04 0.053566 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00017hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00017hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.001e-01 CC threshold: 0.735 Mean Std: 39.01 6.67 Num Hot pixels: 236 Hot pixel threshold: 79.02 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.882072 Iteration 2 Error: 0.211948 Iteration 3 Error: 0.042969 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.15 -0.08 ...... Frame ( 3) shift: -0.31 -0.17 ...... Frame ( 4) shift: -0.46 -0.25 ...... Frame ( 5) shift: -0.61 -0.34 ...... Frame ( 6) shift: -0.68 -0.36 ...... Frame ( 7) shift: -0.65 -0.30 ...... Frame ( 8) shift: -0.62 -0.25 ...... Frame ( 9) shift: -0.61 -0.22 ...... Frame ( 10) shift: -0.61 -0.20 ...... Frame ( 11) shift: -0.61 -0.19 ...... Frame ( 12) shift: -0.64 -0.16 ...... Frame ( 13) shift: -0.71 -0.12 ...... Frame ( 14) shift: -0.78 -0.08 ...... Frame ( 15) shift: -0.80 -0.02 ...... Frame ( 16) shift: -0.76 0.08 ...... Frame ( 17) shift: -0.73 0.18 ...... Frame ( 18) shift: -0.68 0.26 ...... Frame ( 19) shift: -0.62 0.31 ...... Frame ( 20) shift: -0.56 0.37 ...... Frame ( 21) shift: -0.53 0.43 ...... Frame ( 22) shift: -0.54 0.49 ...... Frame ( 23) shift: -0.56 0.56 ...... Frame ( 24) shift: -0.54 0.60 ...... Frame ( 25) shift: -0.49 0.63 ...... Frame ( 26) shift: -0.44 0.66 ...... Frame ( 27) shift: -0.40 0.67 ...... Frame ( 28) shift: -0.36 0.67 ...... Frame ( 29) shift: -0.33 0.66 ...... Frame ( 30) shift: -0.27 0.69 ...... Frame ( 31) shift: -0.18 0.77 ...... Frame ( 32) shift: -0.09 0.84 ...... Frame ( 33) shift: 0.00 0.92 ...... Frame ( 34) shift: 0.10 1.00 ...... Frame ( 35) shift: 0.20 1.08 ...... Frame ( 36) shift: 0.25 1.12 ...... Frame ( 37) shift: 0.25 1.13 ...... Frame ( 38) shift: 0.25 1.13 ...... Frame ( 39) shift: 0.25 1.13 ...... Frame ( 40) shift: 0.25 1.13 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.791284 Iteration 2 Error: 0.217966 Iteration 3 Error: 0.060181 Iteration 4 Error: 0.028405 Align patch 2 23 left Iteration 1 Error: 0.651498 Iteration 2 Error: 0.121076 Iteration 3 Error: 0.030994 Align patch 3 22 left Iteration 1 Error: 0.898747 Iteration 2 Error: 0.133290 Iteration 3 Error: 0.021809 Align patch 4 21 left Iteration 1 Error: 0.800684 Iteration 2 Error: 0.140821 Iteration 3 Error: 0.034506 Align patch 5 20 left Iteration 1 Error: 0.675431 Iteration 2 Error: 0.155409 Iteration 3 Error: 0.041257 Align patch 6 19 left Iteration 1 Error: 0.760562 Iteration 2 Error: 0.092317 Iteration 3 Error: 0.025494 Align patch 7 18 left Iteration 1 Error: 0.685227 Iteration 2 Error: 0.105038 Iteration 3 Error: 0.029073 Align patch 8 17 left Iteration 1 Error: 0.774374 Iteration 2 Error: 0.248735 Iteration 3 Error: 0.072627 Iteration 4 Error: 0.029984 Align patch 9 16 left Iteration 1 Error: 1.091686 Iteration 2 Error: 0.131872 Iteration 3 Error: 0.036747 Align patch 10 15 left Iteration 1 Error: 0.680210 Iteration 2 Error: 0.131510 Iteration 3 Error: 0.032744 Align patch 11 14 left Iteration 1 Error: 0.743971 Iteration 2 Error: 0.104699 Iteration 3 Error: 0.023795 Align patch 12 13 left Iteration 1 Error: 0.924059 Iteration 2 Error: 0.110577 Iteration 3 Error: 0.034168 Align patch 13 12 left Iteration 1 Error: 0.539044 Iteration 2 Error: 0.114852 Iteration 3 Error: 0.029175 Align patch 14 11 left Iteration 1 Error: 0.540697 Iteration 2 Error: 0.126628 Iteration 3 Error: 0.035278 Align patch 15 10 left Iteration 1 Error: 0.870201 Iteration 2 Error: 0.132444 Iteration 3 Error: 0.029745 Align patch 16 9 left Iteration 1 Error: 0.880789 Iteration 2 Error: 0.222148 Iteration 3 Error: 0.057830 Iteration 4 Error: 0.024523 Align patch 17 8 left Iteration 1 Error: 0.586814 Iteration 2 Error: 0.097816 Iteration 3 Error: 0.020472 Align patch 18 7 left Iteration 1 Error: 0.882169 Iteration 2 Error: 0.159693 Iteration 3 Error: 0.048613 Align patch 19 6 left Iteration 1 Error: 0.745481 Iteration 2 Error: 0.091173 Iteration 3 Error: 0.036275 Align patch 20 5 left Iteration 1 Error: 0.984294 Iteration 2 Error: 0.197582 Iteration 3 Error: 0.041784 Align patch 21 4 left Iteration 1 Error: 0.807862 Iteration 2 Error: 0.146876 Iteration 3 Error: 0.045426 Align patch 22 3 left Iteration 1 Error: 0.551024 Iteration 2 Error: 0.103725 Iteration 3 Error: 0.032622 Align patch 23 2 left Iteration 1 Error: 1.134124 Iteration 2 Error: 0.161045 Iteration 3 Error: 0.027755 Align patch 24 1 left Iteration 1 Error: 0.458772 Iteration 2 Error: 0.081824 Iteration 3 Error: 0.033276 Align patch 25 0 left Iteration 1 Error: 1.136696 Iteration 2 Error: 0.245625 Iteration 3 Error: 0.044075 3D Fitting completed. Patch alignment time: 12.11(sec) Local motion has been corrected. Process thread exits. Computational time: 21.181984 sec Total time: 28.683826 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00017hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00017hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.466974s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00017hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.720704s ........................................ >>>>>>TIME<<<<<< FFT: 0.903206s Defocus_U Defocus_V Angle CCC 10027.35 10019.53 40.05 0.026116 Final Values Defocus_U Defocus_V Angle CCC 10340.45 9603.53 86.19 0.051281 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00018hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00018hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 38.95 6.67 Num Hot pixels: 224 Hot pixel threshold: 78.94 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.881974 Iteration 2 Error: 0.180778 Iteration 3 Error: 0.044955 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.04 -0.02 ...... Frame ( 3) shift: -0.09 -0.05 ...... Frame ( 4) shift: -0.13 -0.07 ...... Frame ( 5) shift: -0.17 -0.10 ...... Frame ( 6) shift: -0.18 -0.12 ...... Frame ( 7) shift: -0.16 -0.13 ...... Frame ( 8) shift: -0.14 -0.15 ...... Frame ( 9) shift: -0.13 -0.13 ...... Frame ( 10) shift: -0.12 -0.08 ...... Frame ( 11) shift: -0.11 -0.02 ...... Frame ( 12) shift: -0.10 0.01 ...... Frame ( 13) shift: -0.08 0.01 ...... Frame ( 14) shift: -0.07 0.01 ...... Frame ( 15) shift: -0.03 0.07 ...... Frame ( 16) shift: 0.04 0.19 ...... Frame ( 17) shift: 0.10 0.31 ...... Frame ( 18) shift: 0.18 0.37 ...... Frame ( 19) shift: 0.29 0.38 ...... Frame ( 20) shift: 0.40 0.39 ...... Frame ( 21) shift: 0.47 0.41 ...... Frame ( 22) shift: 0.49 0.46 ...... Frame ( 23) shift: 0.51 0.50 ...... Frame ( 24) shift: 0.53 0.54 ...... Frame ( 25) shift: 0.56 0.57 ...... Frame ( 26) shift: 0.59 0.60 ...... Frame ( 27) shift: 0.64 0.65 ...... Frame ( 28) shift: 0.71 0.71 ...... Frame ( 29) shift: 0.78 0.76 ...... Frame ( 30) shift: 0.84 0.77 ...... Frame ( 31) shift: 0.89 0.72 ...... Frame ( 32) shift: 0.95 0.68 ...... Frame ( 33) shift: 1.00 0.68 ...... Frame ( 34) shift: 1.04 0.72 ...... Frame ( 35) shift: 1.09 0.77 ...... Frame ( 36) shift: 1.14 0.81 ...... Frame ( 37) shift: 1.19 0.84 ...... Frame ( 38) shift: 1.24 0.86 ...... Frame ( 39) shift: 1.28 0.89 ...... Frame ( 40) shift: 1.33 0.92 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.094327 Iteration 2 Error: 0.101700 Iteration 3 Error: 0.030412 Align patch 2 23 left Iteration 1 Error: 0.682646 Iteration 2 Error: 0.117581 Iteration 3 Error: 0.033985 Align patch 3 22 left Iteration 1 Error: 0.408606 Iteration 2 Error: 0.072110 Iteration 3 Error: 0.022251 Align patch 4 21 left Iteration 1 Error: 0.820488 Iteration 2 Error: 0.130087 Iteration 3 Error: 0.029398 Align patch 5 20 left Iteration 1 Error: 0.672676 Iteration 2 Error: 0.075235 Iteration 3 Error: 0.008354 Align patch 6 19 left Iteration 1 Error: 0.853635 Iteration 2 Error: 0.185629 Iteration 3 Error: 0.072898 Iteration 4 Error: 0.027258 Align patch 7 18 left Iteration 1 Error: 0.702338 Iteration 2 Error: 0.195178 Iteration 3 Error: 0.057828 Iteration 4 Error: 0.020823 Align patch 8 17 left Iteration 1 Error: 0.505527 Iteration 2 Error: 0.097659 Iteration 3 Error: 0.021393 Align patch 9 16 left Iteration 1 Error: 0.919815 Iteration 2 Error: 0.119596 Iteration 3 Error: 0.026406 Align patch 10 15 left Iteration 1 Error: 0.633777 Iteration 2 Error: 0.109137 Iteration 3 Error: 0.019501 Align patch 11 14 left Iteration 1 Error: 0.635156 Iteration 2 Error: 0.080539 Iteration 3 Error: 0.025975 Align patch 12 13 left Iteration 1 Error: 0.709581 Iteration 2 Error: 0.150115 Iteration 3 Error: 0.028917 Align patch 13 12 left Iteration 1 Error: 0.779342 Iteration 2 Error: 0.153520 Iteration 3 Error: 0.034939 Align patch 14 11 left Iteration 1 Error: 0.993998 Iteration 2 Error: 0.093745 Iteration 3 Error: 0.024355 Align patch 15 10 left Iteration 1 Error: 0.851129 Iteration 2 Error: 0.208900 Iteration 3 Error: 0.042341 Align patch 16 9 left Iteration 1 Error: 1.068813 Iteration 2 Error: 0.279226 Iteration 3 Error: 0.063523 Iteration 4 Error: 0.016951 Align patch 17 8 left Iteration 1 Error: 0.779777 Iteration 2 Error: 0.215338 Iteration 3 Error: 0.080432 Iteration 4 Error: 0.024999 Align patch 18 7 left Iteration 1 Error: 0.784588 Iteration 2 Error: 0.171328 Iteration 3 Error: 0.045072 Align patch 19 6 left Iteration 1 Error: 0.717449 Iteration 2 Error: 0.093557 Iteration 3 Error: 0.023566 Align patch 20 5 left Iteration 1 Error: 0.601978 Iteration 2 Error: 0.082495 Iteration 3 Error: 0.019741 Align patch 21 4 left Iteration 1 Error: 0.704637 Iteration 2 Error: 0.126398 Iteration 3 Error: 0.034099 Align patch 22 3 left Iteration 1 Error: 0.666059 Iteration 2 Error: 0.120993 Iteration 3 Error: 0.027234 Align patch 23 2 left Iteration 1 Error: 0.904485 Iteration 2 Error: 0.247356 Iteration 3 Error: 0.064086 Iteration 4 Error: 0.017274 Align patch 24 1 left Iteration 1 Error: 0.796030 Iteration 2 Error: 0.100769 Iteration 3 Error: 0.024322 Align patch 25 0 left Iteration 1 Error: 0.802990 Iteration 2 Error: 0.122091 Iteration 3 Error: 0.045068 3D Fitting completed. Patch alignment time: 11.99(sec) Local motion has been corrected. Process thread exits. Computational time: 22.249960 sec Total time: 29.042660 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00018hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00018hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.486882s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00018hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.628102s ........................................ >>>>>>TIME<<<<<< FFT: 0.909149s Defocus_U Defocus_V Angle CCC 10712.91 11505.88 11.22 0.038330 Final Values Defocus_U Defocus_V Angle CCC 10701.96 11541.85 12.16 0.061985 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00018hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00018hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 28.01 5.69 Num Hot pixels: 204 Hot pixel threshold: 62.14 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.152984 Iteration 2 Error: 0.190481 Iteration 3 Error: 0.055023 Iteration 4 Error: 0.016714 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.10 0.30 ...... Frame ( 3) shift: -0.20 0.61 ...... Frame ( 4) shift: -0.31 0.91 ...... Frame ( 5) shift: -0.41 1.21 ...... Frame ( 6) shift: -0.47 1.39 ...... Frame ( 7) shift: -0.50 1.43 ...... Frame ( 8) shift: -0.52 1.48 ...... Frame ( 9) shift: -0.48 1.46 ...... Frame ( 10) shift: -0.38 1.39 ...... Frame ( 11) shift: -0.27 1.32 ...... Frame ( 12) shift: -0.25 1.29 ...... Frame ( 13) shift: -0.32 1.29 ...... Frame ( 14) shift: -0.39 1.30 ...... Frame ( 15) shift: -0.41 1.32 ...... Frame ( 16) shift: -0.40 1.35 ...... Frame ( 17) shift: -0.39 1.38 ...... Frame ( 18) shift: -0.35 1.44 ...... Frame ( 19) shift: -0.29 1.52 ...... Frame ( 20) shift: -0.23 1.61 ...... Frame ( 21) shift: -0.20 1.70 ...... Frame ( 22) shift: -0.19 1.80 ...... Frame ( 23) shift: -0.19 1.89 ...... Frame ( 24) shift: -0.13 1.92 ...... Frame ( 25) shift: -0.01 1.87 ...... Frame ( 26) shift: 0.11 1.83 ...... Frame ( 27) shift: 0.22 1.82 ...... Frame ( 28) shift: 0.30 1.85 ...... Frame ( 29) shift: 0.39 1.89 ...... Frame ( 30) shift: 0.45 1.94 ...... Frame ( 31) shift: 0.49 2.02 ...... Frame ( 32) shift: 0.53 2.10 ...... Frame ( 33) shift: 0.53 2.14 ...... Frame ( 34) shift: 0.49 2.14 ...... Frame ( 35) shift: 0.44 2.14 ...... Frame ( 36) shift: 0.48 2.19 ...... Frame ( 37) shift: 0.60 2.29 ...... Frame ( 38) shift: 0.71 2.40 ...... Frame ( 39) shift: 0.83 2.50 ...... Frame ( 40) shift: 0.95 2.60 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.122072 Iteration 2 Error: 0.343756 Iteration 3 Error: 0.106627 Iteration 4 Error: 0.039040 Align patch 2 23 left Iteration 1 Error: 1.068398 Iteration 2 Error: 0.173464 Iteration 3 Error: 0.070451 Iteration 4 Error: 0.027991 Align patch 3 22 left Iteration 1 Error: 0.784116 Iteration 2 Error: 0.185822 Iteration 3 Error: 0.047664 Align patch 4 21 left Iteration 1 Error: 1.213701 Iteration 2 Error: 0.203073 Iteration 3 Error: 0.099495 Iteration 4 Error: 0.043373 Align patch 5 20 left Iteration 1 Error: 0.744136 Iteration 2 Error: 0.035016 Align patch 6 19 left Iteration 1 Error: 1.053799 Iteration 2 Error: 0.290082 Iteration 3 Error: 0.079944 Iteration 4 Error: 0.032009 Align patch 7 18 left Iteration 1 Error: 0.852501 Iteration 2 Error: 0.258271 Iteration 3 Error: 0.114731 Iteration 4 Error: 0.048259 Align patch 8 17 left Iteration 1 Error: 0.930133 Iteration 2 Error: 0.325593 Iteration 3 Error: 0.216616 Iteration 4 Error: 0.087052 Iteration 5 Error: 0.053340 Align patch 8 17 left Iteration 1 Error: 0.666612 Iteration 2 Error: 0.095707 Iteration 3 Error: 0.046158 Align patch 9 16 left Iteration 1 Error: 0.934314 Iteration 2 Error: 0.158931 Iteration 3 Error: 0.076417 Iteration 4 Error: 0.018602 Align patch 10 15 left Iteration 1 Error: 1.260882 Iteration 2 Error: 0.267882 Iteration 3 Error: 0.047490 Align patch 11 14 left Iteration 1 Error: 1.501828 Iteration 2 Error: 0.244903 Iteration 3 Error: 0.052951 Iteration 4 Error: 0.032460 Align patch 12 13 left Iteration 1 Error: 0.712287 Iteration 2 Error: 0.265693 Iteration 3 Error: 0.109300 Iteration 4 Error: 0.046717 Align patch 13 12 left Iteration 1 Error: 1.381286 Iteration 2 Error: 0.359378 Iteration 3 Error: 0.098555 Iteration 4 Error: 0.059008 Iteration 5 Error: 0.022020 Align patch 14 11 left Iteration 1 Error: 1.380082 Iteration 2 Error: 0.388361 Iteration 3 Error: 0.133187 Iteration 4 Error: 0.048022 Align patch 15 10 left Iteration 1 Error: 1.797088 Iteration 2 Error: 0.248223 Iteration 3 Error: 0.164591 Iteration 4 Error: 0.072477 Iteration 5 Error: 0.044533 Align patch 16 9 left Iteration 1 Error: 1.117297 Iteration 2 Error: 0.380950 Iteration 3 Error: 0.220152 Iteration 4 Error: 0.101369 Iteration 5 Error: 0.048740 Align patch 17 8 left Iteration 1 Error: 0.855322 Iteration 2 Error: 0.180067 Iteration 3 Error: 0.050239 Iteration 4 Error: 0.020757 Align patch 18 7 left Iteration 1 Error: 1.961278 Iteration 2 Error: 0.243669 Iteration 3 Error: 0.068973 Iteration 4 Error: 0.017077 Align patch 19 6 left Iteration 1 Error: 1.874885 Iteration 2 Error: 0.320440 Iteration 3 Error: 0.080889 Iteration 4 Error: 0.039600 Align patch 20 5 left Iteration 1 Error: 1.956708 Iteration 2 Error: 0.397822 Iteration 3 Error: 0.098892 Iteration 4 Error: 0.038907 Align patch 21 4 left Iteration 1 Error: 1.518859 Iteration 2 Error: 0.431058 Iteration 3 Error: 0.145354 Iteration 4 Error: 0.066111 Iteration 5 Error: 0.027144 Align patch 22 3 left Iteration 1 Error: 1.548984 Iteration 2 Error: 0.262910 Iteration 3 Error: 0.071624 Iteration 4 Error: 0.026691 Align patch 23 2 left Iteration 1 Error: 0.746507 Iteration 2 Error: 0.176347 Iteration 3 Error: 0.046495 Align patch 24 1 left Iteration 1 Error: 1.520194 Iteration 2 Error: 0.270800 Iteration 3 Error: 0.054022 Iteration 4 Error: 0.026778 Align patch 25 0 left Iteration 1 Error: 1.448424 Iteration 2 Error: 0.323138 Iteration 3 Error: 0.089074 Iteration 4 Error: 0.025399 3D Fitting completed. Patch alignment time: 13.58(sec) Local motion has been corrected. Process thread exits. Computational time: 24.194254 sec Total time: 30.772995 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00018hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00018hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.780021s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00018hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.438534s ........................................ >>>>>>TIME<<<<<< FFT: 0.940137s Defocus_U Defocus_V Angle CCC 9966.84 9603.51 81.79 0.009739 Final Values Defocus_U Defocus_V Angle CCC 9963.73 9587.90 81.17 0.013464 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00018hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00018hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 37.46 6.50 Num Hot pixels: 221 Hot pixel threshold: 76.44 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.565560 Iteration 2 Error: 0.101857 Iteration 3 Error: 0.024047 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.06 0.03 ...... Frame ( 3) shift: -0.13 0.07 ...... Frame ( 4) shift: -0.19 0.10 ...... Frame ( 5) shift: -0.26 0.14 ...... Frame ( 6) shift: -0.25 0.16 ...... Frame ( 7) shift: -0.18 0.17 ...... Frame ( 8) shift: -0.11 0.18 ...... Frame ( 9) shift: -0.07 0.21 ...... Frame ( 10) shift: -0.06 0.28 ...... Frame ( 11) shift: -0.06 0.34 ...... Frame ( 12) shift: -0.04 0.36 ...... Frame ( 13) shift: -0.01 0.32 ...... Frame ( 14) shift: 0.01 0.28 ...... Frame ( 15) shift: 0.05 0.28 ...... Frame ( 16) shift: 0.11 0.30 ...... Frame ( 17) shift: 0.16 0.32 ...... Frame ( 18) shift: 0.22 0.33 ...... Frame ( 19) shift: 0.29 0.32 ...... Frame ( 20) shift: 0.35 0.31 ...... Frame ( 21) shift: 0.41 0.32 ...... Frame ( 22) shift: 0.46 0.33 ...... Frame ( 23) shift: 0.52 0.34 ...... Frame ( 24) shift: 0.55 0.35 ...... Frame ( 25) shift: 0.55 0.38 ...... Frame ( 26) shift: 0.56 0.40 ...... Frame ( 27) shift: 0.57 0.42 ...... Frame ( 28) shift: 0.57 0.45 ...... Frame ( 29) shift: 0.58 0.47 ...... Frame ( 30) shift: 0.58 0.46 ...... Frame ( 31) shift: 0.57 0.40 ...... Frame ( 32) shift: 0.55 0.33 ...... Frame ( 33) shift: 0.61 0.34 ...... Frame ( 34) shift: 0.73 0.41 ...... Frame ( 35) shift: 0.85 0.48 ...... Frame ( 36) shift: 0.88 0.52 ...... Frame ( 37) shift: 0.81 0.53 ...... Frame ( 38) shift: 0.75 0.53 ...... Frame ( 39) shift: 0.69 0.54 ...... Frame ( 40) shift: 0.62 0.54 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.059062 Iteration 2 Error: 0.177900 Iteration 3 Error: 0.044721 Align patch 2 23 left Iteration 1 Error: 1.462255 Iteration 2 Error: 0.169214 Iteration 3 Error: 0.041695 Align patch 3 22 left Iteration 1 Error: 0.516880 Iteration 2 Error: 0.091973 Iteration 3 Error: 0.025353 Align patch 4 21 left Iteration 1 Error: 0.885181 Iteration 2 Error: 0.164739 Iteration 3 Error: 0.035419 Align patch 5 20 left Iteration 1 Error: 0.843914 Iteration 2 Error: 0.118655 Iteration 3 Error: 0.024252 Align patch 6 19 left Iteration 1 Error: 0.936183 Iteration 2 Error: 0.142351 Iteration 3 Error: 0.039433 Align patch 7 18 left Iteration 1 Error: 1.099748 Iteration 2 Error: 0.148336 Iteration 3 Error: 0.029436 Align patch 8 17 left Iteration 1 Error: 0.914382 Iteration 2 Error: 0.120659 Iteration 3 Error: 0.037039 Align patch 9 16 left Iteration 1 Error: 0.758603 Iteration 2 Error: 0.208953 Iteration 3 Error: 0.046016 Align patch 10 15 left Iteration 1 Error: 0.691260 Iteration 2 Error: 0.138452 Iteration 3 Error: 0.043448 Align patch 11 14 left Iteration 1 Error: 0.813166 Iteration 2 Error: 0.123636 Iteration 3 Error: 0.026804 Align patch 12 13 left Iteration 1 Error: 0.756383 Iteration 2 Error: 0.138638 Iteration 3 Error: 0.054464 Iteration 4 Error: 0.018747 Align patch 13 12 left Iteration 1 Error: 0.746008 Iteration 2 Error: 0.149100 Iteration 3 Error: 0.040652 Align patch 14 11 left Iteration 1 Error: 0.721254 Iteration 2 Error: 0.149913 Iteration 3 Error: 0.032850 Align patch 15 10 left Iteration 1 Error: 1.035587 Iteration 2 Error: 0.225677 Iteration 3 Error: 0.044356 Align patch 16 9 left Iteration 1 Error: 0.739270 Iteration 2 Error: 0.098124 Iteration 3 Error: 0.022541 Align patch 17 8 left Iteration 1 Error: 0.471217 Iteration 2 Error: 0.075993 Iteration 3 Error: 0.025145 Align patch 18 7 left Iteration 1 Error: 0.662107 Iteration 2 Error: 0.126874 Iteration 3 Error: 0.038625 Align patch 19 6 left Iteration 1 Error: 0.766457 Iteration 2 Error: 0.189134 Iteration 3 Error: 0.042373 Align patch 20 5 left Iteration 1 Error: 0.614854 Iteration 2 Error: 0.094247 Iteration 3 Error: 0.027992 Align patch 21 4 left Iteration 1 Error: 0.978335 Iteration 2 Error: 0.192078 Iteration 3 Error: 0.055334 Iteration 4 Error: 0.016797 Align patch 22 3 left Iteration 1 Error: 0.766490 Iteration 2 Error: 0.159251 Iteration 3 Error: 0.029034 Align patch 23 2 left Iteration 1 Error: 0.790125 Iteration 2 Error: 0.122463 Iteration 3 Error: 0.026430 Align patch 24 1 left Iteration 1 Error: 1.088064 Iteration 2 Error: 0.283993 Iteration 3 Error: 0.041200 Align patch 25 0 left Iteration 1 Error: 0.762888 Iteration 2 Error: 0.148964 Iteration 3 Error: 0.029900 3D Fitting completed. Patch alignment time: 12.25(sec) Local motion has been corrected. Process thread exits. Computational time: 22.578430 sec Total time: 30.399521 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00018hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00018hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.470920s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00018hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.644876s ........................................ >>>>>>TIME<<<<<< FFT: 0.936757s Defocus_U Defocus_V Angle CCC 13009.77 13994.14 17.69 0.027196 Final Values Defocus_U Defocus_V Angle CCC 13106.66 13978.54 22.70 0.038975 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00019hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00019hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.002e-01 CC threshold: 0.736 Mean Std: 40.57 6.89 Num Hot pixels: 239 Hot pixel threshold: 81.93 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.436880 Iteration 2 Error: 0.292963 Iteration 3 Error: 0.078721 Iteration 4 Error: 0.019745 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.11 0.06 ...... Frame ( 3) shift: -0.22 0.12 ...... Frame ( 4) shift: -0.34 0.18 ...... Frame ( 5) shift: -0.45 0.24 ...... Frame ( 6) shift: -0.51 0.31 ...... Frame ( 7) shift: -0.51 0.40 ...... Frame ( 8) shift: -0.51 0.49 ...... Frame ( 9) shift: -0.48 0.60 ...... Frame ( 10) shift: -0.43 0.73 ...... Frame ( 11) shift: -0.38 0.87 ...... Frame ( 12) shift: -0.31 0.99 ...... Frame ( 13) shift: -0.24 1.11 ...... Frame ( 14) shift: -0.16 1.23 ...... Frame ( 15) shift: -0.08 1.34 ...... Frame ( 16) shift: -0.01 1.45 ...... Frame ( 17) shift: 0.06 1.55 ...... Frame ( 18) shift: 0.13 1.67 ...... Frame ( 19) shift: 0.18 1.80 ...... Frame ( 20) shift: 0.24 1.92 ...... Frame ( 21) shift: 0.30 2.01 ...... Frame ( 22) shift: 0.37 2.06 ...... Frame ( 23) shift: 0.43 2.11 ...... Frame ( 24) shift: 0.49 2.18 ...... Frame ( 25) shift: 0.54 2.26 ...... Frame ( 26) shift: 0.58 2.34 ...... Frame ( 27) shift: 0.63 2.38 ...... Frame ( 28) shift: 0.67 2.39 ...... Frame ( 29) shift: 0.71 2.41 ...... Frame ( 30) shift: 0.74 2.44 ...... Frame ( 31) shift: 0.77 2.50 ...... Frame ( 32) shift: 0.79 2.56 ...... Frame ( 33) shift: 0.83 2.62 ...... Frame ( 34) shift: 0.88 2.68 ...... Frame ( 35) shift: 0.94 2.74 ...... Frame ( 36) shift: 0.95 2.78 ...... Frame ( 37) shift: 0.93 2.80 ...... Frame ( 38) shift: 0.90 2.82 ...... Frame ( 39) shift: 0.88 2.84 ...... Frame ( 40) shift: 0.86 2.86 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.900433 Iteration 2 Error: 0.153363 Iteration 3 Error: 0.057561 Iteration 4 Error: 0.022514 Align patch 2 23 left Iteration 1 Error: 0.594389 Iteration 2 Error: 0.077914 Iteration 3 Error: 0.024719 Align patch 3 22 left Iteration 1 Error: 0.496403 Iteration 2 Error: 0.069673 Iteration 3 Error: 0.014526 Align patch 4 21 left Iteration 1 Error: 0.810371 Iteration 2 Error: 0.079541 Iteration 3 Error: 0.021277 Align patch 5 20 left Iteration 1 Error: 0.346909 Iteration 2 Error: 0.075559 Iteration 3 Error: 0.025428 Align patch 6 19 left Iteration 1 Error: 0.705091 Iteration 2 Error: 0.167717 Iteration 3 Error: 0.043266 Align patch 7 18 left Iteration 1 Error: 0.586815 Iteration 2 Error: 0.052106 Iteration 3 Error: 0.015638 Align patch 8 17 left Iteration 1 Error: 0.518010 Iteration 2 Error: 0.085688 Iteration 3 Error: 0.020874 Align patch 9 16 left Iteration 1 Error: 0.595128 Iteration 2 Error: 0.119622 Iteration 3 Error: 0.030495 Align patch 10 15 left Iteration 1 Error: 0.440232 Iteration 2 Error: 0.073589 Iteration 3 Error: 0.013840 Align patch 11 14 left Iteration 1 Error: 0.789481 Iteration 2 Error: 0.153285 Iteration 3 Error: 0.042508 Align patch 12 13 left Iteration 1 Error: 0.830691 Iteration 2 Error: 0.109928 Iteration 3 Error: 0.031634 Align patch 13 12 left Iteration 1 Error: 1.043644 Iteration 2 Error: 0.107860 Iteration 3 Error: 0.027514 Align patch 14 11 left Iteration 1 Error: 0.720402 Iteration 2 Error: 0.076243 Iteration 3 Error: 0.015628 Align patch 15 10 left Iteration 1 Error: 0.400647 Iteration 2 Error: 0.073358 Iteration 3 Error: 0.010194 Align patch 16 9 left Iteration 1 Error: 0.542616 Iteration 2 Error: 0.121193 Iteration 3 Error: 0.052122 Iteration 4 Error: 0.015146 Align patch 17 8 left Iteration 1 Error: 0.525210 Iteration 2 Error: 0.053732 Iteration 3 Error: 0.019204 Align patch 18 7 left Iteration 1 Error: 0.636871 Iteration 2 Error: 0.067760 Iteration 3 Error: 0.013980 Align patch 19 6 left Iteration 1 Error: 0.687916 Iteration 2 Error: 0.061773 Iteration 3 Error: 0.013416 Align patch 20 5 left Iteration 1 Error: 0.398880 Iteration 2 Error: 0.106101 Iteration 3 Error: 0.032427 Align patch 21 4 left Iteration 1 Error: 0.846904 Iteration 2 Error: 0.116481 Iteration 3 Error: 0.036945 Align patch 22 3 left Iteration 1 Error: 0.873078 Iteration 2 Error: 0.146417 Iteration 3 Error: 0.033156 Align patch 23 2 left Iteration 1 Error: 0.665489 Iteration 2 Error: 0.091930 Iteration 3 Error: 0.024638 Align patch 24 1 left Iteration 1 Error: 0.511437 Iteration 2 Error: 0.082291 Iteration 3 Error: 0.018369 Align patch 25 0 left Iteration 1 Error: 0.642583 Iteration 2 Error: 0.099002 Iteration 3 Error: 0.022470 3D Fitting completed. Patch alignment time: 12.25(sec) Local motion has been corrected. Process thread exits. Computational time: 23.483042 sec Total time: 30.814257 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00019hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00019hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.592314s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00019hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.805452s ........................................ >>>>>>TIME<<<<<< FFT: 0.960825s Defocus_U Defocus_V Angle CCC 12824.22 12316.41 87.19 0.063102 Final Values Defocus_U Defocus_V Angle CCC 12841.41 12314.85 86.56 0.101412 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00019hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00019hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 38.77 6.69 Num Hot pixels: 240 Hot pixel threshold: 78.93 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.256499 Iteration 2 Error: 0.201289 Iteration 3 Error: 0.040845 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.18 -0.06 ...... Frame ( 3) shift: -0.36 -0.13 ...... Frame ( 4) shift: -0.53 -0.19 ...... Frame ( 5) shift: -0.71 -0.25 ...... Frame ( 6) shift: -0.74 -0.23 ...... Frame ( 7) shift: -0.63 -0.13 ...... Frame ( 8) shift: -0.51 -0.04 ...... Frame ( 9) shift: -0.39 0.07 ...... Frame ( 10) shift: -0.27 0.20 ...... Frame ( 11) shift: -0.15 0.32 ...... Frame ( 12) shift: -0.10 0.42 ...... Frame ( 13) shift: -0.14 0.51 ...... Frame ( 14) shift: -0.17 0.59 ...... Frame ( 15) shift: -0.14 0.65 ...... Frame ( 16) shift: -0.05 0.69 ...... Frame ( 17) shift: 0.04 0.73 ...... Frame ( 18) shift: 0.13 0.75 ...... Frame ( 19) shift: 0.21 0.75 ...... Frame ( 20) shift: 0.30 0.76 ...... Frame ( 21) shift: 0.32 0.80 ...... Frame ( 22) shift: 0.27 0.88 ...... Frame ( 23) shift: 0.22 0.97 ...... Frame ( 24) shift: 0.23 1.03 ...... Frame ( 25) shift: 0.29 1.07 ...... Frame ( 26) shift: 0.35 1.10 ...... Frame ( 27) shift: 0.40 1.17 ...... Frame ( 28) shift: 0.44 1.27 ...... Frame ( 29) shift: 0.49 1.37 ...... Frame ( 30) shift: 0.50 1.41 ...... Frame ( 31) shift: 0.48 1.41 ...... Frame ( 32) shift: 0.46 1.40 ...... Frame ( 33) shift: 0.50 1.43 ...... Frame ( 34) shift: 0.60 1.48 ...... Frame ( 35) shift: 0.69 1.54 ...... Frame ( 36) shift: 0.78 1.59 ...... Frame ( 37) shift: 0.87 1.63 ...... Frame ( 38) shift: 0.95 1.67 ...... Frame ( 39) shift: 1.03 1.71 ...... Frame ( 40) shift: 1.12 1.75 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.837141 Iteration 2 Error: 0.178281 Iteration 3 Error: 0.026179 Align patch 2 23 left Iteration 1 Error: 0.774087 Iteration 2 Error: 0.128334 Iteration 3 Error: 0.032984 Align patch 3 22 left Iteration 1 Error: 0.462945 Iteration 2 Error: 0.055832 Iteration 3 Error: 0.015179 Align patch 4 21 left Iteration 1 Error: 0.619621 Iteration 2 Error: 0.085574 Iteration 3 Error: 0.022432 Align patch 5 20 left Iteration 1 Error: 0.599116 Iteration 2 Error: 0.109841 Iteration 3 Error: 0.020656 Align patch 6 19 left Iteration 1 Error: 0.809704 Iteration 2 Error: 0.174386 Iteration 3 Error: 0.042143 Align patch 7 18 left Iteration 1 Error: 0.443539 Iteration 2 Error: 0.097822 Iteration 3 Error: 0.021497 Align patch 8 17 left Iteration 1 Error: 0.690079 Iteration 2 Error: 0.077193 Iteration 3 Error: 0.015799 Align patch 9 16 left Iteration 1 Error: 0.406295 Iteration 2 Error: 0.099401 Iteration 3 Error: 0.020404 Align patch 10 15 left Iteration 1 Error: 0.773845 Iteration 2 Error: 0.100186 Iteration 3 Error: 0.028574 Align patch 11 14 left Iteration 1 Error: 1.050999 Iteration 2 Error: 0.146781 Iteration 3 Error: 0.041870 Align patch 12 13 left Iteration 1 Error: 0.706191 Iteration 2 Error: 0.107246 Iteration 3 Error: 0.041239 Align patch 13 12 left Iteration 1 Error: 0.853203 Iteration 2 Error: 0.191425 Iteration 3 Error: 0.071247 Iteration 4 Error: 0.026700 Align patch 14 11 left Iteration 1 Error: 0.434524 Iteration 2 Error: 0.053326 Iteration 3 Error: 0.019908 Align patch 15 10 left Iteration 1 Error: 0.768612 Iteration 2 Error: 0.119816 Iteration 3 Error: 0.048744 Align patch 16 9 left Iteration 1 Error: 0.641768 Iteration 2 Error: 0.168395 Iteration 3 Error: 0.039376 Align patch 17 8 left Iteration 1 Error: 0.800970 Iteration 2 Error: 0.140336 Iteration 3 Error: 0.030282 Align patch 18 7 left Iteration 1 Error: 0.477881 Iteration 2 Error: 0.078947 Iteration 3 Error: 0.019504 Align patch 19 6 left Iteration 1 Error: 0.673625 Iteration 2 Error: 0.087138 Iteration 3 Error: 0.017052 Align patch 20 5 left Iteration 1 Error: 0.655299 Iteration 2 Error: 0.103837 Iteration 3 Error: 0.039606 Align patch 21 4 left Iteration 1 Error: 0.711802 Iteration 2 Error: 0.102943 Iteration 3 Error: 0.021807 Align patch 22 3 left Iteration 1 Error: 0.716621 Iteration 2 Error: 0.104561 Iteration 3 Error: 0.021094 Align patch 23 2 left Iteration 1 Error: 0.828683 Iteration 2 Error: 0.136775 Iteration 3 Error: 0.029430 Align patch 24 1 left Iteration 1 Error: 0.713629 Iteration 2 Error: 0.090300 Iteration 3 Error: 0.014709 Align patch 25 0 left Iteration 1 Error: 1.039249 Iteration 2 Error: 0.117801 Iteration 3 Error: 0.021432 3D Fitting completed. Patch alignment time: 12.01(sec) Local motion has been corrected. Process thread exits. Computational time: 24.084303 sec Total time: 31.357508 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00019hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00019hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.799951s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00019hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.937582s ........................................ >>>>>>TIME<<<<<< FFT: 1.327153s Defocus_U Defocus_V Angle CCC 12283.25 13283.25 4.26 0.041497 Final Values Defocus_U Defocus_V Angle CCC 12295.76 13295.76 3.32 0.062594 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00019hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00019hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 40.77 6.82 Num Hot pixels: 238 Hot pixel threshold: 81.69 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.921099 Iteration 2 Error: 0.179783 Iteration 3 Error: 0.051763 Iteration 4 Error: 0.012381 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.05 0.05 ...... Frame ( 3) shift: -0.11 0.09 ...... Frame ( 4) shift: -0.16 0.14 ...... Frame ( 5) shift: -0.21 0.19 ...... Frame ( 6) shift: -0.20 0.23 ...... Frame ( 7) shift: -0.11 0.27 ...... Frame ( 8) shift: -0.03 0.31 ...... Frame ( 9) shift: 0.05 0.36 ...... Frame ( 10) shift: 0.12 0.43 ...... Frame ( 11) shift: 0.19 0.49 ...... Frame ( 12) shift: 0.27 0.56 ...... Frame ( 13) shift: 0.37 0.64 ...... Frame ( 14) shift: 0.47 0.71 ...... Frame ( 15) shift: 0.53 0.80 ...... Frame ( 16) shift: 0.56 0.88 ...... Frame ( 17) shift: 0.59 0.97 ...... Frame ( 18) shift: 0.64 1.01 ...... Frame ( 19) shift: 0.70 0.99 ...... Frame ( 20) shift: 0.77 0.98 ...... Frame ( 21) shift: 0.83 1.00 ...... Frame ( 22) shift: 0.89 1.05 ...... Frame ( 23) shift: 0.94 1.10 ...... Frame ( 24) shift: 0.97 1.14 ...... Frame ( 25) shift: 0.97 1.18 ...... Frame ( 26) shift: 0.96 1.21 ...... Frame ( 27) shift: 0.98 1.24 ...... Frame ( 28) shift: 1.01 1.26 ...... Frame ( 29) shift: 1.05 1.27 ...... Frame ( 30) shift: 1.06 1.28 ...... Frame ( 31) shift: 1.03 1.28 ...... Frame ( 32) shift: 1.00 1.28 ...... Frame ( 33) shift: 1.02 1.34 ...... Frame ( 34) shift: 1.08 1.48 ...... Frame ( 35) shift: 1.14 1.62 ...... Frame ( 36) shift: 1.21 1.67 ...... Frame ( 37) shift: 1.28 1.63 ...... Frame ( 38) shift: 1.36 1.59 ...... Frame ( 39) shift: 1.43 1.55 ...... Frame ( 40) shift: 1.51 1.51 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.018898 Iteration 2 Error: 0.280778 Iteration 3 Error: 0.034158 Align patch 2 23 left Iteration 1 Error: 0.913231 Iteration 2 Error: 0.218035 Iteration 3 Error: 0.085199 Iteration 4 Error: 0.037186 Align patch 3 22 left Iteration 1 Error: 0.807669 Iteration 2 Error: 0.182826 Iteration 3 Error: 0.081974 Iteration 4 Error: 0.037304 Align patch 4 21 left Iteration 1 Error: 0.996239 Iteration 2 Error: 0.155893 Iteration 3 Error: 0.062599 Iteration 4 Error: 0.018100 Align patch 5 20 left Iteration 1 Error: 0.585816 Iteration 2 Error: 0.096055 Iteration 3 Error: 0.036074 Align patch 6 19 left Iteration 1 Error: 0.707802 Iteration 2 Error: 0.129892 Iteration 3 Error: 0.046347 Align patch 7 18 left Iteration 1 Error: 0.540262 Iteration 2 Error: 0.164198 Iteration 3 Error: 0.054040 Iteration 4 Error: 0.018307 Align patch 8 17 left Iteration 1 Error: 0.590805 Iteration 2 Error: 0.102953 Iteration 3 Error: 0.019640 Align patch 9 16 left Iteration 1 Error: 0.523332 Iteration 2 Error: 0.072817 Iteration 3 Error: 0.013043 Align patch 10 15 left Iteration 1 Error: 0.678789 Iteration 2 Error: 0.105047 Iteration 3 Error: 0.027825 Align patch 11 14 left Iteration 1 Error: 0.842962 Iteration 2 Error: 0.152602 Iteration 3 Error: 0.055625 Iteration 4 Error: 0.028381 Align patch 12 13 left Iteration 1 Error: 0.847477 Iteration 2 Error: 0.147640 Iteration 3 Error: 0.047716 Align patch 13 12 left Iteration 1 Error: 0.906096 Iteration 2 Error: 0.107166 Iteration 3 Error: 0.023963 Align patch 14 11 left Iteration 1 Error: 0.569463 Iteration 2 Error: 0.077567 Iteration 3 Error: 0.015732 Align patch 15 10 left Iteration 1 Error: 0.868421 Iteration 2 Error: 0.088756 Iteration 3 Error: 0.020723 Align patch 16 9 left Iteration 1 Error: 0.734475 Iteration 2 Error: 0.133318 Iteration 3 Error: 0.035866 Align patch 17 8 left Iteration 1 Error: 0.814326 Iteration 2 Error: 0.225382 Iteration 3 Error: 0.059832 Iteration 4 Error: 0.027547 Align patch 18 7 left Iteration 1 Error: 0.678058 Iteration 2 Error: 0.075946 Iteration 3 Error: 0.013875 Align patch 19 6 left Iteration 1 Error: 0.747082 Iteration 2 Error: 0.107353 Iteration 3 Error: 0.019257 Align patch 20 5 left Iteration 1 Error: 1.021299 Iteration 2 Error: 0.280520 Iteration 3 Error: 0.046250 Align patch 21 4 left Iteration 1 Error: 0.712247 Iteration 2 Error: 0.127034 Iteration 3 Error: 0.029266 Align patch 22 3 left Iteration 1 Error: 0.902615 Iteration 2 Error: 0.222242 Iteration 3 Error: 0.057708 Iteration 4 Error: 0.020180 Align patch 23 2 left Iteration 1 Error: 0.641023 Iteration 2 Error: 0.104541 Iteration 3 Error: 0.020583 Align patch 24 1 left Iteration 1 Error: 0.639502 Iteration 2 Error: 0.080392 Iteration 3 Error: 0.016961 Align patch 25 0 left Iteration 1 Error: 0.751874 Iteration 2 Error: 0.155013 Iteration 3 Error: 0.022424 3D Fitting completed. Patch alignment time: 12.02(sec) Local motion has been corrected. Process thread exits. Computational time: 22.976650 sec Total time: 31.234602 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00019hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00019hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.763989s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00019hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.612945s ........................................ >>>>>>TIME<<<<<< FFT: 0.992356s Defocus_U Defocus_V Angle CCC 10662.11 10025.39 85.91 0.044585 Final Values Defocus_U Defocus_V Angle CCC 10683.99 10028.51 85.91 0.078519 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00020hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00020hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 39.64 6.77 Num Hot pixels: 241 Hot pixel threshold: 80.28 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.371653 Iteration 2 Error: 0.240991 Iteration 3 Error: 0.060993 Iteration 4 Error: 0.015142 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.18 -0.04 ...... Frame ( 3) shift: -0.37 -0.07 ...... Frame ( 4) shift: -0.55 -0.11 ...... Frame ( 5) shift: -0.74 -0.14 ...... Frame ( 6) shift: -0.81 -0.10 ...... Frame ( 7) shift: -0.75 0.01 ...... Frame ( 8) shift: -0.70 0.13 ...... Frame ( 9) shift: -0.64 0.19 ...... Frame ( 10) shift: -0.58 0.20 ...... Frame ( 11) shift: -0.51 0.21 ...... Frame ( 12) shift: -0.46 0.24 ...... Frame ( 13) shift: -0.41 0.29 ...... Frame ( 14) shift: -0.36 0.34 ...... Frame ( 15) shift: -0.29 0.41 ...... Frame ( 16) shift: -0.19 0.51 ...... Frame ( 17) shift: -0.09 0.61 ...... Frame ( 18) shift: -0.03 0.68 ...... Frame ( 19) shift: 0.00 0.72 ...... Frame ( 20) shift: 0.03 0.76 ...... Frame ( 21) shift: 0.09 0.82 ...... Frame ( 22) shift: 0.17 0.91 ...... Frame ( 23) shift: 0.26 1.00 ...... Frame ( 24) shift: 0.30 1.12 ...... Frame ( 25) shift: 0.30 1.27 ...... Frame ( 26) shift: 0.30 1.41 ...... Frame ( 27) shift: 0.33 1.54 ...... Frame ( 28) shift: 0.40 1.63 ...... Frame ( 29) shift: 0.47 1.73 ...... Frame ( 30) shift: 0.50 1.81 ...... Frame ( 31) shift: 0.49 1.88 ...... Frame ( 32) shift: 0.48 1.94 ...... Frame ( 33) shift: 0.48 2.01 ...... Frame ( 34) shift: 0.51 2.07 ...... Frame ( 35) shift: 0.53 2.14 ...... Frame ( 36) shift: 0.57 2.19 ...... Frame ( 37) shift: 0.63 2.22 ...... Frame ( 38) shift: 0.69 2.25 ...... Frame ( 39) shift: 0.75 2.28 ...... Frame ( 40) shift: 0.81 2.31 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.584264 Iteration 2 Error: 0.210194 Iteration 3 Error: 0.064934 Iteration 4 Error: 0.029596 Align patch 2 23 left Iteration 1 Error: 0.897425 Iteration 2 Error: 0.151646 Iteration 3 Error: 0.037341 Align patch 3 22 left Iteration 1 Error: 0.488504 Iteration 2 Error: 0.092722 Iteration 3 Error: 0.021743 Align patch 4 21 left Iteration 1 Error: 0.669521 Iteration 2 Error: 0.081710 Iteration 3 Error: 0.021027 Align patch 5 20 left Iteration 1 Error: 0.517269 Iteration 2 Error: 0.095289 Iteration 3 Error: 0.019820 Align patch 6 19 left Iteration 1 Error: 1.024405 Iteration 2 Error: 0.205629 Iteration 3 Error: 0.042424 Align patch 7 18 left Iteration 1 Error: 0.705842 Iteration 2 Error: 0.100441 Iteration 3 Error: 0.020988 Align patch 8 17 left Iteration 1 Error: 0.601575 Iteration 2 Error: 0.075237 Iteration 3 Error: 0.009040 Align patch 9 16 left Iteration 1 Error: 0.822051 Iteration 2 Error: 0.146058 Iteration 3 Error: 0.036110 Align patch 10 15 left Iteration 1 Error: 0.610759 Iteration 2 Error: 0.062082 Iteration 3 Error: 0.014239 Align patch 11 14 left Iteration 1 Error: 0.734448 Iteration 2 Error: 0.124329 Iteration 3 Error: 0.025684 Align patch 12 13 left Iteration 1 Error: 0.412644 Iteration 2 Error: 0.042335 Align patch 13 12 left Iteration 1 Error: 0.666310 Iteration 2 Error: 0.106564 Iteration 3 Error: 0.020591 Align patch 14 11 left Iteration 1 Error: 0.490569 Iteration 2 Error: 0.076181 Iteration 3 Error: 0.019334 Align patch 15 10 left Iteration 1 Error: 0.583289 Iteration 2 Error: 0.038075 Align patch 16 9 left Iteration 1 Error: 0.842358 Iteration 2 Error: 0.101201 Iteration 3 Error: 0.020168 Align patch 17 8 left Iteration 1 Error: 0.488308 Iteration 2 Error: 0.108069 Iteration 3 Error: 0.019193 Align patch 18 7 left Iteration 1 Error: 0.676578 Iteration 2 Error: 0.057588 Iteration 3 Error: 0.014388 Align patch 19 6 left Iteration 1 Error: 0.478935 Iteration 2 Error: 0.065870 Iteration 3 Error: 0.015962 Align patch 20 5 left Iteration 1 Error: 0.569373 Iteration 2 Error: 0.053501 Iteration 3 Error: 0.009890 Align patch 21 4 left Iteration 1 Error: 0.669291 Iteration 2 Error: 0.065645 Iteration 3 Error: 0.010629 Align patch 22 3 left Iteration 1 Error: 0.425794 Iteration 2 Error: 0.091007 Iteration 3 Error: 0.016457 Align patch 23 2 left Iteration 1 Error: 0.601212 Iteration 2 Error: 0.079272 Iteration 3 Error: 0.014099 Align patch 24 1 left Iteration 1 Error: 0.687605 Iteration 2 Error: 0.102026 Iteration 3 Error: 0.026866 Align patch 25 0 left Iteration 1 Error: 0.386887 Iteration 2 Error: 0.063295 Iteration 3 Error: 0.014268 3D Fitting completed. Patch alignment time: 12.28(sec) Local motion has been corrected. Process thread exits. Computational time: 24.483343 sec Total time: 30.538424 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00020hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00020hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.786731s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00020hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.546731s ........................................ >>>>>>TIME<<<<<< FFT: 0.961084s Defocus_U Defocus_V Angle CCC 10298.85 11209.02 13.01 0.060265 Final Values Defocus_U Defocus_V Angle CCC 10305.10 11234.03 12.70 0.098499 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00020hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00020hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 39.75 6.75 Num Hot pixels: 254 Hot pixel threshold: 80.26 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.153345 Iteration 2 Error: 0.211576 Iteration 3 Error: 0.043703 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.13 0.05 ...... Frame ( 3) shift: -0.27 0.10 ...... Frame ( 4) shift: -0.40 0.15 ...... Frame ( 5) shift: -0.54 0.19 ...... Frame ( 6) shift: -0.61 0.26 ...... Frame ( 7) shift: -0.64 0.36 ...... Frame ( 8) shift: -0.66 0.45 ...... Frame ( 9) shift: -0.65 0.56 ...... Frame ( 10) shift: -0.62 0.69 ...... Frame ( 11) shift: -0.58 0.82 ...... Frame ( 12) shift: -0.59 0.91 ...... Frame ( 13) shift: -0.63 0.98 ...... Frame ( 14) shift: -0.68 1.04 ...... Frame ( 15) shift: -0.68 1.12 ...... Frame ( 16) shift: -0.63 1.19 ...... Frame ( 17) shift: -0.58 1.27 ...... Frame ( 18) shift: -0.55 1.33 ...... Frame ( 19) shift: -0.55 1.38 ...... Frame ( 20) shift: -0.54 1.43 ...... Frame ( 21) shift: -0.52 1.47 ...... Frame ( 22) shift: -0.47 1.50 ...... Frame ( 23) shift: -0.43 1.54 ...... Frame ( 24) shift: -0.40 1.59 ...... Frame ( 25) shift: -0.38 1.65 ...... Frame ( 26) shift: -0.37 1.70 ...... Frame ( 27) shift: -0.36 1.77 ...... Frame ( 28) shift: -0.35 1.84 ...... Frame ( 29) shift: -0.34 1.90 ...... Frame ( 30) shift: -0.31 1.97 ...... Frame ( 31) shift: -0.27 2.02 ...... Frame ( 32) shift: -0.23 2.08 ...... Frame ( 33) shift: -0.20 2.13 ...... Frame ( 34) shift: -0.17 2.17 ...... Frame ( 35) shift: -0.14 2.20 ...... Frame ( 36) shift: -0.14 2.25 ...... Frame ( 37) shift: -0.15 2.31 ...... Frame ( 38) shift: -0.16 2.36 ...... Frame ( 39) shift: -0.17 2.42 ...... Frame ( 40) shift: -0.18 2.47 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.963341 Iteration 2 Error: 0.257638 Iteration 3 Error: 0.052988 Iteration 4 Error: 0.023448 Align patch 2 23 left Iteration 1 Error: 0.630202 Iteration 2 Error: 0.135059 Iteration 3 Error: 0.021350 Align patch 3 22 left Iteration 1 Error: 0.691188 Iteration 2 Error: 0.131439 Iteration 3 Error: 0.032179 Align patch 4 21 left Iteration 1 Error: 0.428529 Iteration 2 Error: 0.081026 Iteration 3 Error: 0.019936 Align patch 5 20 left Iteration 1 Error: 0.565670 Iteration 2 Error: 0.123362 Iteration 3 Error: 0.029858 Align patch 6 19 left Iteration 1 Error: 0.492740 Iteration 2 Error: 0.123583 Iteration 3 Error: 0.033257 Align patch 7 18 left Iteration 1 Error: 0.565106 Iteration 2 Error: 0.118643 Iteration 3 Error: 0.025285 Align patch 8 17 left Iteration 1 Error: 0.789008 Iteration 2 Error: 0.148180 Iteration 3 Error: 0.042483 Align patch 9 16 left Iteration 1 Error: 0.506581 Iteration 2 Error: 0.056869 Iteration 3 Error: 0.015671 Align patch 10 15 left Iteration 1 Error: 0.554104 Iteration 2 Error: 0.092210 Iteration 3 Error: 0.025213 Align patch 11 14 left Iteration 1 Error: 0.770517 Iteration 2 Error: 0.136332 Iteration 3 Error: 0.035061 Align patch 12 13 left Iteration 1 Error: 1.200036 Iteration 2 Error: 0.146029 Iteration 3 Error: 0.035724 Align patch 13 12 left Iteration 1 Error: 0.580964 Iteration 2 Error: 0.069675 Iteration 3 Error: 0.021006 Align patch 14 11 left Iteration 1 Error: 0.858750 Iteration 2 Error: 0.104598 Iteration 3 Error: 0.027624 Align patch 15 10 left Iteration 1 Error: 0.688247 Iteration 2 Error: 0.152166 Iteration 3 Error: 0.034471 Align patch 16 9 left Iteration 1 Error: 0.895435 Iteration 2 Error: 0.132168 Iteration 3 Error: 0.032360 Align patch 17 8 left Iteration 1 Error: 0.841119 Iteration 2 Error: 0.122460 Iteration 3 Error: 0.041849 Align patch 18 7 left Iteration 1 Error: 0.507981 Iteration 2 Error: 0.105217 Iteration 3 Error: 0.028818 Align patch 19 6 left Iteration 1 Error: 0.561059 Iteration 2 Error: 0.082287 Iteration 3 Error: 0.017069 Align patch 20 5 left Iteration 1 Error: 0.710043 Iteration 2 Error: 0.116176 Iteration 3 Error: 0.032532 Align patch 21 4 left Iteration 1 Error: 0.891187 Iteration 2 Error: 0.155672 Iteration 3 Error: 0.030793 Align patch 22 3 left Iteration 1 Error: 0.743597 Iteration 2 Error: 0.144075 Iteration 3 Error: 0.021336 Align patch 23 2 left Iteration 1 Error: 0.810950 Iteration 2 Error: 0.102485 Iteration 3 Error: 0.025743 Align patch 24 1 left Iteration 1 Error: 0.617516 Iteration 2 Error: 0.081498 Iteration 3 Error: 0.022187 Align patch 25 0 left Iteration 1 Error: 0.492259 Iteration 2 Error: 0.091651 Iteration 3 Error: 0.013545 3D Fitting completed. Patch alignment time: 12.29(sec) Local motion has been corrected. Process thread exits. Computational time: 24.461691 sec Total time: 31.966604 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00020hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00020hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.466432s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00020hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.712187s ........................................ >>>>>>TIME<<<<<< FFT: 1.055276s Defocus_U Defocus_V Angle CCC 11650.38 12189.47 2.16 0.042933 Final Values Defocus_U Defocus_V Angle CCC 11659.75 12217.60 2.48 0.070191 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00020hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00020hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 40.16 6.79 Num Hot pixels: 229 Hot pixel threshold: 80.88 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.741911 Iteration 2 Error: 0.122958 Iteration 3 Error: 0.024226 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.00 0.04 ...... Frame ( 3) shift: 0.00 0.07 ...... Frame ( 4) shift: 0.00 0.11 ...... Frame ( 5) shift: 0.00 0.15 ...... Frame ( 6) shift: 0.05 0.17 ...... Frame ( 7) shift: 0.14 0.18 ...... Frame ( 8) shift: 0.22 0.19 ...... Frame ( 9) shift: 0.28 0.24 ...... Frame ( 10) shift: 0.30 0.32 ...... Frame ( 11) shift: 0.32 0.41 ...... Frame ( 12) shift: 0.35 0.46 ...... Frame ( 13) shift: 0.39 0.48 ...... Frame ( 14) shift: 0.43 0.50 ...... Frame ( 15) shift: 0.44 0.54 ...... Frame ( 16) shift: 0.43 0.61 ...... Frame ( 17) shift: 0.41 0.67 ...... Frame ( 18) shift: 0.38 0.73 ...... Frame ( 19) shift: 0.33 0.77 ...... Frame ( 20) shift: 0.28 0.82 ...... Frame ( 21) shift: 0.30 0.84 ...... Frame ( 22) shift: 0.39 0.86 ...... Frame ( 23) shift: 0.49 0.87 ...... Frame ( 24) shift: 0.56 0.88 ...... Frame ( 25) shift: 0.60 0.88 ...... Frame ( 26) shift: 0.65 0.89 ...... Frame ( 27) shift: 0.70 0.89 ...... Frame ( 28) shift: 0.76 0.89 ...... Frame ( 29) shift: 0.81 0.89 ...... Frame ( 30) shift: 0.84 0.92 ...... Frame ( 31) shift: 0.85 0.98 ...... Frame ( 32) shift: 0.85 1.03 ...... Frame ( 33) shift: 0.84 1.07 ...... Frame ( 34) shift: 0.83 1.08 ...... Frame ( 35) shift: 0.82 1.09 ...... Frame ( 36) shift: 0.85 1.12 ...... Frame ( 37) shift: 0.92 1.17 ...... Frame ( 38) shift: 0.99 1.23 ...... Frame ( 39) shift: 1.05 1.28 ...... Frame ( 40) shift: 1.12 1.34 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.793928 Iteration 2 Error: 0.149835 Iteration 3 Error: 0.026533 Align patch 2 23 left Iteration 1 Error: 1.109285 Iteration 2 Error: 0.086144 Iteration 3 Error: 0.025363 Align patch 3 22 left Iteration 1 Error: 0.543860 Iteration 2 Error: 0.046247 Align patch 4 21 left Iteration 1 Error: 0.768107 Iteration 2 Error: 0.120215 Iteration 3 Error: 0.032785 Align patch 5 20 left Iteration 1 Error: 0.544136 Iteration 2 Error: 0.082493 Iteration 3 Error: 0.019166 Align patch 6 19 left Iteration 1 Error: 0.623794 Iteration 2 Error: 0.224941 Iteration 3 Error: 0.063153 Iteration 4 Error: 0.026649 Align patch 7 18 left Iteration 1 Error: 0.845304 Iteration 2 Error: 0.165045 Iteration 3 Error: 0.036037 Align patch 8 17 left Iteration 1 Error: 0.643881 Iteration 2 Error: 0.094477 Iteration 3 Error: 0.017252 Align patch 9 16 left Iteration 1 Error: 0.815527 Iteration 2 Error: 0.062448 Iteration 3 Error: 0.019425 Align patch 10 15 left Iteration 1 Error: 0.586062 Iteration 2 Error: 0.147978 Iteration 3 Error: 0.034926 Align patch 11 14 left Iteration 1 Error: 0.565397 Iteration 2 Error: 0.069060 Iteration 3 Error: 0.016797 Align patch 12 13 left Iteration 1 Error: 0.693053 Iteration 2 Error: 0.204109 Iteration 3 Error: 0.052206 Iteration 4 Error: 0.018290 Align patch 13 12 left Iteration 1 Error: 0.621541 Iteration 2 Error: 0.085546 Iteration 3 Error: 0.027855 Align patch 14 11 left Iteration 1 Error: 0.630656 Iteration 2 Error: 0.101500 Iteration 3 Error: 0.016403 Align patch 15 10 left Iteration 1 Error: 0.699811 Iteration 2 Error: 0.167171 Iteration 3 Error: 0.039436 Align patch 16 9 left Iteration 1 Error: 0.696897 Iteration 2 Error: 0.098440 Iteration 3 Error: 0.027771 Align patch 17 8 left Iteration 1 Error: 0.500936 Iteration 2 Error: 0.092215 Iteration 3 Error: 0.017898 Align patch 18 7 left Iteration 1 Error: 0.560121 Iteration 2 Error: 0.078197 Iteration 3 Error: 0.012127 Align patch 19 6 left Iteration 1 Error: 0.433789 Iteration 2 Error: 0.082411 Iteration 3 Error: 0.014707 Align patch 20 5 left Iteration 1 Error: 0.603410 Iteration 2 Error: 0.094478 Iteration 3 Error: 0.019846 Align patch 21 4 left Iteration 1 Error: 0.802842 Iteration 2 Error: 0.119886 Iteration 3 Error: 0.032536 Align patch 22 3 left Iteration 1 Error: 0.594959 Iteration 2 Error: 0.179213 Iteration 3 Error: 0.029876 Align patch 23 2 left Iteration 1 Error: 0.550995 Iteration 2 Error: 0.077161 Iteration 3 Error: 0.015341 Align patch 24 1 left Iteration 1 Error: 0.689420 Iteration 2 Error: 0.189218 Iteration 3 Error: 0.050412 Iteration 4 Error: 0.018558 Align patch 25 0 left Iteration 1 Error: 0.790216 Iteration 2 Error: 0.152222 Iteration 3 Error: 0.034949 3D Fitting completed. Patch alignment time: 11.95(sec) Local motion has been corrected. Process thread exits. Computational time: 25.298407 sec Total time: 32.025513 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00020hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00020hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.737599s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00020hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.589582s ........................................ >>>>>>TIME<<<<<< FFT: 0.952236s Defocus_U Defocus_V Angle CCC 13398.42 14296.89 1.79 0.049245 Final Values Defocus_U Defocus_V Angle CCC 13390.61 14304.71 1.79 0.076515 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00020hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00020hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.999e-02 CC threshold: 0.734 Mean Std: 38.01 6.55 Num Hot pixels: 211 Hot pixel threshold: 77.33 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.732773 Iteration 2 Error: 0.159768 Iteration 3 Error: 0.043130 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.14 0.12 ...... Frame ( 3) shift: -0.28 0.25 ...... Frame ( 4) shift: -0.42 0.37 ...... Frame ( 5) shift: -0.56 0.49 ...... Frame ( 6) shift: -0.59 0.53 ...... Frame ( 7) shift: -0.52 0.47 ...... Frame ( 8) shift: -0.44 0.42 ...... Frame ( 9) shift: -0.40 0.45 ...... Frame ( 10) shift: -0.40 0.56 ...... Frame ( 11) shift: -0.40 0.68 ...... Frame ( 12) shift: -0.39 0.74 ...... Frame ( 13) shift: -0.37 0.75 ...... Frame ( 14) shift: -0.34 0.77 ...... Frame ( 15) shift: -0.31 0.81 ...... Frame ( 16) shift: -0.28 0.87 ...... Frame ( 17) shift: -0.24 0.94 ...... Frame ( 18) shift: -0.22 1.00 ...... Frame ( 19) shift: -0.24 1.05 ...... Frame ( 20) shift: -0.25 1.10 ...... Frame ( 21) shift: -0.25 1.16 ...... Frame ( 22) shift: -0.23 1.23 ...... Frame ( 23) shift: -0.22 1.30 ...... Frame ( 24) shift: -0.15 1.32 ...... Frame ( 25) shift: -0.03 1.28 ...... Frame ( 26) shift: 0.09 1.24 ...... Frame ( 27) shift: 0.13 1.26 ...... Frame ( 28) shift: 0.11 1.34 ...... Frame ( 29) shift: 0.09 1.42 ...... Frame ( 30) shift: 0.12 1.49 ...... Frame ( 31) shift: 0.22 1.55 ...... Frame ( 32) shift: 0.32 1.61 ...... Frame ( 33) shift: 0.37 1.62 ...... Frame ( 34) shift: 0.35 1.57 ...... Frame ( 35) shift: 0.34 1.52 ...... Frame ( 36) shift: 0.34 1.50 ...... Frame ( 37) shift: 0.35 1.53 ...... Frame ( 38) shift: 0.36 1.56 ...... Frame ( 39) shift: 0.37 1.58 ...... Frame ( 40) shift: 0.39 1.61 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.091704 Iteration 2 Error: 0.201582 Iteration 3 Error: 0.041542 Align patch 2 23 left Iteration 1 Error: 0.872704 Iteration 2 Error: 0.156633 Iteration 3 Error: 0.036419 Align patch 3 22 left Iteration 1 Error: 0.793381 Iteration 2 Error: 0.114902 Iteration 3 Error: 0.023404 Align patch 4 21 left Iteration 1 Error: 0.613737 Iteration 2 Error: 0.158731 Iteration 3 Error: 0.063707 Iteration 4 Error: 0.028728 Align patch 5 20 left Iteration 1 Error: 0.841671 Iteration 2 Error: 0.082410 Iteration 3 Error: 0.026185 Align patch 6 19 left Iteration 1 Error: 1.258579 Iteration 2 Error: 0.210760 Iteration 3 Error: 0.055173 Iteration 4 Error: 0.023173 Align patch 7 18 left Iteration 1 Error: 0.907930 Iteration 2 Error: 0.175334 Iteration 3 Error: 0.033795 Align patch 8 17 left Iteration 1 Error: 1.067587 Iteration 2 Error: 0.244063 Iteration 3 Error: 0.059136 Iteration 4 Error: 0.025522 Align patch 9 16 left Iteration 1 Error: 1.172904 Iteration 2 Error: 0.273147 Iteration 3 Error: 0.091243 Iteration 4 Error: 0.034626 Align patch 10 15 left Iteration 1 Error: 0.735135 Iteration 2 Error: 0.178889 Iteration 3 Error: 0.054173 Iteration 4 Error: 0.011899 Align patch 11 14 left Iteration 1 Error: 2.145770 Iteration 2 Error: 0.227396 Iteration 3 Error: 0.062492 Iteration 4 Error: 0.019699 Align patch 12 13 left Iteration 1 Error: 1.073906 Iteration 2 Error: 0.150287 Iteration 3 Error: 0.033664 Align patch 13 12 left Iteration 1 Error: 0.802065 Iteration 2 Error: 0.135420 Iteration 3 Error: 0.040579 Align patch 14 11 left Iteration 1 Error: 0.723433 Iteration 2 Error: 0.132792 Iteration 3 Error: 0.044077 Align patch 15 10 left Iteration 1 Error: 0.697830 Iteration 2 Error: 0.119901 Iteration 3 Error: 0.021170 Align patch 16 9 left Iteration 1 Error: 1.019735 Iteration 2 Error: 0.325935 Iteration 3 Error: 0.111858 Iteration 4 Error: 0.030728 Align patch 17 8 left Iteration 1 Error: 0.744420 Iteration 2 Error: 0.099541 Iteration 3 Error: 0.046888 Align patch 18 7 left Iteration 1 Error: 0.513463 Iteration 2 Error: 0.180312 Iteration 3 Error: 0.059184 Iteration 4 Error: 0.023312 Align patch 19 6 left Iteration 1 Error: 1.083820 Iteration 2 Error: 0.170452 Iteration 3 Error: 0.073967 Iteration 4 Error: 0.028492 Align patch 20 5 left Iteration 1 Error: 0.996474 Iteration 2 Error: 0.224481 Iteration 3 Error: 0.029663 Align patch 21 4 left Iteration 1 Error: 1.168208 Iteration 2 Error: 0.288747 Iteration 3 Error: 0.086094 Iteration 4 Error: 0.028774 Align patch 22 3 left Iteration 1 Error: 1.050711 Iteration 2 Error: 0.221537 Iteration 3 Error: 0.085453 Iteration 4 Error: 0.029426 Align patch 23 2 left Iteration 1 Error: 0.873233 Iteration 2 Error: 0.123797 Iteration 3 Error: 0.035095 Align patch 24 1 left Iteration 1 Error: 0.670816 Iteration 2 Error: 0.216977 Iteration 3 Error: 0.038020 Align patch 25 0 left Iteration 1 Error: 1.053546 Iteration 2 Error: 0.238128 Iteration 3 Error: 0.097109 Iteration 4 Error: 0.029558 3D Fitting completed. Patch alignment time: 13.54(sec) Local motion has been corrected. Process thread exits. Computational time: 24.881060 sec Total time: 31.118696 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00020hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00020hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.581726s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00020hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.315146s ........................................ >>>>>>TIME<<<<<< FFT: 1.012589s Defocus_U Defocus_V Angle CCC 11054.83 10418.01 72.69 0.024103 Final Values Defocus_U Defocus_V Angle CCC 11032.97 10458.72 67.82 0.039779 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00021hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00021hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.371e-01 1.018e-01 CC threshold: 0.748 Mean Std: 12.50 11.70 Num Hot pixels: 27 Hot pixel threshold: 82.67 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.656686 Iteration 2 Error: 0.211247 Iteration 3 Error: 0.042088 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.08 0.05 ...... Frame ( 3) shift: 0.15 0.09 ...... Frame ( 4) shift: 0.23 0.14 ...... Frame ( 5) shift: 0.31 0.19 ...... Frame ( 6) shift: 0.36 0.20 ...... Frame ( 7) shift: 0.40 0.18 ...... Frame ( 8) shift: 0.44 0.15 ...... Frame ( 9) shift: 0.48 0.17 ...... Frame ( 10) shift: 0.52 0.24 ...... Frame ( 11) shift: 0.56 0.30 ...... Frame ( 12) shift: 0.61 0.34 ...... Frame ( 13) shift: 0.66 0.37 ...... Frame ( 14) shift: 0.71 0.40 ...... Frame ( 15) shift: 0.76 0.43 ...... Frame ( 16) shift: 0.82 0.46 ...... Frame ( 17) shift: 0.88 0.49 ...... Frame ( 18) shift: 0.89 0.53 ...... Frame ( 19) shift: 0.86 0.56 ...... Frame ( 20) shift: 0.82 0.60 ...... Frame ( 21) shift: 0.86 0.68 ...... Frame ( 22) shift: 0.96 0.83 ...... Frame ( 23) shift: 1.07 0.97 ...... Frame ( 24) shift: 1.12 1.03 ...... Frame ( 25) shift: 1.14 0.99 ...... Frame ( 26) shift: 1.15 0.96 ...... Frame ( 27) shift: 1.15 0.95 ...... Frame ( 28) shift: 1.15 0.94 ...... Frame ( 29) shift: 1.15 0.94 ...... Frame ( 30) shift: 1.17 0.91 ...... Frame ( 31) shift: 1.22 0.84 ...... Frame ( 32) shift: 1.26 0.78 ...... Frame ( 33) shift: 1.36 0.75 ...... Frame ( 34) shift: 1.51 0.76 ...... Frame ( 35) shift: 1.67 0.76 ...... Frame ( 36) shift: 1.84 0.83 ...... Frame ( 37) shift: 2.02 0.95 ...... Frame ( 38) shift: 2.21 1.07 ...... Frame ( 39) shift: 2.40 1.19 ...... Frame ( 40) shift: 2.59 1.32 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.347833 Iteration 2 Error: 0.330860 Iteration 3 Error: 0.103538 Iteration 4 Error: 0.041234 Align patch 2 23 left Iteration 1 Error: 0.589512 Iteration 2 Error: 0.034456 Align patch 3 22 left Iteration 1 Error: 0.453800 Iteration 2 Error: 0.037915 Align patch 4 21 left Iteration 1 Error: 0.895242 Iteration 2 Error: 0.136380 Iteration 3 Error: 0.022887 Align patch 5 20 left Iteration 1 Error: 0.674637 Iteration 2 Error: 0.120277 Iteration 3 Error: 0.029677 Align patch 6 19 left Iteration 1 Error: 0.796433 Iteration 2 Error: 0.164447 Iteration 3 Error: 0.031908 Align patch 7 18 left Iteration 1 Error: 0.565442 Iteration 2 Error: 0.101923 Iteration 3 Error: 0.019406 Align patch 8 17 left Iteration 1 Error: 0.414008 Iteration 2 Error: 0.106408 Iteration 3 Error: 0.024577 Align patch 9 16 left Iteration 1 Error: 0.688546 Iteration 2 Error: 0.121205 Iteration 3 Error: 0.022299 Align patch 10 15 left Iteration 1 Error: 0.838498 Iteration 2 Error: 0.051247 Iteration 3 Error: 0.007555 Align patch 11 14 left Iteration 1 Error: 0.607371 Iteration 2 Error: 0.107400 Iteration 3 Error: 0.015957 Align patch 12 13 left Iteration 1 Error: 0.600538 Iteration 2 Error: 0.225949 Iteration 3 Error: 0.073027 Iteration 4 Error: 0.026631 Align patch 13 12 left Iteration 1 Error: 0.533308 Iteration 2 Error: 0.062652 Iteration 3 Error: 0.007464 Align patch 14 11 left Iteration 1 Error: 0.642474 Iteration 2 Error: 0.041070 Align patch 15 10 left Iteration 1 Error: 1.002833 Iteration 2 Error: 0.079300 Iteration 3 Error: 0.009652 Align patch 16 9 left Iteration 1 Error: 0.198998 Iteration 2 Error: 0.057793 Iteration 3 Error: 0.016600 Align patch 17 8 left Iteration 1 Error: 0.608497 Iteration 2 Error: 0.206493 Iteration 3 Error: 0.058898 Iteration 4 Error: 0.018711 Align patch 18 7 left Iteration 1 Error: 1.347592 Iteration 2 Error: 0.084837 Iteration 3 Error: 0.011087 Align patch 19 6 left Iteration 1 Error: 1.613362 Iteration 2 Error: 0.150814 Iteration 3 Error: 0.042181 Align patch 20 5 left Iteration 1 Error: 0.789536 Iteration 2 Error: 0.059586 Iteration 3 Error: 0.007510 Align patch 21 4 left Iteration 1 Error: 0.329164 Iteration 2 Error: 0.129549 Iteration 3 Error: 0.051771 Iteration 4 Error: 0.020411 Align patch 22 3 left Iteration 1 Error: 0.643189 Iteration 2 Error: 0.065490 Iteration 3 Error: 0.006433 Align patch 23 2 left Iteration 1 Error: 1.307830 Iteration 2 Error: 0.067916 Iteration 3 Error: 0.008805 Align patch 24 1 left Iteration 1 Error: 0.805126 Iteration 2 Error: 0.081183 Iteration 3 Error: 0.011206 Align patch 25 0 left Iteration 1 Error: 0.661359 Iteration 2 Error: 0.060431 Iteration 3 Error: 0.006781 3D Fitting completed. Patch alignment time: 11.13(sec) Local motion has been corrected. Process thread exits. Computational time: 23.301744 sec Total time: 30.652391 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00021hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00021hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.760865s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00021hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.933928s ........................................ >>>>>>TIME<<<<<< FFT: 0.956097s Defocus_U Defocus_V Angle CCC 9855.51 10703.17 10.47 0.024745 Final Values Defocus_U Defocus_V Angle CCC 9891.48 10726.63 9.53 0.048337 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00022hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00022hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 34.87 6.28 Num Hot pixels: 230 Hot pixel threshold: 72.55 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.371716 Iteration 2 Error: 0.170113 Iteration 3 Error: 0.035194 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.12 0.20 ...... Frame ( 3) shift: -0.24 0.40 ...... Frame ( 4) shift: -0.36 0.61 ...... Frame ( 5) shift: -0.47 0.81 ...... Frame ( 6) shift: -0.50 0.95 ...... Frame ( 7) shift: -0.44 1.04 ...... Frame ( 8) shift: -0.38 1.12 ...... Frame ( 9) shift: -0.34 1.19 ...... Frame ( 10) shift: -0.33 1.25 ...... Frame ( 11) shift: -0.32 1.30 ...... Frame ( 12) shift: -0.31 1.37 ...... Frame ( 13) shift: -0.30 1.45 ...... Frame ( 14) shift: -0.28 1.53 ...... Frame ( 15) shift: -0.25 1.60 ...... Frame ( 16) shift: -0.20 1.65 ...... Frame ( 17) shift: -0.15 1.71 ...... Frame ( 18) shift: -0.11 1.77 ...... Frame ( 19) shift: -0.09 1.83 ...... Frame ( 20) shift: -0.06 1.88 ...... Frame ( 21) shift: -0.07 1.95 ...... Frame ( 22) shift: -0.11 2.01 ...... Frame ( 23) shift: -0.15 2.08 ...... Frame ( 24) shift: -0.12 2.13 ...... Frame ( 25) shift: -0.02 2.16 ...... Frame ( 26) shift: 0.08 2.18 ...... Frame ( 27) shift: 0.13 2.22 ...... Frame ( 28) shift: 0.13 2.26 ...... Frame ( 29) shift: 0.14 2.30 ...... Frame ( 30) shift: 0.19 2.34 ...... Frame ( 31) shift: 0.29 2.35 ...... Frame ( 32) shift: 0.39 2.37 ...... Frame ( 33) shift: 0.38 2.42 ...... Frame ( 34) shift: 0.28 2.50 ...... Frame ( 35) shift: 0.18 2.57 ...... Frame ( 36) shift: 0.17 2.60 ...... Frame ( 37) shift: 0.26 2.59 ...... Frame ( 38) shift: 0.35 2.57 ...... Frame ( 39) shift: 0.44 2.56 ...... Frame ( 40) shift: 0.53 2.55 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.189536 Iteration 2 Error: 0.238232 Iteration 3 Error: 0.084607 Iteration 4 Error: 0.037742 Align patch 2 23 left Iteration 1 Error: 0.805210 Iteration 2 Error: 0.264630 Iteration 3 Error: 0.069815 Iteration 4 Error: 0.045128 Align patch 3 22 left Iteration 1 Error: 0.851251 Iteration 2 Error: 0.228879 Iteration 3 Error: 0.057438 Iteration 4 Error: 0.021759 Align patch 4 21 left Iteration 1 Error: 0.721254 Iteration 2 Error: 0.168723 Iteration 3 Error: 0.057251 Iteration 4 Error: 0.031587 Align patch 5 20 left Iteration 1 Error: 1.013320 Iteration 2 Error: 0.156713 Iteration 3 Error: 0.057302 Iteration 4 Error: 0.019812 Align patch 6 19 left Iteration 1 Error: 1.418756 Iteration 2 Error: 0.271442 Iteration 3 Error: 0.078450 Iteration 4 Error: 0.037137 Align patch 7 18 left Iteration 1 Error: 0.822590 Iteration 2 Error: 0.158112 Iteration 3 Error: 0.035600 Align patch 8 17 left Iteration 1 Error: 0.971591 Iteration 2 Error: 0.213302 Iteration 3 Error: 0.074192 Iteration 4 Error: 0.038974 Align patch 9 16 left Iteration 1 Error: 0.767414 Iteration 2 Error: 0.169140 Iteration 3 Error: 0.032140 Align patch 10 15 left Iteration 1 Error: 0.974444 Iteration 2 Error: 0.102130 Iteration 3 Error: 0.031172 Align patch 11 14 left Iteration 1 Error: 1.689098 Iteration 2 Error: 0.391500 Iteration 3 Error: 0.081174 Iteration 4 Error: 0.030149 Align patch 12 13 left Iteration 1 Error: 1.105979 Iteration 2 Error: 0.164057 Iteration 3 Error: 0.036676 Align patch 13 12 left Iteration 1 Error: 0.668270 Iteration 2 Error: 0.123638 Iteration 3 Error: 0.028710 Align patch 14 11 left Iteration 1 Error: 0.647646 Iteration 2 Error: 0.124461 Iteration 3 Error: 0.035477 Align patch 15 10 left Iteration 1 Error: 0.992687 Iteration 2 Error: 0.213055 Iteration 3 Error: 0.041447 Align patch 16 9 left Iteration 1 Error: 0.662554 Iteration 2 Error: 0.176149 Iteration 3 Error: 0.056407 Iteration 4 Error: 0.015299 Align patch 17 8 left Iteration 1 Error: 1.604033 Iteration 2 Error: 0.406302 Iteration 3 Error: 0.128658 Iteration 4 Error: 0.037198 Align patch 18 7 left Iteration 1 Error: 1.273322 Iteration 2 Error: 0.194576 Iteration 3 Error: 0.053887 Iteration 4 Error: 0.018388 Align patch 19 6 left Iteration 1 Error: 1.359569 Iteration 2 Error: 0.180483 Iteration 3 Error: 0.027012 Align patch 20 5 left Iteration 1 Error: 1.002784 Iteration 2 Error: 0.205613 Iteration 3 Error: 0.075409 Iteration 4 Error: 0.023785 Align patch 21 4 left Iteration 1 Error: 1.850418 Iteration 2 Error: 0.229630 Iteration 3 Error: 0.077775 Iteration 4 Error: 0.013840 Align patch 22 3 left Iteration 1 Error: 0.906564 Iteration 2 Error: 0.210649 Iteration 3 Error: 0.053947 Iteration 4 Error: 0.012338 Align patch 23 2 left Iteration 1 Error: 1.035709 Iteration 2 Error: 0.209931 Iteration 3 Error: 0.046848 Align patch 24 1 left Iteration 1 Error: 1.005294 Iteration 2 Error: 0.141659 Iteration 3 Error: 0.033986 Align patch 25 0 left Iteration 1 Error: 0.844787 Iteration 2 Error: 0.462412 Iteration 3 Error: 0.244782 Iteration 4 Error: 0.139518 Iteration 5 Error: 0.070673 Align patch 25 0 left Iteration 1 Error: 0.990519 Iteration 2 Error: 0.366420 Iteration 3 Error: 0.152809 Iteration 4 Error: 0.051614 Iteration 5 Error: 0.015746 3D Fitting completed. Patch alignment time: 13.29(sec) Local motion has been corrected. Process thread exits. Computational time: 26.240545 sec Total time: 33.058456 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00022hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00022hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.613823s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00022hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.092387s ........................................ >>>>>>TIME<<<<<< FFT: 0.959203s Defocus_U Defocus_V Angle CCC 10654.29 11345.71 16.50 0.020959 Final Values Defocus_U Defocus_V Angle CCC 10576.17 11280.09 16.19 0.031657 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00004sq_v01_00022hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00022hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 38.16 6.56 Num Hot pixels: 262 Hot pixel threshold: 77.49 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.234347 Iteration 2 Error: 0.209349 Iteration 3 Error: 0.086397 Iteration 4 Error: 0.020943 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.00 0.10 ...... Frame ( 3) shift: 0.00 0.21 ...... Frame ( 4) shift: 0.01 0.31 ...... Frame ( 5) shift: 0.01 0.41 ...... Frame ( 6) shift: 0.01 0.55 ...... Frame ( 7) shift: 0.01 0.71 ...... Frame ( 8) shift: 0.01 0.88 ...... Frame ( 9) shift: 0.02 0.97 ...... Frame ( 10) shift: 0.05 1.00 ...... Frame ( 11) shift: 0.08 1.03 ...... Frame ( 12) shift: 0.09 1.09 ...... Frame ( 13) shift: 0.07 1.18 ...... Frame ( 14) shift: 0.05 1.28 ...... Frame ( 15) shift: 0.05 1.38 ...... Frame ( 16) shift: 0.06 1.47 ...... Frame ( 17) shift: 0.07 1.57 ...... Frame ( 18) shift: 0.10 1.66 ...... Frame ( 19) shift: 0.16 1.74 ...... Frame ( 20) shift: 0.21 1.81 ...... Frame ( 21) shift: 0.27 1.87 ...... Frame ( 22) shift: 0.34 1.91 ...... Frame ( 23) shift: 0.41 1.95 ...... Frame ( 24) shift: 0.38 2.00 ...... Frame ( 25) shift: 0.24 2.06 ...... Frame ( 26) shift: 0.10 2.12 ...... Frame ( 27) shift: 0.06 2.19 ...... Frame ( 28) shift: 0.10 2.27 ...... Frame ( 29) shift: 0.14 2.35 ...... Frame ( 30) shift: 0.17 2.41 ...... Frame ( 31) shift: 0.20 2.46 ...... Frame ( 32) shift: 0.22 2.51 ...... Frame ( 33) shift: 0.19 2.54 ...... Frame ( 34) shift: 0.10 2.55 ...... Frame ( 35) shift: 0.00 2.56 ...... Frame ( 36) shift: -0.03 2.56 ...... Frame ( 37) shift: -0.01 2.56 ...... Frame ( 38) shift: 0.02 2.56 ...... Frame ( 39) shift: 0.05 2.56 ...... Frame ( 40) shift: 0.08 2.55 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.062977 Iteration 2 Error: 0.270308 Iteration 3 Error: 0.138425 Iteration 4 Error: 0.048880 Align patch 2 23 left Iteration 1 Error: 0.711742 Iteration 2 Error: 0.193604 Iteration 3 Error: 0.072624 Iteration 4 Error: 0.032032 Align patch 3 22 left Iteration 1 Error: 0.921327 Iteration 2 Error: 0.277071 Iteration 3 Error: 0.133555 Iteration 4 Error: 0.060868 Iteration 5 Error: 0.033156 Align patch 4 21 left Iteration 1 Error: 0.768754 Iteration 2 Error: 0.338805 Iteration 3 Error: 0.083712 Iteration 4 Error: 0.049272 Align patch 5 20 left Iteration 1 Error: 1.088715 Iteration 2 Error: 0.181139 Iteration 3 Error: 0.040316 Align patch 6 19 left Iteration 1 Error: 0.556879 Iteration 2 Error: 0.110929 Iteration 3 Error: 0.037580 Align patch 7 18 left Iteration 1 Error: 0.976218 Iteration 2 Error: 0.190864 Iteration 3 Error: 0.101819 Iteration 4 Error: 0.032220 Align patch 8 17 left Iteration 1 Error: 0.754965 Iteration 2 Error: 0.205431 Iteration 3 Error: 0.073035 Iteration 4 Error: 0.038647 Align patch 9 16 left Iteration 1 Error: 0.812020 Iteration 2 Error: 0.182160 Iteration 3 Error: 0.092904 Iteration 4 Error: 0.015376 Align patch 10 15 left Iteration 1 Error: 1.011838 Iteration 2 Error: 0.186901 Iteration 3 Error: 0.036701 Align patch 11 14 left Iteration 1 Error: 0.674659 Iteration 2 Error: 0.179887 Iteration 3 Error: 0.051963 Iteration 4 Error: 0.029096 Align patch 12 13 left Iteration 1 Error: 1.840924 Iteration 2 Error: 0.292097 Iteration 3 Error: 0.101318 Iteration 4 Error: 0.036342 Align patch 13 12 left Iteration 1 Error: 1.037913 Iteration 2 Error: 0.124501 Iteration 3 Error: 0.029617 Align patch 14 11 left Iteration 1 Error: 0.921705 Iteration 2 Error: 0.220535 Iteration 3 Error: 0.059016 Iteration 4 Error: 0.027532 Align patch 15 10 left Iteration 1 Error: 0.658193 Iteration 2 Error: 0.192269 Iteration 3 Error: 0.050325 Iteration 4 Error: 0.022219 Align patch 16 9 left Iteration 1 Error: 0.749088 Iteration 2 Error: 0.113009 Iteration 3 Error: 0.055892 Iteration 4 Error: 0.018823 Align patch 17 8 left Iteration 1 Error: 1.135212 Iteration 2 Error: 0.269840 Iteration 3 Error: 0.080121 Iteration 4 Error: 0.024397 Align patch 18 7 left Iteration 1 Error: 0.744778 Iteration 2 Error: 0.144273 Iteration 3 Error: 0.040392 Align patch 19 6 left Iteration 1 Error: 1.005418 Iteration 2 Error: 0.150704 Iteration 3 Error: 0.039477 Align patch 20 5 left Iteration 1 Error: 1.048061 Iteration 2 Error: 0.108139 Iteration 3 Error: 0.024315 Align patch 21 4 left Iteration 1 Error: 0.820006 Iteration 2 Error: 0.262327 Iteration 3 Error: 0.086330 Iteration 4 Error: 0.040847 Align patch 22 3 left Iteration 1 Error: 1.052256 Iteration 2 Error: 0.203436 Iteration 3 Error: 0.050750 Iteration 4 Error: 0.010813 Align patch 23 2 left Iteration 1 Error: 0.756331 Iteration 2 Error: 0.127223 Iteration 3 Error: 0.039513 Align patch 24 1 left Iteration 1 Error: 1.027576 Iteration 2 Error: 0.211287 Iteration 3 Error: 0.050149 Iteration 4 Error: 0.012817 Align patch 25 0 left Iteration 1 Error: 0.790291 Iteration 2 Error: 0.137682 Iteration 3 Error: 0.038548 3D Fitting completed. Patch alignment time: 13.26(sec) Local motion has been corrected. Process thread exits. Computational time: 25.971275 sec Total time: 31.911924 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00022hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00022hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.572370s Reading file: gc_18feb27f_CTD_g1_00012gr_00004sq_v01_00022hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.657240s ........................................ >>>>>>TIME<<<<<< FFT: 0.957201s Defocus_U Defocus_V Angle CCC 8724.59 9185.57 7.28 0.020196 Final Values Defocus_U Defocus_V Angle CCC 8780.84 9173.07 6.05 0.036596 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00005sq_v01_00002hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00002hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.997e-02 CC threshold: 0.734 Mean Std: 39.29 6.74 Num Hot pixels: 235 Hot pixel threshold: 79.73 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.978348 Iteration 2 Error: 0.564698 Iteration 3 Error: 0.181822 Iteration 4 Error: 0.092483 Iteration 5 Error: 0.047350 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.12 0.08 ...... Frame ( 3) shift: -0.25 0.16 ...... Frame ( 4) shift: -0.37 0.24 ...... Frame ( 5) shift: -0.49 0.32 ...... Frame ( 6) shift: -0.48 0.43 ...... Frame ( 7) shift: -0.33 0.56 ...... Frame ( 8) shift: -0.18 0.69 ...... Frame ( 9) shift: -0.06 0.85 ...... Frame ( 10) shift: 0.03 1.04 ...... Frame ( 11) shift: 0.11 1.23 ...... Frame ( 12) shift: 0.19 1.39 ...... Frame ( 13) shift: 0.28 1.50 ...... Frame ( 14) shift: 0.36 1.62 ...... Frame ( 15) shift: 0.43 1.70 ...... Frame ( 16) shift: 0.49 1.76 ...... Frame ( 17) shift: 0.56 1.82 ...... Frame ( 18) shift: 0.63 1.94 ...... Frame ( 19) shift: 0.72 2.12 ...... Frame ( 20) shift: 0.81 2.31 ...... Frame ( 21) shift: 0.89 2.42 ...... Frame ( 22) shift: 0.97 2.44 ...... Frame ( 23) shift: 1.05 2.47 ...... Frame ( 24) shift: 1.12 2.53 ...... Frame ( 25) shift: 1.18 2.63 ...... Frame ( 26) shift: 1.24 2.74 ...... Frame ( 27) shift: 1.32 2.84 ...... Frame ( 28) shift: 1.40 2.95 ...... Frame ( 29) shift: 1.49 3.06 ...... Frame ( 30) shift: 1.57 3.17 ...... Frame ( 31) shift: 1.64 3.30 ...... Frame ( 32) shift: 1.72 3.42 ...... Frame ( 33) shift: 1.81 3.51 ...... Frame ( 34) shift: 1.91 3.56 ...... Frame ( 35) shift: 2.01 3.60 ...... Frame ( 36) shift: 2.09 3.68 ...... Frame ( 37) shift: 2.17 3.79 ...... Frame ( 38) shift: 2.24 3.90 ...... Frame ( 39) shift: 2.31 4.01 ...... Frame ( 40) shift: 2.38 4.12 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.507841 Iteration 2 Error: 0.585723 Iteration 3 Error: 0.275920 Iteration 4 Error: 0.130530 Iteration 5 Error: 0.074024 Align patch 1 24 left Iteration 1 Error: 1.427579 Iteration 2 Error: 0.292965 Iteration 3 Error: 0.097124 Iteration 4 Error: 0.029983 Align patch 2 23 left Iteration 1 Error: 2.464237 Iteration 2 Error: 0.482763 Iteration 3 Error: 0.205761 Iteration 4 Error: 0.132718 Iteration 5 Error: 0.063665 Align patch 2 23 left Iteration 1 Error: 1.394081 Iteration 2 Error: 0.276543 Iteration 3 Error: 0.092401 Iteration 4 Error: 0.028472 Align patch 3 22 left Iteration 1 Error: 0.688504 Iteration 2 Error: 0.189431 Iteration 3 Error: 0.067997 Iteration 4 Error: 0.053685 Iteration 5 Error: 0.033186 Align patch 4 21 left Iteration 1 Error: 0.575943 Iteration 2 Error: 0.128570 Iteration 3 Error: 0.028580 Align patch 5 20 left Iteration 1 Error: 0.894966 Iteration 2 Error: 0.173543 Iteration 3 Error: 0.082434 Iteration 4 Error: 0.021679 Align patch 6 19 left Iteration 1 Error: 1.092542 Iteration 2 Error: 0.309865 Iteration 3 Error: 0.166261 Iteration 4 Error: 0.078054 Iteration 5 Error: 0.043366 Align patch 7 18 left Iteration 1 Error: 0.914904 Iteration 2 Error: 0.303749 Iteration 3 Error: 0.113374 Iteration 4 Error: 0.072881 Iteration 5 Error: 0.040351 Align patch 8 17 left Iteration 1 Error: 1.032432 Iteration 2 Error: 0.222922 Iteration 3 Error: 0.052890 Iteration 4 Error: 0.032841 Align patch 9 16 left Iteration 1 Error: 1.020284 Iteration 2 Error: 0.277266 Iteration 3 Error: 0.095790 Iteration 4 Error: 0.048526 Align patch 10 15 left Iteration 1 Error: 0.758823 Iteration 2 Error: 0.305644 Iteration 3 Error: 0.132187 Iteration 4 Error: 0.055630 Iteration 5 Error: 0.029451 Align patch 11 14 left Iteration 1 Error: 0.592492 Iteration 2 Error: 0.104820 Iteration 3 Error: 0.045423 Align patch 12 13 left Iteration 1 Error: 0.596322 Iteration 2 Error: 0.162335 Iteration 3 Error: 0.061159 Iteration 4 Error: 0.024841 Align patch 13 12 left Iteration 1 Error: 0.788518 Iteration 2 Error: 0.121533 Iteration 3 Error: 0.052362 Iteration 4 Error: 0.023034 Align patch 14 11 left Iteration 1 Error: 1.046766 Iteration 2 Error: 0.295079 Iteration 3 Error: 0.104220 Iteration 4 Error: 0.058134 Iteration 5 Error: 0.044368 Align patch 15 10 left Iteration 1 Error: 0.772171 Iteration 2 Error: 0.287244 Iteration 3 Error: 0.083531 Iteration 4 Error: 0.033941 Align patch 16 9 left Iteration 1 Error: 1.102688 Iteration 2 Error: 0.259807 Iteration 3 Error: 0.091332 Iteration 4 Error: 0.041015 Align patch 17 8 left Iteration 1 Error: 0.830406 Iteration 2 Error: 0.205941 Iteration 3 Error: 0.108069 Iteration 4 Error: 0.056297 Iteration 5 Error: 0.038369 Align patch 18 7 left Iteration 1 Error: 0.959922 Iteration 2 Error: 0.183059 Iteration 3 Error: 0.045302 Align patch 19 6 left Iteration 1 Error: 0.871577 Iteration 2 Error: 0.210031 Iteration 3 Error: 0.061797 Iteration 4 Error: 0.015540 Align patch 20 5 left Iteration 1 Error: 0.843897 Iteration 2 Error: 0.289228 Iteration 3 Error: 0.088431 Iteration 4 Error: 0.034573 Align patch 21 4 left Iteration 1 Error: 1.443953 Iteration 2 Error: 0.302132 Iteration 3 Error: 0.068994 Iteration 4 Error: 0.021919 Align patch 22 3 left Iteration 1 Error: 1.397757 Iteration 2 Error: 0.316564 Iteration 3 Error: 0.122363 Iteration 4 Error: 0.061187 Iteration 5 Error: 0.048279 Align patch 23 2 left Iteration 1 Error: 0.841405 Iteration 2 Error: 0.234354 Iteration 3 Error: 0.095130 Iteration 4 Error: 0.035798 Align patch 24 1 left Iteration 1 Error: 0.571425 Iteration 2 Error: 0.112131 Iteration 3 Error: 0.039014 Align patch 25 0 left Iteration 1 Error: 0.616109 Iteration 2 Error: 0.132217 Iteration 3 Error: 0.036771 3D Fitting completed. Patch alignment time: 14.96(sec) Local motion has been corrected. Process thread exits. Computational time: 27.150675 sec Total time: 33.408264 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00002hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00002hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.979217s Reading file: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00002hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.585152s ........................................ >>>>>>TIME<<<<<< FFT: 0.989092s Defocus_U Defocus_V Angle CCC 8519.48 9410.21 10.56 0.027090 Final Values Defocus_U Defocus_V Angle CCC 8531.98 9410.22 10.56 0.053370 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00005sq_v01_00002hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00002hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 39.01 6.69 Num Hot pixels: 240 Hot pixel threshold: 79.16 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.045711 Iteration 2 Error: 0.215613 Iteration 3 Error: 0.056281 Iteration 4 Error: 0.021258 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.03 0.05 ...... Frame ( 3) shift: -0.05 0.10 ...... Frame ( 4) shift: -0.08 0.15 ...... Frame ( 5) shift: -0.10 0.21 ...... Frame ( 6) shift: -0.13 0.24 ...... Frame ( 7) shift: -0.16 0.26 ...... Frame ( 8) shift: -0.20 0.28 ...... Frame ( 9) shift: -0.22 0.30 ...... Frame ( 10) shift: -0.24 0.31 ...... Frame ( 11) shift: -0.27 0.33 ...... Frame ( 12) shift: -0.24 0.37 ...... Frame ( 13) shift: -0.16 0.46 ...... Frame ( 14) shift: -0.08 0.54 ...... Frame ( 15) shift: -0.02 0.60 ...... Frame ( 16) shift: 0.03 0.64 ...... Frame ( 17) shift: 0.08 0.67 ...... Frame ( 18) shift: 0.10 0.71 ...... Frame ( 19) shift: 0.08 0.74 ...... Frame ( 20) shift: 0.06 0.78 ...... Frame ( 21) shift: 0.10 0.81 ...... Frame ( 22) shift: 0.19 0.82 ...... Frame ( 23) shift: 0.28 0.84 ...... Frame ( 24) shift: 0.34 0.90 ...... Frame ( 25) shift: 0.36 1.02 ...... Frame ( 26) shift: 0.39 1.15 ...... Frame ( 27) shift: 0.43 1.22 ...... Frame ( 28) shift: 0.49 1.25 ...... Frame ( 29) shift: 0.56 1.29 ...... Frame ( 30) shift: 0.60 1.34 ...... Frame ( 31) shift: 0.61 1.42 ...... Frame ( 32) shift: 0.62 1.50 ...... Frame ( 33) shift: 0.66 1.57 ...... Frame ( 34) shift: 0.72 1.62 ...... Frame ( 35) shift: 0.78 1.67 ...... Frame ( 36) shift: 0.85 1.73 ...... Frame ( 37) shift: 0.92 1.79 ...... Frame ( 38) shift: 0.98 1.86 ...... Frame ( 39) shift: 1.05 1.93 ...... Frame ( 40) shift: 1.12 1.99 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.926393 Iteration 2 Error: 0.169455 Iteration 3 Error: 0.047158 Align patch 2 23 left Iteration 1 Error: 0.951746 Iteration 2 Error: 0.142947 Iteration 3 Error: 0.035621 Align patch 3 22 left Iteration 1 Error: 0.770119 Iteration 2 Error: 0.142208 Iteration 3 Error: 0.030847 Align patch 4 21 left Iteration 1 Error: 0.705898 Iteration 2 Error: 0.114830 Iteration 3 Error: 0.024956 Align patch 5 20 left Iteration 1 Error: 1.633530 Iteration 2 Error: 0.345017 Iteration 3 Error: 0.084879 Iteration 4 Error: 0.037722 Align patch 6 19 left Iteration 1 Error: 1.048050 Iteration 2 Error: 0.141565 Iteration 3 Error: 0.030737 Align patch 7 18 left Iteration 1 Error: 0.430709 Iteration 2 Error: 0.110694 Iteration 3 Error: 0.024047 Align patch 8 17 left Iteration 1 Error: 0.755391 Iteration 2 Error: 0.181099 Iteration 3 Error: 0.062065 Iteration 4 Error: 0.035866 Align patch 9 16 left Iteration 1 Error: 0.616118 Iteration 2 Error: 0.096767 Iteration 3 Error: 0.022042 Align patch 10 15 left Iteration 1 Error: 1.327546 Iteration 2 Error: 0.209231 Iteration 3 Error: 0.058849 Iteration 4 Error: 0.022253 Align patch 11 14 left Iteration 1 Error: 1.141267 Iteration 2 Error: 0.160693 Iteration 3 Error: 0.037092 Align patch 12 13 left Iteration 1 Error: 0.660853 Iteration 2 Error: 0.110051 Iteration 3 Error: 0.023645 Align patch 13 12 left Iteration 1 Error: 0.480373 Iteration 2 Error: 0.135000 Iteration 3 Error: 0.057715 Iteration 4 Error: 0.019193 Align patch 14 11 left Iteration 1 Error: 1.037583 Iteration 2 Error: 0.124507 Iteration 3 Error: 0.032893 Align patch 15 10 left Iteration 1 Error: 1.062211 Iteration 2 Error: 0.189848 Iteration 3 Error: 0.047658 Align patch 16 9 left Iteration 1 Error: 0.544608 Iteration 2 Error: 0.084924 Iteration 3 Error: 0.018700 Align patch 17 8 left Iteration 1 Error: 0.475592 Iteration 2 Error: 0.081569 Iteration 3 Error: 0.026299 Align patch 18 7 left Iteration 1 Error: 1.117906 Iteration 2 Error: 0.112062 Iteration 3 Error: 0.028895 Align patch 19 6 left Iteration 1 Error: 0.811125 Iteration 2 Error: 0.134326 Iteration 3 Error: 0.022297 Align patch 20 5 left Iteration 1 Error: 0.979393 Iteration 2 Error: 0.175305 Iteration 3 Error: 0.029995 Align patch 21 4 left Iteration 1 Error: 0.675517 Iteration 2 Error: 0.174044 Iteration 3 Error: 0.063148 Iteration 4 Error: 0.026414 Align patch 22 3 left Iteration 1 Error: 0.618006 Iteration 2 Error: 0.135147 Iteration 3 Error: 0.033624 Align patch 23 2 left Iteration 1 Error: 0.536837 Iteration 2 Error: 0.138112 Iteration 3 Error: 0.025622 Align patch 24 1 left Iteration 1 Error: 0.559231 Iteration 2 Error: 0.125358 Iteration 3 Error: 0.021907 Align patch 25 0 left Iteration 1 Error: 0.765086 Iteration 2 Error: 0.185379 Iteration 3 Error: 0.039328 3D Fitting completed. Patch alignment time: 11.96(sec) Local motion has been corrected. Process thread exits. Computational time: 24.386494 sec Total time: 30.968340 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00002hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00002hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.870384s Reading file: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00002hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.466477s ........................................ >>>>>>TIME<<<<<< FFT: 0.975211s Defocus_U Defocus_V Angle CCC 13158.19 13681.67 4.13 0.038983 Final Values Defocus_U Defocus_V Angle CCC 13164.45 13706.68 4.44 0.060248 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00005sq_v01_00002hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00002hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 41.13 6.93 Num Hot pixels: 239 Hot pixel threshold: 82.73 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.699474 Iteration 2 Error: 0.412482 Iteration 3 Error: 0.141899 Iteration 4 Error: 0.061461 Iteration 5 Error: 0.034186 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.17 -0.03 ...... Frame ( 3) shift: -0.34 -0.05 ...... Frame ( 4) shift: -0.51 -0.08 ...... Frame ( 5) shift: -0.69 -0.10 ...... Frame ( 6) shift: -0.78 -0.09 ...... Frame ( 7) shift: -0.79 -0.05 ...... Frame ( 8) shift: -0.81 -0.00 ...... Frame ( 9) shift: -0.79 0.10 ...... Frame ( 10) shift: -0.73 0.26 ...... Frame ( 11) shift: -0.68 0.43 ...... Frame ( 12) shift: -0.58 0.58 ...... Frame ( 13) shift: -0.42 0.73 ...... Frame ( 14) shift: -0.27 0.88 ...... Frame ( 15) shift: -0.18 1.05 ...... Frame ( 16) shift: -0.14 1.23 ...... Frame ( 17) shift: -0.10 1.40 ...... Frame ( 18) shift: -0.03 1.53 ...... Frame ( 19) shift: 0.08 1.60 ...... Frame ( 20) shift: 0.19 1.67 ...... Frame ( 21) shift: 0.27 1.75 ...... Frame ( 22) shift: 0.33 1.84 ...... Frame ( 23) shift: 0.40 1.92 ...... Frame ( 24) shift: 0.46 2.00 ...... Frame ( 25) shift: 0.53 2.08 ...... Frame ( 26) shift: 0.59 2.16 ...... Frame ( 27) shift: 0.67 2.25 ...... Frame ( 28) shift: 0.78 2.37 ...... Frame ( 29) shift: 0.88 2.48 ...... Frame ( 30) shift: 0.92 2.57 ...... Frame ( 31) shift: 0.91 2.63 ...... Frame ( 32) shift: 0.89 2.68 ...... Frame ( 33) shift: 0.90 2.73 ...... Frame ( 34) shift: 0.94 2.78 ...... Frame ( 35) shift: 0.98 2.83 ...... Frame ( 36) shift: 1.05 2.90 ...... Frame ( 37) shift: 1.16 2.98 ...... Frame ( 38) shift: 1.27 3.06 ...... Frame ( 39) shift: 1.38 3.14 ...... Frame ( 40) shift: 1.49 3.22 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 3.075297 Iteration 2 Error: 0.757902 Iteration 3 Error: 0.279087 Iteration 4 Error: 0.127505 Iteration 5 Error: 0.053683 Align patch 1 24 left Iteration 1 Error: 2.920061 Iteration 2 Error: 0.357698 Iteration 3 Error: 0.087996 Iteration 4 Error: 0.023366 Align patch 2 23 left Iteration 1 Error: 1.991452 Iteration 2 Error: 0.475631 Iteration 3 Error: 0.186229 Iteration 4 Error: 0.100955 Iteration 5 Error: 0.038977 Align patch 3 22 left Iteration 1 Error: 0.664403 Iteration 2 Error: 0.223767 Iteration 3 Error: 0.122504 Iteration 4 Error: 0.052462 Iteration 5 Error: 0.028076 Align patch 4 21 left Iteration 1 Error: 0.694173 Iteration 2 Error: 0.155417 Iteration 3 Error: 0.047517 Align patch 5 20 left Iteration 1 Error: 0.728337 Iteration 2 Error: 0.106346 Iteration 3 Error: 0.032397 Align patch 6 19 left Iteration 1 Error: 2.905746 Iteration 2 Error: 0.489132 Iteration 3 Error: 0.211517 Iteration 4 Error: 0.088261 Iteration 5 Error: 0.039400 Align patch 7 18 left Iteration 1 Error: 2.194310 Iteration 2 Error: 0.594955 Iteration 3 Error: 0.200350 Iteration 4 Error: 0.109095 Iteration 5 Error: 0.052614 Align patch 7 18 left Iteration 1 Error: 1.705451 Iteration 2 Error: 0.253822 Iteration 3 Error: 0.058842 Iteration 4 Error: 0.021062 Align patch 8 17 left Iteration 1 Error: 1.168152 Iteration 2 Error: 0.222886 Iteration 3 Error: 0.112956 Iteration 4 Error: 0.062570 Iteration 5 Error: 0.038336 Align patch 9 16 left Iteration 1 Error: 0.895359 Iteration 2 Error: 0.123911 Iteration 3 Error: 0.033158 Align patch 10 15 left Iteration 1 Error: 0.617522 Iteration 2 Error: 0.155207 Iteration 3 Error: 0.046282 Align patch 11 14 left Iteration 1 Error: 2.203630 Iteration 2 Error: 0.470444 Iteration 3 Error: 0.244079 Iteration 4 Error: 0.197640 Iteration 5 Error: 0.107604 Align patch 11 14 left Iteration 1 Error: 2.730663 Iteration 2 Error: 0.437827 Iteration 3 Error: 0.089089 Iteration 4 Error: 0.023838 Align patch 12 13 left Iteration 1 Error: 0.954455 Iteration 2 Error: 0.344753 Iteration 3 Error: 0.161350 Iteration 4 Error: 0.103910 Iteration 5 Error: 0.057041 Align patch 12 13 left Iteration 1 Error: 1.382602 Iteration 2 Error: 0.317335 Iteration 3 Error: 0.097022 Iteration 4 Error: 0.030085 Align patch 13 12 left Iteration 1 Error: 0.512995 Iteration 2 Error: 0.134043 Iteration 3 Error: 0.051641 Iteration 4 Error: 0.021393 Align patch 14 11 left Iteration 1 Error: 1.519997 Iteration 2 Error: 0.296931 Iteration 3 Error: 0.100483 Iteration 4 Error: 0.036373 Align patch 15 10 left Iteration 1 Error: 1.111548 Iteration 2 Error: 0.215086 Iteration 3 Error: 0.095628 Iteration 4 Error: 0.024530 Align patch 16 9 left Iteration 1 Error: 2.114967 Iteration 2 Error: 0.609151 Iteration 3 Error: 0.253486 Iteration 4 Error: 0.153029 Iteration 5 Error: 0.109250 Align patch 16 9 left Iteration 1 Error: 1.583790 Iteration 2 Error: 0.334621 Iteration 3 Error: 0.088777 Iteration 4 Error: 0.031890 Align patch 17 8 left Iteration 1 Error: 0.721696 Iteration 2 Error: 0.163845 Iteration 3 Error: 0.073489 Iteration 4 Error: 0.040013 Align patch 18 7 left Iteration 1 Error: 0.715186 Iteration 2 Error: 0.201224 Iteration 3 Error: 0.098598 Iteration 4 Error: 0.066874 Iteration 5 Error: 0.048836 Align patch 19 6 left Iteration 1 Error: 0.848375 Iteration 2 Error: 0.328469 Iteration 3 Error: 0.133814 Iteration 4 Error: 0.075045 Iteration 5 Error: 0.029394 Align patch 20 5 left Iteration 1 Error: 1.146074 Iteration 2 Error: 0.258775 Iteration 3 Error: 0.065839 Iteration 4 Error: 0.020039 Align patch 21 4 left Iteration 1 Error: 1.018111 Iteration 2 Error: 0.168223 Iteration 3 Error: 0.056219 Iteration 4 Error: 0.031503 Align patch 22 3 left Iteration 1 Error: 0.723977 Iteration 2 Error: 0.083307 Iteration 3 Error: 0.020661 Align patch 23 2 left Iteration 1 Error: 0.622141 Iteration 2 Error: 0.154232 Iteration 3 Error: 0.047167 Align patch 24 1 left Iteration 1 Error: 1.150603 Iteration 2 Error: 0.235240 Iteration 3 Error: 0.064330 Iteration 4 Error: 0.023377 Align patch 25 0 left Iteration 1 Error: 1.114954 Iteration 2 Error: 0.204693 Iteration 3 Error: 0.058288 Iteration 4 Error: 0.015270 3D Fitting completed. Patch alignment time: 17.05(sec) Local motion has been corrected. Process thread exits. Computational time: 30.422970 sec Total time: 38.610596 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00002hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00002hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.742601s Reading file: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00002hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.870417s ........................................ >>>>>>TIME<<<<<< FFT: 1.008233s Defocus_U Defocus_V Angle CCC 10355.48 11222.67 5.15 0.052564 Final Values Defocus_U Defocus_V Angle CCC 10378.92 11236.73 5.47 0.092789 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00005sq_v01_00002hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00002hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.002e-01 CC threshold: 0.736 Mean Std: 41.65 6.98 Num Hot pixels: 244 Hot pixel threshold: 83.51 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.995368 Iteration 2 Error: 0.179648 Iteration 3 Error: 0.041326 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.07 0.08 ...... Frame ( 3) shift: -0.14 0.16 ...... Frame ( 4) shift: -0.21 0.24 ...... Frame ( 5) shift: -0.28 0.32 ...... Frame ( 6) shift: -0.28 0.40 ...... Frame ( 7) shift: -0.20 0.49 ...... Frame ( 8) shift: -0.12 0.57 ...... Frame ( 9) shift: -0.07 0.64 ...... Frame ( 10) shift: -0.04 0.69 ...... Frame ( 11) shift: -0.00 0.74 ...... Frame ( 12) shift: 0.05 0.78 ...... Frame ( 13) shift: 0.12 0.81 ...... Frame ( 14) shift: 0.19 0.84 ...... Frame ( 15) shift: 0.28 0.89 ...... Frame ( 16) shift: 0.37 0.96 ...... Frame ( 17) shift: 0.46 1.04 ...... Frame ( 18) shift: 0.51 1.09 ...... Frame ( 19) shift: 0.52 1.13 ...... Frame ( 20) shift: 0.53 1.16 ...... Frame ( 21) shift: 0.56 1.19 ...... Frame ( 22) shift: 0.62 1.23 ...... Frame ( 23) shift: 0.68 1.27 ...... Frame ( 24) shift: 0.70 1.31 ...... Frame ( 25) shift: 0.70 1.34 ...... Frame ( 26) shift: 0.69 1.38 ...... Frame ( 27) shift: 0.68 1.42 ...... Frame ( 28) shift: 0.67 1.48 ...... Frame ( 29) shift: 0.66 1.53 ...... Frame ( 30) shift: 0.66 1.57 ...... Frame ( 31) shift: 0.68 1.58 ...... Frame ( 32) shift: 0.69 1.59 ...... Frame ( 33) shift: 0.72 1.65 ...... Frame ( 34) shift: 0.77 1.75 ...... Frame ( 35) shift: 0.82 1.85 ...... Frame ( 36) shift: 0.86 1.94 ...... Frame ( 37) shift: 0.88 2.00 ...... Frame ( 38) shift: 0.91 2.06 ...... Frame ( 39) shift: 0.93 2.12 ...... Frame ( 40) shift: 0.96 2.19 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.954831 Iteration 2 Error: 0.215950 Iteration 3 Error: 0.081875 Iteration 4 Error: 0.036616 Align patch 2 23 left Iteration 1 Error: 0.908423 Iteration 2 Error: 0.217730 Iteration 3 Error: 0.088180 Iteration 4 Error: 0.028694 Align patch 3 22 left Iteration 1 Error: 0.462885 Iteration 2 Error: 0.091479 Iteration 3 Error: 0.025010 Align patch 4 21 left Iteration 1 Error: 0.634872 Iteration 2 Error: 0.102744 Iteration 3 Error: 0.019998 Align patch 5 20 left Iteration 1 Error: 0.662493 Iteration 2 Error: 0.112172 Iteration 3 Error: 0.030761 Align patch 6 19 left Iteration 1 Error: 1.178091 Iteration 2 Error: 0.189828 Iteration 3 Error: 0.066876 Iteration 4 Error: 0.028987 Align patch 7 18 left Iteration 1 Error: 0.595516 Iteration 2 Error: 0.120231 Iteration 3 Error: 0.039163 Align patch 8 17 left Iteration 1 Error: 0.664757 Iteration 2 Error: 0.157345 Iteration 3 Error: 0.052326 Iteration 4 Error: 0.016318 Align patch 9 16 left Iteration 1 Error: 0.803174 Iteration 2 Error: 0.138834 Iteration 3 Error: 0.040184 Align patch 10 15 left Iteration 1 Error: 0.807090 Iteration 2 Error: 0.142560 Iteration 3 Error: 0.045322 Align patch 11 14 left Iteration 1 Error: 1.345597 Iteration 2 Error: 0.134134 Iteration 3 Error: 0.027007 Align patch 12 13 left Iteration 1 Error: 1.170241 Iteration 2 Error: 0.213966 Iteration 3 Error: 0.037035 Align patch 13 12 left Iteration 1 Error: 1.046308 Iteration 2 Error: 0.392325 Iteration 3 Error: 0.137464 Iteration 4 Error: 0.052852 Iteration 5 Error: 0.015312 Align patch 14 11 left Iteration 1 Error: 0.997919 Iteration 2 Error: 0.117868 Iteration 3 Error: 0.019873 Align patch 15 10 left Iteration 1 Error: 0.603474 Iteration 2 Error: 0.070890 Iteration 3 Error: 0.015099 Align patch 16 9 left Iteration 1 Error: 0.798451 Iteration 2 Error: 0.210156 Iteration 3 Error: 0.075534 Iteration 4 Error: 0.033719 Align patch 17 8 left Iteration 1 Error: 0.902865 Iteration 2 Error: 0.086876 Iteration 3 Error: 0.025697 Align patch 18 7 left Iteration 1 Error: 0.541998 Iteration 2 Error: 0.117191 Iteration 3 Error: 0.029630 Align patch 19 6 left Iteration 1 Error: 0.973672 Iteration 2 Error: 0.200145 Iteration 3 Error: 0.029590 Align patch 20 5 left Iteration 1 Error: 1.097826 Iteration 2 Error: 0.140946 Iteration 3 Error: 0.022644 Align patch 21 4 left Iteration 1 Error: 0.655776 Iteration 2 Error: 0.064744 Iteration 3 Error: 0.025389 Align patch 22 3 left Iteration 1 Error: 0.697791 Iteration 2 Error: 0.161414 Iteration 3 Error: 0.035971 Align patch 23 2 left Iteration 1 Error: 0.427281 Iteration 2 Error: 0.061992 Iteration 3 Error: 0.016415 Align patch 24 1 left Iteration 1 Error: 0.692726 Iteration 2 Error: 0.129205 Iteration 3 Error: 0.024201 Align patch 25 0 left Iteration 1 Error: 1.033374 Iteration 2 Error: 0.160884 Iteration 3 Error: 0.018617 3D Fitting completed. Patch alignment time: 11.75(sec) Local motion has been corrected. Process thread exits. Computational time: 25.103415 sec Total time: 31.635246 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00002hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00002hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.857598s Reading file: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00002hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.596966s ........................................ >>>>>>TIME<<<<<< FFT: 0.970447s Defocus_U Defocus_V Angle CCC 10570.03 9871.41 84.85 0.048332 Final Values Defocus_U Defocus_V Angle CCC 10588.78 9871.41 85.47 0.088953 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00005sq_v01_00003hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00003hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.001e-01 CC threshold: 0.735 Mean Std: 39.30 6.78 Num Hot pixels: 201 Hot pixel threshold: 79.96 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.583814 Iteration 2 Error: 0.397609 Iteration 3 Error: 0.119706 Iteration 4 Error: 0.044730 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.34 -0.18 ...... Frame ( 3) shift: -0.68 -0.37 ...... Frame ( 4) shift: -1.02 -0.55 ...... Frame ( 5) shift: -1.36 -0.73 ...... Frame ( 6) shift: -1.51 -0.78 ...... Frame ( 7) shift: -1.47 -0.69 ...... Frame ( 8) shift: -1.42 -0.59 ...... Frame ( 9) shift: -1.38 -0.53 ...... Frame ( 10) shift: -1.34 -0.51 ...... Frame ( 11) shift: -1.29 -0.48 ...... Frame ( 12) shift: -1.18 -0.39 ...... Frame ( 13) shift: -1.01 -0.24 ...... Frame ( 14) shift: -0.83 -0.09 ...... Frame ( 15) shift: -0.70 0.05 ...... Frame ( 16) shift: -0.61 0.17 ...... Frame ( 17) shift: -0.51 0.29 ...... Frame ( 18) shift: -0.43 0.39 ...... Frame ( 19) shift: -0.36 0.47 ...... Frame ( 20) shift: -0.29 0.55 ...... Frame ( 21) shift: -0.22 0.62 ...... Frame ( 22) shift: -0.16 0.69 ...... Frame ( 23) shift: -0.10 0.76 ...... Frame ( 24) shift: -0.04 0.84 ...... Frame ( 25) shift: 0.00 0.95 ...... Frame ( 26) shift: 0.04 1.06 ...... Frame ( 27) shift: 0.08 1.13 ...... Frame ( 28) shift: 0.12 1.17 ...... Frame ( 29) shift: 0.16 1.22 ...... Frame ( 30) shift: 0.24 1.30 ...... Frame ( 31) shift: 0.36 1.41 ...... Frame ( 32) shift: 0.48 1.53 ...... Frame ( 33) shift: 0.52 1.62 ...... Frame ( 34) shift: 0.48 1.67 ...... Frame ( 35) shift: 0.44 1.73 ...... Frame ( 36) shift: 0.47 1.78 ...... Frame ( 37) shift: 0.56 1.84 ...... Frame ( 38) shift: 0.65 1.89 ...... Frame ( 39) shift: 0.74 1.95 ...... Frame ( 40) shift: 0.83 2.00 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.516600 Iteration 2 Error: 0.074641 Iteration 3 Error: 0.020097 Align patch 2 23 left Iteration 1 Error: 0.721035 Iteration 2 Error: 0.096546 Iteration 3 Error: 0.030881 Align patch 3 22 left Iteration 1 Error: 1.591540 Iteration 2 Error: 0.268196 Iteration 3 Error: 0.083748 Iteration 4 Error: 0.026391 Align patch 4 21 left Iteration 1 Error: 0.609841 Iteration 2 Error: 0.116972 Iteration 3 Error: 0.028106 Align patch 5 20 left Iteration 1 Error: 0.729099 Iteration 2 Error: 0.234379 Iteration 3 Error: 0.068536 Iteration 4 Error: 0.023551 Align patch 6 19 left Iteration 1 Error: 0.619135 Iteration 2 Error: 0.140087 Iteration 3 Error: 0.039888 Align patch 7 18 left Iteration 1 Error: 0.931640 Iteration 2 Error: 0.265333 Iteration 3 Error: 0.098469 Iteration 4 Error: 0.031862 Align patch 8 17 left Iteration 1 Error: 0.918167 Iteration 2 Error: 0.170981 Iteration 3 Error: 0.058253 Iteration 4 Error: 0.027166 Align patch 9 16 left Iteration 1 Error: 1.084700 Iteration 2 Error: 0.187664 Iteration 3 Error: 0.061103 Iteration 4 Error: 0.027287 Align patch 10 15 left Iteration 1 Error: 1.029761 Iteration 2 Error: 0.207008 Iteration 3 Error: 0.057075 Iteration 4 Error: 0.020136 Align patch 11 14 left Iteration 1 Error: 0.640630 Iteration 2 Error: 0.129086 Iteration 3 Error: 0.041620 Align patch 12 13 left Iteration 1 Error: 0.928750 Iteration 2 Error: 0.330632 Iteration 3 Error: 0.121734 Iteration 4 Error: 0.051224 Iteration 5 Error: 0.033366 Align patch 13 12 left Iteration 1 Error: 0.927177 Iteration 2 Error: 0.253637 Iteration 3 Error: 0.171336 Iteration 4 Error: 0.071477 Iteration 5 Error: 0.040384 Align patch 14 11 left Iteration 1 Error: 0.646582 Iteration 2 Error: 0.166011 Iteration 3 Error: 0.041323 Align patch 15 10 left Iteration 1 Error: 0.588896 Iteration 2 Error: 0.178151 Iteration 3 Error: 0.038450 Align patch 16 9 left Iteration 1 Error: 1.327131 Iteration 2 Error: 0.256272 Iteration 3 Error: 0.071647 Iteration 4 Error: 0.036990 Align patch 17 8 left Iteration 1 Error: 1.078883 Iteration 2 Error: 0.225360 Iteration 3 Error: 0.096588 Iteration 4 Error: 0.041645 Align patch 18 7 left Iteration 1 Error: 0.801350 Iteration 2 Error: 0.090528 Iteration 3 Error: 0.029247 Align patch 19 6 left Iteration 1 Error: 1.229498 Iteration 2 Error: 0.162982 Iteration 3 Error: 0.042330 Align patch 20 5 left Iteration 1 Error: 0.781495 Iteration 2 Error: 0.102313 Iteration 3 Error: 0.029972 Align patch 21 4 left Iteration 1 Error: 1.273005 Iteration 2 Error: 0.195749 Iteration 3 Error: 0.049327 Align patch 22 3 left Iteration 1 Error: 0.858715 Iteration 2 Error: 0.206360 Iteration 3 Error: 0.072711 Iteration 4 Error: 0.035839 Align patch 23 2 left Iteration 1 Error: 1.022541 Iteration 2 Error: 0.225651 Iteration 3 Error: 0.045819 Align patch 24 1 left Iteration 1 Error: 1.080926 Iteration 2 Error: 0.210598 Iteration 3 Error: 0.032786 Align patch 25 0 left Iteration 1 Error: 0.741759 Iteration 2 Error: 0.114928 Iteration 3 Error: 0.027581 3D Fitting completed. Patch alignment time: 12.33(sec) Local motion has been corrected. Process thread exits. Computational time: 25.287842 sec Total time: 33.393551 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00003hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00003hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.466328s Reading file: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00003hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.079355s ........................................ >>>>>>TIME<<<<<< FFT: 0.964334s Defocus_U Defocus_V Angle CCC 8761.76 9574.26 11.74 0.034061 Final Values Defocus_U Defocus_V Angle CCC 8769.59 9607.09 11.13 0.062696 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00005sq_v01_00003hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00003hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.003e-01 CC threshold: 0.736 Mean Std: 39.55 6.91 Num Hot pixels: 229 Hot pixel threshold: 81.00 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.778146 Iteration 2 Error: 0.409469 Iteration 3 Error: 0.093578 Iteration 4 Error: 0.033475 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.28 -0.10 ...... Frame ( 3) shift: -0.55 -0.20 ...... Frame ( 4) shift: -0.83 -0.30 ...... Frame ( 5) shift: -1.10 -0.40 ...... Frame ( 6) shift: -1.29 -0.45 ...... Frame ( 7) shift: -1.38 -0.46 ...... Frame ( 8) shift: -1.46 -0.47 ...... Frame ( 9) shift: -1.43 -0.45 ...... Frame ( 10) shift: -1.27 -0.40 ...... Frame ( 11) shift: -1.11 -0.34 ...... Frame ( 12) shift: -0.97 -0.29 ...... Frame ( 13) shift: -0.84 -0.25 ...... Frame ( 14) shift: -0.70 -0.20 ...... Frame ( 15) shift: -0.62 -0.17 ...... Frame ( 16) shift: -0.57 -0.15 ...... Frame ( 17) shift: -0.53 -0.13 ...... Frame ( 18) shift: -0.44 -0.07 ...... Frame ( 19) shift: -0.32 0.01 ...... Frame ( 20) shift: -0.19 0.10 ...... Frame ( 21) shift: -0.08 0.19 ...... Frame ( 22) shift: 0.01 0.29 ...... Frame ( 23) shift: 0.11 0.39 ...... Frame ( 24) shift: 0.19 0.44 ...... Frame ( 25) shift: 0.25 0.44 ...... Frame ( 26) shift: 0.31 0.43 ...... Frame ( 27) shift: 0.40 0.44 ...... Frame ( 28) shift: 0.53 0.46 ...... Frame ( 29) shift: 0.65 0.48 ...... Frame ( 30) shift: 0.76 0.52 ...... Frame ( 31) shift: 0.84 0.60 ...... Frame ( 32) shift: 0.92 0.68 ...... Frame ( 33) shift: 1.01 0.77 ...... Frame ( 34) shift: 1.11 0.88 ...... Frame ( 35) shift: 1.21 0.98 ...... Frame ( 36) shift: 1.30 1.07 ...... Frame ( 37) shift: 1.38 1.16 ...... Frame ( 38) shift: 1.46 1.24 ...... Frame ( 39) shift: 1.54 1.32 ...... Frame ( 40) shift: 1.62 1.41 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.237142 Iteration 2 Error: 0.833836 Iteration 3 Error: 0.279272 Iteration 4 Error: 0.114306 Iteration 5 Error: 0.040419 Align patch 2 23 left Iteration 1 Error: 2.116095 Iteration 2 Error: 0.481150 Iteration 3 Error: 0.179216 Iteration 4 Error: 0.077453 Iteration 5 Error: 0.037278 Align patch 3 22 left Iteration 1 Error: 0.718299 Iteration 2 Error: 0.290418 Iteration 3 Error: 0.069447 Iteration 4 Error: 0.033605 Align patch 4 21 left Iteration 1 Error: 0.685619 Iteration 2 Error: 0.136465 Iteration 3 Error: 0.048135 Align patch 5 20 left Iteration 1 Error: 1.142837 Iteration 2 Error: 0.242653 Iteration 3 Error: 0.104118 Iteration 4 Error: 0.041150 Align patch 6 19 left Iteration 1 Error: 2.983509 Iteration 2 Error: 0.787721 Iteration 3 Error: 0.195594 Iteration 4 Error: 0.059565 Iteration 5 Error: 0.026190 Align patch 7 18 left Iteration 1 Error: 1.432988 Iteration 2 Error: 0.473476 Iteration 3 Error: 0.213191 Iteration 4 Error: 0.117397 Iteration 5 Error: 0.059141 Align patch 7 18 left Iteration 1 Error: 1.660661 Iteration 2 Error: 0.347740 Iteration 3 Error: 0.100172 Iteration 4 Error: 0.027026 Align patch 8 17 left Iteration 1 Error: 0.971158 Iteration 2 Error: 0.147926 Iteration 3 Error: 0.052808 Iteration 4 Error: 0.030219 Align patch 9 16 left Iteration 1 Error: 0.711697 Iteration 2 Error: 0.209289 Iteration 3 Error: 0.068825 Iteration 4 Error: 0.034831 Align patch 10 15 left Iteration 1 Error: 0.882373 Iteration 2 Error: 0.208189 Iteration 3 Error: 0.055987 Iteration 4 Error: 0.023368 Align patch 11 14 left Iteration 1 Error: 1.660291 Iteration 2 Error: 0.395900 Iteration 3 Error: 0.165560 Iteration 4 Error: 0.087173 Iteration 5 Error: 0.031882 Align patch 12 13 left Iteration 1 Error: 1.452122 Iteration 2 Error: 0.483769 Iteration 3 Error: 0.186895 Iteration 4 Error: 0.099508 Iteration 5 Error: 0.043444 Align patch 13 12 left Iteration 1 Error: 0.703500 Iteration 2 Error: 0.234572 Iteration 3 Error: 0.112134 Iteration 4 Error: 0.045288 Align patch 14 11 left Iteration 1 Error: 0.902591 Iteration 2 Error: 0.187431 Iteration 3 Error: 0.074037 Iteration 4 Error: 0.034663 Align patch 15 10 left Iteration 1 Error: 0.810710 Iteration 2 Error: 0.134897 Iteration 3 Error: 0.043349 Align patch 16 9 left Iteration 1 Error: 1.607831 Iteration 2 Error: 0.631175 Iteration 3 Error: 0.224329 Iteration 4 Error: 0.101043 Iteration 5 Error: 0.042597 Align patch 17 8 left Iteration 1 Error: 0.797904 Iteration 2 Error: 0.143067 Iteration 3 Error: 0.053762 Iteration 4 Error: 0.027735 Align patch 18 7 left Iteration 1 Error: 0.601862 Iteration 2 Error: 0.098247 Iteration 3 Error: 0.029074 Align patch 19 6 left Iteration 1 Error: 1.166886 Iteration 2 Error: 0.239480 Iteration 3 Error: 0.063598 Iteration 4 Error: 0.029026 Align patch 20 5 left Iteration 1 Error: 1.349962 Iteration 2 Error: 0.278524 Iteration 3 Error: 0.052422 Iteration 4 Error: 0.023457 Align patch 21 4 left Iteration 1 Error: 1.798768 Iteration 2 Error: 0.515932 Iteration 3 Error: 0.198105 Iteration 4 Error: 0.120917 Iteration 5 Error: 0.053192 Align patch 21 4 left Iteration 1 Error: 1.613677 Iteration 2 Error: 0.323950 Iteration 3 Error: 0.068233 Iteration 4 Error: 0.029252 Align patch 22 3 left Iteration 1 Error: 1.209225 Iteration 2 Error: 0.224165 Iteration 3 Error: 0.060132 Iteration 4 Error: 0.025776 Align patch 23 2 left Iteration 1 Error: 0.463458 Iteration 2 Error: 0.084209 Iteration 3 Error: 0.030752 Align patch 24 1 left Iteration 1 Error: 0.822139 Iteration 2 Error: 0.174891 Iteration 3 Error: 0.045458 Align patch 25 0 left Iteration 1 Error: 0.800846 Iteration 2 Error: 0.079854 Iteration 3 Error: 0.009797 3D Fitting completed. Patch alignment time: 14.19(sec) Local motion has been corrected. Process thread exits. Computational time: 24.417471 sec Total time: 33.030163 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00003hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00003hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.449165s Reading file: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00003hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.335163s ........................................ >>>>>>TIME<<<<<< FFT: 0.938701s Defocus_U Defocus_V Angle CCC 10535.18 11031.28 2.47 0.050081 Final Values Defocus_U Defocus_V Angle CCC 10541.43 11078.18 1.22 0.085484 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00005sq_v01_00003hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00003hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.002e-01 CC threshold: 0.736 Mean Std: 40.09 6.95 Num Hot pixels: 212 Hot pixel threshold: 81.82 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.747708 Iteration 2 Error: 0.411706 Iteration 3 Error: 0.097946 Iteration 4 Error: 0.037886 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.26 -0.23 ...... Frame ( 3) shift: -0.52 -0.46 ...... Frame ( 4) shift: -0.78 -0.69 ...... Frame ( 5) shift: -1.04 -0.91 ...... Frame ( 6) shift: -1.19 -1.03 ...... Frame ( 7) shift: -1.23 -1.03 ...... Frame ( 8) shift: -1.27 -1.04 ...... Frame ( 9) shift: -1.25 -1.00 ...... Frame ( 10) shift: -1.15 -0.91 ...... Frame ( 11) shift: -1.06 -0.83 ...... Frame ( 12) shift: -0.94 -0.72 ...... Frame ( 13) shift: -0.82 -0.58 ...... Frame ( 14) shift: -0.69 -0.44 ...... Frame ( 15) shift: -0.57 -0.32 ...... Frame ( 16) shift: -0.44 -0.23 ...... Frame ( 17) shift: -0.32 -0.14 ...... Frame ( 18) shift: -0.21 -0.02 ...... Frame ( 19) shift: -0.11 0.14 ...... Frame ( 20) shift: -0.02 0.29 ...... Frame ( 21) shift: 0.07 0.43 ...... Frame ( 22) shift: 0.16 0.55 ...... Frame ( 23) shift: 0.25 0.67 ...... Frame ( 24) shift: 0.31 0.78 ...... Frame ( 25) shift: 0.34 0.89 ...... Frame ( 26) shift: 0.37 0.99 ...... Frame ( 27) shift: 0.39 1.05 ...... Frame ( 28) shift: 0.38 1.07 ...... Frame ( 29) shift: 0.37 1.08 ...... Frame ( 30) shift: 0.43 1.09 ...... Frame ( 31) shift: 0.55 1.09 ...... Frame ( 32) shift: 0.67 1.09 ...... Frame ( 33) shift: 0.77 1.12 ...... Frame ( 34) shift: 0.84 1.19 ...... Frame ( 35) shift: 0.92 1.26 ...... Frame ( 36) shift: 1.02 1.33 ...... Frame ( 37) shift: 1.14 1.39 ...... Frame ( 38) shift: 1.25 1.45 ...... Frame ( 39) shift: 1.37 1.51 ...... Frame ( 40) shift: 1.48 1.56 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.074503 Iteration 2 Error: 0.204933 Iteration 3 Error: 0.064006 Iteration 4 Error: 0.027466 Align patch 2 23 left Iteration 1 Error: 0.840491 Iteration 2 Error: 0.234516 Iteration 3 Error: 0.096177 Iteration 4 Error: 0.040722 Align patch 3 22 left Iteration 1 Error: 1.112756 Iteration 2 Error: 0.162468 Iteration 3 Error: 0.060551 Iteration 4 Error: 0.023327 Align patch 4 21 left Iteration 1 Error: 0.837239 Iteration 2 Error: 0.086181 Iteration 3 Error: 0.023607 Align patch 5 20 left Iteration 1 Error: 0.558566 Iteration 2 Error: 0.086921 Iteration 3 Error: 0.023016 Align patch 6 19 left Iteration 1 Error: 1.179854 Iteration 2 Error: 0.175644 Iteration 3 Error: 0.054696 Iteration 4 Error: 0.019808 Align patch 7 18 left Iteration 1 Error: 1.023135 Iteration 2 Error: 0.241658 Iteration 3 Error: 0.097932 Iteration 4 Error: 0.050791 Iteration 5 Error: 0.022708 Align patch 8 17 left Iteration 1 Error: 0.909598 Iteration 2 Error: 0.193611 Iteration 3 Error: 0.087739 Iteration 4 Error: 0.030238 Align patch 9 16 left Iteration 1 Error: 0.716752 Iteration 2 Error: 0.141275 Iteration 3 Error: 0.040959 Align patch 10 15 left Iteration 1 Error: 0.646021 Iteration 2 Error: 0.095276 Iteration 3 Error: 0.043516 Align patch 11 14 left Iteration 1 Error: 0.747874 Iteration 2 Error: 0.233686 Iteration 3 Error: 0.088970 Iteration 4 Error: 0.029228 Align patch 12 13 left Iteration 1 Error: 0.682584 Iteration 2 Error: 0.148525 Iteration 3 Error: 0.043953 Align patch 13 12 left Iteration 1 Error: 0.567757 Iteration 2 Error: 0.069640 Iteration 3 Error: 0.016056 Align patch 14 11 left Iteration 1 Error: 0.463946 Iteration 2 Error: 0.098855 Iteration 3 Error: 0.025750 Align patch 15 10 left Iteration 1 Error: 1.003977 Iteration 2 Error: 0.196722 Iteration 3 Error: 0.051839 Iteration 4 Error: 0.017988 Align patch 16 9 left Iteration 1 Error: 0.801850 Iteration 2 Error: 0.129439 Iteration 3 Error: 0.037085 Align patch 17 8 left Iteration 1 Error: 0.815407 Iteration 2 Error: 0.195620 Iteration 3 Error: 0.061187 Iteration 4 Error: 0.025620 Align patch 18 7 left Iteration 1 Error: 0.390499 Iteration 2 Error: 0.099084 Iteration 3 Error: 0.037744 Align patch 19 6 left Iteration 1 Error: 0.683910 Iteration 2 Error: 0.166217 Iteration 3 Error: 0.063588 Iteration 4 Error: 0.031538 Align patch 20 5 left Iteration 1 Error: 1.124132 Iteration 2 Error: 0.175870 Iteration 3 Error: 0.045077 Align patch 21 4 left Iteration 1 Error: 0.492570 Iteration 2 Error: 0.105947 Iteration 3 Error: 0.041421 Align patch 22 3 left Iteration 1 Error: 0.553496 Iteration 2 Error: 0.114394 Iteration 3 Error: 0.026427 Align patch 23 2 left Iteration 1 Error: 0.793086 Iteration 2 Error: 0.085517 Iteration 3 Error: 0.033346 Align patch 24 1 left Iteration 1 Error: 0.537507 Iteration 2 Error: 0.099394 Iteration 3 Error: 0.021334 Align patch 25 0 left Iteration 1 Error: 0.690616 Iteration 2 Error: 0.085349 Iteration 3 Error: 0.024016 3D Fitting completed. Patch alignment time: 12.65(sec) Local motion has been corrected. Process thread exits. Computational time: 22.735291 sec Total time: 28.887590 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00003hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00003hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.578682s Reading file: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00003hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.326308s ........................................ >>>>>>TIME<<<<<< FFT: 0.914029s Defocus_U Defocus_V Angle CCC 10039.06 10898.44 6.37 0.053093 Final Values Defocus_U Defocus_V Angle CCC 10039.07 10923.45 6.06 0.090186 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00005sq_v01_00003hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00003hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 40.72 7.08 Num Hot pixels: 220 Hot pixel threshold: 83.21 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.396914 Iteration 2 Error: 0.624552 Iteration 3 Error: 0.203048 Iteration 4 Error: 0.071548 Iteration 5 Error: 0.026681 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.25 -0.30 ...... Frame ( 3) shift: -0.49 -0.60 ...... Frame ( 4) shift: -0.74 -0.90 ...... Frame ( 5) shift: -0.99 -1.19 ...... Frame ( 6) shift: -1.00 -1.38 ...... Frame ( 7) shift: -0.78 -1.46 ...... Frame ( 8) shift: -0.56 -1.53 ...... Frame ( 9) shift: -0.34 -1.59 ...... Frame ( 10) shift: -0.14 -1.62 ...... Frame ( 11) shift: 0.06 -1.64 ...... Frame ( 12) shift: 0.30 -1.62 ...... Frame ( 13) shift: 0.58 -1.55 ...... Frame ( 14) shift: 0.85 -1.48 ...... Frame ( 15) shift: 1.12 -1.44 ...... Frame ( 16) shift: 1.37 -1.43 ...... Frame ( 17) shift: 1.63 -1.42 ...... Frame ( 18) shift: 1.85 -1.42 ...... Frame ( 19) shift: 2.04 -1.43 ...... Frame ( 20) shift: 2.24 -1.44 ...... Frame ( 21) shift: 2.43 -1.43 ...... Frame ( 22) shift: 2.62 -1.39 ...... Frame ( 23) shift: 2.81 -1.35 ...... Frame ( 24) shift: 2.96 -1.30 ...... Frame ( 25) shift: 3.07 -1.25 ...... Frame ( 26) shift: 3.19 -1.19 ...... Frame ( 27) shift: 3.36 -1.14 ...... Frame ( 28) shift: 3.59 -1.08 ...... Frame ( 29) shift: 3.82 -1.02 ...... Frame ( 30) shift: 4.00 -0.97 ...... Frame ( 31) shift: 4.12 -0.94 ...... Frame ( 32) shift: 4.24 -0.90 ...... Frame ( 33) shift: 4.35 -0.86 ...... Frame ( 34) shift: 4.44 -0.83 ...... Frame ( 35) shift: 4.53 -0.79 ...... Frame ( 36) shift: 4.60 -0.76 ...... Frame ( 37) shift: 4.66 -0.73 ...... Frame ( 38) shift: 4.72 -0.69 ...... Frame ( 39) shift: 4.78 -0.66 ...... Frame ( 40) shift: 4.84 -0.62 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 3.906932 Iteration 2 Error: 1.155156 Iteration 3 Error: 0.291466 Iteration 4 Error: 0.086429 Iteration 5 Error: 0.031309 Align patch 2 23 left Iteration 1 Error: 2.686382 Iteration 2 Error: 0.537187 Iteration 3 Error: 0.118220 Iteration 4 Error: 0.038087 Align patch 3 22 left Iteration 1 Error: 1.227598 Iteration 2 Error: 0.320719 Iteration 3 Error: 0.126357 Iteration 4 Error: 0.069280 Iteration 5 Error: 0.042086 Align patch 4 21 left Iteration 1 Error: 1.166864 Iteration 2 Error: 0.256405 Iteration 3 Error: 0.102498 Iteration 4 Error: 0.030247 Align patch 5 20 left Iteration 1 Error: 1.471362 Iteration 2 Error: 0.332228 Iteration 3 Error: 0.093204 Iteration 4 Error: 0.027429 Align patch 6 19 left Iteration 1 Error: 4.205290 Iteration 2 Error: 0.995428 Iteration 3 Error: 0.315335 Iteration 4 Error: 0.121146 Iteration 5 Error: 0.041566 Align patch 7 18 left Iteration 1 Error: 2.412234 Iteration 2 Error: 0.414985 Iteration 3 Error: 0.192344 Iteration 4 Error: 0.084624 Iteration 5 Error: 0.041219 Align patch 8 17 left Iteration 1 Error: 1.759427 Iteration 2 Error: 0.429169 Iteration 3 Error: 0.209001 Iteration 4 Error: 0.114827 Iteration 5 Error: 0.050628 Align patch 8 17 left Iteration 1 Error: 1.450721 Iteration 2 Error: 0.202902 Iteration 3 Error: 0.047944 Align patch 9 16 left Iteration 1 Error: 1.360886 Iteration 2 Error: 0.237427 Iteration 3 Error: 0.094011 Iteration 4 Error: 0.029192 Align patch 10 15 left Iteration 1 Error: 0.852751 Iteration 2 Error: 0.175196 Iteration 3 Error: 0.051178 Iteration 4 Error: 0.018166 Align patch 11 14 left Iteration 1 Error: 3.507533 Iteration 2 Error: 0.947169 Iteration 3 Error: 0.382076 Iteration 4 Error: 0.219520 Iteration 5 Error: 0.099789 Align patch 11 14 left Iteration 1 Error: 3.121462 Iteration 2 Error: 0.424766 Iteration 3 Error: 0.115384 Iteration 4 Error: 0.033901 Align patch 12 13 left Iteration 1 Error: 2.505894 Iteration 2 Error: 0.399473 Iteration 3 Error: 0.203224 Iteration 4 Error: 0.098315 Iteration 5 Error: 0.042950 Align patch 13 12 left Iteration 1 Error: 1.449130 Iteration 2 Error: 0.282146 Iteration 3 Error: 0.104050 Iteration 4 Error: 0.050738 Iteration 5 Error: 0.027253 Align patch 14 11 left Iteration 1 Error: 0.664656 Iteration 2 Error: 0.161535 Iteration 3 Error: 0.062054 Iteration 4 Error: 0.024920 Align patch 15 10 left Iteration 1 Error: 0.686857 Iteration 2 Error: 0.504003 Iteration 3 Error: 0.243647 Iteration 4 Error: 0.199186 Iteration 5 Error: 0.115929 Align patch 15 10 left Iteration 1 Error: 0.824162 Iteration 2 Error: 0.225729 Iteration 3 Error: 0.060150 Iteration 4 Error: 0.030493 Align patch 16 9 left Iteration 1 Error: 2.566206 Iteration 2 Error: 0.504330 Iteration 3 Error: 0.147746 Iteration 4 Error: 0.071474 Iteration 5 Error: 0.039827 Align patch 17 8 left Iteration 1 Error: 1.757094 Iteration 2 Error: 0.482371 Iteration 3 Error: 0.167511 Iteration 4 Error: 0.074622 Iteration 5 Error: 0.032377 Align patch 18 7 left Iteration 1 Error: 1.119954 Iteration 2 Error: 0.346878 Iteration 3 Error: 0.131410 Iteration 4 Error: 0.056494 Iteration 5 Error: 0.032619 Align patch 19 6 left Iteration 1 Error: 0.694679 Iteration 2 Error: 0.157435 Iteration 3 Error: 0.031943 Align patch 20 5 left Iteration 1 Error: 1.573243 Iteration 2 Error: 0.194167 Iteration 3 Error: 0.030267 Align patch 21 4 left Iteration 1 Error: 1.692821 Iteration 2 Error: 0.374154 Iteration 3 Error: 0.210657 Iteration 4 Error: 0.084114 Iteration 5 Error: 0.048857 Align patch 22 3 left Iteration 1 Error: 1.425277 Iteration 2 Error: 0.466861 Iteration 3 Error: 0.186928 Iteration 4 Error: 0.085786 Iteration 5 Error: 0.042915 Align patch 23 2 left Iteration 1 Error: 0.602711 Iteration 2 Error: 0.194057 Iteration 3 Error: 0.066384 Iteration 4 Error: 0.030175 Align patch 24 1 left Iteration 1 Error: 1.577795 Iteration 2 Error: 0.170791 Iteration 3 Error: 0.036879 Align patch 25 0 left Iteration 1 Error: 1.603315 Iteration 2 Error: 0.046572 3D Fitting completed. Patch alignment time: 14.85(sec) Local motion has been corrected. Process thread exits. Computational time: 25.284349 sec Total time: 31.776331 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00003hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00003hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.662350s Reading file: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00003hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.913965s ........................................ >>>>>>TIME<<<<<< FFT: 1.040291s Defocus_U Defocus_V Angle CCC 12316.43 11589.82 84.66 0.066083 Final Values Defocus_U Defocus_V Angle CCC 12322.68 11599.20 84.35 0.114587 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00005sq_v01_00004hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00004hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 38.47 6.68 Num Hot pixels: 225 Hot pixel threshold: 78.54 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.029808 Iteration 2 Error: 0.222872 Iteration 3 Error: 0.083757 Iteration 4 Error: 0.030930 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.19 0.01 ...... Frame ( 3) shift: -0.39 0.02 ...... Frame ( 4) shift: -0.58 0.03 ...... Frame ( 5) shift: -0.78 0.04 ...... Frame ( 6) shift: -0.86 0.05 ...... Frame ( 7) shift: -0.83 0.07 ...... Frame ( 8) shift: -0.80 0.09 ...... Frame ( 9) shift: -0.73 0.14 ...... Frame ( 10) shift: -0.61 0.24 ...... Frame ( 11) shift: -0.49 0.33 ...... Frame ( 12) shift: -0.42 0.39 ...... Frame ( 13) shift: -0.40 0.43 ...... Frame ( 14) shift: -0.38 0.48 ...... Frame ( 15) shift: -0.31 0.48 ...... Frame ( 16) shift: -0.20 0.46 ...... Frame ( 17) shift: -0.09 0.43 ...... Frame ( 18) shift: -0.01 0.46 ...... Frame ( 19) shift: 0.04 0.54 ...... Frame ( 20) shift: 0.09 0.62 ...... Frame ( 21) shift: 0.16 0.68 ...... Frame ( 22) shift: 0.24 0.72 ...... Frame ( 23) shift: 0.32 0.76 ...... Frame ( 24) shift: 0.40 0.79 ...... Frame ( 25) shift: 0.49 0.80 ...... Frame ( 26) shift: 0.57 0.81 ...... Frame ( 27) shift: 0.61 0.81 ...... Frame ( 28) shift: 0.62 0.78 ...... Frame ( 29) shift: 0.62 0.75 ...... Frame ( 30) shift: 0.67 0.73 ...... Frame ( 31) shift: 0.77 0.70 ...... Frame ( 32) shift: 0.86 0.68 ...... Frame ( 33) shift: 0.97 0.70 ...... Frame ( 34) shift: 1.10 0.77 ...... Frame ( 35) shift: 1.23 0.84 ...... Frame ( 36) shift: 1.30 0.93 ...... Frame ( 37) shift: 1.30 1.04 ...... Frame ( 38) shift: 1.31 1.15 ...... Frame ( 39) shift: 1.31 1.26 ...... Frame ( 40) shift: 1.32 1.38 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.763049 Iteration 2 Error: 0.125596 Iteration 3 Error: 0.048487 Align patch 2 23 left Iteration 1 Error: 1.112292 Iteration 2 Error: 0.242936 Iteration 3 Error: 0.069998 Iteration 4 Error: 0.021667 Align patch 3 22 left Iteration 1 Error: 0.835632 Iteration 2 Error: 0.191746 Iteration 3 Error: 0.069574 Iteration 4 Error: 0.032998 Align patch 4 21 left Iteration 1 Error: 0.736939 Iteration 2 Error: 0.150734 Iteration 3 Error: 0.029776 Align patch 5 20 left Iteration 1 Error: 0.610742 Iteration 2 Error: 0.084886 Iteration 3 Error: 0.027320 Align patch 6 19 left Iteration 1 Error: 0.857442 Iteration 2 Error: 0.145118 Iteration 3 Error: 0.057766 Iteration 4 Error: 0.020438 Align patch 7 18 left Iteration 1 Error: 0.681668 Iteration 2 Error: 0.099296 Iteration 3 Error: 0.033024 Align patch 8 17 left Iteration 1 Error: 0.834210 Iteration 2 Error: 0.124728 Iteration 3 Error: 0.024278 Align patch 9 16 left Iteration 1 Error: 0.698323 Iteration 2 Error: 0.084137 Iteration 3 Error: 0.039006 Align patch 10 15 left Iteration 1 Error: 1.006602 Iteration 2 Error: 0.165969 Iteration 3 Error: 0.045065 Align patch 11 14 left Iteration 1 Error: 1.243207 Iteration 2 Error: 0.243069 Iteration 3 Error: 0.077207 Iteration 4 Error: 0.021066 Align patch 12 13 left Iteration 1 Error: 0.993128 Iteration 2 Error: 0.230438 Iteration 3 Error: 0.056994 Iteration 4 Error: 0.031341 Align patch 13 12 left Iteration 1 Error: 0.643530 Iteration 2 Error: 0.128573 Iteration 3 Error: 0.043034 Align patch 14 11 left Iteration 1 Error: 0.593372 Iteration 2 Error: 0.105867 Iteration 3 Error: 0.030364 Align patch 15 10 left Iteration 1 Error: 0.664318 Iteration 2 Error: 0.098384 Iteration 3 Error: 0.027173 Align patch 16 9 left Iteration 1 Error: 0.667681 Iteration 2 Error: 0.153107 Iteration 3 Error: 0.050091 Iteration 4 Error: 0.040766 Align patch 17 8 left Iteration 1 Error: 1.065995 Iteration 2 Error: 0.233618 Iteration 3 Error: 0.050813 Iteration 4 Error: 0.014994 Align patch 18 7 left Iteration 1 Error: 0.806066 Iteration 2 Error: 0.264981 Iteration 3 Error: 0.050419 Iteration 4 Error: 0.017025 Align patch 19 6 left Iteration 1 Error: 0.749678 Iteration 2 Error: 0.142793 Iteration 3 Error: 0.036461 Align patch 20 5 left Iteration 1 Error: 0.840715 Iteration 2 Error: 0.094467 Iteration 3 Error: 0.023517 Align patch 21 4 left Iteration 1 Error: 0.936674 Iteration 2 Error: 0.263505 Iteration 3 Error: 0.087461 Iteration 4 Error: 0.030222 Align patch 22 3 left Iteration 1 Error: 0.838804 Iteration 2 Error: 0.131232 Iteration 3 Error: 0.051842 Iteration 4 Error: 0.016296 Align patch 23 2 left Iteration 1 Error: 0.851889 Iteration 2 Error: 0.177068 Iteration 3 Error: 0.069431 Iteration 4 Error: 0.026110 Align patch 24 1 left Iteration 1 Error: 1.155072 Iteration 2 Error: 0.240586 Iteration 3 Error: 0.066143 Iteration 4 Error: 0.018509 Align patch 25 0 left Iteration 1 Error: 0.954587 Iteration 2 Error: 0.173889 Iteration 3 Error: 0.050705 Iteration 4 Error: 0.044911 3D Fitting completed. Patch alignment time: 11.52(sec) Local motion has been corrected. Process thread exits. Computational time: 21.315500 sec Total time: 27.892452 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00004hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00004hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.487110s Reading file: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00004hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.095973s ........................................ >>>>>>TIME<<<<<< FFT: 1.030268s Defocus_U Defocus_V Angle CCC 8822.35 9318.45 0.96 0.022376 Final Values Defocus_U Defocus_V Angle CCC 8845.85 9307.61 0.65 0.041427 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00005sq_v01_00004hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00004hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.001e-01 CC threshold: 0.735 Mean Std: 37.45 6.51 Num Hot pixels: 229 Hot pixel threshold: 76.50 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.607093 Iteration 2 Error: 0.110360 Iteration 3 Error: 0.025309 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.02 -0.06 ...... Frame ( 3) shift: 0.04 -0.12 ...... Frame ( 4) shift: 0.06 -0.18 ...... Frame ( 5) shift: 0.07 -0.24 ...... Frame ( 6) shift: 0.09 -0.28 ...... Frame ( 7) shift: 0.12 -0.29 ...... Frame ( 8) shift: 0.14 -0.30 ...... Frame ( 9) shift: 0.16 -0.31 ...... Frame ( 10) shift: 0.19 -0.32 ...... Frame ( 11) shift: 0.22 -0.33 ...... Frame ( 12) shift: 0.26 -0.35 ...... Frame ( 13) shift: 0.31 -0.40 ...... Frame ( 14) shift: 0.37 -0.44 ...... Frame ( 15) shift: 0.39 -0.47 ...... Frame ( 16) shift: 0.38 -0.47 ...... Frame ( 17) shift: 0.37 -0.47 ...... Frame ( 18) shift: 0.40 -0.47 ...... Frame ( 19) shift: 0.46 -0.47 ...... Frame ( 20) shift: 0.52 -0.46 ...... Frame ( 21) shift: 0.59 -0.44 ...... Frame ( 22) shift: 0.68 -0.42 ...... Frame ( 23) shift: 0.76 -0.40 ...... Frame ( 24) shift: 0.79 -0.38 ...... Frame ( 25) shift: 0.76 -0.37 ...... Frame ( 26) shift: 0.73 -0.36 ...... Frame ( 27) shift: 0.75 -0.33 ...... Frame ( 28) shift: 0.83 -0.28 ...... Frame ( 29) shift: 0.91 -0.23 ...... Frame ( 30) shift: 0.95 -0.21 ...... Frame ( 31) shift: 0.97 -0.21 ...... Frame ( 32) shift: 0.98 -0.21 ...... Frame ( 33) shift: 0.99 -0.18 ...... Frame ( 34) shift: 0.99 -0.14 ...... Frame ( 35) shift: 0.98 -0.09 ...... Frame ( 36) shift: 1.00 -0.04 ...... Frame ( 37) shift: 1.05 0.01 ...... Frame ( 38) shift: 1.10 0.05 ...... Frame ( 39) shift: 1.14 0.10 ...... Frame ( 40) shift: 1.19 0.15 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.774834 Iteration 2 Error: 0.097454 Iteration 3 Error: 0.022188 Align patch 2 23 left Iteration 1 Error: 0.968474 Iteration 2 Error: 0.098966 Iteration 3 Error: 0.019412 Align patch 3 22 left Iteration 1 Error: 0.646524 Iteration 2 Error: 0.101675 Iteration 3 Error: 0.024899 Align patch 4 21 left Iteration 1 Error: 0.539457 Iteration 2 Error: 0.117618 Iteration 3 Error: 0.028037 Align patch 5 20 left Iteration 1 Error: 0.479229 Iteration 2 Error: 0.117928 Iteration 3 Error: 0.027704 Align patch 6 19 left Iteration 1 Error: 0.703165 Iteration 2 Error: 0.130043 Iteration 3 Error: 0.026598 Align patch 7 18 left Iteration 1 Error: 0.737351 Iteration 2 Error: 0.170043 Iteration 3 Error: 0.053643 Iteration 4 Error: 0.016075 Align patch 8 17 left Iteration 1 Error: 0.664886 Iteration 2 Error: 0.161169 Iteration 3 Error: 0.047228 Align patch 9 16 left Iteration 1 Error: 0.892801 Iteration 2 Error: 0.131284 Iteration 3 Error: 0.046293 Align patch 10 15 left Iteration 1 Error: 0.698102 Iteration 2 Error: 0.126086 Iteration 3 Error: 0.028758 Align patch 11 14 left Iteration 1 Error: 0.585481 Iteration 2 Error: 0.104665 Iteration 3 Error: 0.046439 Align patch 12 13 left Iteration 1 Error: 1.127649 Iteration 2 Error: 0.244953 Iteration 3 Error: 0.044813 Align patch 13 12 left Iteration 1 Error: 0.715581 Iteration 2 Error: 0.245187 Iteration 3 Error: 0.070974 Iteration 4 Error: 0.041208 Align patch 14 11 left Iteration 1 Error: 0.584092 Iteration 2 Error: 0.110917 Iteration 3 Error: 0.033042 Align patch 15 10 left Iteration 1 Error: 1.127817 Iteration 2 Error: 0.175044 Iteration 3 Error: 0.037050 Align patch 16 9 left Iteration 1 Error: 1.052612 Iteration 2 Error: 0.116199 Iteration 3 Error: 0.029009 Align patch 17 8 left Iteration 1 Error: 0.938453 Iteration 2 Error: 0.156929 Iteration 3 Error: 0.054693 Iteration 4 Error: 0.018707 Align patch 18 7 left Iteration 1 Error: 1.072116 Iteration 2 Error: 0.255044 Iteration 3 Error: 0.090589 Iteration 4 Error: 0.025838 Align patch 19 6 left Iteration 1 Error: 0.681422 Iteration 2 Error: 0.147946 Iteration 3 Error: 0.030618 Align patch 20 5 left Iteration 1 Error: 0.707518 Iteration 2 Error: 0.204083 Iteration 3 Error: 0.054920 Iteration 4 Error: 0.022159 Align patch 21 4 left Iteration 1 Error: 0.521033 Iteration 2 Error: 0.105661 Iteration 3 Error: 0.024750 Align patch 22 3 left Iteration 1 Error: 0.783421 Iteration 2 Error: 0.195711 Iteration 3 Error: 0.051926 Iteration 4 Error: 0.017776 Align patch 23 2 left Iteration 1 Error: 0.892628 Iteration 2 Error: 0.194057 Iteration 3 Error: 0.072565 Iteration 4 Error: 0.028433 Align patch 24 1 left Iteration 1 Error: 1.022826 Iteration 2 Error: 0.153269 Iteration 3 Error: 0.048413 Align patch 25 0 left Iteration 1 Error: 0.823873 Iteration 2 Error: 0.145700 Iteration 3 Error: 0.023326 3D Fitting completed. Patch alignment time: 11.68(sec) Local motion has been corrected. Process thread exits. Computational time: 22.531490 sec Total time: 30.220100 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00004hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00004hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.614845s Reading file: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00004hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.640426s ........................................ >>>>>>TIME<<<<<< FFT: 0.920749s Defocus_U Defocus_V Angle CCC 14011.72 14937.50 10.37 0.032159 Final Values Defocus_U Defocus_V Angle CCC 14028.76 14923.58 12.27 0.044968 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00005sq_v01_00004hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00004hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 40.38 6.87 Num Hot pixels: 252 Hot pixel threshold: 81.57 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.002854 Iteration 2 Error: 0.189745 Iteration 3 Error: 0.047263 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.25 -0.12 ...... Frame ( 3) shift: -0.50 -0.24 ...... Frame ( 4) shift: -0.74 -0.37 ...... Frame ( 5) shift: -0.99 -0.49 ...... Frame ( 6) shift: -1.11 -0.55 ...... Frame ( 7) shift: -1.11 -0.55 ...... Frame ( 8) shift: -1.10 -0.55 ...... Frame ( 9) shift: -1.07 -0.47 ...... Frame ( 10) shift: -1.01 -0.30 ...... Frame ( 11) shift: -0.95 -0.13 ...... Frame ( 12) shift: -0.88 -0.00 ...... Frame ( 13) shift: -0.80 0.08 ...... Frame ( 14) shift: -0.72 0.16 ...... Frame ( 15) shift: -0.66 0.23 ...... Frame ( 16) shift: -0.62 0.29 ...... Frame ( 17) shift: -0.57 0.35 ...... Frame ( 18) shift: -0.53 0.40 ...... Frame ( 19) shift: -0.48 0.46 ...... Frame ( 20) shift: -0.44 0.52 ...... Frame ( 21) shift: -0.36 0.56 ...... Frame ( 22) shift: -0.26 0.59 ...... Frame ( 23) shift: -0.16 0.62 ...... Frame ( 24) shift: -0.09 0.65 ...... Frame ( 25) shift: -0.04 0.69 ...... Frame ( 26) shift: 0.01 0.72 ...... Frame ( 27) shift: 0.06 0.76 ...... Frame ( 28) shift: 0.09 0.79 ...... Frame ( 29) shift: 0.12 0.83 ...... Frame ( 30) shift: 0.16 0.84 ...... Frame ( 31) shift: 0.20 0.82 ...... Frame ( 32) shift: 0.24 0.81 ...... Frame ( 33) shift: 0.30 0.82 ...... Frame ( 34) shift: 0.36 0.86 ...... Frame ( 35) shift: 0.43 0.91 ...... Frame ( 36) shift: 0.44 0.95 ...... Frame ( 37) shift: 0.42 0.99 ...... Frame ( 38) shift: 0.39 1.03 ...... Frame ( 39) shift: 0.36 1.07 ...... Frame ( 40) shift: 0.33 1.12 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.739000 Iteration 2 Error: 0.137774 Iteration 3 Error: 0.031935 Align patch 2 23 left Iteration 1 Error: 0.643796 Iteration 2 Error: 0.089910 Iteration 3 Error: 0.022304 Align patch 3 22 left Iteration 1 Error: 0.560820 Iteration 2 Error: 0.085505 Iteration 3 Error: 0.018696 Align patch 4 21 left Iteration 1 Error: 0.679180 Iteration 2 Error: 0.083838 Iteration 3 Error: 0.024034 Align patch 5 20 left Iteration 1 Error: 0.642221 Iteration 2 Error: 0.102289 Iteration 3 Error: 0.024752 Align patch 6 19 left Iteration 1 Error: 0.527588 Iteration 2 Error: 0.071220 Iteration 3 Error: 0.023771 Align patch 7 18 left Iteration 1 Error: 0.460657 Iteration 2 Error: 0.078863 Iteration 3 Error: 0.033431 Align patch 8 17 left Iteration 1 Error: 0.599648 Iteration 2 Error: 0.130428 Iteration 3 Error: 0.036323 Align patch 9 16 left Iteration 1 Error: 0.555796 Iteration 2 Error: 0.093901 Iteration 3 Error: 0.014638 Align patch 10 15 left Iteration 1 Error: 0.616229 Iteration 2 Error: 0.094094 Iteration 3 Error: 0.024728 Align patch 11 14 left Iteration 1 Error: 0.823416 Iteration 2 Error: 0.059955 Iteration 3 Error: 0.015228 Align patch 12 13 left Iteration 1 Error: 0.613119 Iteration 2 Error: 0.070812 Iteration 3 Error: 0.018988 Align patch 13 12 left Iteration 1 Error: 0.623699 Iteration 2 Error: 0.118215 Iteration 3 Error: 0.035753 Align patch 14 11 left Iteration 1 Error: 0.518641 Iteration 2 Error: 0.079644 Iteration 3 Error: 0.024536 Align patch 15 10 left Iteration 1 Error: 0.545829 Iteration 2 Error: 0.104294 Iteration 3 Error: 0.033789 Align patch 16 9 left Iteration 1 Error: 0.887018 Iteration 2 Error: 0.128409 Iteration 3 Error: 0.031713 Align patch 17 8 left Iteration 1 Error: 0.990167 Iteration 2 Error: 0.139921 Iteration 3 Error: 0.025314 Align patch 18 7 left Iteration 1 Error: 0.618890 Iteration 2 Error: 0.115419 Iteration 3 Error: 0.029578 Align patch 19 6 left Iteration 1 Error: 0.685535 Iteration 2 Error: 0.186428 Iteration 3 Error: 0.037273 Align patch 20 5 left Iteration 1 Error: 0.673169 Iteration 2 Error: 0.120776 Iteration 3 Error: 0.033331 Align patch 21 4 left Iteration 1 Error: 1.211102 Iteration 2 Error: 0.101014 Iteration 3 Error: 0.019315 Align patch 22 3 left Iteration 1 Error: 1.139147 Iteration 2 Error: 0.165546 Iteration 3 Error: 0.034084 Align patch 23 2 left Iteration 1 Error: 0.775446 Iteration 2 Error: 0.097358 Iteration 3 Error: 0.021820 Align patch 24 1 left Iteration 1 Error: 0.905942 Iteration 2 Error: 0.180712 Iteration 3 Error: 0.037187 Align patch 25 0 left Iteration 1 Error: 0.810339 Iteration 2 Error: 0.111081 Iteration 3 Error: 0.026184 3D Fitting completed. Patch alignment time: 11.09(sec) Local motion has been corrected. Process thread exits. Computational time: 22.072834 sec Total time: 29.540501 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00004hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00004hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.739631s Reading file: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00004hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.544544s ........................................ >>>>>>TIME<<<<<< FFT: 1.003297s Defocus_U Defocus_V Angle CCC 12828.12 12140.62 86.03 0.051871 Final Values Defocus_U Defocus_V Angle CCC 12848.46 12148.46 86.34 0.087061 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00005sq_v01_00005hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00005hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.350e-01 1.004e-01 CC threshold: 0.737 Mean Std: 41.92 7.11 Num Hot pixels: 226 Hot pixel threshold: 84.59 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.234023 Iteration 2 Error: 0.192359 Iteration 3 Error: 0.036819 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.08 0.05 ...... Frame ( 3) shift: -0.16 0.10 ...... Frame ( 4) shift: -0.24 0.14 ...... Frame ( 5) shift: -0.33 0.19 ...... Frame ( 6) shift: -0.36 0.27 ...... Frame ( 7) shift: -0.36 0.39 ...... Frame ( 8) shift: -0.35 0.52 ...... Frame ( 9) shift: -0.29 0.62 ...... Frame ( 10) shift: -0.17 0.72 ...... Frame ( 11) shift: -0.04 0.81 ...... Frame ( 12) shift: 0.01 0.88 ...... Frame ( 13) shift: 0.01 0.93 ...... Frame ( 14) shift: 0.00 0.98 ...... Frame ( 15) shift: 0.08 1.02 ...... Frame ( 16) shift: 0.26 1.05 ...... Frame ( 17) shift: 0.43 1.08 ...... Frame ( 18) shift: 0.52 1.09 ...... Frame ( 19) shift: 0.51 1.09 ...... Frame ( 20) shift: 0.51 1.08 ...... Frame ( 21) shift: 0.53 1.08 ...... Frame ( 22) shift: 0.57 1.08 ...... Frame ( 23) shift: 0.62 1.07 ...... Frame ( 24) shift: 0.65 1.10 ...... Frame ( 25) shift: 0.67 1.15 ...... Frame ( 26) shift: 0.70 1.20 ...... Frame ( 27) shift: 0.75 1.22 ...... Frame ( 28) shift: 0.82 1.21 ...... Frame ( 29) shift: 0.90 1.19 ...... Frame ( 30) shift: 0.95 1.21 ...... Frame ( 31) shift: 0.99 1.27 ...... Frame ( 32) shift: 1.02 1.32 ...... Frame ( 33) shift: 1.07 1.38 ...... Frame ( 34) shift: 1.15 1.43 ...... Frame ( 35) shift: 1.22 1.49 ...... Frame ( 36) shift: 1.31 1.54 ...... Frame ( 37) shift: 1.41 1.57 ...... Frame ( 38) shift: 1.51 1.61 ...... Frame ( 39) shift: 1.61 1.64 ...... Frame ( 40) shift: 1.71 1.68 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.154532 Iteration 2 Error: 0.314389 Iteration 3 Error: 0.090824 Iteration 4 Error: 0.031051 Align patch 2 23 left Iteration 1 Error: 1.067124 Iteration 2 Error: 0.234231 Iteration 3 Error: 0.127843 Iteration 4 Error: 0.036958 Align patch 3 22 left Iteration 1 Error: 0.688125 Iteration 2 Error: 0.129285 Iteration 3 Error: 0.036964 Align patch 4 21 left Iteration 1 Error: 0.453727 Iteration 2 Error: 0.091410 Iteration 3 Error: 0.012415 Align patch 5 20 left Iteration 1 Error: 0.403993 Iteration 2 Error: 0.084792 Iteration 3 Error: 0.020854 Align patch 6 19 left Iteration 1 Error: 1.636457 Iteration 2 Error: 0.274277 Iteration 3 Error: 0.081521 Iteration 4 Error: 0.020108 Align patch 7 18 left Iteration 1 Error: 0.614313 Iteration 2 Error: 0.132441 Iteration 3 Error: 0.030782 Align patch 8 17 left Iteration 1 Error: 0.640733 Iteration 2 Error: 0.099683 Iteration 3 Error: 0.025890 Align patch 9 16 left Iteration 1 Error: 0.486311 Iteration 2 Error: 0.074767 Iteration 3 Error: 0.019940 Align patch 10 15 left Iteration 1 Error: 0.571585 Iteration 2 Error: 0.071924 Iteration 3 Error: 0.011840 Align patch 11 14 left Iteration 1 Error: 0.732121 Iteration 2 Error: 0.103654 Iteration 3 Error: 0.051078 Iteration 4 Error: 0.014496 Align patch 12 13 left Iteration 1 Error: 0.579888 Iteration 2 Error: 0.102741 Iteration 3 Error: 0.017915 Align patch 13 12 left Iteration 1 Error: 0.477609 Iteration 2 Error: 0.040994 Align patch 14 11 left Iteration 1 Error: 0.437538 Iteration 2 Error: 0.044390 Align patch 15 10 left Iteration 1 Error: 0.421111 Iteration 2 Error: 0.061894 Iteration 3 Error: 0.011239 Align patch 16 9 left Iteration 1 Error: 0.748734 Iteration 2 Error: 0.106761 Iteration 3 Error: 0.034028 Align patch 17 8 left Iteration 1 Error: 0.642450 Iteration 2 Error: 0.069545 Iteration 3 Error: 0.014296 Align patch 18 7 left Iteration 1 Error: 0.580662 Iteration 2 Error: 0.074857 Iteration 3 Error: 0.018196 Align patch 19 6 left Iteration 1 Error: 0.545087 Iteration 2 Error: 0.062014 Iteration 3 Error: 0.011576 Align patch 20 5 left Iteration 1 Error: 0.644133 Iteration 2 Error: 0.065793 Iteration 3 Error: 0.014313 Align patch 21 4 left Iteration 1 Error: 0.489298 Iteration 2 Error: 0.050893 Iteration 3 Error: 0.012357 Align patch 22 3 left Iteration 1 Error: 0.722935 Iteration 2 Error: 0.184615 Iteration 3 Error: 0.028154 Align patch 23 2 left Iteration 1 Error: 0.870290 Iteration 2 Error: 0.086398 Iteration 3 Error: 0.017978 Align patch 24 1 left Iteration 1 Error: 0.738311 Iteration 2 Error: 0.085686 Iteration 3 Error: 0.013402 Align patch 25 0 left Iteration 1 Error: 0.563465 Iteration 2 Error: 0.077035 Iteration 3 Error: 0.013835 3D Fitting completed. Patch alignment time: 11.36(sec) Local motion has been corrected. Process thread exits. Computational time: 22.622660 sec Total time: 29.968065 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00005hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00005hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.579866s Reading file: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00005hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.864779s ........................................ >>>>>>TIME<<<<<< FFT: 1.002000s Defocus_U Defocus_V Angle CCC 12896.48 13720.70 12.02 0.069601 Final Values Defocus_U Defocus_V Angle CCC 12905.86 13720.71 12.34 0.113475 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00005sq_v01_00005hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00005hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.350e-01 1.004e-01 CC threshold: 0.737 Mean Std: 40.97 7.05 Num Hot pixels: 231 Hot pixel threshold: 83.26 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.763051 Iteration 2 Error: 0.122081 Iteration 3 Error: 0.027890 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.13 0.10 ...... Frame ( 3) shift: -0.27 0.20 ...... Frame ( 4) shift: -0.40 0.30 ...... Frame ( 5) shift: -0.54 0.39 ...... Frame ( 6) shift: -0.61 0.45 ...... Frame ( 7) shift: -0.62 0.46 ...... Frame ( 8) shift: -0.63 0.48 ...... Frame ( 9) shift: -0.64 0.53 ...... Frame ( 10) shift: -0.66 0.61 ...... Frame ( 11) shift: -0.69 0.70 ...... Frame ( 12) shift: -0.69 0.74 ...... Frame ( 13) shift: -0.67 0.73 ...... Frame ( 14) shift: -0.65 0.73 ...... Frame ( 15) shift: -0.64 0.75 ...... Frame ( 16) shift: -0.62 0.78 ...... Frame ( 17) shift: -0.60 0.82 ...... Frame ( 18) shift: -0.55 0.87 ...... Frame ( 19) shift: -0.44 0.93 ...... Frame ( 20) shift: -0.34 1.00 ...... Frame ( 21) shift: -0.27 1.05 ...... Frame ( 22) shift: -0.21 1.08 ...... Frame ( 23) shift: -0.16 1.12 ...... Frame ( 24) shift: -0.11 1.15 ...... Frame ( 25) shift: -0.06 1.18 ...... Frame ( 26) shift: -0.02 1.21 ...... Frame ( 27) shift: 0.01 1.23 ...... Frame ( 28) shift: 0.00 1.23 ...... Frame ( 29) shift: -0.00 1.23 ...... Frame ( 30) shift: 0.03 1.25 ...... Frame ( 31) shift: 0.09 1.29 ...... Frame ( 32) shift: 0.16 1.33 ...... Frame ( 33) shift: 0.21 1.32 ...... Frame ( 34) shift: 0.25 1.28 ...... Frame ( 35) shift: 0.29 1.23 ...... Frame ( 36) shift: 0.34 1.22 ...... Frame ( 37) shift: 0.40 1.26 ...... Frame ( 38) shift: 0.45 1.29 ...... Frame ( 39) shift: 0.51 1.33 ...... Frame ( 40) shift: 0.57 1.37 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.182053 Iteration 2 Error: 0.393010 Iteration 3 Error: 0.192787 Iteration 4 Error: 0.095870 Iteration 5 Error: 0.043432 Align patch 2 23 left Iteration 1 Error: 0.750891 Iteration 2 Error: 0.161304 Iteration 3 Error: 0.059345 Iteration 4 Error: 0.022280 Align patch 3 22 left Iteration 1 Error: 0.398778 Iteration 2 Error: 0.079635 Iteration 3 Error: 0.023602 Align patch 4 21 left Iteration 1 Error: 0.508842 Iteration 2 Error: 0.066046 Iteration 3 Error: 0.009819 Align patch 5 20 left Iteration 1 Error: 1.004863 Iteration 2 Error: 0.266900 Iteration 3 Error: 0.084819 Iteration 4 Error: 0.028354 Align patch 6 19 left Iteration 1 Error: 1.321443 Iteration 2 Error: 0.312842 Iteration 3 Error: 0.112119 Iteration 4 Error: 0.043285 Align patch 7 18 left Iteration 1 Error: 1.151984 Iteration 2 Error: 0.167545 Iteration 3 Error: 0.045265 Align patch 8 17 left Iteration 1 Error: 0.418811 Iteration 2 Error: 0.070688 Iteration 3 Error: 0.013896 Align patch 9 16 left Iteration 1 Error: 0.470244 Iteration 2 Error: 0.049479 Align patch 10 15 left Iteration 1 Error: 0.694259 Iteration 2 Error: 0.126058 Iteration 3 Error: 0.026229 Align patch 11 14 left Iteration 1 Error: 0.742536 Iteration 2 Error: 0.200018 Iteration 3 Error: 0.070224 Iteration 4 Error: 0.025691 Align patch 12 13 left Iteration 1 Error: 0.759940 Iteration 2 Error: 0.152902 Iteration 3 Error: 0.034479 Align patch 13 12 left Iteration 1 Error: 0.343531 Iteration 2 Error: 0.059785 Iteration 3 Error: 0.015718 Align patch 14 11 left Iteration 1 Error: 0.675442 Iteration 2 Error: 0.071488 Iteration 3 Error: 0.012475 Align patch 15 10 left Iteration 1 Error: 0.684172 Iteration 2 Error: 0.111802 Iteration 3 Error: 0.013819 Align patch 16 9 left Iteration 1 Error: 0.555066 Iteration 2 Error: 0.085892 Iteration 3 Error: 0.023878 Align patch 17 8 left Iteration 1 Error: 0.603379 Iteration 2 Error: 0.124034 Iteration 3 Error: 0.017916 Align patch 18 7 left Iteration 1 Error: 0.466034 Iteration 2 Error: 0.044475 Align patch 19 6 left Iteration 1 Error: 0.385499 Iteration 2 Error: 0.048264 Align patch 20 5 left Iteration 1 Error: 0.459522 Iteration 2 Error: 0.040362 Align patch 21 4 left Iteration 1 Error: 0.705307 Iteration 2 Error: 0.107184 Iteration 3 Error: 0.037026 Align patch 22 3 left Iteration 1 Error: 1.088310 Iteration 2 Error: 0.099911 Iteration 3 Error: 0.024287 Align patch 23 2 left Iteration 1 Error: 0.497434 Iteration 2 Error: 0.071240 Iteration 3 Error: 0.012944 Align patch 24 1 left Iteration 1 Error: 0.651209 Iteration 2 Error: 0.089479 Iteration 3 Error: 0.019043 Align patch 25 0 left Iteration 1 Error: 0.715902 Iteration 2 Error: 0.099473 Iteration 3 Error: 0.026464 3D Fitting completed. Patch alignment time: 11.23(sec) Local motion has been corrected. Process thread exits. Computational time: 21.984402 sec Total time: 29.159153 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00005hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00005hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.519092s Reading file: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00005hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.773102s ........................................ >>>>>>TIME<<<<<< FFT: 0.989490s Defocus_U Defocus_V Angle CCC 10216.75 10666.09 3.42 0.057085 Final Values Defocus_U Defocus_V Angle CCC 10235.51 10684.85 2.17 0.099682 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00005sq_v01_00005hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00005hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.002e-01 CC threshold: 0.736 Mean Std: 43.55 7.27 Num Hot pixels: 234 Hot pixel threshold: 87.18 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.083818 Iteration 2 Error: 0.183456 Iteration 3 Error: 0.039536 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.19 -0.09 ...... Frame ( 3) shift: -0.38 -0.17 ...... Frame ( 4) shift: -0.57 -0.26 ...... Frame ( 5) shift: -0.76 -0.34 ...... Frame ( 6) shift: -0.83 -0.37 ...... Frame ( 7) shift: -0.77 -0.33 ...... Frame ( 8) shift: -0.71 -0.29 ...... Frame ( 9) shift: -0.67 -0.20 ...... Frame ( 10) shift: -0.63 -0.07 ...... Frame ( 11) shift: -0.60 0.06 ...... Frame ( 12) shift: -0.53 0.16 ...... Frame ( 13) shift: -0.43 0.22 ...... Frame ( 14) shift: -0.33 0.27 ...... Frame ( 15) shift: -0.22 0.34 ...... Frame ( 16) shift: -0.07 0.43 ...... Frame ( 17) shift: 0.07 0.51 ...... Frame ( 18) shift: 0.16 0.58 ...... Frame ( 19) shift: 0.21 0.64 ...... Frame ( 20) shift: 0.25 0.70 ...... Frame ( 21) shift: 0.32 0.73 ...... Frame ( 22) shift: 0.39 0.73 ...... Frame ( 23) shift: 0.47 0.73 ...... Frame ( 24) shift: 0.53 0.72 ...... Frame ( 25) shift: 0.55 0.71 ...... Frame ( 26) shift: 0.57 0.69 ...... Frame ( 27) shift: 0.61 0.69 ...... Frame ( 28) shift: 0.65 0.71 ...... Frame ( 29) shift: 0.70 0.73 ...... Frame ( 30) shift: 0.75 0.75 ...... Frame ( 31) shift: 0.78 0.77 ...... Frame ( 32) shift: 0.82 0.80 ...... Frame ( 33) shift: 0.87 0.79 ...... Frame ( 34) shift: 0.92 0.77 ...... Frame ( 35) shift: 0.97 0.74 ...... Frame ( 36) shift: 1.01 0.73 ...... Frame ( 37) shift: 1.04 0.74 ...... Frame ( 38) shift: 1.07 0.74 ...... Frame ( 39) shift: 1.10 0.75 ...... Frame ( 40) shift: 1.13 0.76 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.470906 Iteration 2 Error: 0.341040 Iteration 3 Error: 0.097995 Iteration 4 Error: 0.045843 Align patch 2 23 left Iteration 1 Error: 2.078713 Iteration 2 Error: 0.218841 Iteration 3 Error: 0.084225 Iteration 4 Error: 0.029493 Align patch 3 22 left Iteration 1 Error: 1.028105 Iteration 2 Error: 0.209247 Iteration 3 Error: 0.068829 Iteration 4 Error: 0.026573 Align patch 4 21 left Iteration 1 Error: 0.483442 Iteration 2 Error: 0.063014 Iteration 3 Error: 0.012644 Align patch 5 20 left Iteration 1 Error: 0.521379 Iteration 2 Error: 0.069711 Iteration 3 Error: 0.013049 Align patch 6 19 left Iteration 1 Error: 1.592606 Iteration 2 Error: 0.229525 Iteration 3 Error: 0.055380 Iteration 4 Error: 0.019128 Align patch 7 18 left Iteration 1 Error: 1.431612 Iteration 2 Error: 0.260348 Iteration 3 Error: 0.066086 Iteration 4 Error: 0.025001 Align patch 8 17 left Iteration 1 Error: 0.579088 Iteration 2 Error: 0.120070 Iteration 3 Error: 0.040805 Align patch 9 16 left Iteration 1 Error: 0.545406 Iteration 2 Error: 0.102983 Iteration 3 Error: 0.013070 Align patch 10 15 left Iteration 1 Error: 0.402981 Iteration 2 Error: 0.040982 Align patch 11 14 left Iteration 1 Error: 0.841831 Iteration 2 Error: 0.237803 Iteration 3 Error: 0.083153 Iteration 4 Error: 0.025530 Align patch 12 13 left Iteration 1 Error: 1.178816 Iteration 2 Error: 0.143928 Iteration 3 Error: 0.044355 Align patch 13 12 left Iteration 1 Error: 0.524901 Iteration 2 Error: 0.091922 Iteration 3 Error: 0.020070 Align patch 14 11 left Iteration 1 Error: 0.413475 Iteration 2 Error: 0.049249 Align patch 15 10 left Iteration 1 Error: 0.526972 Iteration 2 Error: 0.063179 Iteration 3 Error: 0.020628 Align patch 16 9 left Iteration 1 Error: 0.748076 Iteration 2 Error: 0.159445 Iteration 3 Error: 0.051777 Iteration 4 Error: 0.026840 Align patch 17 8 left Iteration 1 Error: 0.779842 Iteration 2 Error: 0.110171 Iteration 3 Error: 0.022638 Align patch 18 7 left Iteration 1 Error: 0.582950 Iteration 2 Error: 0.064359 Iteration 3 Error: 0.012503 Align patch 19 6 left Iteration 1 Error: 0.428321 Iteration 2 Error: 0.079899 Iteration 3 Error: 0.015753 Align patch 20 5 left Iteration 1 Error: 0.770296 Iteration 2 Error: 0.158638 Iteration 3 Error: 0.023205 Align patch 21 4 left Iteration 1 Error: 0.895339 Iteration 2 Error: 0.105526 Iteration 3 Error: 0.030507 Align patch 22 3 left Iteration 1 Error: 0.941976 Iteration 2 Error: 0.092694 Iteration 3 Error: 0.018973 Align patch 23 2 left Iteration 1 Error: 0.945740 Iteration 2 Error: 0.095485 Iteration 3 Error: 0.028700 Align patch 24 1 left Iteration 1 Error: 1.098869 Iteration 2 Error: 0.125166 Iteration 3 Error: 0.024358 Align patch 25 0 left Iteration 1 Error: 0.901070 Iteration 2 Error: 0.155252 Iteration 3 Error: 0.029934 3D Fitting completed. Patch alignment time: 11.87(sec) Local motion has been corrected. Process thread exits. Computational time: 21.139147 sec Total time: 27.898956 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00005hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00005hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.665404s Reading file: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00005hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.357472s ........................................ >>>>>>TIME<<<<<< FFT: 0.965611s Defocus_U Defocus_V Angle CCC 14093.76 14964.85 3.82 0.068874 Final Values Defocus_U Defocus_V Angle CCC 14095.32 14941.41 3.82 0.111096 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00005sq_v01_00005hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00005hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 42.61 7.26 Num Hot pixels: 223 Hot pixel threshold: 86.17 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.583362 Iteration 2 Error: 0.058764 Iteration 3 Error: 0.011377 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.15 0.07 ...... Frame ( 3) shift: -0.30 0.14 ...... Frame ( 4) shift: -0.46 0.21 ...... Frame ( 5) shift: -0.61 0.28 ...... Frame ( 6) shift: -0.69 0.34 ...... Frame ( 7) shift: -0.70 0.40 ...... Frame ( 8) shift: -0.71 0.46 ...... Frame ( 9) shift: -0.69 0.54 ...... Frame ( 10) shift: -0.62 0.66 ...... Frame ( 11) shift: -0.56 0.77 ...... Frame ( 12) shift: -0.52 0.82 ...... Frame ( 13) shift: -0.50 0.81 ...... Frame ( 14) shift: -0.49 0.81 ...... Frame ( 15) shift: -0.47 0.80 ...... Frame ( 16) shift: -0.46 0.80 ...... Frame ( 17) shift: -0.45 0.80 ...... Frame ( 18) shift: -0.42 0.78 ...... Frame ( 19) shift: -0.39 0.77 ...... Frame ( 20) shift: -0.35 0.75 ...... Frame ( 21) shift: -0.33 0.76 ...... Frame ( 22) shift: -0.34 0.80 ...... Frame ( 23) shift: -0.35 0.85 ...... Frame ( 24) shift: -0.32 0.86 ...... Frame ( 25) shift: -0.24 0.85 ...... Frame ( 26) shift: -0.17 0.83 ...... Frame ( 27) shift: -0.14 0.82 ...... Frame ( 28) shift: -0.16 0.80 ...... Frame ( 29) shift: -0.18 0.78 ...... Frame ( 30) shift: -0.18 0.75 ...... Frame ( 31) shift: -0.16 0.73 ...... Frame ( 32) shift: -0.13 0.71 ...... Frame ( 33) shift: -0.12 0.68 ...... Frame ( 34) shift: -0.13 0.63 ...... Frame ( 35) shift: -0.14 0.58 ...... Frame ( 36) shift: -0.14 0.58 ...... Frame ( 37) shift: -0.13 0.63 ...... Frame ( 38) shift: -0.11 0.69 ...... Frame ( 39) shift: -0.10 0.75 ...... Frame ( 40) shift: -0.09 0.80 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.759294 Iteration 2 Error: 0.199146 Iteration 3 Error: 0.054072 Iteration 4 Error: 0.016542 Align patch 2 23 left Iteration 1 Error: 1.241009 Iteration 2 Error: 0.230521 Iteration 3 Error: 0.045375 Align patch 3 22 left Iteration 1 Error: 0.855261 Iteration 2 Error: 0.129031 Iteration 3 Error: 0.035388 Align patch 4 21 left Iteration 1 Error: 0.535976 Iteration 2 Error: 0.046570 Align patch 5 20 left Iteration 1 Error: 0.608701 Iteration 2 Error: 0.062832 Iteration 3 Error: 0.007517 Align patch 6 19 left Iteration 1 Error: 0.960332 Iteration 2 Error: 0.107851 Iteration 3 Error: 0.036496 Align patch 7 18 left Iteration 1 Error: 0.651090 Iteration 2 Error: 0.173596 Iteration 3 Error: 0.044682 Align patch 8 17 left Iteration 1 Error: 0.723558 Iteration 2 Error: 0.116439 Iteration 3 Error: 0.034051 Align patch 9 16 left Iteration 1 Error: 0.588559 Iteration 2 Error: 0.099254 Iteration 3 Error: 0.011394 Align patch 10 15 left Iteration 1 Error: 0.570142 Iteration 2 Error: 0.076799 Iteration 3 Error: 0.015158 Align patch 11 14 left Iteration 1 Error: 0.663863 Iteration 2 Error: 0.081820 Iteration 3 Error: 0.018722 Align patch 12 13 left Iteration 1 Error: 0.654895 Iteration 2 Error: 0.093737 Iteration 3 Error: 0.014747 Align patch 13 12 left Iteration 1 Error: 0.655456 Iteration 2 Error: 0.109629 Iteration 3 Error: 0.018656 Align patch 14 11 left Iteration 1 Error: 0.466609 Iteration 2 Error: 0.047392 Align patch 15 10 left Iteration 1 Error: 0.506094 Iteration 2 Error: 0.057707 Iteration 3 Error: 0.011516 Align patch 16 9 left Iteration 1 Error: 0.680166 Iteration 2 Error: 0.074788 Iteration 3 Error: 0.014492 Align patch 17 8 left Iteration 1 Error: 0.711852 Iteration 2 Error: 0.083316 Iteration 3 Error: 0.017968 Align patch 18 7 left Iteration 1 Error: 0.720327 Iteration 2 Error: 0.081871 Iteration 3 Error: 0.021589 Align patch 19 6 left Iteration 1 Error: 0.573182 Iteration 2 Error: 0.041059 Align patch 20 5 left Iteration 1 Error: 0.629164 Iteration 2 Error: 0.089474 Iteration 3 Error: 0.011187 Align patch 21 4 left Iteration 1 Error: 0.592094 Iteration 2 Error: 0.062568 Iteration 3 Error: 0.015409 Align patch 22 3 left Iteration 1 Error: 0.657486 Iteration 2 Error: 0.107570 Iteration 3 Error: 0.025540 Align patch 23 2 left Iteration 1 Error: 0.773465 Iteration 2 Error: 0.113864 Iteration 3 Error: 0.028314 Align patch 24 1 left Iteration 1 Error: 0.613005 Iteration 2 Error: 0.115299 Iteration 3 Error: 0.026722 Align patch 25 0 left Iteration 1 Error: 0.661755 Iteration 2 Error: 0.061196 Iteration 3 Error: 0.010830 3D Fitting completed. Patch alignment time: 11.89(sec) Local motion has been corrected. Process thread exits. Computational time: 21.906981 sec Total time: 30.942446 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00005hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00005hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.613732s Reading file: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00005hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.870022s ........................................ >>>>>>TIME<<<<<< FFT: 1.011429s Defocus_U Defocus_V Angle CCC 14608.68 15098.35 8.12 0.066023 Final Values Defocus_U Defocus_V Angle CCC 15170.28 14521.13 84.79 0.106958 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00005sq_v01_00006hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00006hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.002e-01 CC threshold: 0.736 Mean Std: 42.62 7.19 Num Hot pixels: 233 Hot pixel threshold: 85.76 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.919750 Iteration 2 Error: 0.424113 Iteration 3 Error: 0.099910 Iteration 4 Error: 0.036219 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.20 -0.06 ...... Frame ( 3) shift: -0.41 -0.12 ...... Frame ( 4) shift: -0.61 -0.17 ...... Frame ( 5) shift: -0.81 -0.23 ...... Frame ( 6) shift: -0.85 -0.19 ...... Frame ( 7) shift: -0.74 -0.05 ...... Frame ( 8) shift: -0.62 0.09 ...... Frame ( 9) shift: -0.51 0.23 ...... Frame ( 10) shift: -0.40 0.37 ...... Frame ( 11) shift: -0.30 0.51 ...... Frame ( 12) shift: -0.22 0.63 ...... Frame ( 13) shift: -0.16 0.72 ...... Frame ( 14) shift: -0.10 0.82 ...... Frame ( 15) shift: -0.01 0.93 ...... Frame ( 16) shift: 0.13 1.08 ...... Frame ( 17) shift: 0.27 1.22 ...... Frame ( 18) shift: 0.37 1.35 ...... Frame ( 19) shift: 0.46 1.46 ...... Frame ( 20) shift: 0.54 1.58 ...... Frame ( 21) shift: 0.60 1.67 ...... Frame ( 22) shift: 0.66 1.73 ...... Frame ( 23) shift: 0.71 1.79 ...... Frame ( 24) shift: 0.77 1.88 ...... Frame ( 25) shift: 0.85 1.99 ...... Frame ( 26) shift: 0.92 2.11 ...... Frame ( 27) shift: 0.97 2.21 ...... Frame ( 28) shift: 1.00 2.30 ...... Frame ( 29) shift: 1.04 2.39 ...... Frame ( 30) shift: 1.07 2.47 ...... Frame ( 31) shift: 1.11 2.55 ...... Frame ( 32) shift: 1.15 2.62 ...... Frame ( 33) shift: 1.20 2.68 ...... Frame ( 34) shift: 1.25 2.71 ...... Frame ( 35) shift: 1.31 2.74 ...... Frame ( 36) shift: 1.36 2.82 ...... Frame ( 37) shift: 1.42 2.92 ...... Frame ( 38) shift: 1.48 3.03 ...... Frame ( 39) shift: 1.54 3.14 ...... Frame ( 40) shift: 1.60 3.25 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.844928 Iteration 2 Error: 0.556040 Iteration 3 Error: 0.232588 Iteration 4 Error: 0.099725 Iteration 5 Error: 0.040142 Align patch 2 23 left Iteration 1 Error: 1.784278 Iteration 2 Error: 0.408784 Iteration 3 Error: 0.087047 Iteration 4 Error: 0.038039 Align patch 3 22 left Iteration 1 Error: 0.813741 Iteration 2 Error: 0.204705 Iteration 3 Error: 0.048560 Align patch 4 21 left Iteration 1 Error: 0.367610 Iteration 2 Error: 0.064914 Iteration 3 Error: 0.009964 Align patch 5 20 left Iteration 1 Error: 0.722030 Iteration 2 Error: 0.083360 Iteration 3 Error: 0.021260 Align patch 6 19 left Iteration 1 Error: 3.533891 Iteration 2 Error: 0.742354 Iteration 3 Error: 0.158152 Iteration 4 Error: 0.068384 Iteration 5 Error: 0.036046 Align patch 7 18 left Iteration 1 Error: 1.608158 Iteration 2 Error: 0.360220 Iteration 3 Error: 0.084312 Iteration 4 Error: 0.033681 Align patch 8 17 left Iteration 1 Error: 0.773872 Iteration 2 Error: 0.132443 Iteration 3 Error: 0.042874 Align patch 9 16 left Iteration 1 Error: 0.378262 Iteration 2 Error: 0.032048 Align patch 10 15 left Iteration 1 Error: 0.454626 Iteration 2 Error: 0.078509 Iteration 3 Error: 0.015654 Align patch 11 14 left Iteration 1 Error: 2.439472 Iteration 2 Error: 0.306051 Iteration 3 Error: 0.108659 Iteration 4 Error: 0.048005 Align patch 12 13 left Iteration 1 Error: 0.641258 Iteration 2 Error: 0.086216 Iteration 3 Error: 0.033996 Align patch 13 12 left Iteration 1 Error: 0.621938 Iteration 2 Error: 0.143051 Iteration 3 Error: 0.035125 Align patch 14 11 left Iteration 1 Error: 0.672571 Iteration 2 Error: 0.099760 Iteration 3 Error: 0.029526 Align patch 15 10 left Iteration 1 Error: 0.626057 Iteration 2 Error: 0.167233 Iteration 3 Error: 0.026407 Align patch 16 9 left Iteration 1 Error: 0.783362 Iteration 2 Error: 0.289378 Iteration 3 Error: 0.084754 Iteration 4 Error: 0.036537 Align patch 17 8 left Iteration 1 Error: 0.572866 Iteration 2 Error: 0.093332 Iteration 3 Error: 0.024569 Align patch 18 7 left Iteration 1 Error: 0.600527 Iteration 2 Error: 0.192707 Iteration 3 Error: 0.044849 Align patch 19 6 left Iteration 1 Error: 0.533271 Iteration 2 Error: 0.108055 Iteration 3 Error: 0.026399 Align patch 20 5 left Iteration 1 Error: 0.709582 Iteration 2 Error: 0.123239 Iteration 3 Error: 0.043274 Align patch 21 4 left Iteration 1 Error: 1.065510 Iteration 2 Error: 0.223254 Iteration 3 Error: 0.065066 Iteration 4 Error: 0.019119 Align patch 22 3 left Iteration 1 Error: 0.620520 Iteration 2 Error: 0.080298 Iteration 3 Error: 0.020268 Align patch 23 2 left Iteration 1 Error: 0.936836 Iteration 2 Error: 0.160314 Iteration 3 Error: 0.041183 Align patch 24 1 left Iteration 1 Error: 0.761129 Iteration 2 Error: 0.166672 Iteration 3 Error: 0.046356 Align patch 25 0 left Iteration 1 Error: 0.675011 Iteration 2 Error: 0.207390 Iteration 3 Error: 0.053926 Iteration 4 Error: 0.019719 3D Fitting completed. Patch alignment time: 11.65(sec) Local motion has been corrected. Process thread exits. Computational time: 23.022215 sec Total time: 31.128719 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00006hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00006hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.652775s Reading file: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00006hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.354051s ........................................ >>>>>>TIME<<<<<< FFT: 0.941113s Defocus_U Defocus_V Angle CCC 11511.72 12386.72 13.75 0.065368 Final Values Defocus_U Defocus_V Angle CCC 11527.35 12396.10 13.75 0.114247 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00005sq_v01_00006hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00006hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 42.86 7.22 Num Hot pixels: 221 Hot pixel threshold: 86.15 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.344909 Iteration 2 Error: 0.171759 Iteration 3 Error: 0.036612 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.24 -0.05 ...... Frame ( 3) shift: -0.48 -0.10 ...... Frame ( 4) shift: -0.72 -0.15 ...... Frame ( 5) shift: -0.96 -0.19 ...... Frame ( 6) shift: -1.04 -0.18 ...... Frame ( 7) shift: -0.96 -0.09 ...... Frame ( 8) shift: -0.88 -0.01 ...... Frame ( 9) shift: -0.82 0.11 ...... Frame ( 10) shift: -0.76 0.26 ...... Frame ( 11) shift: -0.71 0.41 ...... Frame ( 12) shift: -0.65 0.55 ...... Frame ( 13) shift: -0.57 0.68 ...... Frame ( 14) shift: -0.49 0.80 ...... Frame ( 15) shift: -0.45 0.92 ...... Frame ( 16) shift: -0.43 1.03 ...... Frame ( 17) shift: -0.41 1.14 ...... Frame ( 18) shift: -0.34 1.21 ...... Frame ( 19) shift: -0.24 1.24 ...... Frame ( 20) shift: -0.13 1.28 ...... Frame ( 21) shift: -0.06 1.34 ...... Frame ( 22) shift: -0.03 1.44 ...... Frame ( 23) shift: -0.00 1.53 ...... Frame ( 24) shift: 0.05 1.57 ...... Frame ( 25) shift: 0.12 1.54 ...... Frame ( 26) shift: 0.19 1.52 ...... Frame ( 27) shift: 0.17 1.52 ...... Frame ( 28) shift: 0.06 1.54 ...... Frame ( 29) shift: -0.06 1.55 ...... Frame ( 30) shift: -0.09 1.57 ...... Frame ( 31) shift: -0.04 1.60 ...... Frame ( 32) shift: 0.01 1.63 ...... Frame ( 33) shift: 0.05 1.66 ...... Frame ( 34) shift: 0.07 1.69 ...... Frame ( 35) shift: 0.10 1.73 ...... Frame ( 36) shift: 0.11 1.74 ...... Frame ( 37) shift: 0.10 1.73 ...... Frame ( 38) shift: 0.09 1.72 ...... Frame ( 39) shift: 0.09 1.70 ...... Frame ( 40) shift: 0.08 1.69 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.561568 Iteration 2 Error: 0.292097 Iteration 3 Error: 0.147662 Iteration 4 Error: 0.085139 Iteration 5 Error: 0.040707 Align patch 2 23 left Iteration 1 Error: 1.205048 Iteration 2 Error: 0.226933 Iteration 3 Error: 0.066080 Iteration 4 Error: 0.019275 Align patch 3 22 left Iteration 1 Error: 0.742395 Iteration 2 Error: 0.128135 Iteration 3 Error: 0.052164 Iteration 4 Error: 0.013713 Align patch 4 21 left Iteration 1 Error: 0.630891 Iteration 2 Error: 0.074556 Iteration 3 Error: 0.019057 Align patch 5 20 left Iteration 1 Error: 0.376051 Iteration 2 Error: 0.059258 Iteration 3 Error: 0.013018 Align patch 6 19 left Iteration 1 Error: 2.428366 Iteration 2 Error: 0.280027 Iteration 3 Error: 0.079853 Iteration 4 Error: 0.031376 Align patch 7 18 left Iteration 1 Error: 0.934115 Iteration 2 Error: 0.230217 Iteration 3 Error: 0.078461 Iteration 4 Error: 0.026932 Align patch 8 17 left Iteration 1 Error: 0.648942 Iteration 2 Error: 0.080360 Iteration 3 Error: 0.024094 Align patch 9 16 left Iteration 1 Error: 0.599284 Iteration 2 Error: 0.061893 Iteration 3 Error: 0.018569 Align patch 10 15 left Iteration 1 Error: 0.470480 Iteration 2 Error: 0.057079 Iteration 3 Error: 0.012885 Align patch 11 14 left Iteration 1 Error: 1.599435 Iteration 2 Error: 0.191909 Iteration 3 Error: 0.051975 Iteration 4 Error: 0.015874 Align patch 12 13 left Iteration 1 Error: 0.671094 Iteration 2 Error: 0.140401 Iteration 3 Error: 0.039692 Align patch 13 12 left Iteration 1 Error: 0.505285 Iteration 2 Error: 0.078079 Iteration 3 Error: 0.012416 Align patch 14 11 left Iteration 1 Error: 0.393321 Iteration 2 Error: 0.038535 Align patch 15 10 left Iteration 1 Error: 0.461145 Iteration 2 Error: 0.075260 Iteration 3 Error: 0.011801 Align patch 16 9 left Iteration 1 Error: 1.018719 Iteration 2 Error: 0.153393 Iteration 3 Error: 0.036953 Align patch 17 8 left Iteration 1 Error: 0.569904 Iteration 2 Error: 0.060779 Iteration 3 Error: 0.017021 Align patch 18 7 left Iteration 1 Error: 0.726969 Iteration 2 Error: 0.108528 Iteration 3 Error: 0.020986 Align patch 19 6 left Iteration 1 Error: 0.626025 Iteration 2 Error: 0.087527 Iteration 3 Error: 0.015728 Align patch 20 5 left Iteration 1 Error: 0.743320 Iteration 2 Error: 0.078443 Iteration 3 Error: 0.013576 Align patch 21 4 left Iteration 1 Error: 0.749516 Iteration 2 Error: 0.117315 Iteration 3 Error: 0.032932 Align patch 22 3 left Iteration 1 Error: 0.699116 Iteration 2 Error: 0.123371 Iteration 3 Error: 0.023034 Align patch 23 2 left Iteration 1 Error: 0.638808 Iteration 2 Error: 0.131859 Iteration 3 Error: 0.016190 Align patch 24 1 left Iteration 1 Error: 1.123963 Iteration 2 Error: 0.120798 Iteration 3 Error: 0.021793 Align patch 25 0 left Iteration 1 Error: 0.844128 Iteration 2 Error: 0.133265 Iteration 3 Error: 0.025534 3D Fitting completed. Patch alignment time: 11.39(sec) Local motion has been corrected. Process thread exits. Computational time: 21.661495 sec Total time: 28.652348 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00006hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00006hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.614414s Reading file: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00006hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.639646s ........................................ >>>>>>TIME<<<<<< FFT: 0.989843s Defocus_U Defocus_V Angle CCC 10791.03 11337.90 2.77 0.058513 Final Values Defocus_U Defocus_V Angle CCC 10836.37 11345.74 2.46 0.102632 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00005sq_v01_00006hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00006hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.736 Mean Std: 43.06 7.24 Num Hot pixels: 234 Hot pixel threshold: 86.52 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.151344 Iteration 2 Error: 0.153112 Iteration 3 Error: 0.030757 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.18 0.06 ...... Frame ( 3) shift: -0.35 0.12 ...... Frame ( 4) shift: -0.53 0.18 ...... Frame ( 5) shift: -0.70 0.24 ...... Frame ( 6) shift: -0.77 0.33 ...... Frame ( 7) shift: -0.75 0.44 ...... Frame ( 8) shift: -0.72 0.56 ...... Frame ( 9) shift: -0.71 0.68 ...... Frame ( 10) shift: -0.73 0.81 ...... Frame ( 11) shift: -0.74 0.95 ...... Frame ( 12) shift: -0.72 1.03 ...... Frame ( 13) shift: -0.67 1.08 ...... Frame ( 14) shift: -0.63 1.12 ...... Frame ( 15) shift: -0.63 1.10 ...... Frame ( 16) shift: -0.68 1.04 ...... Frame ( 17) shift: -0.72 0.97 ...... Frame ( 18) shift: -0.73 0.95 ...... Frame ( 19) shift: -0.71 0.97 ...... Frame ( 20) shift: -0.68 1.00 ...... Frame ( 21) shift: -0.65 1.06 ...... Frame ( 22) shift: -0.61 1.18 ...... Frame ( 23) shift: -0.58 1.30 ...... Frame ( 24) shift: -0.56 1.43 ...... Frame ( 25) shift: -0.57 1.58 ...... Frame ( 26) shift: -0.57 1.74 ...... Frame ( 27) shift: -0.58 1.84 ...... Frame ( 28) shift: -0.60 1.88 ...... Frame ( 29) shift: -0.61 1.93 ...... Frame ( 30) shift: -0.61 1.97 ...... Frame ( 31) shift: -0.58 2.00 ...... Frame ( 32) shift: -0.55 2.02 ...... Frame ( 33) shift: -0.53 2.04 ...... Frame ( 34) shift: -0.53 2.04 ...... Frame ( 35) shift: -0.52 2.04 ...... Frame ( 36) shift: -0.50 2.07 ...... Frame ( 37) shift: -0.45 2.11 ...... Frame ( 38) shift: -0.40 2.16 ...... Frame ( 39) shift: -0.35 2.21 ...... Frame ( 40) shift: -0.31 2.25 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.101607 Iteration 2 Error: 0.373679 Iteration 3 Error: 0.074519 Iteration 4 Error: 0.032271 Align patch 2 23 left Iteration 1 Error: 1.045227 Iteration 2 Error: 0.261051 Iteration 3 Error: 0.071589 Iteration 4 Error: 0.027380 Align patch 3 22 left Iteration 1 Error: 0.725121 Iteration 2 Error: 0.143377 Iteration 3 Error: 0.030301 Align patch 4 21 left Iteration 1 Error: 0.626895 Iteration 2 Error: 0.070664 Iteration 3 Error: 0.019517 Align patch 5 20 left Iteration 1 Error: 0.494043 Iteration 2 Error: 0.085182 Iteration 3 Error: 0.018425 Align patch 6 19 left Iteration 1 Error: 1.597251 Iteration 2 Error: 0.350421 Iteration 3 Error: 0.056112 Iteration 4 Error: 0.013803 Align patch 7 18 left Iteration 1 Error: 1.047743 Iteration 2 Error: 0.241089 Iteration 3 Error: 0.048599 Align patch 8 17 left Iteration 1 Error: 0.734957 Iteration 2 Error: 0.099987 Iteration 3 Error: 0.017529 Align patch 9 16 left Iteration 1 Error: 0.604529 Iteration 2 Error: 0.077807 Iteration 3 Error: 0.023306 Align patch 10 15 left Iteration 1 Error: 0.574832 Iteration 2 Error: 0.076963 Iteration 3 Error: 0.016133 Align patch 11 14 left Iteration 1 Error: 0.597933 Iteration 2 Error: 0.113992 Iteration 3 Error: 0.021880 Align patch 12 13 left Iteration 1 Error: 0.556708 Iteration 2 Error: 0.111650 Iteration 3 Error: 0.018372 Align patch 13 12 left Iteration 1 Error: 0.474288 Iteration 2 Error: 0.062033 Iteration 3 Error: 0.022030 Align patch 14 11 left Iteration 1 Error: 0.608978 Iteration 2 Error: 0.100464 Iteration 3 Error: 0.017032 Align patch 15 10 left Iteration 1 Error: 0.398479 Iteration 2 Error: 0.045980 Align patch 16 9 left Iteration 1 Error: 1.002202 Iteration 2 Error: 0.124827 Iteration 3 Error: 0.025659 Align patch 17 8 left Iteration 1 Error: 0.549207 Iteration 2 Error: 0.078931 Iteration 3 Error: 0.023337 Align patch 18 7 left Iteration 1 Error: 0.637999 Iteration 2 Error: 0.079139 Iteration 3 Error: 0.021451 Align patch 19 6 left Iteration 1 Error: 0.615999 Iteration 2 Error: 0.102119 Iteration 3 Error: 0.020166 Align patch 20 5 left Iteration 1 Error: 0.522401 Iteration 2 Error: 0.079690 Iteration 3 Error: 0.019337 Align patch 21 4 left Iteration 1 Error: 1.455192 Iteration 2 Error: 0.158047 Iteration 3 Error: 0.033423 Align patch 22 3 left Iteration 1 Error: 0.865353 Iteration 2 Error: 0.124462 Iteration 3 Error: 0.023563 Align patch 23 2 left Iteration 1 Error: 0.570373 Iteration 2 Error: 0.065673 Iteration 3 Error: 0.012087 Align patch 24 1 left Iteration 1 Error: 0.563760 Iteration 2 Error: 0.068841 Iteration 3 Error: 0.012781 Align patch 25 0 left Iteration 1 Error: 0.706874 Iteration 2 Error: 0.073097 Iteration 3 Error: 0.014085 3D Fitting completed. Patch alignment time: 11.87(sec) Local motion has been corrected. Process thread exits. Computational time: 24.471275 sec Total time: 31.622818 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00006hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00006hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.513666s Reading file: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00006hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.705183s ........................................ >>>>>>TIME<<<<<< FFT: 1.087090s Defocus_U Defocus_V Angle CCC 10064.45 10943.36 6.06 0.060061 Final Values Defocus_U Defocus_V Angle CCC 10084.77 10954.30 6.06 0.110332 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00005sq_v01_00006hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00006hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 42.86 7.27 Num Hot pixels: 239 Hot pixel threshold: 86.49 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.895971 Iteration 2 Error: 0.120718 Iteration 3 Error: 0.021861 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.26 -0.05 ...... Frame ( 3) shift: -0.53 -0.10 ...... Frame ( 4) shift: -0.79 -0.15 ...... Frame ( 5) shift: -1.06 -0.20 ...... Frame ( 6) shift: -1.17 -0.20 ...... Frame ( 7) shift: -1.12 -0.14 ...... Frame ( 8) shift: -1.08 -0.08 ...... Frame ( 9) shift: -1.04 -0.01 ...... Frame ( 10) shift: -1.00 0.06 ...... Frame ( 11) shift: -0.97 0.14 ...... Frame ( 12) shift: -0.94 0.23 ...... Frame ( 13) shift: -0.92 0.34 ...... Frame ( 14) shift: -0.90 0.45 ...... Frame ( 15) shift: -0.84 0.57 ...... Frame ( 16) shift: -0.75 0.68 ...... Frame ( 17) shift: -0.66 0.80 ...... Frame ( 18) shift: -0.62 0.87 ...... Frame ( 19) shift: -0.64 0.91 ...... Frame ( 20) shift: -0.66 0.94 ...... Frame ( 21) shift: -0.65 0.95 ...... Frame ( 22) shift: -0.63 0.92 ...... Frame ( 23) shift: -0.61 0.90 ...... Frame ( 24) shift: -0.60 0.88 ...... Frame ( 25) shift: -0.58 0.87 ...... Frame ( 26) shift: -0.56 0.86 ...... Frame ( 27) shift: -0.52 0.87 ...... Frame ( 28) shift: -0.46 0.90 ...... Frame ( 29) shift: -0.39 0.93 ...... Frame ( 30) shift: -0.36 0.94 ...... Frame ( 31) shift: -0.35 0.94 ...... Frame ( 32) shift: -0.34 0.93 ...... Frame ( 33) shift: -0.33 0.93 ...... Frame ( 34) shift: -0.31 0.94 ...... Frame ( 35) shift: -0.28 0.96 ...... Frame ( 36) shift: -0.25 0.99 ...... Frame ( 37) shift: -0.19 1.03 ...... Frame ( 38) shift: -0.14 1.08 ...... Frame ( 39) shift: -0.08 1.12 ...... Frame ( 40) shift: -0.03 1.17 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.991049 Iteration 2 Error: 0.497562 Iteration 3 Error: 0.220363 Iteration 4 Error: 0.069033 Iteration 5 Error: 0.036067 Align patch 2 23 left Iteration 1 Error: 2.008869 Iteration 2 Error: 0.223469 Iteration 3 Error: 0.055412 Iteration 4 Error: 0.013080 Align patch 3 22 left Iteration 1 Error: 0.713318 Iteration 2 Error: 0.094552 Iteration 3 Error: 0.026256 Align patch 4 21 left Iteration 1 Error: 0.421106 Iteration 2 Error: 0.060233 Iteration 3 Error: 0.011533 Align patch 5 20 left Iteration 1 Error: 0.497493 Iteration 2 Error: 0.063794 Iteration 3 Error: 0.007885 Align patch 6 19 left Iteration 1 Error: 1.458504 Iteration 2 Error: 0.185329 Iteration 3 Error: 0.054852 Iteration 4 Error: 0.015031 Align patch 7 18 left Iteration 1 Error: 1.306198 Iteration 2 Error: 0.145658 Iteration 3 Error: 0.031994 Align patch 8 17 left Iteration 1 Error: 0.908602 Iteration 2 Error: 0.172847 Iteration 3 Error: 0.040506 Align patch 9 16 left Iteration 1 Error: 0.637514 Iteration 2 Error: 0.088998 Iteration 3 Error: 0.023371 Align patch 10 15 left Iteration 1 Error: 0.733454 Iteration 2 Error: 0.093444 Iteration 3 Error: 0.018664 Align patch 11 14 left Iteration 1 Error: 0.893997 Iteration 2 Error: 0.164030 Iteration 3 Error: 0.058346 Iteration 4 Error: 0.017127 Align patch 12 13 left Iteration 1 Error: 0.549047 Iteration 2 Error: 0.086282 Iteration 3 Error: 0.014236 Align patch 13 12 left Iteration 1 Error: 0.882247 Iteration 2 Error: 0.055681 Iteration 3 Error: 0.013263 Align patch 14 11 left Iteration 1 Error: 0.638440 Iteration 2 Error: 0.082543 Iteration 3 Error: 0.016604 Align patch 15 10 left Iteration 1 Error: 0.708652 Iteration 2 Error: 0.086613 Iteration 3 Error: 0.016127 Align patch 16 9 left Iteration 1 Error: 0.674724 Iteration 2 Error: 0.093790 Iteration 3 Error: 0.021879 Align patch 17 8 left Iteration 1 Error: 0.641590 Iteration 2 Error: 0.089416 Iteration 3 Error: 0.032852 Align patch 18 7 left Iteration 1 Error: 0.863153 Iteration 2 Error: 0.127887 Iteration 3 Error: 0.023965 Align patch 19 6 left Iteration 1 Error: 0.635031 Iteration 2 Error: 0.094825 Iteration 3 Error: 0.015896 Align patch 20 5 left Iteration 1 Error: 0.768035 Iteration 2 Error: 0.117293 Iteration 3 Error: 0.025436 Align patch 21 4 left Iteration 1 Error: 1.117145 Iteration 2 Error: 0.157397 Iteration 3 Error: 0.038242 Align patch 22 3 left Iteration 1 Error: 0.912839 Iteration 2 Error: 0.095186 Iteration 3 Error: 0.021182 Align patch 23 2 left Iteration 1 Error: 0.580125 Iteration 2 Error: 0.071092 Iteration 3 Error: 0.014390 Align patch 24 1 left Iteration 1 Error: 0.598273 Iteration 2 Error: 0.060903 Iteration 3 Error: 0.010978 Align patch 25 0 left Iteration 1 Error: 0.681057 Iteration 2 Error: 0.090052 Iteration 3 Error: 0.016404 3D Fitting completed. Patch alignment time: 11.35(sec) Local motion has been corrected. Process thread exits. Computational time: 23.380281 sec Total time: 31.052868 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00006hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00006hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.613988s Reading file: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00006hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.338134s ........................................ >>>>>>TIME<<<<<< FFT: 0.947759s Defocus_U Defocus_V Angle CCC 14044.95 13330.11 84.06 0.069566 Final Values Defocus_U Defocus_V Angle CCC 14048.08 13336.36 85.32 0.114460 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00005sq_v01_00007hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00007hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.002e-01 CC threshold: 0.736 Mean Std: 40.69 6.93 Num Hot pixels: 231 Hot pixel threshold: 82.28 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.568805 Iteration 2 Error: 0.302729 Iteration 3 Error: 0.105405 Iteration 4 Error: 0.037389 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.19 -0.08 ...... Frame ( 3) shift: -0.38 -0.17 ...... Frame ( 4) shift: -0.57 -0.25 ...... Frame ( 5) shift: -0.76 -0.34 ...... Frame ( 6) shift: -0.83 -0.36 ...... Frame ( 7) shift: -0.78 -0.32 ...... Frame ( 8) shift: -0.74 -0.28 ...... Frame ( 9) shift: -0.66 -0.19 ...... Frame ( 10) shift: -0.54 -0.06 ...... Frame ( 11) shift: -0.42 0.07 ...... Frame ( 12) shift: -0.31 0.18 ...... Frame ( 13) shift: -0.22 0.26 ...... Frame ( 14) shift: -0.12 0.34 ...... Frame ( 15) shift: -0.03 0.39 ...... Frame ( 16) shift: 0.04 0.41 ...... Frame ( 17) shift: 0.11 0.43 ...... Frame ( 18) shift: 0.14 0.51 ...... Frame ( 19) shift: 0.14 0.65 ...... Frame ( 20) shift: 0.13 0.79 ...... Frame ( 21) shift: 0.16 0.90 ...... Frame ( 22) shift: 0.23 0.98 ...... Frame ( 23) shift: 0.30 1.05 ...... Frame ( 24) shift: 0.39 1.14 ...... Frame ( 25) shift: 0.48 1.23 ...... Frame ( 26) shift: 0.57 1.33 ...... Frame ( 27) shift: 0.62 1.41 ...... Frame ( 28) shift: 0.62 1.49 ...... Frame ( 29) shift: 0.62 1.56 ...... Frame ( 30) shift: 0.65 1.64 ...... Frame ( 31) shift: 0.69 1.70 ...... Frame ( 32) shift: 0.74 1.77 ...... Frame ( 33) shift: 0.81 1.85 ...... Frame ( 34) shift: 0.90 1.95 ...... Frame ( 35) shift: 0.99 2.05 ...... Frame ( 36) shift: 1.06 2.14 ...... Frame ( 37) shift: 1.11 2.22 ...... Frame ( 38) shift: 1.16 2.31 ...... Frame ( 39) shift: 1.21 2.40 ...... Frame ( 40) shift: 1.26 2.48 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.437090 Iteration 2 Error: 0.260766 Iteration 3 Error: 0.070058 Iteration 4 Error: 0.027112 Align patch 2 23 left Iteration 1 Error: 1.064648 Iteration 2 Error: 0.280842 Iteration 3 Error: 0.129354 Iteration 4 Error: 0.063360 Iteration 5 Error: 0.022124 Align patch 3 22 left Iteration 1 Error: 0.558156 Iteration 2 Error: 0.086278 Iteration 3 Error: 0.019328 Align patch 4 21 left Iteration 1 Error: 0.637840 Iteration 2 Error: 0.141889 Iteration 3 Error: 0.033683 Align patch 5 20 left Iteration 1 Error: 0.579193 Iteration 2 Error: 0.167919 Iteration 3 Error: 0.043139 Align patch 6 19 left Iteration 1 Error: 1.613777 Iteration 2 Error: 0.361660 Iteration 3 Error: 0.133910 Iteration 4 Error: 0.071138 Iteration 5 Error: 0.035878 Align patch 7 18 left Iteration 1 Error: 0.734497 Iteration 2 Error: 0.226491 Iteration 3 Error: 0.113703 Iteration 4 Error: 0.053644 Iteration 5 Error: 0.023779 Align patch 8 17 left Iteration 1 Error: 0.548400 Iteration 2 Error: 0.129759 Iteration 3 Error: 0.051079 Iteration 4 Error: 0.022903 Align patch 9 16 left Iteration 1 Error: 0.551463 Iteration 2 Error: 0.119427 Iteration 3 Error: 0.024794 Align patch 10 15 left Iteration 1 Error: 0.605390 Iteration 2 Error: 0.062718 Iteration 3 Error: 0.025451 Align patch 11 14 left Iteration 1 Error: 0.972512 Iteration 2 Error: 0.280351 Iteration 3 Error: 0.111451 Iteration 4 Error: 0.054020 Iteration 5 Error: 0.035231 Align patch 12 13 left Iteration 1 Error: 0.685548 Iteration 2 Error: 0.193944 Iteration 3 Error: 0.090794 Iteration 4 Error: 0.053477 Iteration 5 Error: 0.019022 Align patch 13 12 left Iteration 1 Error: 0.506480 Iteration 2 Error: 0.148815 Iteration 3 Error: 0.043392 Align patch 14 11 left Iteration 1 Error: 0.558596 Iteration 2 Error: 0.094652 Iteration 3 Error: 0.037300 Align patch 15 10 left Iteration 1 Error: 1.239791 Iteration 2 Error: 0.219611 Iteration 3 Error: 0.059856 Iteration 4 Error: 0.019554 Align patch 16 9 left Iteration 1 Error: 0.868776 Iteration 2 Error: 0.181854 Iteration 3 Error: 0.073669 Iteration 4 Error: 0.016932 Align patch 17 8 left Iteration 1 Error: 0.632241 Iteration 2 Error: 0.150606 Iteration 3 Error: 0.052760 Iteration 4 Error: 0.029107 Align patch 18 7 left Iteration 1 Error: 0.493332 Iteration 2 Error: 0.177809 Iteration 3 Error: 0.054118 Iteration 4 Error: 0.024628 Align patch 19 6 left Iteration 1 Error: 0.686701 Iteration 2 Error: 0.115715 Iteration 3 Error: 0.032526 Align patch 20 5 left Iteration 1 Error: 1.077797 Iteration 2 Error: 0.177324 Iteration 3 Error: 0.030665 Align patch 21 4 left Iteration 1 Error: 0.583300 Iteration 2 Error: 0.101522 Iteration 3 Error: 0.026065 Align patch 22 3 left Iteration 1 Error: 0.568983 Iteration 2 Error: 0.127096 Iteration 3 Error: 0.023618 Align patch 23 2 left Iteration 1 Error: 0.762751 Iteration 2 Error: 0.068509 Iteration 3 Error: 0.019286 Align patch 24 1 left Iteration 1 Error: 0.905735 Iteration 2 Error: 0.137662 Iteration 3 Error: 0.055678 Iteration 4 Error: 0.020302 Align patch 25 0 left Iteration 1 Error: 0.966323 Iteration 2 Error: 0.135447 Iteration 3 Error: 0.032205 3D Fitting completed. Patch alignment time: 12.11(sec) Local motion has been corrected. Process thread exits. Computational time: 24.364960 sec Total time: 31.444204 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00007hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00007hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.885482s Reading file: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00007hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.428885s ........................................ >>>>>>TIME<<<<<< FFT: 0.996576s Defocus_U Defocus_V Angle CCC 9335.94 10179.69 11.33 0.045143 Final Values Defocus_U Defocus_V Angle CCC 9343.76 10184.38 11.02 0.083062 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00005sq_v01_00007hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00007hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.350e-01 1.003e-01 CC threshold: 0.737 Mean Std: 41.18 7.11 Num Hot pixels: 236 Hot pixel threshold: 83.84 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.469863 Iteration 2 Error: 0.246174 Iteration 3 Error: 0.049207 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.19 -0.15 ...... Frame ( 3) shift: -0.39 -0.31 ...... Frame ( 4) shift: -0.58 -0.46 ...... Frame ( 5) shift: -0.78 -0.62 ...... Frame ( 6) shift: -0.83 -0.76 ...... Frame ( 7) shift: -0.74 -0.90 ...... Frame ( 8) shift: -0.64 -1.04 ...... Frame ( 9) shift: -0.56 -1.12 ...... Frame ( 10) shift: -0.48 -1.14 ...... Frame ( 11) shift: -0.40 -1.17 ...... Frame ( 12) shift: -0.33 -1.23 ...... Frame ( 13) shift: -0.26 -1.33 ...... Frame ( 14) shift: -0.20 -1.43 ...... Frame ( 15) shift: -0.14 -1.47 ...... Frame ( 16) shift: -0.10 -1.46 ...... Frame ( 17) shift: -0.05 -1.45 ...... Frame ( 18) shift: 0.01 -1.46 ...... Frame ( 19) shift: 0.10 -1.49 ...... Frame ( 20) shift: 0.19 -1.52 ...... Frame ( 21) shift: 0.24 -1.54 ...... Frame ( 22) shift: 0.25 -1.55 ...... Frame ( 23) shift: 0.26 -1.56 ...... Frame ( 24) shift: 0.31 -1.56 ...... Frame ( 25) shift: 0.42 -1.56 ...... Frame ( 26) shift: 0.52 -1.55 ...... Frame ( 27) shift: 0.64 -1.57 ...... Frame ( 28) shift: 0.78 -1.62 ...... Frame ( 29) shift: 0.91 -1.67 ...... Frame ( 30) shift: 1.04 -1.72 ...... Frame ( 31) shift: 1.15 -1.79 ...... Frame ( 32) shift: 1.27 -1.85 ...... Frame ( 33) shift: 1.34 -1.90 ...... Frame ( 34) shift: 1.36 -1.94 ...... Frame ( 35) shift: 1.39 -1.98 ...... Frame ( 36) shift: 1.46 -1.96 ...... Frame ( 37) shift: 1.59 -1.90 ...... Frame ( 38) shift: 1.71 -1.84 ...... Frame ( 39) shift: 1.84 -1.79 ...... Frame ( 40) shift: 1.97 -1.73 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.067034 Iteration 2 Error: 0.257041 Iteration 3 Error: 0.080992 Iteration 4 Error: 0.033948 Align patch 2 23 left Iteration 1 Error: 0.966054 Iteration 2 Error: 0.162481 Iteration 3 Error: 0.060138 Iteration 4 Error: 0.011902 Align patch 3 22 left Iteration 1 Error: 0.699150 Iteration 2 Error: 0.148862 Iteration 3 Error: 0.034709 Align patch 4 21 left Iteration 1 Error: 0.544978 Iteration 2 Error: 0.094791 Iteration 3 Error: 0.018168 Align patch 5 20 left Iteration 1 Error: 1.334605 Iteration 2 Error: 0.193683 Iteration 3 Error: 0.042133 Align patch 6 19 left Iteration 1 Error: 1.737056 Iteration 2 Error: 0.384491 Iteration 3 Error: 0.144539 Iteration 4 Error: 0.051637 Iteration 5 Error: 0.026699 Align patch 7 18 left Iteration 1 Error: 1.208457 Iteration 2 Error: 0.272639 Iteration 3 Error: 0.061211 Iteration 4 Error: 0.022166 Align patch 8 17 left Iteration 1 Error: 1.143982 Iteration 2 Error: 0.179422 Iteration 3 Error: 0.048771 Align patch 9 16 left Iteration 1 Error: 0.413649 Iteration 2 Error: 0.084505 Iteration 3 Error: 0.013883 Align patch 10 15 left Iteration 1 Error: 1.066270 Iteration 2 Error: 0.157969 Iteration 3 Error: 0.027887 Align patch 11 14 left Iteration 1 Error: 1.804357 Iteration 2 Error: 0.643478 Iteration 3 Error: 0.220562 Iteration 4 Error: 0.087938 Iteration 5 Error: 0.042721 Align patch 12 13 left Iteration 1 Error: 1.988328 Iteration 2 Error: 0.558533 Iteration 3 Error: 0.198446 Iteration 4 Error: 0.074673 Iteration 5 Error: 0.033941 Align patch 13 12 left Iteration 1 Error: 0.714534 Iteration 2 Error: 0.138313 Iteration 3 Error: 0.033144 Align patch 14 11 left Iteration 1 Error: 0.611553 Iteration 2 Error: 0.105068 Iteration 3 Error: 0.016114 Align patch 15 10 left Iteration 1 Error: 1.001155 Iteration 2 Error: 0.143267 Iteration 3 Error: 0.036417 Align patch 16 9 left Iteration 1 Error: 2.519366 Iteration 2 Error: 0.906659 Iteration 3 Error: 0.385175 Iteration 4 Error: 0.169459 Iteration 5 Error: 0.089249 Align patch 16 9 left Iteration 1 Error: 3.296948 Iteration 2 Error: 0.568719 Iteration 3 Error: 0.169071 Iteration 4 Error: 0.060249 Iteration 5 Error: 0.018445 Align patch 17 8 left Iteration 1 Error: 1.840812 Iteration 2 Error: 0.378512 Iteration 3 Error: 0.136467 Iteration 4 Error: 0.060865 Iteration 5 Error: 0.029760 Align patch 18 7 left Iteration 1 Error: 0.534551 Iteration 2 Error: 0.063834 Iteration 3 Error: 0.016363 Align patch 19 6 left Iteration 1 Error: 0.855457 Iteration 2 Error: 0.105313 Iteration 3 Error: 0.018118 Align patch 20 5 left Iteration 1 Error: 0.899147 Iteration 2 Error: 0.157337 Iteration 3 Error: 0.019866 Align patch 21 4 left Iteration 1 Error: 1.894941 Iteration 2 Error: 0.373588 Iteration 3 Error: 0.077867 Iteration 4 Error: 0.030910 Align patch 22 3 left Iteration 1 Error: 1.558900 Iteration 2 Error: 0.306151 Iteration 3 Error: 0.065847 Iteration 4 Error: 0.030241 Align patch 23 2 left Iteration 1 Error: 0.610565 Iteration 2 Error: 0.097692 Iteration 3 Error: 0.027337 Align patch 24 1 left Iteration 1 Error: 0.791531 Iteration 2 Error: 0.127396 Iteration 3 Error: 0.021300 Align patch 25 0 left Iteration 1 Error: 0.812857 Iteration 2 Error: 0.118638 Iteration 3 Error: 0.012643 3D Fitting completed. Patch alignment time: 12.61(sec) Local motion has been corrected. Process thread exits. Computational time: 25.704653 sec Total time: 33.186813 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00007hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00007hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.635774s Reading file: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00007hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.179626s ........................................ >>>>>>TIME<<<<<< FFT: 1.002176s Defocus_U Defocus_V Angle CCC 13710.94 13210.94 89.08 0.070057 Final Values Defocus_U Defocus_V Angle CCC 13710.94 13207.81 89.08 0.115293 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00005sq_v01_00007hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00007hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 40.79 6.97 Num Hot pixels: 243 Hot pixel threshold: 82.59 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.661588 Iteration 2 Error: 0.130692 Iteration 3 Error: 0.029630 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.24 -0.14 ...... Frame ( 3) shift: -0.47 -0.27 ...... Frame ( 4) shift: -0.71 -0.41 ...... Frame ( 5) shift: -0.94 -0.54 ...... Frame ( 6) shift: -1.05 -0.61 ...... Frame ( 7) shift: -1.02 -0.61 ...... Frame ( 8) shift: -0.99 -0.61 ...... Frame ( 9) shift: -0.96 -0.58 ...... Frame ( 10) shift: -0.94 -0.51 ...... Frame ( 11) shift: -0.91 -0.44 ...... Frame ( 12) shift: -0.88 -0.40 ...... Frame ( 13) shift: -0.84 -0.39 ...... Frame ( 14) shift: -0.80 -0.37 ...... Frame ( 15) shift: -0.79 -0.34 ...... Frame ( 16) shift: -0.81 -0.28 ...... Frame ( 17) shift: -0.83 -0.22 ...... Frame ( 18) shift: -0.85 -0.15 ...... Frame ( 19) shift: -0.85 -0.06 ...... Frame ( 20) shift: -0.86 0.02 ...... Frame ( 21) shift: -0.84 0.11 ...... Frame ( 22) shift: -0.79 0.19 ...... Frame ( 23) shift: -0.73 0.28 ...... Frame ( 24) shift: -0.68 0.36 ...... Frame ( 25) shift: -0.64 0.43 ...... Frame ( 26) shift: -0.60 0.50 ...... Frame ( 27) shift: -0.58 0.55 ...... Frame ( 28) shift: -0.59 0.58 ...... Frame ( 29) shift: -0.60 0.61 ...... Frame ( 30) shift: -0.60 0.64 ...... Frame ( 31) shift: -0.57 0.66 ...... Frame ( 32) shift: -0.55 0.67 ...... Frame ( 33) shift: -0.52 0.67 ...... Frame ( 34) shift: -0.49 0.64 ...... Frame ( 35) shift: -0.46 0.61 ...... Frame ( 36) shift: -0.46 0.63 ...... Frame ( 37) shift: -0.51 0.69 ...... Frame ( 38) shift: -0.55 0.75 ...... Frame ( 39) shift: -0.59 0.81 ...... Frame ( 40) shift: -0.63 0.86 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.243958 Iteration 2 Error: 0.176556 Iteration 3 Error: 0.048292 Align patch 2 23 left Iteration 1 Error: 0.711287 Iteration 2 Error: 0.106257 Iteration 3 Error: 0.031714 Align patch 3 22 left Iteration 1 Error: 0.600747 Iteration 2 Error: 0.084891 Iteration 3 Error: 0.019272 Align patch 4 21 left Iteration 1 Error: 0.904828 Iteration 2 Error: 0.065557 Iteration 3 Error: 0.014166 Align patch 5 20 left Iteration 1 Error: 0.509606 Iteration 2 Error: 0.160161 Iteration 3 Error: 0.030703 Align patch 6 19 left Iteration 1 Error: 1.186343 Iteration 2 Error: 0.220838 Iteration 3 Error: 0.067821 Iteration 4 Error: 0.017974 Align patch 7 18 left Iteration 1 Error: 0.677620 Iteration 2 Error: 0.126137 Iteration 3 Error: 0.022822 Align patch 8 17 left Iteration 1 Error: 0.544537 Iteration 2 Error: 0.125599 Iteration 3 Error: 0.028852 Align patch 9 16 left Iteration 1 Error: 0.558213 Iteration 2 Error: 0.118817 Iteration 3 Error: 0.037570 Align patch 10 15 left Iteration 1 Error: 1.431392 Iteration 2 Error: 0.141459 Iteration 3 Error: 0.031126 Align patch 11 14 left Iteration 1 Error: 0.582572 Iteration 2 Error: 0.089548 Iteration 3 Error: 0.024049 Align patch 12 13 left Iteration 1 Error: 0.988258 Iteration 2 Error: 0.116167 Iteration 3 Error: 0.033376 Align patch 13 12 left Iteration 1 Error: 0.727527 Iteration 2 Error: 0.112458 Iteration 3 Error: 0.018687 Align patch 14 11 left Iteration 1 Error: 0.646622 Iteration 2 Error: 0.108621 Iteration 3 Error: 0.026513 Align patch 15 10 left Iteration 1 Error: 0.737622 Iteration 2 Error: 0.103951 Iteration 3 Error: 0.039457 Align patch 16 9 left Iteration 1 Error: 0.815694 Iteration 2 Error: 0.197472 Iteration 3 Error: 0.060190 Iteration 4 Error: 0.012912 Align patch 17 8 left Iteration 1 Error: 0.518185 Iteration 2 Error: 0.088976 Iteration 3 Error: 0.032194 Align patch 18 7 left Iteration 1 Error: 0.978360 Iteration 2 Error: 0.125924 Iteration 3 Error: 0.032785 Align patch 19 6 left Iteration 1 Error: 0.478571 Iteration 2 Error: 0.063922 Iteration 3 Error: 0.015671 Align patch 20 5 left Iteration 1 Error: 0.817598 Iteration 2 Error: 0.091945 Iteration 3 Error: 0.021007 Align patch 21 4 left Iteration 1 Error: 1.041056 Iteration 2 Error: 0.160108 Iteration 3 Error: 0.029262 Align patch 22 3 left Iteration 1 Error: 1.007190 Iteration 2 Error: 0.159614 Iteration 3 Error: 0.019490 Align patch 23 2 left Iteration 1 Error: 0.637182 Iteration 2 Error: 0.114106 Iteration 3 Error: 0.031291 Align patch 24 1 left Iteration 1 Error: 0.585720 Iteration 2 Error: 0.109046 Iteration 3 Error: 0.024743 Align patch 25 0 left Iteration 1 Error: 0.732093 Iteration 2 Error: 0.084603 Iteration 3 Error: 0.014102 3D Fitting completed. Patch alignment time: 11.07(sec) Local motion has been corrected. Process thread exits. Computational time: 23.544294 sec Total time: 30.397747 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00007hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00007hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.866768s Reading file: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00007hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.661667s ........................................ >>>>>>TIME<<<<<< FFT: 0.998011s Defocus_U Defocus_V Angle CCC 14765.64 15648.45 4.60 0.058382 Final Values Defocus_U Defocus_V Angle CCC 14760.95 15653.14 4.92 0.093009 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00005sq_v01_00007hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00007hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.351e-01 1.004e-01 CC threshold: 0.738 Mean Std: 42.36 7.16 Num Hot pixels: 220 Hot pixel threshold: 85.29 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.687742 Iteration 2 Error: 0.074224 Iteration 3 Error: 0.011291 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.24 -0.16 ...... Frame ( 3) shift: -0.48 -0.31 ...... Frame ( 4) shift: -0.72 -0.47 ...... Frame ( 5) shift: -0.96 -0.62 ...... Frame ( 6) shift: -1.09 -0.68 ...... Frame ( 7) shift: -1.09 -0.64 ...... Frame ( 8) shift: -1.10 -0.60 ...... Frame ( 9) shift: -1.10 -0.53 ...... Frame ( 10) shift: -1.08 -0.42 ...... Frame ( 11) shift: -1.07 -0.31 ...... Frame ( 12) shift: -1.07 -0.24 ...... Frame ( 13) shift: -1.08 -0.22 ...... Frame ( 14) shift: -1.09 -0.20 ...... Frame ( 15) shift: -1.08 -0.17 ...... Frame ( 16) shift: -1.06 -0.15 ...... Frame ( 17) shift: -1.03 -0.13 ...... Frame ( 18) shift: -1.02 -0.10 ...... Frame ( 19) shift: -1.04 -0.08 ...... Frame ( 20) shift: -1.05 -0.06 ...... Frame ( 21) shift: -1.06 -0.03 ...... Frame ( 22) shift: -1.06 0.02 ...... Frame ( 23) shift: -1.05 0.06 ...... Frame ( 24) shift: -1.06 0.09 ...... Frame ( 25) shift: -1.07 0.11 ...... Frame ( 26) shift: -1.08 0.13 ...... Frame ( 27) shift: -1.08 0.14 ...... Frame ( 28) shift: -1.07 0.15 ...... Frame ( 29) shift: -1.07 0.16 ...... Frame ( 30) shift: -1.05 0.17 ...... Frame ( 31) shift: -1.03 0.16 ...... Frame ( 32) shift: -1.01 0.16 ...... Frame ( 33) shift: -1.01 0.17 ...... Frame ( 34) shift: -1.03 0.20 ...... Frame ( 35) shift: -1.05 0.22 ...... Frame ( 36) shift: -1.06 0.24 ...... Frame ( 37) shift: -1.06 0.24 ...... Frame ( 38) shift: -1.07 0.25 ...... Frame ( 39) shift: -1.07 0.25 ...... Frame ( 40) shift: -1.07 0.25 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.595695 Iteration 2 Error: 0.287236 Iteration 3 Error: 0.052229 Iteration 4 Error: 0.008805 Align patch 2 23 left Iteration 1 Error: 0.974283 Iteration 2 Error: 0.119983 Iteration 3 Error: 0.020927 Align patch 3 22 left Iteration 1 Error: 1.157504 Iteration 2 Error: 0.112644 Iteration 3 Error: 0.022389 Align patch 4 21 left Iteration 1 Error: 0.376378 Iteration 2 Error: 0.065522 Iteration 3 Error: 0.012609 Align patch 5 20 left Iteration 1 Error: 0.510305 Iteration 2 Error: 0.043876 Align patch 6 19 left Iteration 1 Error: 0.831538 Iteration 2 Error: 0.105589 Iteration 3 Error: 0.022475 Align patch 7 18 left Iteration 1 Error: 0.978179 Iteration 2 Error: 0.102407 Iteration 3 Error: 0.014577 Align patch 8 17 left Iteration 1 Error: 0.949645 Iteration 2 Error: 0.100608 Iteration 3 Error: 0.031144 Align patch 9 16 left Iteration 1 Error: 0.663830 Iteration 2 Error: 0.108416 Iteration 3 Error: 0.021065 Align patch 10 15 left Iteration 1 Error: 0.560008 Iteration 2 Error: 0.101134 Iteration 3 Error: 0.019369 Align patch 11 14 left Iteration 1 Error: 0.773849 Iteration 2 Error: 0.137915 Iteration 3 Error: 0.020968 Align patch 12 13 left Iteration 1 Error: 0.569782 Iteration 2 Error: 0.054689 Iteration 3 Error: 0.017372 Align patch 13 12 left Iteration 1 Error: 0.643984 Iteration 2 Error: 0.077477 Iteration 3 Error: 0.022587 Align patch 14 11 left Iteration 1 Error: 0.396798 Iteration 2 Error: 0.070005 Iteration 3 Error: 0.016337 Align patch 15 10 left Iteration 1 Error: 1.263029 Iteration 2 Error: 0.078080 Iteration 3 Error: 0.012730 Align patch 16 9 left Iteration 1 Error: 0.494853 Iteration 2 Error: 0.061823 Iteration 3 Error: 0.018309 Align patch 17 8 left Iteration 1 Error: 0.467457 Iteration 2 Error: 0.068478 Iteration 3 Error: 0.020330 Align patch 18 7 left Iteration 1 Error: 0.455943 Iteration 2 Error: 0.041215 Align patch 19 6 left Iteration 1 Error: 0.500350 Iteration 2 Error: 0.083638 Iteration 3 Error: 0.019063 Align patch 20 5 left Iteration 1 Error: 0.492624 Iteration 2 Error: 0.038784 Align patch 21 4 left Iteration 1 Error: 1.034786 Iteration 2 Error: 0.154445 Iteration 3 Error: 0.020450 Align patch 22 3 left Iteration 1 Error: 0.717328 Iteration 2 Error: 0.095798 Iteration 3 Error: 0.018457 Align patch 23 2 left Iteration 1 Error: 0.701950 Iteration 2 Error: 0.117436 Iteration 3 Error: 0.012061 Align patch 24 1 left Iteration 1 Error: 0.871944 Iteration 2 Error: 0.075206 Iteration 3 Error: 0.019359 Align patch 25 0 left Iteration 1 Error: 0.474005 Iteration 2 Error: 0.045424 3D Fitting completed. Patch alignment time: 11.34(sec) Local motion has been corrected. Process thread exits. Computational time: 21.820223 sec Total time: 29.487780 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00007hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00007hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.681523s Reading file: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00007hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.827279s ........................................ >>>>>>TIME<<<<<< FFT: 0.935340s Defocus_U Defocus_V Angle CCC 11572.28 10876.96 84.67 0.059497 Final Values Defocus_U Defocus_V Angle CCC 11589.47 10884.78 84.67 0.104811 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00005sq_v01_00008hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00008hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.734 Mean Std: 33.43 6.13 Num Hot pixels: 222 Hot pixel threshold: 70.19 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.066965 Iteration 2 Error: 0.224509 Iteration 3 Error: 0.054384 Iteration 4 Error: 0.022082 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.06 -0.09 ...... Frame ( 3) shift: 0.13 -0.18 ...... Frame ( 4) shift: 0.19 -0.27 ...... Frame ( 5) shift: 0.25 -0.36 ...... Frame ( 6) shift: 0.37 -0.37 ...... Frame ( 7) shift: 0.55 -0.31 ...... Frame ( 8) shift: 0.72 -0.24 ...... Frame ( 9) shift: 0.86 -0.18 ...... Frame ( 10) shift: 0.97 -0.13 ...... Frame ( 11) shift: 1.08 -0.07 ...... Frame ( 12) shift: 1.14 -0.01 ...... Frame ( 13) shift: 1.15 0.06 ...... Frame ( 14) shift: 1.15 0.14 ...... Frame ( 15) shift: 1.16 0.21 ...... Frame ( 16) shift: 1.17 0.27 ...... Frame ( 17) shift: 1.17 0.34 ...... Frame ( 18) shift: 1.17 0.36 ...... Frame ( 19) shift: 1.16 0.32 ...... Frame ( 20) shift: 1.16 0.28 ...... Frame ( 21) shift: 1.17 0.25 ...... Frame ( 22) shift: 1.20 0.23 ...... Frame ( 23) shift: 1.23 0.21 ...... Frame ( 24) shift: 1.32 0.25 ...... Frame ( 25) shift: 1.46 0.36 ...... Frame ( 26) shift: 1.61 0.46 ...... Frame ( 27) shift: 1.71 0.56 ...... Frame ( 28) shift: 1.76 0.66 ...... Frame ( 29) shift: 1.82 0.76 ...... Frame ( 30) shift: 1.84 0.84 ...... Frame ( 31) shift: 1.83 0.91 ...... Frame ( 32) shift: 1.83 0.97 ...... Frame ( 33) shift: 1.87 1.03 ...... Frame ( 34) shift: 1.95 1.09 ...... Frame ( 35) shift: 2.03 1.14 ...... Frame ( 36) shift: 2.08 1.20 ...... Frame ( 37) shift: 2.08 1.26 ...... Frame ( 38) shift: 2.08 1.31 ...... Frame ( 39) shift: 2.09 1.37 ...... Frame ( 40) shift: 2.09 1.42 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.416025 Iteration 2 Error: 0.359380 Iteration 3 Error: 0.097177 Iteration 4 Error: 0.046862 Align patch 2 23 left Iteration 1 Error: 0.847769 Iteration 2 Error: 0.129315 Iteration 3 Error: 0.049663 Align patch 3 22 left Iteration 1 Error: 1.408193 Iteration 2 Error: 0.178953 Iteration 3 Error: 0.039007 Align patch 4 21 left Iteration 1 Error: 1.133578 Iteration 2 Error: 0.204921 Iteration 3 Error: 0.080331 Iteration 4 Error: 0.026433 Align patch 5 20 left Iteration 1 Error: 0.802327 Iteration 2 Error: 0.228611 Iteration 3 Error: 0.068007 Iteration 4 Error: 0.046385 Align patch 6 19 left Iteration 1 Error: 0.867233 Iteration 2 Error: 0.267570 Iteration 3 Error: 0.093859 Iteration 4 Error: 0.041013 Align patch 7 18 left Iteration 1 Error: 0.954274 Iteration 2 Error: 0.126312 Iteration 3 Error: 0.034400 Align patch 8 17 left Iteration 1 Error: 1.173476 Iteration 2 Error: 0.356156 Iteration 3 Error: 0.088629 Iteration 4 Error: 0.026531 Align patch 9 16 left Iteration 1 Error: 0.802735 Iteration 2 Error: 0.180915 Iteration 3 Error: 0.047492 Align patch 10 15 left Iteration 1 Error: 0.869342 Iteration 2 Error: 0.157639 Iteration 3 Error: 0.059128 Iteration 4 Error: 0.022378 Align patch 11 14 left Iteration 1 Error: 1.064830 Iteration 2 Error: 0.184275 Iteration 3 Error: 0.039979 Align patch 12 13 left Iteration 1 Error: 0.699505 Iteration 2 Error: 0.347840 Iteration 3 Error: 0.104399 Iteration 4 Error: 0.049904 Align patch 13 12 left Iteration 1 Error: 1.178612 Iteration 2 Error: 0.208247 Iteration 3 Error: 0.045090 Align patch 14 11 left Iteration 1 Error: 1.330862 Iteration 2 Error: 0.298856 Iteration 3 Error: 0.084900 Iteration 4 Error: 0.031947 Align patch 15 10 left Iteration 1 Error: 1.051507 Iteration 2 Error: 0.151231 Iteration 3 Error: 0.028708 Align patch 16 9 left Iteration 1 Error: 0.775600 Iteration 2 Error: 0.172430 Iteration 3 Error: 0.046496 Align patch 17 8 left Iteration 1 Error: 1.124477 Iteration 2 Error: 0.106363 Iteration 3 Error: 0.034424 Align patch 18 7 left Iteration 1 Error: 1.097061 Iteration 2 Error: 0.232646 Iteration 3 Error: 0.054273 Iteration 4 Error: 0.020320 Align patch 19 6 left Iteration 1 Error: 0.683393 Iteration 2 Error: 0.136022 Iteration 3 Error: 0.057194 Iteration 4 Error: 0.023234 Align patch 20 5 left Iteration 1 Error: 0.952899 Iteration 2 Error: 0.164488 Iteration 3 Error: 0.046944 Align patch 21 4 left Iteration 1 Error: 0.882476 Iteration 2 Error: 0.093662 Iteration 3 Error: 0.029002 Align patch 22 3 left Iteration 1 Error: 1.201079 Iteration 2 Error: 0.147286 Iteration 3 Error: 0.062144 Iteration 4 Error: 0.014192 Align patch 23 2 left Iteration 1 Error: 0.600398 Iteration 2 Error: 0.107693 Iteration 3 Error: 0.038344 Align patch 24 1 left Iteration 1 Error: 0.940790 Iteration 2 Error: 0.349863 Iteration 3 Error: 0.177253 Iteration 4 Error: 0.053038 Iteration 5 Error: 0.018701 Align patch 25 0 left Iteration 1 Error: 0.907524 Iteration 2 Error: 0.246208 Iteration 3 Error: 0.068048 Iteration 4 Error: 0.024631 3D Fitting completed. Patch alignment time: 13.82(sec) Local motion has been corrected. Process thread exits. Computational time: 27.109255 sec Total time: 35.788208 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00008hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00008hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.613923s Reading file: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00008hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.422708s ........................................ >>>>>>TIME<<<<<< FFT: 1.100026s Defocus_U Defocus_V Angle CCC 13196.03 12737.61 75.73 0.020839 Final Values Defocus_U Defocus_V Angle CCC 13286.80 12737.66 62.34 0.028659 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00005sq_v01_00008hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00008hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.001e-01 CC threshold: 0.736 Mean Std: 38.83 6.70 Num Hot pixels: 219 Hot pixel threshold: 79.05 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.145091 Iteration 2 Error: 0.210919 Iteration 3 Error: 0.042132 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.21 -0.02 ...... Frame ( 3) shift: -0.41 -0.04 ...... Frame ( 4) shift: -0.62 -0.07 ...... Frame ( 5) shift: -0.82 -0.09 ...... Frame ( 6) shift: -0.93 -0.12 ...... Frame ( 7) shift: -0.95 -0.15 ...... Frame ( 8) shift: -0.96 -0.18 ...... Frame ( 9) shift: -0.96 -0.18 ...... Frame ( 10) shift: -0.96 -0.16 ...... Frame ( 11) shift: -0.95 -0.13 ...... Frame ( 12) shift: -0.94 -0.14 ...... Frame ( 13) shift: -0.91 -0.20 ...... Frame ( 14) shift: -0.88 -0.26 ...... Frame ( 15) shift: -0.83 -0.30 ...... Frame ( 16) shift: -0.74 -0.33 ...... Frame ( 17) shift: -0.66 -0.36 ...... Frame ( 18) shift: -0.58 -0.36 ...... Frame ( 19) shift: -0.51 -0.33 ...... Frame ( 20) shift: -0.44 -0.30 ...... Frame ( 21) shift: -0.36 -0.28 ...... Frame ( 22) shift: -0.28 -0.25 ...... Frame ( 23) shift: -0.19 -0.23 ...... Frame ( 24) shift: -0.10 -0.21 ...... Frame ( 25) shift: -0.01 -0.19 ...... Frame ( 26) shift: 0.08 -0.17 ...... Frame ( 27) shift: 0.14 -0.16 ...... Frame ( 28) shift: 0.16 -0.14 ...... Frame ( 29) shift: 0.18 -0.13 ...... Frame ( 30) shift: 0.21 -0.07 ...... Frame ( 31) shift: 0.24 0.04 ...... Frame ( 32) shift: 0.27 0.15 ...... Frame ( 33) shift: 0.31 0.23 ...... Frame ( 34) shift: 0.35 0.26 ...... Frame ( 35) shift: 0.39 0.29 ...... Frame ( 36) shift: 0.46 0.34 ...... Frame ( 37) shift: 0.57 0.41 ...... Frame ( 38) shift: 0.68 0.47 ...... Frame ( 39) shift: 0.80 0.54 ...... Frame ( 40) shift: 0.91 0.60 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.865842 Iteration 2 Error: 0.129957 Iteration 3 Error: 0.043324 Align patch 2 23 left Iteration 1 Error: 0.691337 Iteration 2 Error: 0.101913 Iteration 3 Error: 0.021208 Align patch 3 22 left Iteration 1 Error: 0.887545 Iteration 2 Error: 0.135145 Iteration 3 Error: 0.024498 Align patch 4 21 left Iteration 1 Error: 1.003025 Iteration 2 Error: 0.102175 Iteration 3 Error: 0.018989 Align patch 5 20 left Iteration 1 Error: 0.961733 Iteration 2 Error: 0.182283 Iteration 3 Error: 0.038047 Align patch 6 19 left Iteration 1 Error: 0.704143 Iteration 2 Error: 0.114559 Iteration 3 Error: 0.033298 Align patch 7 18 left Iteration 1 Error: 0.558656 Iteration 2 Error: 0.139326 Iteration 3 Error: 0.029055 Align patch 8 17 left Iteration 1 Error: 0.996606 Iteration 2 Error: 0.089415 Iteration 3 Error: 0.035438 Align patch 9 16 left Iteration 1 Error: 0.644840 Iteration 2 Error: 0.116546 Iteration 3 Error: 0.027451 Align patch 10 15 left Iteration 1 Error: 1.130783 Iteration 2 Error: 0.139074 Iteration 3 Error: 0.044498 Align patch 11 14 left Iteration 1 Error: 1.131035 Iteration 2 Error: 0.173670 Iteration 3 Error: 0.048266 Align patch 12 13 left Iteration 1 Error: 0.690655 Iteration 2 Error: 0.096328 Iteration 3 Error: 0.019738 Align patch 13 12 left Iteration 1 Error: 0.564455 Iteration 2 Error: 0.096086 Iteration 3 Error: 0.018517 Align patch 14 11 left Iteration 1 Error: 0.741951 Iteration 2 Error: 0.136368 Iteration 3 Error: 0.034907 Align patch 15 10 left Iteration 1 Error: 0.718666 Iteration 2 Error: 0.127321 Iteration 3 Error: 0.037926 Align patch 16 9 left Iteration 1 Error: 0.719430 Iteration 2 Error: 0.115791 Iteration 3 Error: 0.016023 Align patch 17 8 left Iteration 1 Error: 0.612010 Iteration 2 Error: 0.099770 Iteration 3 Error: 0.017182 Align patch 18 7 left Iteration 1 Error: 0.659298 Iteration 2 Error: 0.104714 Iteration 3 Error: 0.036740 Align patch 19 6 left Iteration 1 Error: 0.856506 Iteration 2 Error: 0.155534 Iteration 3 Error: 0.066049 Iteration 4 Error: 0.030691 Align patch 20 5 left Iteration 1 Error: 0.629211 Iteration 2 Error: 0.110655 Iteration 3 Error: 0.027180 Align patch 21 4 left Iteration 1 Error: 0.914053 Iteration 2 Error: 0.137762 Iteration 3 Error: 0.048338 Align patch 22 3 left Iteration 1 Error: 0.631337 Iteration 2 Error: 0.129300 Iteration 3 Error: 0.046371 Align patch 23 2 left Iteration 1 Error: 0.794894 Iteration 2 Error: 0.107959 Iteration 3 Error: 0.027757 Align patch 24 1 left Iteration 1 Error: 0.724543 Iteration 2 Error: 0.131711 Iteration 3 Error: 0.043227 Align patch 25 0 left Iteration 1 Error: 0.765105 Iteration 2 Error: 0.111998 Iteration 3 Error: 0.024732 3D Fitting completed. Patch alignment time: 12.41(sec) Local motion has been corrected. Process thread exits. Computational time: 21.978453 sec Total time: 29.465075 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00008hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00008hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.541118s Reading file: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00008hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.505249s ........................................ >>>>>>TIME<<<<<< FFT: 0.987136s Defocus_U Defocus_V Angle CCC 9150.41 8607.40 88.50 0.026447 Final Values Defocus_U Defocus_V Angle CCC 9136.35 8643.35 89.44 0.049647 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00005sq_v01_00008hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00008hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 35.51 6.33 Num Hot pixels: 244 Hot pixel threshold: 73.47 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.869003 Iteration 2 Error: 0.144548 Iteration 3 Error: 0.036740 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.03 -0.11 ...... Frame ( 3) shift: -0.07 -0.21 ...... Frame ( 4) shift: -0.10 -0.32 ...... Frame ( 5) shift: -0.13 -0.43 ...... Frame ( 6) shift: -0.16 -0.54 ...... Frame ( 7) shift: -0.17 -0.66 ...... Frame ( 8) shift: -0.19 -0.78 ...... Frame ( 9) shift: -0.13 -0.82 ...... Frame ( 10) shift: 0.01 -0.79 ...... Frame ( 11) shift: 0.15 -0.75 ...... Frame ( 12) shift: 0.27 -0.75 ...... Frame ( 13) shift: 0.40 -0.79 ...... Frame ( 14) shift: 0.52 -0.83 ...... Frame ( 15) shift: 0.61 -0.88 ...... Frame ( 16) shift: 0.67 -0.94 ...... Frame ( 17) shift: 0.72 -1.00 ...... Frame ( 18) shift: 0.78 -1.00 ...... Frame ( 19) shift: 0.85 -0.95 ...... Frame ( 20) shift: 0.91 -0.90 ...... Frame ( 21) shift: 0.95 -0.91 ...... Frame ( 22) shift: 0.97 -0.97 ...... Frame ( 23) shift: 1.00 -1.03 ...... Frame ( 24) shift: 1.04 -1.03 ...... Frame ( 25) shift: 1.10 -0.99 ...... Frame ( 26) shift: 1.15 -0.95 ...... Frame ( 27) shift: 1.18 -0.93 ...... Frame ( 28) shift: 1.19 -0.93 ...... Frame ( 29) shift: 1.19 -0.94 ...... Frame ( 30) shift: 1.17 -0.94 ...... Frame ( 31) shift: 1.14 -0.93 ...... Frame ( 32) shift: 1.11 -0.93 ...... Frame ( 33) shift: 1.12 -0.94 ...... Frame ( 34) shift: 1.17 -0.97 ...... Frame ( 35) shift: 1.22 -1.00 ...... Frame ( 36) shift: 1.27 -1.01 ...... Frame ( 37) shift: 1.31 -1.01 ...... Frame ( 38) shift: 1.35 -1.00 ...... Frame ( 39) shift: 1.40 -1.00 ...... Frame ( 40) shift: 1.44 -0.99 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.062117 Iteration 2 Error: 0.234059 Iteration 3 Error: 0.056152 Iteration 4 Error: 0.017190 Align patch 2 23 left Iteration 1 Error: 0.914507 Iteration 2 Error: 0.191684 Iteration 3 Error: 0.049043 Align patch 3 22 left Iteration 1 Error: 0.750472 Iteration 2 Error: 0.114589 Iteration 3 Error: 0.030696 Align patch 4 21 left Iteration 1 Error: 1.003614 Iteration 2 Error: 0.089560 Iteration 3 Error: 0.021292 Align patch 5 20 left Iteration 1 Error: 1.262266 Iteration 2 Error: 0.196304 Iteration 3 Error: 0.045759 Align patch 6 19 left Iteration 1 Error: 1.445179 Iteration 2 Error: 0.191611 Iteration 3 Error: 0.044507 Align patch 7 18 left Iteration 1 Error: 0.538673 Iteration 2 Error: 0.114637 Iteration 3 Error: 0.039400 Align patch 8 17 left Iteration 1 Error: 0.876940 Iteration 2 Error: 0.141460 Iteration 3 Error: 0.052611 Iteration 4 Error: 0.013678 Align patch 9 16 left Iteration 1 Error: 1.053555 Iteration 2 Error: 0.196241 Iteration 3 Error: 0.062228 Iteration 4 Error: 0.015724 Align patch 10 15 left Iteration 1 Error: 0.734187 Iteration 2 Error: 0.095397 Iteration 3 Error: 0.024706 Align patch 11 14 left Iteration 1 Error: 0.788085 Iteration 2 Error: 0.193660 Iteration 3 Error: 0.062941 Iteration 4 Error: 0.021608 Align patch 12 13 left Iteration 1 Error: 0.921003 Iteration 2 Error: 0.157503 Iteration 3 Error: 0.064884 Iteration 4 Error: 0.028595 Align patch 13 12 left Iteration 1 Error: 1.088583 Iteration 2 Error: 0.258774 Iteration 3 Error: 0.070468 Iteration 4 Error: 0.039182 Align patch 14 11 left Iteration 1 Error: 0.782559 Iteration 2 Error: 0.127772 Iteration 3 Error: 0.036532 Align patch 15 10 left Iteration 1 Error: 0.742344 Iteration 2 Error: 0.135129 Iteration 3 Error: 0.030920 Align patch 16 9 left Iteration 1 Error: 0.547253 Iteration 2 Error: 0.125932 Iteration 3 Error: 0.022016 Align patch 17 8 left Iteration 1 Error: 0.895776 Iteration 2 Error: 0.186560 Iteration 3 Error: 0.041581 Align patch 18 7 left Iteration 1 Error: 0.641305 Iteration 2 Error: 0.158725 Iteration 3 Error: 0.036883 Align patch 19 6 left Iteration 1 Error: 0.690838 Iteration 2 Error: 0.095701 Iteration 3 Error: 0.021916 Align patch 20 5 left Iteration 1 Error: 0.818894 Iteration 2 Error: 0.219607 Iteration 3 Error: 0.054745 Iteration 4 Error: 0.030115 Align patch 21 4 left Iteration 1 Error: 0.643541 Iteration 2 Error: 0.149590 Iteration 3 Error: 0.038200 Align patch 22 3 left Iteration 1 Error: 0.871846 Iteration 2 Error: 0.271188 Iteration 3 Error: 0.080114 Iteration 4 Error: 0.037945 Align patch 23 2 left Iteration 1 Error: 0.947344 Iteration 2 Error: 0.213045 Iteration 3 Error: 0.073716 Iteration 4 Error: 0.025877 Align patch 24 1 left Iteration 1 Error: 0.714312 Iteration 2 Error: 0.163401 Iteration 3 Error: 0.048613 Align patch 25 0 left Iteration 1 Error: 0.909208 Iteration 2 Error: 0.158353 Iteration 3 Error: 0.034577 3D Fitting completed. Patch alignment time: 11.90(sec) Local motion has been corrected. Process thread exits. Computational time: 24.060837 sec Total time: 30.309198 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00008hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00008hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.586547s Reading file: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00008hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.348299s ........................................ >>>>>>TIME<<<<<< FFT: 0.919631s Defocus_U Defocus_V Angle CCC 12160.18 13386.76 8.55 0.022717 Final Values Defocus_U Defocus_V Angle CCC 12482.06 13412.17 0.11 0.033869 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00005sq_v01_00008hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00008hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 40.06 6.79 Num Hot pixels: 234 Hot pixel threshold: 80.83 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.716679 Iteration 2 Error: 0.126048 Iteration 3 Error: 0.028263 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.17 0.02 ...... Frame ( 3) shift: -0.35 0.03 ...... Frame ( 4) shift: -0.52 0.05 ...... Frame ( 5) shift: -0.69 0.06 ...... Frame ( 6) shift: -0.82 0.08 ...... Frame ( 7) shift: -0.89 0.09 ...... Frame ( 8) shift: -0.97 0.11 ...... Frame ( 9) shift: -0.97 0.08 ...... Frame ( 10) shift: -0.91 0.02 ...... Frame ( 11) shift: -0.85 -0.04 ...... Frame ( 12) shift: -0.79 -0.03 ...... Frame ( 13) shift: -0.73 0.03 ...... Frame ( 14) shift: -0.68 0.10 ...... Frame ( 15) shift: -0.67 0.15 ...... Frame ( 16) shift: -0.72 0.18 ...... Frame ( 17) shift: -0.76 0.20 ...... Frame ( 18) shift: -0.75 0.23 ...... Frame ( 19) shift: -0.69 0.26 ...... Frame ( 20) shift: -0.63 0.29 ...... Frame ( 21) shift: -0.57 0.33 ...... Frame ( 22) shift: -0.50 0.36 ...... Frame ( 23) shift: -0.44 0.40 ...... Frame ( 24) shift: -0.38 0.43 ...... Frame ( 25) shift: -0.34 0.47 ...... Frame ( 26) shift: -0.29 0.51 ...... Frame ( 27) shift: -0.25 0.53 ...... Frame ( 28) shift: -0.21 0.54 ...... Frame ( 29) shift: -0.17 0.54 ...... Frame ( 30) shift: -0.11 0.54 ...... Frame ( 31) shift: -0.03 0.55 ...... Frame ( 32) shift: 0.05 0.55 ...... Frame ( 33) shift: 0.08 0.58 ...... Frame ( 34) shift: 0.05 0.62 ...... Frame ( 35) shift: 0.02 0.67 ...... Frame ( 36) shift: 0.03 0.73 ...... Frame ( 37) shift: 0.06 0.80 ...... Frame ( 38) shift: 0.09 0.87 ...... Frame ( 39) shift: 0.13 0.94 ...... Frame ( 40) shift: 0.16 1.01 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.687990 Iteration 2 Error: 0.074096 Iteration 3 Error: 0.014800 Align patch 2 23 left Iteration 1 Error: 0.707474 Iteration 2 Error: 0.085636 Iteration 3 Error: 0.019659 Align patch 3 22 left Iteration 1 Error: 0.674053 Iteration 2 Error: 0.163790 Iteration 3 Error: 0.053011 Iteration 4 Error: 0.012348 Align patch 4 21 left Iteration 1 Error: 0.686765 Iteration 2 Error: 0.061358 Iteration 3 Error: 0.010063 Align patch 5 20 left Iteration 1 Error: 1.367014 Iteration 2 Error: 0.179155 Iteration 3 Error: 0.071447 Iteration 4 Error: 0.032840 Align patch 6 19 left Iteration 1 Error: 0.607305 Iteration 2 Error: 0.120005 Iteration 3 Error: 0.029584 Align patch 7 18 left Iteration 1 Error: 0.904688 Iteration 2 Error: 0.125796 Iteration 3 Error: 0.022114 Align patch 8 17 left Iteration 1 Error: 0.664981 Iteration 2 Error: 0.094107 Iteration 3 Error: 0.034381 Align patch 9 16 left Iteration 1 Error: 0.808776 Iteration 2 Error: 0.145167 Iteration 3 Error: 0.021545 Align patch 10 15 left Iteration 1 Error: 0.785120 Iteration 2 Error: 0.162844 Iteration 3 Error: 0.036478 Align patch 11 14 left Iteration 1 Error: 0.962391 Iteration 2 Error: 0.078114 Iteration 3 Error: 0.019900 Align patch 12 13 left Iteration 1 Error: 0.564270 Iteration 2 Error: 0.086180 Iteration 3 Error: 0.018222 Align patch 13 12 left Iteration 1 Error: 0.696859 Iteration 2 Error: 0.160707 Iteration 3 Error: 0.046547 Align patch 14 11 left Iteration 1 Error: 0.600798 Iteration 2 Error: 0.083096 Iteration 3 Error: 0.018148 Align patch 15 10 left Iteration 1 Error: 0.796880 Iteration 2 Error: 0.249248 Iteration 3 Error: 0.077146 Iteration 4 Error: 0.033906 Align patch 16 9 left Iteration 1 Error: 0.687787 Iteration 2 Error: 0.094860 Iteration 3 Error: 0.025499 Align patch 17 8 left Iteration 1 Error: 1.351377 Iteration 2 Error: 0.185142 Iteration 3 Error: 0.038606 Align patch 18 7 left Iteration 1 Error: 1.074801 Iteration 2 Error: 0.117229 Iteration 3 Error: 0.017098 Align patch 19 6 left Iteration 1 Error: 0.653697 Iteration 2 Error: 0.146265 Iteration 3 Error: 0.021634 Align patch 20 5 left Iteration 1 Error: 1.012275 Iteration 2 Error: 0.169974 Iteration 3 Error: 0.052299 Iteration 4 Error: 0.010989 Align patch 21 4 left Iteration 1 Error: 0.827248 Iteration 2 Error: 0.117391 Iteration 3 Error: 0.030748 Align patch 22 3 left Iteration 1 Error: 0.706494 Iteration 2 Error: 0.138007 Iteration 3 Error: 0.027118 Align patch 23 2 left Iteration 1 Error: 0.590794 Iteration 2 Error: 0.099141 Iteration 3 Error: 0.025250 Align patch 24 1 left Iteration 1 Error: 0.862492 Iteration 2 Error: 0.081724 Iteration 3 Error: 0.015140 Align patch 25 0 left Iteration 1 Error: 0.935764 Iteration 2 Error: 0.196467 Iteration 3 Error: 0.049414 3D Fitting completed. Patch alignment time: 11.85(sec) Local motion has been corrected. Process thread exits. Computational time: 24.307913 sec Total time: 31.709219 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00008hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00008hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.601529s Reading file: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00008hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.134518s ........................................ >>>>>>TIME<<<<<< FFT: 1.118557s Defocus_U Defocus_V Angle CCC 11697.33 10998.02 87.41 0.042233 Final Values Defocus_U Defocus_V Angle CCC 11723.89 11024.58 86.79 0.071379 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00005sq_v01_00009hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00009hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 42.09 7.23 Num Hot pixels: 208 Hot pixel threshold: 85.46 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.303971 Iteration 2 Error: 0.152897 Iteration 3 Error: 0.030311 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.21 0.01 ...... Frame ( 3) shift: -0.42 0.02 ...... Frame ( 4) shift: -0.62 0.03 ...... Frame ( 5) shift: -0.83 0.04 ...... Frame ( 6) shift: -0.89 0.10 ...... Frame ( 7) shift: -0.80 0.22 ...... Frame ( 8) shift: -0.71 0.33 ...... Frame ( 9) shift: -0.64 0.47 ...... Frame ( 10) shift: -0.59 0.62 ...... Frame ( 11) shift: -0.53 0.78 ...... Frame ( 12) shift: -0.47 0.90 ...... Frame ( 13) shift: -0.41 1.00 ...... Frame ( 14) shift: -0.35 1.11 ...... Frame ( 15) shift: -0.30 1.20 ...... Frame ( 16) shift: -0.27 1.28 ...... Frame ( 17) shift: -0.23 1.37 ...... Frame ( 18) shift: -0.19 1.44 ...... Frame ( 19) shift: -0.13 1.50 ...... Frame ( 20) shift: -0.07 1.56 ...... Frame ( 21) shift: -0.00 1.58 ...... Frame ( 22) shift: 0.06 1.56 ...... Frame ( 23) shift: 0.12 1.54 ...... Frame ( 24) shift: 0.15 1.56 ...... Frame ( 25) shift: 0.15 1.60 ...... Frame ( 26) shift: 0.16 1.65 ...... Frame ( 27) shift: 0.15 1.67 ...... Frame ( 28) shift: 0.15 1.66 ...... Frame ( 29) shift: 0.15 1.65 ...... Frame ( 30) shift: 0.17 1.66 ...... Frame ( 31) shift: 0.22 1.69 ...... Frame ( 32) shift: 0.26 1.72 ...... Frame ( 33) shift: 0.28 1.76 ...... Frame ( 34) shift: 0.27 1.81 ...... Frame ( 35) shift: 0.26 1.87 ...... Frame ( 36) shift: 0.26 1.91 ...... Frame ( 37) shift: 0.26 1.94 ...... Frame ( 38) shift: 0.26 1.97 ...... Frame ( 39) shift: 0.26 1.99 ...... Frame ( 40) shift: 0.27 2.02 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.100686 Iteration 2 Error: 0.206758 Iteration 3 Error: 0.048363 Align patch 2 23 left Iteration 1 Error: 0.852641 Iteration 2 Error: 0.090206 Iteration 3 Error: 0.017948 Align patch 3 22 left Iteration 1 Error: 0.926081 Iteration 2 Error: 0.122895 Iteration 3 Error: 0.028743 Align patch 4 21 left Iteration 1 Error: 0.633827 Iteration 2 Error: 0.093864 Iteration 3 Error: 0.018775 Align patch 5 20 left Iteration 1 Error: 0.571003 Iteration 2 Error: 0.063208 Iteration 3 Error: 0.013697 Align patch 6 19 left Iteration 1 Error: 1.527246 Iteration 2 Error: 0.257366 Iteration 3 Error: 0.090182 Iteration 4 Error: 0.027204 Align patch 7 18 left Iteration 1 Error: 0.524064 Iteration 2 Error: 0.083886 Iteration 3 Error: 0.026181 Align patch 8 17 left Iteration 1 Error: 0.928414 Iteration 2 Error: 0.123783 Iteration 3 Error: 0.026468 Align patch 9 16 left Iteration 1 Error: 0.359903 Iteration 2 Error: 0.043372 Align patch 10 15 left Iteration 1 Error: 0.418079 Iteration 2 Error: 0.063859 Iteration 3 Error: 0.016206 Align patch 11 14 left Iteration 1 Error: 0.738370 Iteration 2 Error: 0.111962 Iteration 3 Error: 0.035054 Align patch 12 13 left Iteration 1 Error: 0.496260 Iteration 2 Error: 0.069468 Iteration 3 Error: 0.019703 Align patch 13 12 left Iteration 1 Error: 0.652643 Iteration 2 Error: 0.092361 Iteration 3 Error: 0.020338 Align patch 14 11 left Iteration 1 Error: 0.460802 Iteration 2 Error: 0.069419 Iteration 3 Error: 0.017556 Align patch 15 10 left Iteration 1 Error: 0.442025 Iteration 2 Error: 0.065779 Iteration 3 Error: 0.012003 Align patch 16 9 left Iteration 1 Error: 1.012739 Iteration 2 Error: 0.259951 Iteration 3 Error: 0.075416 Iteration 4 Error: 0.034705 Align patch 17 8 left Iteration 1 Error: 0.648076 Iteration 2 Error: 0.103313 Iteration 3 Error: 0.037186 Align patch 18 7 left Iteration 1 Error: 0.556128 Iteration 2 Error: 0.101181 Iteration 3 Error: 0.013347 Align patch 19 6 left Iteration 1 Error: 0.544485 Iteration 2 Error: 0.050658 Iteration 3 Error: 0.013788 Align patch 20 5 left Iteration 1 Error: 0.594491 Iteration 2 Error: 0.048910 Align patch 21 4 left Iteration 1 Error: 0.997620 Iteration 2 Error: 0.119179 Iteration 3 Error: 0.053108 Iteration 4 Error: 0.011899 Align patch 22 3 left Iteration 1 Error: 0.633154 Iteration 2 Error: 0.112827 Iteration 3 Error: 0.026867 Align patch 23 2 left Iteration 1 Error: 0.691850 Iteration 2 Error: 0.124805 Iteration 3 Error: 0.018765 Align patch 24 1 left Iteration 1 Error: 1.064961 Iteration 2 Error: 0.095804 Iteration 3 Error: 0.017794 Align patch 25 0 left Iteration 1 Error: 0.521415 Iteration 2 Error: 0.057814 Iteration 3 Error: 0.013582 3D Fitting completed. Patch alignment time: 11.87(sec) Local motion has been corrected. Process thread exits. Computational time: 24.229689 sec Total time: 31.130968 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00009hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00009hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.595352s Reading file: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00009hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.642862s ........................................ >>>>>>TIME<<<<<< FFT: 0.947901s Defocus_U Defocus_V Angle CCC 10796.90 11617.21 12.69 0.054368 Final Values Defocus_U Defocus_V Angle CCC 10812.53 11661.00 12.38 0.093566 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00005sq_v01_00009hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00009hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 41.24 7.19 Num Hot pixels: 227 Hot pixel threshold: 84.37 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.540389 Iteration 2 Error: 0.189805 Iteration 3 Error: 0.035102 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.16 0.19 ...... Frame ( 3) shift: -0.32 0.37 ...... Frame ( 4) shift: -0.47 0.56 ...... Frame ( 5) shift: -0.63 0.75 ...... Frame ( 6) shift: -0.69 0.90 ...... Frame ( 7) shift: -0.65 1.02 ...... Frame ( 8) shift: -0.61 1.14 ...... Frame ( 9) shift: -0.54 1.28 ...... Frame ( 10) shift: -0.46 1.42 ...... Frame ( 11) shift: -0.37 1.57 ...... Frame ( 12) shift: -0.30 1.67 ...... Frame ( 13) shift: -0.26 1.73 ...... Frame ( 14) shift: -0.21 1.79 ...... Frame ( 15) shift: -0.16 1.83 ...... Frame ( 16) shift: -0.08 1.84 ...... Frame ( 17) shift: -0.01 1.86 ...... Frame ( 18) shift: 0.02 1.88 ...... Frame ( 19) shift: 0.01 1.91 ...... Frame ( 20) shift: -0.00 1.95 ...... Frame ( 21) shift: 0.01 2.00 ...... Frame ( 22) shift: 0.04 2.06 ...... Frame ( 23) shift: 0.07 2.13 ...... Frame ( 24) shift: 0.09 2.17 ...... Frame ( 25) shift: 0.09 2.20 ...... Frame ( 26) shift: 0.10 2.22 ...... Frame ( 27) shift: 0.10 2.27 ...... Frame ( 28) shift: 0.11 2.34 ...... Frame ( 29) shift: 0.13 2.42 ...... Frame ( 30) shift: 0.15 2.45 ...... Frame ( 31) shift: 0.19 2.43 ...... Frame ( 32) shift: 0.24 2.41 ...... Frame ( 33) shift: 0.28 2.41 ...... Frame ( 34) shift: 0.32 2.44 ...... Frame ( 35) shift: 0.37 2.47 ...... Frame ( 36) shift: 0.39 2.52 ...... Frame ( 37) shift: 0.41 2.60 ...... Frame ( 38) shift: 0.42 2.67 ...... Frame ( 39) shift: 0.43 2.74 ...... Frame ( 40) shift: 0.44 2.81 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.195660 Iteration 2 Error: 0.244993 Iteration 3 Error: 0.070211 Iteration 4 Error: 0.024713 Align patch 2 23 left Iteration 1 Error: 0.550125 Iteration 2 Error: 0.121215 Iteration 3 Error: 0.031096 Align patch 3 22 left Iteration 1 Error: 0.499700 Iteration 2 Error: 0.090964 Iteration 3 Error: 0.017152 Align patch 4 21 left Iteration 1 Error: 0.463322 Iteration 2 Error: 0.042914 Align patch 5 20 left Iteration 1 Error: 0.465744 Iteration 2 Error: 0.055561 Iteration 3 Error: 0.010008 Align patch 6 19 left Iteration 1 Error: 0.721477 Iteration 2 Error: 0.184832 Iteration 3 Error: 0.042389 Align patch 7 18 left Iteration 1 Error: 0.656610 Iteration 2 Error: 0.115552 Iteration 3 Error: 0.018645 Align patch 8 17 left Iteration 1 Error: 0.671090 Iteration 2 Error: 0.119284 Iteration 3 Error: 0.026476 Align patch 9 16 left Iteration 1 Error: 0.354419 Iteration 2 Error: 0.069838 Iteration 3 Error: 0.013611 Align patch 10 15 left Iteration 1 Error: 0.757416 Iteration 2 Error: 0.135461 Iteration 3 Error: 0.032967 Align patch 11 14 left Iteration 1 Error: 1.292281 Iteration 2 Error: 0.228327 Iteration 3 Error: 0.052966 Iteration 4 Error: 0.020461 Align patch 12 13 left Iteration 1 Error: 0.477150 Iteration 2 Error: 0.089252 Iteration 3 Error: 0.019028 Align patch 13 12 left Iteration 1 Error: 0.749062 Iteration 2 Error: 0.076148 Iteration 3 Error: 0.016459 Align patch 14 11 left Iteration 1 Error: 0.555611 Iteration 2 Error: 0.068855 Iteration 3 Error: 0.017467 Align patch 15 10 left Iteration 1 Error: 0.650930 Iteration 2 Error: 0.071587 Iteration 3 Error: 0.012947 Align patch 16 9 left Iteration 1 Error: 0.674993 Iteration 2 Error: 0.118673 Iteration 3 Error: 0.029550 Align patch 17 8 left Iteration 1 Error: 0.693888 Iteration 2 Error: 0.148906 Iteration 3 Error: 0.037489 Align patch 18 7 left Iteration 1 Error: 0.687412 Iteration 2 Error: 0.142301 Iteration 3 Error: 0.030566 Align patch 19 6 left Iteration 1 Error: 0.595111 Iteration 2 Error: 0.107922 Iteration 3 Error: 0.022637 Align patch 20 5 left Iteration 1 Error: 0.698370 Iteration 2 Error: 0.058159 Iteration 3 Error: 0.016446 Align patch 21 4 left Iteration 1 Error: 0.724746 Iteration 2 Error: 0.080173 Iteration 3 Error: 0.013205 Align patch 22 3 left Iteration 1 Error: 0.766314 Iteration 2 Error: 0.093188 Iteration 3 Error: 0.026295 Align patch 23 2 left Iteration 1 Error: 0.692303 Iteration 2 Error: 0.113007 Iteration 3 Error: 0.017344 Align patch 24 1 left Iteration 1 Error: 0.547835 Iteration 2 Error: 0.054852 Iteration 3 Error: 0.011693 Align patch 25 0 left Iteration 1 Error: 0.580331 Iteration 2 Error: 0.064722 Iteration 3 Error: 0.011551 3D Fitting completed. Patch alignment time: 11.18(sec) Local motion has been corrected. Process thread exits. Computational time: 23.397032 sec Total time: 30.200373 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00009hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00009hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.543566s Reading file: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00009hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.007882s ........................................ >>>>>>TIME<<<<<< FFT: 0.952977s Defocus_U Defocus_V Angle CCC 12388.68 11951.18 86.76 0.053728 Final Values Defocus_U Defocus_V Angle CCC 12396.49 11977.76 86.46 0.089953 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00005sq_v01_00009hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00009hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.002e-01 CC threshold: 0.736 Mean Std: 42.78 7.26 Num Hot pixels: 233 Hot pixel threshold: 86.36 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.099102 Iteration 2 Error: 0.170600 Iteration 3 Error: 0.033890 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.21 0.06 ...... Frame ( 3) shift: -0.41 0.13 ...... Frame ( 4) shift: -0.62 0.19 ...... Frame ( 5) shift: -0.83 0.26 ...... Frame ( 6) shift: -0.92 0.31 ...... Frame ( 7) shift: -0.90 0.36 ...... Frame ( 8) shift: -0.87 0.41 ...... Frame ( 9) shift: -0.82 0.50 ...... Frame ( 10) shift: -0.74 0.64 ...... Frame ( 11) shift: -0.66 0.78 ...... Frame ( 12) shift: -0.57 0.90 ...... Frame ( 13) shift: -0.46 1.01 ...... Frame ( 14) shift: -0.36 1.12 ...... Frame ( 15) shift: -0.29 1.20 ...... Frame ( 16) shift: -0.26 1.26 ...... Frame ( 17) shift: -0.24 1.31 ...... Frame ( 18) shift: -0.21 1.37 ...... Frame ( 19) shift: -0.18 1.43 ...... Frame ( 20) shift: -0.15 1.49 ...... Frame ( 21) shift: -0.10 1.53 ...... Frame ( 22) shift: -0.03 1.53 ...... Frame ( 23) shift: 0.04 1.54 ...... Frame ( 24) shift: 0.06 1.57 ...... Frame ( 25) shift: 0.03 1.62 ...... Frame ( 26) shift: -0.01 1.68 ...... Frame ( 27) shift: 0.02 1.71 ...... Frame ( 28) shift: 0.09 1.73 ...... Frame ( 29) shift: 0.17 1.74 ...... Frame ( 30) shift: 0.19 1.77 ...... Frame ( 31) shift: 0.13 1.80 ...... Frame ( 32) shift: 0.08 1.83 ...... Frame ( 33) shift: 0.05 1.86 ...... Frame ( 34) shift: 0.04 1.90 ...... Frame ( 35) shift: 0.04 1.94 ...... Frame ( 36) shift: 0.04 1.96 ...... Frame ( 37) shift: 0.04 1.97 ...... Frame ( 38) shift: 0.04 1.98 ...... Frame ( 39) shift: 0.03 1.98 ...... Frame ( 40) shift: 0.03 1.99 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.120357 Iteration 2 Error: 0.257282 Iteration 3 Error: 0.069519 Iteration 4 Error: 0.023841 Align patch 2 23 left Iteration 1 Error: 1.471403 Iteration 2 Error: 0.156838 Iteration 3 Error: 0.063418 Iteration 4 Error: 0.016739 Align patch 3 22 left Iteration 1 Error: 0.648167 Iteration 2 Error: 0.106752 Iteration 3 Error: 0.012934 Align patch 4 21 left Iteration 1 Error: 0.663606 Iteration 2 Error: 0.064048 Iteration 3 Error: 0.016347 Align patch 5 20 left Iteration 1 Error: 0.597196 Iteration 2 Error: 0.081064 Iteration 3 Error: 0.013562 Align patch 6 19 left Iteration 1 Error: 1.580637 Iteration 2 Error: 0.206311 Iteration 3 Error: 0.104074 Iteration 4 Error: 0.020511 Align patch 7 18 left Iteration 1 Error: 0.982596 Iteration 2 Error: 0.138305 Iteration 3 Error: 0.041566 Align patch 8 17 left Iteration 1 Error: 0.576250 Iteration 2 Error: 0.096451 Iteration 3 Error: 0.025447 Align patch 9 16 left Iteration 1 Error: 0.566560 Iteration 2 Error: 0.086464 Iteration 3 Error: 0.024619 Align patch 10 15 left Iteration 1 Error: 0.718405 Iteration 2 Error: 0.066579 Iteration 3 Error: 0.016505 Align patch 11 14 left Iteration 1 Error: 1.036898 Iteration 2 Error: 0.315590 Iteration 3 Error: 0.086199 Iteration 4 Error: 0.032901 Align patch 12 13 left Iteration 1 Error: 0.825037 Iteration 2 Error: 0.215324 Iteration 3 Error: 0.059851 Iteration 4 Error: 0.025640 Align patch 13 12 left Iteration 1 Error: 0.688136 Iteration 2 Error: 0.086026 Iteration 3 Error: 0.020112 Align patch 14 11 left Iteration 1 Error: 0.729935 Iteration 2 Error: 0.108025 Iteration 3 Error: 0.025089 Align patch 15 10 left Iteration 1 Error: 0.655259 Iteration 2 Error: 0.113468 Iteration 3 Error: 0.023752 Align patch 16 9 left Iteration 1 Error: 1.074821 Iteration 2 Error: 0.129921 Iteration 3 Error: 0.031310 Align patch 17 8 left Iteration 1 Error: 0.715670 Iteration 2 Error: 0.133636 Iteration 3 Error: 0.039782 Align patch 18 7 left Iteration 1 Error: 0.804378 Iteration 2 Error: 0.098508 Iteration 3 Error: 0.018449 Align patch 19 6 left Iteration 1 Error: 0.608930 Iteration 2 Error: 0.142290 Iteration 3 Error: 0.032702 Align patch 20 5 left Iteration 1 Error: 0.552320 Iteration 2 Error: 0.079562 Iteration 3 Error: 0.021215 Align patch 21 4 left Iteration 1 Error: 0.839122 Iteration 2 Error: 0.105028 Iteration 3 Error: 0.014972 Align patch 22 3 left Iteration 1 Error: 1.057395 Iteration 2 Error: 0.134160 Iteration 3 Error: 0.023441 Align patch 23 2 left Iteration 1 Error: 1.026886 Iteration 2 Error: 0.137495 Iteration 3 Error: 0.022001 Align patch 24 1 left Iteration 1 Error: 0.614664 Iteration 2 Error: 0.074811 Iteration 3 Error: 0.016561 Align patch 25 0 left Iteration 1 Error: 0.498892 Iteration 2 Error: 0.044619 3D Fitting completed. Patch alignment time: 11.79(sec) Local motion has been corrected. Process thread exits. Computational time: 23.637657 sec Total time: 30.423174 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00009hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00009hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.705171s Reading file: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00009hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.917805s ........................................ >>>>>>TIME<<<<<< FFT: 0.927234s Defocus_U Defocus_V Angle CCC 11761.72 12601.56 5.53 0.057922 Final Values Defocus_U Defocus_V Angle CCC 11775.78 12590.63 5.53 0.097877 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00005sq_v01_00009hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00009hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 41.81 7.15 Num Hot pixels: 248 Hot pixel threshold: 84.71 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.902511 Iteration 2 Error: 0.152116 Iteration 3 Error: 0.026156 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.30 -0.12 ...... Frame ( 3) shift: -0.61 -0.23 ...... Frame ( 4) shift: -0.91 -0.35 ...... Frame ( 5) shift: -1.22 -0.46 ...... Frame ( 6) shift: -1.37 -0.53 ...... Frame ( 7) shift: -1.38 -0.56 ...... Frame ( 8) shift: -1.38 -0.59 ...... Frame ( 9) shift: -1.33 -0.54 ...... Frame ( 10) shift: -1.21 -0.42 ...... Frame ( 11) shift: -1.09 -0.31 ...... Frame ( 12) shift: -1.03 -0.22 ...... Frame ( 13) shift: -1.04 -0.16 ...... Frame ( 14) shift: -1.04 -0.10 ...... Frame ( 15) shift: -0.96 -0.00 ...... Frame ( 16) shift: -0.81 0.13 ...... Frame ( 17) shift: -0.65 0.26 ...... Frame ( 18) shift: -0.61 0.36 ...... Frame ( 19) shift: -0.69 0.45 ...... Frame ( 20) shift: -0.77 0.53 ...... Frame ( 21) shift: -0.81 0.60 ...... Frame ( 22) shift: -0.83 0.66 ...... Frame ( 23) shift: -0.84 0.72 ...... Frame ( 24) shift: -0.84 0.74 ...... Frame ( 25) shift: -0.80 0.71 ...... Frame ( 26) shift: -0.77 0.69 ...... Frame ( 27) shift: -0.73 0.72 ...... Frame ( 28) shift: -0.68 0.79 ...... Frame ( 29) shift: -0.64 0.87 ...... Frame ( 30) shift: -0.61 0.91 ...... Frame ( 31) shift: -0.59 0.91 ...... Frame ( 32) shift: -0.58 0.91 ...... Frame ( 33) shift: -0.61 0.93 ...... Frame ( 34) shift: -0.69 0.96 ...... Frame ( 35) shift: -0.76 1.00 ...... Frame ( 36) shift: -0.82 0.98 ...... Frame ( 37) shift: -0.87 0.89 ...... Frame ( 38) shift: -0.91 0.79 ...... Frame ( 39) shift: -0.95 0.70 ...... Frame ( 40) shift: -1.00 0.61 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.377828 Iteration 2 Error: 0.190484 Iteration 3 Error: 0.047591 Align patch 2 23 left Iteration 1 Error: 0.927140 Iteration 2 Error: 0.239289 Iteration 3 Error: 0.065983 Iteration 4 Error: 0.019805 Align patch 3 22 left Iteration 1 Error: 0.379030 Iteration 2 Error: 0.049953 Align patch 4 21 left Iteration 1 Error: 0.648022 Iteration 2 Error: 0.058685 Iteration 3 Error: 0.011241 Align patch 5 20 left Iteration 1 Error: 0.856046 Iteration 2 Error: 0.166252 Iteration 3 Error: 0.034007 Align patch 6 19 left Iteration 1 Error: 1.345867 Iteration 2 Error: 0.202404 Iteration 3 Error: 0.053328 Iteration 4 Error: 0.020654 Align patch 7 18 left Iteration 1 Error: 0.844125 Iteration 2 Error: 0.186241 Iteration 3 Error: 0.035376 Align patch 8 17 left Iteration 1 Error: 0.408192 Iteration 2 Error: 0.055720 Iteration 3 Error: 0.010861 Align patch 9 16 left Iteration 1 Error: 0.629062 Iteration 2 Error: 0.063754 Iteration 3 Error: 0.016376 Align patch 10 15 left Iteration 1 Error: 0.511254 Iteration 2 Error: 0.081726 Iteration 3 Error: 0.022840 Align patch 11 14 left Iteration 1 Error: 0.966476 Iteration 2 Error: 0.169524 Iteration 3 Error: 0.057182 Iteration 4 Error: 0.020526 Align patch 12 13 left Iteration 1 Error: 1.031917 Iteration 2 Error: 0.179131 Iteration 3 Error: 0.045685 Align patch 13 12 left Iteration 1 Error: 0.390432 Iteration 2 Error: 0.048823 Align patch 14 11 left Iteration 1 Error: 0.333756 Iteration 2 Error: 0.072936 Iteration 3 Error: 0.015100 Align patch 15 10 left Iteration 1 Error: 0.554736 Iteration 2 Error: 0.082450 Iteration 3 Error: 0.023794 Align patch 16 9 left Iteration 1 Error: 0.945899 Iteration 2 Error: 0.209941 Iteration 3 Error: 0.051476 Iteration 4 Error: 0.017481 Align patch 17 8 left Iteration 1 Error: 1.030403 Iteration 2 Error: 0.165763 Iteration 3 Error: 0.038515 Align patch 18 7 left Iteration 1 Error: 0.574600 Iteration 2 Error: 0.091796 Iteration 3 Error: 0.017093 Align patch 19 6 left Iteration 1 Error: 0.672381 Iteration 2 Error: 0.073267 Iteration 3 Error: 0.014974 Align patch 20 5 left Iteration 1 Error: 0.646169 Iteration 2 Error: 0.065433 Iteration 3 Error: 0.012571 Align patch 21 4 left Iteration 1 Error: 0.720235 Iteration 2 Error: 0.108822 Iteration 3 Error: 0.032145 Align patch 22 3 left Iteration 1 Error: 0.479000 Iteration 2 Error: 0.065362 Iteration 3 Error: 0.016119 Align patch 23 2 left Iteration 1 Error: 0.569620 Iteration 2 Error: 0.073711 Iteration 3 Error: 0.008938 Align patch 24 1 left Iteration 1 Error: 0.593562 Iteration 2 Error: 0.068847 Iteration 3 Error: 0.014586 Align patch 25 0 left Iteration 1 Error: 0.708723 Iteration 2 Error: 0.119414 Iteration 3 Error: 0.023308 3D Fitting completed. Patch alignment time: 11.32(sec) Local motion has been corrected. Process thread exits. Computational time: 24.306458 sec Total time: 30.827660 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00009hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00009hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.501072s Reading file: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00009hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.040383s ........................................ >>>>>>TIME<<<<<< FFT: 0.942102s Defocus_U Defocus_V Angle CCC 11705.08 11076.18 83.29 0.055481 Final Values Defocus_U Defocus_V Angle CCC 11711.34 11107.44 82.35 0.095833 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00005sq_v01_00010hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00010hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.002e-01 CC threshold: 0.736 Mean Std: 43.09 7.28 Num Hot pixels: 210 Hot pixel threshold: 86.75 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.609495 Iteration 2 Error: 0.247292 Iteration 3 Error: 0.046486 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.18 -0.12 ...... Frame ( 3) shift: -0.36 -0.23 ...... Frame ( 4) shift: -0.53 -0.35 ...... Frame ( 5) shift: -0.71 -0.46 ...... Frame ( 6) shift: -0.76 -0.49 ...... Frame ( 7) shift: -0.68 -0.44 ...... Frame ( 8) shift: -0.59 -0.38 ...... Frame ( 9) shift: -0.52 -0.36 ...... Frame ( 10) shift: -0.47 -0.37 ...... Frame ( 11) shift: -0.41 -0.38 ...... Frame ( 12) shift: -0.37 -0.31 ...... Frame ( 13) shift: -0.34 -0.16 ...... Frame ( 14) shift: -0.30 -0.01 ...... Frame ( 15) shift: -0.24 0.11 ...... Frame ( 16) shift: -0.14 0.19 ...... Frame ( 17) shift: -0.04 0.28 ...... Frame ( 18) shift: 0.01 0.33 ...... Frame ( 19) shift: -0.01 0.35 ...... Frame ( 20) shift: -0.02 0.38 ...... Frame ( 21) shift: 0.04 0.39 ...... Frame ( 22) shift: 0.15 0.39 ...... Frame ( 23) shift: 0.27 0.40 ...... Frame ( 24) shift: 0.36 0.37 ...... Frame ( 25) shift: 0.40 0.31 ...... Frame ( 26) shift: 0.44 0.25 ...... Frame ( 27) shift: 0.49 0.24 ...... Frame ( 28) shift: 0.56 0.26 ...... Frame ( 29) shift: 0.63 0.28 ...... Frame ( 30) shift: 0.69 0.29 ...... Frame ( 31) shift: 0.74 0.28 ...... Frame ( 32) shift: 0.80 0.27 ...... Frame ( 33) shift: 0.87 0.31 ...... Frame ( 34) shift: 0.94 0.40 ...... Frame ( 35) shift: 1.02 0.49 ...... Frame ( 36) shift: 1.14 0.61 ...... Frame ( 37) shift: 1.29 0.77 ...... Frame ( 38) shift: 1.45 0.93 ...... Frame ( 39) shift: 1.60 1.09 ...... Frame ( 40) shift: 1.76 1.25 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.120407 Iteration 2 Error: 0.253400 Iteration 3 Error: 0.083438 Iteration 4 Error: 0.028235 Align patch 2 23 left Iteration 1 Error: 1.310157 Iteration 2 Error: 0.186683 Iteration 3 Error: 0.059984 Iteration 4 Error: 0.024791 Align patch 3 22 left Iteration 1 Error: 0.692650 Iteration 2 Error: 0.082671 Iteration 3 Error: 0.017027 Align patch 4 21 left Iteration 1 Error: 0.524375 Iteration 2 Error: 0.052471 Iteration 3 Error: 0.019276 Align patch 5 20 left Iteration 1 Error: 0.428444 Iteration 2 Error: 0.061919 Iteration 3 Error: 0.010965 Align patch 6 19 left Iteration 1 Error: 0.794637 Iteration 2 Error: 0.142997 Iteration 3 Error: 0.026688 Align patch 7 18 left Iteration 1 Error: 0.852824 Iteration 2 Error: 0.130499 Iteration 3 Error: 0.031130 Align patch 8 17 left Iteration 1 Error: 0.565955 Iteration 2 Error: 0.098967 Iteration 3 Error: 0.033009 Align patch 9 16 left Iteration 1 Error: 0.619839 Iteration 2 Error: 0.097412 Iteration 3 Error: 0.023808 Align patch 10 15 left Iteration 1 Error: 0.537413 Iteration 2 Error: 0.072479 Iteration 3 Error: 0.014201 Align patch 11 14 left Iteration 1 Error: 0.967929 Iteration 2 Error: 0.115564 Iteration 3 Error: 0.032079 Align patch 12 13 left Iteration 1 Error: 0.924147 Iteration 2 Error: 0.108399 Iteration 3 Error: 0.028814 Align patch 13 12 left Iteration 1 Error: 0.591063 Iteration 2 Error: 0.072784 Iteration 3 Error: 0.027143 Align patch 14 11 left Iteration 1 Error: 0.501073 Iteration 2 Error: 0.052376 Iteration 3 Error: 0.012072 Align patch 15 10 left Iteration 1 Error: 0.482068 Iteration 2 Error: 0.063536 Iteration 3 Error: 0.012337 Align patch 16 9 left Iteration 1 Error: 0.664158 Iteration 2 Error: 0.117138 Iteration 3 Error: 0.029510 Align patch 17 8 left Iteration 1 Error: 0.750842 Iteration 2 Error: 0.102341 Iteration 3 Error: 0.023100 Align patch 18 7 left Iteration 1 Error: 1.048405 Iteration 2 Error: 0.150659 Iteration 3 Error: 0.048772 Align patch 19 6 left Iteration 1 Error: 0.748367 Iteration 2 Error: 0.126360 Iteration 3 Error: 0.028282 Align patch 20 5 left Iteration 1 Error: 0.475611 Iteration 2 Error: 0.104770 Iteration 3 Error: 0.030152 Align patch 21 4 left Iteration 1 Error: 0.670052 Iteration 2 Error: 0.141632 Iteration 3 Error: 0.031923 Align patch 22 3 left Iteration 1 Error: 0.970548 Iteration 2 Error: 0.121107 Iteration 3 Error: 0.048939 Align patch 23 2 left Iteration 1 Error: 0.832885 Iteration 2 Error: 0.143554 Iteration 3 Error: 0.030035 Align patch 24 1 left Iteration 1 Error: 0.555096 Iteration 2 Error: 0.061997 Iteration 3 Error: 0.014144 Align patch 25 0 left Iteration 1 Error: 0.478989 Iteration 2 Error: 0.076123 Iteration 3 Error: 0.021973 3D Fitting completed. Patch alignment time: 12.41(sec) Local motion has been corrected. Process thread exits. Computational time: 25.395872 sec Total time: 32.282410 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00010hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00010hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.928009s Reading file: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00010hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.776889s ........................................ >>>>>>TIME<<<<<< FFT: 0.931186s Defocus_U Defocus_V Angle CCC 10382.84 11253.94 11.81 0.061154 Final Values Defocus_U Defocus_V Angle CCC 10393.79 11271.13 12.13 0.110309 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00005sq_v01_00010hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00010hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.003e-01 CC threshold: 0.736 Mean Std: 42.59 7.34 Num Hot pixels: 229 Hot pixel threshold: 86.65 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.006773 Iteration 2 Error: 0.210368 Iteration 3 Error: 0.046669 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.20 0.03 ...... Frame ( 3) shift: -0.40 0.07 ...... Frame ( 4) shift: -0.60 0.10 ...... Frame ( 5) shift: -0.80 0.13 ...... Frame ( 6) shift: -0.86 0.15 ...... Frame ( 7) shift: -0.78 0.15 ...... Frame ( 8) shift: -0.70 0.15 ...... Frame ( 9) shift: -0.65 0.21 ...... Frame ( 10) shift: -0.63 0.32 ...... Frame ( 11) shift: -0.60 0.44 ...... Frame ( 12) shift: -0.55 0.53 ...... Frame ( 13) shift: -0.46 0.59 ...... Frame ( 14) shift: -0.38 0.64 ...... Frame ( 15) shift: -0.31 0.70 ...... Frame ( 16) shift: -0.26 0.74 ...... Frame ( 17) shift: -0.22 0.79 ...... Frame ( 18) shift: -0.18 0.88 ...... Frame ( 19) shift: -0.14 1.00 ...... Frame ( 20) shift: -0.10 1.12 ...... Frame ( 21) shift: -0.03 1.19 ...... Frame ( 22) shift: 0.09 1.22 ...... Frame ( 23) shift: 0.21 1.24 ...... Frame ( 24) shift: 0.27 1.30 ...... Frame ( 25) shift: 0.27 1.39 ...... Frame ( 26) shift: 0.28 1.48 ...... Frame ( 27) shift: 0.29 1.56 ...... Frame ( 28) shift: 0.32 1.62 ...... Frame ( 29) shift: 0.34 1.69 ...... Frame ( 30) shift: 0.35 1.74 ...... Frame ( 31) shift: 0.35 1.77 ...... Frame ( 32) shift: 0.35 1.80 ...... Frame ( 33) shift: 0.36 1.81 ...... Frame ( 34) shift: 0.38 1.81 ...... Frame ( 35) shift: 0.41 1.80 ...... Frame ( 36) shift: 0.41 1.83 ...... Frame ( 37) shift: 0.39 1.88 ...... Frame ( 38) shift: 0.36 1.94 ...... Frame ( 39) shift: 0.34 1.99 ...... Frame ( 40) shift: 0.31 2.05 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.523552 Iteration 2 Error: 0.126900 Iteration 3 Error: 0.037847 Align patch 2 23 left Iteration 1 Error: 0.947793 Iteration 2 Error: 0.132845 Iteration 3 Error: 0.045043 Align patch 3 22 left Iteration 1 Error: 0.535796 Iteration 2 Error: 0.090415 Iteration 3 Error: 0.025456 Align patch 4 21 left Iteration 1 Error: 0.687602 Iteration 2 Error: 0.084590 Iteration 3 Error: 0.026513 Align patch 5 20 left Iteration 1 Error: 0.653146 Iteration 2 Error: 0.085500 Iteration 3 Error: 0.016125 Align patch 6 19 left Iteration 1 Error: 0.995786 Iteration 2 Error: 0.111524 Iteration 3 Error: 0.026822 Align patch 7 18 left Iteration 1 Error: 0.619863 Iteration 2 Error: 0.079899 Iteration 3 Error: 0.032753 Align patch 8 17 left Iteration 1 Error: 0.556019 Iteration 2 Error: 0.060417 Iteration 3 Error: 0.021417 Align patch 9 16 left Iteration 1 Error: 0.550427 Iteration 2 Error: 0.080362 Iteration 3 Error: 0.012439 Align patch 10 15 left Iteration 1 Error: 0.494868 Iteration 2 Error: 0.106278 Iteration 3 Error: 0.030365 Align patch 11 14 left Iteration 1 Error: 1.039559 Iteration 2 Error: 0.222347 Iteration 3 Error: 0.041840 Align patch 12 13 left Iteration 1 Error: 0.578472 Iteration 2 Error: 0.129386 Iteration 3 Error: 0.037394 Align patch 13 12 left Iteration 1 Error: 0.456360 Iteration 2 Error: 0.090803 Iteration 3 Error: 0.023207 Align patch 14 11 left Iteration 1 Error: 0.625329 Iteration 2 Error: 0.079503 Iteration 3 Error: 0.018175 Align patch 15 10 left Iteration 1 Error: 0.509081 Iteration 2 Error: 0.073174 Iteration 3 Error: 0.022328 Align patch 16 9 left Iteration 1 Error: 0.772294 Iteration 2 Error: 0.178394 Iteration 3 Error: 0.034085 Align patch 17 8 left Iteration 1 Error: 0.562923 Iteration 2 Error: 0.072676 Iteration 3 Error: 0.023067 Align patch 18 7 left Iteration 1 Error: 0.612968 Iteration 2 Error: 0.064772 Iteration 3 Error: 0.018427 Align patch 19 6 left Iteration 1 Error: 0.701493 Iteration 2 Error: 0.087934 Iteration 3 Error: 0.019577 Align patch 20 5 left Iteration 1 Error: 0.698813 Iteration 2 Error: 0.098754 Iteration 3 Error: 0.030923 Align patch 21 4 left Iteration 1 Error: 0.791574 Iteration 2 Error: 0.094927 Iteration 3 Error: 0.031620 Align patch 22 3 left Iteration 1 Error: 0.726504 Iteration 2 Error: 0.071169 Iteration 3 Error: 0.025636 Align patch 23 2 left Iteration 1 Error: 0.768253 Iteration 2 Error: 0.113914 Iteration 3 Error: 0.039193 Align patch 24 1 left Iteration 1 Error: 0.990075 Iteration 2 Error: 0.175119 Iteration 3 Error: 0.035217 Align patch 25 0 left Iteration 1 Error: 0.878183 Iteration 2 Error: 0.124231 Iteration 3 Error: 0.028239 3D Fitting completed. Patch alignment time: 11.52(sec) Local motion has been corrected. Process thread exits. Computational time: 23.162079 sec Total time: 30.007353 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00010hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00010hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.561770s Reading file: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00010hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.734709s ........................................ >>>>>>TIME<<<<<< FFT: 1.049586s Defocus_U Defocus_V Angle CCC 8919.95 9396.51 2.84 0.042123 Final Values Defocus_U Defocus_V Angle CCC 8921.51 9398.07 2.84 0.083167 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00005sq_v01_00010hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00010hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.003e-01 CC threshold: 0.737 Mean Std: 43.59 7.27 Num Hot pixels: 240 Hot pixel threshold: 87.22 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.085096 Iteration 2 Error: 0.164464 Iteration 3 Error: 0.025621 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.25 0.01 ...... Frame ( 3) shift: -0.50 0.02 ...... Frame ( 4) shift: -0.76 0.03 ...... Frame ( 5) shift: -1.01 0.03 ...... Frame ( 6) shift: -1.13 0.09 ...... Frame ( 7) shift: -1.13 0.20 ...... Frame ( 8) shift: -1.13 0.32 ...... Frame ( 9) shift: -1.11 0.43 ...... Frame ( 10) shift: -1.07 0.54 ...... Frame ( 11) shift: -1.02 0.65 ...... Frame ( 12) shift: -1.01 0.73 ...... Frame ( 13) shift: -1.03 0.76 ...... Frame ( 14) shift: -1.05 0.80 ...... Frame ( 15) shift: -1.08 0.84 ...... Frame ( 16) shift: -1.12 0.89 ...... Frame ( 17) shift: -1.17 0.93 ...... Frame ( 18) shift: -1.17 0.99 ...... Frame ( 19) shift: -1.14 1.04 ...... Frame ( 20) shift: -1.11 1.10 ...... Frame ( 21) shift: -1.08 1.17 ...... Frame ( 22) shift: -1.03 1.25 ...... Frame ( 23) shift: -0.98 1.33 ...... Frame ( 24) shift: -0.95 1.38 ...... Frame ( 25) shift: -0.94 1.40 ...... Frame ( 26) shift: -0.92 1.41 ...... Frame ( 27) shift: -0.94 1.43 ...... Frame ( 28) shift: -0.98 1.45 ...... Frame ( 29) shift: -1.02 1.47 ...... Frame ( 30) shift: -1.02 1.50 ...... Frame ( 31) shift: -0.97 1.53 ...... Frame ( 32) shift: -0.92 1.57 ...... Frame ( 33) shift: -0.90 1.62 ...... Frame ( 34) shift: -0.93 1.68 ...... Frame ( 35) shift: -0.95 1.73 ...... Frame ( 36) shift: -0.97 1.81 ...... Frame ( 37) shift: -0.97 1.90 ...... Frame ( 38) shift: -0.98 1.99 ...... Frame ( 39) shift: -0.98 2.08 ...... Frame ( 40) shift: -0.99 2.17 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.130760 Iteration 2 Error: 0.102809 Iteration 3 Error: 0.017412 Align patch 2 23 left Iteration 1 Error: 1.079927 Iteration 2 Error: 0.207689 Iteration 3 Error: 0.068398 Iteration 4 Error: 0.019476 Align patch 3 22 left Iteration 1 Error: 1.060255 Iteration 2 Error: 0.136048 Iteration 3 Error: 0.034118 Align patch 4 21 left Iteration 1 Error: 0.918582 Iteration 2 Error: 0.083445 Iteration 3 Error: 0.018516 Align patch 5 20 left Iteration 1 Error: 0.532505 Iteration 2 Error: 0.090040 Iteration 3 Error: 0.023991 Align patch 6 19 left Iteration 1 Error: 0.844418 Iteration 2 Error: 0.096905 Iteration 3 Error: 0.024780 Align patch 7 18 left Iteration 1 Error: 0.727146 Iteration 2 Error: 0.174149 Iteration 3 Error: 0.049022 Align patch 8 17 left Iteration 1 Error: 0.499429 Iteration 2 Error: 0.084685 Iteration 3 Error: 0.020629 Align patch 9 16 left Iteration 1 Error: 0.664253 Iteration 2 Error: 0.080863 Iteration 3 Error: 0.020097 Align patch 10 15 left Iteration 1 Error: 0.587714 Iteration 2 Error: 0.068074 Iteration 3 Error: 0.009645 Align patch 11 14 left Iteration 1 Error: 0.838487 Iteration 2 Error: 0.119573 Iteration 3 Error: 0.041818 Align patch 12 13 left Iteration 1 Error: 0.653227 Iteration 2 Error: 0.103976 Iteration 3 Error: 0.028928 Align patch 13 12 left Iteration 1 Error: 1.017236 Iteration 2 Error: 0.120477 Iteration 3 Error: 0.030655 Align patch 14 11 left Iteration 1 Error: 0.437033 Iteration 2 Error: 0.159147 Iteration 3 Error: 0.026430 Align patch 15 10 left Iteration 1 Error: 0.486118 Iteration 2 Error: 0.058235 Iteration 3 Error: 0.022455 Align patch 16 9 left Iteration 1 Error: 0.717676 Iteration 2 Error: 0.108154 Iteration 3 Error: 0.023388 Align patch 17 8 left Iteration 1 Error: 0.668020 Iteration 2 Error: 0.108150 Iteration 3 Error: 0.019420 Align patch 18 7 left Iteration 1 Error: 0.569007 Iteration 2 Error: 0.114686 Iteration 3 Error: 0.022639 Align patch 19 6 left Iteration 1 Error: 0.610252 Iteration 2 Error: 0.128989 Iteration 3 Error: 0.018516 Align patch 20 5 left Iteration 1 Error: 0.491723 Iteration 2 Error: 0.076888 Iteration 3 Error: 0.015766 Align patch 21 4 left Iteration 1 Error: 0.756795 Iteration 2 Error: 0.125165 Iteration 3 Error: 0.038896 Align patch 22 3 left Iteration 1 Error: 0.803537 Iteration 2 Error: 0.175601 Iteration 3 Error: 0.045112 Align patch 23 2 left Iteration 1 Error: 0.632343 Iteration 2 Error: 0.065279 Iteration 3 Error: 0.015276 Align patch 24 1 left Iteration 1 Error: 0.948851 Iteration 2 Error: 0.136116 Iteration 3 Error: 0.022461 Align patch 25 0 left Iteration 1 Error: 0.598771 Iteration 2 Error: 0.101529 Iteration 3 Error: 0.017425 3D Fitting completed. Patch alignment time: 11.10(sec) Local motion has been corrected. Process thread exits. Computational time: 23.012665 sec Total time: 28.785740 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00010hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00010hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.522354s Reading file: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00010hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.851636s ........................................ >>>>>>TIME<<<<<< FFT: 1.011390s Defocus_U Defocus_V Angle CCC 9593.75 10437.50 7.89 0.051433 Final Values Defocus_U Defocus_V Angle CCC 9590.62 10456.27 7.58 0.097365 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00005sq_v01_00010hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00010hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 43.13 7.29 Num Hot pixels: 216 Hot pixel threshold: 86.90 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.002091 Iteration 2 Error: 0.170461 Iteration 3 Error: 0.032346 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.28 -0.04 ...... Frame ( 3) shift: -0.55 -0.07 ...... Frame ( 4) shift: -0.83 -0.11 ...... Frame ( 5) shift: -1.11 -0.15 ...... Frame ( 6) shift: -1.24 -0.15 ...... Frame ( 7) shift: -1.23 -0.11 ...... Frame ( 8) shift: -1.21 -0.07 ...... Frame ( 9) shift: -1.15 -0.00 ...... Frame ( 10) shift: -1.02 0.09 ...... Frame ( 11) shift: -0.90 0.19 ...... Frame ( 12) shift: -0.78 0.29 ...... Frame ( 13) shift: -0.65 0.40 ...... Frame ( 14) shift: -0.52 0.51 ...... Frame ( 15) shift: -0.47 0.61 ...... Frame ( 16) shift: -0.48 0.71 ...... Frame ( 17) shift: -0.50 0.80 ...... Frame ( 18) shift: -0.48 0.88 ...... Frame ( 19) shift: -0.42 0.94 ...... Frame ( 20) shift: -0.37 1.00 ...... Frame ( 21) shift: -0.35 1.05 ...... Frame ( 22) shift: -0.36 1.09 ...... Frame ( 23) shift: -0.38 1.14 ...... Frame ( 24) shift: -0.36 1.16 ...... Frame ( 25) shift: -0.30 1.18 ...... Frame ( 26) shift: -0.25 1.19 ...... Frame ( 27) shift: -0.23 1.20 ...... Frame ( 28) shift: -0.24 1.19 ...... Frame ( 29) shift: -0.25 1.18 ...... Frame ( 30) shift: -0.23 1.18 ...... Frame ( 31) shift: -0.19 1.19 ...... Frame ( 32) shift: -0.14 1.19 ...... Frame ( 33) shift: -0.14 1.22 ...... Frame ( 34) shift: -0.17 1.27 ...... Frame ( 35) shift: -0.21 1.32 ...... Frame ( 36) shift: -0.21 1.37 ...... Frame ( 37) shift: -0.18 1.42 ...... Frame ( 38) shift: -0.15 1.46 ...... Frame ( 39) shift: -0.11 1.51 ...... Frame ( 40) shift: -0.08 1.55 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.441361 Iteration 2 Error: 0.128865 Iteration 3 Error: 0.029994 Align patch 2 23 left Iteration 1 Error: 1.532709 Iteration 2 Error: 0.188103 Iteration 3 Error: 0.041681 Align patch 3 22 left Iteration 1 Error: 0.745487 Iteration 2 Error: 0.108862 Iteration 3 Error: 0.019380 Align patch 4 21 left Iteration 1 Error: 0.598990 Iteration 2 Error: 0.092635 Iteration 3 Error: 0.021358 Align patch 5 20 left Iteration 1 Error: 0.670009 Iteration 2 Error: 0.137872 Iteration 3 Error: 0.019070 Align patch 6 19 left Iteration 1 Error: 0.963208 Iteration 2 Error: 0.121733 Iteration 3 Error: 0.033950 Align patch 7 18 left Iteration 1 Error: 0.835903 Iteration 2 Error: 0.116525 Iteration 3 Error: 0.032981 Align patch 8 17 left Iteration 1 Error: 0.548685 Iteration 2 Error: 0.057630 Iteration 3 Error: 0.018147 Align patch 9 16 left Iteration 1 Error: 0.645176 Iteration 2 Error: 0.119199 Iteration 3 Error: 0.041828 Align patch 10 15 left Iteration 1 Error: 0.555277 Iteration 2 Error: 0.062772 Iteration 3 Error: 0.013734 Align patch 11 14 left Iteration 1 Error: 0.898429 Iteration 2 Error: 0.141751 Iteration 3 Error: 0.039359 Align patch 12 13 left Iteration 1 Error: 0.870346 Iteration 2 Error: 0.122166 Iteration 3 Error: 0.028480 Align patch 13 12 left Iteration 1 Error: 0.634925 Iteration 2 Error: 0.180409 Iteration 3 Error: 0.043343 Align patch 14 11 left Iteration 1 Error: 0.410448 Iteration 2 Error: 0.058216 Iteration 3 Error: 0.015058 Align patch 15 10 left Iteration 1 Error: 0.559387 Iteration 2 Error: 0.100887 Iteration 3 Error: 0.028817 Align patch 16 9 left Iteration 1 Error: 0.789753 Iteration 2 Error: 0.111407 Iteration 3 Error: 0.024725 Align patch 17 8 left Iteration 1 Error: 0.723077 Iteration 2 Error: 0.180508 Iteration 3 Error: 0.058040 Iteration 4 Error: 0.023237 Align patch 18 7 left Iteration 1 Error: 0.631713 Iteration 2 Error: 0.107605 Iteration 3 Error: 0.035011 Align patch 19 6 left Iteration 1 Error: 0.606955 Iteration 2 Error: 0.087533 Iteration 3 Error: 0.021317 Align patch 20 5 left Iteration 1 Error: 0.933946 Iteration 2 Error: 0.129364 Iteration 3 Error: 0.022376 Align patch 21 4 left Iteration 1 Error: 0.642536 Iteration 2 Error: 0.099816 Iteration 3 Error: 0.022177 Align patch 22 3 left Iteration 1 Error: 0.776653 Iteration 2 Error: 0.137407 Iteration 3 Error: 0.041492 Align patch 23 2 left Iteration 1 Error: 0.838527 Iteration 2 Error: 0.128449 Iteration 3 Error: 0.035726 Align patch 24 1 left Iteration 1 Error: 0.716920 Iteration 2 Error: 0.128193 Iteration 3 Error: 0.039470 Align patch 25 0 left Iteration 1 Error: 1.176219 Iteration 2 Error: 0.080281 Iteration 3 Error: 0.014974 3D Fitting completed. Patch alignment time: 10.97(sec) Local motion has been corrected. Process thread exits. Computational time: 23.147320 sec Total time: 30.152750 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00010hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00010hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.549309s Reading file: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00010hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.498978s ........................................ >>>>>>TIME<<<<<< FFT: 1.026225s Defocus_U Defocus_V Angle CCC 13202.14 12536.15 84.15 0.063004 Final Values Defocus_U Defocus_V Angle CCC 13205.27 12533.03 84.78 0.107947 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00005sq_v01_00011hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00011hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.350e-01 1.004e-01 CC threshold: 0.737 Mean Std: 41.92 7.14 Num Hot pixels: 218 Hot pixel threshold: 84.77 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.849555 Iteration 2 Error: 0.132326 Iteration 3 Error: 0.022513 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.22 0.00 ...... Frame ( 3) shift: -0.43 0.01 ...... Frame ( 4) shift: -0.65 0.01 ...... Frame ( 5) shift: -0.87 0.02 ...... Frame ( 6) shift: -0.95 0.02 ...... Frame ( 7) shift: -0.90 0.03 ...... Frame ( 8) shift: -0.85 0.04 ...... Frame ( 9) shift: -0.81 0.09 ...... Frame ( 10) shift: -0.76 0.21 ...... Frame ( 11) shift: -0.72 0.32 ...... Frame ( 12) shift: -0.70 0.43 ...... Frame ( 13) shift: -0.69 0.53 ...... Frame ( 14) shift: -0.68 0.64 ...... Frame ( 15) shift: -0.64 0.72 ...... Frame ( 16) shift: -0.57 0.78 ...... Frame ( 17) shift: -0.50 0.83 ...... Frame ( 18) shift: -0.48 0.91 ...... Frame ( 19) shift: -0.52 1.00 ...... Frame ( 20) shift: -0.56 1.09 ...... Frame ( 21) shift: -0.55 1.17 ...... Frame ( 22) shift: -0.49 1.24 ...... Frame ( 23) shift: -0.43 1.31 ...... Frame ( 24) shift: -0.37 1.35 ...... Frame ( 25) shift: -0.31 1.37 ...... Frame ( 26) shift: -0.24 1.40 ...... Frame ( 27) shift: -0.22 1.38 ...... Frame ( 28) shift: -0.23 1.33 ...... Frame ( 29) shift: -0.24 1.27 ...... Frame ( 30) shift: -0.23 1.25 ...... Frame ( 31) shift: -0.20 1.26 ...... Frame ( 32) shift: -0.17 1.27 ...... Frame ( 33) shift: -0.15 1.29 ...... Frame ( 34) shift: -0.15 1.30 ...... Frame ( 35) shift: -0.14 1.32 ...... Frame ( 36) shift: -0.14 1.36 ...... Frame ( 37) shift: -0.14 1.43 ...... Frame ( 38) shift: -0.13 1.49 ...... Frame ( 39) shift: -0.13 1.55 ...... Frame ( 40) shift: -0.12 1.62 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.099248 Iteration 2 Error: 0.265440 Iteration 3 Error: 0.058179 Iteration 4 Error: 0.017324 Align patch 2 23 left Iteration 1 Error: 1.127812 Iteration 2 Error: 0.163962 Iteration 3 Error: 0.063602 Iteration 4 Error: 0.024636 Align patch 3 22 left Iteration 1 Error: 1.243347 Iteration 2 Error: 0.196074 Iteration 3 Error: 0.053188 Iteration 4 Error: 0.027340 Align patch 4 21 left Iteration 1 Error: 0.604053 Iteration 2 Error: 0.126739 Iteration 3 Error: 0.028598 Align patch 5 20 left Iteration 1 Error: 0.635785 Iteration 2 Error: 0.062144 Iteration 3 Error: 0.017237 Align patch 6 19 left Iteration 1 Error: 1.093240 Iteration 2 Error: 0.134376 Iteration 3 Error: 0.034547 Align patch 7 18 left Iteration 1 Error: 0.494130 Iteration 2 Error: 0.090799 Iteration 3 Error: 0.019329 Align patch 8 17 left Iteration 1 Error: 0.885162 Iteration 2 Error: 0.097091 Iteration 3 Error: 0.029221 Align patch 9 16 left Iteration 1 Error: 0.728253 Iteration 2 Error: 0.068895 Iteration 3 Error: 0.014192 Align patch 10 15 left Iteration 1 Error: 0.608527 Iteration 2 Error: 0.086303 Iteration 3 Error: 0.018662 Align patch 11 14 left Iteration 1 Error: 0.640403 Iteration 2 Error: 0.067711 Iteration 3 Error: 0.009295 Align patch 12 13 left Iteration 1 Error: 0.588208 Iteration 2 Error: 0.101305 Iteration 3 Error: 0.026194 Align patch 13 12 left Iteration 1 Error: 0.790800 Iteration 2 Error: 0.110187 Iteration 3 Error: 0.026418 Align patch 14 11 left Iteration 1 Error: 0.588934 Iteration 2 Error: 0.038091 Align patch 15 10 left Iteration 1 Error: 0.652915 Iteration 2 Error: 0.058346 Iteration 3 Error: 0.015857 Align patch 16 9 left Iteration 1 Error: 0.817633 Iteration 2 Error: 0.095862 Iteration 3 Error: 0.024963 Align patch 17 8 left Iteration 1 Error: 0.599073 Iteration 2 Error: 0.040395 Align patch 18 7 left Iteration 1 Error: 0.564329 Iteration 2 Error: 0.055310 Iteration 3 Error: 0.016770 Align patch 19 6 left Iteration 1 Error: 0.616357 Iteration 2 Error: 0.083292 Iteration 3 Error: 0.016112 Align patch 20 5 left Iteration 1 Error: 0.793271 Iteration 2 Error: 0.093209 Iteration 3 Error: 0.016436 Align patch 21 4 left Iteration 1 Error: 1.240341 Iteration 2 Error: 0.142460 Iteration 3 Error: 0.037340 Align patch 22 3 left Iteration 1 Error: 1.177832 Iteration 2 Error: 0.166872 Iteration 3 Error: 0.036468 Align patch 23 2 left Iteration 1 Error: 0.507347 Iteration 2 Error: 0.117601 Iteration 3 Error: 0.021825 Align patch 24 1 left Iteration 1 Error: 0.745785 Iteration 2 Error: 0.112139 Iteration 3 Error: 0.018809 Align patch 25 0 left Iteration 1 Error: 0.487558 Iteration 2 Error: 0.087311 Iteration 3 Error: 0.016552 3D Fitting completed. Patch alignment time: 11.55(sec) Local motion has been corrected. Process thread exits. Computational time: 23.376520 sec Total time: 30.464401 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00011hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00011hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.639880s Reading file: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00011hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.305342s ........................................ >>>>>>TIME<<<<<< FFT: 1.253272s Defocus_U Defocus_V Angle CCC 9757.82 10605.48 14.14 0.056214 Final Values Defocus_U Defocus_V Angle CCC 9773.45 10605.48 13.83 0.103850 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00005sq_v01_00011hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00011hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.352e-01 1.005e-01 CC threshold: 0.738 Mean Std: 41.36 7.19 Num Hot pixels: 212 Hot pixel threshold: 84.47 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.056247 Iteration 2 Error: 0.100838 Iteration 3 Error: 0.021698 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.20 0.00 ...... Frame ( 3) shift: -0.40 0.00 ...... Frame ( 4) shift: -0.60 0.00 ...... Frame ( 5) shift: -0.80 0.00 ...... Frame ( 6) shift: -0.94 0.02 ...... Frame ( 7) shift: -1.02 0.05 ...... Frame ( 8) shift: -1.10 0.08 ...... Frame ( 9) shift: -1.14 0.15 ...... Frame ( 10) shift: -1.16 0.25 ...... Frame ( 11) shift: -1.18 0.35 ...... Frame ( 12) shift: -1.15 0.43 ...... Frame ( 13) shift: -1.06 0.49 ...... Frame ( 14) shift: -0.97 0.56 ...... Frame ( 15) shift: -0.94 0.61 ...... Frame ( 16) shift: -0.98 0.67 ...... Frame ( 17) shift: -1.01 0.72 ...... Frame ( 18) shift: -1.03 0.78 ...... Frame ( 19) shift: -1.02 0.85 ...... Frame ( 20) shift: -1.02 0.92 ...... Frame ( 21) shift: -1.03 0.98 ...... Frame ( 22) shift: -1.07 1.03 ...... Frame ( 23) shift: -1.10 1.09 ...... Frame ( 24) shift: -1.13 1.13 ...... Frame ( 25) shift: -1.14 1.15 ...... Frame ( 26) shift: -1.15 1.17 ...... Frame ( 27) shift: -1.20 1.19 ...... Frame ( 28) shift: -1.28 1.21 ...... Frame ( 29) shift: -1.37 1.22 ...... Frame ( 30) shift: -1.42 1.21 ...... Frame ( 31) shift: -1.45 1.18 ...... Frame ( 32) shift: -1.48 1.15 ...... Frame ( 33) shift: -1.47 1.15 ...... Frame ( 34) shift: -1.44 1.17 ...... Frame ( 35) shift: -1.41 1.20 ...... Frame ( 36) shift: -1.38 1.23 ...... Frame ( 37) shift: -1.36 1.26 ...... Frame ( 38) shift: -1.33 1.29 ...... Frame ( 39) shift: -1.30 1.32 ...... Frame ( 40) shift: -1.28 1.35 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.581133 Iteration 2 Error: 0.082969 Iteration 3 Error: 0.025377 Align patch 2 23 left Iteration 1 Error: 1.001758 Iteration 2 Error: 0.112220 Iteration 3 Error: 0.031362 Align patch 3 22 left Iteration 1 Error: 0.478647 Iteration 2 Error: 0.063052 Iteration 3 Error: 0.007738 Align patch 4 21 left Iteration 1 Error: 0.411746 Iteration 2 Error: 0.051588 Iteration 3 Error: 0.007908 Align patch 5 20 left Iteration 1 Error: 0.639449 Iteration 2 Error: 0.165488 Iteration 3 Error: 0.033663 Align patch 6 19 left Iteration 1 Error: 0.621357 Iteration 2 Error: 0.064521 Iteration 3 Error: 0.012796 Align patch 7 18 left Iteration 1 Error: 0.776801 Iteration 2 Error: 0.088937 Iteration 3 Error: 0.025167 Align patch 8 17 left Iteration 1 Error: 0.561766 Iteration 2 Error: 0.102967 Iteration 3 Error: 0.022132 Align patch 9 16 left Iteration 1 Error: 0.460112 Iteration 2 Error: 0.054081 Iteration 3 Error: 0.007682 Align patch 10 15 left Iteration 1 Error: 0.787374 Iteration 2 Error: 0.079188 Iteration 3 Error: 0.013460 Align patch 11 14 left Iteration 1 Error: 0.652150 Iteration 2 Error: 0.068115 Iteration 3 Error: 0.016093 Align patch 12 13 left Iteration 1 Error: 0.645702 Iteration 2 Error: 0.094436 Iteration 3 Error: 0.023262 Align patch 13 12 left Iteration 1 Error: 0.437824 Iteration 2 Error: 0.057782 Iteration 3 Error: 0.007977 Align patch 14 11 left Iteration 1 Error: 0.532128 Iteration 2 Error: 0.069108 Iteration 3 Error: 0.013334 Align patch 15 10 left Iteration 1 Error: 0.399366 Iteration 2 Error: 0.038920 Align patch 16 9 left Iteration 1 Error: 0.514035 Iteration 2 Error: 0.052017 Iteration 3 Error: 0.011549 Align patch 17 8 left Iteration 1 Error: 0.534126 Iteration 2 Error: 0.088905 Iteration 3 Error: 0.017246 Align patch 18 7 left Iteration 1 Error: 0.392981 Iteration 2 Error: 0.070246 Iteration 3 Error: 0.014890 Align patch 19 6 left Iteration 1 Error: 0.550154 Iteration 2 Error: 0.060396 Iteration 3 Error: 0.013325 Align patch 20 5 left Iteration 1 Error: 0.376204 Iteration 2 Error: 0.039985 Align patch 21 4 left Iteration 1 Error: 1.028736 Iteration 2 Error: 0.115904 Iteration 3 Error: 0.023912 Align patch 22 3 left Iteration 1 Error: 0.820771 Iteration 2 Error: 0.161558 Iteration 3 Error: 0.029517 Align patch 23 2 left Iteration 1 Error: 0.402908 Iteration 2 Error: 0.051896 Iteration 3 Error: 0.010622 Align patch 24 1 left Iteration 1 Error: 0.542397 Iteration 2 Error: 0.049279 Align patch 25 0 left Iteration 1 Error: 0.580477 Iteration 2 Error: 0.063922 Iteration 3 Error: 0.012729 3D Fitting completed. Patch alignment time: 10.95(sec) Local motion has been corrected. Process thread exits. Computational time: 24.462837 sec Total time: 31.779692 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00011hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00011hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.022264s Reading file: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00011hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.395329s ........................................ >>>>>>TIME<<<<<< FFT: 1.026734s Defocus_U Defocus_V Angle CCC 9699.22 10160.16 0.81 0.053071 Final Values Defocus_U Defocus_V Angle CCC 9707.04 10171.10 0.81 0.099256 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00005sq_v01_00011hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00011hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.003e-01 CC threshold: 0.736 Mean Std: 41.31 7.01 Num Hot pixels: 245 Hot pixel threshold: 83.36 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.058606 Iteration 2 Error: 0.153122 Iteration 3 Error: 0.031237 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.19 0.01 ...... Frame ( 3) shift: -0.38 0.01 ...... Frame ( 4) shift: -0.57 0.02 ...... Frame ( 5) shift: -0.76 0.02 ...... Frame ( 6) shift: -0.87 0.06 ...... Frame ( 7) shift: -0.90 0.12 ...... Frame ( 8) shift: -0.92 0.17 ...... Frame ( 9) shift: -0.94 0.27 ...... Frame ( 10) shift: -0.97 0.40 ...... Frame ( 11) shift: -0.99 0.53 ...... Frame ( 12) shift: -0.97 0.62 ...... Frame ( 13) shift: -0.93 0.66 ...... Frame ( 14) shift: -0.88 0.70 ...... Frame ( 15) shift: -0.85 0.80 ...... Frame ( 16) shift: -0.84 0.94 ...... Frame ( 17) shift: -0.83 1.08 ...... Frame ( 18) shift: -0.82 1.19 ...... Frame ( 19) shift: -0.80 1.26 ...... Frame ( 20) shift: -0.78 1.32 ...... Frame ( 21) shift: -0.74 1.38 ...... Frame ( 22) shift: -0.66 1.43 ...... Frame ( 23) shift: -0.59 1.47 ...... Frame ( 24) shift: -0.57 1.51 ...... Frame ( 25) shift: -0.61 1.54 ...... Frame ( 26) shift: -0.64 1.57 ...... Frame ( 27) shift: -0.65 1.62 ...... Frame ( 28) shift: -0.61 1.70 ...... Frame ( 29) shift: -0.58 1.78 ...... Frame ( 30) shift: -0.59 1.82 ...... Frame ( 31) shift: -0.63 1.80 ...... Frame ( 32) shift: -0.67 1.79 ...... Frame ( 33) shift: -0.70 1.78 ...... Frame ( 34) shift: -0.70 1.77 ...... Frame ( 35) shift: -0.70 1.76 ...... Frame ( 36) shift: -0.70 1.77 ...... Frame ( 37) shift: -0.69 1.80 ...... Frame ( 38) shift: -0.68 1.83 ...... Frame ( 39) shift: -0.67 1.85 ...... Frame ( 40) shift: -0.67 1.88 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.569216 Iteration 2 Error: 0.246586 Iteration 3 Error: 0.045663 Align patch 2 23 left Iteration 1 Error: 0.702501 Iteration 2 Error: 0.129248 Iteration 3 Error: 0.034986 Align patch 3 22 left Iteration 1 Error: 0.602983 Iteration 2 Error: 0.122243 Iteration 3 Error: 0.041510 Align patch 4 21 left Iteration 1 Error: 0.875701 Iteration 2 Error: 0.087793 Iteration 3 Error: 0.022473 Align patch 5 20 left Iteration 1 Error: 0.768694 Iteration 2 Error: 0.100993 Iteration 3 Error: 0.023430 Align patch 6 19 left Iteration 1 Error: 0.966413 Iteration 2 Error: 0.188496 Iteration 3 Error: 0.048428 Align patch 7 18 left Iteration 1 Error: 0.657565 Iteration 2 Error: 0.153322 Iteration 3 Error: 0.045416 Align patch 8 17 left Iteration 1 Error: 0.461892 Iteration 2 Error: 0.072498 Iteration 3 Error: 0.026121 Align patch 9 16 left Iteration 1 Error: 0.525082 Iteration 2 Error: 0.083204 Iteration 3 Error: 0.019560 Align patch 10 15 left Iteration 1 Error: 0.501985 Iteration 2 Error: 0.071860 Iteration 3 Error: 0.015076 Align patch 11 14 left Iteration 1 Error: 0.831785 Iteration 2 Error: 0.109924 Iteration 3 Error: 0.024571 Align patch 12 13 left Iteration 1 Error: 0.738554 Iteration 2 Error: 0.090533 Iteration 3 Error: 0.020059 Align patch 13 12 left Iteration 1 Error: 0.778797 Iteration 2 Error: 0.106805 Iteration 3 Error: 0.024948 Align patch 14 11 left Iteration 1 Error: 0.801644 Iteration 2 Error: 0.100259 Iteration 3 Error: 0.024880 Align patch 15 10 left Iteration 1 Error: 0.811438 Iteration 2 Error: 0.074214 Iteration 3 Error: 0.015561 Align patch 16 9 left Iteration 1 Error: 0.889767 Iteration 2 Error: 0.170045 Iteration 3 Error: 0.035096 Align patch 17 8 left Iteration 1 Error: 0.693611 Iteration 2 Error: 0.087928 Iteration 3 Error: 0.023121 Align patch 18 7 left Iteration 1 Error: 0.576268 Iteration 2 Error: 0.084882 Iteration 3 Error: 0.015409 Align patch 19 6 left Iteration 1 Error: 0.448662 Iteration 2 Error: 0.067885 Iteration 3 Error: 0.010425 Align patch 20 5 left Iteration 1 Error: 0.538478 Iteration 2 Error: 0.101643 Iteration 3 Error: 0.033814 Align patch 21 4 left Iteration 1 Error: 1.025998 Iteration 2 Error: 0.202041 Iteration 3 Error: 0.060820 Iteration 4 Error: 0.021030 Align patch 22 3 left Iteration 1 Error: 0.668046 Iteration 2 Error: 0.103092 Iteration 3 Error: 0.024362 Align patch 23 2 left Iteration 1 Error: 0.556113 Iteration 2 Error: 0.079326 Iteration 3 Error: 0.021977 Align patch 24 1 left Iteration 1 Error: 0.426392 Iteration 2 Error: 0.094163 Iteration 3 Error: 0.014152 Align patch 25 0 left Iteration 1 Error: 1.327137 Iteration 2 Error: 0.309462 Iteration 3 Error: 0.096487 Iteration 4 Error: 0.033349 3D Fitting completed. Patch alignment time: 11.43(sec) Local motion has been corrected. Process thread exits. Computational time: 24.376148 sec Total time: 31.796026 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00011hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00011hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.829999s Reading file: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00011hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.964215s ........................................ >>>>>>TIME<<<<<< FFT: 0.971036s Defocus_U Defocus_V Angle CCC 13796.93 14714.89 6.57 0.058970 Final Values Defocus_U Defocus_V Angle CCC 13803.18 14708.64 6.89 0.096381 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00005sq_v01_00011hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00011hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.350e-01 1.003e-01 CC threshold: 0.737 Mean Std: 41.90 7.10 Num Hot pixels: 231 Hot pixel threshold: 84.51 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.826002 Iteration 2 Error: 0.047839 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.24 -0.02 ...... Frame ( 3) shift: -0.48 -0.05 ...... Frame ( 4) shift: -0.71 -0.07 ...... Frame ( 5) shift: -0.95 -0.09 ...... Frame ( 6) shift: -1.08 -0.10 ...... Frame ( 7) shift: -1.11 -0.10 ...... Frame ( 8) shift: -1.13 -0.09 ...... Frame ( 9) shift: -1.13 -0.09 ...... Frame ( 10) shift: -1.10 -0.10 ...... Frame ( 11) shift: -1.07 -0.11 ...... Frame ( 12) shift: -1.08 -0.10 ...... Frame ( 13) shift: -1.13 -0.07 ...... Frame ( 14) shift: -1.18 -0.05 ...... Frame ( 15) shift: -1.21 -0.01 ...... Frame ( 16) shift: -1.22 0.04 ...... Frame ( 17) shift: -1.24 0.09 ...... Frame ( 18) shift: -1.28 0.13 ...... Frame ( 19) shift: -1.35 0.18 ...... Frame ( 20) shift: -1.41 0.22 ...... Frame ( 21) shift: -1.41 0.23 ...... Frame ( 22) shift: -1.34 0.21 ...... Frame ( 23) shift: -1.27 0.20 ...... Frame ( 24) shift: -1.25 0.15 ...... Frame ( 25) shift: -1.28 0.09 ...... Frame ( 26) shift: -1.31 0.02 ...... Frame ( 27) shift: -1.32 0.01 ...... Frame ( 28) shift: -1.31 0.05 ...... Frame ( 29) shift: -1.30 0.09 ...... Frame ( 30) shift: -1.25 0.12 ...... Frame ( 31) shift: -1.15 0.14 ...... Frame ( 32) shift: -1.06 0.15 ...... Frame ( 33) shift: -1.05 0.19 ...... Frame ( 34) shift: -1.13 0.25 ...... Frame ( 35) shift: -1.21 0.31 ...... Frame ( 36) shift: -1.25 0.36 ...... Frame ( 37) shift: -1.26 0.38 ...... Frame ( 38) shift: -1.27 0.41 ...... Frame ( 39) shift: -1.29 0.43 ...... Frame ( 40) shift: -1.30 0.45 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.696060 Iteration 2 Error: 0.120777 Iteration 3 Error: 0.017652 Align patch 2 23 left Iteration 1 Error: 0.555218 Iteration 2 Error: 0.062969 Iteration 3 Error: 0.014696 Align patch 3 22 left Iteration 1 Error: 0.890613 Iteration 2 Error: 0.081679 Iteration 3 Error: 0.015246 Align patch 4 21 left Iteration 1 Error: 0.543711 Iteration 2 Error: 0.075712 Iteration 3 Error: 0.017136 Align patch 5 20 left Iteration 1 Error: 0.736898 Iteration 2 Error: 0.103752 Iteration 3 Error: 0.023477 Align patch 6 19 left Iteration 1 Error: 0.934868 Iteration 2 Error: 0.097932 Iteration 3 Error: 0.014039 Align patch 7 18 left Iteration 1 Error: 1.076518 Iteration 2 Error: 0.168869 Iteration 3 Error: 0.031832 Align patch 8 17 left Iteration 1 Error: 0.860986 Iteration 2 Error: 0.094524 Iteration 3 Error: 0.019373 Align patch 9 16 left Iteration 1 Error: 0.722007 Iteration 2 Error: 0.090339 Iteration 3 Error: 0.019836 Align patch 10 15 left Iteration 1 Error: 0.703053 Iteration 2 Error: 0.106422 Iteration 3 Error: 0.030222 Align patch 11 14 left Iteration 1 Error: 1.001655 Iteration 2 Error: 0.156953 Iteration 3 Error: 0.024278 Align patch 12 13 left Iteration 1 Error: 0.732408 Iteration 2 Error: 0.082116 Iteration 3 Error: 0.025053 Align patch 13 12 left Iteration 1 Error: 0.578269 Iteration 2 Error: 0.081802 Iteration 3 Error: 0.017552 Align patch 14 11 left Iteration 1 Error: 0.494350 Iteration 2 Error: 0.065697 Iteration 3 Error: 0.009487 Align patch 15 10 left Iteration 1 Error: 0.579069 Iteration 2 Error: 0.046706 Align patch 16 9 left Iteration 1 Error: 0.476400 Iteration 2 Error: 0.056020 Iteration 3 Error: 0.015920 Align patch 17 8 left Iteration 1 Error: 0.808212 Iteration 2 Error: 0.050951 Iteration 3 Error: 0.012109 Align patch 18 7 left Iteration 1 Error: 0.467054 Iteration 2 Error: 0.057046 Iteration 3 Error: 0.012475 Align patch 19 6 left Iteration 1 Error: 0.493858 Iteration 2 Error: 0.086324 Iteration 3 Error: 0.015443 Align patch 20 5 left Iteration 1 Error: 0.471077 Iteration 2 Error: 0.082186 Iteration 3 Error: 0.018990 Align patch 21 4 left Iteration 1 Error: 0.657618 Iteration 2 Error: 0.088213 Iteration 3 Error: 0.012905 Align patch 22 3 left Iteration 1 Error: 0.524858 Iteration 2 Error: 0.072802 Iteration 3 Error: 0.022345 Align patch 23 2 left Iteration 1 Error: 0.433236 Iteration 2 Error: 0.070957 Iteration 3 Error: 0.016890 Align patch 24 1 left Iteration 1 Error: 0.823956 Iteration 2 Error: 0.097324 Iteration 3 Error: 0.018358 Align patch 25 0 left Iteration 1 Error: 0.508048 Iteration 2 Error: 0.066234 Iteration 3 Error: 0.012575 3D Fitting completed. Patch alignment time: 10.97(sec) Local motion has been corrected. Process thread exits. Computational time: 23.138119 sec Total time: 29.976191 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00011hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00011hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.456861s Reading file: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00011hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.079358s ........................................ >>>>>>TIME<<<<<< FFT: 0.915129s Defocus_U Defocus_V Angle CCC 14025.41 13345.72 84.11 0.066646 Final Values Defocus_U Defocus_V Angle CCC 14023.85 13344.16 84.42 0.107771 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00005sq_v01_00012hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00012hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.001e-01 CC threshold: 0.735 Mean Std: 38.97 6.67 Num Hot pixels: 148 Hot pixel threshold: 79.00 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.738409 Iteration 2 Error: 0.132148 Iteration 3 Error: 0.029067 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.21 -0.07 ...... Frame ( 3) shift: -0.42 -0.14 ...... Frame ( 4) shift: -0.63 -0.21 ...... Frame ( 5) shift: -0.85 -0.28 ...... Frame ( 6) shift: -0.96 -0.33 ...... Frame ( 7) shift: -0.96 -0.35 ...... Frame ( 8) shift: -0.97 -0.37 ...... Frame ( 9) shift: -0.95 -0.40 ...... Frame ( 10) shift: -0.90 -0.43 ...... Frame ( 11) shift: -0.85 -0.46 ...... Frame ( 12) shift: -0.81 -0.45 ...... Frame ( 13) shift: -0.77 -0.40 ...... Frame ( 14) shift: -0.73 -0.34 ...... Frame ( 15) shift: -0.67 -0.31 ...... Frame ( 16) shift: -0.61 -0.29 ...... Frame ( 17) shift: -0.54 -0.27 ...... Frame ( 18) shift: -0.47 -0.27 ...... Frame ( 19) shift: -0.40 -0.29 ...... Frame ( 20) shift: -0.33 -0.32 ...... Frame ( 21) shift: -0.27 -0.31 ...... Frame ( 22) shift: -0.20 -0.27 ...... Frame ( 23) shift: -0.14 -0.23 ...... Frame ( 24) shift: -0.10 -0.23 ...... Frame ( 25) shift: -0.09 -0.27 ...... Frame ( 26) shift: -0.08 -0.31 ...... Frame ( 27) shift: -0.04 -0.32 ...... Frame ( 28) shift: 0.04 -0.30 ...... Frame ( 29) shift: 0.12 -0.28 ...... Frame ( 30) shift: 0.18 -0.26 ...... Frame ( 31) shift: 0.22 -0.22 ...... Frame ( 32) shift: 0.26 -0.18 ...... Frame ( 33) shift: 0.27 -0.13 ...... Frame ( 34) shift: 0.26 -0.07 ...... Frame ( 35) shift: 0.24 -0.01 ...... Frame ( 36) shift: 0.26 0.04 ...... Frame ( 37) shift: 0.31 0.08 ...... Frame ( 38) shift: 0.37 0.13 ...... Frame ( 39) shift: 0.42 0.17 ...... Frame ( 40) shift: 0.48 0.22 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.033617 Iteration 2 Error: 0.104332 Iteration 3 Error: 0.032803 Align patch 2 23 left Iteration 1 Error: 0.790214 Iteration 2 Error: 0.159867 Iteration 3 Error: 0.043827 Align patch 3 22 left Iteration 1 Error: 0.752266 Iteration 2 Error: 0.094498 Iteration 3 Error: 0.028585 Align patch 4 21 left Iteration 1 Error: 0.502298 Iteration 2 Error: 0.128384 Iteration 3 Error: 0.029084 Align patch 5 20 left Iteration 1 Error: 0.747671 Iteration 2 Error: 0.098018 Iteration 3 Error: 0.020481 Align patch 6 19 left Iteration 1 Error: 1.201069 Iteration 2 Error: 0.206963 Iteration 3 Error: 0.063054 Iteration 4 Error: 0.021096 Align patch 7 18 left Iteration 1 Error: 0.777325 Iteration 2 Error: 0.203237 Iteration 3 Error: 0.059072 Iteration 4 Error: 0.035178 Align patch 8 17 left Iteration 1 Error: 0.596352 Iteration 2 Error: 0.146833 Iteration 3 Error: 0.034729 Align patch 9 16 left Iteration 1 Error: 0.781047 Iteration 2 Error: 0.126379 Iteration 3 Error: 0.026395 Align patch 10 15 left Iteration 1 Error: 0.779868 Iteration 2 Error: 0.163685 Iteration 3 Error: 0.031265 Align patch 11 14 left Iteration 1 Error: 0.651958 Iteration 2 Error: 0.082196 Iteration 3 Error: 0.029890 Align patch 12 13 left Iteration 1 Error: 0.769742 Iteration 2 Error: 0.122977 Iteration 3 Error: 0.036502 Align patch 13 12 left Iteration 1 Error: 0.521506 Iteration 2 Error: 0.071050 Iteration 3 Error: 0.015668 Align patch 14 11 left Iteration 1 Error: 0.631126 Iteration 2 Error: 0.127824 Iteration 3 Error: 0.022882 Align patch 15 10 left Iteration 1 Error: 0.631503 Iteration 2 Error: 0.251367 Iteration 3 Error: 0.056732 Iteration 4 Error: 0.017014 Align patch 16 9 left Iteration 1 Error: 1.411148 Iteration 2 Error: 0.294142 Iteration 3 Error: 0.074100 Iteration 4 Error: 0.025992 Align patch 17 8 left Iteration 1 Error: 0.594565 Iteration 2 Error: 0.259049 Iteration 3 Error: 0.044552 Align patch 18 7 left Iteration 1 Error: 0.632776 Iteration 2 Error: 0.186097 Iteration 3 Error: 0.041033 Align patch 19 6 left Iteration 1 Error: 0.779580 Iteration 2 Error: 0.132778 Iteration 3 Error: 0.037929 Align patch 20 5 left Iteration 1 Error: 0.535914 Iteration 2 Error: 0.096802 Iteration 3 Error: 0.016232 Align patch 21 4 left Iteration 1 Error: 1.062740 Iteration 2 Error: 0.123592 Iteration 3 Error: 0.038206 Align patch 22 3 left Iteration 1 Error: 0.766917 Iteration 2 Error: 0.111138 Iteration 3 Error: 0.026076 Align patch 23 2 left Iteration 1 Error: 0.444108 Iteration 2 Error: 0.076240 Iteration 3 Error: 0.017041 Align patch 24 1 left Iteration 1 Error: 0.710659 Iteration 2 Error: 0.091510 Iteration 3 Error: 0.020257 Align patch 25 0 left Iteration 1 Error: 1.152545 Iteration 2 Error: 0.094409 Iteration 3 Error: 0.017238 3D Fitting completed. Patch alignment time: 12.08(sec) Local motion has been corrected. Process thread exits. Computational time: 25.257982 sec Total time: 31.678331 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00012hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00012hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.550502s Reading file: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00012hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.925298s ........................................ >>>>>>TIME<<<<<< FFT: 0.983659s Defocus_U Defocus_V Angle CCC 13712.89 14646.49 9.52 0.044704 Final Values Defocus_U Defocus_V Angle CCC 13672.25 14677.76 9.21 0.068210 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00005sq_v01_00012hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00012hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 40.20 6.83 Num Hot pixels: 126 Hot pixel threshold: 81.20 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.972199 Iteration 2 Error: 0.180778 Iteration 3 Error: 0.040527 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.17 -0.06 ...... Frame ( 3) shift: -0.33 -0.11 ...... Frame ( 4) shift: -0.50 -0.17 ...... Frame ( 5) shift: -0.66 -0.23 ...... Frame ( 6) shift: -0.71 -0.21 ...... Frame ( 7) shift: -0.64 -0.11 ...... Frame ( 8) shift: -0.58 -0.02 ...... Frame ( 9) shift: -0.50 0.05 ...... Frame ( 10) shift: -0.42 0.10 ...... Frame ( 11) shift: -0.33 0.14 ...... Frame ( 12) shift: -0.24 0.20 ...... Frame ( 13) shift: -0.15 0.26 ...... Frame ( 14) shift: -0.06 0.32 ...... Frame ( 15) shift: 0.00 0.40 ...... Frame ( 16) shift: 0.03 0.49 ...... Frame ( 17) shift: 0.06 0.58 ...... Frame ( 18) shift: 0.10 0.60 ...... Frame ( 19) shift: 0.15 0.55 ...... Frame ( 20) shift: 0.20 0.50 ...... Frame ( 21) shift: 0.24 0.50 ...... Frame ( 22) shift: 0.28 0.53 ...... Frame ( 23) shift: 0.31 0.57 ...... Frame ( 24) shift: 0.35 0.61 ...... Frame ( 25) shift: 0.39 0.66 ...... Frame ( 26) shift: 0.44 0.71 ...... Frame ( 27) shift: 0.47 0.73 ...... Frame ( 28) shift: 0.49 0.71 ...... Frame ( 29) shift: 0.51 0.69 ...... Frame ( 30) shift: 0.55 0.67 ...... Frame ( 31) shift: 0.62 0.65 ...... Frame ( 32) shift: 0.68 0.62 ...... Frame ( 33) shift: 0.77 0.61 ...... Frame ( 34) shift: 0.88 0.63 ...... Frame ( 35) shift: 0.99 0.64 ...... Frame ( 36) shift: 1.04 0.64 ...... Frame ( 37) shift: 1.03 0.62 ...... Frame ( 38) shift: 1.02 0.59 ...... Frame ( 39) shift: 1.01 0.57 ...... Frame ( 40) shift: 1.00 0.55 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.384590 Iteration 2 Error: 0.204636 Iteration 3 Error: 0.050670 Iteration 4 Error: 0.016804 Align patch 2 23 left Iteration 1 Error: 0.861278 Iteration 2 Error: 0.155973 Iteration 3 Error: 0.041259 Align patch 3 22 left Iteration 1 Error: 0.673452 Iteration 2 Error: 0.192029 Iteration 3 Error: 0.050519 Iteration 4 Error: 0.014692 Align patch 4 21 left Iteration 1 Error: 0.879390 Iteration 2 Error: 0.124066 Iteration 3 Error: 0.030150 Align patch 5 20 left Iteration 1 Error: 0.724071 Iteration 2 Error: 0.095533 Iteration 3 Error: 0.019750 Align patch 6 19 left Iteration 1 Error: 0.875426 Iteration 2 Error: 0.183095 Iteration 3 Error: 0.085736 Iteration 4 Error: 0.028954 Align patch 7 18 left Iteration 1 Error: 0.901188 Iteration 2 Error: 0.158885 Iteration 3 Error: 0.049038 Align patch 8 17 left Iteration 1 Error: 0.689655 Iteration 2 Error: 0.220147 Iteration 3 Error: 0.057635 Iteration 4 Error: 0.028497 Align patch 9 16 left Iteration 1 Error: 0.602437 Iteration 2 Error: 0.154244 Iteration 3 Error: 0.039366 Align patch 10 15 left Iteration 1 Error: 0.769261 Iteration 2 Error: 0.099641 Iteration 3 Error: 0.022961 Align patch 11 14 left Iteration 1 Error: 1.600499 Iteration 2 Error: 0.465178 Iteration 3 Error: 0.130821 Iteration 4 Error: 0.039729 Align patch 12 13 left Iteration 1 Error: 0.518303 Iteration 2 Error: 0.124605 Iteration 3 Error: 0.035592 Align patch 13 12 left Iteration 1 Error: 0.517223 Iteration 2 Error: 0.125852 Iteration 3 Error: 0.024877 Align patch 14 11 left Iteration 1 Error: 0.859241 Iteration 2 Error: 0.091107 Iteration 3 Error: 0.024208 Align patch 15 10 left Iteration 1 Error: 0.754696 Iteration 2 Error: 0.109557 Iteration 3 Error: 0.043207 Align patch 16 9 left Iteration 1 Error: 0.804107 Iteration 2 Error: 0.122556 Iteration 3 Error: 0.026464 Align patch 17 8 left Iteration 1 Error: 0.532158 Iteration 2 Error: 0.090068 Iteration 3 Error: 0.026248 Align patch 18 7 left Iteration 1 Error: 0.559068 Iteration 2 Error: 0.071759 Iteration 3 Error: 0.027556 Align patch 19 6 left Iteration 1 Error: 0.773465 Iteration 2 Error: 0.113046 Iteration 3 Error: 0.030881 Align patch 20 5 left Iteration 1 Error: 0.546525 Iteration 2 Error: 0.099382 Iteration 3 Error: 0.019718 Align patch 21 4 left Iteration 1 Error: 0.988904 Iteration 2 Error: 0.212743 Iteration 3 Error: 0.075970 Iteration 4 Error: 0.029046 Align patch 22 3 left Iteration 1 Error: 0.666038 Iteration 2 Error: 0.106866 Iteration 3 Error: 0.034831 Align patch 23 2 left Iteration 1 Error: 0.986570 Iteration 2 Error: 0.112021 Iteration 3 Error: 0.032984 Align patch 24 1 left Iteration 1 Error: 0.890724 Iteration 2 Error: 0.118065 Iteration 3 Error: 0.024810 Align patch 25 0 left Iteration 1 Error: 1.131961 Iteration 2 Error: 0.102406 Iteration 3 Error: 0.020120 3D Fitting completed. Patch alignment time: 11.82(sec) Local motion has been corrected. Process thread exits. Computational time: 24.593397 sec Total time: 31.919249 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00012hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00012hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.040340s Reading file: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00012hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.130065s ........................................ >>>>>>TIME<<<<<< FFT: 0.965908s Defocus_U Defocus_V Angle CCC 13220.70 12701.17 89.24 0.050387 Final Values Defocus_U Defocus_V Angle CCC 13236.33 12723.05 87.37 0.080294 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00005sq_v01_00012hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00012hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.998e-02 CC threshold: 0.734 Mean Std: 36.72 6.40 Num Hot pixels: 128 Hot pixel threshold: 75.14 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.447734 Iteration 2 Error: 0.247923 Iteration 3 Error: 0.070695 Iteration 4 Error: 0.020585 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.08 0.02 ...... Frame ( 3) shift: 0.17 0.05 ...... Frame ( 4) shift: 0.25 0.07 ...... Frame ( 5) shift: 0.33 0.10 ...... Frame ( 6) shift: 0.35 0.11 ...... Frame ( 7) shift: 0.29 0.10 ...... Frame ( 8) shift: 0.24 0.09 ...... Frame ( 9) shift: 0.24 0.13 ...... Frame ( 10) shift: 0.28 0.21 ...... Frame ( 11) shift: 0.32 0.29 ...... Frame ( 12) shift: 0.37 0.32 ...... Frame ( 13) shift: 0.42 0.31 ...... Frame ( 14) shift: 0.47 0.29 ...... Frame ( 15) shift: 0.52 0.33 ...... Frame ( 16) shift: 0.55 0.41 ...... Frame ( 17) shift: 0.58 0.50 ...... Frame ( 18) shift: 0.65 0.57 ...... Frame ( 19) shift: 0.77 0.63 ...... Frame ( 20) shift: 0.88 0.69 ...... Frame ( 21) shift: 1.01 0.73 ...... Frame ( 22) shift: 1.14 0.76 ...... Frame ( 23) shift: 1.28 0.78 ...... Frame ( 24) shift: 1.37 0.82 ...... Frame ( 25) shift: 1.42 0.86 ...... Frame ( 26) shift: 1.47 0.90 ...... Frame ( 27) shift: 1.52 0.97 ...... Frame ( 28) shift: 1.57 1.06 ...... Frame ( 29) shift: 1.62 1.15 ...... Frame ( 30) shift: 1.67 1.19 ...... Frame ( 31) shift: 1.72 1.17 ...... Frame ( 32) shift: 1.76 1.14 ...... Frame ( 33) shift: 1.81 1.13 ...... Frame ( 34) shift: 1.86 1.12 ...... Frame ( 35) shift: 1.91 1.11 ...... Frame ( 36) shift: 2.00 1.16 ...... Frame ( 37) shift: 2.13 1.28 ...... Frame ( 38) shift: 2.26 1.39 ...... Frame ( 39) shift: 2.39 1.51 ...... Frame ( 40) shift: 2.52 1.63 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.209997 Iteration 2 Error: 0.353200 Iteration 3 Error: 0.136457 Iteration 4 Error: 0.060769 Iteration 5 Error: 0.036439 Align patch 2 23 left Iteration 1 Error: 1.022235 Iteration 2 Error: 0.192520 Iteration 3 Error: 0.052012 Iteration 4 Error: 0.019116 Align patch 3 22 left Iteration 1 Error: 1.039377 Iteration 2 Error: 0.139515 Iteration 3 Error: 0.041118 Align patch 4 21 left Iteration 1 Error: 0.642192 Iteration 2 Error: 0.119857 Iteration 3 Error: 0.033140 Align patch 5 20 left Iteration 1 Error: 0.850028 Iteration 2 Error: 0.156151 Iteration 3 Error: 0.036600 Align patch 6 19 left Iteration 1 Error: 1.329067 Iteration 2 Error: 0.254473 Iteration 3 Error: 0.120420 Iteration 4 Error: 0.052103 Iteration 5 Error: 0.042753 Align patch 7 18 left Iteration 1 Error: 0.792189 Iteration 2 Error: 0.187358 Iteration 3 Error: 0.049658 Align patch 8 17 left Iteration 1 Error: 0.728155 Iteration 2 Error: 0.101746 Iteration 3 Error: 0.047441 Align patch 9 16 left Iteration 1 Error: 1.028555 Iteration 2 Error: 0.198559 Iteration 3 Error: 0.035995 Align patch 10 15 left Iteration 1 Error: 0.813497 Iteration 2 Error: 0.139350 Iteration 3 Error: 0.034231 Align patch 11 14 left Iteration 1 Error: 1.621811 Iteration 2 Error: 0.356391 Iteration 3 Error: 0.116462 Iteration 4 Error: 0.042133 Align patch 12 13 left Iteration 1 Error: 0.649359 Iteration 2 Error: 0.211555 Iteration 3 Error: 0.072239 Iteration 4 Error: 0.052705 Iteration 5 Error: 0.025502 Align patch 13 12 left Iteration 1 Error: 1.591787 Iteration 2 Error: 0.241755 Iteration 3 Error: 0.035973 Align patch 14 11 left Iteration 1 Error: 1.000999 Iteration 2 Error: 0.255511 Iteration 3 Error: 0.073403 Iteration 4 Error: 0.031984 Align patch 15 10 left Iteration 1 Error: 0.737574 Iteration 2 Error: 0.154890 Iteration 3 Error: 0.033577 Align patch 16 9 left Iteration 1 Error: 1.250058 Iteration 2 Error: 0.188283 Iteration 3 Error: 0.062853 Iteration 4 Error: 0.018665 Align patch 17 8 left Iteration 1 Error: 1.046972 Iteration 2 Error: 0.269420 Iteration 3 Error: 0.074755 Iteration 4 Error: 0.037786 Align patch 18 7 left Iteration 1 Error: 0.748709 Iteration 2 Error: 0.126346 Iteration 3 Error: 0.039457 Align patch 19 6 left Iteration 1 Error: 0.633737 Iteration 2 Error: 0.095852 Iteration 3 Error: 0.021800 Align patch 20 5 left Iteration 1 Error: 0.887222 Iteration 2 Error: 0.189630 Iteration 3 Error: 0.039737 Align patch 21 4 left Iteration 1 Error: 0.634982 Iteration 2 Error: 0.080149 Iteration 3 Error: 0.033368 Align patch 22 3 left Iteration 1 Error: 0.795964 Iteration 2 Error: 0.118284 Iteration 3 Error: 0.039092 Align patch 23 2 left Iteration 1 Error: 0.713673 Iteration 2 Error: 0.156580 Iteration 3 Error: 0.041270 Align patch 24 1 left Iteration 1 Error: 0.632847 Iteration 2 Error: 0.178580 Iteration 3 Error: 0.043820 Align patch 25 0 left Iteration 1 Error: 1.299657 Iteration 2 Error: 0.285907 Iteration 3 Error: 0.073294 Iteration 4 Error: 0.022800 3D Fitting completed. Patch alignment time: 12.45(sec) Local motion has been corrected. Process thread exits. Computational time: 24.575802 sec Total time: 32.461433 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00012hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00012hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.591629s Reading file: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00012hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.569997s ........................................ >>>>>>TIME<<<<<< FFT: 0.922059s Defocus_U Defocus_V Angle CCC 11855.43 12761.76 10.53 0.032232 Final Values Defocus_U Defocus_V Angle CCC 11872.64 12738.38 14.60 0.045876 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00005sq_v01_00012hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00012hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 1.000e-01 CC threshold: 0.734 Mean Std: 38.77 6.65 Num Hot pixels: 142 Hot pixel threshold: 78.64 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.954524 Iteration 2 Error: 0.244073 Iteration 3 Error: 0.070658 Iteration 4 Error: 0.018982 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.22 -0.02 ...... Frame ( 3) shift: -0.43 -0.04 ...... Frame ( 4) shift: -0.65 -0.06 ...... Frame ( 5) shift: -0.87 -0.09 ...... Frame ( 6) shift: -0.99 -0.09 ...... Frame ( 7) shift: -1.01 -0.08 ...... Frame ( 8) shift: -1.03 -0.07 ...... Frame ( 9) shift: -0.96 -0.06 ...... Frame ( 10) shift: -0.78 -0.06 ...... Frame ( 11) shift: -0.60 -0.05 ...... Frame ( 12) shift: -0.49 -0.00 ...... Frame ( 13) shift: -0.45 0.10 ...... Frame ( 14) shift: -0.40 0.20 ...... Frame ( 15) shift: -0.37 0.29 ...... Frame ( 16) shift: -0.35 0.36 ...... Frame ( 17) shift: -0.33 0.43 ...... Frame ( 18) shift: -0.28 0.50 ...... Frame ( 19) shift: -0.20 0.57 ...... Frame ( 20) shift: -0.12 0.63 ...... Frame ( 21) shift: -0.06 0.69 ...... Frame ( 22) shift: -0.02 0.74 ...... Frame ( 23) shift: 0.03 0.79 ...... Frame ( 24) shift: 0.07 0.80 ...... Frame ( 25) shift: 0.13 0.77 ...... Frame ( 26) shift: 0.19 0.75 ...... Frame ( 27) shift: 0.24 0.77 ...... Frame ( 28) shift: 0.28 0.85 ...... Frame ( 29) shift: 0.33 0.93 ...... Frame ( 30) shift: 0.40 0.97 ...... Frame ( 31) shift: 0.51 0.99 ...... Frame ( 32) shift: 0.61 1.00 ...... Frame ( 33) shift: 0.70 1.00 ...... Frame ( 34) shift: 0.78 0.99 ...... Frame ( 35) shift: 0.86 0.98 ...... Frame ( 36) shift: 0.92 0.99 ...... Frame ( 37) shift: 0.94 1.03 ...... Frame ( 38) shift: 0.97 1.08 ...... Frame ( 39) shift: 0.99 1.12 ...... Frame ( 40) shift: 1.02 1.16 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.521472 Iteration 2 Error: 0.309222 Iteration 3 Error: 0.102368 Iteration 4 Error: 0.061030 Iteration 5 Error: 0.021776 Align patch 2 23 left Iteration 1 Error: 1.035466 Iteration 2 Error: 0.200617 Iteration 3 Error: 0.068244 Iteration 4 Error: 0.035797 Align patch 3 22 left Iteration 1 Error: 0.863165 Iteration 2 Error: 0.198159 Iteration 3 Error: 0.052442 Iteration 4 Error: 0.021664 Align patch 4 21 left Iteration 1 Error: 0.964748 Iteration 2 Error: 0.236317 Iteration 3 Error: 0.069035 Iteration 4 Error: 0.027034 Align patch 5 20 left Iteration 1 Error: 0.814840 Iteration 2 Error: 0.097372 Iteration 3 Error: 0.027856 Align patch 6 19 left Iteration 1 Error: 1.502774 Iteration 2 Error: 0.270028 Iteration 3 Error: 0.082275 Iteration 4 Error: 0.021081 Align patch 7 18 left Iteration 1 Error: 1.103528 Iteration 2 Error: 0.281715 Iteration 3 Error: 0.104938 Iteration 4 Error: 0.038479 Align patch 8 17 left Iteration 1 Error: 0.769661 Iteration 2 Error: 0.156149 Iteration 3 Error: 0.058150 Iteration 4 Error: 0.025898 Align patch 9 16 left Iteration 1 Error: 0.946842 Iteration 2 Error: 0.257952 Iteration 3 Error: 0.057628 Iteration 4 Error: 0.020347 Align patch 10 15 left Iteration 1 Error: 0.816521 Iteration 2 Error: 0.142706 Iteration 3 Error: 0.035485 Align patch 11 14 left Iteration 1 Error: 0.670937 Iteration 2 Error: 0.171026 Iteration 3 Error: 0.052850 Iteration 4 Error: 0.015468 Align patch 12 13 left Iteration 1 Error: 1.011591 Iteration 2 Error: 0.176407 Iteration 3 Error: 0.032696 Align patch 13 12 left Iteration 1 Error: 0.660607 Iteration 2 Error: 0.086832 Iteration 3 Error: 0.023988 Align patch 14 11 left Iteration 1 Error: 0.617236 Iteration 2 Error: 0.118277 Iteration 3 Error: 0.032958 Align patch 15 10 left Iteration 1 Error: 0.922178 Iteration 2 Error: 0.227314 Iteration 3 Error: 0.057891 Iteration 4 Error: 0.024018 Align patch 16 9 left Iteration 1 Error: 0.736968 Iteration 2 Error: 0.279658 Iteration 3 Error: 0.108266 Iteration 4 Error: 0.045346 Align patch 17 8 left Iteration 1 Error: 1.161873 Iteration 2 Error: 0.263854 Iteration 3 Error: 0.085128 Iteration 4 Error: 0.036348 Align patch 18 7 left Iteration 1 Error: 0.447769 Iteration 2 Error: 0.074483 Iteration 3 Error: 0.028549 Align patch 19 6 left Iteration 1 Error: 0.972198 Iteration 2 Error: 0.169659 Iteration 3 Error: 0.036835 Align patch 20 5 left Iteration 1 Error: 1.014065 Iteration 2 Error: 0.217750 Iteration 3 Error: 0.035462 Align patch 21 4 left Iteration 1 Error: 1.117496 Iteration 2 Error: 0.140126 Iteration 3 Error: 0.027001 Align patch 22 3 left Iteration 1 Error: 0.755653 Iteration 2 Error: 0.167901 Iteration 3 Error: 0.044692 Align patch 23 2 left Iteration 1 Error: 0.880481 Iteration 2 Error: 0.164292 Iteration 3 Error: 0.046626 Align patch 24 1 left Iteration 1 Error: 1.195980 Iteration 2 Error: 0.161089 Iteration 3 Error: 0.067213 Iteration 4 Error: 0.018826 Align patch 25 0 left Iteration 1 Error: 1.077961 Iteration 2 Error: 0.175589 Iteration 3 Error: 0.034420 3D Fitting completed. Patch alignment time: 12.03(sec) Local motion has been corrected. Process thread exits. Computational time: 25.846485 sec Total time: 32.953480 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00012hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00012hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.700521s Reading file: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00012hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.476439s ........................................ >>>>>>TIME<<<<<< FFT: 1.261507s Defocus_U Defocus_V Angle CCC 11736.56 11076.08 82.81 0.032753 Final Values Defocus_U Defocus_V Angle CCC 11731.87 11105.77 79.73 0.053783 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00005sq_v01_00013hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00013hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 42.17 7.10 Num Hot pixels: 153 Hot pixel threshold: 84.79 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.689517 Iteration 2 Error: 0.370195 Iteration 3 Error: 0.113559 Iteration 4 Error: 0.047163 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.13 -0.05 ...... Frame ( 3) shift: -0.26 -0.10 ...... Frame ( 4) shift: -0.39 -0.15 ...... Frame ( 5) shift: -0.51 -0.20 ...... Frame ( 6) shift: -0.52 -0.20 ...... Frame ( 7) shift: -0.40 -0.15 ...... Frame ( 8) shift: -0.28 -0.10 ...... Frame ( 9) shift: -0.16 -0.00 ...... Frame ( 10) shift: -0.04 0.15 ...... Frame ( 11) shift: 0.08 0.30 ...... Frame ( 12) shift: 0.20 0.43 ...... Frame ( 13) shift: 0.31 0.53 ...... Frame ( 14) shift: 0.42 0.63 ...... Frame ( 15) shift: 0.52 0.74 ...... Frame ( 16) shift: 0.60 0.86 ...... Frame ( 17) shift: 0.68 0.98 ...... Frame ( 18) shift: 0.76 1.08 ...... Frame ( 19) shift: 0.86 1.14 ...... Frame ( 20) shift: 0.95 1.20 ...... Frame ( 21) shift: 1.05 1.24 ...... Frame ( 22) shift: 1.16 1.26 ...... Frame ( 23) shift: 1.26 1.28 ...... Frame ( 24) shift: 1.36 1.28 ...... Frame ( 25) shift: 1.46 1.27 ...... Frame ( 26) shift: 1.55 1.26 ...... Frame ( 27) shift: 1.63 1.28 ...... Frame ( 28) shift: 1.70 1.34 ...... Frame ( 29) shift: 1.78 1.40 ...... Frame ( 30) shift: 1.89 1.44 ...... Frame ( 31) shift: 2.05 1.48 ...... Frame ( 32) shift: 2.20 1.51 ...... Frame ( 33) shift: 2.31 1.55 ...... Frame ( 34) shift: 2.36 1.60 ...... Frame ( 35) shift: 2.41 1.64 ...... Frame ( 36) shift: 2.49 1.71 ...... Frame ( 37) shift: 2.59 1.79 ...... Frame ( 38) shift: 2.69 1.87 ...... Frame ( 39) shift: 2.79 1.95 ...... Frame ( 40) shift: 2.89 2.04 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.301615 Iteration 2 Error: 0.377679 Iteration 3 Error: 0.112189 Iteration 4 Error: 0.050139 Iteration 5 Error: 0.024555 Align patch 2 23 left Iteration 1 Error: 1.254652 Iteration 2 Error: 0.172032 Iteration 3 Error: 0.083088 Iteration 4 Error: 0.026120 Align patch 3 22 left Iteration 1 Error: 0.820613 Iteration 2 Error: 0.158216 Iteration 3 Error: 0.049954 Align patch 4 21 left Iteration 1 Error: 0.492543 Iteration 2 Error: 0.097432 Iteration 3 Error: 0.025422 Align patch 5 20 left Iteration 1 Error: 0.704838 Iteration 2 Error: 0.091378 Iteration 3 Error: 0.031517 Align patch 6 19 left Iteration 1 Error: 0.847827 Iteration 2 Error: 0.282233 Iteration 3 Error: 0.149995 Iteration 4 Error: 0.072943 Iteration 5 Error: 0.040957 Align patch 7 18 left Iteration 1 Error: 1.253852 Iteration 2 Error: 0.341610 Iteration 3 Error: 0.113570 Iteration 4 Error: 0.053810 Iteration 5 Error: 0.027808 Align patch 8 17 left Iteration 1 Error: 0.609467 Iteration 2 Error: 0.094811 Iteration 3 Error: 0.018334 Align patch 9 16 left Iteration 1 Error: 0.430383 Iteration 2 Error: 0.124341 Iteration 3 Error: 0.038067 Align patch 10 15 left Iteration 1 Error: 0.536834 Iteration 2 Error: 0.113639 Iteration 3 Error: 0.041551 Align patch 11 14 left Iteration 1 Error: 1.365291 Iteration 2 Error: 0.362493 Iteration 3 Error: 0.085883 Iteration 4 Error: 0.036920 Align patch 12 13 left Iteration 1 Error: 1.331546 Iteration 2 Error: 0.144800 Iteration 3 Error: 0.043294 Align patch 13 12 left Iteration 1 Error: 0.833191 Iteration 2 Error: 0.135849 Iteration 3 Error: 0.033968 Align patch 14 11 left Iteration 1 Error: 0.814909 Iteration 2 Error: 0.080938 Iteration 3 Error: 0.017591 Align patch 15 10 left Iteration 1 Error: 0.660424 Iteration 2 Error: 0.147068 Iteration 3 Error: 0.052350 Iteration 4 Error: 0.017078 Align patch 16 9 left Iteration 1 Error: 1.140168 Iteration 2 Error: 0.152647 Iteration 3 Error: 0.043228 Align patch 17 8 left Iteration 1 Error: 0.827855 Iteration 2 Error: 0.092042 Iteration 3 Error: 0.023123 Align patch 18 7 left Iteration 1 Error: 0.660651 Iteration 2 Error: 0.178539 Iteration 3 Error: 0.058226 Iteration 4 Error: 0.014638 Align patch 19 6 left Iteration 1 Error: 0.740607 Iteration 2 Error: 0.092856 Iteration 3 Error: 0.032885 Align patch 20 5 left Iteration 1 Error: 0.646316 Iteration 2 Error: 0.133084 Iteration 3 Error: 0.047152 Align patch 21 4 left Iteration 1 Error: 0.586485 Iteration 2 Error: 0.139154 Iteration 3 Error: 0.060384 Iteration 4 Error: 0.019724 Align patch 22 3 left Iteration 1 Error: 0.767888 Iteration 2 Error: 0.194868 Iteration 3 Error: 0.074144 Iteration 4 Error: 0.020349 Align patch 23 2 left Iteration 1 Error: 0.533140 Iteration 2 Error: 0.114683 Iteration 3 Error: 0.043856 Align patch 24 1 left Iteration 1 Error: 0.847588 Iteration 2 Error: 0.150806 Iteration 3 Error: 0.038965 Align patch 25 0 left Iteration 1 Error: 0.840980 Iteration 2 Error: 0.119907 Iteration 3 Error: 0.029033 3D Fitting completed. Patch alignment time: 11.92(sec) Local motion has been corrected. Process thread exits. Computational time: 25.745403 sec Total time: 32.867371 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00013hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00013hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.653975s Reading file: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00013hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.227483s ........................................ >>>>>>TIME<<<<<< FFT: 0.982230s Defocus_U Defocus_V Angle CCC 13421.88 14281.25 12.43 0.067047 Final Values Defocus_U Defocus_V Angle CCC 13426.56 14273.44 12.74 0.107354 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00005sq_v01_00013hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00013hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.736 Mean Std: 41.53 7.76 Num Hot pixels: 107 Hot pixel threshold: 88.08 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.096316 Iteration 2 Error: 0.229989 Iteration 3 Error: 0.050124 Iteration 4 Error: 0.017567 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.01 0.01 ...... Frame ( 3) shift: 0.02 0.01 ...... Frame ( 4) shift: 0.04 0.02 ...... Frame ( 5) shift: 0.05 0.02 ...... Frame ( 6) shift: 0.06 0.04 ...... Frame ( 7) shift: 0.09 0.08 ...... Frame ( 8) shift: 0.11 0.12 ...... Frame ( 9) shift: 0.17 0.20 ...... Frame ( 10) shift: 0.27 0.33 ...... Frame ( 11) shift: 0.36 0.46 ...... Frame ( 12) shift: 0.45 0.55 ...... Frame ( 13) shift: 0.53 0.58 ...... Frame ( 14) shift: 0.61 0.61 ...... Frame ( 15) shift: 0.69 0.63 ...... Frame ( 16) shift: 0.78 0.64 ...... Frame ( 17) shift: 0.86 0.65 ...... Frame ( 18) shift: 0.93 0.69 ...... Frame ( 19) shift: 0.99 0.76 ...... Frame ( 20) shift: 1.05 0.82 ...... Frame ( 21) shift: 1.11 0.86 ...... Frame ( 22) shift: 1.16 0.86 ...... Frame ( 23) shift: 1.20 0.87 ...... Frame ( 24) shift: 1.27 0.89 ...... Frame ( 25) shift: 1.37 0.93 ...... Frame ( 26) shift: 1.47 0.97 ...... Frame ( 27) shift: 1.58 0.97 ...... Frame ( 28) shift: 1.72 0.93 ...... Frame ( 29) shift: 1.85 0.89 ...... Frame ( 30) shift: 1.92 0.91 ...... Frame ( 31) shift: 1.91 0.97 ...... Frame ( 32) shift: 1.91 1.04 ...... Frame ( 33) shift: 1.93 1.04 ...... Frame ( 34) shift: 1.97 0.98 ...... Frame ( 35) shift: 2.01 0.91 ...... Frame ( 36) shift: 2.05 0.91 ...... Frame ( 37) shift: 2.07 0.97 ...... Frame ( 38) shift: 2.10 1.04 ...... Frame ( 39) shift: 2.13 1.10 ...... Frame ( 40) shift: 2.15 1.16 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.753822 Iteration 2 Error: 0.351380 Iteration 3 Error: 0.234838 Iteration 4 Error: 0.116563 Iteration 5 Error: 0.057993 Align patch 1 24 left Iteration 1 Error: 1.713501 Iteration 2 Error: 0.216496 Iteration 3 Error: 0.047705 Align patch 2 23 left Iteration 1 Error: 1.479738 Iteration 2 Error: 0.368253 Iteration 3 Error: 0.096518 Iteration 4 Error: 0.041280 Align patch 3 22 left Iteration 1 Error: 0.895371 Iteration 2 Error: 0.214045 Iteration 3 Error: 0.064311 Iteration 4 Error: 0.029063 Align patch 4 21 left Iteration 1 Error: 0.571945 Iteration 2 Error: 0.143128 Iteration 3 Error: 0.039810 Align patch 5 20 left Iteration 1 Error: 0.617689 Iteration 2 Error: 0.221497 Iteration 3 Error: 0.075966 Iteration 4 Error: 0.026837 Align patch 6 19 left Iteration 1 Error: 1.296095 Iteration 2 Error: 0.247713 Iteration 3 Error: 0.080545 Iteration 4 Error: 0.030226 Align patch 7 18 left Iteration 1 Error: 1.003372 Iteration 2 Error: 0.145939 Iteration 3 Error: 0.051540 Iteration 4 Error: 0.013518 Align patch 8 17 left Iteration 1 Error: 0.615409 Iteration 2 Error: 0.162098 Iteration 3 Error: 0.031865 Align patch 9 16 left Iteration 1 Error: 0.844870 Iteration 2 Error: 0.133512 Iteration 3 Error: 0.032385 Align patch 10 15 left Iteration 1 Error: 0.576268 Iteration 2 Error: 0.180817 Iteration 3 Error: 0.068264 Iteration 4 Error: 0.026695 Align patch 11 14 left Iteration 1 Error: 0.627150 Iteration 2 Error: 0.176873 Iteration 3 Error: 0.052196 Iteration 4 Error: 0.013901 Align patch 12 13 left Iteration 1 Error: 1.828771 Iteration 2 Error: 0.173037 Iteration 3 Error: 0.050980 Iteration 4 Error: 0.019262 Align patch 13 12 left Iteration 1 Error: 1.107825 Iteration 2 Error: 0.282989 Iteration 3 Error: 0.073232 Iteration 4 Error: 0.024563 Align patch 14 11 left Iteration 1 Error: 0.913698 Iteration 2 Error: 0.223066 Iteration 3 Error: 0.063555 Iteration 4 Error: 0.025356 Align patch 15 10 left Iteration 1 Error: 0.653863 Iteration 2 Error: 0.085094 Iteration 3 Error: 0.019702 Align patch 16 9 left Iteration 1 Error: 0.787414 Iteration 2 Error: 0.070231 Iteration 3 Error: 0.016030 Align patch 17 8 left Iteration 1 Error: 0.591367 Iteration 2 Error: 0.109560 Iteration 3 Error: 0.038440 Align patch 18 7 left Iteration 1 Error: 0.576631 Iteration 2 Error: 0.202282 Iteration 3 Error: 0.063355 Iteration 4 Error: 0.015142 Align patch 19 6 left Iteration 1 Error: 0.506825 Iteration 2 Error: 0.092896 Iteration 3 Error: 0.048223 Align patch 20 5 left Iteration 1 Error: 0.451821 Iteration 2 Error: 0.072159 Iteration 3 Error: 0.015574 Align patch 21 4 left Iteration 1 Error: 0.632602 Iteration 2 Error: 0.169781 Iteration 3 Error: 0.036869 Align patch 22 3 left Iteration 1 Error: 0.839780 Iteration 2 Error: 0.121779 Iteration 3 Error: 0.022342 Align patch 23 2 left Iteration 1 Error: 0.681656 Iteration 2 Error: 0.105142 Iteration 3 Error: 0.030494 Align patch 24 1 left Iteration 1 Error: 0.615429 Iteration 2 Error: 0.062549 Iteration 3 Error: 0.019016 Align patch 25 0 left Iteration 1 Error: 0.844961 Iteration 2 Error: 0.156155 Iteration 3 Error: 0.026543 3D Fitting completed. Patch alignment time: 13.13(sec) Local motion has been corrected. Process thread exits. Computational time: 26.982849 sec Total time: 34.614639 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00013hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00013hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.471692s Reading file: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00013hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 4.899955s ........................................ >>>>>>TIME<<<<<< FFT: 1.192985s Defocus_U Defocus_V Angle CCC 10562.51 11082.04 0.52 0.041971 Final Values Defocus_U Defocus_V Angle CCC 10589.07 11086.73 1.14 0.077814 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00005sq_v01_00013hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00013hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 43.07 7.10 Num Hot pixels: 159 Hot pixel threshold: 85.70 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.756873 Iteration 2 Error: 0.304262 Iteration 3 Error: 0.084650 Iteration 4 Error: 0.026775 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.16 -0.07 ...... Frame ( 3) shift: -0.33 -0.13 ...... Frame ( 4) shift: -0.49 -0.20 ...... Frame ( 5) shift: -0.65 -0.26 ...... Frame ( 6) shift: -0.65 -0.26 ...... Frame ( 7) shift: -0.49 -0.20 ...... Frame ( 8) shift: -0.33 -0.13 ...... Frame ( 9) shift: -0.18 -0.06 ...... Frame ( 10) shift: -0.03 0.02 ...... Frame ( 11) shift: 0.11 0.11 ...... Frame ( 12) shift: 0.25 0.21 ...... Frame ( 13) shift: 0.37 0.33 ...... Frame ( 14) shift: 0.49 0.45 ...... Frame ( 15) shift: 0.56 0.56 ...... Frame ( 16) shift: 0.60 0.65 ...... Frame ( 17) shift: 0.63 0.74 ...... Frame ( 18) shift: 0.67 0.80 ...... Frame ( 19) shift: 0.73 0.83 ...... Frame ( 20) shift: 0.79 0.86 ...... Frame ( 21) shift: 0.90 0.92 ...... Frame ( 22) shift: 1.06 0.99 ...... Frame ( 23) shift: 1.23 1.07 ...... Frame ( 24) shift: 1.37 1.15 ...... Frame ( 25) shift: 1.49 1.24 ...... Frame ( 26) shift: 1.61 1.32 ...... Frame ( 27) shift: 1.65 1.40 ...... Frame ( 28) shift: 1.63 1.48 ...... Frame ( 29) shift: 1.60 1.56 ...... Frame ( 30) shift: 1.64 1.63 ...... Frame ( 31) shift: 1.76 1.69 ...... Frame ( 32) shift: 1.88 1.75 ...... Frame ( 33) shift: 1.94 1.75 ...... Frame ( 34) shift: 1.96 1.67 ...... Frame ( 35) shift: 1.97 1.60 ...... Frame ( 36) shift: 2.01 1.57 ...... Frame ( 37) shift: 2.07 1.59 ...... Frame ( 38) shift: 2.13 1.60 ...... Frame ( 39) shift: 2.19 1.62 ...... Frame ( 40) shift: 2.24 1.63 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.972564 Iteration 2 Error: 0.294915 Iteration 3 Error: 0.066530 Iteration 4 Error: 0.025793 Align patch 2 23 left Iteration 1 Error: 0.721389 Iteration 2 Error: 0.133334 Iteration 3 Error: 0.029975 Align patch 3 22 left Iteration 1 Error: 0.628455 Iteration 2 Error: 0.100412 Iteration 3 Error: 0.020115 Align patch 4 21 left Iteration 1 Error: 0.542104 Iteration 2 Error: 0.106418 Iteration 3 Error: 0.035627 Align patch 5 20 left Iteration 1 Error: 0.785925 Iteration 2 Error: 0.086559 Iteration 3 Error: 0.024265 Align patch 6 19 left Iteration 1 Error: 0.751690 Iteration 2 Error: 0.141604 Iteration 3 Error: 0.026522 Align patch 7 18 left Iteration 1 Error: 0.599570 Iteration 2 Error: 0.106970 Iteration 3 Error: 0.020466 Align patch 8 17 left Iteration 1 Error: 0.669927 Iteration 2 Error: 0.115833 Iteration 3 Error: 0.035532 Align patch 9 16 left Iteration 1 Error: 0.383518 Iteration 2 Error: 0.055981 Iteration 3 Error: 0.011161 Align patch 10 15 left Iteration 1 Error: 1.034813 Iteration 2 Error: 0.080996 Iteration 3 Error: 0.021261 Align patch 11 14 left Iteration 1 Error: 0.612292 Iteration 2 Error: 0.141635 Iteration 3 Error: 0.045033 Align patch 12 13 left Iteration 1 Error: 0.925457 Iteration 2 Error: 0.178904 Iteration 3 Error: 0.052144 Iteration 4 Error: 0.022181 Align patch 13 12 left Iteration 1 Error: 0.712055 Iteration 2 Error: 0.099580 Iteration 3 Error: 0.020876 Align patch 14 11 left Iteration 1 Error: 0.824202 Iteration 2 Error: 0.093866 Iteration 3 Error: 0.021386 Align patch 15 10 left Iteration 1 Error: 0.755571 Iteration 2 Error: 0.136285 Iteration 3 Error: 0.048581 Align patch 16 9 left Iteration 1 Error: 0.654670 Iteration 2 Error: 0.141269 Iteration 3 Error: 0.035275 Align patch 17 8 left Iteration 1 Error: 0.731977 Iteration 2 Error: 0.239439 Iteration 3 Error: 0.061855 Iteration 4 Error: 0.028507 Align patch 18 7 left Iteration 1 Error: 0.861454 Iteration 2 Error: 0.141191 Iteration 3 Error: 0.040610 Align patch 19 6 left Iteration 1 Error: 0.523631 Iteration 2 Error: 0.065491 Iteration 3 Error: 0.029229 Align patch 20 5 left Iteration 1 Error: 0.833665 Iteration 2 Error: 0.115861 Iteration 3 Error: 0.037981 Align patch 21 4 left Iteration 1 Error: 0.876930 Iteration 2 Error: 0.203871 Iteration 3 Error: 0.079051 Iteration 4 Error: 0.032996 Align patch 22 3 left Iteration 1 Error: 0.619642 Iteration 2 Error: 0.127711 Iteration 3 Error: 0.025088 Align patch 23 2 left Iteration 1 Error: 0.468475 Iteration 2 Error: 0.073886 Iteration 3 Error: 0.020729 Align patch 24 1 left Iteration 1 Error: 0.896663 Iteration 2 Error: 0.150653 Iteration 3 Error: 0.030270 Align patch 25 0 left Iteration 1 Error: 1.037498 Iteration 2 Error: 0.187825 Iteration 3 Error: 0.065122 Iteration 4 Error: 0.022103 3D Fitting completed. Patch alignment time: 11.11(sec) Local motion has been corrected. Process thread exits. Computational time: 25.021851 sec Total time: 35.927177 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00013hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00013hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.632331s Reading file: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00013hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.047835s ........................................ >>>>>>TIME<<<<<< FFT: 1.279332s Defocus_U Defocus_V Angle CCC 10650.39 11533.21 6.11 0.060178 Final Values Defocus_U Defocus_V Angle CCC 10670.70 11541.02 6.43 0.108181 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00005sq_v01_00013hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00013hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.001e-01 CC threshold: 0.735 Mean Std: 42.38 7.03 Num Hot pixels: 172 Hot pixel threshold: 84.56 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.734426 Iteration 2 Error: 0.347685 Iteration 3 Error: 0.104112 Iteration 4 Error: 0.033540 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.11 -0.05 ...... Frame ( 3) shift: -0.22 -0.10 ...... Frame ( 4) shift: -0.32 -0.15 ...... Frame ( 5) shift: -0.43 -0.21 ...... Frame ( 6) shift: -0.42 -0.21 ...... Frame ( 7) shift: -0.28 -0.16 ...... Frame ( 8) shift: -0.15 -0.11 ...... Frame ( 9) shift: 0.02 -0.03 ...... Frame ( 10) shift: 0.20 0.07 ...... Frame ( 11) shift: 0.39 0.17 ...... Frame ( 12) shift: 0.53 0.28 ...... Frame ( 13) shift: 0.63 0.38 ...... Frame ( 14) shift: 0.73 0.49 ...... Frame ( 15) shift: 0.81 0.60 ...... Frame ( 16) shift: 0.89 0.70 ...... Frame ( 17) shift: 0.96 0.79 ...... Frame ( 18) shift: 1.08 0.83 ...... Frame ( 19) shift: 1.23 0.79 ...... Frame ( 20) shift: 1.39 0.75 ...... Frame ( 21) shift: 1.51 0.75 ...... Frame ( 22) shift: 1.58 0.78 ...... Frame ( 23) shift: 1.65 0.81 ...... Frame ( 24) shift: 1.76 0.86 ...... Frame ( 25) shift: 1.91 0.92 ...... Frame ( 26) shift: 2.06 0.98 ...... Frame ( 27) shift: 2.21 1.01 ...... Frame ( 28) shift: 2.37 0.99 ...... Frame ( 29) shift: 2.53 0.97 ...... Frame ( 30) shift: 2.67 0.97 ...... Frame ( 31) shift: 2.79 0.98 ...... Frame ( 32) shift: 2.91 1.00 ...... Frame ( 33) shift: 3.00 0.98 ...... Frame ( 34) shift: 3.04 0.94 ...... Frame ( 35) shift: 3.09 0.90 ...... Frame ( 36) shift: 3.17 0.89 ...... Frame ( 37) shift: 3.28 0.92 ...... Frame ( 38) shift: 3.38 0.95 ...... Frame ( 39) shift: 3.49 0.97 ...... Frame ( 40) shift: 3.60 1.00 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.069243 Iteration 2 Error: 0.201868 Iteration 3 Error: 0.049000 Align patch 2 23 left Iteration 1 Error: 0.904802 Iteration 2 Error: 0.263334 Iteration 3 Error: 0.077710 Iteration 4 Error: 0.035079 Align patch 3 22 left Iteration 1 Error: 0.607828 Iteration 2 Error: 0.173622 Iteration 3 Error: 0.073845 Iteration 4 Error: 0.022337 Align patch 4 21 left Iteration 1 Error: 0.801206 Iteration 2 Error: 0.122625 Iteration 3 Error: 0.018345 Align patch 5 20 left Iteration 1 Error: 0.524053 Iteration 2 Error: 0.113714 Iteration 3 Error: 0.016000 Align patch 6 19 left Iteration 1 Error: 1.430331 Iteration 2 Error: 0.223947 Iteration 3 Error: 0.077698 Iteration 4 Error: 0.023315 Align patch 7 18 left Iteration 1 Error: 1.145684 Iteration 2 Error: 0.187501 Iteration 3 Error: 0.057862 Iteration 4 Error: 0.022166 Align patch 8 17 left Iteration 1 Error: 0.884458 Iteration 2 Error: 0.179548 Iteration 3 Error: 0.084042 Iteration 4 Error: 0.027629 Align patch 9 16 left Iteration 1 Error: 0.752985 Iteration 2 Error: 0.118887 Iteration 3 Error: 0.048600 Align patch 10 15 left Iteration 1 Error: 0.757090 Iteration 2 Error: 0.144178 Iteration 3 Error: 0.044427 Align patch 11 14 left Iteration 1 Error: 0.878040 Iteration 2 Error: 0.133302 Iteration 3 Error: 0.053703 Iteration 4 Error: 0.027839 Align patch 12 13 left Iteration 1 Error: 0.654770 Iteration 2 Error: 0.140873 Iteration 3 Error: 0.041034 Align patch 13 12 left Iteration 1 Error: 0.632937 Iteration 2 Error: 0.110413 Iteration 3 Error: 0.050251 Iteration 4 Error: 0.015461 Align patch 14 11 left Iteration 1 Error: 0.737382 Iteration 2 Error: 0.122923 Iteration 3 Error: 0.043151 Align patch 15 10 left Iteration 1 Error: 0.777853 Iteration 2 Error: 0.108958 Iteration 3 Error: 0.030037 Align patch 16 9 left Iteration 1 Error: 0.450778 Iteration 2 Error: 0.120361 Iteration 3 Error: 0.033305 Align patch 17 8 left Iteration 1 Error: 0.635325 Iteration 2 Error: 0.175593 Iteration 3 Error: 0.044528 Align patch 18 7 left Iteration 1 Error: 0.600638 Iteration 2 Error: 0.160965 Iteration 3 Error: 0.061041 Iteration 4 Error: 0.018871 Align patch 19 6 left Iteration 1 Error: 0.635923 Iteration 2 Error: 0.127291 Iteration 3 Error: 0.037494 Align patch 20 5 left Iteration 1 Error: 0.949083 Iteration 2 Error: 0.171570 Iteration 3 Error: 0.068221 Iteration 4 Error: 0.017935 Align patch 21 4 left Iteration 1 Error: 1.732821 Iteration 2 Error: 0.273037 Iteration 3 Error: 0.096935 Iteration 4 Error: 0.035965 Align patch 22 3 left Iteration 1 Error: 0.678824 Iteration 2 Error: 0.154976 Iteration 3 Error: 0.048357 Align patch 23 2 left Iteration 1 Error: 1.132375 Iteration 2 Error: 0.135689 Iteration 3 Error: 0.045849 Align patch 24 1 left Iteration 1 Error: 0.567642 Iteration 2 Error: 0.097211 Iteration 3 Error: 0.046246 Align patch 25 0 left Iteration 1 Error: 0.709541 Iteration 2 Error: 0.125128 Iteration 3 Error: 0.029490 3D Fitting completed. Patch alignment time: 11.86(sec) Local motion has been corrected. Process thread exits. Computational time: 24.974449 sec Total time: 32.471226 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00013hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00013hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.589159s Reading file: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00013hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.902151s ........................................ >>>>>>TIME<<<<<< FFT: 0.959545s Defocus_U Defocus_V Angle CCC 11824.22 11082.03 81.75 0.056876 Final Values Defocus_U Defocus_V Angle CCC 11833.60 11107.04 82.06 0.100732 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00005sq_v01_00014hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00014hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 9.999e-02 CC threshold: 0.734 Mean Std: 43.24 7.21 Num Hot pixels: 166 Hot pixel threshold: 86.48 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.100844 Iteration 2 Error: 0.383317 Iteration 3 Error: 0.116922 Iteration 4 Error: 0.039926 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.13 0.11 ...... Frame ( 3) shift: -0.26 0.21 ...... Frame ( 4) shift: -0.38 0.32 ...... Frame ( 5) shift: -0.51 0.42 ...... Frame ( 6) shift: -0.54 0.54 ...... Frame ( 7) shift: -0.47 0.66 ...... Frame ( 8) shift: -0.40 0.78 ...... Frame ( 9) shift: -0.28 0.93 ...... Frame ( 10) shift: -0.10 1.09 ...... Frame ( 11) shift: 0.09 1.26 ...... Frame ( 12) shift: 0.23 1.39 ...... Frame ( 13) shift: 0.34 1.48 ...... Frame ( 14) shift: 0.44 1.57 ...... Frame ( 15) shift: 0.55 1.64 ...... Frame ( 16) shift: 0.64 1.69 ...... Frame ( 17) shift: 0.74 1.75 ...... Frame ( 18) shift: 0.82 1.85 ...... Frame ( 19) shift: 0.87 2.01 ...... Frame ( 20) shift: 0.93 2.16 ...... Frame ( 21) shift: 1.02 2.25 ...... Frame ( 22) shift: 1.14 2.29 ...... Frame ( 23) shift: 1.27 2.32 ...... Frame ( 24) shift: 1.36 2.35 ...... Frame ( 25) shift: 1.44 2.39 ...... Frame ( 26) shift: 1.51 2.42 ...... Frame ( 27) shift: 1.61 2.48 ...... Frame ( 28) shift: 1.73 2.55 ...... Frame ( 29) shift: 1.85 2.63 ...... Frame ( 30) shift: 1.95 2.69 ...... Frame ( 31) shift: 2.01 2.75 ...... Frame ( 32) shift: 2.07 2.81 ...... Frame ( 33) shift: 2.16 2.87 ...... Frame ( 34) shift: 2.29 2.94 ...... Frame ( 35) shift: 2.42 3.01 ...... Frame ( 36) shift: 2.55 3.09 ...... Frame ( 37) shift: 2.67 3.18 ...... Frame ( 38) shift: 2.79 3.28 ...... Frame ( 39) shift: 2.91 3.37 ...... Frame ( 40) shift: 3.04 3.46 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.161617 Iteration 2 Error: 0.270224 Iteration 3 Error: 0.117807 Iteration 4 Error: 0.054079 Iteration 5 Error: 0.035678 Align patch 2 23 left Iteration 1 Error: 1.328547 Iteration 2 Error: 0.146249 Iteration 3 Error: 0.051341 Iteration 4 Error: 0.014636 Align patch 3 22 left Iteration 1 Error: 0.868459 Iteration 2 Error: 0.316265 Iteration 3 Error: 0.121280 Iteration 4 Error: 0.060179 Iteration 5 Error: 0.027453 Align patch 4 21 left Iteration 1 Error: 0.744178 Iteration 2 Error: 0.144052 Iteration 3 Error: 0.055797 Iteration 4 Error: 0.027790 Align patch 5 20 left Iteration 1 Error: 0.723612 Iteration 2 Error: 0.120053 Iteration 3 Error: 0.038458 Align patch 6 19 left Iteration 1 Error: 0.965615 Iteration 2 Error: 0.285213 Iteration 3 Error: 0.090066 Iteration 4 Error: 0.048775 Align patch 7 18 left Iteration 1 Error: 0.779256 Iteration 2 Error: 0.267123 Iteration 3 Error: 0.086497 Iteration 4 Error: 0.024514 Align patch 8 17 left Iteration 1 Error: 0.680050 Iteration 2 Error: 0.255872 Iteration 3 Error: 0.098218 Iteration 4 Error: 0.045278 Align patch 9 16 left Iteration 1 Error: 0.798028 Iteration 2 Error: 0.187927 Iteration 3 Error: 0.057130 Iteration 4 Error: 0.022392 Align patch 10 15 left Iteration 1 Error: 0.789040 Iteration 2 Error: 0.162867 Iteration 3 Error: 0.050513 Iteration 4 Error: 0.017185 Align patch 11 14 left Iteration 1 Error: 0.924687 Iteration 2 Error: 0.255014 Iteration 3 Error: 0.079794 Iteration 4 Error: 0.030407 Align patch 12 13 left Iteration 1 Error: 0.726185 Iteration 2 Error: 0.227875 Iteration 3 Error: 0.055656 Iteration 4 Error: 0.025932 Align patch 13 12 left Iteration 1 Error: 0.680003 Iteration 2 Error: 0.126992 Iteration 3 Error: 0.040887 Align patch 14 11 left Iteration 1 Error: 0.769321 Iteration 2 Error: 0.157287 Iteration 3 Error: 0.057451 Iteration 4 Error: 0.022579 Align patch 15 10 left Iteration 1 Error: 0.657074 Iteration 2 Error: 0.104492 Iteration 3 Error: 0.022787 Align patch 16 9 left Iteration 1 Error: 1.328995 Iteration 2 Error: 0.317997 Iteration 3 Error: 0.098890 Iteration 4 Error: 0.042750 Align patch 17 8 left Iteration 1 Error: 0.603235 Iteration 2 Error: 0.134710 Iteration 3 Error: 0.033201 Align patch 18 7 left Iteration 1 Error: 0.446757 Iteration 2 Error: 0.158066 Iteration 3 Error: 0.038553 Align patch 19 6 left Iteration 1 Error: 0.674358 Iteration 2 Error: 0.181928 Iteration 3 Error: 0.047017 Align patch 20 5 left Iteration 1 Error: 1.036276 Iteration 2 Error: 0.134710 Iteration 3 Error: 0.034791 Align patch 21 4 left Iteration 1 Error: 0.805039 Iteration 2 Error: 0.151398 Iteration 3 Error: 0.034447 Align patch 22 3 left Iteration 1 Error: 0.755382 Iteration 2 Error: 0.117928 Iteration 3 Error: 0.031071 Align patch 23 2 left Iteration 1 Error: 0.711933 Iteration 2 Error: 0.102359 Iteration 3 Error: 0.024759 Align patch 24 1 left Iteration 1 Error: 1.137601 Iteration 2 Error: 0.116517 Iteration 3 Error: 0.025915 Align patch 25 0 left Iteration 1 Error: 0.883899 Iteration 2 Error: 0.103862 Iteration 3 Error: 0.020924 3D Fitting completed. Patch alignment time: 12.00(sec) Local motion has been corrected. Process thread exits. Computational time: 25.642435 sec Total time: 35.121334 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00014hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00014hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.608339s Reading file: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00014hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.248489s ........................................ >>>>>>TIME<<<<<< FFT: 1.082486s Defocus_U Defocus_V Angle CCC 10775.40 11658.22 13.34 0.059373 Final Values Defocus_U Defocus_V Angle CCC 10794.16 11667.60 13.04 0.105464 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00005sq_v01_00014hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00014hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 41.90 7.21 Num Hot pixels: 144 Hot pixel threshold: 85.19 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.114568 Iteration 2 Error: 0.249370 Iteration 3 Error: 0.061011 Iteration 4 Error: 0.016178 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.16 0.07 ...... Frame ( 3) shift: -0.31 0.15 ...... Frame ( 4) shift: -0.47 0.22 ...... Frame ( 5) shift: -0.62 0.30 ...... Frame ( 6) shift: -0.67 0.36 ...... Frame ( 7) shift: -0.60 0.42 ...... Frame ( 8) shift: -0.54 0.48 ...... Frame ( 9) shift: -0.46 0.55 ...... Frame ( 10) shift: -0.38 0.64 ...... Frame ( 11) shift: -0.29 0.73 ...... Frame ( 12) shift: -0.24 0.82 ...... Frame ( 13) shift: -0.21 0.90 ...... Frame ( 14) shift: -0.19 0.98 ...... Frame ( 15) shift: -0.13 1.03 ...... Frame ( 16) shift: -0.05 1.05 ...... Frame ( 17) shift: 0.03 1.07 ...... Frame ( 18) shift: 0.13 1.12 ...... Frame ( 19) shift: 0.24 1.21 ...... Frame ( 20) shift: 0.35 1.30 ...... Frame ( 21) shift: 0.44 1.41 ...... Frame ( 22) shift: 0.51 1.54 ...... Frame ( 23) shift: 0.58 1.66 ...... Frame ( 24) shift: 0.65 1.75 ...... Frame ( 25) shift: 0.71 1.82 ...... Frame ( 26) shift: 0.78 1.88 ...... Frame ( 27) shift: 0.82 1.92 ...... Frame ( 28) shift: 0.85 1.96 ...... Frame ( 29) shift: 0.88 1.99 ...... Frame ( 30) shift: 0.90 2.03 ...... Frame ( 31) shift: 0.90 2.09 ...... Frame ( 32) shift: 0.90 2.15 ...... Frame ( 33) shift: 0.95 2.16 ...... Frame ( 34) shift: 1.06 2.12 ...... Frame ( 35) shift: 1.16 2.09 ...... Frame ( 36) shift: 1.24 2.07 ...... Frame ( 37) shift: 1.29 2.07 ...... Frame ( 38) shift: 1.34 2.07 ...... Frame ( 39) shift: 1.39 2.07 ...... Frame ( 40) shift: 1.45 2.07 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.575980 Iteration 2 Error: 0.133627 Iteration 3 Error: 0.045095 Align patch 2 23 left Iteration 1 Error: 0.681962 Iteration 2 Error: 0.214718 Iteration 3 Error: 0.054330 Iteration 4 Error: 0.027692 Align patch 3 22 left Iteration 1 Error: 0.617103 Iteration 2 Error: 0.132742 Iteration 3 Error: 0.041187 Align patch 4 21 left Iteration 1 Error: 0.585568 Iteration 2 Error: 0.105243 Iteration 3 Error: 0.015655 Align patch 5 20 left Iteration 1 Error: 0.897031 Iteration 2 Error: 0.102104 Iteration 3 Error: 0.017023 Align patch 6 19 left Iteration 1 Error: 0.871071 Iteration 2 Error: 0.211438 Iteration 3 Error: 0.093591 Iteration 4 Error: 0.044697 Align patch 7 18 left Iteration 1 Error: 0.896647 Iteration 2 Error: 0.245318 Iteration 3 Error: 0.107267 Iteration 4 Error: 0.055368 Iteration 5 Error: 0.027452 Align patch 8 17 left Iteration 1 Error: 1.038206 Iteration 2 Error: 0.136950 Iteration 3 Error: 0.054123 Iteration 4 Error: 0.014588 Align patch 9 16 left Iteration 1 Error: 0.492680 Iteration 2 Error: 0.085108 Iteration 3 Error: 0.020014 Align patch 10 15 left Iteration 1 Error: 0.681615 Iteration 2 Error: 0.183036 Iteration 3 Error: 0.037823 Align patch 11 14 left Iteration 1 Error: 1.503976 Iteration 2 Error: 0.137158 Iteration 3 Error: 0.054794 Iteration 4 Error: 0.021152 Align patch 12 13 left Iteration 1 Error: 1.048839 Iteration 2 Error: 0.207574 Iteration 3 Error: 0.058764 Iteration 4 Error: 0.023223 Align patch 13 12 left Iteration 1 Error: 0.699957 Iteration 2 Error: 0.147770 Iteration 3 Error: 0.033318 Align patch 14 11 left Iteration 1 Error: 0.599523 Iteration 2 Error: 0.078519 Iteration 3 Error: 0.013983 Align patch 15 10 left Iteration 1 Error: 0.753280 Iteration 2 Error: 0.079503 Iteration 3 Error: 0.016071 Align patch 16 9 left Iteration 1 Error: 0.886985 Iteration 2 Error: 0.123889 Iteration 3 Error: 0.040933 Align patch 17 8 left Iteration 1 Error: 0.544242 Iteration 2 Error: 0.068327 Iteration 3 Error: 0.020205 Align patch 18 7 left Iteration 1 Error: 0.658362 Iteration 2 Error: 0.127938 Iteration 3 Error: 0.059227 Iteration 4 Error: 0.030103 Align patch 19 6 left Iteration 1 Error: 0.543782 Iteration 2 Error: 0.090277 Iteration 3 Error: 0.036436 Align patch 20 5 left Iteration 1 Error: 0.471571 Iteration 2 Error: 0.051962 Iteration 3 Error: 0.011491 Align patch 21 4 left Iteration 1 Error: 0.525453 Iteration 2 Error: 0.149444 Iteration 3 Error: 0.027382 Align patch 22 3 left Iteration 1 Error: 0.592399 Iteration 2 Error: 0.070888 Iteration 3 Error: 0.016769 Align patch 23 2 left Iteration 1 Error: 0.750325 Iteration 2 Error: 0.114866 Iteration 3 Error: 0.033635 Align patch 24 1 left Iteration 1 Error: 0.804137 Iteration 2 Error: 0.077836 Iteration 3 Error: 0.013961 Align patch 25 0 left Iteration 1 Error: 0.472110 Iteration 2 Error: 0.079042 Iteration 3 Error: 0.021931 3D Fitting completed. Patch alignment time: 11.43(sec) Local motion has been corrected. Process thread exits. Computational time: 26.637205 sec Total time: 33.509041 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00014hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00014hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.669610s Reading file: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00014hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.131261s ........................................ >>>>>>TIME<<<<<< FFT: 1.017494s Defocus_U Defocus_V Angle CCC 12810.55 13306.64 2.19 0.056267 Final Values Defocus_U Defocus_V Angle CCC 12808.99 13314.46 2.19 0.095002 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00005sq_v01_00014hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00014hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.001e-01 CC threshold: 0.735 Mean Std: 41.24 7.01 Num Hot pixels: 162 Hot pixel threshold: 83.28 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.629783 Iteration 2 Error: 0.284991 Iteration 3 Error: 0.058724 Iteration 4 Error: 0.023281 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.20 0.11 ...... Frame ( 3) shift: -0.40 0.22 ...... Frame ( 4) shift: -0.60 0.33 ...... Frame ( 5) shift: -0.80 0.45 ...... Frame ( 6) shift: -0.87 0.53 ...... Frame ( 7) shift: -0.80 0.58 ...... Frame ( 8) shift: -0.73 0.63 ...... Frame ( 9) shift: -0.68 0.71 ...... Frame ( 10) shift: -0.65 0.84 ...... Frame ( 11) shift: -0.61 0.96 ...... Frame ( 12) shift: -0.58 1.04 ...... Frame ( 13) shift: -0.54 1.08 ...... Frame ( 14) shift: -0.49 1.11 ...... Frame ( 15) shift: -0.45 1.19 ...... Frame ( 16) shift: -0.39 1.30 ...... Frame ( 17) shift: -0.33 1.42 ...... Frame ( 18) shift: -0.30 1.49 ...... Frame ( 19) shift: -0.31 1.52 ...... Frame ( 20) shift: -0.31 1.55 ...... Frame ( 21) shift: -0.27 1.60 ...... Frame ( 22) shift: -0.20 1.68 ...... Frame ( 23) shift: -0.12 1.75 ...... Frame ( 24) shift: -0.03 1.83 ...... Frame ( 25) shift: 0.09 1.90 ...... Frame ( 26) shift: 0.21 1.97 ...... Frame ( 27) shift: 0.30 2.00 ...... Frame ( 28) shift: 0.37 1.97 ...... Frame ( 29) shift: 0.44 1.95 ...... Frame ( 30) shift: 0.52 1.99 ...... Frame ( 31) shift: 0.59 2.08 ...... Frame ( 32) shift: 0.66 2.17 ...... Frame ( 33) shift: 0.69 2.23 ...... Frame ( 34) shift: 0.67 2.25 ...... Frame ( 35) shift: 0.65 2.27 ...... Frame ( 36) shift: 0.70 2.34 ...... Frame ( 37) shift: 0.82 2.47 ...... Frame ( 38) shift: 0.93 2.60 ...... Frame ( 39) shift: 1.05 2.73 ...... Frame ( 40) shift: 1.16 2.86 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.587859 Iteration 2 Error: 0.311985 Iteration 3 Error: 0.218650 Iteration 4 Error: 0.080165 Iteration 5 Error: 0.060934 Align patch 1 24 left Iteration 1 Error: 1.593731 Iteration 2 Error: 0.255262 Iteration 3 Error: 0.075772 Iteration 4 Error: 0.027888 Align patch 2 23 left Iteration 1 Error: 0.795185 Iteration 2 Error: 0.229915 Iteration 3 Error: 0.082072 Iteration 4 Error: 0.044940 Align patch 3 22 left Iteration 1 Error: 0.850038 Iteration 2 Error: 0.234258 Iteration 3 Error: 0.095456 Iteration 4 Error: 0.040730 Align patch 4 21 left Iteration 1 Error: 0.743661 Iteration 2 Error: 0.168393 Iteration 3 Error: 0.045785 Align patch 5 20 left Iteration 1 Error: 0.620299 Iteration 2 Error: 0.063776 Iteration 3 Error: 0.013422 Align patch 6 19 left Iteration 1 Error: 1.788175 Iteration 2 Error: 0.443492 Iteration 3 Error: 0.207402 Iteration 4 Error: 0.088754 Iteration 5 Error: 0.034189 Align patch 7 18 left Iteration 1 Error: 0.789647 Iteration 2 Error: 0.366736 Iteration 3 Error: 0.117583 Iteration 4 Error: 0.062545 Iteration 5 Error: 0.029911 Align patch 8 17 left Iteration 1 Error: 0.904796 Iteration 2 Error: 0.201085 Iteration 3 Error: 0.046537 Align patch 9 16 left Iteration 1 Error: 0.832411 Iteration 2 Error: 0.179554 Iteration 3 Error: 0.043992 Align patch 10 15 left Iteration 1 Error: 0.430600 Iteration 2 Error: 0.085436 Iteration 3 Error: 0.025570 Align patch 11 14 left Iteration 1 Error: 0.556919 Iteration 2 Error: 0.096792 Iteration 3 Error: 0.035288 Align patch 12 13 left Iteration 1 Error: 0.929292 Iteration 2 Error: 0.110548 Iteration 3 Error: 0.027460 Align patch 13 12 left Iteration 1 Error: 0.782207 Iteration 2 Error: 0.103657 Iteration 3 Error: 0.029108 Align patch 14 11 left Iteration 1 Error: 0.628689 Iteration 2 Error: 0.106406 Iteration 3 Error: 0.025913 Align patch 15 10 left Iteration 1 Error: 0.654931 Iteration 2 Error: 0.070667 Iteration 3 Error: 0.010018 Align patch 16 9 left Iteration 1 Error: 0.619211 Iteration 2 Error: 0.137936 Iteration 3 Error: 0.032543 Align patch 17 8 left Iteration 1 Error: 0.609557 Iteration 2 Error: 0.054835 Iteration 3 Error: 0.016109 Align patch 18 7 left Iteration 1 Error: 0.677578 Iteration 2 Error: 0.083609 Iteration 3 Error: 0.023976 Align patch 19 6 left Iteration 1 Error: 0.560263 Iteration 2 Error: 0.092477 Iteration 3 Error: 0.027589 Align patch 20 5 left Iteration 1 Error: 0.637111 Iteration 2 Error: 0.118298 Iteration 3 Error: 0.019446 Align patch 21 4 left Iteration 1 Error: 0.875791 Iteration 2 Error: 0.081570 Iteration 3 Error: 0.022994 Align patch 22 3 left Iteration 1 Error: 1.042899 Iteration 2 Error: 0.137444 Iteration 3 Error: 0.032661 Align patch 23 2 left Iteration 1 Error: 1.240186 Iteration 2 Error: 0.299627 Iteration 3 Error: 0.047836 Align patch 24 1 left Iteration 1 Error: 0.576940 Iteration 2 Error: 0.078610 Iteration 3 Error: 0.017021 Align patch 25 0 left Iteration 1 Error: 0.413926 Iteration 2 Error: 0.054853 Iteration 3 Error: 0.008173 3D Fitting completed. Patch alignment time: 12.25(sec) Local motion has been corrected. Process thread exits. Computational time: 26.901217 sec Total time: 33.894215 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00014hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00014hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.595754s Reading file: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00014hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.871766s ........................................ >>>>>>TIME<<<<<< FFT: 1.068009s Defocus_U Defocus_V Angle CCC 9525.40 10361.34 6.82 0.045501 Final Values Defocus_U Defocus_V Angle CCC 9523.84 10384.78 6.82 0.082470 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00005sq_v01_00014hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00014hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.001e-01 CC threshold: 0.736 Mean Std: 41.95 7.08 Num Hot pixels: 157 Hot pixel threshold: 84.44 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.241723 Iteration 2 Error: 0.169751 Iteration 3 Error: 0.037534 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.11 -0.07 ...... Frame ( 3) shift: -0.23 -0.15 ...... Frame ( 4) shift: -0.34 -0.22 ...... Frame ( 5) shift: -0.45 -0.30 ...... Frame ( 6) shift: -0.48 -0.31 ...... Frame ( 7) shift: -0.43 -0.25 ...... Frame ( 8) shift: -0.37 -0.20 ...... Frame ( 9) shift: -0.30 -0.11 ...... Frame ( 10) shift: -0.21 0.01 ...... Frame ( 11) shift: -0.12 0.13 ...... Frame ( 12) shift: -0.03 0.27 ...... Frame ( 13) shift: 0.06 0.44 ...... Frame ( 14) shift: 0.16 0.60 ...... Frame ( 15) shift: 0.24 0.75 ...... Frame ( 16) shift: 0.29 0.87 ...... Frame ( 17) shift: 0.35 0.98 ...... Frame ( 18) shift: 0.38 1.04 ...... Frame ( 19) shift: 0.39 1.03 ...... Frame ( 20) shift: 0.40 1.01 ...... Frame ( 21) shift: 0.40 1.01 ...... Frame ( 22) shift: 0.41 1.03 ...... Frame ( 23) shift: 0.41 1.04 ...... Frame ( 24) shift: 0.42 1.06 ...... Frame ( 25) shift: 0.44 1.10 ...... Frame ( 26) shift: 0.45 1.14 ...... Frame ( 27) shift: 0.51 1.19 ...... Frame ( 28) shift: 0.60 1.24 ...... Frame ( 29) shift: 0.70 1.29 ...... Frame ( 30) shift: 0.74 1.33 ...... Frame ( 31) shift: 0.74 1.35 ...... Frame ( 32) shift: 0.74 1.37 ...... Frame ( 33) shift: 0.77 1.38 ...... Frame ( 34) shift: 0.84 1.39 ...... Frame ( 35) shift: 0.90 1.40 ...... Frame ( 36) shift: 0.97 1.41 ...... Frame ( 37) shift: 1.05 1.40 ...... Frame ( 38) shift: 1.13 1.40 ...... Frame ( 39) shift: 1.21 1.40 ...... Frame ( 40) shift: 1.28 1.39 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.733916 Iteration 2 Error: 0.106730 Iteration 3 Error: 0.022461 Align patch 2 23 left Iteration 1 Error: 0.569149 Iteration 2 Error: 0.137281 Iteration 3 Error: 0.024347 Align patch 3 22 left Iteration 1 Error: 0.705086 Iteration 2 Error: 0.056358 Iteration 3 Error: 0.017033 Align patch 4 21 left Iteration 1 Error: 0.677261 Iteration 2 Error: 0.086303 Iteration 3 Error: 0.017720 Align patch 5 20 left Iteration 1 Error: 0.639486 Iteration 2 Error: 0.085835 Iteration 3 Error: 0.015472 Align patch 6 19 left Iteration 1 Error: 1.480682 Iteration 2 Error: 0.183209 Iteration 3 Error: 0.036983 Align patch 7 18 left Iteration 1 Error: 1.070484 Iteration 2 Error: 0.136861 Iteration 3 Error: 0.028371 Align patch 8 17 left Iteration 1 Error: 0.463976 Iteration 2 Error: 0.098743 Iteration 3 Error: 0.017740 Align patch 9 16 left Iteration 1 Error: 0.740742 Iteration 2 Error: 0.104795 Iteration 3 Error: 0.040231 Align patch 10 15 left Iteration 1 Error: 0.773416 Iteration 2 Error: 0.106290 Iteration 3 Error: 0.022505 Align patch 11 14 left Iteration 1 Error: 0.849119 Iteration 2 Error: 0.152226 Iteration 3 Error: 0.031254 Align patch 12 13 left Iteration 1 Error: 0.960683 Iteration 2 Error: 0.122730 Iteration 3 Error: 0.040046 Align patch 13 12 left Iteration 1 Error: 0.739727 Iteration 2 Error: 0.077176 Iteration 3 Error: 0.016442 Align patch 14 11 left Iteration 1 Error: 0.531066 Iteration 2 Error: 0.062632 Iteration 3 Error: 0.015861 Align patch 15 10 left Iteration 1 Error: 0.747179 Iteration 2 Error: 0.062515 Iteration 3 Error: 0.010374 Align patch 16 9 left Iteration 1 Error: 0.729926 Iteration 2 Error: 0.117768 Iteration 3 Error: 0.030410 Align patch 17 8 left Iteration 1 Error: 0.948820 Iteration 2 Error: 0.137311 Iteration 3 Error: 0.027651 Align patch 18 7 left Iteration 1 Error: 0.623848 Iteration 2 Error: 0.128564 Iteration 3 Error: 0.034096 Align patch 19 6 left Iteration 1 Error: 0.529528 Iteration 2 Error: 0.088065 Iteration 3 Error: 0.014873 Align patch 20 5 left Iteration 1 Error: 0.530106 Iteration 2 Error: 0.098690 Iteration 3 Error: 0.022704 Align patch 21 4 left Iteration 1 Error: 0.658425 Iteration 2 Error: 0.094554 Iteration 3 Error: 0.020783 Align patch 22 3 left Iteration 1 Error: 0.664415 Iteration 2 Error: 0.108002 Iteration 3 Error: 0.021570 Align patch 23 2 left Iteration 1 Error: 0.871216 Iteration 2 Error: 0.172076 Iteration 3 Error: 0.022164 Align patch 24 1 left Iteration 1 Error: 0.469723 Iteration 2 Error: 0.072344 Iteration 3 Error: 0.019224 Align patch 25 0 left Iteration 1 Error: 0.753690 Iteration 2 Error: 0.105897 Iteration 3 Error: 0.020316 3D Fitting completed. Patch alignment time: 11.26(sec) Local motion has been corrected. Process thread exits. Computational time: 24.722139 sec Total time: 32.305107 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00014hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00014hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.634164s Reading file: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00014hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.064266s ........................................ >>>>>>TIME<<<<<< FFT: 0.940039s Defocus_U Defocus_V Angle CCC 15207.08 14546.83 84.18 0.065476 Final Values Defocus_U Defocus_V Angle CCC 15211.76 14548.40 84.49 0.107071 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00005sq_v01_00015hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00015hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.003e-01 CC threshold: 0.736 Mean Std: 40.02 6.90 Num Hot pixels: 166 Hot pixel threshold: 81.41 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.124701 Iteration 2 Error: 0.187972 Iteration 3 Error: 0.043057 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.26 -0.05 ...... Frame ( 3) shift: -0.52 -0.10 ...... Frame ( 4) shift: -0.78 -0.16 ...... Frame ( 5) shift: -1.03 -0.21 ...... Frame ( 6) shift: -1.16 -0.26 ...... Frame ( 7) shift: -1.16 -0.31 ...... Frame ( 8) shift: -1.16 -0.36 ...... Frame ( 9) shift: -1.13 -0.34 ...... Frame ( 10) shift: -1.07 -0.25 ...... Frame ( 11) shift: -1.01 -0.17 ...... Frame ( 12) shift: -0.93 -0.10 ...... Frame ( 13) shift: -0.84 -0.05 ...... Frame ( 14) shift: -0.74 0.01 ...... Frame ( 15) shift: -0.65 0.08 ...... Frame ( 16) shift: -0.57 0.17 ...... Frame ( 17) shift: -0.48 0.26 ...... Frame ( 18) shift: -0.39 0.34 ...... Frame ( 19) shift: -0.29 0.41 ...... Frame ( 20) shift: -0.20 0.47 ...... Frame ( 21) shift: -0.12 0.51 ...... Frame ( 22) shift: -0.05 0.53 ...... Frame ( 23) shift: 0.01 0.55 ...... Frame ( 24) shift: 0.07 0.60 ...... Frame ( 25) shift: 0.10 0.69 ...... Frame ( 26) shift: 0.14 0.79 ...... Frame ( 27) shift: 0.19 0.84 ...... Frame ( 28) shift: 0.24 0.85 ...... Frame ( 29) shift: 0.29 0.86 ...... Frame ( 30) shift: 0.34 0.87 ...... Frame ( 31) shift: 0.39 0.89 ...... Frame ( 32) shift: 0.44 0.90 ...... Frame ( 33) shift: 0.48 0.92 ...... Frame ( 34) shift: 0.51 0.94 ...... Frame ( 35) shift: 0.54 0.96 ...... Frame ( 36) shift: 0.58 1.01 ...... Frame ( 37) shift: 0.63 1.09 ...... Frame ( 38) shift: 0.68 1.18 ...... Frame ( 39) shift: 0.74 1.26 ...... Frame ( 40) shift: 0.79 1.35 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.863262 Iteration 2 Error: 0.229415 Iteration 3 Error: 0.103809 Iteration 4 Error: 0.039173 Align patch 2 23 left Iteration 1 Error: 0.645592 Iteration 2 Error: 0.194165 Iteration 3 Error: 0.076011 Iteration 4 Error: 0.030882 Align patch 3 22 left Iteration 1 Error: 0.557065 Iteration 2 Error: 0.083680 Iteration 3 Error: 0.017837 Align patch 4 21 left Iteration 1 Error: 0.735414 Iteration 2 Error: 0.142650 Iteration 3 Error: 0.033570 Align patch 5 20 left Iteration 1 Error: 0.706237 Iteration 2 Error: 0.093251 Iteration 3 Error: 0.014510 Align patch 6 19 left Iteration 1 Error: 0.994405 Iteration 2 Error: 0.108963 Iteration 3 Error: 0.031412 Align patch 7 18 left Iteration 1 Error: 0.489779 Iteration 2 Error: 0.079430 Iteration 3 Error: 0.028245 Align patch 8 17 left Iteration 1 Error: 0.772990 Iteration 2 Error: 0.113902 Iteration 3 Error: 0.025604 Align patch 9 16 left Iteration 1 Error: 0.592918 Iteration 2 Error: 0.108753 Iteration 3 Error: 0.025444 Align patch 10 15 left Iteration 1 Error: 0.378233 Iteration 2 Error: 0.049680 Align patch 11 14 left Iteration 1 Error: 0.656110 Iteration 2 Error: 0.125478 Iteration 3 Error: 0.027990 Align patch 12 13 left Iteration 1 Error: 0.553835 Iteration 2 Error: 0.155870 Iteration 3 Error: 0.050273 Iteration 4 Error: 0.023155 Align patch 13 12 left Iteration 1 Error: 0.979810 Iteration 2 Error: 0.100021 Iteration 3 Error: 0.018229 Align patch 14 11 left Iteration 1 Error: 0.440998 Iteration 2 Error: 0.120216 Iteration 3 Error: 0.022078 Align patch 15 10 left Iteration 1 Error: 0.618964 Iteration 2 Error: 0.117502 Iteration 3 Error: 0.030908 Align patch 16 9 left Iteration 1 Error: 0.738936 Iteration 2 Error: 0.134658 Iteration 3 Error: 0.048850 Align patch 17 8 left Iteration 1 Error: 0.567627 Iteration 2 Error: 0.063460 Iteration 3 Error: 0.016079 Align patch 18 7 left Iteration 1 Error: 0.520384 Iteration 2 Error: 0.069621 Iteration 3 Error: 0.012014 Align patch 19 6 left Iteration 1 Error: 0.365791 Iteration 2 Error: 0.090422 Iteration 3 Error: 0.029223 Align patch 20 5 left Iteration 1 Error: 0.682476 Iteration 2 Error: 0.094810 Iteration 3 Error: 0.030082 Align patch 21 4 left Iteration 1 Error: 0.536306 Iteration 2 Error: 0.079787 Iteration 3 Error: 0.012492 Align patch 22 3 left Iteration 1 Error: 0.779621 Iteration 2 Error: 0.086805 Iteration 3 Error: 0.027448 Align patch 23 2 left Iteration 1 Error: 0.859523 Iteration 2 Error: 0.116663 Iteration 3 Error: 0.019763 Align patch 24 1 left Iteration 1 Error: 0.555608 Iteration 2 Error: 0.054787 Iteration 3 Error: 0.013546 Align patch 25 0 left Iteration 1 Error: 0.653895 Iteration 2 Error: 0.078319 Iteration 3 Error: 0.017539 3D Fitting completed. Patch alignment time: 12.11(sec) Local motion has been corrected. Process thread exits. Computational time: 22.496101 sec Total time: 30.768717 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00015hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00015hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.644953s Reading file: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00015hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.491162s ........................................ >>>>>>TIME<<<<<< FFT: 0.938956s Defocus_U Defocus_V Angle CCC 13173.84 13998.06 12.61 0.059115 Final Values Defocus_U Defocus_V Angle CCC 13184.78 13999.63 12.92 0.093713 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00005sq_v01_00015hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00015hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 40.12 6.88 Num Hot pixels: 165 Hot pixel threshold: 81.37 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.950387 Iteration 2 Error: 0.256867 Iteration 3 Error: 0.065542 Iteration 4 Error: 0.025286 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.06 0.05 ...... Frame ( 3) shift: -0.13 0.09 ...... Frame ( 4) shift: -0.19 0.14 ...... Frame ( 5) shift: -0.26 0.19 ...... Frame ( 6) shift: -0.24 0.21 ...... Frame ( 7) shift: -0.15 0.22 ...... Frame ( 8) shift: -0.05 0.22 ...... Frame ( 9) shift: 0.01 0.25 ...... Frame ( 10) shift: 0.04 0.31 ...... Frame ( 11) shift: 0.06 0.36 ...... Frame ( 12) shift: 0.14 0.40 ...... Frame ( 13) shift: 0.26 0.42 ...... Frame ( 14) shift: 0.38 0.44 ...... Frame ( 15) shift: 0.44 0.52 ...... Frame ( 16) shift: 0.46 0.66 ...... Frame ( 17) shift: 0.48 0.80 ...... Frame ( 18) shift: 0.52 0.87 ...... Frame ( 19) shift: 0.58 0.86 ...... Frame ( 20) shift: 0.65 0.85 ...... Frame ( 21) shift: 0.74 0.88 ...... Frame ( 22) shift: 0.87 0.96 ...... Frame ( 23) shift: 0.99 1.04 ...... Frame ( 24) shift: 1.08 1.12 ...... Frame ( 25) shift: 1.15 1.20 ...... Frame ( 26) shift: 1.22 1.28 ...... Frame ( 27) shift: 1.28 1.36 ...... Frame ( 28) shift: 1.33 1.44 ...... Frame ( 29) shift: 1.38 1.52 ...... Frame ( 30) shift: 1.41 1.59 ...... Frame ( 31) shift: 1.41 1.64 ...... Frame ( 32) shift: 1.42 1.69 ...... Frame ( 33) shift: 1.44 1.72 ...... Frame ( 34) shift: 1.49 1.71 ...... Frame ( 35) shift: 1.54 1.70 ...... Frame ( 36) shift: 1.56 1.69 ...... Frame ( 37) shift: 1.56 1.68 ...... Frame ( 38) shift: 1.56 1.67 ...... Frame ( 39) shift: 1.56 1.66 ...... Frame ( 40) shift: 1.56 1.64 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.332282 Iteration 2 Error: 0.382248 Iteration 3 Error: 0.084100 Iteration 4 Error: 0.037518 Align patch 2 23 left Iteration 1 Error: 1.377948 Iteration 2 Error: 0.213044 Iteration 3 Error: 0.056749 Iteration 4 Error: 0.029386 Align patch 3 22 left Iteration 1 Error: 1.051126 Iteration 2 Error: 0.118443 Iteration 3 Error: 0.027790 Align patch 4 21 left Iteration 1 Error: 0.507624 Iteration 2 Error: 0.055400 Iteration 3 Error: 0.011376 Align patch 5 20 left Iteration 1 Error: 0.671055 Iteration 2 Error: 0.095493 Iteration 3 Error: 0.034546 Align patch 6 19 left Iteration 1 Error: 0.676237 Iteration 2 Error: 0.201075 Iteration 3 Error: 0.070243 Iteration 4 Error: 0.037251 Align patch 7 18 left Iteration 1 Error: 0.754312 Iteration 2 Error: 0.193709 Iteration 3 Error: 0.096932 Iteration 4 Error: 0.036726 Align patch 8 17 left Iteration 1 Error: 0.591937 Iteration 2 Error: 0.108006 Iteration 3 Error: 0.020013 Align patch 9 16 left Iteration 1 Error: 0.419733 Iteration 2 Error: 0.078703 Iteration 3 Error: 0.032131 Align patch 10 15 left Iteration 1 Error: 0.448513 Iteration 2 Error: 0.076969 Iteration 3 Error: 0.010940 Align patch 11 14 left Iteration 1 Error: 0.597466 Iteration 2 Error: 0.145346 Iteration 3 Error: 0.046573 Align patch 12 13 left Iteration 1 Error: 0.444529 Iteration 2 Error: 0.100241 Iteration 3 Error: 0.023799 Align patch 13 12 left Iteration 1 Error: 0.821456 Iteration 2 Error: 0.102707 Iteration 3 Error: 0.022126 Align patch 14 11 left Iteration 1 Error: 0.526375 Iteration 2 Error: 0.088915 Iteration 3 Error: 0.021880 Align patch 15 10 left Iteration 1 Error: 0.562570 Iteration 2 Error: 0.070706 Iteration 3 Error: 0.008914 Align patch 16 9 left Iteration 1 Error: 0.645112 Iteration 2 Error: 0.120355 Iteration 3 Error: 0.023497 Align patch 17 8 left Iteration 1 Error: 0.568236 Iteration 2 Error: 0.064535 Iteration 3 Error: 0.012398 Align patch 18 7 left Iteration 1 Error: 0.847806 Iteration 2 Error: 0.144351 Iteration 3 Error: 0.034441 Align patch 19 6 left Iteration 1 Error: 0.581601 Iteration 2 Error: 0.072030 Iteration 3 Error: 0.015172 Align patch 20 5 left Iteration 1 Error: 0.496961 Iteration 2 Error: 0.062474 Iteration 3 Error: 0.015373 Align patch 21 4 left Iteration 1 Error: 0.833320 Iteration 2 Error: 0.143140 Iteration 3 Error: 0.036926 Align patch 22 3 left Iteration 1 Error: 0.621953 Iteration 2 Error: 0.099157 Iteration 3 Error: 0.020105 Align patch 23 2 left Iteration 1 Error: 0.492031 Iteration 2 Error: 0.099842 Iteration 3 Error: 0.016231 Align patch 24 1 left Iteration 1 Error: 0.376188 Iteration 2 Error: 0.067110 Iteration 3 Error: 0.031363 Align patch 25 0 left Iteration 1 Error: 0.717253 Iteration 2 Error: 0.228347 Iteration 3 Error: 0.051646 Iteration 4 Error: 0.010399 3D Fitting completed. Patch alignment time: 11.51(sec) Local motion has been corrected. Process thread exits. Computational time: 22.464785 sec Total time: 28.604298 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00015hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00015hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.516815s Reading file: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00015hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.273799s ........................................ >>>>>>TIME<<<<<< FFT: 0.900332s Defocus_U Defocus_V Angle CCC 9882.83 10312.52 0.14 0.044003 Final Values Defocus_U Defocus_V Angle CCC 10335.97 9896.90 89.20 0.075710 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00005sq_v01_00015hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00015hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.996e-02 CC threshold: 0.734 Mean Std: 38.34 6.63 Num Hot pixels: 189 Hot pixel threshold: 78.11 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.086017 Iteration 2 Error: 0.298472 Iteration 3 Error: 0.066148 Iteration 4 Error: 0.016986 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.30 -0.12 ...... Frame ( 3) shift: -0.60 -0.24 ...... Frame ( 4) shift: -0.90 -0.35 ...... Frame ( 5) shift: -1.20 -0.47 ...... Frame ( 6) shift: -1.35 -0.51 ...... Frame ( 7) shift: -1.37 -0.46 ...... Frame ( 8) shift: -1.38 -0.41 ...... Frame ( 9) shift: -1.38 -0.35 ...... Frame ( 10) shift: -1.38 -0.26 ...... Frame ( 11) shift: -1.37 -0.17 ...... Frame ( 12) shift: -1.34 -0.11 ...... Frame ( 13) shift: -1.27 -0.08 ...... Frame ( 14) shift: -1.21 -0.05 ...... Frame ( 15) shift: -1.15 -0.01 ...... Frame ( 16) shift: -1.11 0.05 ...... Frame ( 17) shift: -1.06 0.11 ...... Frame ( 18) shift: -1.01 0.15 ...... Frame ( 19) shift: -0.95 0.16 ...... Frame ( 20) shift: -0.90 0.17 ...... Frame ( 21) shift: -0.82 0.23 ...... Frame ( 22) shift: -0.73 0.35 ...... Frame ( 23) shift: -0.63 0.47 ...... Frame ( 24) shift: -0.57 0.52 ...... Frame ( 25) shift: -0.53 0.50 ...... Frame ( 26) shift: -0.49 0.48 ...... Frame ( 27) shift: -0.45 0.52 ...... Frame ( 28) shift: -0.41 0.64 ...... Frame ( 29) shift: -0.37 0.77 ...... Frame ( 30) shift: -0.32 0.90 ...... Frame ( 31) shift: -0.25 1.03 ...... Frame ( 32) shift: -0.18 1.17 ...... Frame ( 33) shift: -0.09 1.24 ...... Frame ( 34) shift: 0.02 1.24 ...... Frame ( 35) shift: 0.13 1.23 ...... Frame ( 36) shift: 0.16 1.26 ...... Frame ( 37) shift: 0.11 1.30 ...... Frame ( 38) shift: 0.05 1.35 ...... Frame ( 39) shift: 0.00 1.40 ...... Frame ( 40) shift: -0.05 1.45 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.120371 Iteration 2 Error: 0.354309 Iteration 3 Error: 0.091067 Iteration 4 Error: 0.051273 Iteration 5 Error: 0.030748 Align patch 2 23 left Iteration 1 Error: 1.560497 Iteration 2 Error: 0.232397 Iteration 3 Error: 0.079512 Iteration 4 Error: 0.025049 Align patch 3 22 left Iteration 1 Error: 0.827860 Iteration 2 Error: 0.081985 Iteration 3 Error: 0.022044 Align patch 4 21 left Iteration 1 Error: 0.603215 Iteration 2 Error: 0.120495 Iteration 3 Error: 0.023805 Align patch 5 20 left Iteration 1 Error: 0.527646 Iteration 2 Error: 0.101270 Iteration 3 Error: 0.016940 Align patch 6 19 left Iteration 1 Error: 0.865667 Iteration 2 Error: 0.139855 Iteration 3 Error: 0.062485 Iteration 4 Error: 0.026315 Align patch 7 18 left Iteration 1 Error: 0.709071 Iteration 2 Error: 0.115329 Iteration 3 Error: 0.028810 Align patch 8 17 left Iteration 1 Error: 0.734667 Iteration 2 Error: 0.178387 Iteration 3 Error: 0.058464 Iteration 4 Error: 0.031500 Align patch 9 16 left Iteration 1 Error: 1.027459 Iteration 2 Error: 0.201641 Iteration 3 Error: 0.062835 Iteration 4 Error: 0.024632 Align patch 10 15 left Iteration 1 Error: 0.608298 Iteration 2 Error: 0.115160 Iteration 3 Error: 0.020010 Align patch 11 14 left Iteration 1 Error: 0.724371 Iteration 2 Error: 0.252437 Iteration 3 Error: 0.108306 Iteration 4 Error: 0.078354 Iteration 5 Error: 0.032079 Align patch 12 13 left Iteration 1 Error: 1.179736 Iteration 2 Error: 0.150286 Iteration 3 Error: 0.041608 Align patch 13 12 left Iteration 1 Error: 1.200891 Iteration 2 Error: 0.272627 Iteration 3 Error: 0.052516 Iteration 4 Error: 0.016888 Align patch 14 11 left Iteration 1 Error: 1.010501 Iteration 2 Error: 0.146266 Iteration 3 Error: 0.049900 Align patch 15 10 left Iteration 1 Error: 0.572396 Iteration 2 Error: 0.069270 Iteration 3 Error: 0.013176 Align patch 16 9 left Iteration 1 Error: 0.678012 Iteration 2 Error: 0.135511 Iteration 3 Error: 0.034403 Align patch 17 8 left Iteration 1 Error: 0.670463 Iteration 2 Error: 0.148412 Iteration 3 Error: 0.033635 Align patch 18 7 left Iteration 1 Error: 0.544690 Iteration 2 Error: 0.094670 Iteration 3 Error: 0.017822 Align patch 19 6 left Iteration 1 Error: 0.549435 Iteration 2 Error: 0.057423 Iteration 3 Error: 0.016752 Align patch 20 5 left Iteration 1 Error: 0.920052 Iteration 2 Error: 0.131131 Iteration 3 Error: 0.034419 Align patch 21 4 left Iteration 1 Error: 0.879532 Iteration 2 Error: 0.224381 Iteration 3 Error: 0.035695 Align patch 22 3 left Iteration 1 Error: 0.609662 Iteration 2 Error: 0.110203 Iteration 3 Error: 0.029395 Align patch 23 2 left Iteration 1 Error: 0.710067 Iteration 2 Error: 0.083638 Iteration 3 Error: 0.015985 Align patch 24 1 left Iteration 1 Error: 0.495642 Iteration 2 Error: 0.079884 Iteration 3 Error: 0.021819 Align patch 25 0 left Iteration 1 Error: 0.598720 Iteration 2 Error: 0.123887 Iteration 3 Error: 0.038157 3D Fitting completed. Patch alignment time: 11.94(sec) Local motion has been corrected. Process thread exits. Computational time: 22.738617 sec Total time: 31.829712 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00015hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00015hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.689276s Reading file: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00015hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.870935s ........................................ >>>>>>TIME<<<<<< FFT: 1.148671s Defocus_U Defocus_V Angle CCC 13835.92 14687.52 5.15 0.040044 Final Values Defocus_U Defocus_V Angle CCC 13824.95 14736.00 4.84 0.059648 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00005sq_v01_00015hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00015hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 40.03 6.74 Num Hot pixels: 177 Hot pixel threshold: 80.46 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.890807 Iteration 2 Error: 0.143337 Iteration 3 Error: 0.031953 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.01 0.12 ...... Frame ( 3) shift: -0.02 0.23 ...... Frame ( 4) shift: -0.03 0.35 ...... Frame ( 5) shift: -0.03 0.47 ...... Frame ( 6) shift: 0.01 0.55 ...... Frame ( 7) shift: 0.10 0.60 ...... Frame ( 8) shift: 0.20 0.64 ...... Frame ( 9) shift: 0.25 0.69 ...... Frame ( 10) shift: 0.27 0.74 ...... Frame ( 11) shift: 0.29 0.79 ...... Frame ( 12) shift: 0.32 0.85 ...... Frame ( 13) shift: 0.37 0.93 ...... Frame ( 14) shift: 0.42 1.00 ...... Frame ( 15) shift: 0.45 1.00 ...... Frame ( 16) shift: 0.45 0.93 ...... Frame ( 17) shift: 0.46 0.86 ...... Frame ( 18) shift: 0.48 0.86 ...... Frame ( 19) shift: 0.53 0.93 ...... Frame ( 20) shift: 0.58 1.01 ...... Frame ( 21) shift: 0.62 1.05 ...... Frame ( 22) shift: 0.66 1.07 ...... Frame ( 23) shift: 0.70 1.08 ...... Frame ( 24) shift: 0.70 1.14 ...... Frame ( 25) shift: 0.67 1.23 ...... Frame ( 26) shift: 0.63 1.32 ...... Frame ( 27) shift: 0.64 1.37 ...... Frame ( 28) shift: 0.70 1.37 ...... Frame ( 29) shift: 0.75 1.37 ...... Frame ( 30) shift: 0.80 1.39 ...... Frame ( 31) shift: 0.84 1.44 ...... Frame ( 32) shift: 0.88 1.49 ...... Frame ( 33) shift: 0.93 1.50 ...... Frame ( 34) shift: 0.99 1.49 ...... Frame ( 35) shift: 1.04 1.47 ...... Frame ( 36) shift: 1.07 1.50 ...... Frame ( 37) shift: 1.06 1.56 ...... Frame ( 38) shift: 1.05 1.63 ...... Frame ( 39) shift: 1.05 1.69 ...... Frame ( 40) shift: 1.04 1.76 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.773264 Iteration 2 Error: 0.317041 Iteration 3 Error: 0.107828 Iteration 4 Error: 0.054408 Iteration 5 Error: 0.023509 Align patch 2 23 left Iteration 1 Error: 1.175770 Iteration 2 Error: 0.148951 Iteration 3 Error: 0.050038 Iteration 4 Error: 0.014223 Align patch 3 22 left Iteration 1 Error: 1.410199 Iteration 2 Error: 0.133723 Iteration 3 Error: 0.025669 Align patch 4 21 left Iteration 1 Error: 0.613095 Iteration 2 Error: 0.090831 Iteration 3 Error: 0.021398 Align patch 5 20 left Iteration 1 Error: 0.847084 Iteration 2 Error: 0.106823 Iteration 3 Error: 0.023401 Align patch 6 19 left Iteration 1 Error: 0.971248 Iteration 2 Error: 0.248920 Iteration 3 Error: 0.073270 Iteration 4 Error: 0.033066 Align patch 7 18 left Iteration 1 Error: 0.762898 Iteration 2 Error: 0.176408 Iteration 3 Error: 0.037683 Align patch 8 17 left Iteration 1 Error: 0.855764 Iteration 2 Error: 0.149914 Iteration 3 Error: 0.031267 Align patch 9 16 left Iteration 1 Error: 0.769637 Iteration 2 Error: 0.151463 Iteration 3 Error: 0.038387 Align patch 10 15 left Iteration 1 Error: 0.606299 Iteration 2 Error: 0.080713 Iteration 3 Error: 0.021706 Align patch 11 14 left Iteration 1 Error: 0.557138 Iteration 2 Error: 0.107927 Iteration 3 Error: 0.032767 Align patch 12 13 left Iteration 1 Error: 0.550008 Iteration 2 Error: 0.133687 Iteration 3 Error: 0.027478 Align patch 13 12 left Iteration 1 Error: 0.942714 Iteration 2 Error: 0.118460 Iteration 3 Error: 0.023347 Align patch 14 11 left Iteration 1 Error: 0.823728 Iteration 2 Error: 0.085187 Iteration 3 Error: 0.033137 Align patch 15 10 left Iteration 1 Error: 0.550441 Iteration 2 Error: 0.131523 Iteration 3 Error: 0.033217 Align patch 16 9 left Iteration 1 Error: 0.642039 Iteration 2 Error: 0.137199 Iteration 3 Error: 0.030362 Align patch 17 8 left Iteration 1 Error: 1.203698 Iteration 2 Error: 0.165708 Iteration 3 Error: 0.032629 Align patch 18 7 left Iteration 1 Error: 0.805272 Iteration 2 Error: 0.125022 Iteration 3 Error: 0.038736 Align patch 19 6 left Iteration 1 Error: 0.725868 Iteration 2 Error: 0.112548 Iteration 3 Error: 0.035311 Align patch 20 5 left Iteration 1 Error: 0.904364 Iteration 2 Error: 0.158426 Iteration 3 Error: 0.039851 Align patch 21 4 left Iteration 1 Error: 0.573955 Iteration 2 Error: 0.110020 Iteration 3 Error: 0.031319 Align patch 22 3 left Iteration 1 Error: 0.651051 Iteration 2 Error: 0.106969 Iteration 3 Error: 0.028889 Align patch 23 2 left Iteration 1 Error: 0.935724 Iteration 2 Error: 0.170518 Iteration 3 Error: 0.021916 Align patch 24 1 left Iteration 1 Error: 0.760940 Iteration 2 Error: 0.081006 Iteration 3 Error: 0.028917 Align patch 25 0 left Iteration 1 Error: 1.103637 Iteration 2 Error: 0.374297 Iteration 3 Error: 0.180089 Iteration 4 Error: 0.061906 Iteration 5 Error: 0.026803 3D Fitting completed. Patch alignment time: 11.18(sec) Local motion has been corrected. Process thread exits. Computational time: 22.070555 sec Total time: 29.375578 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00015hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00015hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.597051s Reading file: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00015hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.664005s ........................................ >>>>>>TIME<<<<<< FFT: 1.020968s Defocus_U Defocus_V Angle CCC 14388.69 13759.77 83.90 0.046359 Final Values Defocus_U Defocus_V Angle CCC 14382.43 13766.03 83.90 0.071288 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00005sq_v01_00016hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00016hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.996e-02 CC threshold: 0.734 Mean Std: 34.03 6.16 Num Hot pixels: 169 Hot pixel threshold: 70.97 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.160661 Iteration 2 Error: 0.250086 Iteration 3 Error: 0.075974 Iteration 4 Error: 0.032664 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.10 0.05 ...... Frame ( 3) shift: -0.20 0.09 ...... Frame ( 4) shift: -0.29 0.14 ...... Frame ( 5) shift: -0.39 0.18 ...... Frame ( 6) shift: -0.45 0.22 ...... Frame ( 7) shift: -0.47 0.24 ...... Frame ( 8) shift: -0.49 0.26 ...... Frame ( 9) shift: -0.43 0.27 ...... Frame ( 10) shift: -0.30 0.26 ...... Frame ( 11) shift: -0.16 0.25 ...... Frame ( 12) shift: -0.11 0.32 ...... Frame ( 13) shift: -0.15 0.47 ...... Frame ( 14) shift: -0.19 0.62 ...... Frame ( 15) shift: -0.16 0.72 ...... Frame ( 16) shift: -0.06 0.77 ...... Frame ( 17) shift: 0.04 0.83 ...... Frame ( 18) shift: 0.13 0.87 ...... Frame ( 19) shift: 0.20 0.91 ...... Frame ( 20) shift: 0.27 0.96 ...... Frame ( 21) shift: 0.31 1.00 ...... Frame ( 22) shift: 0.33 1.03 ...... Frame ( 23) shift: 0.34 1.07 ...... Frame ( 24) shift: 0.41 1.14 ...... Frame ( 25) shift: 0.53 1.23 ...... Frame ( 26) shift: 0.66 1.33 ...... Frame ( 27) shift: 0.77 1.39 ...... Frame ( 28) shift: 0.85 1.42 ...... Frame ( 29) shift: 0.94 1.45 ...... Frame ( 30) shift: 1.01 1.51 ...... Frame ( 31) shift: 1.05 1.59 ...... Frame ( 32) shift: 1.09 1.67 ...... Frame ( 33) shift: 1.14 1.65 ...... Frame ( 34) shift: 1.19 1.53 ...... Frame ( 35) shift: 1.24 1.41 ...... Frame ( 36) shift: 1.30 1.43 ...... Frame ( 37) shift: 1.36 1.58 ...... Frame ( 38) shift: 1.42 1.72 ...... Frame ( 39) shift: 1.48 1.87 ...... Frame ( 40) shift: 1.54 2.02 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.531371 Iteration 2 Error: 0.372716 Iteration 3 Error: 0.118370 Iteration 4 Error: 0.041516 Align patch 2 23 left Iteration 1 Error: 0.816359 Iteration 2 Error: 0.213372 Iteration 3 Error: 0.048370 Align patch 3 22 left Iteration 1 Error: 1.065078 Iteration 2 Error: 0.257650 Iteration 3 Error: 0.099015 Iteration 4 Error: 0.030763 Align patch 4 21 left Iteration 1 Error: 0.876569 Iteration 2 Error: 0.208595 Iteration 3 Error: 0.069800 Iteration 4 Error: 0.015879 Align patch 5 20 left Iteration 1 Error: 0.746511 Iteration 2 Error: 0.240464 Iteration 3 Error: 0.083534 Iteration 4 Error: 0.030421 Align patch 6 19 left Iteration 1 Error: 1.913191 Iteration 2 Error: 0.325081 Iteration 3 Error: 0.083923 Iteration 4 Error: 0.030769 Align patch 7 18 left Iteration 1 Error: 1.086236 Iteration 2 Error: 0.249161 Iteration 3 Error: 0.050561 Iteration 4 Error: 0.027247 Align patch 8 17 left Iteration 1 Error: 0.962652 Iteration 2 Error: 0.128982 Iteration 3 Error: 0.042024 Align patch 9 16 left Iteration 1 Error: 0.566205 Iteration 2 Error: 0.155744 Iteration 3 Error: 0.060667 Iteration 4 Error: 0.033177 Align patch 10 15 left Iteration 1 Error: 1.322988 Iteration 2 Error: 0.248004 Iteration 3 Error: 0.135985 Iteration 4 Error: 0.044322 Align patch 11 14 left Iteration 1 Error: 1.060853 Iteration 2 Error: 0.203657 Iteration 3 Error: 0.066860 Iteration 4 Error: 0.025526 Align patch 12 13 left Iteration 1 Error: 1.146273 Iteration 2 Error: 0.317270 Iteration 3 Error: 0.110922 Iteration 4 Error: 0.050416 Iteration 5 Error: 0.021336 Align patch 13 12 left Iteration 1 Error: 1.011406 Iteration 2 Error: 0.259922 Iteration 3 Error: 0.067160 Iteration 4 Error: 0.030669 Align patch 14 11 left Iteration 1 Error: 1.551282 Iteration 2 Error: 0.209768 Iteration 3 Error: 0.090217 Iteration 4 Error: 0.044866 Align patch 15 10 left Iteration 1 Error: 3.839632 Iteration 2 Error: 0.463455 Iteration 3 Error: 0.145450 Iteration 4 Error: 0.067923 Iteration 5 Error: 0.039257 Align patch 16 9 left Iteration 1 Error: 1.418816 Iteration 2 Error: 0.413511 Iteration 3 Error: 0.071328 Iteration 4 Error: 0.052576 Iteration 5 Error: 0.019093 Align patch 17 8 left Iteration 1 Error: 0.912055 Iteration 2 Error: 0.217161 Iteration 3 Error: 0.065581 Iteration 4 Error: 0.020998 Align patch 18 7 left Iteration 1 Error: 0.857269 Iteration 2 Error: 0.289770 Iteration 3 Error: 0.030818 Align patch 19 6 left Iteration 1 Error: 1.094394 Iteration 2 Error: 0.158126 Iteration 3 Error: 0.033185 Align patch 20 5 left Iteration 1 Error: 1.370415 Iteration 2 Error: 0.280259 Iteration 3 Error: 0.072526 Iteration 4 Error: 0.031267 Align patch 21 4 left Iteration 1 Error: 0.889686 Iteration 2 Error: 0.252607 Iteration 3 Error: 0.109290 Iteration 4 Error: 0.042206 Align patch 22 3 left Iteration 1 Error: 0.790236 Iteration 2 Error: 0.188829 Iteration 3 Error: 0.040324 Align patch 23 2 left Iteration 1 Error: 0.862058 Iteration 2 Error: 0.208890 Iteration 3 Error: 0.060170 Iteration 4 Error: 0.031174 Align patch 24 1 left Iteration 1 Error: 0.767728 Iteration 2 Error: 0.186722 Iteration 3 Error: 0.065569 Iteration 4 Error: 0.046555 Align patch 25 0 left Iteration 1 Error: 1.113279 Iteration 2 Error: 0.323187 Iteration 3 Error: 0.111986 Iteration 4 Error: 0.055272 Iteration 5 Error: 0.020742 3D Fitting completed. Patch alignment time: 14.45(sec) Local motion has been corrected. Process thread exits. Computational time: 26.833836 sec Total time: 36.585793 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00016hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00016hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.608845s Reading file: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00016hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.355116s ........................................ >>>>>>TIME<<<<<< FFT: 0.960405s Defocus_U Defocus_V Angle CCC 12894.52 14160.21 25.97 0.025343 Final Values Defocus_U Defocus_V Angle CCC 12852.26 14252.47 28.16 0.035450 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00005sq_v01_00016hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00016hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.997e-02 CC threshold: 0.734 Mean Std: 39.05 6.63 Num Hot pixels: 164 Hot pixel threshold: 78.84 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.963397 Iteration 2 Error: 0.252094 Iteration 3 Error: 0.091805 Iteration 4 Error: 0.041459 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.11 0.06 ...... Frame ( 3) shift: -0.22 0.12 ...... Frame ( 4) shift: -0.34 0.18 ...... Frame ( 5) shift: -0.45 0.23 ...... Frame ( 6) shift: -0.51 0.28 ...... Frame ( 7) shift: -0.53 0.31 ...... Frame ( 8) shift: -0.55 0.34 ...... Frame ( 9) shift: -0.56 0.41 ...... Frame ( 10) shift: -0.54 0.50 ...... Frame ( 11) shift: -0.52 0.60 ...... Frame ( 12) shift: -0.45 0.70 ...... Frame ( 13) shift: -0.35 0.81 ...... Frame ( 14) shift: -0.24 0.91 ...... Frame ( 15) shift: -0.19 1.03 ...... Frame ( 16) shift: -0.18 1.15 ...... Frame ( 17) shift: -0.18 1.28 ...... Frame ( 18) shift: -0.15 1.35 ...... Frame ( 19) shift: -0.08 1.38 ...... Frame ( 20) shift: -0.02 1.41 ...... Frame ( 21) shift: 0.04 1.44 ...... Frame ( 22) shift: 0.09 1.47 ...... Frame ( 23) shift: 0.13 1.51 ...... Frame ( 24) shift: 0.19 1.56 ...... Frame ( 25) shift: 0.25 1.64 ...... Frame ( 26) shift: 0.32 1.71 ...... Frame ( 27) shift: 0.34 1.79 ...... Frame ( 28) shift: 0.30 1.87 ...... Frame ( 29) shift: 0.27 1.96 ...... Frame ( 30) shift: 0.27 2.02 ...... Frame ( 31) shift: 0.30 2.06 ...... Frame ( 32) shift: 0.34 2.10 ...... Frame ( 33) shift: 0.37 2.13 ...... Frame ( 34) shift: 0.40 2.14 ...... Frame ( 35) shift: 0.43 2.16 ...... Frame ( 36) shift: 0.46 2.19 ...... Frame ( 37) shift: 0.48 2.25 ...... Frame ( 38) shift: 0.49 2.31 ...... Frame ( 39) shift: 0.51 2.37 ...... Frame ( 40) shift: 0.53 2.43 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.027127 Iteration 2 Error: 0.513026 Iteration 3 Error: 0.209684 Iteration 4 Error: 0.121869 Iteration 5 Error: 0.066352 Align patch 1 24 left Iteration 1 Error: 1.475910 Iteration 2 Error: 0.350865 Iteration 3 Error: 0.102348 Iteration 4 Error: 0.048117 Align patch 2 23 left Iteration 1 Error: 0.715883 Iteration 2 Error: 0.174189 Iteration 3 Error: 0.076830 Iteration 4 Error: 0.042462 Align patch 3 22 left Iteration 1 Error: 0.983023 Iteration 2 Error: 0.277143 Iteration 3 Error: 0.085463 Iteration 4 Error: 0.037293 Align patch 4 21 left Iteration 1 Error: 1.074507 Iteration 2 Error: 0.250229 Iteration 3 Error: 0.056282 Iteration 4 Error: 0.017191 Align patch 5 20 left Iteration 1 Error: 0.669254 Iteration 2 Error: 0.175741 Iteration 3 Error: 0.042642 Align patch 6 19 left Iteration 1 Error: 1.285046 Iteration 2 Error: 0.403254 Iteration 3 Error: 0.233386 Iteration 4 Error: 0.120231 Iteration 5 Error: 0.079567 Align patch 6 19 left Iteration 1 Error: 1.699549 Iteration 2 Error: 0.345642 Iteration 3 Error: 0.160631 Iteration 4 Error: 0.065064 Iteration 5 Error: 0.036319 Align patch 7 18 left Iteration 1 Error: 1.224565 Iteration 2 Error: 0.390974 Iteration 3 Error: 0.129865 Iteration 4 Error: 0.065408 Iteration 5 Error: 0.023124 Align patch 8 17 left Iteration 1 Error: 0.950615 Iteration 2 Error: 0.336371 Iteration 3 Error: 0.179120 Iteration 4 Error: 0.077093 Iteration 5 Error: 0.040069 Align patch 9 16 left Iteration 1 Error: 0.723776 Iteration 2 Error: 0.141937 Iteration 3 Error: 0.027804 Align patch 10 15 left Iteration 1 Error: 0.821685 Iteration 2 Error: 0.142731 Iteration 3 Error: 0.057291 Iteration 4 Error: 0.023887 Align patch 11 14 left Iteration 1 Error: 1.137147 Iteration 2 Error: 0.354413 Iteration 3 Error: 0.165807 Iteration 4 Error: 0.076403 Iteration 5 Error: 0.050946 Align patch 11 14 left Iteration 1 Error: 1.791905 Iteration 2 Error: 0.241306 Iteration 3 Error: 0.079912 Iteration 4 Error: 0.029469 Align patch 12 13 left Iteration 1 Error: 0.990556 Iteration 2 Error: 0.251672 Iteration 3 Error: 0.057706 Iteration 4 Error: 0.024705 Align patch 13 12 left Iteration 1 Error: 0.968878 Iteration 2 Error: 0.310326 Iteration 3 Error: 0.139954 Iteration 4 Error: 0.073207 Iteration 5 Error: 0.039399 Align patch 14 11 left Iteration 1 Error: 0.627168 Iteration 2 Error: 0.176293 Iteration 3 Error: 0.030426 Align patch 15 10 left Iteration 1 Error: 0.817091 Iteration 2 Error: 0.137445 Iteration 3 Error: 0.030994 Align patch 16 9 left Iteration 1 Error: 0.906219 Iteration 2 Error: 0.342672 Iteration 3 Error: 0.173086 Iteration 4 Error: 0.074403 Iteration 5 Error: 0.033953 Align patch 17 8 left Iteration 1 Error: 1.005464 Iteration 2 Error: 0.313892 Iteration 3 Error: 0.077072 Iteration 4 Error: 0.040009 Align patch 18 7 left Iteration 1 Error: 0.956189 Iteration 2 Error: 0.255372 Iteration 3 Error: 0.081541 Iteration 4 Error: 0.035518 Align patch 19 6 left Iteration 1 Error: 0.380437 Iteration 2 Error: 0.079960 Iteration 3 Error: 0.022435 Align patch 20 5 left Iteration 1 Error: 0.848590 Iteration 2 Error: 0.120451 Iteration 3 Error: 0.041411 Align patch 21 4 left Iteration 1 Error: 1.450997 Iteration 2 Error: 0.195913 Iteration 3 Error: 0.054297 Iteration 4 Error: 0.017234 Align patch 22 3 left Iteration 1 Error: 0.745228 Iteration 2 Error: 0.203660 Iteration 3 Error: 0.109107 Iteration 4 Error: 0.041584 Align patch 23 2 left Iteration 1 Error: 0.706947 Iteration 2 Error: 0.182334 Iteration 3 Error: 0.061056 Iteration 4 Error: 0.019866 Align patch 24 1 left Iteration 1 Error: 1.044210 Iteration 2 Error: 0.217074 Iteration 3 Error: 0.065627 Iteration 4 Error: 0.020931 Align patch 25 0 left Iteration 1 Error: 1.461966 Iteration 2 Error: 0.276254 Iteration 3 Error: 0.051473 Iteration 4 Error: 0.015423 3D Fitting completed. Patch alignment time: 14.52(sec) Local motion has been corrected. Process thread exits. Computational time: 24.432440 sec Total time: 31.037275 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00016hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00016hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.506270s Reading file: gc_18feb27f_CTD_g1_00012gr_00005sq_v01_00016hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.525641s ........................................ >>>>>>TIME<<<<<< FFT: 0.907823s Defocus_U Defocus_V Angle CCC 8887.20 8374.70 88.92 0.017561 Final Values Defocus_U Defocus_V Angle CCC 8926.24 8345.04 88.29 0.034231 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00002hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00002hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.306e-01 9.739e-02 CC threshold: 0.715 Mean Std: 42.23 7.53 Num Hot pixels: 139 Hot pixel threshold: 87.43 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.801884 Iteration 2 Error: 0.105169 Iteration 3 Error: 0.021126 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.07 0.11 ...... Frame ( 3) shift: -0.14 0.22 ...... Frame ( 4) shift: -0.21 0.33 ...... Frame ( 5) shift: -0.28 0.44 ...... Frame ( 6) shift: -0.37 0.52 ...... Frame ( 7) shift: -0.47 0.57 ...... Frame ( 8) shift: -0.57 0.62 ...... Frame ( 9) shift: -0.61 0.68 ...... Frame ( 10) shift: -0.59 0.74 ...... Frame ( 11) shift: -0.57 0.79 ...... Frame ( 12) shift: -0.56 0.82 ...... Frame ( 13) shift: -0.55 0.81 ...... Frame ( 14) shift: -0.55 0.81 ...... Frame ( 15) shift: -0.55 0.84 ...... Frame ( 16) shift: -0.56 0.92 ...... Frame ( 17) shift: -0.56 0.99 ...... Frame ( 18) shift: -0.58 1.02 ...... Frame ( 19) shift: -0.59 1.01 ...... Frame ( 20) shift: -0.61 1.00 ...... Frame ( 21) shift: -0.60 1.03 ...... Frame ( 22) shift: -0.56 1.12 ...... Frame ( 23) shift: -0.52 1.21 ...... Frame ( 24) shift: -0.46 1.24 ...... Frame ( 25) shift: -0.39 1.22 ...... Frame ( 26) shift: -0.32 1.19 ...... Frame ( 27) shift: -0.27 1.20 ...... Frame ( 28) shift: -0.23 1.22 ...... Frame ( 29) shift: -0.19 1.25 ...... Frame ( 30) shift: -0.16 1.29 ...... Frame ( 31) shift: -0.13 1.33 ...... Frame ( 32) shift: -0.10 1.38 ...... Frame ( 33) shift: -0.07 1.40 ...... Frame ( 34) shift: -0.05 1.39 ...... Frame ( 35) shift: -0.03 1.39 ...... Frame ( 36) shift: 0.00 1.39 ...... Frame ( 37) shift: 0.05 1.39 ...... Frame ( 38) shift: 0.10 1.40 ...... Frame ( 39) shift: 0.15 1.41 ...... Frame ( 40) shift: 0.20 1.41 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.672837 Iteration 2 Error: 0.076834 Iteration 3 Error: 0.022644 Align patch 2 23 left Iteration 1 Error: 0.832715 Iteration 2 Error: 0.120411 Iteration 3 Error: 0.054737 Iteration 4 Error: 0.017181 Align patch 3 22 left Iteration 1 Error: 0.711584 Iteration 2 Error: 0.111170 Iteration 3 Error: 0.022268 Align patch 4 21 left Iteration 1 Error: 0.464600 Iteration 2 Error: 0.066331 Iteration 3 Error: 0.014176 Align patch 5 20 left Iteration 1 Error: 0.550889 Iteration 2 Error: 0.111645 Iteration 3 Error: 0.033516 Align patch 6 19 left Iteration 1 Error: 0.955105 Iteration 2 Error: 0.129014 Iteration 3 Error: 0.028032 Align patch 7 18 left Iteration 1 Error: 0.863155 Iteration 2 Error: 0.166911 Iteration 3 Error: 0.040139 Align patch 8 17 left Iteration 1 Error: 0.640412 Iteration 2 Error: 0.095386 Iteration 3 Error: 0.031073 Align patch 9 16 left Iteration 1 Error: 0.828979 Iteration 2 Error: 0.112013 Iteration 3 Error: 0.027644 Align patch 10 15 left Iteration 1 Error: 0.636639 Iteration 2 Error: 0.128783 Iteration 3 Error: 0.037892 Align patch 11 14 left Iteration 1 Error: 0.699036 Iteration 2 Error: 0.124947 Iteration 3 Error: 0.039366 Align patch 12 13 left Iteration 1 Error: 0.686360 Iteration 2 Error: 0.163548 Iteration 3 Error: 0.056235 Iteration 4 Error: 0.020133 Align patch 13 12 left Iteration 1 Error: 0.632746 Iteration 2 Error: 0.175823 Iteration 3 Error: 0.044714 Align patch 14 11 left Iteration 1 Error: 0.528184 Iteration 2 Error: 0.114448 Iteration 3 Error: 0.017433 Align patch 15 10 left Iteration 1 Error: 0.447189 Iteration 2 Error: 0.060060 Iteration 3 Error: 0.019199 Align patch 16 9 left Iteration 1 Error: 0.884081 Iteration 2 Error: 0.235593 Iteration 3 Error: 0.056511 Iteration 4 Error: 0.020557 Align patch 17 8 left Iteration 1 Error: 0.533762 Iteration 2 Error: 0.079126 Iteration 3 Error: 0.024803 Align patch 18 7 left Iteration 1 Error: 0.854580 Iteration 2 Error: 0.093175 Iteration 3 Error: 0.018178 Align patch 19 6 left Iteration 1 Error: 0.726731 Iteration 2 Error: 0.136215 Iteration 3 Error: 0.028988 Align patch 20 5 left Iteration 1 Error: 0.896325 Iteration 2 Error: 0.136686 Iteration 3 Error: 0.024803 Align patch 21 4 left Iteration 1 Error: 0.908614 Iteration 2 Error: 0.149143 Iteration 3 Error: 0.051284 Iteration 4 Error: 0.022132 Align patch 22 3 left Iteration 1 Error: 0.753333 Iteration 2 Error: 0.125409 Iteration 3 Error: 0.031922 Align patch 23 2 left Iteration 1 Error: 0.580106 Iteration 2 Error: 0.135358 Iteration 3 Error: 0.041671 Align patch 24 1 left Iteration 1 Error: 0.930430 Iteration 2 Error: 0.132810 Iteration 3 Error: 0.024290 Align patch 25 0 left Iteration 1 Error: 0.618840 Iteration 2 Error: 0.087556 Iteration 3 Error: 0.014105 3D Fitting completed. Patch alignment time: 11.32(sec) Local motion has been corrected. Process thread exits. Computational time: 23.533443 sec Total time: 32.538532 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00002hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00002hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.690497s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00002hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.892922s ........................................ >>>>>>TIME<<<<<< FFT: 1.001814s Defocus_U Defocus_V Angle CCC 13587.89 14404.30 9.56 -0.018821 Final Values Defocus_U Defocus_V Angle CCC 13581.64 14410.55 10.19 -0.167746 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00002hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00002hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.306e-01 9.746e-02 CC threshold: 0.715 Mean Std: 42.79 7.54 Num Hot pixels: 142 Hot pixel threshold: 88.01 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.799283 Iteration 2 Error: 0.096338 Iteration 3 Error: 0.021760 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.03 0.11 ...... Frame ( 3) shift: -0.07 0.22 ...... Frame ( 4) shift: -0.10 0.34 ...... Frame ( 5) shift: -0.14 0.45 ...... Frame ( 6) shift: -0.19 0.50 ...... Frame ( 7) shift: -0.27 0.49 ...... Frame ( 8) shift: -0.34 0.48 ...... Frame ( 9) shift: -0.35 0.50 ...... Frame ( 10) shift: -0.29 0.53 ...... Frame ( 11) shift: -0.23 0.57 ...... Frame ( 12) shift: -0.21 0.59 ...... Frame ( 13) shift: -0.22 0.58 ...... Frame ( 14) shift: -0.22 0.57 ...... Frame ( 15) shift: -0.25 0.61 ...... Frame ( 16) shift: -0.28 0.69 ...... Frame ( 17) shift: -0.32 0.77 ...... Frame ( 18) shift: -0.34 0.82 ...... Frame ( 19) shift: -0.35 0.84 ...... Frame ( 20) shift: -0.35 0.86 ...... Frame ( 21) shift: -0.29 0.88 ...... Frame ( 22) shift: -0.14 0.91 ...... Frame ( 23) shift: 0.01 0.94 ...... Frame ( 24) shift: 0.09 0.95 ...... Frame ( 25) shift: 0.12 0.94 ...... Frame ( 26) shift: 0.15 0.94 ...... Frame ( 27) shift: 0.18 0.94 ...... Frame ( 28) shift: 0.21 0.95 ...... Frame ( 29) shift: 0.24 0.96 ...... Frame ( 30) shift: 0.26 0.96 ...... Frame ( 31) shift: 0.26 0.96 ...... Frame ( 32) shift: 0.27 0.95 ...... Frame ( 33) shift: 0.34 1.00 ...... Frame ( 34) shift: 0.48 1.10 ...... Frame ( 35) shift: 0.61 1.20 ...... Frame ( 36) shift: 0.69 1.24 ...... Frame ( 37) shift: 0.72 1.21 ...... Frame ( 38) shift: 0.75 1.19 ...... Frame ( 39) shift: 0.79 1.17 ...... Frame ( 40) shift: 0.82 1.15 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.801064 Iteration 2 Error: 0.106472 Iteration 3 Error: 0.023935 Align patch 2 23 left Iteration 1 Error: 0.739643 Iteration 2 Error: 0.145771 Iteration 3 Error: 0.022726 Align patch 3 22 left Iteration 1 Error: 0.810610 Iteration 2 Error: 0.101913 Iteration 3 Error: 0.036300 Align patch 4 21 left Iteration 1 Error: 0.835757 Iteration 2 Error: 0.112368 Iteration 3 Error: 0.017278 Align patch 5 20 left Iteration 1 Error: 0.570906 Iteration 2 Error: 0.088191 Iteration 3 Error: 0.021315 Align patch 6 19 left Iteration 1 Error: 0.789969 Iteration 2 Error: 0.092041 Iteration 3 Error: 0.017148 Align patch 7 18 left Iteration 1 Error: 0.582321 Iteration 2 Error: 0.078711 Iteration 3 Error: 0.016519 Align patch 8 17 left Iteration 1 Error: 0.585201 Iteration 2 Error: 0.081453 Iteration 3 Error: 0.025228 Align patch 9 16 left Iteration 1 Error: 0.605009 Iteration 2 Error: 0.107888 Iteration 3 Error: 0.032686 Align patch 10 15 left Iteration 1 Error: 0.874304 Iteration 2 Error: 0.138459 Iteration 3 Error: 0.039579 Align patch 11 14 left Iteration 1 Error: 0.723384 Iteration 2 Error: 0.133639 Iteration 3 Error: 0.039771 Align patch 12 13 left Iteration 1 Error: 0.676760 Iteration 2 Error: 0.150553 Iteration 3 Error: 0.058519 Iteration 4 Error: 0.021150 Align patch 13 12 left Iteration 1 Error: 0.663070 Iteration 2 Error: 0.092284 Iteration 3 Error: 0.027690 Align patch 14 11 left Iteration 1 Error: 0.557876 Iteration 2 Error: 0.075522 Iteration 3 Error: 0.026568 Align patch 15 10 left Iteration 1 Error: 0.705117 Iteration 2 Error: 0.081963 Iteration 3 Error: 0.023130 Align patch 16 9 left Iteration 1 Error: 0.674052 Iteration 2 Error: 0.130271 Iteration 3 Error: 0.038023 Align patch 17 8 left Iteration 1 Error: 0.813892 Iteration 2 Error: 0.152963 Iteration 3 Error: 0.035560 Align patch 18 7 left Iteration 1 Error: 0.715025 Iteration 2 Error: 0.159707 Iteration 3 Error: 0.059609 Iteration 4 Error: 0.032359 Align patch 19 6 left Iteration 1 Error: 0.548052 Iteration 2 Error: 0.101628 Iteration 3 Error: 0.016700 Align patch 20 5 left Iteration 1 Error: 1.176236 Iteration 2 Error: 0.133996 Iteration 3 Error: 0.037785 Align patch 21 4 left Iteration 1 Error: 1.424123 Iteration 2 Error: 0.210309 Iteration 3 Error: 0.059539 Iteration 4 Error: 0.025152 Align patch 22 3 left Iteration 1 Error: 0.797916 Iteration 2 Error: 0.177816 Iteration 3 Error: 0.061285 Iteration 4 Error: 0.020464 Align patch 23 2 left Iteration 1 Error: 0.703606 Iteration 2 Error: 0.108782 Iteration 3 Error: 0.025924 Align patch 24 1 left Iteration 1 Error: 0.585549 Iteration 2 Error: 0.120750 Iteration 3 Error: 0.030832 Align patch 25 0 left Iteration 1 Error: 1.416495 Iteration 2 Error: 0.220803 Iteration 3 Error: 0.033382 3D Fitting completed. Patch alignment time: 11.95(sec) Local motion has been corrected. Process thread exits. Computational time: 30.048710 sec Total time: 37.276726 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00002hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00002hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.475211s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00002hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 5.374457s ........................................ >>>>>>TIME<<<<<< FFT: 1.162282s Defocus_U Defocus_V Angle CCC 11849.66 11267.54 88.64 -0.021669 Final Values Defocus_U Defocus_V Angle CCC 11868.39 11283.19 89.27 -0.162426 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00002hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00002hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 45.40 7.58 Num Hot pixels: 160 Hot pixel threshold: 90.89 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.851452 Iteration 2 Error: 0.049870 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.25 -0.04 ...... Frame ( 3) shift: -0.51 -0.09 ...... Frame ( 4) shift: -0.76 -0.13 ...... Frame ( 5) shift: -1.01 -0.18 ...... Frame ( 6) shift: -1.19 -0.19 ...... Frame ( 7) shift: -1.29 -0.16 ...... Frame ( 8) shift: -1.40 -0.14 ...... Frame ( 9) shift: -1.42 -0.12 ...... Frame ( 10) shift: -1.37 -0.11 ...... Frame ( 11) shift: -1.33 -0.09 ...... Frame ( 12) shift: -1.32 -0.08 ...... Frame ( 13) shift: -1.35 -0.09 ...... Frame ( 14) shift: -1.39 -0.10 ...... Frame ( 15) shift: -1.41 -0.11 ...... Frame ( 16) shift: -1.43 -0.11 ...... Frame ( 17) shift: -1.44 -0.11 ...... Frame ( 18) shift: -1.43 -0.09 ...... Frame ( 19) shift: -1.38 -0.05 ...... Frame ( 20) shift: -1.34 -0.01 ...... Frame ( 21) shift: -1.30 0.00 ...... Frame ( 22) shift: -1.26 0.00 ...... Frame ( 23) shift: -1.22 0.01 ...... Frame ( 24) shift: -1.21 0.03 ...... Frame ( 25) shift: -1.22 0.07 ...... Frame ( 26) shift: -1.24 0.11 ...... Frame ( 27) shift: -1.23 0.14 ...... Frame ( 28) shift: -1.19 0.16 ...... Frame ( 29) shift: -1.16 0.18 ...... Frame ( 30) shift: -1.12 0.20 ...... Frame ( 31) shift: -1.09 0.22 ...... Frame ( 32) shift: -1.05 0.24 ...... Frame ( 33) shift: -1.05 0.26 ...... Frame ( 34) shift: -1.08 0.27 ...... Frame ( 35) shift: -1.12 0.28 ...... Frame ( 36) shift: -1.13 0.27 ...... Frame ( 37) shift: -1.10 0.23 ...... Frame ( 38) shift: -1.08 0.20 ...... Frame ( 39) shift: -1.06 0.16 ...... Frame ( 40) shift: -1.04 0.12 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.680491 Iteration 2 Error: 0.131306 Iteration 3 Error: 0.028761 Align patch 2 23 left Iteration 1 Error: 0.823697 Iteration 2 Error: 0.120956 Iteration 3 Error: 0.032754 Align patch 3 22 left Iteration 1 Error: 0.627841 Iteration 2 Error: 0.081658 Iteration 3 Error: 0.022784 Align patch 4 21 left Iteration 1 Error: 1.201433 Iteration 2 Error: 0.145708 Iteration 3 Error: 0.040132 Align patch 5 20 left Iteration 1 Error: 0.838380 Iteration 2 Error: 0.132907 Iteration 3 Error: 0.030244 Align patch 6 19 left Iteration 1 Error: 0.820451 Iteration 2 Error: 0.107581 Iteration 3 Error: 0.033149 Align patch 7 18 left Iteration 1 Error: 0.736850 Iteration 2 Error: 0.161816 Iteration 3 Error: 0.061489 Iteration 4 Error: 0.024306 Align patch 8 17 left Iteration 1 Error: 0.648860 Iteration 2 Error: 0.074289 Iteration 3 Error: 0.022810 Align patch 9 16 left Iteration 1 Error: 0.814759 Iteration 2 Error: 0.151708 Iteration 3 Error: 0.053710 Iteration 4 Error: 0.019715 Align patch 10 15 left Iteration 1 Error: 0.580290 Iteration 2 Error: 0.161744 Iteration 3 Error: 0.031679 Align patch 11 14 left Iteration 1 Error: 1.002417 Iteration 2 Error: 0.190126 Iteration 3 Error: 0.057891 Iteration 4 Error: 0.018740 Align patch 12 13 left Iteration 1 Error: 0.724790 Iteration 2 Error: 0.120885 Iteration 3 Error: 0.028487 Align patch 13 12 left Iteration 1 Error: 0.675697 Iteration 2 Error: 0.117794 Iteration 3 Error: 0.032896 Align patch 14 11 left Iteration 1 Error: 0.863427 Iteration 2 Error: 0.157099 Iteration 3 Error: 0.050186 Iteration 4 Error: 0.010092 Align patch 15 10 left Iteration 1 Error: 0.444467 Iteration 2 Error: 0.077152 Iteration 3 Error: 0.015903 Align patch 16 9 left Iteration 1 Error: 0.882198 Iteration 2 Error: 0.236592 Iteration 3 Error: 0.037177 Align patch 17 8 left Iteration 1 Error: 1.219614 Iteration 2 Error: 0.136728 Iteration 3 Error: 0.048780 Align patch 18 7 left Iteration 1 Error: 0.730287 Iteration 2 Error: 0.153244 Iteration 3 Error: 0.024856 Align patch 19 6 left Iteration 1 Error: 0.670719 Iteration 2 Error: 0.087433 Iteration 3 Error: 0.038029 Align patch 20 5 left Iteration 1 Error: 0.804515 Iteration 2 Error: 0.112991 Iteration 3 Error: 0.035653 Align patch 21 4 left Iteration 1 Error: 1.519770 Iteration 2 Error: 0.221026 Iteration 3 Error: 0.050983 Iteration 4 Error: 0.027366 Align patch 22 3 left Iteration 1 Error: 1.807955 Iteration 2 Error: 0.353519 Iteration 3 Error: 0.057608 Iteration 4 Error: 0.023512 Align patch 23 2 left Iteration 1 Error: 0.829791 Iteration 2 Error: 0.144794 Iteration 3 Error: 0.032310 Align patch 24 1 left Iteration 1 Error: 0.547169 Iteration 2 Error: 0.068687 Iteration 3 Error: 0.023461 Align patch 25 0 left Iteration 1 Error: 0.780340 Iteration 2 Error: 0.171416 Iteration 3 Error: 0.039247 3D Fitting completed. Patch alignment time: 11.99(sec) Local motion has been corrected. Process thread exits. Computational time: 24.210716 sec Total time: 33.410164 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00002hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00002hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.699148s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00002hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.605408s ........................................ >>>>>>TIME<<<<<< FFT: 0.975421s Defocus_U Defocus_V Angle CCC 9976.56 10828.12 5.21 0.042439 Final Values Defocus_U Defocus_V Angle CCC 9971.85 10851.59 5.21 0.079853 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00002hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00002hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 45.61 7.61 Num Hot pixels: 159 Hot pixel threshold: 91.26 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.761782 Iteration 2 Error: 0.046665 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.30 -0.05 ...... Frame ( 3) shift: -0.60 -0.09 ...... Frame ( 4) shift: -0.90 -0.14 ...... Frame ( 5) shift: -1.20 -0.19 ...... Frame ( 6) shift: -1.37 -0.19 ...... Frame ( 7) shift: -1.40 -0.15 ...... Frame ( 8) shift: -1.43 -0.10 ...... Frame ( 9) shift: -1.42 -0.10 ...... Frame ( 10) shift: -1.38 -0.15 ...... Frame ( 11) shift: -1.34 -0.20 ...... Frame ( 12) shift: -1.32 -0.24 ...... Frame ( 13) shift: -1.34 -0.28 ...... Frame ( 14) shift: -1.35 -0.32 ...... Frame ( 15) shift: -1.35 -0.32 ...... Frame ( 16) shift: -1.33 -0.29 ...... Frame ( 17) shift: -1.31 -0.25 ...... Frame ( 18) shift: -1.27 -0.26 ...... Frame ( 19) shift: -1.20 -0.29 ...... Frame ( 20) shift: -1.14 -0.33 ...... Frame ( 21) shift: -1.12 -0.33 ...... Frame ( 22) shift: -1.15 -0.29 ...... Frame ( 23) shift: -1.18 -0.25 ...... Frame ( 24) shift: -1.19 -0.22 ...... Frame ( 25) shift: -1.17 -0.19 ...... Frame ( 26) shift: -1.15 -0.16 ...... Frame ( 27) shift: -1.15 -0.12 ...... Frame ( 28) shift: -1.16 -0.06 ...... Frame ( 29) shift: -1.18 0.01 ...... Frame ( 30) shift: -1.17 0.05 ...... Frame ( 31) shift: -1.13 0.07 ...... Frame ( 32) shift: -1.10 0.10 ...... Frame ( 33) shift: -1.09 0.08 ...... Frame ( 34) shift: -1.09 0.03 ...... Frame ( 35) shift: -1.09 -0.02 ...... Frame ( 36) shift: -1.07 -0.03 ...... Frame ( 37) shift: -1.03 0.02 ...... Frame ( 38) shift: -0.99 0.06 ...... Frame ( 39) shift: -0.94 0.10 ...... Frame ( 40) shift: -0.90 0.14 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.723126 Iteration 2 Error: 0.131262 Iteration 3 Error: 0.032319 Align patch 2 23 left Iteration 1 Error: 0.984013 Iteration 2 Error: 0.149115 Iteration 3 Error: 0.037899 Align patch 3 22 left Iteration 1 Error: 0.732596 Iteration 2 Error: 0.131825 Iteration 3 Error: 0.027141 Align patch 4 21 left Iteration 1 Error: 0.855125 Iteration 2 Error: 0.125523 Iteration 3 Error: 0.038508 Align patch 5 20 left Iteration 1 Error: 0.873040 Iteration 2 Error: 0.127651 Iteration 3 Error: 0.047580 Align patch 6 19 left Iteration 1 Error: 0.972160 Iteration 2 Error: 0.181148 Iteration 3 Error: 0.045131 Align patch 7 18 left Iteration 1 Error: 0.847567 Iteration 2 Error: 0.099113 Iteration 3 Error: 0.030304 Align patch 8 17 left Iteration 1 Error: 0.698523 Iteration 2 Error: 0.143469 Iteration 3 Error: 0.041890 Align patch 9 16 left Iteration 1 Error: 0.536259 Iteration 2 Error: 0.131881 Iteration 3 Error: 0.029127 Align patch 10 15 left Iteration 1 Error: 0.880236 Iteration 2 Error: 0.165865 Iteration 3 Error: 0.054433 Iteration 4 Error: 0.018567 Align patch 11 14 left Iteration 1 Error: 1.171499 Iteration 2 Error: 0.203982 Iteration 3 Error: 0.037524 Align patch 12 13 left Iteration 1 Error: 0.846272 Iteration 2 Error: 0.178731 Iteration 3 Error: 0.057249 Iteration 4 Error: 0.020929 Align patch 13 12 left Iteration 1 Error: 0.926562 Iteration 2 Error: 0.129666 Iteration 3 Error: 0.025096 Align patch 14 11 left Iteration 1 Error: 0.958275 Iteration 2 Error: 0.136808 Iteration 3 Error: 0.034448 Align patch 15 10 left Iteration 1 Error: 0.891159 Iteration 2 Error: 0.166717 Iteration 3 Error: 0.020504 Align patch 16 9 left Iteration 1 Error: 1.196226 Iteration 2 Error: 0.155925 Iteration 3 Error: 0.045681 Align patch 17 8 left Iteration 1 Error: 0.829269 Iteration 2 Error: 0.103637 Iteration 3 Error: 0.027644 Align patch 18 7 left Iteration 1 Error: 0.619217 Iteration 2 Error: 0.121153 Iteration 3 Error: 0.028431 Align patch 19 6 left Iteration 1 Error: 0.703858 Iteration 2 Error: 0.099171 Iteration 3 Error: 0.025861 Align patch 20 5 left Iteration 1 Error: 0.651405 Iteration 2 Error: 0.153412 Iteration 3 Error: 0.034356 Align patch 21 4 left Iteration 1 Error: 1.024615 Iteration 2 Error: 0.183453 Iteration 3 Error: 0.036320 Align patch 22 3 left Iteration 1 Error: 2.078606 Iteration 2 Error: 0.160322 Iteration 3 Error: 0.041763 Align patch 23 2 left Iteration 1 Error: 1.260384 Iteration 2 Error: 0.198480 Iteration 3 Error: 0.036740 Align patch 24 1 left Iteration 1 Error: 0.901637 Iteration 2 Error: 0.141386 Iteration 3 Error: 0.037826 Align patch 25 0 left Iteration 1 Error: 1.123634 Iteration 2 Error: 0.165313 Iteration 3 Error: 0.038244 3D Fitting completed. Patch alignment time: 12.83(sec) Local motion has been corrected. Process thread exits. Computational time: 26.917597 sec Total time: 36.570793 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00002hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00002hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.580386s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00002hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.846024s ........................................ >>>>>>TIME<<<<<< FFT: 1.061067s Defocus_U Defocus_V Angle CCC 12269.60 11609.40 82.89 0.042993 Final Values Defocus_U Defocus_V Angle CCC 12286.79 11617.21 82.27 0.082609 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00003hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00003hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.330e-01 9.906e-02 CC threshold: 0.727 Mean Std: 40.83 7.13 Num Hot pixels: 135 Hot pixel threshold: 83.62 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.754506 Iteration 2 Error: 0.235404 Iteration 3 Error: 0.067426 Iteration 4 Error: 0.021636 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.28 -0.08 ...... Frame ( 3) shift: -0.56 -0.16 ...... Frame ( 4) shift: -0.84 -0.24 ...... Frame ( 5) shift: -1.12 -0.32 ...... Frame ( 6) shift: -1.27 -0.47 ...... Frame ( 7) shift: -1.28 -0.70 ...... Frame ( 8) shift: -1.29 -0.93 ...... Frame ( 9) shift: -1.31 -1.12 ...... Frame ( 10) shift: -1.33 -1.28 ...... Frame ( 11) shift: -1.35 -1.44 ...... Frame ( 12) shift: -1.35 -1.57 ...... Frame ( 13) shift: -1.34 -1.66 ...... Frame ( 14) shift: -1.33 -1.75 ...... Frame ( 15) shift: -1.33 -1.86 ...... Frame ( 16) shift: -1.35 -2.00 ...... Frame ( 17) shift: -1.37 -2.13 ...... Frame ( 18) shift: -1.37 -2.22 ...... Frame ( 19) shift: -1.35 -2.25 ...... Frame ( 20) shift: -1.33 -2.29 ...... Frame ( 21) shift: -1.31 -2.32 ...... Frame ( 22) shift: -1.30 -2.37 ...... Frame ( 23) shift: -1.28 -2.41 ...... Frame ( 24) shift: -1.28 -2.44 ...... Frame ( 25) shift: -1.29 -2.47 ...... Frame ( 26) shift: -1.31 -2.50 ...... Frame ( 27) shift: -1.30 -2.54 ...... Frame ( 28) shift: -1.29 -2.61 ...... Frame ( 29) shift: -1.27 -2.67 ...... Frame ( 30) shift: -1.23 -2.72 ...... Frame ( 31) shift: -1.16 -2.75 ...... Frame ( 32) shift: -1.10 -2.78 ...... Frame ( 33) shift: -1.08 -2.80 ...... Frame ( 34) shift: -1.09 -2.83 ...... Frame ( 35) shift: -1.11 -2.85 ...... Frame ( 36) shift: -1.09 -2.89 ...... Frame ( 37) shift: -1.03 -2.93 ...... Frame ( 38) shift: -0.97 -2.97 ...... Frame ( 39) shift: -0.92 -3.01 ...... Frame ( 40) shift: -0.86 -3.06 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.612584 Iteration 2 Error: 0.143150 Iteration 3 Error: 0.045986 Align patch 2 23 left Iteration 1 Error: 0.589489 Iteration 2 Error: 0.186265 Iteration 3 Error: 0.055107 Iteration 4 Error: 0.020327 Align patch 3 22 left Iteration 1 Error: 1.015970 Iteration 2 Error: 0.208331 Iteration 3 Error: 0.063928 Iteration 4 Error: 0.029049 Align patch 4 21 left Iteration 1 Error: 1.393381 Iteration 2 Error: 0.213903 Iteration 3 Error: 0.073124 Iteration 4 Error: 0.015002 Align patch 5 20 left Iteration 1 Error: 1.457448 Iteration 2 Error: 0.338882 Iteration 3 Error: 0.056675 Iteration 4 Error: 0.016513 Align patch 6 19 left Iteration 1 Error: 1.039621 Iteration 2 Error: 0.255932 Iteration 3 Error: 0.169395 Iteration 4 Error: 0.054733 Iteration 5 Error: 0.034163 Align patch 7 18 left Iteration 1 Error: 0.527374 Iteration 2 Error: 0.145113 Iteration 3 Error: 0.038675 Align patch 8 17 left Iteration 1 Error: 0.564349 Iteration 2 Error: 0.093315 Iteration 3 Error: 0.033480 Align patch 9 16 left Iteration 1 Error: 0.581451 Iteration 2 Error: 0.093539 Iteration 3 Error: 0.025841 Align patch 10 15 left Iteration 1 Error: 1.500954 Iteration 2 Error: 0.224379 Iteration 3 Error: 0.052329 Iteration 4 Error: 0.014907 Align patch 11 14 left Iteration 1 Error: 1.867680 Iteration 2 Error: 0.563065 Iteration 3 Error: 0.164027 Iteration 4 Error: 0.083098 Iteration 5 Error: 0.025867 Align patch 12 13 left Iteration 1 Error: 1.762616 Iteration 2 Error: 0.294646 Iteration 3 Error: 0.118558 Iteration 4 Error: 0.028864 Align patch 13 12 left Iteration 1 Error: 0.897442 Iteration 2 Error: 0.268767 Iteration 3 Error: 0.109708 Iteration 4 Error: 0.050979 Iteration 5 Error: 0.018481 Align patch 14 11 left Iteration 1 Error: 0.664437 Iteration 2 Error: 0.099114 Iteration 3 Error: 0.042348 Align patch 15 10 left Iteration 1 Error: 0.818811 Iteration 2 Error: 0.201189 Iteration 3 Error: 0.055633 Iteration 4 Error: 0.019960 Align patch 16 9 left Iteration 1 Error: 1.777741 Iteration 2 Error: 0.381070 Iteration 3 Error: 0.230369 Iteration 4 Error: 0.097790 Iteration 5 Error: 0.056045 Align patch 16 9 left Iteration 1 Error: 1.525139 Iteration 2 Error: 0.289361 Iteration 3 Error: 0.088571 Iteration 4 Error: 0.025942 Align patch 17 8 left Iteration 1 Error: 2.093028 Iteration 2 Error: 0.457334 Iteration 3 Error: 0.118390 Iteration 4 Error: 0.061083 Iteration 5 Error: 0.027810 Align patch 18 7 left Iteration 1 Error: 1.689135 Iteration 2 Error: 0.259731 Iteration 3 Error: 0.083001 Iteration 4 Error: 0.033093 Align patch 19 6 left Iteration 1 Error: 1.239577 Iteration 2 Error: 0.246430 Iteration 3 Error: 0.059785 Iteration 4 Error: 0.019360 Align patch 20 5 left Iteration 1 Error: 0.802352 Iteration 2 Error: 0.248703 Iteration 3 Error: 0.064273 Iteration 4 Error: 0.022850 Align patch 21 4 left Iteration 1 Error: 1.362908 Iteration 2 Error: 0.359253 Iteration 3 Error: 0.128156 Iteration 4 Error: 0.060405 Iteration 5 Error: 0.039018 Align patch 22 3 left Iteration 1 Error: 1.591088 Iteration 2 Error: 0.561023 Iteration 3 Error: 0.238118 Iteration 4 Error: 0.118736 Iteration 5 Error: 0.062061 Align patch 22 3 left Iteration 1 Error: 1.921700 Iteration 2 Error: 0.560990 Iteration 3 Error: 0.185407 Iteration 4 Error: 0.092813 Iteration 5 Error: 0.038889 Align patch 23 2 left Iteration 1 Error: 0.748352 Iteration 2 Error: 0.187953 Iteration 3 Error: 0.082863 Iteration 4 Error: 0.050982 Iteration 5 Error: 0.029450 Align patch 24 1 left Iteration 1 Error: 1.717901 Iteration 2 Error: 0.215569 Iteration 3 Error: 0.049331 Align patch 25 0 left Iteration 1 Error: 2.031683 Iteration 2 Error: 0.212886 Iteration 3 Error: 0.055993 Iteration 4 Error: 0.014455 3D Fitting completed. Patch alignment time: 15.05(sec) Local motion has been corrected. Process thread exits. Computational time: 29.243105 sec Total time: 36.324905 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00003hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00003hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.614056s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00003hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.394619s ........................................ >>>>>>TIME<<<<<< FFT: 1.085342s Defocus_U Defocus_V Angle CCC 11275.44 12134.81 11.76 0.008246 Final Values Defocus_U Defocus_V Angle CCC 11281.69 12141.06 10.83 -0.048000 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00003hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00003hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 1.000e-01 CC threshold: 0.735 Mean Std: 42.05 7.38 Num Hot pixels: 137 Hot pixel threshold: 86.30 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.590635 Iteration 2 Error: 0.070874 Iteration 3 Error: 0.013682 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.26 -0.00 ...... Frame ( 3) shift: -0.51 -0.01 ...... Frame ( 4) shift: -0.77 -0.01 ...... Frame ( 5) shift: -1.03 -0.02 ...... Frame ( 6) shift: -1.18 -0.07 ...... Frame ( 7) shift: -1.23 -0.19 ...... Frame ( 8) shift: -1.27 -0.30 ...... Frame ( 9) shift: -1.28 -0.36 ...... Frame ( 10) shift: -1.25 -0.38 ...... Frame ( 11) shift: -1.22 -0.39 ...... Frame ( 12) shift: -1.18 -0.41 ...... Frame ( 13) shift: -1.15 -0.43 ...... Frame ( 14) shift: -1.11 -0.45 ...... Frame ( 15) shift: -1.10 -0.45 ...... Frame ( 16) shift: -1.12 -0.44 ...... Frame ( 17) shift: -1.14 -0.43 ...... Frame ( 18) shift: -1.10 -0.45 ...... Frame ( 19) shift: -1.01 -0.50 ...... Frame ( 20) shift: -0.92 -0.55 ...... Frame ( 21) shift: -0.84 -0.57 ...... Frame ( 22) shift: -0.78 -0.56 ...... Frame ( 23) shift: -0.72 -0.55 ...... Frame ( 24) shift: -0.68 -0.56 ...... Frame ( 25) shift: -0.65 -0.57 ...... Frame ( 26) shift: -0.63 -0.59 ...... Frame ( 27) shift: -0.59 -0.59 ...... Frame ( 28) shift: -0.54 -0.57 ...... Frame ( 29) shift: -0.49 -0.55 ...... Frame ( 30) shift: -0.45 -0.54 ...... Frame ( 31) shift: -0.42 -0.53 ...... Frame ( 32) shift: -0.39 -0.52 ...... Frame ( 33) shift: -0.37 -0.52 ...... Frame ( 34) shift: -0.36 -0.53 ...... Frame ( 35) shift: -0.34 -0.54 ...... Frame ( 36) shift: -0.32 -0.55 ...... Frame ( 37) shift: -0.30 -0.55 ...... Frame ( 38) shift: -0.28 -0.55 ...... Frame ( 39) shift: -0.26 -0.54 ...... Frame ( 40) shift: -0.23 -0.54 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.739567 Iteration 2 Error: 0.093206 Iteration 3 Error: 0.020856 Align patch 2 23 left Iteration 1 Error: 0.927786 Iteration 2 Error: 0.111415 Iteration 3 Error: 0.035442 Align patch 3 22 left Iteration 1 Error: 0.803554 Iteration 2 Error: 0.147578 Iteration 3 Error: 0.037728 Align patch 4 21 left Iteration 1 Error: 0.729955 Iteration 2 Error: 0.097401 Iteration 3 Error: 0.026012 Align patch 5 20 left Iteration 1 Error: 1.668586 Iteration 2 Error: 0.256463 Iteration 3 Error: 0.056528 Iteration 4 Error: 0.014623 Align patch 6 19 left Iteration 1 Error: 0.730853 Iteration 2 Error: 0.247822 Iteration 3 Error: 0.062607 Iteration 4 Error: 0.024457 Align patch 7 18 left Iteration 1 Error: 0.725585 Iteration 2 Error: 0.100960 Iteration 3 Error: 0.024856 Align patch 8 17 left Iteration 1 Error: 0.627832 Iteration 2 Error: 0.084170 Iteration 3 Error: 0.017474 Align patch 9 16 left Iteration 1 Error: 0.875318 Iteration 2 Error: 0.190098 Iteration 3 Error: 0.040816 Align patch 10 15 left Iteration 1 Error: 0.968763 Iteration 2 Error: 0.128178 Iteration 3 Error: 0.011918 Align patch 11 14 left Iteration 1 Error: 1.507557 Iteration 2 Error: 0.222277 Iteration 3 Error: 0.103708 Iteration 4 Error: 0.030075 Align patch 12 13 left Iteration 1 Error: 1.107706 Iteration 2 Error: 0.290856 Iteration 3 Error: 0.064993 Iteration 4 Error: 0.026582 Align patch 13 12 left Iteration 1 Error: 1.355052 Iteration 2 Error: 0.295152 Iteration 3 Error: 0.075302 Iteration 4 Error: 0.039758 Align patch 14 11 left Iteration 1 Error: 0.949894 Iteration 2 Error: 0.114181 Iteration 3 Error: 0.018565 Align patch 15 10 left Iteration 1 Error: 0.817448 Iteration 2 Error: 0.192432 Iteration 3 Error: 0.042132 Align patch 16 9 left Iteration 1 Error: 1.908688 Iteration 2 Error: 0.270070 Iteration 3 Error: 0.077578 Iteration 4 Error: 0.029206 Align patch 17 8 left Iteration 1 Error: 1.829528 Iteration 2 Error: 0.244538 Iteration 3 Error: 0.051451 Iteration 4 Error: 0.022091 Align patch 18 7 left Iteration 1 Error: 1.018789 Iteration 2 Error: 0.125922 Iteration 3 Error: 0.023640 Align patch 19 6 left Iteration 1 Error: 1.322296 Iteration 2 Error: 0.239543 Iteration 3 Error: 0.103934 Iteration 4 Error: 0.040275 Align patch 20 5 left Iteration 1 Error: 0.680207 Iteration 2 Error: 0.122589 Iteration 3 Error: 0.026238 Align patch 21 4 left Iteration 1 Error: 1.640333 Iteration 2 Error: 0.281253 Iteration 3 Error: 0.072829 Iteration 4 Error: 0.034334 Align patch 22 3 left Iteration 1 Error: 0.606806 Iteration 2 Error: 0.106952 Iteration 3 Error: 0.019355 Align patch 23 2 left Iteration 1 Error: 1.283468 Iteration 2 Error: 0.212222 Iteration 3 Error: 0.030547 Align patch 24 1 left Iteration 1 Error: 0.721866 Iteration 2 Error: 0.052815 Iteration 3 Error: 0.010693 Align patch 25 0 left Iteration 1 Error: 0.734047 Iteration 2 Error: 0.089918 Iteration 3 Error: 0.020486 3D Fitting completed. Patch alignment time: 13.17(sec) Local motion has been corrected. Process thread exits. Computational time: 24.142647 sec Total time: 33.576088 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00003hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00003hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.606895s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00003hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.566129s ........................................ >>>>>>TIME<<<<<< FFT: 0.895497s Defocus_U Defocus_V Angle CCC 12058.71 11531.21 87.05 0.038423 Final Values Defocus_U Defocus_V Angle CCC 12060.29 11551.55 87.05 0.068029 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00003hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00003hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.998e-02 CC threshold: 0.734 Mean Std: 43.27 7.32 Num Hot pixels: 157 Hot pixel threshold: 87.17 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.705327 Iteration 2 Error: 0.084205 Iteration 3 Error: 0.025681 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.39 -0.22 ...... Frame ( 3) shift: -0.77 -0.44 ...... Frame ( 4) shift: -1.16 -0.65 ...... Frame ( 5) shift: -1.55 -0.87 ...... Frame ( 6) shift: -1.71 -0.96 ...... Frame ( 7) shift: -1.66 -0.92 ...... Frame ( 8) shift: -1.60 -0.87 ...... Frame ( 9) shift: -1.54 -0.87 ...... Frame ( 10) shift: -1.45 -0.90 ...... Frame ( 11) shift: -1.37 -0.93 ...... Frame ( 12) shift: -1.30 -0.92 ...... Frame ( 13) shift: -1.23 -0.87 ...... Frame ( 14) shift: -1.17 -0.82 ...... Frame ( 15) shift: -1.12 -0.76 ...... Frame ( 16) shift: -1.08 -0.68 ...... Frame ( 17) shift: -1.05 -0.61 ...... Frame ( 18) shift: -1.04 -0.53 ...... Frame ( 19) shift: -1.07 -0.45 ...... Frame ( 20) shift: -1.09 -0.37 ...... Frame ( 21) shift: -1.11 -0.36 ...... Frame ( 22) shift: -1.13 -0.43 ...... Frame ( 23) shift: -1.14 -0.50 ...... Frame ( 24) shift: -1.13 -0.50 ...... Frame ( 25) shift: -1.07 -0.44 ...... Frame ( 26) shift: -1.02 -0.38 ...... Frame ( 27) shift: -1.02 -0.32 ...... Frame ( 28) shift: -1.07 -0.28 ...... Frame ( 29) shift: -1.11 -0.23 ...... Frame ( 30) shift: -1.15 -0.20 ...... Frame ( 31) shift: -1.17 -0.20 ...... Frame ( 32) shift: -1.20 -0.20 ...... Frame ( 33) shift: -1.25 -0.19 ...... Frame ( 34) shift: -1.32 -0.17 ...... Frame ( 35) shift: -1.39 -0.15 ...... Frame ( 36) shift: -1.41 -0.12 ...... Frame ( 37) shift: -1.38 -0.06 ...... Frame ( 38) shift: -1.35 -0.01 ...... Frame ( 39) shift: -1.32 0.05 ...... Frame ( 40) shift: -1.29 0.10 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.335728 Iteration 2 Error: 0.242653 Iteration 3 Error: 0.070028 Iteration 4 Error: 0.015993 Align patch 2 23 left Iteration 1 Error: 1.602034 Iteration 2 Error: 0.216200 Iteration 3 Error: 0.052531 Iteration 4 Error: 0.020536 Align patch 3 22 left Iteration 1 Error: 1.077984 Iteration 2 Error: 0.316265 Iteration 3 Error: 0.098410 Iteration 4 Error: 0.047563 Align patch 4 21 left Iteration 1 Error: 1.242259 Iteration 2 Error: 0.278578 Iteration 3 Error: 0.062940 Iteration 4 Error: 0.021456 Align patch 5 20 left Iteration 1 Error: 1.858841 Iteration 2 Error: 0.490435 Iteration 3 Error: 0.159119 Iteration 4 Error: 0.069466 Iteration 5 Error: 0.032740 Align patch 6 19 left Iteration 1 Error: 1.120190 Iteration 2 Error: 0.178002 Iteration 3 Error: 0.036648 Align patch 7 18 left Iteration 1 Error: 1.376283 Iteration 2 Error: 0.204080 Iteration 3 Error: 0.037133 Align patch 8 17 left Iteration 1 Error: 1.350978 Iteration 2 Error: 0.244183 Iteration 3 Error: 0.069682 Iteration 4 Error: 0.021820 Align patch 9 16 left Iteration 1 Error: 0.844477 Iteration 2 Error: 0.174906 Iteration 3 Error: 0.053706 Iteration 4 Error: 0.019090 Align patch 10 15 left Iteration 1 Error: 2.463059 Iteration 2 Error: 1.054968 Iteration 3 Error: 0.459088 Iteration 4 Error: 0.285868 Iteration 5 Error: 0.177552 Align patch 10 15 left Iteration 1 Error: 1.865330 Iteration 2 Error: 0.341841 Iteration 3 Error: 0.057756 Iteration 4 Error: 0.016232 Align patch 11 14 left Iteration 1 Error: 0.833826 Iteration 2 Error: 0.169930 Iteration 3 Error: 0.033176 Align patch 12 13 left Iteration 1 Error: 0.705108 Iteration 2 Error: 0.102227 Iteration 3 Error: 0.035349 Align patch 13 12 left Iteration 1 Error: 0.970458 Iteration 2 Error: 0.205747 Iteration 3 Error: 0.070571 Iteration 4 Error: 0.019264 Align patch 14 11 left Iteration 1 Error: 1.210068 Iteration 2 Error: 0.235538 Iteration 3 Error: 0.043188 Align patch 15 10 left Iteration 1 Error: 0.810963 Iteration 2 Error: 0.236173 Iteration 3 Error: 0.064359 Iteration 4 Error: 0.018371 Align patch 16 9 left Iteration 1 Error: 1.371269 Iteration 2 Error: 0.241955 Iteration 3 Error: 0.079204 Iteration 4 Error: 0.024591 Align patch 17 8 left Iteration 1 Error: 1.118605 Iteration 2 Error: 0.156551 Iteration 3 Error: 0.039278 Align patch 18 7 left Iteration 1 Error: 0.773446 Iteration 2 Error: 0.161888 Iteration 3 Error: 0.038337 Align patch 19 6 left Iteration 1 Error: 0.967840 Iteration 2 Error: 0.141462 Iteration 3 Error: 0.035865 Align patch 20 5 left Iteration 1 Error: 1.003673 Iteration 2 Error: 0.109372 Iteration 3 Error: 0.020134 Align patch 21 4 left Iteration 1 Error: 0.941292 Iteration 2 Error: 0.197659 Iteration 3 Error: 0.059308 Iteration 4 Error: 0.017356 Align patch 22 3 left Iteration 1 Error: 1.318805 Iteration 2 Error: 0.280021 Iteration 3 Error: 0.048379 Align patch 23 2 left Iteration 1 Error: 1.007107 Iteration 2 Error: 0.173740 Iteration 3 Error: 0.040198 Align patch 24 1 left Iteration 1 Error: 0.866300 Iteration 2 Error: 0.201584 Iteration 3 Error: 0.043223 Align patch 25 0 left Iteration 1 Error: 1.124382 Iteration 2 Error: 0.181656 Iteration 3 Error: 0.046628 3D Fitting completed. Patch alignment time: 12.66(sec) Local motion has been corrected. Process thread exits. Computational time: 24.633888 sec Total time: 31.189631 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00003hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00003hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.435371s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00003hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.379379s ........................................ >>>>>>TIME<<<<<< FFT: 1.101151s Defocus_U Defocus_V Angle CCC 14835.94 15699.22 2.50 0.042231 Final Values Defocus_U Defocus_V Angle CCC 14835.94 15714.89 2.19 0.071197 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00003hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00003hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 45.67 7.64 Num Hot pixels: 170 Hot pixel threshold: 91.53 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.936238 Iteration 2 Error: 0.107017 Iteration 3 Error: 0.029010 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.42 0.10 ...... Frame ( 3) shift: -0.85 0.20 ...... Frame ( 4) shift: -1.27 0.30 ...... Frame ( 5) shift: -1.70 0.40 ...... Frame ( 6) shift: -1.91 0.46 ...... Frame ( 7) shift: -1.92 0.47 ...... Frame ( 8) shift: -1.93 0.49 ...... Frame ( 9) shift: -1.87 0.53 ...... Frame ( 10) shift: -1.75 0.61 ...... Frame ( 11) shift: -1.62 0.69 ...... Frame ( 12) shift: -1.55 0.73 ...... Frame ( 13) shift: -1.53 0.74 ...... Frame ( 14) shift: -1.51 0.74 ...... Frame ( 15) shift: -1.47 0.75 ...... Frame ( 16) shift: -1.42 0.76 ...... Frame ( 17) shift: -1.36 0.76 ...... Frame ( 18) shift: -1.32 0.77 ...... Frame ( 19) shift: -1.30 0.78 ...... Frame ( 20) shift: -1.27 0.80 ...... Frame ( 21) shift: -1.26 0.83 ...... Frame ( 22) shift: -1.27 0.89 ...... Frame ( 23) shift: -1.27 0.95 ...... Frame ( 24) shift: -1.25 0.99 ...... Frame ( 25) shift: -1.20 1.01 ...... Frame ( 26) shift: -1.15 1.04 ...... Frame ( 27) shift: -1.10 1.07 ...... Frame ( 28) shift: -1.06 1.11 ...... Frame ( 29) shift: -1.02 1.15 ...... Frame ( 30) shift: -1.00 1.15 ...... Frame ( 31) shift: -1.01 1.10 ...... Frame ( 32) shift: -1.01 1.06 ...... Frame ( 33) shift: -1.01 1.06 ...... Frame ( 34) shift: -0.99 1.11 ...... Frame ( 35) shift: -0.97 1.15 ...... Frame ( 36) shift: -0.96 1.18 ...... Frame ( 37) shift: -0.95 1.20 ...... Frame ( 38) shift: -0.95 1.21 ...... Frame ( 39) shift: -0.94 1.23 ...... Frame ( 40) shift: -0.94 1.25 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.380714 Iteration 2 Error: 0.238685 Iteration 3 Error: 0.088292 Iteration 4 Error: 0.030527 Align patch 2 23 left Iteration 1 Error: 0.817286 Iteration 2 Error: 0.178312 Iteration 3 Error: 0.050267 Iteration 4 Error: 0.029671 Align patch 3 22 left Iteration 1 Error: 0.820162 Iteration 2 Error: 0.167820 Iteration 3 Error: 0.069219 Iteration 4 Error: 0.022370 Align patch 4 21 left Iteration 1 Error: 0.751149 Iteration 2 Error: 0.132516 Iteration 3 Error: 0.035279 Align patch 5 20 left Iteration 1 Error: 0.572453 Iteration 2 Error: 0.097666 Iteration 3 Error: 0.032356 Align patch 6 19 left Iteration 1 Error: 1.255549 Iteration 2 Error: 0.167208 Iteration 3 Error: 0.060838 Iteration 4 Error: 0.016883 Align patch 7 18 left Iteration 1 Error: 0.892767 Iteration 2 Error: 0.159993 Iteration 3 Error: 0.035960 Align patch 8 17 left Iteration 1 Error: 0.956942 Iteration 2 Error: 0.144966 Iteration 3 Error: 0.042392 Align patch 9 16 left Iteration 1 Error: 0.560356 Iteration 2 Error: 0.115472 Iteration 3 Error: 0.050531 Iteration 4 Error: 0.011463 Align patch 10 15 left Iteration 1 Error: 0.630977 Iteration 2 Error: 0.081548 Iteration 3 Error: 0.023173 Align patch 11 14 left Iteration 1 Error: 0.719697 Iteration 2 Error: 0.126752 Iteration 3 Error: 0.020136 Align patch 12 13 left Iteration 1 Error: 1.021926 Iteration 2 Error: 0.121381 Iteration 3 Error: 0.022031 Align patch 13 12 left Iteration 1 Error: 0.776916 Iteration 2 Error: 0.174680 Iteration 3 Error: 0.078638 Iteration 4 Error: 0.021738 Align patch 14 11 left Iteration 1 Error: 0.557810 Iteration 2 Error: 0.066619 Iteration 3 Error: 0.023620 Align patch 15 10 left Iteration 1 Error: 0.593892 Iteration 2 Error: 0.074881 Iteration 3 Error: 0.016758 Align patch 16 9 left Iteration 1 Error: 1.022175 Iteration 2 Error: 0.197353 Iteration 3 Error: 0.045361 Align patch 17 8 left Iteration 1 Error: 0.812738 Iteration 2 Error: 0.232742 Iteration 3 Error: 0.065681 Iteration 4 Error: 0.032488 Align patch 18 7 left Iteration 1 Error: 1.020824 Iteration 2 Error: 0.171987 Iteration 3 Error: 0.043385 Align patch 19 6 left Iteration 1 Error: 0.685643 Iteration 2 Error: 0.099529 Iteration 3 Error: 0.022929 Align patch 20 5 left Iteration 1 Error: 0.701754 Iteration 2 Error: 0.115428 Iteration 3 Error: 0.029682 Align patch 21 4 left Iteration 1 Error: 0.986037 Iteration 2 Error: 0.138851 Iteration 3 Error: 0.046840 Align patch 22 3 left Iteration 1 Error: 0.907979 Iteration 2 Error: 0.175104 Iteration 3 Error: 0.035913 Align patch 23 2 left Iteration 1 Error: 0.942032 Iteration 2 Error: 0.110661 Iteration 3 Error: 0.022732 Align patch 24 1 left Iteration 1 Error: 0.823202 Iteration 2 Error: 0.114306 Iteration 3 Error: 0.017584 Align patch 25 0 left Iteration 1 Error: 0.632130 Iteration 2 Error: 0.103210 Iteration 3 Error: 0.020184 3D Fitting completed. Patch alignment time: 12.48(sec) Local motion has been corrected. Process thread exits. Computational time: 22.034037 sec Total time: 29.138601 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00003hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00003hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.618192s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00003hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.534249s ........................................ >>>>>>TIME<<<<<< FFT: 0.912762s Defocus_U Defocus_V Angle CCC 10582.07 9882.85 84.68 0.046032 Final Values Defocus_U Defocus_V Angle CCC 10588.32 9885.98 84.68 0.087510 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00004hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00004hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.990e-02 CC threshold: 0.734 Mean Std: 39.84 6.84 Num Hot pixels: 165 Hot pixel threshold: 80.89 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.388592 Iteration 2 Error: 0.279180 Iteration 3 Error: 0.078387 Iteration 4 Error: 0.033012 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.29 -0.22 ...... Frame ( 3) shift: -0.58 -0.43 ...... Frame ( 4) shift: -0.87 -0.65 ...... Frame ( 5) shift: -1.16 -0.87 ...... Frame ( 6) shift: -1.31 -1.03 ...... Frame ( 7) shift: -1.30 -1.13 ...... Frame ( 8) shift: -1.30 -1.23 ...... Frame ( 9) shift: -1.23 -1.26 ...... Frame ( 10) shift: -1.12 -1.24 ...... Frame ( 11) shift: -1.00 -1.22 ...... Frame ( 12) shift: -0.93 -1.17 ...... Frame ( 13) shift: -0.91 -1.10 ...... Frame ( 14) shift: -0.88 -1.03 ...... Frame ( 15) shift: -0.84 -0.93 ...... Frame ( 16) shift: -0.79 -0.79 ...... Frame ( 17) shift: -0.73 -0.65 ...... Frame ( 18) shift: -0.67 -0.56 ...... Frame ( 19) shift: -0.60 -0.52 ...... Frame ( 20) shift: -0.53 -0.48 ...... Frame ( 21) shift: -0.42 -0.46 ...... Frame ( 22) shift: -0.28 -0.46 ...... Frame ( 23) shift: -0.13 -0.47 ...... Frame ( 24) shift: -0.02 -0.45 ...... Frame ( 25) shift: 0.07 -0.43 ...... Frame ( 26) shift: 0.15 -0.40 ...... Frame ( 27) shift: 0.21 -0.35 ...... Frame ( 28) shift: 0.25 -0.26 ...... Frame ( 29) shift: 0.29 -0.18 ...... Frame ( 30) shift: 0.35 -0.13 ...... Frame ( 31) shift: 0.45 -0.10 ...... Frame ( 32) shift: 0.54 -0.08 ...... Frame ( 33) shift: 0.60 -0.03 ...... Frame ( 34) shift: 0.62 0.05 ...... Frame ( 35) shift: 0.64 0.12 ...... Frame ( 36) shift: 0.70 0.20 ...... Frame ( 37) shift: 0.82 0.28 ...... Frame ( 38) shift: 0.94 0.35 ...... Frame ( 39) shift: 1.05 0.43 ...... Frame ( 40) shift: 1.17 0.51 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.876892 Iteration 2 Error: 0.274461 Iteration 3 Error: 0.086947 Iteration 4 Error: 0.028401 Align patch 2 23 left Iteration 1 Error: 0.797271 Iteration 2 Error: 0.237568 Iteration 3 Error: 0.080342 Iteration 4 Error: 0.023184 Align patch 3 22 left Iteration 1 Error: 1.556299 Iteration 2 Error: 0.190832 Iteration 3 Error: 0.081594 Iteration 4 Error: 0.019737 Align patch 4 21 left Iteration 1 Error: 0.912050 Iteration 2 Error: 0.209687 Iteration 3 Error: 0.052227 Iteration 4 Error: 0.014395 Align patch 5 20 left Iteration 1 Error: 0.899659 Iteration 2 Error: 0.140757 Iteration 3 Error: 0.040759 Align patch 6 19 left Iteration 1 Error: 1.345042 Iteration 2 Error: 0.260348 Iteration 3 Error: 0.155028 Iteration 4 Error: 0.054087 Iteration 5 Error: 0.023313 Align patch 7 18 left Iteration 1 Error: 1.161434 Iteration 2 Error: 0.294975 Iteration 3 Error: 0.144975 Iteration 4 Error: 0.045684 Align patch 8 17 left Iteration 1 Error: 0.917902 Iteration 2 Error: 0.152343 Iteration 3 Error: 0.052662 Iteration 4 Error: 0.028266 Align patch 9 16 left Iteration 1 Error: 0.924380 Iteration 2 Error: 0.191309 Iteration 3 Error: 0.080660 Iteration 4 Error: 0.025413 Align patch 10 15 left Iteration 1 Error: 0.869182 Iteration 2 Error: 0.154389 Iteration 3 Error: 0.045801 Align patch 11 14 left Iteration 1 Error: 1.397557 Iteration 2 Error: 0.327553 Iteration 3 Error: 0.126403 Iteration 4 Error: 0.054085 Iteration 5 Error: 0.027104 Align patch 12 13 left Iteration 1 Error: 0.718240 Iteration 2 Error: 0.238964 Iteration 3 Error: 0.074803 Iteration 4 Error: 0.033982 Align patch 13 12 left Iteration 1 Error: 0.800669 Iteration 2 Error: 0.199902 Iteration 3 Error: 0.074219 Iteration 4 Error: 0.034495 Align patch 14 11 left Iteration 1 Error: 0.606132 Iteration 2 Error: 0.131266 Iteration 3 Error: 0.024238 Align patch 15 10 left Iteration 1 Error: 1.065849 Iteration 2 Error: 0.141967 Iteration 3 Error: 0.047434 Align patch 16 9 left Iteration 1 Error: 0.882910 Iteration 2 Error: 0.153852 Iteration 3 Error: 0.042949 Align patch 17 8 left Iteration 1 Error: 0.578207 Iteration 2 Error: 0.135507 Iteration 3 Error: 0.048596 Align patch 18 7 left Iteration 1 Error: 0.977537 Iteration 2 Error: 0.191661 Iteration 3 Error: 0.044911 Align patch 19 6 left Iteration 1 Error: 0.826291 Iteration 2 Error: 0.163752 Iteration 3 Error: 0.041293 Align patch 20 5 left Iteration 1 Error: 1.066066 Iteration 2 Error: 0.195014 Iteration 3 Error: 0.045127 Align patch 21 4 left Iteration 1 Error: 0.990775 Iteration 2 Error: 0.327103 Iteration 3 Error: 0.112549 Iteration 4 Error: 0.053972 Iteration 5 Error: 0.023079 Align patch 22 3 left Iteration 1 Error: 1.261152 Iteration 2 Error: 0.356385 Iteration 3 Error: 0.074471 Iteration 4 Error: 0.022801 Align patch 23 2 left Iteration 1 Error: 0.926179 Iteration 2 Error: 0.152656 Iteration 3 Error: 0.027483 Align patch 24 1 left Iteration 1 Error: 0.824115 Iteration 2 Error: 0.278526 Iteration 3 Error: 0.087088 Iteration 4 Error: 0.032537 Align patch 25 0 left Iteration 1 Error: 0.779279 Iteration 2 Error: 0.195138 Iteration 3 Error: 0.084886 Iteration 4 Error: 0.021771 3D Fitting completed. Patch alignment time: 11.98(sec) Local motion has been corrected. Process thread exits. Computational time: 24.391878 sec Total time: 31.716850 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00004hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00004hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.600393s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00004hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.810679s ........................................ >>>>>>TIME<<<<<< FFT: 1.132050s Defocus_U Defocus_V Angle CCC 12785.15 13324.28 7.50 0.035093 Final Values Defocus_U Defocus_V Angle CCC 12810.17 13349.30 8.44 0.056188 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00004hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00004hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.994e-02 CC threshold: 0.734 Mean Std: 40.64 6.85 Num Hot pixels: 195 Hot pixel threshold: 81.71 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.568489 Iteration 2 Error: 0.379732 Iteration 3 Error: 0.119276 Iteration 4 Error: 0.061153 Iteration 5 Error: 0.024584 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.30 -0.31 ...... Frame ( 3) shift: -0.59 -0.61 ...... Frame ( 4) shift: -0.89 -0.92 ...... Frame ( 5) shift: -1.18 -1.22 ...... Frame ( 6) shift: -1.34 -1.37 ...... Frame ( 7) shift: -1.37 -1.35 ...... Frame ( 8) shift: -1.39 -1.33 ...... Frame ( 9) shift: -1.38 -1.28 ...... Frame ( 10) shift: -1.34 -1.20 ...... Frame ( 11) shift: -1.30 -1.12 ...... Frame ( 12) shift: -1.22 -1.03 ...... Frame ( 13) shift: -1.09 -0.93 ...... Frame ( 14) shift: -0.96 -0.83 ...... Frame ( 15) shift: -0.80 -0.73 ...... Frame ( 16) shift: -0.63 -0.62 ...... Frame ( 17) shift: -0.46 -0.50 ...... Frame ( 18) shift: -0.37 -0.39 ...... Frame ( 19) shift: -0.36 -0.27 ...... Frame ( 20) shift: -0.34 -0.15 ...... Frame ( 21) shift: -0.30 -0.03 ...... Frame ( 22) shift: -0.21 0.08 ...... Frame ( 23) shift: -0.13 0.19 ...... Frame ( 24) shift: -0.09 0.27 ...... Frame ( 25) shift: -0.10 0.32 ...... Frame ( 26) shift: -0.10 0.36 ...... Frame ( 27) shift: -0.05 0.43 ...... Frame ( 28) shift: 0.04 0.51 ...... Frame ( 29) shift: 0.14 0.59 ...... Frame ( 30) shift: 0.22 0.66 ...... Frame ( 31) shift: 0.29 0.72 ...... Frame ( 32) shift: 0.35 0.79 ...... Frame ( 33) shift: 0.42 0.83 ...... Frame ( 34) shift: 0.51 0.84 ...... Frame ( 35) shift: 0.60 0.86 ...... Frame ( 36) shift: 0.67 0.91 ...... Frame ( 37) shift: 0.74 1.01 ...... Frame ( 38) shift: 0.81 1.10 ...... Frame ( 39) shift: 0.88 1.20 ...... Frame ( 40) shift: 0.95 1.29 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.148702 Iteration 2 Error: 0.342651 Iteration 3 Error: 0.155255 Iteration 4 Error: 0.067105 Iteration 5 Error: 0.047679 Align patch 2 23 left Iteration 1 Error: 1.392645 Iteration 2 Error: 0.301259 Iteration 3 Error: 0.144110 Iteration 4 Error: 0.099965 Iteration 5 Error: 0.060217 Align patch 2 23 left Iteration 1 Error: 1.546878 Iteration 2 Error: 0.330582 Iteration 3 Error: 0.056102 Iteration 4 Error: 0.020267 Align patch 3 22 left Iteration 1 Error: 0.938130 Iteration 2 Error: 0.224605 Iteration 3 Error: 0.068098 Iteration 4 Error: 0.022932 Align patch 4 21 left Iteration 1 Error: 1.049189 Iteration 2 Error: 0.183153 Iteration 3 Error: 0.070782 Iteration 4 Error: 0.024585 Align patch 5 20 left Iteration 1 Error: 1.214350 Iteration 2 Error: 0.199190 Iteration 3 Error: 0.067528 Iteration 4 Error: 0.015889 Align patch 6 19 left Iteration 1 Error: 1.854802 Iteration 2 Error: 0.495802 Iteration 3 Error: 0.226799 Iteration 4 Error: 0.071443 Iteration 5 Error: 0.040176 Align patch 7 18 left Iteration 1 Error: 1.187752 Iteration 2 Error: 0.370249 Iteration 3 Error: 0.126896 Iteration 4 Error: 0.049804 Align patch 8 17 left Iteration 1 Error: 1.062590 Iteration 2 Error: 0.392261 Iteration 3 Error: 0.147147 Iteration 4 Error: 0.049527 Align patch 9 16 left Iteration 1 Error: 1.011448 Iteration 2 Error: 0.348344 Iteration 3 Error: 0.109616 Iteration 4 Error: 0.039107 Align patch 10 15 left Iteration 1 Error: 1.554954 Iteration 2 Error: 0.392834 Iteration 3 Error: 0.175222 Iteration 4 Error: 0.049697 Align patch 11 14 left Iteration 1 Error: 2.060565 Iteration 2 Error: 0.465235 Iteration 3 Error: 0.179658 Iteration 4 Error: 0.072692 Iteration 5 Error: 0.049196 Align patch 12 13 left Iteration 1 Error: 1.123538 Iteration 2 Error: 0.243692 Iteration 3 Error: 0.103448 Iteration 4 Error: 0.047534 Align patch 13 12 left Iteration 1 Error: 0.732053 Iteration 2 Error: 0.166400 Iteration 3 Error: 0.053325 Iteration 4 Error: 0.026152 Align patch 14 11 left Iteration 1 Error: 0.751996 Iteration 2 Error: 0.209120 Iteration 3 Error: 0.063450 Iteration 4 Error: 0.023792 Align patch 15 10 left Iteration 1 Error: 1.027289 Iteration 2 Error: 0.531572 Iteration 3 Error: 0.161249 Iteration 4 Error: 0.092441 Iteration 5 Error: 0.035573 Align patch 16 9 left Iteration 1 Error: 1.135991 Iteration 2 Error: 0.134785 Iteration 3 Error: 0.035383 Align patch 17 8 left Iteration 1 Error: 0.907927 Iteration 2 Error: 0.191431 Iteration 3 Error: 0.097795 Iteration 4 Error: 0.034547 Align patch 18 7 left Iteration 1 Error: 0.955349 Iteration 2 Error: 0.399755 Iteration 3 Error: 0.208413 Iteration 4 Error: 0.110911 Iteration 5 Error: 0.056516 Align patch 18 7 left Iteration 1 Error: 0.978478 Iteration 2 Error: 0.168413 Iteration 3 Error: 0.060535 Iteration 4 Error: 0.025421 Align patch 19 6 left Iteration 1 Error: 0.866058 Iteration 2 Error: 0.162965 Iteration 3 Error: 0.047235 Align patch 20 5 left Iteration 1 Error: 1.111100 Iteration 2 Error: 0.345730 Iteration 3 Error: 0.093428 Iteration 4 Error: 0.042943 Align patch 21 4 left Iteration 1 Error: 0.715881 Iteration 2 Error: 0.154382 Iteration 3 Error: 0.042171 Align patch 22 3 left Iteration 1 Error: 0.897330 Iteration 2 Error: 0.254549 Iteration 3 Error: 0.122724 Iteration 4 Error: 0.070668 Iteration 5 Error: 0.052649 Align patch 22 3 left Iteration 1 Error: 0.794083 Iteration 2 Error: 0.155341 Iteration 3 Error: 0.066309 Iteration 4 Error: 0.028959 Align patch 23 2 left Iteration 1 Error: 0.919089 Iteration 2 Error: 0.208501 Iteration 3 Error: 0.091509 Iteration 4 Error: 0.037452 Align patch 24 1 left Iteration 1 Error: 1.014116 Iteration 2 Error: 0.240697 Iteration 3 Error: 0.080547 Iteration 4 Error: 0.024753 Align patch 25 0 left Iteration 1 Error: 1.788727 Iteration 2 Error: 0.443074 Iteration 3 Error: 0.134016 Iteration 4 Error: 0.050250 Iteration 5 Error: 0.022023 3D Fitting completed. Patch alignment time: 14.86(sec) Local motion has been corrected. Process thread exits. Computational time: 27.631775 sec Total time: 34.984638 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00004hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00004hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.489993s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00004hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.464641s ........................................ >>>>>>TIME<<<<<< FFT: 1.216347s Defocus_U Defocus_V Angle CCC 11187.50 10562.50 88.29 0.034047 Final Values Defocus_U Defocus_V Angle CCC 11218.77 10609.41 89.55 0.060434 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00005hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00005hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.339e-01 9.963e-02 CC threshold: 0.732 Mean Std: 44.95 7.55 Num Hot pixels: 182 Hot pixel threshold: 90.27 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.792631 Iteration 2 Error: 0.129494 Iteration 3 Error: 0.019954 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.32 -0.17 ...... Frame ( 3) shift: -0.64 -0.35 ...... Frame ( 4) shift: -0.96 -0.52 ...... Frame ( 5) shift: -1.28 -0.70 ...... Frame ( 6) shift: -1.50 -0.83 ...... Frame ( 7) shift: -1.62 -0.93 ...... Frame ( 8) shift: -1.74 -1.03 ...... Frame ( 9) shift: -1.79 -1.13 ...... Frame ( 10) shift: -1.78 -1.22 ...... Frame ( 11) shift: -1.77 -1.31 ...... Frame ( 12) shift: -1.79 -1.37 ...... Frame ( 13) shift: -1.86 -1.39 ...... Frame ( 14) shift: -1.92 -1.41 ...... Frame ( 15) shift: -1.93 -1.44 ...... Frame ( 16) shift: -1.90 -1.47 ...... Frame ( 17) shift: -1.87 -1.51 ...... Frame ( 18) shift: -1.86 -1.56 ...... Frame ( 19) shift: -1.86 -1.63 ...... Frame ( 20) shift: -1.86 -1.70 ...... Frame ( 21) shift: -1.87 -1.73 ...... Frame ( 22) shift: -1.89 -1.70 ...... Frame ( 23) shift: -1.91 -1.68 ...... Frame ( 24) shift: -1.89 -1.67 ...... Frame ( 25) shift: -1.85 -1.67 ...... Frame ( 26) shift: -1.80 -1.67 ...... Frame ( 27) shift: -1.76 -1.68 ...... Frame ( 28) shift: -1.73 -1.69 ...... Frame ( 29) shift: -1.69 -1.71 ...... Frame ( 30) shift: -1.66 -1.74 ...... Frame ( 31) shift: -1.64 -1.79 ...... Frame ( 32) shift: -1.63 -1.83 ...... Frame ( 33) shift: -1.60 -1.84 ...... Frame ( 34) shift: -1.57 -1.81 ...... Frame ( 35) shift: -1.53 -1.79 ...... Frame ( 36) shift: -1.49 -1.78 ...... Frame ( 37) shift: -1.45 -1.79 ...... Frame ( 38) shift: -1.40 -1.80 ...... Frame ( 39) shift: -1.36 -1.82 ...... Frame ( 40) shift: -1.31 -1.83 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.545429 Iteration 2 Error: 0.169306 Iteration 3 Error: 0.063060 Iteration 4 Error: 0.027323 Align patch 2 23 left Iteration 1 Error: 0.741565 Iteration 2 Error: 0.149207 Iteration 3 Error: 0.030240 Align patch 3 22 left Iteration 1 Error: 0.814498 Iteration 2 Error: 0.166828 Iteration 3 Error: 0.047752 Align patch 4 21 left Iteration 1 Error: 0.738090 Iteration 2 Error: 0.127570 Iteration 3 Error: 0.036272 Align patch 5 20 left Iteration 1 Error: 1.249046 Iteration 2 Error: 0.250471 Iteration 3 Error: 0.052195 Iteration 4 Error: 0.025489 Align patch 6 19 left Iteration 1 Error: 1.089323 Iteration 2 Error: 0.258597 Iteration 3 Error: 0.069979 Iteration 4 Error: 0.025010 Align patch 7 18 left Iteration 1 Error: 1.409525 Iteration 2 Error: 0.129435 Iteration 3 Error: 0.040448 Align patch 8 17 left Iteration 1 Error: 1.006964 Iteration 2 Error: 0.163343 Iteration 3 Error: 0.039647 Align patch 9 16 left Iteration 1 Error: 0.606202 Iteration 2 Error: 0.092266 Iteration 3 Error: 0.045810 Align patch 10 15 left Iteration 1 Error: 0.676376 Iteration 2 Error: 0.097250 Iteration 3 Error: 0.038163 Align patch 11 14 left Iteration 1 Error: 0.941997 Iteration 2 Error: 0.157982 Iteration 3 Error: 0.045701 Align patch 12 13 left Iteration 1 Error: 1.432637 Iteration 2 Error: 0.111748 Iteration 3 Error: 0.032810 Align patch 13 12 left Iteration 1 Error: 1.010562 Iteration 2 Error: 0.282943 Iteration 3 Error: 0.089564 Iteration 4 Error: 0.023079 Align patch 14 11 left Iteration 1 Error: 0.694793 Iteration 2 Error: 0.157394 Iteration 3 Error: 0.024690 Align patch 15 10 left Iteration 1 Error: 0.629314 Iteration 2 Error: 0.133784 Iteration 3 Error: 0.031824 Align patch 16 9 left Iteration 1 Error: 2.360933 Iteration 2 Error: 0.224707 Iteration 3 Error: 0.041336 Align patch 17 8 left Iteration 1 Error: 2.688652 Iteration 2 Error: 0.280505 Iteration 3 Error: 0.093185 Iteration 4 Error: 0.034182 Align patch 18 7 left Iteration 1 Error: 0.838618 Iteration 2 Error: 0.137045 Iteration 3 Error: 0.035601 Align patch 19 6 left Iteration 1 Error: 0.951354 Iteration 2 Error: 0.180010 Iteration 3 Error: 0.041910 Align patch 20 5 left Iteration 1 Error: 1.067743 Iteration 2 Error: 0.158904 Iteration 3 Error: 0.032690 Align patch 21 4 left Iteration 1 Error: 1.576806 Iteration 2 Error: 0.158879 Iteration 3 Error: 0.060022 Iteration 4 Error: 0.021939 Align patch 22 3 left Iteration 1 Error: 1.549263 Iteration 2 Error: 0.285931 Iteration 3 Error: 0.098573 Iteration 4 Error: 0.032987 Align patch 23 2 left Iteration 1 Error: 0.782990 Iteration 2 Error: 0.146365 Iteration 3 Error: 0.062509 Iteration 4 Error: 0.042076 Align patch 24 1 left Iteration 1 Error: 0.958220 Iteration 2 Error: 0.172731 Iteration 3 Error: 0.053321 Iteration 4 Error: 0.017573 Align patch 25 0 left Iteration 1 Error: 0.954269 Iteration 2 Error: 0.111007 Iteration 3 Error: 0.021359 3D Fitting completed. Patch alignment time: 11.60(sec) Local motion has been corrected. Process thread exits. Computational time: 24.066269 sec Total time: 31.060572 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00005hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00005hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.463738s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00005hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.207214s ........................................ >>>>>>TIME<<<<<< FFT: 1.009692s Defocus_U Defocus_V Angle CCC 12660.16 13539.07 13.49 0.039955 Final Values Defocus_U Defocus_V Angle CCC 12672.66 13539.07 13.18 0.049308 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00005hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00005hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.325e-01 9.873e-02 CC threshold: 0.725 Mean Std: 44.70 7.58 Num Hot pixels: 164 Hot pixel threshold: 90.16 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.987488 Iteration 2 Error: 0.261106 Iteration 3 Error: 0.055506 Iteration 4 Error: 0.018327 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.24 -0.13 ...... Frame ( 3) shift: -0.49 -0.26 ...... Frame ( 4) shift: -0.73 -0.39 ...... Frame ( 5) shift: -0.97 -0.52 ...... Frame ( 6) shift: -1.17 -0.64 ...... Frame ( 7) shift: -1.32 -0.76 ...... Frame ( 8) shift: -1.47 -0.88 ...... Frame ( 9) shift: -1.58 -0.99 ...... Frame ( 10) shift: -1.63 -1.07 ...... Frame ( 11) shift: -1.69 -1.15 ...... Frame ( 12) shift: -1.78 -1.22 ...... Frame ( 13) shift: -1.91 -1.26 ...... Frame ( 14) shift: -2.03 -1.30 ...... Frame ( 15) shift: -2.10 -1.34 ...... Frame ( 16) shift: -2.10 -1.40 ...... Frame ( 17) shift: -2.10 -1.46 ...... Frame ( 18) shift: -2.11 -1.51 ...... Frame ( 19) shift: -2.15 -1.58 ...... Frame ( 20) shift: -2.19 -1.64 ...... Frame ( 21) shift: -2.22 -1.67 ...... Frame ( 22) shift: -2.24 -1.67 ...... Frame ( 23) shift: -2.27 -1.67 ...... Frame ( 24) shift: -2.27 -1.69 ...... Frame ( 25) shift: -2.24 -1.74 ...... Frame ( 26) shift: -2.21 -1.78 ...... Frame ( 27) shift: -2.21 -1.83 ...... Frame ( 28) shift: -2.23 -1.89 ...... Frame ( 29) shift: -2.25 -1.95 ...... Frame ( 30) shift: -2.28 -1.98 ...... Frame ( 31) shift: -2.31 -2.00 ...... Frame ( 32) shift: -2.33 -2.02 ...... Frame ( 33) shift: -2.30 -2.04 ...... Frame ( 34) shift: -2.20 -2.06 ...... Frame ( 35) shift: -2.11 -2.09 ...... Frame ( 36) shift: -2.05 -2.13 ...... Frame ( 37) shift: -2.02 -2.17 ...... Frame ( 38) shift: -1.99 -2.22 ...... Frame ( 39) shift: -1.96 -2.27 ...... Frame ( 40) shift: -1.93 -2.32 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.508055 Iteration 2 Error: 0.333435 Iteration 3 Error: 0.165710 Iteration 4 Error: 0.096799 Iteration 5 Error: 0.035275 Align patch 2 23 left Iteration 1 Error: 1.473988 Iteration 2 Error: 0.434111 Iteration 3 Error: 0.100832 Iteration 4 Error: 0.042070 Align patch 3 22 left Iteration 1 Error: 1.479014 Iteration 2 Error: 0.262382 Iteration 3 Error: 0.118475 Iteration 4 Error: 0.037426 Align patch 4 21 left Iteration 1 Error: 0.704779 Iteration 2 Error: 0.150716 Iteration 3 Error: 0.030435 Align patch 5 20 left Iteration 1 Error: 0.455265 Iteration 2 Error: 0.100895 Iteration 3 Error: 0.024780 Align patch 6 19 left Iteration 1 Error: 1.564511 Iteration 2 Error: 0.340856 Iteration 3 Error: 0.158450 Iteration 4 Error: 0.143682 Iteration 5 Error: 0.130616 Align patch 6 19 left Iteration 1 Error: 1.547236 Iteration 2 Error: 0.374390 Iteration 3 Error: 0.101282 Iteration 4 Error: 0.044568 Align patch 7 18 left Iteration 1 Error: 2.302669 Iteration 2 Error: 0.585853 Iteration 3 Error: 0.240341 Iteration 4 Error: 0.127320 Iteration 5 Error: 0.110700 Align patch 7 18 left Iteration 1 Error: 1.460384 Iteration 2 Error: 0.344663 Iteration 3 Error: 0.093803 Iteration 4 Error: 0.026904 Align patch 8 17 left Iteration 1 Error: 2.141413 Iteration 2 Error: 0.365891 Iteration 3 Error: 0.137524 Iteration 4 Error: 0.085148 Iteration 5 Error: 0.027907 Align patch 9 16 left Iteration 1 Error: 0.698129 Iteration 2 Error: 0.106062 Iteration 3 Error: 0.027884 Align patch 10 15 left Iteration 1 Error: 0.786209 Iteration 2 Error: 0.089063 Iteration 3 Error: 0.026216 Align patch 11 14 left Iteration 1 Error: 2.330407 Iteration 2 Error: 0.631849 Iteration 3 Error: 0.278570 Iteration 4 Error: 0.140360 Iteration 5 Error: 0.077539 Align patch 11 14 left Iteration 1 Error: 3.197168 Iteration 2 Error: 0.389107 Iteration 3 Error: 0.117267 Iteration 4 Error: 0.031900 Align patch 12 13 left Iteration 1 Error: 2.668600 Iteration 2 Error: 0.825094 Iteration 3 Error: 0.309354 Iteration 4 Error: 0.181096 Iteration 5 Error: 0.107359 Align patch 12 13 left Iteration 1 Error: 2.471325 Iteration 2 Error: 0.466269 Iteration 3 Error: 0.107551 Iteration 4 Error: 0.042332 Align patch 13 12 left Iteration 1 Error: 1.296476 Iteration 2 Error: 0.212220 Iteration 3 Error: 0.083321 Iteration 4 Error: 0.027573 Align patch 14 11 left Iteration 1 Error: 0.761278 Iteration 2 Error: 0.173379 Iteration 3 Error: 0.042830 Align patch 15 10 left Iteration 1 Error: 1.189373 Iteration 2 Error: 0.189456 Iteration 3 Error: 0.033419 Align patch 16 9 left Iteration 1 Error: 4.683307 Iteration 2 Error: 0.719308 Iteration 3 Error: 0.345502 Iteration 4 Error: 0.176150 Iteration 5 Error: 0.096615 Align patch 16 9 left Iteration 1 Error: 3.507588 Iteration 2 Error: 0.375624 Iteration 3 Error: 0.063569 Iteration 4 Error: 0.025567 Align patch 17 8 left Iteration 1 Error: 3.393515 Iteration 2 Error: 0.301255 Iteration 3 Error: 0.117798 Iteration 4 Error: 0.051396 Iteration 5 Error: 0.022647 Align patch 18 7 left Iteration 1 Error: 1.101251 Iteration 2 Error: 0.205650 Iteration 3 Error: 0.073200 Iteration 4 Error: 0.039335 Align patch 19 6 left Iteration 1 Error: 0.604715 Iteration 2 Error: 0.179883 Iteration 3 Error: 0.032851 Align patch 20 5 left Iteration 1 Error: 1.134254 Iteration 2 Error: 0.225389 Iteration 3 Error: 0.042031 Align patch 21 4 left Iteration 1 Error: 2.570922 Iteration 2 Error: 0.507855 Iteration 3 Error: 0.401236 Iteration 4 Error: 0.164711 Iteration 5 Error: 0.085808 Align patch 21 4 left Iteration 1 Error: 2.882872 Iteration 2 Error: 0.317076 Iteration 3 Error: 0.078131 Iteration 4 Error: 0.036290 Align patch 22 3 left Iteration 1 Error: 2.097364 Iteration 2 Error: 0.419000 Iteration 3 Error: 0.165315 Iteration 4 Error: 0.043484 Align patch 23 2 left Iteration 1 Error: 0.852620 Iteration 2 Error: 0.177421 Iteration 3 Error: 0.055683 Iteration 4 Error: 0.027847 Align patch 24 1 left Iteration 1 Error: 0.694648 Iteration 2 Error: 0.091907 Iteration 3 Error: 0.034856 Align patch 25 0 left Iteration 1 Error: 1.707245 Iteration 2 Error: 0.127753 Iteration 3 Error: 0.017423 3D Fitting completed. Patch alignment time: 16.22(sec) Local motion has been corrected. Process thread exits. Computational time: 29.798174 sec Total time: 39.857914 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00005hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00005hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.596080s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00005hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.008502s ........................................ >>>>>>TIME<<<<<< FFT: 0.979899s Defocus_U Defocus_V Angle CCC 13003.88 13558.62 1.03 0.017668 Final Values Defocus_U Defocus_V Angle CCC 13007.01 13558.62 1.66 -0.041615 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00005hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00005hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 1.000e-01 CC threshold: 0.734 Mean Std: 47.43 7.57 Num Hot pixels: 179 Hot pixel threshold: 92.85 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.970517 Iteration 2 Error: 0.138855 Iteration 3 Error: 0.027107 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.34 -0.09 ...... Frame ( 3) shift: -0.68 -0.18 ...... Frame ( 4) shift: -1.03 -0.28 ...... Frame ( 5) shift: -1.37 -0.37 ...... Frame ( 6) shift: -1.57 -0.46 ...... Frame ( 7) shift: -1.62 -0.54 ...... Frame ( 8) shift: -1.67 -0.62 ...... Frame ( 9) shift: -1.67 -0.65 ...... Frame ( 10) shift: -1.60 -0.62 ...... Frame ( 11) shift: -1.54 -0.60 ...... Frame ( 12) shift: -1.49 -0.64 ...... Frame ( 13) shift: -1.46 -0.74 ...... Frame ( 14) shift: -1.43 -0.84 ...... Frame ( 15) shift: -1.43 -0.92 ...... Frame ( 16) shift: -1.46 -0.96 ...... Frame ( 17) shift: -1.49 -1.01 ...... Frame ( 18) shift: -1.48 -1.08 ...... Frame ( 19) shift: -1.43 -1.16 ...... Frame ( 20) shift: -1.39 -1.24 ...... Frame ( 21) shift: -1.34 -1.28 ...... Frame ( 22) shift: -1.28 -1.27 ...... Frame ( 23) shift: -1.22 -1.25 ...... Frame ( 24) shift: -1.19 -1.23 ...... Frame ( 25) shift: -1.20 -1.19 ...... Frame ( 26) shift: -1.21 -1.15 ...... Frame ( 27) shift: -1.21 -1.16 ...... Frame ( 28) shift: -1.20 -1.22 ...... Frame ( 29) shift: -1.19 -1.28 ...... Frame ( 30) shift: -1.16 -1.29 ...... Frame ( 31) shift: -1.09 -1.27 ...... Frame ( 32) shift: -1.02 -1.25 ...... Frame ( 33) shift: -1.01 -1.22 ...... Frame ( 34) shift: -1.05 -1.18 ...... Frame ( 35) shift: -1.10 -1.14 ...... Frame ( 36) shift: -1.08 -1.12 ...... Frame ( 37) shift: -1.00 -1.12 ...... Frame ( 38) shift: -0.93 -1.13 ...... Frame ( 39) shift: -0.85 -1.13 ...... Frame ( 40) shift: -0.77 -1.13 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.985113 Iteration 2 Error: 0.105282 Iteration 3 Error: 0.032710 Align patch 2 23 left Iteration 1 Error: 1.017443 Iteration 2 Error: 0.194878 Iteration 3 Error: 0.070120 Iteration 4 Error: 0.029009 Align patch 3 22 left Iteration 1 Error: 0.809456 Iteration 2 Error: 0.161852 Iteration 3 Error: 0.029863 Align patch 4 21 left Iteration 1 Error: 0.824133 Iteration 2 Error: 0.151386 Iteration 3 Error: 0.044112 Align patch 5 20 left Iteration 1 Error: 0.934742 Iteration 2 Error: 0.127511 Iteration 3 Error: 0.035869 Align patch 6 19 left Iteration 1 Error: 1.227796 Iteration 2 Error: 0.158227 Iteration 3 Error: 0.036891 Align patch 7 18 left Iteration 1 Error: 1.116714 Iteration 2 Error: 0.119703 Iteration 3 Error: 0.037160 Align patch 8 17 left Iteration 1 Error: 0.807524 Iteration 2 Error: 0.141770 Iteration 3 Error: 0.022643 Align patch 9 16 left Iteration 1 Error: 0.814991 Iteration 2 Error: 0.143121 Iteration 3 Error: 0.064088 Iteration 4 Error: 0.021752 Align patch 10 15 left Iteration 1 Error: 0.867115 Iteration 2 Error: 0.184820 Iteration 3 Error: 0.053185 Iteration 4 Error: 0.017941 Align patch 11 14 left Iteration 1 Error: 0.832032 Iteration 2 Error: 0.177475 Iteration 3 Error: 0.103406 Iteration 4 Error: 0.051613 Iteration 5 Error: 0.013874 Align patch 12 13 left Iteration 1 Error: 1.024867 Iteration 2 Error: 0.269245 Iteration 3 Error: 0.097875 Iteration 4 Error: 0.016581 Align patch 13 12 left Iteration 1 Error: 0.870712 Iteration 2 Error: 0.186055 Iteration 3 Error: 0.071156 Iteration 4 Error: 0.034449 Align patch 14 11 left Iteration 1 Error: 0.745879 Iteration 2 Error: 0.106398 Iteration 3 Error: 0.031513 Align patch 15 10 left Iteration 1 Error: 0.820770 Iteration 2 Error: 0.104736 Iteration 3 Error: 0.067585 Iteration 4 Error: 0.020344 Align patch 16 9 left Iteration 1 Error: 0.912041 Iteration 2 Error: 0.190280 Iteration 3 Error: 0.064146 Iteration 4 Error: 0.018551 Align patch 17 8 left Iteration 1 Error: 1.157132 Iteration 2 Error: 0.294983 Iteration 3 Error: 0.084973 Iteration 4 Error: 0.041238 Align patch 18 7 left Iteration 1 Error: 1.047880 Iteration 2 Error: 0.183318 Iteration 3 Error: 0.047683 Align patch 19 6 left Iteration 1 Error: 0.684062 Iteration 2 Error: 0.129156 Iteration 3 Error: 0.031297 Align patch 20 5 left Iteration 1 Error: 0.744991 Iteration 2 Error: 0.088448 Iteration 3 Error: 0.013641 Align patch 21 4 left Iteration 1 Error: 1.040441 Iteration 2 Error: 0.250082 Iteration 3 Error: 0.074958 Iteration 4 Error: 0.025483 Align patch 22 3 left Iteration 1 Error: 1.212795 Iteration 2 Error: 0.216175 Iteration 3 Error: 0.072031 Iteration 4 Error: 0.026500 Align patch 23 2 left Iteration 1 Error: 0.928905 Iteration 2 Error: 0.128244 Iteration 3 Error: 0.053299 Iteration 4 Error: 0.021242 Align patch 24 1 left Iteration 1 Error: 0.517032 Iteration 2 Error: 0.126699 Iteration 3 Error: 0.035494 Align patch 25 0 left Iteration 1 Error: 0.502024 Iteration 2 Error: 0.073404 Iteration 3 Error: 0.018591 3D Fitting completed. Patch alignment time: 11.99(sec) Local motion has been corrected. Process thread exits. Computational time: 25.063179 sec Total time: 35.640060 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00005hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00005hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.559587s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00005hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.641438s ........................................ >>>>>>TIME<<<<<< FFT: 0.992876s Defocus_U Defocus_V Angle CCC 11619.15 12556.65 4.61 0.045598 Final Values Defocus_U Defocus_V Angle CCC 11641.04 12550.41 4.61 0.084723 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00005hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00005hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.998e-02 CC threshold: 0.734 Mean Std: 46.68 7.64 Num Hot pixels: 172 Hot pixel threshold: 92.50 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.925509 Iteration 2 Error: 0.086932 Iteration 3 Error: 0.023893 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.31 -0.02 ...... Frame ( 3) shift: -0.63 -0.03 ...... Frame ( 4) shift: -0.94 -0.05 ...... Frame ( 5) shift: -1.25 -0.06 ...... Frame ( 6) shift: -1.44 -0.08 ...... Frame ( 7) shift: -1.52 -0.10 ...... Frame ( 8) shift: -1.59 -0.12 ...... Frame ( 9) shift: -1.62 -0.14 ...... Frame ( 10) shift: -1.61 -0.14 ...... Frame ( 11) shift: -1.61 -0.15 ...... Frame ( 12) shift: -1.61 -0.18 ...... Frame ( 13) shift: -1.61 -0.23 ...... Frame ( 14) shift: -1.62 -0.28 ...... Frame ( 15) shift: -1.60 -0.31 ...... Frame ( 16) shift: -1.57 -0.34 ...... Frame ( 17) shift: -1.54 -0.36 ...... Frame ( 18) shift: -1.52 -0.42 ...... Frame ( 19) shift: -1.50 -0.52 ...... Frame ( 20) shift: -1.48 -0.62 ...... Frame ( 21) shift: -1.43 -0.70 ...... Frame ( 22) shift: -1.36 -0.76 ...... Frame ( 23) shift: -1.29 -0.82 ...... Frame ( 24) shift: -1.24 -0.81 ...... Frame ( 25) shift: -1.21 -0.75 ...... Frame ( 26) shift: -1.17 -0.68 ...... Frame ( 27) shift: -1.16 -0.66 ...... Frame ( 28) shift: -1.15 -0.67 ...... Frame ( 29) shift: -1.15 -0.69 ...... Frame ( 30) shift: -1.16 -0.72 ...... Frame ( 31) shift: -1.18 -0.77 ...... Frame ( 32) shift: -1.20 -0.81 ...... Frame ( 33) shift: -1.20 -0.83 ...... Frame ( 34) shift: -1.17 -0.81 ...... Frame ( 35) shift: -1.14 -0.79 ...... Frame ( 36) shift: -1.10 -0.77 ...... Frame ( 37) shift: -1.04 -0.73 ...... Frame ( 38) shift: -0.99 -0.70 ...... Frame ( 39) shift: -0.94 -0.67 ...... Frame ( 40) shift: -0.88 -0.64 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.448431 Iteration 2 Error: 0.473242 Iteration 3 Error: 0.110144 Iteration 4 Error: 0.058457 Iteration 5 Error: 0.026701 Align patch 2 23 left Iteration 1 Error: 0.862128 Iteration 2 Error: 0.193806 Iteration 3 Error: 0.073091 Iteration 4 Error: 0.020361 Align patch 3 22 left Iteration 1 Error: 0.704892 Iteration 2 Error: 0.130379 Iteration 3 Error: 0.048271 Align patch 4 21 left Iteration 1 Error: 0.888963 Iteration 2 Error: 0.213324 Iteration 3 Error: 0.063221 Iteration 4 Error: 0.031537 Align patch 5 20 left Iteration 1 Error: 0.844582 Iteration 2 Error: 0.100183 Iteration 3 Error: 0.021986 Align patch 6 19 left Iteration 1 Error: 0.918279 Iteration 2 Error: 0.378690 Iteration 3 Error: 0.102218 Iteration 4 Error: 0.059534 Iteration 5 Error: 0.019775 Align patch 7 18 left Iteration 1 Error: 0.758932 Iteration 2 Error: 0.163759 Iteration 3 Error: 0.066302 Iteration 4 Error: 0.037355 Align patch 8 17 left Iteration 1 Error: 0.977674 Iteration 2 Error: 0.164162 Iteration 3 Error: 0.047513 Align patch 9 16 left Iteration 1 Error: 0.992827 Iteration 2 Error: 0.211685 Iteration 3 Error: 0.062049 Iteration 4 Error: 0.013928 Align patch 10 15 left Iteration 1 Error: 0.771320 Iteration 2 Error: 0.130344 Iteration 3 Error: 0.033960 Align patch 11 14 left Iteration 1 Error: 0.882017 Iteration 2 Error: 0.192227 Iteration 3 Error: 0.034122 Align patch 12 13 left Iteration 1 Error: 0.925763 Iteration 2 Error: 0.233821 Iteration 3 Error: 0.065925 Iteration 4 Error: 0.015005 Align patch 13 12 left Iteration 1 Error: 0.698627 Iteration 2 Error: 0.205083 Iteration 3 Error: 0.102678 Iteration 4 Error: 0.035375 Align patch 14 11 left Iteration 1 Error: 0.586551 Iteration 2 Error: 0.065872 Iteration 3 Error: 0.020509 Align patch 15 10 left Iteration 1 Error: 0.878883 Iteration 2 Error: 0.077223 Iteration 3 Error: 0.019371 Align patch 16 9 left Iteration 1 Error: 1.056342 Iteration 2 Error: 0.161930 Iteration 3 Error: 0.072466 Iteration 4 Error: 0.017980 Align patch 17 8 left Iteration 1 Error: 1.403208 Iteration 2 Error: 0.192654 Iteration 3 Error: 0.066745 Iteration 4 Error: 0.049143 Align patch 18 7 left Iteration 1 Error: 0.786107 Iteration 2 Error: 0.179698 Iteration 3 Error: 0.028777 Align patch 19 6 left Iteration 1 Error: 0.748920 Iteration 2 Error: 0.092977 Iteration 3 Error: 0.025080 Align patch 20 5 left Iteration 1 Error: 0.619701 Iteration 2 Error: 0.100619 Iteration 3 Error: 0.034284 Align patch 21 4 left Iteration 1 Error: 0.808916 Iteration 2 Error: 0.227704 Iteration 3 Error: 0.043201 Align patch 22 3 left Iteration 1 Error: 1.644868 Iteration 2 Error: 0.197838 Iteration 3 Error: 0.157287 Iteration 4 Error: 0.084808 Iteration 5 Error: 0.064786 Align patch 22 3 left Iteration 1 Error: 1.407581 Iteration 2 Error: 0.140176 Iteration 3 Error: 0.040755 Align patch 23 2 left Iteration 1 Error: 0.861041 Iteration 2 Error: 0.209455 Iteration 3 Error: 0.066907 Iteration 4 Error: 0.020015 Align patch 24 1 left Iteration 1 Error: 0.646765 Iteration 2 Error: 0.156308 Iteration 3 Error: 0.038185 Align patch 25 0 left Iteration 1 Error: 0.714379 Iteration 2 Error: 0.184666 Iteration 3 Error: 0.055228 Iteration 4 Error: 0.021432 3D Fitting completed. Patch alignment time: 12.77(sec) Local motion has been corrected. Process thread exits. Computational time: 26.086910 sec Total time: 33.652470 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00005hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00005hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.546487s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00005hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.110848s ........................................ >>>>>>TIME<<<<<< FFT: 0.943485s Defocus_U Defocus_V Angle CCC 10312.07 9621.54 86.90 0.042432 Final Values Defocus_U Defocus_V Angle CCC 10352.70 9634.06 86.90 0.084439 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00006hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00006hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 46.43 7.76 Num Hot pixels: 142 Hot pixel threshold: 93.00 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.000058 Iteration 2 Error: 0.075387 Iteration 3 Error: 0.014148 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.37 -0.03 ...... Frame ( 3) shift: -0.74 -0.06 ...... Frame ( 4) shift: -1.11 -0.10 ...... Frame ( 5) shift: -1.48 -0.13 ...... Frame ( 6) shift: -1.67 -0.14 ...... Frame ( 7) shift: -1.67 -0.13 ...... Frame ( 8) shift: -1.68 -0.11 ...... Frame ( 9) shift: -1.66 -0.04 ...... Frame ( 10) shift: -1.63 0.08 ...... Frame ( 11) shift: -1.60 0.20 ...... Frame ( 12) shift: -1.58 0.28 ...... Frame ( 13) shift: -1.58 0.31 ...... Frame ( 14) shift: -1.58 0.34 ...... Frame ( 15) shift: -1.56 0.39 ...... Frame ( 16) shift: -1.53 0.46 ...... Frame ( 17) shift: -1.50 0.52 ...... Frame ( 18) shift: -1.49 0.55 ...... Frame ( 19) shift: -1.49 0.53 ...... Frame ( 20) shift: -1.49 0.50 ...... Frame ( 21) shift: -1.49 0.51 ...... Frame ( 22) shift: -1.48 0.53 ...... Frame ( 23) shift: -1.47 0.56 ...... Frame ( 24) shift: -1.48 0.58 ...... Frame ( 25) shift: -1.50 0.60 ...... Frame ( 26) shift: -1.52 0.61 ...... Frame ( 27) shift: -1.50 0.63 ...... Frame ( 28) shift: -1.44 0.65 ...... Frame ( 29) shift: -1.38 0.67 ...... Frame ( 30) shift: -1.36 0.67 ...... Frame ( 31) shift: -1.38 0.65 ...... Frame ( 32) shift: -1.40 0.63 ...... Frame ( 33) shift: -1.40 0.61 ...... Frame ( 34) shift: -1.37 0.60 ...... Frame ( 35) shift: -1.35 0.58 ...... Frame ( 36) shift: -1.34 0.60 ...... Frame ( 37) shift: -1.32 0.65 ...... Frame ( 38) shift: -1.31 0.70 ...... Frame ( 39) shift: -1.30 0.75 ...... Frame ( 40) shift: -1.29 0.80 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.967162 Iteration 2 Error: 0.188908 Iteration 3 Error: 0.060422 Iteration 4 Error: 0.016732 Align patch 2 23 left Iteration 1 Error: 0.783540 Iteration 2 Error: 0.165702 Iteration 3 Error: 0.077161 Iteration 4 Error: 0.034771 Align patch 3 22 left Iteration 1 Error: 0.799790 Iteration 2 Error: 0.215625 Iteration 3 Error: 0.070787 Iteration 4 Error: 0.045381 Align patch 4 21 left Iteration 1 Error: 1.009166 Iteration 2 Error: 0.137439 Iteration 3 Error: 0.027263 Align patch 5 20 left Iteration 1 Error: 1.022212 Iteration 2 Error: 0.157733 Iteration 3 Error: 0.031181 Align patch 6 19 left Iteration 1 Error: 0.684917 Iteration 2 Error: 0.125853 Iteration 3 Error: 0.031511 Align patch 7 18 left Iteration 1 Error: 0.827544 Iteration 2 Error: 0.192221 Iteration 3 Error: 0.047486 Align patch 8 17 left Iteration 1 Error: 0.650498 Iteration 2 Error: 0.082548 Iteration 3 Error: 0.024786 Align patch 9 16 left Iteration 1 Error: 1.064794 Iteration 2 Error: 0.194080 Iteration 3 Error: 0.080414 Iteration 4 Error: 0.023798 Align patch 10 15 left Iteration 1 Error: 1.021309 Iteration 2 Error: 0.144724 Iteration 3 Error: 0.031198 Align patch 11 14 left Iteration 1 Error: 1.036443 Iteration 2 Error: 0.163226 Iteration 3 Error: 0.034193 Align patch 12 13 left Iteration 1 Error: 0.857192 Iteration 2 Error: 0.230402 Iteration 3 Error: 0.116472 Iteration 4 Error: 0.031679 Align patch 13 12 left Iteration 1 Error: 1.273736 Iteration 2 Error: 0.134128 Iteration 3 Error: 0.029767 Align patch 14 11 left Iteration 1 Error: 0.763214 Iteration 2 Error: 0.120935 Iteration 3 Error: 0.028614 Align patch 15 10 left Iteration 1 Error: 0.742674 Iteration 2 Error: 0.106062 Iteration 3 Error: 0.024475 Align patch 16 9 left Iteration 1 Error: 1.220284 Iteration 2 Error: 0.326485 Iteration 3 Error: 0.071394 Iteration 4 Error: 0.052031 Iteration 5 Error: 0.023737 Align patch 17 8 left Iteration 1 Error: 0.917143 Iteration 2 Error: 0.193917 Iteration 3 Error: 0.036953 Align patch 18 7 left Iteration 1 Error: 0.777907 Iteration 2 Error: 0.148899 Iteration 3 Error: 0.031668 Align patch 19 6 left Iteration 1 Error: 0.491245 Iteration 2 Error: 0.050729 Iteration 3 Error: 0.012343 Align patch 20 5 left Iteration 1 Error: 0.676962 Iteration 2 Error: 0.110143 Iteration 3 Error: 0.018604 Align patch 21 4 left Iteration 1 Error: 1.070262 Iteration 2 Error: 0.252783 Iteration 3 Error: 0.077255 Iteration 4 Error: 0.039647 Align patch 22 3 left Iteration 1 Error: 0.728381 Iteration 2 Error: 0.162511 Iteration 3 Error: 0.036963 Align patch 23 2 left Iteration 1 Error: 0.725609 Iteration 2 Error: 0.117716 Iteration 3 Error: 0.023671 Align patch 24 1 left Iteration 1 Error: 0.651707 Iteration 2 Error: 0.102003 Iteration 3 Error: 0.018853 Align patch 25 0 left Iteration 1 Error: 0.575575 Iteration 2 Error: 0.106765 Iteration 3 Error: 0.018491 3D Fitting completed. Patch alignment time: 11.57(sec) Local motion has been corrected. Process thread exits. Computational time: 25.032030 sec Total time: 35.403042 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00006hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00006hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.600915s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00006hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.656908s ........................................ >>>>>>TIME<<<<<< FFT: 0.927366s Defocus_U Defocus_V Angle CCC 12220.72 13044.98 10.06 0.049287 Final Values Defocus_U Defocus_V Angle CCC 12216.17 13065.42 10.06 0.089312 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00006hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00006hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 1.000e-01 CC threshold: 0.734 Mean Std: 46.20 7.77 Num Hot pixels: 153 Hot pixel threshold: 92.82 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.800473 Iteration 2 Error: 0.074921 Iteration 3 Error: 0.014418 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.32 -0.07 ...... Frame ( 3) shift: -0.65 -0.14 ...... Frame ( 4) shift: -0.97 -0.21 ...... Frame ( 5) shift: -1.30 -0.28 ...... Frame ( 6) shift: -1.48 -0.37 ...... Frame ( 7) shift: -1.51 -0.48 ...... Frame ( 8) shift: -1.54 -0.59 ...... Frame ( 9) shift: -1.55 -0.67 ...... Frame ( 10) shift: -1.53 -0.73 ...... Frame ( 11) shift: -1.52 -0.79 ...... Frame ( 12) shift: -1.51 -0.81 ...... Frame ( 13) shift: -1.53 -0.80 ...... Frame ( 14) shift: -1.54 -0.78 ...... Frame ( 15) shift: -1.53 -0.81 ...... Frame ( 16) shift: -1.50 -0.89 ...... Frame ( 17) shift: -1.47 -0.96 ...... Frame ( 18) shift: -1.42 -0.99 ...... Frame ( 19) shift: -1.35 -0.97 ...... Frame ( 20) shift: -1.28 -0.94 ...... Frame ( 21) shift: -1.22 -0.92 ...... Frame ( 22) shift: -1.19 -0.89 ...... Frame ( 23) shift: -1.16 -0.86 ...... Frame ( 24) shift: -1.12 -0.85 ...... Frame ( 25) shift: -1.07 -0.85 ...... Frame ( 26) shift: -1.02 -0.85 ...... Frame ( 27) shift: -0.98 -0.86 ...... Frame ( 28) shift: -0.94 -0.87 ...... Frame ( 29) shift: -0.91 -0.89 ...... Frame ( 30) shift: -0.85 -0.89 ...... Frame ( 31) shift: -0.76 -0.88 ...... Frame ( 32) shift: -0.68 -0.86 ...... Frame ( 33) shift: -0.61 -0.80 ...... Frame ( 34) shift: -0.55 -0.68 ...... Frame ( 35) shift: -0.49 -0.56 ...... Frame ( 36) shift: -0.44 -0.48 ...... Frame ( 37) shift: -0.40 -0.45 ...... Frame ( 38) shift: -0.35 -0.41 ...... Frame ( 39) shift: -0.31 -0.38 ...... Frame ( 40) shift: -0.26 -0.34 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.959424 Iteration 2 Error: 0.144282 Iteration 3 Error: 0.040158 Align patch 2 23 left Iteration 1 Error: 1.211737 Iteration 2 Error: 0.163563 Iteration 3 Error: 0.052452 Iteration 4 Error: 0.016965 Align patch 3 22 left Iteration 1 Error: 0.530883 Iteration 2 Error: 0.096712 Iteration 3 Error: 0.017332 Align patch 4 21 left Iteration 1 Error: 0.557698 Iteration 2 Error: 0.069593 Iteration 3 Error: 0.013599 Align patch 5 20 left Iteration 1 Error: 0.958169 Iteration 2 Error: 0.101847 Iteration 3 Error: 0.021291 Align patch 6 19 left Iteration 1 Error: 0.749303 Iteration 2 Error: 0.177814 Iteration 3 Error: 0.041214 Align patch 7 18 left Iteration 1 Error: 0.725618 Iteration 2 Error: 0.199066 Iteration 3 Error: 0.055308 Iteration 4 Error: 0.017927 Align patch 8 17 left Iteration 1 Error: 0.580978 Iteration 2 Error: 0.132422 Iteration 3 Error: 0.034641 Align patch 9 16 left Iteration 1 Error: 1.293027 Iteration 2 Error: 0.155304 Iteration 3 Error: 0.030479 Align patch 10 15 left Iteration 1 Error: 0.807393 Iteration 2 Error: 0.171482 Iteration 3 Error: 0.036467 Align patch 11 14 left Iteration 1 Error: 2.021889 Iteration 2 Error: 0.358297 Iteration 3 Error: 0.102259 Iteration 4 Error: 0.040811 Align patch 12 13 left Iteration 1 Error: 1.053764 Iteration 2 Error: 0.323743 Iteration 3 Error: 0.083623 Iteration 4 Error: 0.042182 Align patch 13 12 left Iteration 1 Error: 0.794971 Iteration 2 Error: 0.147750 Iteration 3 Error: 0.039463 Align patch 14 11 left Iteration 1 Error: 0.912324 Iteration 2 Error: 0.101366 Iteration 3 Error: 0.029835 Align patch 15 10 left Iteration 1 Error: 0.949508 Iteration 2 Error: 0.164448 Iteration 3 Error: 0.041936 Align patch 16 9 left Iteration 1 Error: 1.027393 Iteration 2 Error: 0.241649 Iteration 3 Error: 0.044637 Align patch 17 8 left Iteration 1 Error: 1.041388 Iteration 2 Error: 0.162174 Iteration 3 Error: 0.048464 Align patch 18 7 left Iteration 1 Error: 1.642666 Iteration 2 Error: 0.209639 Iteration 3 Error: 0.020237 Align patch 19 6 left Iteration 1 Error: 0.894611 Iteration 2 Error: 0.166423 Iteration 3 Error: 0.024284 Align patch 20 5 left Iteration 1 Error: 0.956416 Iteration 2 Error: 0.168153 Iteration 3 Error: 0.034142 Align patch 21 4 left Iteration 1 Error: 1.701817 Iteration 2 Error: 0.123070 Iteration 3 Error: 0.038005 Align patch 22 3 left Iteration 1 Error: 1.429855 Iteration 2 Error: 0.170639 Iteration 3 Error: 0.045291 Align patch 23 2 left Iteration 1 Error: 0.707361 Iteration 2 Error: 0.085681 Iteration 3 Error: 0.023116 Align patch 24 1 left Iteration 1 Error: 0.934194 Iteration 2 Error: 0.148534 Iteration 3 Error: 0.033315 Align patch 25 0 left Iteration 1 Error: 0.890519 Iteration 2 Error: 0.154750 Iteration 3 Error: 0.050221 Iteration 4 Error: 0.019577 3D Fitting completed. Patch alignment time: 11.58(sec) Local motion has been corrected. Process thread exits. Computational time: 22.605844 sec Total time: 29.991421 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00006hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00006hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.590688s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00006hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.805232s ........................................ >>>>>>TIME<<<<<< FFT: 0.900444s Defocus_U Defocus_V Angle CCC 9521.50 10021.50 1.59 0.040396 Final Values Defocus_U Defocus_V Angle CCC 9523.06 10029.31 0.65 0.081209 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00006hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00006hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 47.69 7.68 Num Hot pixels: 186 Hot pixel threshold: 93.77 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.989508 Iteration 2 Error: 0.062004 Iteration 3 Error: 0.014029 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.35 -0.02 ...... Frame ( 3) shift: -0.70 -0.04 ...... Frame ( 4) shift: -1.05 -0.05 ...... Frame ( 5) shift: -1.40 -0.07 ...... Frame ( 6) shift: -1.57 -0.08 ...... Frame ( 7) shift: -1.57 -0.09 ...... Frame ( 8) shift: -1.57 -0.09 ...... Frame ( 9) shift: -1.59 -0.02 ...... Frame ( 10) shift: -1.64 0.13 ...... Frame ( 11) shift: -1.69 0.28 ...... Frame ( 12) shift: -1.66 0.37 ...... Frame ( 13) shift: -1.57 0.40 ...... Frame ( 14) shift: -1.48 0.43 ...... Frame ( 15) shift: -1.43 0.46 ...... Frame ( 16) shift: -1.42 0.47 ...... Frame ( 17) shift: -1.41 0.49 ...... Frame ( 18) shift: -1.40 0.50 ...... Frame ( 19) shift: -1.41 0.50 ...... Frame ( 20) shift: -1.41 0.50 ...... Frame ( 21) shift: -1.41 0.48 ...... Frame ( 22) shift: -1.41 0.44 ...... Frame ( 23) shift: -1.40 0.41 ...... Frame ( 24) shift: -1.42 0.39 ...... Frame ( 25) shift: -1.47 0.39 ...... Frame ( 26) shift: -1.52 0.40 ...... Frame ( 27) shift: -1.55 0.40 ...... Frame ( 28) shift: -1.55 0.41 ...... Frame ( 29) shift: -1.54 0.42 ...... Frame ( 30) shift: -1.51 0.44 ...... Frame ( 31) shift: -1.44 0.48 ...... Frame ( 32) shift: -1.38 0.51 ...... Frame ( 33) shift: -1.34 0.50 ...... Frame ( 34) shift: -1.33 0.44 ...... Frame ( 35) shift: -1.32 0.39 ...... Frame ( 36) shift: -1.34 0.34 ...... Frame ( 37) shift: -1.39 0.30 ...... Frame ( 38) shift: -1.44 0.27 ...... Frame ( 39) shift: -1.49 0.23 ...... Frame ( 40) shift: -1.54 0.19 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.001117 Iteration 2 Error: 0.317541 Iteration 3 Error: 0.095593 Iteration 4 Error: 0.031661 Align patch 2 23 left Iteration 1 Error: 1.294703 Iteration 2 Error: 0.182470 Iteration 3 Error: 0.042802 Align patch 3 22 left Iteration 1 Error: 2.066776 Iteration 2 Error: 0.282221 Iteration 3 Error: 0.196227 Iteration 4 Error: 0.089964 Iteration 5 Error: 0.048547 Align patch 4 21 left Iteration 1 Error: 0.742364 Iteration 2 Error: 0.166289 Iteration 3 Error: 0.052878 Iteration 4 Error: 0.023625 Align patch 5 20 left Iteration 1 Error: 0.583387 Iteration 2 Error: 0.136578 Iteration 3 Error: 0.018909 Align patch 6 19 left Iteration 1 Error: 1.376250 Iteration 2 Error: 0.252194 Iteration 3 Error: 0.042268 Align patch 7 18 left Iteration 1 Error: 0.731423 Iteration 2 Error: 0.096393 Iteration 3 Error: 0.040124 Align patch 8 17 left Iteration 1 Error: 0.777364 Iteration 2 Error: 0.212891 Iteration 3 Error: 0.073379 Iteration 4 Error: 0.035148 Align patch 9 16 left Iteration 1 Error: 0.726976 Iteration 2 Error: 0.102767 Iteration 3 Error: 0.017522 Align patch 10 15 left Iteration 1 Error: 0.912388 Iteration 2 Error: 0.123761 Iteration 3 Error: 0.015671 Align patch 11 14 left Iteration 1 Error: 1.367920 Iteration 2 Error: 0.173380 Iteration 3 Error: 0.041028 Align patch 12 13 left Iteration 1 Error: 1.127362 Iteration 2 Error: 0.146152 Iteration 3 Error: 0.019702 Align patch 13 12 left Iteration 1 Error: 1.457897 Iteration 2 Error: 0.237798 Iteration 3 Error: 0.041092 Align patch 14 11 left Iteration 1 Error: 0.671063 Iteration 2 Error: 0.099534 Iteration 3 Error: 0.023247 Align patch 15 10 left Iteration 1 Error: 0.718210 Iteration 2 Error: 0.113572 Iteration 3 Error: 0.028174 Align patch 16 9 left Iteration 1 Error: 1.539645 Iteration 2 Error: 0.188110 Iteration 3 Error: 0.055703 Iteration 4 Error: 0.009982 Align patch 17 8 left Iteration 1 Error: 0.926821 Iteration 2 Error: 0.231092 Iteration 3 Error: 0.063485 Iteration 4 Error: 0.021471 Align patch 18 7 left Iteration 1 Error: 0.721690 Iteration 2 Error: 0.140808 Iteration 3 Error: 0.025415 Align patch 19 6 left Iteration 1 Error: 0.835178 Iteration 2 Error: 0.087781 Iteration 3 Error: 0.025649 Align patch 20 5 left Iteration 1 Error: 0.707280 Iteration 2 Error: 0.095814 Iteration 3 Error: 0.024754 Align patch 21 4 left Iteration 1 Error: 1.117627 Iteration 2 Error: 0.186776 Iteration 3 Error: 0.025473 Align patch 22 3 left Iteration 1 Error: 1.220286 Iteration 2 Error: 0.242784 Iteration 3 Error: 0.080202 Iteration 4 Error: 0.028529 Align patch 23 2 left Iteration 1 Error: 1.277302 Iteration 2 Error: 0.230575 Iteration 3 Error: 0.047306 Align patch 24 1 left Iteration 1 Error: 0.773976 Iteration 2 Error: 0.073233 Iteration 3 Error: 0.022545 Align patch 25 0 left Iteration 1 Error: 0.744796 Iteration 2 Error: 0.158875 Iteration 3 Error: 0.035322 3D Fitting completed. Patch alignment time: 12.11(sec) Local motion has been corrected. Process thread exits. Computational time: 22.943512 sec Total time: 31.126492 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00006hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00006hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.889765s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00006hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.839310s ........................................ >>>>>>TIME<<<<<< FFT: 1.069553s Defocus_U Defocus_V Angle CCC 10351.60 11257.85 5.07 0.048125 Final Values Defocus_U Defocus_V Angle CCC 10356.26 11271.94 5.38 0.089658 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00006hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00006hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 47.60 7.67 Num Hot pixels: 174 Hot pixel threshold: 93.59 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.354721 Iteration 2 Error: 0.082768 Iteration 3 Error: 0.010967 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.37 0.03 ...... Frame ( 3) shift: -0.75 0.06 ...... Frame ( 4) shift: -1.12 0.09 ...... Frame ( 5) shift: -1.50 0.12 ...... Frame ( 6) shift: -1.72 0.15 ...... Frame ( 7) shift: -1.79 0.18 ...... Frame ( 8) shift: -1.86 0.21 ...... Frame ( 9) shift: -1.89 0.20 ...... Frame ( 10) shift: -1.87 0.14 ...... Frame ( 11) shift: -1.86 0.08 ...... Frame ( 12) shift: -1.89 0.08 ...... Frame ( 13) shift: -1.96 0.14 ...... Frame ( 14) shift: -2.03 0.19 ...... Frame ( 15) shift: -2.03 0.22 ...... Frame ( 16) shift: -1.95 0.21 ...... Frame ( 17) shift: -1.87 0.19 ...... Frame ( 18) shift: -1.83 0.19 ...... Frame ( 19) shift: -1.82 0.20 ...... Frame ( 20) shift: -1.81 0.21 ...... Frame ( 21) shift: -1.83 0.23 ...... Frame ( 22) shift: -1.87 0.25 ...... Frame ( 23) shift: -1.91 0.28 ...... Frame ( 24) shift: -1.93 0.29 ...... Frame ( 25) shift: -1.94 0.29 ...... Frame ( 26) shift: -1.95 0.28 ...... Frame ( 27) shift: -1.97 0.29 ...... Frame ( 28) shift: -2.00 0.32 ...... Frame ( 29) shift: -2.03 0.34 ...... Frame ( 30) shift: -2.02 0.38 ...... Frame ( 31) shift: -1.98 0.43 ...... Frame ( 32) shift: -1.95 0.48 ...... Frame ( 33) shift: -1.93 0.51 ...... Frame ( 34) shift: -1.94 0.52 ...... Frame ( 35) shift: -1.94 0.53 ...... Frame ( 36) shift: -1.96 0.53 ...... Frame ( 37) shift: -2.00 0.54 ...... Frame ( 38) shift: -2.04 0.54 ...... Frame ( 39) shift: -2.07 0.54 ...... Frame ( 40) shift: -2.11 0.55 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.030038 Iteration 2 Error: 0.163456 Iteration 3 Error: 0.041934 Align patch 2 23 left Iteration 1 Error: 1.351413 Iteration 2 Error: 0.181561 Iteration 3 Error: 0.046281 Align patch 3 22 left Iteration 1 Error: 1.100376 Iteration 2 Error: 0.120988 Iteration 3 Error: 0.027581 Align patch 4 21 left Iteration 1 Error: 1.350296 Iteration 2 Error: 0.142995 Iteration 3 Error: 0.040003 Align patch 5 20 left Iteration 1 Error: 0.696702 Iteration 2 Error: 0.117589 Iteration 3 Error: 0.024429 Align patch 6 19 left Iteration 1 Error: 1.111056 Iteration 2 Error: 0.150455 Iteration 3 Error: 0.030241 Align patch 7 18 left Iteration 1 Error: 0.750579 Iteration 2 Error: 0.088797 Iteration 3 Error: 0.020879 Align patch 8 17 left Iteration 1 Error: 1.091244 Iteration 2 Error: 0.175559 Iteration 3 Error: 0.044720 Align patch 9 16 left Iteration 1 Error: 0.649971 Iteration 2 Error: 0.137804 Iteration 3 Error: 0.047667 Align patch 10 15 left Iteration 1 Error: 0.966715 Iteration 2 Error: 0.129197 Iteration 3 Error: 0.031583 Align patch 11 14 left Iteration 1 Error: 0.874804 Iteration 2 Error: 0.131482 Iteration 3 Error: 0.043202 Align patch 12 13 left Iteration 1 Error: 0.653345 Iteration 2 Error: 0.127828 Iteration 3 Error: 0.069746 Iteration 4 Error: 0.024186 Align patch 13 12 left Iteration 1 Error: 0.777428 Iteration 2 Error: 0.129731 Iteration 3 Error: 0.029486 Align patch 14 11 left Iteration 1 Error: 0.631750 Iteration 2 Error: 0.175657 Iteration 3 Error: 0.040376 Align patch 15 10 left Iteration 1 Error: 0.459281 Iteration 2 Error: 0.082811 Iteration 3 Error: 0.016514 Align patch 16 9 left Iteration 1 Error: 2.149878 Iteration 2 Error: 0.250642 Iteration 3 Error: 0.120049 Iteration 4 Error: 0.044419 Align patch 17 8 left Iteration 1 Error: 1.933878 Iteration 2 Error: 0.179074 Iteration 3 Error: 0.042449 Align patch 18 7 left Iteration 1 Error: 1.136869 Iteration 2 Error: 0.213767 Iteration 3 Error: 0.040359 Align patch 19 6 left Iteration 1 Error: 0.472474 Iteration 2 Error: 0.107987 Iteration 3 Error: 0.018613 Align patch 20 5 left Iteration 1 Error: 0.672154 Iteration 2 Error: 0.119794 Iteration 3 Error: 0.022847 Align patch 21 4 left Iteration 1 Error: 2.363978 Iteration 2 Error: 0.275861 Iteration 3 Error: 0.089090 Iteration 4 Error: 0.031815 Align patch 22 3 left Iteration 1 Error: 1.160208 Iteration 2 Error: 0.191543 Iteration 3 Error: 0.034928 Align patch 23 2 left Iteration 1 Error: 1.851439 Iteration 2 Error: 0.134738 Iteration 3 Error: 0.046895 Align patch 24 1 left Iteration 1 Error: 0.798751 Iteration 2 Error: 0.114514 Iteration 3 Error: 0.037547 Align patch 25 0 left Iteration 1 Error: 0.699701 Iteration 2 Error: 0.115793 Iteration 3 Error: 0.019619 3D Fitting completed. Patch alignment time: 11.82(sec) Local motion has been corrected. Process thread exits. Computational time: 23.087507 sec Total time: 30.050003 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00006hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00006hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.600049s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00006hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.783528s ........................................ >>>>>>TIME<<<<<< FFT: 0.920328s Defocus_U Defocus_V Angle CCC 14521.67 13876.79 83.52 0.052272 Final Values Defocus_U Defocus_V Angle CCC 14537.30 13879.92 81.65 0.092286 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00007hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00007hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 45.95 7.83 Num Hot pixels: 176 Hot pixel threshold: 92.93 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.693297 Iteration 2 Error: 0.267509 Iteration 3 Error: 0.087499 Iteration 4 Error: 0.041890 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.30 -0.06 ...... Frame ( 3) shift: -0.59 -0.12 ...... Frame ( 4) shift: -0.89 -0.18 ...... Frame ( 5) shift: -1.19 -0.24 ...... Frame ( 6) shift: -1.23 -0.22 ...... Frame ( 7) shift: -1.03 -0.13 ...... Frame ( 8) shift: -0.83 -0.04 ...... Frame ( 9) shift: -0.67 0.06 ...... Frame ( 10) shift: -0.56 0.17 ...... Frame ( 11) shift: -0.45 0.27 ...... Frame ( 12) shift: -0.36 0.33 ...... Frame ( 13) shift: -0.29 0.34 ...... Frame ( 14) shift: -0.23 0.35 ...... Frame ( 15) shift: -0.16 0.44 ...... Frame ( 16) shift: -0.09 0.60 ...... Frame ( 17) shift: -0.02 0.75 ...... Frame ( 18) shift: 0.06 0.85 ...... Frame ( 19) shift: 0.14 0.90 ...... Frame ( 20) shift: 0.22 0.94 ...... Frame ( 21) shift: 0.30 0.99 ...... Frame ( 22) shift: 0.38 1.05 ...... Frame ( 23) shift: 0.45 1.10 ...... Frame ( 24) shift: 0.52 1.14 ...... Frame ( 25) shift: 0.57 1.16 ...... Frame ( 26) shift: 0.63 1.18 ...... Frame ( 27) shift: 0.66 1.21 ...... Frame ( 28) shift: 0.66 1.25 ...... Frame ( 29) shift: 0.65 1.29 ...... Frame ( 30) shift: 0.68 1.35 ...... Frame ( 31) shift: 0.73 1.42 ...... Frame ( 32) shift: 0.79 1.48 ...... Frame ( 33) shift: 0.80 1.55 ...... Frame ( 34) shift: 0.76 1.63 ...... Frame ( 35) shift: 0.72 1.70 ...... Frame ( 36) shift: 0.72 1.76 ...... Frame ( 37) shift: 0.77 1.81 ...... Frame ( 38) shift: 0.81 1.86 ...... Frame ( 39) shift: 0.86 1.90 ...... Frame ( 40) shift: 0.90 1.95 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.024247 Iteration 2 Error: 0.200532 Iteration 3 Error: 0.056735 Iteration 4 Error: 0.037343 Align patch 2 23 left Iteration 1 Error: 1.695652 Iteration 2 Error: 0.312045 Iteration 3 Error: 0.095774 Iteration 4 Error: 0.033152 Align patch 3 22 left Iteration 1 Error: 1.332612 Iteration 2 Error: 0.221863 Iteration 3 Error: 0.081297 Iteration 4 Error: 0.028679 Align patch 4 21 left Iteration 1 Error: 0.684154 Iteration 2 Error: 0.150281 Iteration 3 Error: 0.057502 Iteration 4 Error: 0.013912 Align patch 5 20 left Iteration 1 Error: 0.415313 Iteration 2 Error: 0.062066 Iteration 3 Error: 0.013841 Align patch 6 19 left Iteration 1 Error: 1.080733 Iteration 2 Error: 0.180204 Iteration 3 Error: 0.063200 Iteration 4 Error: 0.020438 Align patch 7 18 left Iteration 1 Error: 1.214208 Iteration 2 Error: 0.227860 Iteration 3 Error: 0.132799 Iteration 4 Error: 0.044857 Align patch 8 17 left Iteration 1 Error: 1.111634 Iteration 2 Error: 0.183510 Iteration 3 Error: 0.061079 Iteration 4 Error: 0.025600 Align patch 9 16 left Iteration 1 Error: 1.043010 Iteration 2 Error: 0.119804 Iteration 3 Error: 0.040803 Align patch 10 15 left Iteration 1 Error: 0.578593 Iteration 2 Error: 0.162875 Iteration 3 Error: 0.043216 Align patch 11 14 left Iteration 1 Error: 1.422518 Iteration 2 Error: 0.247428 Iteration 3 Error: 0.081125 Iteration 4 Error: 0.030201 Align patch 12 13 left Iteration 1 Error: 1.200541 Iteration 2 Error: 0.250561 Iteration 3 Error: 0.083570 Iteration 4 Error: 0.039135 Align patch 13 12 left Iteration 1 Error: 1.136188 Iteration 2 Error: 0.208386 Iteration 3 Error: 0.053347 Iteration 4 Error: 0.024125 Align patch 14 11 left Iteration 1 Error: 0.749024 Iteration 2 Error: 0.168454 Iteration 3 Error: 0.058867 Iteration 4 Error: 0.023635 Align patch 15 10 left Iteration 1 Error: 0.835735 Iteration 2 Error: 0.143356 Iteration 3 Error: 0.035145 Align patch 16 9 left Iteration 1 Error: 1.534786 Iteration 2 Error: 0.245844 Iteration 3 Error: 0.069904 Iteration 4 Error: 0.021730 Align patch 17 8 left Iteration 1 Error: 0.950262 Iteration 2 Error: 0.203091 Iteration 3 Error: 0.054116 Iteration 4 Error: 0.019385 Align patch 18 7 left Iteration 1 Error: 0.834106 Iteration 2 Error: 0.126233 Iteration 3 Error: 0.028461 Align patch 19 6 left Iteration 1 Error: 0.439099 Iteration 2 Error: 0.115111 Iteration 3 Error: 0.031021 Align patch 20 5 left Iteration 1 Error: 2.037813 Iteration 2 Error: 0.509812 Iteration 3 Error: 0.191830 Iteration 4 Error: 0.081712 Iteration 5 Error: 0.029829 Align patch 21 4 left Iteration 1 Error: 1.572370 Iteration 2 Error: 0.281721 Iteration 3 Error: 0.060297 Iteration 4 Error: 0.017037 Align patch 22 3 left Iteration 1 Error: 1.384992 Iteration 2 Error: 0.258939 Iteration 3 Error: 0.071229 Iteration 4 Error: 0.029440 Align patch 23 2 left Iteration 1 Error: 0.748400 Iteration 2 Error: 0.164235 Iteration 3 Error: 0.044367 Align patch 24 1 left Iteration 1 Error: 0.696751 Iteration 2 Error: 0.251443 Iteration 3 Error: 0.038650 Align patch 25 0 left Iteration 1 Error: 2.594755 Iteration 2 Error: 0.470377 Iteration 3 Error: 0.128361 Iteration 4 Error: 0.035129 3D Fitting completed. Patch alignment time: 11.90(sec) Local motion has been corrected. Process thread exits. Computational time: 23.081074 sec Total time: 30.299957 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00007hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00007hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.801788s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00007hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.589594s ........................................ >>>>>>TIME<<<<<< FFT: 0.984475s Defocus_U Defocus_V Angle CCC 9394.54 10238.29 10.79 0.044448 Final Values Defocus_U Defocus_V Angle CCC 9378.91 10244.55 11.73 0.083930 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00007hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00007hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.001e-01 CC threshold: 0.735 Mean Std: 46.60 7.75 Num Hot pixels: 169 Hot pixel threshold: 93.13 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.987275 Iteration 2 Error: 0.100027 Iteration 3 Error: 0.023536 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.30 0.05 ...... Frame ( 3) shift: -0.61 0.10 ...... Frame ( 4) shift: -0.91 0.15 ...... Frame ( 5) shift: -1.21 0.20 ...... Frame ( 6) shift: -1.34 0.27 ...... Frame ( 7) shift: -1.27 0.37 ...... Frame ( 8) shift: -1.21 0.47 ...... Frame ( 9) shift: -1.16 0.56 ...... Frame ( 10) shift: -1.12 0.63 ...... Frame ( 11) shift: -1.09 0.70 ...... Frame ( 12) shift: -1.08 0.76 ...... Frame ( 13) shift: -1.10 0.82 ...... Frame ( 14) shift: -1.13 0.87 ...... Frame ( 15) shift: -1.12 0.92 ...... Frame ( 16) shift: -1.07 0.98 ...... Frame ( 17) shift: -1.03 1.03 ...... Frame ( 18) shift: -1.01 1.09 ...... Frame ( 19) shift: -1.01 1.14 ...... Frame ( 20) shift: -1.01 1.20 ...... Frame ( 21) shift: -1.02 1.22 ...... Frame ( 22) shift: -1.04 1.19 ...... Frame ( 23) shift: -1.07 1.17 ...... Frame ( 24) shift: -1.02 1.20 ...... Frame ( 25) shift: -0.92 1.27 ...... Frame ( 26) shift: -0.81 1.34 ...... Frame ( 27) shift: -0.77 1.36 ...... Frame ( 28) shift: -0.78 1.33 ...... Frame ( 29) shift: -0.79 1.30 ...... Frame ( 30) shift: -0.78 1.32 ...... Frame ( 31) shift: -0.75 1.38 ...... Frame ( 32) shift: -0.72 1.44 ...... Frame ( 33) shift: -0.72 1.48 ...... Frame ( 34) shift: -0.73 1.49 ...... Frame ( 35) shift: -0.75 1.50 ...... Frame ( 36) shift: -0.73 1.52 ...... Frame ( 37) shift: -0.66 1.55 ...... Frame ( 38) shift: -0.59 1.58 ...... Frame ( 39) shift: -0.53 1.61 ...... Frame ( 40) shift: -0.46 1.64 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.424599 Iteration 2 Error: 0.371228 Iteration 3 Error: 0.101447 Iteration 4 Error: 0.055116 Iteration 5 Error: 0.014504 Align patch 2 23 left Iteration 1 Error: 0.865012 Iteration 2 Error: 0.097727 Iteration 3 Error: 0.017521 Align patch 3 22 left Iteration 1 Error: 1.820403 Iteration 2 Error: 0.172143 Iteration 3 Error: 0.049599 Align patch 4 21 left Iteration 1 Error: 0.632744 Iteration 2 Error: 0.115216 Iteration 3 Error: 0.023900 Align patch 5 20 left Iteration 1 Error: 0.608411 Iteration 2 Error: 0.098491 Iteration 3 Error: 0.022449 Align patch 6 19 left Iteration 1 Error: 1.372909 Iteration 2 Error: 0.347245 Iteration 3 Error: 0.107923 Iteration 4 Error: 0.029335 Align patch 7 18 left Iteration 1 Error: 0.994819 Iteration 2 Error: 0.154596 Iteration 3 Error: 0.053534 Iteration 4 Error: 0.016113 Align patch 8 17 left Iteration 1 Error: 0.723509 Iteration 2 Error: 0.117986 Iteration 3 Error: 0.040878 Align patch 9 16 left Iteration 1 Error: 0.798914 Iteration 2 Error: 0.113743 Iteration 3 Error: 0.041617 Align patch 10 15 left Iteration 1 Error: 0.592610 Iteration 2 Error: 0.076757 Iteration 3 Error: 0.012555 Align patch 11 14 left Iteration 1 Error: 1.194349 Iteration 2 Error: 0.294043 Iteration 3 Error: 0.093495 Iteration 4 Error: 0.026532 Align patch 12 13 left Iteration 1 Error: 0.925636 Iteration 2 Error: 0.189704 Iteration 3 Error: 0.048512 Align patch 13 12 left Iteration 1 Error: 0.824210 Iteration 2 Error: 0.196755 Iteration 3 Error: 0.086861 Iteration 4 Error: 0.026168 Align patch 14 11 left Iteration 1 Error: 0.765792 Iteration 2 Error: 0.079994 Iteration 3 Error: 0.020772 Align patch 15 10 left Iteration 1 Error: 0.496735 Iteration 2 Error: 0.107284 Iteration 3 Error: 0.019676 Align patch 16 9 left Iteration 1 Error: 0.945541 Iteration 2 Error: 0.265626 Iteration 3 Error: 0.063874 Iteration 4 Error: 0.020427 Align patch 17 8 left Iteration 1 Error: 0.659538 Iteration 2 Error: 0.147405 Iteration 3 Error: 0.043803 Align patch 18 7 left Iteration 1 Error: 0.876085 Iteration 2 Error: 0.121779 Iteration 3 Error: 0.037679 Align patch 19 6 left Iteration 1 Error: 0.888494 Iteration 2 Error: 0.142984 Iteration 3 Error: 0.045171 Align patch 20 5 left Iteration 1 Error: 0.693758 Iteration 2 Error: 0.099127 Iteration 3 Error: 0.027902 Align patch 21 4 left Iteration 1 Error: 1.805700 Iteration 2 Error: 0.254277 Iteration 3 Error: 0.058954 Iteration 4 Error: 0.022611 Align patch 22 3 left Iteration 1 Error: 0.672585 Iteration 2 Error: 0.107948 Iteration 3 Error: 0.030658 Align patch 23 2 left Iteration 1 Error: 1.096446 Iteration 2 Error: 0.119518 Iteration 3 Error: 0.045138 Align patch 24 1 left Iteration 1 Error: 0.807243 Iteration 2 Error: 0.120585 Iteration 3 Error: 0.022229 Align patch 25 0 left Iteration 1 Error: 0.655799 Iteration 2 Error: 0.087312 Iteration 3 Error: 0.018920 3D Fitting completed. Patch alignment time: 12.12(sec) Local motion has been corrected. Process thread exits. Computational time: 22.597740 sec Total time: 31.007362 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00007hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00007hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.607666s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00007hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.667471s ........................................ >>>>>>TIME<<<<<< FFT: 1.171470s Defocus_U Defocus_V Angle CCC 10976.60 10503.95 89.07 0.046806 Final Values Defocus_U Defocus_V Angle CCC 11003.18 10518.03 89.70 0.085817 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00007hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00007hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.997e-02 CC threshold: 0.734 Mean Std: 48.02 7.61 Num Hot pixels: 200 Hot pixel threshold: 93.68 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.885968 Iteration 2 Error: 0.119426 Iteration 3 Error: 0.023732 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.16 0.09 ...... Frame ( 3) shift: -0.32 0.19 ...... Frame ( 4) shift: -0.47 0.28 ...... Frame ( 5) shift: -0.63 0.37 ...... Frame ( 6) shift: -0.64 0.46 ...... Frame ( 7) shift: -0.50 0.54 ...... Frame ( 8) shift: -0.35 0.63 ...... Frame ( 9) shift: -0.21 0.74 ...... Frame ( 10) shift: -0.08 0.88 ...... Frame ( 11) shift: 0.05 1.02 ...... Frame ( 12) shift: 0.11 1.06 ...... Frame ( 13) shift: 0.09 0.99 ...... Frame ( 14) shift: 0.07 0.92 ...... Frame ( 15) shift: 0.08 0.90 ...... Frame ( 16) shift: 0.12 0.93 ...... Frame ( 17) shift: 0.16 0.96 ...... Frame ( 18) shift: 0.18 0.98 ...... Frame ( 19) shift: 0.19 0.98 ...... Frame ( 20) shift: 0.20 0.99 ...... Frame ( 21) shift: 0.22 1.02 ...... Frame ( 22) shift: 0.26 1.09 ...... Frame ( 23) shift: 0.29 1.15 ...... Frame ( 24) shift: 0.30 1.17 ...... Frame ( 25) shift: 0.29 1.15 ...... Frame ( 26) shift: 0.27 1.13 ...... Frame ( 27) shift: 0.28 1.13 ...... Frame ( 28) shift: 0.30 1.15 ...... Frame ( 29) shift: 0.32 1.18 ...... Frame ( 30) shift: 0.37 1.18 ...... Frame ( 31) shift: 0.45 1.17 ...... Frame ( 32) shift: 0.52 1.16 ...... Frame ( 33) shift: 0.59 1.13 ...... Frame ( 34) shift: 0.64 1.06 ...... Frame ( 35) shift: 0.69 1.00 ...... Frame ( 36) shift: 0.69 0.95 ...... Frame ( 37) shift: 0.62 0.92 ...... Frame ( 38) shift: 0.56 0.90 ...... Frame ( 39) shift: 0.50 0.87 ...... Frame ( 40) shift: 0.43 0.85 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.313854 Iteration 2 Error: 0.587232 Iteration 3 Error: 0.457793 Iteration 4 Error: 0.395858 Iteration 5 Error: 0.309883 Align patch 1 24 left Iteration 1 Error: 3.490351 Iteration 2 Error: 0.282741 Iteration 3 Error: 0.059285 Iteration 4 Error: 0.047300 Align patch 2 23 left Iteration 1 Error: 2.449188 Iteration 2 Error: 0.279733 Iteration 3 Error: 0.135594 Iteration 4 Error: 0.100448 Iteration 5 Error: 0.052686 Align patch 2 23 left Iteration 1 Error: 3.296006 Iteration 2 Error: 0.233217 Iteration 3 Error: 0.059579 Iteration 4 Error: 0.024074 Align patch 3 22 left Iteration 1 Error: 2.293678 Iteration 2 Error: 0.201817 Iteration 3 Error: 0.118234 Iteration 4 Error: 0.083183 Iteration 5 Error: 0.056761 Align patch 3 22 left Iteration 1 Error: 2.831119 Iteration 2 Error: 0.202657 Iteration 3 Error: 0.057067 Iteration 4 Error: 0.027134 Align patch 4 21 left Iteration 1 Error: 0.745325 Iteration 2 Error: 0.153561 Iteration 3 Error: 0.026296 Align patch 5 20 left Iteration 1 Error: 0.952587 Iteration 2 Error: 0.093737 Iteration 3 Error: 0.014190 Align patch 6 19 left Iteration 1 Error: 2.877705 Iteration 2 Error: 0.431078 Iteration 3 Error: 0.529855 Iteration 4 Error: 0.166019 Iteration 5 Error: 0.154577 Align patch 6 19 left Iteration 1 Error: 3.208959 Iteration 2 Error: 0.243440 Iteration 3 Error: 0.052079 Iteration 4 Error: 0.017986 Align patch 7 18 left Iteration 1 Error: 2.586198 Iteration 2 Error: 0.192790 Iteration 3 Error: 0.059005 Iteration 4 Error: 0.060923 Iteration 5 Error: 0.033698 Align patch 8 17 left Iteration 1 Error: 3.302418 Iteration 2 Error: 0.254029 Iteration 3 Error: 0.065411 Iteration 4 Error: 0.039945 Align patch 9 16 left Iteration 1 Error: 1.195443 Iteration 2 Error: 0.135288 Iteration 3 Error: 0.032742 Align patch 10 15 left Iteration 1 Error: 0.800999 Iteration 2 Error: 0.100538 Iteration 3 Error: 0.034862 Align patch 11 14 left Iteration 1 Error: 4.987532 Iteration 2 Error: 0.465821 Iteration 3 Error: 0.224568 Iteration 4 Error: 0.076084 Iteration 5 Error: 0.059101 Align patch 11 14 left Iteration 1 Error: 2.354156 Iteration 2 Error: 0.281091 Iteration 3 Error: 0.083057 Iteration 4 Error: 0.030986 Align patch 12 13 left Iteration 1 Error: 0.891028 Iteration 2 Error: 0.113090 Iteration 3 Error: 0.027053 Align patch 13 12 left Iteration 1 Error: 0.923529 Iteration 2 Error: 0.197952 Iteration 3 Error: 0.053537 Iteration 4 Error: 0.027202 Align patch 14 11 left Iteration 1 Error: 1.388053 Iteration 2 Error: 0.157798 Iteration 3 Error: 0.046714 Align patch 15 10 left Iteration 1 Error: 1.043268 Iteration 2 Error: 0.196667 Iteration 3 Error: 0.048250 Align patch 16 9 left Iteration 1 Error: 1.801014 Iteration 2 Error: 0.223525 Iteration 3 Error: 0.132752 Iteration 4 Error: 0.053821 Iteration 5 Error: 0.035498 Align patch 17 8 left Iteration 1 Error: 1.309185 Iteration 2 Error: 0.211298 Iteration 3 Error: 0.055414 Iteration 4 Error: 0.019713 Align patch 18 7 left Iteration 1 Error: 1.191316 Iteration 2 Error: 0.140827 Iteration 3 Error: 0.027855 Align patch 19 6 left Iteration 1 Error: 0.945391 Iteration 2 Error: 0.149342 Iteration 3 Error: 0.027673 Align patch 20 5 left Iteration 1 Error: 0.954133 Iteration 2 Error: 0.091122 Iteration 3 Error: 0.029190 Align patch 21 4 left Iteration 1 Error: 1.004765 Iteration 2 Error: 0.173112 Iteration 3 Error: 0.072957 Iteration 4 Error: 0.034752 Align patch 22 3 left Iteration 1 Error: 1.087105 Iteration 2 Error: 0.235227 Iteration 3 Error: 0.050223 Iteration 4 Error: 0.021385 Align patch 23 2 left Iteration 1 Error: 0.918773 Iteration 2 Error: 0.178096 Iteration 3 Error: 0.056601 Iteration 4 Error: 0.023063 Align patch 24 1 left Iteration 1 Error: 1.489948 Iteration 2 Error: 0.178639 Iteration 3 Error: 0.041419 Align patch 25 0 left Iteration 1 Error: 1.196210 Iteration 2 Error: 0.099164 Iteration 3 Error: 0.045261 3D Fitting completed. Patch alignment time: 15.59(sec) Local motion has been corrected. Process thread exits. Computational time: 26.144402 sec Total time: 33.545216 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00007hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00007hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.719294s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00007hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.493169s ........................................ >>>>>>TIME<<<<<< FFT: 0.914403s Defocus_U Defocus_V Angle CCC 14873.05 15771.48 7.49 0.051492 Final Values Defocus_U Defocus_V Angle CCC 14888.67 15762.11 7.49 0.089363 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00007hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00007hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.001e-01 CC threshold: 0.735 Mean Std: 47.89 7.66 Num Hot pixels: 201 Hot pixel threshold: 93.84 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.777432 Iteration 2 Error: 0.058162 Iteration 3 Error: 0.012696 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.19 0.13 ...... Frame ( 3) shift: -0.38 0.25 ...... Frame ( 4) shift: -0.57 0.38 ...... Frame ( 5) shift: -0.76 0.50 ...... Frame ( 6) shift: -0.84 0.59 ...... Frame ( 7) shift: -0.80 0.64 ...... Frame ( 8) shift: -0.76 0.69 ...... Frame ( 9) shift: -0.70 0.74 ...... Frame ( 10) shift: -0.62 0.78 ...... Frame ( 11) shift: -0.54 0.82 ...... Frame ( 12) shift: -0.47 0.89 ...... Frame ( 13) shift: -0.42 0.97 ...... Frame ( 14) shift: -0.37 1.06 ...... Frame ( 15) shift: -0.39 1.09 ...... Frame ( 16) shift: -0.48 1.06 ...... Frame ( 17) shift: -0.58 1.03 ...... Frame ( 18) shift: -0.61 1.01 ...... Frame ( 19) shift: -0.60 0.99 ...... Frame ( 20) shift: -0.58 0.97 ...... Frame ( 21) shift: -0.56 0.98 ...... Frame ( 22) shift: -0.53 1.02 ...... Frame ( 23) shift: -0.50 1.07 ...... Frame ( 24) shift: -0.53 1.09 ...... Frame ( 25) shift: -0.60 1.08 ...... Frame ( 26) shift: -0.68 1.08 ...... Frame ( 27) shift: -0.69 1.03 ...... Frame ( 28) shift: -0.64 0.95 ...... Frame ( 29) shift: -0.59 0.86 ...... Frame ( 30) shift: -0.57 0.86 ...... Frame ( 31) shift: -0.58 0.93 ...... Frame ( 32) shift: -0.59 1.01 ...... Frame ( 33) shift: -0.61 1.06 ...... Frame ( 34) shift: -0.65 1.08 ...... Frame ( 35) shift: -0.68 1.10 ...... Frame ( 36) shift: -0.73 1.13 ...... Frame ( 37) shift: -0.79 1.16 ...... Frame ( 38) shift: -0.84 1.20 ...... Frame ( 39) shift: -0.90 1.23 ...... Frame ( 40) shift: -0.96 1.27 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 3.095985 Iteration 2 Error: 0.260923 Iteration 3 Error: 0.046044 Align patch 2 23 left Iteration 1 Error: 1.270114 Iteration 2 Error: 0.197840 Iteration 3 Error: 0.023772 Align patch 3 22 left Iteration 1 Error: 1.305508 Iteration 2 Error: 0.173677 Iteration 3 Error: 0.044933 Align patch 4 21 left Iteration 1 Error: 0.913079 Iteration 2 Error: 0.191347 Iteration 3 Error: 0.037460 Align patch 5 20 left Iteration 1 Error: 0.619604 Iteration 2 Error: 0.079436 Iteration 3 Error: 0.013026 Align patch 6 19 left Iteration 1 Error: 0.979271 Iteration 2 Error: 0.178120 Iteration 3 Error: 0.061825 Iteration 4 Error: 0.019385 Align patch 7 18 left Iteration 1 Error: 1.946787 Iteration 2 Error: 0.308594 Iteration 3 Error: 0.086612 Iteration 4 Error: 0.037414 Align patch 8 17 left Iteration 1 Error: 0.679462 Iteration 2 Error: 0.091874 Iteration 3 Error: 0.023439 Align patch 9 16 left Iteration 1 Error: 1.114168 Iteration 2 Error: 0.119302 Iteration 3 Error: 0.016254 Align patch 10 15 left Iteration 1 Error: 0.678665 Iteration 2 Error: 0.105294 Iteration 3 Error: 0.024568 Align patch 11 14 left Iteration 1 Error: 0.901292 Iteration 2 Error: 0.271957 Iteration 3 Error: 0.089190 Iteration 4 Error: 0.036519 Align patch 12 13 left Iteration 1 Error: 0.855442 Iteration 2 Error: 0.181051 Iteration 3 Error: 0.062599 Iteration 4 Error: 0.031294 Align patch 13 12 left Iteration 1 Error: 0.712608 Iteration 2 Error: 0.095388 Iteration 3 Error: 0.032391 Align patch 14 11 left Iteration 1 Error: 1.030580 Iteration 2 Error: 0.149391 Iteration 3 Error: 0.021166 Align patch 15 10 left Iteration 1 Error: 0.928624 Iteration 2 Error: 0.108332 Iteration 3 Error: 0.018038 Align patch 16 9 left Iteration 1 Error: 0.705725 Iteration 2 Error: 0.116086 Iteration 3 Error: 0.024793 Align patch 17 8 left Iteration 1 Error: 1.015549 Iteration 2 Error: 0.188368 Iteration 3 Error: 0.042408 Align patch 18 7 left Iteration 1 Error: 1.018785 Iteration 2 Error: 0.096759 Iteration 3 Error: 0.027582 Align patch 19 6 left Iteration 1 Error: 0.788434 Iteration 2 Error: 0.121230 Iteration 3 Error: 0.029011 Align patch 20 5 left Iteration 1 Error: 0.657682 Iteration 2 Error: 0.074722 Iteration 3 Error: 0.015197 Align patch 21 4 left Iteration 1 Error: 1.081725 Iteration 2 Error: 0.218067 Iteration 3 Error: 0.053212 Iteration 4 Error: 0.024907 Align patch 22 3 left Iteration 1 Error: 0.960603 Iteration 2 Error: 0.148299 Iteration 3 Error: 0.019107 Align patch 23 2 left Iteration 1 Error: 1.141649 Iteration 2 Error: 0.181755 Iteration 3 Error: 0.048377 Align patch 24 1 left Iteration 1 Error: 1.047608 Iteration 2 Error: 0.134730 Iteration 3 Error: 0.032247 Align patch 25 0 left Iteration 1 Error: 0.623651 Iteration 2 Error: 0.112149 Iteration 3 Error: 0.022099 3D Fitting completed. Patch alignment time: 11.98(sec) Local motion has been corrected. Process thread exits. Computational time: 23.277544 sec Total time: 32.232800 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00007hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00007hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.124647s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00007hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 4.166215s ........................................ >>>>>>TIME<<<<<< FFT: 1.076097s Defocus_U Defocus_V Angle CCC 14177.73 13412.11 84.70 0.053480 Final Values Defocus_U Defocus_V Angle CCC 14169.92 13416.81 85.33 0.090274 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00008hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00008hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.990e-02 CC threshold: 0.734 Mean Std: 43.81 7.39 Num Hot pixels: 171 Hot pixel threshold: 88.16 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.231079 Iteration 2 Error: 0.248657 Iteration 3 Error: 0.072258 Iteration 4 Error: 0.022930 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.27 -0.06 ...... Frame ( 3) shift: -0.54 -0.12 ...... Frame ( 4) shift: -0.81 -0.17 ...... Frame ( 5) shift: -1.08 -0.23 ...... Frame ( 6) shift: -1.22 -0.20 ...... Frame ( 7) shift: -1.21 -0.07 ...... Frame ( 8) shift: -1.20 0.05 ...... Frame ( 9) shift: -1.15 0.17 ...... Frame ( 10) shift: -1.04 0.29 ...... Frame ( 11) shift: -0.94 0.41 ...... Frame ( 12) shift: -0.87 0.52 ...... Frame ( 13) shift: -0.84 0.61 ...... Frame ( 14) shift: -0.81 0.71 ...... Frame ( 15) shift: -0.77 0.83 ...... Frame ( 16) shift: -0.71 0.98 ...... Frame ( 17) shift: -0.65 1.12 ...... Frame ( 18) shift: -0.62 1.22 ...... Frame ( 19) shift: -0.62 1.28 ...... Frame ( 20) shift: -0.62 1.35 ...... Frame ( 21) shift: -0.59 1.38 ...... Frame ( 22) shift: -0.54 1.39 ...... Frame ( 23) shift: -0.49 1.39 ...... Frame ( 24) shift: -0.46 1.40 ...... Frame ( 25) shift: -0.43 1.41 ...... Frame ( 26) shift: -0.40 1.41 ...... Frame ( 27) shift: -0.36 1.42 ...... Frame ( 28) shift: -0.30 1.44 ...... Frame ( 29) shift: -0.25 1.45 ...... Frame ( 30) shift: -0.20 1.53 ...... Frame ( 31) shift: -0.16 1.67 ...... Frame ( 32) shift: -0.12 1.81 ...... Frame ( 33) shift: -0.10 1.90 ...... Frame ( 34) shift: -0.10 1.93 ...... Frame ( 35) shift: -0.10 1.95 ...... Frame ( 36) shift: -0.08 1.96 ...... Frame ( 37) shift: -0.06 1.95 ...... Frame ( 38) shift: -0.03 1.95 ...... Frame ( 39) shift: 0.00 1.94 ...... Frame ( 40) shift: 0.03 1.93 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.932218 Iteration 2 Error: 0.248091 Iteration 3 Error: 0.132138 Iteration 4 Error: 0.039811 Align patch 2 23 left Iteration 1 Error: 0.904935 Iteration 2 Error: 0.205145 Iteration 3 Error: 0.094616 Iteration 4 Error: 0.037400 Align patch 3 22 left Iteration 1 Error: 0.953025 Iteration 2 Error: 0.256310 Iteration 3 Error: 0.093641 Iteration 4 Error: 0.029941 Align patch 4 21 left Iteration 1 Error: 1.009553 Iteration 2 Error: 0.167943 Iteration 3 Error: 0.039706 Align patch 5 20 left Iteration 1 Error: 0.985320 Iteration 2 Error: 0.206826 Iteration 3 Error: 0.069089 Iteration 4 Error: 0.022935 Align patch 6 19 left Iteration 1 Error: 1.313266 Iteration 2 Error: 0.266582 Iteration 3 Error: 0.088381 Iteration 4 Error: 0.033688 Align patch 7 18 left Iteration 1 Error: 1.279000 Iteration 2 Error: 0.378807 Iteration 3 Error: 0.195066 Iteration 4 Error: 0.084301 Iteration 5 Error: 0.044469 Align patch 8 17 left Iteration 1 Error: 0.822401 Iteration 2 Error: 0.312610 Iteration 3 Error: 0.235880 Iteration 4 Error: 0.107788 Iteration 5 Error: 0.074741 Align patch 8 17 left Iteration 1 Error: 1.299909 Iteration 2 Error: 0.222514 Iteration 3 Error: 0.058996 Iteration 4 Error: 0.017972 Align patch 9 16 left Iteration 1 Error: 0.997217 Iteration 2 Error: 0.314174 Iteration 3 Error: 0.100220 Iteration 4 Error: 0.040662 Align patch 10 15 left Iteration 1 Error: 0.772576 Iteration 2 Error: 0.227091 Iteration 3 Error: 0.055072 Iteration 4 Error: 0.020472 Align patch 11 14 left Iteration 1 Error: 0.910524 Iteration 2 Error: 0.197791 Iteration 3 Error: 0.091731 Iteration 4 Error: 0.032265 Align patch 12 13 left Iteration 1 Error: 0.673431 Iteration 2 Error: 0.135209 Iteration 3 Error: 0.052368 Iteration 4 Error: 0.027861 Align patch 13 12 left Iteration 1 Error: 1.119217 Iteration 2 Error: 0.220843 Iteration 3 Error: 0.064474 Iteration 4 Error: 0.029005 Align patch 14 11 left Iteration 1 Error: 0.896734 Iteration 2 Error: 0.193565 Iteration 3 Error: 0.068817 Iteration 4 Error: 0.016240 Align patch 15 10 left Iteration 1 Error: 0.716612 Iteration 2 Error: 0.099891 Iteration 3 Error: 0.020707 Align patch 16 9 left Iteration 1 Error: 1.047928 Iteration 2 Error: 0.162848 Iteration 3 Error: 0.072877 Iteration 4 Error: 0.015748 Align patch 17 8 left Iteration 1 Error: 0.790021 Iteration 2 Error: 0.238211 Iteration 3 Error: 0.074590 Iteration 4 Error: 0.040795 Align patch 18 7 left Iteration 1 Error: 0.956294 Iteration 2 Error: 0.245005 Iteration 3 Error: 0.064408 Iteration 4 Error: 0.023092 Align patch 19 6 left Iteration 1 Error: 0.933436 Iteration 2 Error: 0.141610 Iteration 3 Error: 0.043879 Align patch 20 5 left Iteration 1 Error: 0.919902 Iteration 2 Error: 0.208257 Iteration 3 Error: 0.039554 Align patch 21 4 left Iteration 1 Error: 0.634687 Iteration 2 Error: 0.166526 Iteration 3 Error: 0.043485 Align patch 22 3 left Iteration 1 Error: 0.943569 Iteration 2 Error: 0.174708 Iteration 3 Error: 0.062089 Iteration 4 Error: 0.030591 Align patch 23 2 left Iteration 1 Error: 1.551068 Iteration 2 Error: 0.171172 Iteration 3 Error: 0.042265 Align patch 24 1 left Iteration 1 Error: 1.679713 Iteration 2 Error: 0.239120 Iteration 3 Error: 0.043532 Align patch 25 0 left Iteration 1 Error: 0.768963 Iteration 2 Error: 0.186656 Iteration 3 Error: 0.039842 3D Fitting completed. Patch alignment time: 12.71(sec) Local motion has been corrected. Process thread exits. Computational time: 25.079510 sec Total time: 32.632175 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00008hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00008hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.867668s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00008hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.805746s ........................................ >>>>>>TIME<<<<<< FFT: 1.028502s Defocus_U Defocus_V Angle CCC 12519.53 13421.88 14.39 0.040992 Final Values Defocus_U Defocus_V Angle CCC 12516.41 13418.75 14.08 0.073023 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00008hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00008hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.998e-02 CC threshold: 0.734 Mean Std: 45.64 7.69 Num Hot pixels: 169 Hot pixel threshold: 91.81 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.209773 Iteration 2 Error: 0.183057 Iteration 3 Error: 0.054668 Iteration 4 Error: 0.018447 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.27 0.07 ...... Frame ( 3) shift: -0.55 0.13 ...... Frame ( 4) shift: -0.82 0.20 ...... Frame ( 5) shift: -1.10 0.26 ...... Frame ( 6) shift: -1.21 0.37 ...... Frame ( 7) shift: -1.15 0.51 ...... Frame ( 8) shift: -1.10 0.65 ...... Frame ( 9) shift: -1.00 0.76 ...... Frame ( 10) shift: -0.87 0.84 ...... Frame ( 11) shift: -0.74 0.91 ...... Frame ( 12) shift: -0.67 0.98 ...... Frame ( 13) shift: -0.64 1.05 ...... Frame ( 14) shift: -0.62 1.11 ...... Frame ( 15) shift: -0.61 1.19 ...... Frame ( 16) shift: -0.61 1.27 ...... Frame ( 17) shift: -0.62 1.36 ...... Frame ( 18) shift: -0.61 1.44 ...... Frame ( 19) shift: -0.59 1.51 ...... Frame ( 20) shift: -0.57 1.57 ...... Frame ( 21) shift: -0.56 1.63 ...... Frame ( 22) shift: -0.56 1.67 ...... Frame ( 23) shift: -0.55 1.71 ...... Frame ( 24) shift: -0.58 1.75 ...... Frame ( 25) shift: -0.64 1.81 ...... Frame ( 26) shift: -0.71 1.86 ...... Frame ( 27) shift: -0.74 1.89 ...... Frame ( 28) shift: -0.75 1.88 ...... Frame ( 29) shift: -0.76 1.88 ...... Frame ( 30) shift: -0.74 1.90 ...... Frame ( 31) shift: -0.71 1.95 ...... Frame ( 32) shift: -0.68 2.00 ...... Frame ( 33) shift: -0.65 2.03 ...... Frame ( 34) shift: -0.62 2.02 ...... Frame ( 35) shift: -0.60 2.02 ...... Frame ( 36) shift: -0.58 2.02 ...... Frame ( 37) shift: -0.56 2.02 ...... Frame ( 38) shift: -0.55 2.02 ...... Frame ( 39) shift: -0.54 2.02 ...... Frame ( 40) shift: -0.53 2.02 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 3.900556 Iteration 2 Error: 0.439830 Iteration 3 Error: 0.155501 Iteration 4 Error: 0.061978 Iteration 5 Error: 0.030193 Align patch 2 23 left Iteration 1 Error: 2.792509 Iteration 2 Error: 0.337040 Iteration 3 Error: 0.215600 Iteration 4 Error: 0.062702 Iteration 5 Error: 0.022505 Align patch 3 22 left Iteration 1 Error: 1.189557 Iteration 2 Error: 0.395067 Iteration 3 Error: 0.159583 Iteration 4 Error: 0.075537 Iteration 5 Error: 0.063514 Align patch 3 22 left Iteration 1 Error: 1.749483 Iteration 2 Error: 0.183489 Iteration 3 Error: 0.034244 Align patch 4 21 left Iteration 1 Error: 0.852251 Iteration 2 Error: 0.146030 Iteration 3 Error: 0.040874 Align patch 5 20 left Iteration 1 Error: 0.591281 Iteration 2 Error: 0.089214 Iteration 3 Error: 0.012036 Align patch 6 19 left Iteration 1 Error: 3.159143 Iteration 2 Error: 0.348347 Iteration 3 Error: 0.125565 Iteration 4 Error: 0.026272 Align patch 7 18 left Iteration 1 Error: 0.899894 Iteration 2 Error: 0.127448 Iteration 3 Error: 0.042807 Align patch 8 17 left Iteration 1 Error: 0.862402 Iteration 2 Error: 0.201136 Iteration 3 Error: 0.108603 Iteration 4 Error: 0.037269 Align patch 9 16 left Iteration 1 Error: 0.650945 Iteration 2 Error: 0.140780 Iteration 3 Error: 0.026952 Align patch 10 15 left Iteration 1 Error: 0.671552 Iteration 2 Error: 0.115437 Iteration 3 Error: 0.028017 Align patch 11 14 left Iteration 1 Error: 1.654124 Iteration 2 Error: 0.248007 Iteration 3 Error: 0.045537 Align patch 12 13 left Iteration 1 Error: 0.974435 Iteration 2 Error: 0.200681 Iteration 3 Error: 0.053345 Iteration 4 Error: 0.012220 Align patch 13 12 left Iteration 1 Error: 0.907068 Iteration 2 Error: 0.148190 Iteration 3 Error: 0.039631 Align patch 14 11 left Iteration 1 Error: 0.802884 Iteration 2 Error: 0.163225 Iteration 3 Error: 0.053591 Iteration 4 Error: 0.014949 Align patch 15 10 left Iteration 1 Error: 0.551958 Iteration 2 Error: 0.083044 Iteration 3 Error: 0.012682 Align patch 16 9 left Iteration 1 Error: 0.881583 Iteration 2 Error: 0.213542 Iteration 3 Error: 0.060162 Iteration 4 Error: 0.016407 Align patch 17 8 left Iteration 1 Error: 1.053944 Iteration 2 Error: 0.147885 Iteration 3 Error: 0.038769 Align patch 18 7 left Iteration 1 Error: 0.700930 Iteration 2 Error: 0.114787 Iteration 3 Error: 0.018927 Align patch 19 6 left Iteration 1 Error: 0.742387 Iteration 2 Error: 0.071777 Iteration 3 Error: 0.035213 Align patch 20 5 left Iteration 1 Error: 1.008877 Iteration 2 Error: 0.172737 Iteration 3 Error: 0.025389 Align patch 21 4 left Iteration 1 Error: 1.031202 Iteration 2 Error: 0.399388 Iteration 3 Error: 0.079396 Iteration 4 Error: 0.041381 Align patch 22 3 left Iteration 1 Error: 1.038771 Iteration 2 Error: 0.193015 Iteration 3 Error: 0.056185 Iteration 4 Error: 0.014509 Align patch 23 2 left Iteration 1 Error: 0.872097 Iteration 2 Error: 0.111423 Iteration 3 Error: 0.028068 Align patch 24 1 left Iteration 1 Error: 0.664918 Iteration 2 Error: 0.126053 Iteration 3 Error: 0.040439 Align patch 25 0 left Iteration 1 Error: 0.728761 Iteration 2 Error: 0.111620 Iteration 3 Error: 0.018536 3D Fitting completed. Patch alignment time: 13.07(sec) Local motion has been corrected. Process thread exits. Computational time: 25.887413 sec Total time: 34.634254 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00008hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00008hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.681189s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00008hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.951040s ........................................ >>>>>>TIME<<<<<< FFT: 1.086322s Defocus_U Defocus_V Angle CCC 8525.39 8970.71 3.30 0.033634 Final Values Defocus_U Defocus_V Angle CCC 8534.77 8973.84 3.30 0.070692 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00008hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00008hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.734 Mean Std: 46.22 7.62 Num Hot pixels: 174 Hot pixel threshold: 91.92 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.926898 Iteration 2 Error: 0.097760 Iteration 3 Error: 0.024857 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.32 0.01 ...... Frame ( 3) shift: -0.64 0.02 ...... Frame ( 4) shift: -0.96 0.03 ...... Frame ( 5) shift: -1.28 0.04 ...... Frame ( 6) shift: -1.44 0.10 ...... Frame ( 7) shift: -1.44 0.21 ...... Frame ( 8) shift: -1.44 0.32 ...... Frame ( 9) shift: -1.40 0.43 ...... Frame ( 10) shift: -1.32 0.54 ...... Frame ( 11) shift: -1.24 0.64 ...... Frame ( 12) shift: -1.18 0.70 ...... Frame ( 13) shift: -1.14 0.72 ...... Frame ( 14) shift: -1.10 0.74 ...... Frame ( 15) shift: -1.09 0.76 ...... Frame ( 16) shift: -1.11 0.79 ...... Frame ( 17) shift: -1.14 0.82 ...... Frame ( 18) shift: -1.14 0.82 ...... Frame ( 19) shift: -1.12 0.79 ...... Frame ( 20) shift: -1.11 0.76 ...... Frame ( 21) shift: -1.10 0.80 ...... Frame ( 22) shift: -1.09 0.92 ...... Frame ( 23) shift: -1.09 1.04 ...... Frame ( 24) shift: -1.08 1.11 ...... Frame ( 25) shift: -1.07 1.12 ...... Frame ( 26) shift: -1.06 1.12 ...... Frame ( 27) shift: -1.04 1.13 ...... Frame ( 28) shift: -1.00 1.13 ...... Frame ( 29) shift: -0.96 1.13 ...... Frame ( 30) shift: -0.91 1.11 ...... Frame ( 31) shift: -0.86 1.09 ...... Frame ( 32) shift: -0.80 1.07 ...... Frame ( 33) shift: -0.80 1.06 ...... Frame ( 34) shift: -0.86 1.05 ...... Frame ( 35) shift: -0.92 1.05 ...... Frame ( 36) shift: -0.95 1.08 ...... Frame ( 37) shift: -0.95 1.16 ...... Frame ( 38) shift: -0.95 1.23 ...... Frame ( 39) shift: -0.95 1.30 ...... Frame ( 40) shift: -0.95 1.37 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.454501 Iteration 2 Error: 0.318155 Iteration 3 Error: 0.068579 Iteration 4 Error: 0.031827 Align patch 2 23 left Iteration 1 Error: 2.052126 Iteration 2 Error: 0.282048 Iteration 3 Error: 0.121817 Iteration 4 Error: 0.025727 Align patch 3 22 left Iteration 1 Error: 0.746181 Iteration 2 Error: 0.148475 Iteration 3 Error: 0.025280 Align patch 4 21 left Iteration 1 Error: 0.908980 Iteration 2 Error: 0.217471 Iteration 3 Error: 0.048308 Align patch 5 20 left Iteration 1 Error: 0.628635 Iteration 2 Error: 0.094081 Iteration 3 Error: 0.022591 Align patch 6 19 left Iteration 1 Error: 1.296286 Iteration 2 Error: 0.256509 Iteration 3 Error: 0.144876 Iteration 4 Error: 0.048019 Align patch 7 18 left Iteration 1 Error: 1.179028 Iteration 2 Error: 0.223951 Iteration 3 Error: 0.068812 Iteration 4 Error: 0.021255 Align patch 8 17 left Iteration 1 Error: 0.711527 Iteration 2 Error: 0.130177 Iteration 3 Error: 0.032066 Align patch 9 16 left Iteration 1 Error: 0.791279 Iteration 2 Error: 0.137313 Iteration 3 Error: 0.033835 Align patch 10 15 left Iteration 1 Error: 0.785645 Iteration 2 Error: 0.085815 Iteration 3 Error: 0.023788 Align patch 11 14 left Iteration 1 Error: 0.795278 Iteration 2 Error: 0.144852 Iteration 3 Error: 0.026948 Align patch 12 13 left Iteration 1 Error: 0.886981 Iteration 2 Error: 0.219160 Iteration 3 Error: 0.050521 Iteration 4 Error: 0.024004 Align patch 13 12 left Iteration 1 Error: 0.887064 Iteration 2 Error: 0.199200 Iteration 3 Error: 0.069589 Iteration 4 Error: 0.024617 Align patch 14 11 left Iteration 1 Error: 1.034981 Iteration 2 Error: 0.133086 Iteration 3 Error: 0.044590 Align patch 15 10 left Iteration 1 Error: 0.369848 Iteration 2 Error: 0.056677 Iteration 3 Error: 0.023835 Align patch 16 9 left Iteration 1 Error: 0.662319 Iteration 2 Error: 0.109593 Iteration 3 Error: 0.044047 Align patch 17 8 left Iteration 1 Error: 0.575375 Iteration 2 Error: 0.196731 Iteration 3 Error: 0.095171 Iteration 4 Error: 0.032716 Align patch 18 7 left Iteration 1 Error: 0.573913 Iteration 2 Error: 0.124445 Iteration 3 Error: 0.044476 Align patch 19 6 left Iteration 1 Error: 0.575499 Iteration 2 Error: 0.150147 Iteration 3 Error: 0.032800 Align patch 20 5 left Iteration 1 Error: 0.916473 Iteration 2 Error: 0.117114 Iteration 3 Error: 0.038289 Align patch 21 4 left Iteration 1 Error: 1.115938 Iteration 2 Error: 0.256764 Iteration 3 Error: 0.056728 Iteration 4 Error: 0.017766 Align patch 22 3 left Iteration 1 Error: 0.862449 Iteration 2 Error: 0.146335 Iteration 3 Error: 0.038936 Align patch 23 2 left Iteration 1 Error: 1.182796 Iteration 2 Error: 0.168987 Iteration 3 Error: 0.052229 Iteration 4 Error: 0.020894 Align patch 24 1 left Iteration 1 Error: 1.197538 Iteration 2 Error: 0.160976 Iteration 3 Error: 0.022955 Align patch 25 0 left Iteration 1 Error: 0.698762 Iteration 2 Error: 0.144273 Iteration 3 Error: 0.048003 3D Fitting completed. Patch alignment time: 11.73(sec) Local motion has been corrected. Process thread exits. Computational time: 22.753691 sec Total time: 30.553810 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00008hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00008hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.638444s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00008hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.428341s ........................................ >>>>>>TIME<<<<<< FFT: 0.951207s Defocus_U Defocus_V Angle CCC 10754.86 11639.69 6.42 0.044139 Final Values Defocus_U Defocus_V Angle CCC 10778.31 11663.14 7.99 0.083694 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00008hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00008hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 46.99 7.69 Num Hot pixels: 176 Hot pixel threshold: 93.12 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.381947 Iteration 2 Error: 0.096195 Iteration 3 Error: 0.024197 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.25 0.14 ...... Frame ( 3) shift: -0.50 0.29 ...... Frame ( 4) shift: -0.75 0.43 ...... Frame ( 5) shift: -1.00 0.57 ...... Frame ( 6) shift: -1.13 0.69 ...... Frame ( 7) shift: -1.14 0.78 ...... Frame ( 8) shift: -1.15 0.87 ...... Frame ( 9) shift: -1.11 1.01 ...... Frame ( 10) shift: -1.02 1.20 ...... Frame ( 11) shift: -0.93 1.38 ...... Frame ( 12) shift: -0.86 1.53 ...... Frame ( 13) shift: -0.81 1.63 ...... Frame ( 14) shift: -0.77 1.73 ...... Frame ( 15) shift: -0.76 1.79 ...... Frame ( 16) shift: -0.80 1.83 ...... Frame ( 17) shift: -0.83 1.86 ...... Frame ( 18) shift: -0.86 1.90 ...... Frame ( 19) shift: -0.87 1.94 ...... Frame ( 20) shift: -0.89 1.98 ...... Frame ( 21) shift: -0.90 1.98 ...... Frame ( 22) shift: -0.90 1.94 ...... Frame ( 23) shift: -0.91 1.90 ...... Frame ( 24) shift: -0.90 1.88 ...... Frame ( 25) shift: -0.87 1.87 ...... Frame ( 26) shift: -0.84 1.87 ...... Frame ( 27) shift: -0.81 1.86 ...... Frame ( 28) shift: -0.76 1.84 ...... Frame ( 29) shift: -0.72 1.83 ...... Frame ( 30) shift: -0.69 1.84 ...... Frame ( 31) shift: -0.68 1.90 ...... Frame ( 32) shift: -0.67 1.95 ...... Frame ( 33) shift: -0.68 1.98 ...... Frame ( 34) shift: -0.71 1.99 ...... Frame ( 35) shift: -0.74 2.00 ...... Frame ( 36) shift: -0.74 2.01 ...... Frame ( 37) shift: -0.69 2.01 ...... Frame ( 38) shift: -0.65 2.01 ...... Frame ( 39) shift: -0.61 2.01 ...... Frame ( 40) shift: -0.57 2.01 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.706519 Iteration 2 Error: 0.535049 Iteration 3 Error: 0.360356 Iteration 4 Error: 0.097040 Iteration 5 Error: 0.063171 Align patch 1 24 left Iteration 1 Error: 2.998572 Iteration 2 Error: 0.154659 Iteration 3 Error: 0.057368 Iteration 4 Error: 0.028759 Align patch 2 23 left Iteration 1 Error: 3.028764 Iteration 2 Error: 0.513983 Iteration 3 Error: 0.303360 Iteration 4 Error: 0.086370 Iteration 5 Error: 0.035029 Align patch 3 22 left Iteration 1 Error: 0.667176 Iteration 2 Error: 0.110825 Iteration 3 Error: 0.036008 Align patch 4 21 left Iteration 1 Error: 0.781895 Iteration 2 Error: 0.150064 Iteration 3 Error: 0.043167 Align patch 5 20 left Iteration 1 Error: 0.496188 Iteration 2 Error: 0.062708 Iteration 3 Error: 0.019521 Align patch 6 19 left Iteration 1 Error: 2.297438 Iteration 2 Error: 0.249935 Iteration 3 Error: 0.082947 Iteration 4 Error: 0.037949 Align patch 7 18 left Iteration 1 Error: 2.961699 Iteration 2 Error: 0.370736 Iteration 3 Error: 0.153256 Iteration 4 Error: 0.039550 Align patch 8 17 left Iteration 1 Error: 1.479254 Iteration 2 Error: 0.186775 Iteration 3 Error: 0.084513 Iteration 4 Error: 0.014686 Align patch 9 16 left Iteration 1 Error: 0.754120 Iteration 2 Error: 0.130695 Iteration 3 Error: 0.058001 Iteration 4 Error: 0.018946 Align patch 10 15 left Iteration 1 Error: 0.735140 Iteration 2 Error: 0.112441 Iteration 3 Error: 0.024892 Align patch 11 14 left Iteration 1 Error: 3.411941 Iteration 2 Error: 0.378361 Iteration 3 Error: 0.247297 Iteration 4 Error: 0.034997 Align patch 12 13 left Iteration 1 Error: 1.859128 Iteration 2 Error: 0.177758 Iteration 3 Error: 0.063562 Iteration 4 Error: 0.018364 Align patch 13 12 left Iteration 1 Error: 0.562551 Iteration 2 Error: 0.098213 Iteration 3 Error: 0.028621 Align patch 14 11 left Iteration 1 Error: 0.866512 Iteration 2 Error: 0.170987 Iteration 3 Error: 0.045638 Align patch 15 10 left Iteration 1 Error: 0.777174 Iteration 2 Error: 0.111254 Iteration 3 Error: 0.018359 Align patch 16 9 left Iteration 1 Error: 1.171755 Iteration 2 Error: 0.183672 Iteration 3 Error: 0.093130 Iteration 4 Error: 0.024666 Align patch 17 8 left Iteration 1 Error: 0.968989 Iteration 2 Error: 0.146566 Iteration 3 Error: 0.036036 Align patch 18 7 left Iteration 1 Error: 1.405368 Iteration 2 Error: 0.207346 Iteration 3 Error: 0.062746 Iteration 4 Error: 0.024292 Align patch 19 6 left Iteration 1 Error: 0.635027 Iteration 2 Error: 0.104718 Iteration 3 Error: 0.035827 Align patch 20 5 left Iteration 1 Error: 0.812163 Iteration 2 Error: 0.092461 Iteration 3 Error: 0.014477 Align patch 21 4 left Iteration 1 Error: 1.538546 Iteration 2 Error: 0.186180 Iteration 3 Error: 0.051264 Iteration 4 Error: 0.011518 Align patch 22 3 left Iteration 1 Error: 1.556537 Iteration 2 Error: 0.248069 Iteration 3 Error: 0.048518 Align patch 23 2 left Iteration 1 Error: 1.183519 Iteration 2 Error: 0.158018 Iteration 3 Error: 0.039863 Align patch 24 1 left Iteration 1 Error: 0.969664 Iteration 2 Error: 0.103183 Iteration 3 Error: 0.025299 Align patch 25 0 left Iteration 1 Error: 0.857892 Iteration 2 Error: 0.078293 Iteration 3 Error: 0.022154 3D Fitting completed. Patch alignment time: 12.79(sec) Local motion has been corrected. Process thread exits. Computational time: 23.437365 sec Total time: 29.696772 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00008hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00008hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.599887s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00008hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.012186s ........................................ >>>>>>TIME<<<<<< FFT: 0.975253s Defocus_U Defocus_V Angle CCC 12579.24 11916.89 85.18 0.047108 Final Values Defocus_U Defocus_V Angle CCC 12580.80 11921.58 85.81 0.085057 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00009hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00009hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.993e-02 CC threshold: 0.734 Mean Std: 46.04 7.87 Num Hot pixels: 173 Hot pixel threshold: 93.27 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.520539 Iteration 2 Error: 0.153638 Iteration 3 Error: 0.045034 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.51 0.03 ...... Frame ( 3) shift: -1.03 0.05 ...... Frame ( 4) shift: -1.54 0.08 ...... Frame ( 5) shift: -2.05 0.11 ...... Frame ( 6) shift: -2.30 0.15 ...... Frame ( 7) shift: -2.30 0.21 ...... Frame ( 8) shift: -2.29 0.27 ...... Frame ( 9) shift: -2.27 0.33 ...... Frame ( 10) shift: -2.26 0.39 ...... Frame ( 11) shift: -2.25 0.44 ...... Frame ( 12) shift: -2.24 0.50 ...... Frame ( 13) shift: -2.24 0.55 ...... Frame ( 14) shift: -2.24 0.61 ...... Frame ( 15) shift: -2.21 0.65 ...... Frame ( 16) shift: -2.14 0.69 ...... Frame ( 17) shift: -2.07 0.73 ...... Frame ( 18) shift: -2.04 0.76 ...... Frame ( 19) shift: -2.03 0.78 ...... Frame ( 20) shift: -2.03 0.81 ...... Frame ( 21) shift: -2.00 0.88 ...... Frame ( 22) shift: -1.94 0.99 ...... Frame ( 23) shift: -1.88 1.10 ...... Frame ( 24) shift: -1.86 1.19 ...... Frame ( 25) shift: -1.86 1.24 ...... Frame ( 26) shift: -1.87 1.29 ...... Frame ( 27) shift: -1.89 1.36 ...... Frame ( 28) shift: -1.93 1.43 ...... Frame ( 29) shift: -1.97 1.50 ...... Frame ( 30) shift: -1.97 1.55 ...... Frame ( 31) shift: -1.94 1.58 ...... Frame ( 32) shift: -1.90 1.61 ...... Frame ( 33) shift: -1.89 1.62 ...... Frame ( 34) shift: -1.90 1.61 ...... Frame ( 35) shift: -1.91 1.60 ...... Frame ( 36) shift: -1.91 1.65 ...... Frame ( 37) shift: -1.92 1.74 ...... Frame ( 38) shift: -1.92 1.84 ...... Frame ( 39) shift: -1.92 1.94 ...... Frame ( 40) shift: -1.92 2.04 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.945683 Iteration 2 Error: 0.221795 Iteration 3 Error: 0.064641 Iteration 4 Error: 0.023013 Align patch 2 23 left Iteration 1 Error: 1.118059 Iteration 2 Error: 0.176836 Iteration 3 Error: 0.044154 Align patch 3 22 left Iteration 1 Error: 0.957704 Iteration 2 Error: 0.190607 Iteration 3 Error: 0.033409 Align patch 4 21 left Iteration 1 Error: 1.869739 Iteration 2 Error: 0.180750 Iteration 3 Error: 0.049150 Align patch 5 20 left Iteration 1 Error: 0.916265 Iteration 2 Error: 0.123562 Iteration 3 Error: 0.032146 Align patch 6 19 left Iteration 1 Error: 1.108052 Iteration 2 Error: 0.280286 Iteration 3 Error: 0.056543 Iteration 4 Error: 0.026334 Align patch 7 18 left Iteration 1 Error: 1.088672 Iteration 2 Error: 0.184349 Iteration 3 Error: 0.036999 Align patch 8 17 left Iteration 1 Error: 1.552060 Iteration 2 Error: 0.236332 Iteration 3 Error: 0.049320 Align patch 9 16 left Iteration 1 Error: 1.833409 Iteration 2 Error: 0.368432 Iteration 3 Error: 0.076988 Iteration 4 Error: 0.028395 Align patch 10 15 left Iteration 1 Error: 0.828552 Iteration 2 Error: 0.108843 Iteration 3 Error: 0.021701 Align patch 11 14 left Iteration 1 Error: 1.216402 Iteration 2 Error: 0.107332 Iteration 3 Error: 0.020470 Align patch 12 13 left Iteration 1 Error: 2.657448 Iteration 2 Error: 0.452254 Iteration 3 Error: 0.219984 Iteration 4 Error: 0.108042 Iteration 5 Error: 0.067229 Align patch 12 13 left Iteration 1 Error: 2.880588 Iteration 2 Error: 0.378790 Iteration 3 Error: 0.084613 Iteration 4 Error: 0.028728 Align patch 13 12 left Iteration 1 Error: 1.755358 Iteration 2 Error: 0.627103 Iteration 3 Error: 0.461486 Iteration 4 Error: 0.355078 Iteration 5 Error: 0.242277 Align patch 13 12 left Iteration 1 Error: 2.462393 Iteration 2 Error: 0.527469 Iteration 3 Error: 0.119833 Iteration 4 Error: 0.031723 Align patch 14 11 left Iteration 1 Error: 1.204333 Iteration 2 Error: 0.224277 Iteration 3 Error: 0.057406 Iteration 4 Error: 0.026367 Align patch 15 10 left Iteration 1 Error: 0.975127 Iteration 2 Error: 0.123796 Iteration 3 Error: 0.033016 Align patch 16 9 left Iteration 1 Error: 1.471582 Iteration 2 Error: 0.234560 Iteration 3 Error: 0.067181 Iteration 4 Error: 0.020887 Align patch 17 8 left Iteration 1 Error: 1.916519 Iteration 2 Error: 0.290406 Iteration 3 Error: 0.077953 Iteration 4 Error: 0.035123 Align patch 18 7 left Iteration 1 Error: 0.991610 Iteration 2 Error: 0.110872 Iteration 3 Error: 0.025938 Align patch 19 6 left Iteration 1 Error: 1.606836 Iteration 2 Error: 0.333166 Iteration 3 Error: 0.089010 Iteration 4 Error: 0.021970 Align patch 20 5 left Iteration 1 Error: 1.329331 Iteration 2 Error: 0.342723 Iteration 3 Error: 0.078403 Iteration 4 Error: 0.037691 Align patch 21 4 left Iteration 1 Error: 1.399151 Iteration 2 Error: 0.317123 Iteration 3 Error: 0.108700 Iteration 4 Error: 0.039030 Align patch 22 3 left Iteration 1 Error: 1.889640 Iteration 2 Error: 0.374712 Iteration 3 Error: 0.069197 Iteration 4 Error: 0.012785 Align patch 23 2 left Iteration 1 Error: 1.919037 Iteration 2 Error: 0.285945 Iteration 3 Error: 0.078640 Iteration 4 Error: 0.015911 Align patch 24 1 left Iteration 1 Error: 1.347823 Iteration 2 Error: 0.414385 Iteration 3 Error: 0.092722 Iteration 4 Error: 0.033287 Align patch 25 0 left Iteration 1 Error: 1.219025 Iteration 2 Error: 0.227523 Iteration 3 Error: 0.051577 Iteration 4 Error: 0.023802 3D Fitting completed. Patch alignment time: 13.76(sec) Local motion has been corrected. Process thread exits. Computational time: 29.096289 sec Total time: 35.820389 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00009hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00009hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.763272s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00009hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.055721s ........................................ >>>>>>TIME<<<<<< FFT: 1.033858s Defocus_U Defocus_V Angle CCC 13355.49 14183.61 15.29 0.043117 Final Values Defocus_U Defocus_V Angle CCC 13347.67 14188.30 15.29 0.074357 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00009hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00009hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.001e-01 CC threshold: 0.735 Mean Std: 46.04 7.73 Num Hot pixels: 178 Hot pixel threshold: 92.42 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.635622 Iteration 2 Error: 0.099473 Iteration 3 Error: 0.021029 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.28 0.07 ...... Frame ( 3) shift: -0.56 0.14 ...... Frame ( 4) shift: -0.85 0.20 ...... Frame ( 5) shift: -1.13 0.27 ...... Frame ( 6) shift: -1.27 0.32 ...... Frame ( 7) shift: -1.26 0.35 ...... Frame ( 8) shift: -1.26 0.38 ...... Frame ( 9) shift: -1.24 0.41 ...... Frame ( 10) shift: -1.23 0.45 ...... Frame ( 11) shift: -1.21 0.49 ...... Frame ( 12) shift: -1.18 0.50 ...... Frame ( 13) shift: -1.15 0.49 ...... Frame ( 14) shift: -1.11 0.47 ...... Frame ( 15) shift: -1.08 0.48 ...... Frame ( 16) shift: -1.04 0.52 ...... Frame ( 17) shift: -1.01 0.56 ...... Frame ( 18) shift: -0.95 0.58 ...... Frame ( 19) shift: -0.87 0.59 ...... Frame ( 20) shift: -0.80 0.60 ...... Frame ( 21) shift: -0.74 0.62 ...... Frame ( 22) shift: -0.71 0.65 ...... Frame ( 23) shift: -0.68 0.67 ...... Frame ( 24) shift: -0.66 0.69 ...... Frame ( 25) shift: -0.64 0.71 ...... Frame ( 26) shift: -0.62 0.72 ...... Frame ( 27) shift: -0.60 0.74 ...... Frame ( 28) shift: -0.58 0.77 ...... Frame ( 29) shift: -0.55 0.81 ...... Frame ( 30) shift: -0.54 0.85 ...... Frame ( 31) shift: -0.54 0.91 ...... Frame ( 32) shift: -0.54 0.97 ...... Frame ( 33) shift: -0.52 0.99 ...... Frame ( 34) shift: -0.48 0.97 ...... Frame ( 35) shift: -0.44 0.95 ...... Frame ( 36) shift: -0.40 0.96 ...... Frame ( 37) shift: -0.37 0.99 ...... Frame ( 38) shift: -0.35 1.03 ...... Frame ( 39) shift: -0.32 1.06 ...... Frame ( 40) shift: -0.29 1.10 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.366863 Iteration 2 Error: 0.201220 Iteration 3 Error: 0.059448 Iteration 4 Error: 0.022923 Align patch 2 23 left Iteration 1 Error: 0.906438 Iteration 2 Error: 0.199361 Iteration 3 Error: 0.056796 Iteration 4 Error: 0.019883 Align patch 3 22 left Iteration 1 Error: 0.980787 Iteration 2 Error: 0.196354 Iteration 3 Error: 0.053677 Iteration 4 Error: 0.021531 Align patch 4 21 left Iteration 1 Error: 0.591363 Iteration 2 Error: 0.097400 Iteration 3 Error: 0.050940 Iteration 4 Error: 0.023866 Align patch 5 20 left Iteration 1 Error: 0.904400 Iteration 2 Error: 0.096590 Iteration 3 Error: 0.022828 Align patch 6 19 left Iteration 1 Error: 1.073495 Iteration 2 Error: 0.178037 Iteration 3 Error: 0.053970 Iteration 4 Error: 0.016013 Align patch 7 18 left Iteration 1 Error: 1.679805 Iteration 2 Error: 0.326157 Iteration 3 Error: 0.066012 Iteration 4 Error: 0.031515 Align patch 8 17 left Iteration 1 Error: 0.591283 Iteration 2 Error: 0.125354 Iteration 3 Error: 0.041582 Align patch 9 16 left Iteration 1 Error: 0.672041 Iteration 2 Error: 0.114509 Iteration 3 Error: 0.037728 Align patch 10 15 left Iteration 1 Error: 1.133587 Iteration 2 Error: 0.123987 Iteration 3 Error: 0.041745 Align patch 11 14 left Iteration 1 Error: 1.126456 Iteration 2 Error: 0.205681 Iteration 3 Error: 0.104411 Iteration 4 Error: 0.062318 Iteration 5 Error: 0.028762 Align patch 12 13 left Iteration 1 Error: 1.285167 Iteration 2 Error: 0.271004 Iteration 3 Error: 0.053541 Iteration 4 Error: 0.018896 Align patch 13 12 left Iteration 1 Error: 0.833579 Iteration 2 Error: 0.125833 Iteration 3 Error: 0.031202 Align patch 14 11 left Iteration 1 Error: 0.679424 Iteration 2 Error: 0.101911 Iteration 3 Error: 0.018480 Align patch 15 10 left Iteration 1 Error: 0.869507 Iteration 2 Error: 0.205497 Iteration 3 Error: 0.033931 Align patch 16 9 left Iteration 1 Error: 0.767594 Iteration 2 Error: 0.117430 Iteration 3 Error: 0.019409 Align patch 17 8 left Iteration 1 Error: 0.788604 Iteration 2 Error: 0.094814 Iteration 3 Error: 0.026638 Align patch 18 7 left Iteration 1 Error: 1.092851 Iteration 2 Error: 0.142271 Iteration 3 Error: 0.042990 Align patch 19 6 left Iteration 1 Error: 0.913795 Iteration 2 Error: 0.140705 Iteration 3 Error: 0.020130 Align patch 20 5 left Iteration 1 Error: 1.046436 Iteration 2 Error: 0.165707 Iteration 3 Error: 0.034102 Align patch 21 4 left Iteration 1 Error: 0.703209 Iteration 2 Error: 0.216534 Iteration 3 Error: 0.059715 Iteration 4 Error: 0.015603 Align patch 22 3 left Iteration 1 Error: 0.715163 Iteration 2 Error: 0.076689 Iteration 3 Error: 0.023167 Align patch 23 2 left Iteration 1 Error: 1.021361 Iteration 2 Error: 0.179747 Iteration 3 Error: 0.039715 Align patch 24 1 left Iteration 1 Error: 0.846600 Iteration 2 Error: 0.157718 Iteration 3 Error: 0.029294 Align patch 25 0 left Iteration 1 Error: 1.006224 Iteration 2 Error: 0.150883 Iteration 3 Error: 0.029501 3D Fitting completed. Patch alignment time: 12.40(sec) Local motion has been corrected. Process thread exits. Computational time: 28.243675 sec Total time: 37.624786 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00009hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00009hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.585459s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00009hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.169422s ........................................ >>>>>>TIME<<<<<< FFT: 1.030289s Defocus_U Defocus_V Angle CCC 13917.97 14437.54 3.05 0.051763 Final Values Defocus_U Defocus_V Angle CCC 13917.97 14428.17 3.37 0.090029 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00009hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00009hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.734 Mean Std: 47.93 7.65 Num Hot pixels: 192 Hot pixel threshold: 93.86 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.644218 Iteration 2 Error: 0.109288 Iteration 3 Error: 0.022115 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.31 -0.02 ...... Frame ( 3) shift: -0.62 -0.03 ...... Frame ( 4) shift: -0.93 -0.05 ...... Frame ( 5) shift: -1.24 -0.07 ...... Frame ( 6) shift: -1.38 -0.09 ...... Frame ( 7) shift: -1.34 -0.13 ...... Frame ( 8) shift: -1.29 -0.16 ...... Frame ( 9) shift: -1.29 -0.11 ...... Frame ( 10) shift: -1.33 0.02 ...... Frame ( 11) shift: -1.37 0.16 ...... Frame ( 12) shift: -1.40 0.20 ...... Frame ( 13) shift: -1.42 0.13 ...... Frame ( 14) shift: -1.43 0.07 ...... Frame ( 15) shift: -1.44 0.06 ...... Frame ( 16) shift: -1.43 0.11 ...... Frame ( 17) shift: -1.42 0.15 ...... Frame ( 18) shift: -1.36 0.19 ...... Frame ( 19) shift: -1.27 0.21 ...... Frame ( 20) shift: -1.18 0.23 ...... Frame ( 21) shift: -1.15 0.23 ...... Frame ( 22) shift: -1.17 0.21 ...... Frame ( 23) shift: -1.19 0.19 ...... Frame ( 24) shift: -1.15 0.20 ...... Frame ( 25) shift: -1.04 0.22 ...... Frame ( 26) shift: -0.93 0.25 ...... Frame ( 27) shift: -0.86 0.27 ...... Frame ( 28) shift: -0.84 0.30 ...... Frame ( 29) shift: -0.82 0.32 ...... Frame ( 30) shift: -0.79 0.37 ...... Frame ( 31) shift: -0.76 0.43 ...... Frame ( 32) shift: -0.73 0.49 ...... Frame ( 33) shift: -0.66 0.53 ...... Frame ( 34) shift: -0.57 0.52 ...... Frame ( 35) shift: -0.47 0.52 ...... Frame ( 36) shift: -0.43 0.55 ...... Frame ( 37) shift: -0.46 0.60 ...... Frame ( 38) shift: -0.48 0.65 ...... Frame ( 39) shift: -0.51 0.70 ...... Frame ( 40) shift: -0.53 0.74 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.352451 Iteration 2 Error: 0.300089 Iteration 3 Error: 0.058135 Iteration 4 Error: 0.020884 Align patch 2 23 left Iteration 1 Error: 0.767737 Iteration 2 Error: 0.145031 Iteration 3 Error: 0.048071 Align patch 3 22 left Iteration 1 Error: 0.982781 Iteration 2 Error: 0.143780 Iteration 3 Error: 0.051250 Iteration 4 Error: 0.010359 Align patch 4 21 left Iteration 1 Error: 1.335883 Iteration 2 Error: 0.243768 Iteration 3 Error: 0.051991 Iteration 4 Error: 0.016897 Align patch 5 20 left Iteration 1 Error: 0.684687 Iteration 2 Error: 0.110895 Iteration 3 Error: 0.030853 Align patch 6 19 left Iteration 1 Error: 1.671177 Iteration 2 Error: 0.231909 Iteration 3 Error: 0.069100 Iteration 4 Error: 0.016579 Align patch 7 18 left Iteration 1 Error: 1.429968 Iteration 2 Error: 0.160041 Iteration 3 Error: 0.046243 Align patch 8 17 left Iteration 1 Error: 1.387256 Iteration 2 Error: 0.223931 Iteration 3 Error: 0.053651 Iteration 4 Error: 0.018293 Align patch 9 16 left Iteration 1 Error: 1.083263 Iteration 2 Error: 0.174517 Iteration 3 Error: 0.038945 Align patch 10 15 left Iteration 1 Error: 0.745757 Iteration 2 Error: 0.078000 Iteration 3 Error: 0.012702 Align patch 11 14 left Iteration 1 Error: 2.333031 Iteration 2 Error: 0.493815 Iteration 3 Error: 0.286456 Iteration 4 Error: 0.156782 Iteration 5 Error: 0.085229 Align patch 11 14 left Iteration 1 Error: 2.666287 Iteration 2 Error: 0.603185 Iteration 3 Error: 0.267206 Iteration 4 Error: 0.121407 Iteration 5 Error: 0.060072 Align patch 12 13 left Iteration 1 Error: 1.260786 Iteration 2 Error: 0.168687 Iteration 3 Error: 0.043152 Align patch 13 12 left Iteration 1 Error: 1.153969 Iteration 2 Error: 0.168236 Iteration 3 Error: 0.046282 Align patch 14 11 left Iteration 1 Error: 0.618339 Iteration 2 Error: 0.092574 Iteration 3 Error: 0.032617 Align patch 15 10 left Iteration 1 Error: 0.749337 Iteration 2 Error: 0.105852 Iteration 3 Error: 0.024484 Align patch 16 9 left Iteration 1 Error: 1.158192 Iteration 2 Error: 0.318624 Iteration 3 Error: 0.095354 Iteration 4 Error: 0.043909 Align patch 17 8 left Iteration 1 Error: 0.641154 Iteration 2 Error: 0.200041 Iteration 3 Error: 0.051988 Iteration 4 Error: 0.017317 Align patch 18 7 left Iteration 1 Error: 0.905593 Iteration 2 Error: 0.148555 Iteration 3 Error: 0.029587 Align patch 19 6 left Iteration 1 Error: 0.864841 Iteration 2 Error: 0.129755 Iteration 3 Error: 0.035780 Align patch 20 5 left Iteration 1 Error: 0.906621 Iteration 2 Error: 0.101522 Iteration 3 Error: 0.026636 Align patch 21 4 left Iteration 1 Error: 1.370119 Iteration 2 Error: 0.264398 Iteration 3 Error: 0.070333 Iteration 4 Error: 0.029806 Align patch 22 3 left Iteration 1 Error: 0.822714 Iteration 2 Error: 0.284686 Iteration 3 Error: 0.044724 Align patch 23 2 left Iteration 1 Error: 1.369888 Iteration 2 Error: 0.185029 Iteration 3 Error: 0.047752 Align patch 24 1 left Iteration 1 Error: 0.918246 Iteration 2 Error: 0.159789 Iteration 3 Error: 0.051151 Iteration 4 Error: 0.017249 Align patch 25 0 left Iteration 1 Error: 0.675197 Iteration 2 Error: 0.087587 Iteration 3 Error: 0.021878 3D Fitting completed. Patch alignment time: 12.46(sec) Local motion has been corrected. Process thread exits. Computational time: 29.744841 sec Total time: 38.879105 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00009hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00009hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.601985s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00009hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.224273s ........................................ >>>>>>TIME<<<<<< FFT: 1.063554s Defocus_U Defocus_V Angle CCC 14548.83 15427.73 4.87 0.049403 Final Values Defocus_U Defocus_V Angle CCC 14542.58 15433.99 6.12 0.088328 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00009hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00009hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 47.34 7.69 Num Hot pixels: 176 Hot pixel threshold: 93.48 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.205998 Iteration 2 Error: 0.050506 Iteration 3 Error: 0.017075 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.35 0.09 ...... Frame ( 3) shift: -0.70 0.19 ...... Frame ( 4) shift: -1.05 0.28 ...... Frame ( 5) shift: -1.40 0.37 ...... Frame ( 6) shift: -1.57 0.46 ...... Frame ( 7) shift: -1.56 0.53 ...... Frame ( 8) shift: -1.54 0.60 ...... Frame ( 9) shift: -1.55 0.65 ...... Frame ( 10) shift: -1.58 0.69 ...... Frame ( 11) shift: -1.61 0.72 ...... Frame ( 12) shift: -1.63 0.75 ...... Frame ( 13) shift: -1.65 0.76 ...... Frame ( 14) shift: -1.67 0.78 ...... Frame ( 15) shift: -1.67 0.79 ...... Frame ( 16) shift: -1.66 0.78 ...... Frame ( 17) shift: -1.66 0.78 ...... Frame ( 18) shift: -1.62 0.77 ...... Frame ( 19) shift: -1.55 0.76 ...... Frame ( 20) shift: -1.49 0.75 ...... Frame ( 21) shift: -1.50 0.77 ...... Frame ( 22) shift: -1.59 0.83 ...... Frame ( 23) shift: -1.68 0.89 ...... Frame ( 24) shift: -1.73 0.90 ...... Frame ( 25) shift: -1.75 0.86 ...... Frame ( 26) shift: -1.77 0.82 ...... Frame ( 27) shift: -1.76 0.83 ...... Frame ( 28) shift: -1.72 0.91 ...... Frame ( 29) shift: -1.69 0.98 ...... Frame ( 30) shift: -1.68 0.98 ...... Frame ( 31) shift: -1.69 0.91 ...... Frame ( 32) shift: -1.70 0.85 ...... Frame ( 33) shift: -1.68 0.80 ...... Frame ( 34) shift: -1.63 0.78 ...... Frame ( 35) shift: -1.58 0.76 ...... Frame ( 36) shift: -1.54 0.79 ...... Frame ( 37) shift: -1.51 0.85 ...... Frame ( 38) shift: -1.49 0.92 ...... Frame ( 39) shift: -1.47 0.98 ...... Frame ( 40) shift: -1.44 1.04 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.367604 Iteration 2 Error: 0.206394 Iteration 3 Error: 0.054701 Iteration 4 Error: 0.021405 Align patch 2 23 left Iteration 1 Error: 1.519375 Iteration 2 Error: 0.170667 Iteration 3 Error: 0.044617 Align patch 3 22 left Iteration 1 Error: 0.757544 Iteration 2 Error: 0.179189 Iteration 3 Error: 0.078025 Iteration 4 Error: 0.021474 Align patch 4 21 left Iteration 1 Error: 0.944501 Iteration 2 Error: 0.124298 Iteration 3 Error: 0.023605 Align patch 5 20 left Iteration 1 Error: 0.939414 Iteration 2 Error: 0.153505 Iteration 3 Error: 0.027251 Align patch 6 19 left Iteration 1 Error: 1.271663 Iteration 2 Error: 0.259777 Iteration 3 Error: 0.070390 Iteration 4 Error: 0.035815 Align patch 7 18 left Iteration 1 Error: 1.467678 Iteration 2 Error: 0.143325 Iteration 3 Error: 0.031560 Align patch 8 17 left Iteration 1 Error: 0.787496 Iteration 2 Error: 0.183179 Iteration 3 Error: 0.054102 Iteration 4 Error: 0.028036 Align patch 9 16 left Iteration 1 Error: 0.550310 Iteration 2 Error: 0.089820 Iteration 3 Error: 0.022171 Align patch 10 15 left Iteration 1 Error: 0.763689 Iteration 2 Error: 0.159587 Iteration 3 Error: 0.043377 Align patch 11 14 left Iteration 1 Error: 1.003989 Iteration 2 Error: 0.138104 Iteration 3 Error: 0.033486 Align patch 12 13 left Iteration 1 Error: 0.942957 Iteration 2 Error: 0.150081 Iteration 3 Error: 0.036669 Align patch 13 12 left Iteration 1 Error: 0.727590 Iteration 2 Error: 0.115669 Iteration 3 Error: 0.036773 Align patch 14 11 left Iteration 1 Error: 0.705850 Iteration 2 Error: 0.189112 Iteration 3 Error: 0.030434 Align patch 15 10 left Iteration 1 Error: 0.654545 Iteration 2 Error: 0.089094 Iteration 3 Error: 0.020698 Align patch 16 9 left Iteration 1 Error: 0.817368 Iteration 2 Error: 0.125493 Iteration 3 Error: 0.037453 Align patch 17 8 left Iteration 1 Error: 1.053838 Iteration 2 Error: 0.135155 Iteration 3 Error: 0.046647 Align patch 18 7 left Iteration 1 Error: 1.044268 Iteration 2 Error: 0.164350 Iteration 3 Error: 0.046148 Align patch 19 6 left Iteration 1 Error: 0.499463 Iteration 2 Error: 0.089720 Iteration 3 Error: 0.023113 Align patch 20 5 left Iteration 1 Error: 0.658358 Iteration 2 Error: 0.152019 Iteration 3 Error: 0.036430 Align patch 21 4 left Iteration 1 Error: 0.868266 Iteration 2 Error: 0.235421 Iteration 3 Error: 0.048724 Align patch 22 3 left Iteration 1 Error: 1.131651 Iteration 2 Error: 0.121102 Iteration 3 Error: 0.039170 Align patch 23 2 left Iteration 1 Error: 1.130908 Iteration 2 Error: 0.232108 Iteration 3 Error: 0.062004 Iteration 4 Error: 0.015673 Align patch 24 1 left Iteration 1 Error: 0.921262 Iteration 2 Error: 0.121424 Iteration 3 Error: 0.019755 Align patch 25 0 left Iteration 1 Error: 0.720592 Iteration 2 Error: 0.076085 Iteration 3 Error: 0.018583 3D Fitting completed. Patch alignment time: 11.79(sec) Local motion has been corrected. Process thread exits. Computational time: 27.000965 sec Total time: 36.349670 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00009hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00009hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.587749s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00009hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.705011s ........................................ >>>>>>TIME<<<<<< FFT: 0.965837s Defocus_U Defocus_V Angle CCC 14935.56 14228.51 83.15 0.054289 Final Values Defocus_U Defocus_V Angle CCC 14937.12 14220.70 82.53 0.094259 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00010hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00010hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 1.000e-01 CC threshold: 0.735 Mean Std: 47.54 7.65 Num Hot pixels: 192 Hot pixel threshold: 93.42 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.054945 Iteration 2 Error: 0.164745 Iteration 3 Error: 0.041010 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.30 0.11 ...... Frame ( 3) shift: -0.61 0.22 ...... Frame ( 4) shift: -0.91 0.33 ...... Frame ( 5) shift: -1.21 0.44 ...... Frame ( 6) shift: -1.34 0.53 ...... Frame ( 7) shift: -1.30 0.61 ...... Frame ( 8) shift: -1.26 0.69 ...... Frame ( 9) shift: -1.23 0.75 ...... Frame ( 10) shift: -1.20 0.80 ...... Frame ( 11) shift: -1.18 0.85 ...... Frame ( 12) shift: -1.18 0.89 ...... Frame ( 13) shift: -1.19 0.91 ...... Frame ( 14) shift: -1.21 0.93 ...... Frame ( 15) shift: -1.20 0.94 ...... Frame ( 16) shift: -1.19 0.94 ...... Frame ( 17) shift: -1.17 0.94 ...... Frame ( 18) shift: -1.13 0.99 ...... Frame ( 19) shift: -1.08 1.09 ...... Frame ( 20) shift: -1.03 1.19 ...... Frame ( 21) shift: -0.96 1.27 ...... Frame ( 22) shift: -0.89 1.33 ...... Frame ( 23) shift: -0.82 1.39 ...... Frame ( 24) shift: -0.79 1.44 ...... Frame ( 25) shift: -0.80 1.48 ...... Frame ( 26) shift: -0.81 1.53 ...... Frame ( 27) shift: -0.80 1.59 ...... Frame ( 28) shift: -0.75 1.67 ...... Frame ( 29) shift: -0.70 1.75 ...... Frame ( 30) shift: -0.65 1.78 ...... Frame ( 31) shift: -0.59 1.77 ...... Frame ( 32) shift: -0.53 1.76 ...... Frame ( 33) shift: -0.49 1.75 ...... Frame ( 34) shift: -0.48 1.74 ...... Frame ( 35) shift: -0.46 1.73 ...... Frame ( 36) shift: -0.45 1.77 ...... Frame ( 37) shift: -0.44 1.86 ...... Frame ( 38) shift: -0.43 1.95 ...... Frame ( 39) shift: -0.42 2.04 ...... Frame ( 40) shift: -0.41 2.13 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.175327 Iteration 2 Error: 0.177996 Iteration 3 Error: 0.033597 Align patch 2 23 left Iteration 1 Error: 1.428677 Iteration 2 Error: 0.200255 Iteration 3 Error: 0.049357 Align patch 3 22 left Iteration 1 Error: 0.993637 Iteration 2 Error: 0.256874 Iteration 3 Error: 0.079110 Iteration 4 Error: 0.030416 Align patch 4 21 left Iteration 1 Error: 0.698193 Iteration 2 Error: 0.132724 Iteration 3 Error: 0.030038 Align patch 5 20 left Iteration 1 Error: 0.384175 Iteration 2 Error: 0.060872 Iteration 3 Error: 0.019101 Align patch 6 19 left Iteration 1 Error: 1.026798 Iteration 2 Error: 0.159287 Iteration 3 Error: 0.066070 Iteration 4 Error: 0.024525 Align patch 7 18 left Iteration 1 Error: 1.257719 Iteration 2 Error: 0.158479 Iteration 3 Error: 0.056569 Iteration 4 Error: 0.022224 Align patch 8 17 left Iteration 1 Error: 0.617641 Iteration 2 Error: 0.120926 Iteration 3 Error: 0.049057 Align patch 9 16 left Iteration 1 Error: 0.867583 Iteration 2 Error: 0.133599 Iteration 3 Error: 0.051243 Iteration 4 Error: 0.020762 Align patch 10 15 left Iteration 1 Error: 0.915000 Iteration 2 Error: 0.088721 Iteration 3 Error: 0.035631 Align patch 11 14 left Iteration 1 Error: 1.231932 Iteration 2 Error: 0.156427 Iteration 3 Error: 0.035775 Align patch 12 13 left Iteration 1 Error: 0.852251 Iteration 2 Error: 0.190611 Iteration 3 Error: 0.093799 Iteration 4 Error: 0.030284 Align patch 13 12 left Iteration 1 Error: 0.782504 Iteration 2 Error: 0.138898 Iteration 3 Error: 0.026907 Align patch 14 11 left Iteration 1 Error: 0.648992 Iteration 2 Error: 0.105802 Iteration 3 Error: 0.032993 Align patch 15 10 left Iteration 1 Error: 0.643563 Iteration 2 Error: 0.156807 Iteration 3 Error: 0.034214 Align patch 16 9 left Iteration 1 Error: 1.294074 Iteration 2 Error: 0.234690 Iteration 3 Error: 0.042781 Align patch 17 8 left Iteration 1 Error: 1.229602 Iteration 2 Error: 0.208885 Iteration 3 Error: 0.048559 Align patch 18 7 left Iteration 1 Error: 1.153716 Iteration 2 Error: 0.283784 Iteration 3 Error: 0.082110 Iteration 4 Error: 0.025860 Align patch 19 6 left Iteration 1 Error: 0.741232 Iteration 2 Error: 0.115484 Iteration 3 Error: 0.016297 Align patch 20 5 left Iteration 1 Error: 0.532777 Iteration 2 Error: 0.094212 Iteration 3 Error: 0.021401 Align patch 21 4 left Iteration 1 Error: 1.162105 Iteration 2 Error: 0.158614 Iteration 3 Error: 0.034361 Align patch 22 3 left Iteration 1 Error: 0.744210 Iteration 2 Error: 0.147295 Iteration 3 Error: 0.048669 Align patch 23 2 left Iteration 1 Error: 1.126022 Iteration 2 Error: 0.243196 Iteration 3 Error: 0.045609 Align patch 24 1 left Iteration 1 Error: 0.726439 Iteration 2 Error: 0.130477 Iteration 3 Error: 0.040489 Align patch 25 0 left Iteration 1 Error: 0.651708 Iteration 2 Error: 0.106969 Iteration 3 Error: 0.051647 Iteration 4 Error: 0.024244 3D Fitting completed. Patch alignment time: 11.79(sec) Local motion has been corrected. Process thread exits. Computational time: 27.086561 sec Total time: 34.490044 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00010hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00010hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.456869s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00010hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.551678s ........................................ >>>>>>TIME<<<<<< FFT: 0.945034s Defocus_U Defocus_V Angle CCC 11349.62 12263.69 11.02 0.048839 Final Values Defocus_U Defocus_V Angle CCC 11382.44 12268.38 11.96 0.089980 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00010hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00010hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 47.24 7.74 Num Hot pixels: 159 Hot pixel threshold: 93.67 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.994459 Iteration 2 Error: 0.069865 Iteration 3 Error: 0.025484 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.31 0.07 ...... Frame ( 3) shift: -0.61 0.15 ...... Frame ( 4) shift: -0.92 0.22 ...... Frame ( 5) shift: -1.23 0.29 ...... Frame ( 6) shift: -1.37 0.37 ...... Frame ( 7) shift: -1.36 0.46 ...... Frame ( 8) shift: -1.35 0.55 ...... Frame ( 9) shift: -1.34 0.62 ...... Frame ( 10) shift: -1.32 0.69 ...... Frame ( 11) shift: -1.30 0.75 ...... Frame ( 12) shift: -1.25 0.81 ...... Frame ( 13) shift: -1.19 0.86 ...... Frame ( 14) shift: -1.13 0.92 ...... Frame ( 15) shift: -1.11 0.94 ...... Frame ( 16) shift: -1.14 0.94 ...... Frame ( 17) shift: -1.17 0.93 ...... Frame ( 18) shift: -1.17 0.91 ...... Frame ( 19) shift: -1.16 0.89 ...... Frame ( 20) shift: -1.14 0.86 ...... Frame ( 21) shift: -1.13 0.88 ...... Frame ( 22) shift: -1.12 0.95 ...... Frame ( 23) shift: -1.11 1.02 ...... Frame ( 24) shift: -1.07 1.06 ...... Frame ( 25) shift: -1.01 1.08 ...... Frame ( 26) shift: -0.95 1.09 ...... Frame ( 27) shift: -0.96 1.09 ...... Frame ( 28) shift: -1.02 1.07 ...... Frame ( 29) shift: -1.09 1.05 ...... Frame ( 30) shift: -1.12 1.05 ...... Frame ( 31) shift: -1.12 1.07 ...... Frame ( 32) shift: -1.11 1.08 ...... Frame ( 33) shift: -1.11 1.10 ...... Frame ( 34) shift: -1.12 1.13 ...... Frame ( 35) shift: -1.13 1.16 ...... Frame ( 36) shift: -1.13 1.20 ...... Frame ( 37) shift: -1.12 1.25 ...... Frame ( 38) shift: -1.10 1.30 ...... Frame ( 39) shift: -1.09 1.36 ...... Frame ( 40) shift: -1.08 1.41 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.655548 Iteration 2 Error: 0.402702 Iteration 3 Error: 0.305038 Iteration 4 Error: 0.086959 Iteration 5 Error: 0.044722 Align patch 2 23 left Iteration 1 Error: 1.505908 Iteration 2 Error: 0.261857 Iteration 3 Error: 0.056636 Iteration 4 Error: 0.020429 Align patch 3 22 left Iteration 1 Error: 0.800354 Iteration 2 Error: 0.154799 Iteration 3 Error: 0.032687 Align patch 4 21 left Iteration 1 Error: 0.795601 Iteration 2 Error: 0.148135 Iteration 3 Error: 0.030032 Align patch 5 20 left Iteration 1 Error: 0.657352 Iteration 2 Error: 0.071410 Iteration 3 Error: 0.016235 Align patch 6 19 left Iteration 1 Error: 3.026551 Iteration 2 Error: 0.352186 Iteration 3 Error: 0.141267 Iteration 4 Error: 0.035471 Align patch 7 18 left Iteration 1 Error: 0.895156 Iteration 2 Error: 0.134907 Iteration 3 Error: 0.032173 Align patch 8 17 left Iteration 1 Error: 1.869785 Iteration 2 Error: 0.229932 Iteration 3 Error: 0.030537 Align patch 9 16 left Iteration 1 Error: 0.954314 Iteration 2 Error: 0.190807 Iteration 3 Error: 0.056495 Iteration 4 Error: 0.027103 Align patch 10 15 left Iteration 1 Error: 0.917124 Iteration 2 Error: 0.138557 Iteration 3 Error: 0.052953 Iteration 4 Error: 0.015955 Align patch 11 14 left Iteration 1 Error: 1.117752 Iteration 2 Error: 0.147292 Iteration 3 Error: 0.042027 Align patch 12 13 left Iteration 1 Error: 1.028294 Iteration 2 Error: 0.153421 Iteration 3 Error: 0.027816 Align patch 13 12 left Iteration 1 Error: 0.957033 Iteration 2 Error: 0.250044 Iteration 3 Error: 0.091468 Iteration 4 Error: 0.033761 Align patch 14 11 left Iteration 1 Error: 0.788079 Iteration 2 Error: 0.143301 Iteration 3 Error: 0.039786 Align patch 15 10 left Iteration 1 Error: 0.593013 Iteration 2 Error: 0.113089 Iteration 3 Error: 0.022222 Align patch 16 9 left Iteration 1 Error: 1.285301 Iteration 2 Error: 0.122950 Iteration 3 Error: 0.038052 Align patch 17 8 left Iteration 1 Error: 1.071115 Iteration 2 Error: 0.214487 Iteration 3 Error: 0.056675 Iteration 4 Error: 0.021605 Align patch 18 7 left Iteration 1 Error: 0.804813 Iteration 2 Error: 0.108703 Iteration 3 Error: 0.022624 Align patch 19 6 left Iteration 1 Error: 0.656361 Iteration 2 Error: 0.129184 Iteration 3 Error: 0.026785 Align patch 20 5 left Iteration 1 Error: 0.798844 Iteration 2 Error: 0.112972 Iteration 3 Error: 0.028897 Align patch 21 4 left Iteration 1 Error: 1.563401 Iteration 2 Error: 0.319517 Iteration 3 Error: 0.080720 Iteration 4 Error: 0.033107 Align patch 22 3 left Iteration 1 Error: 1.833409 Iteration 2 Error: 0.214328 Iteration 3 Error: 0.038436 Align patch 23 2 left Iteration 1 Error: 1.059747 Iteration 2 Error: 0.082636 Iteration 3 Error: 0.014872 Align patch 24 1 left Iteration 1 Error: 0.630081 Iteration 2 Error: 0.095235 Iteration 3 Error: 0.022023 Align patch 25 0 left Iteration 1 Error: 0.794229 Iteration 2 Error: 0.083325 Iteration 3 Error: 0.017740 3D Fitting completed. Patch alignment time: 11.81(sec) Local motion has been corrected. Process thread exits. Computational time: 29.038879 sec Total time: 37.385128 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00010hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00010hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.538093s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00010hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.899693s ........................................ >>>>>>TIME<<<<<< FFT: 1.036552s Defocus_U Defocus_V Angle CCC 10366.32 10786.17 15.43 0.049703 Final Values Defocus_U Defocus_V Angle CCC 10295.88 10844.22 1.93 0.094732 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00010hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00010hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 48.42 7.60 Num Hot pixels: 203 Hot pixel threshold: 94.00 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.613359 Iteration 2 Error: 0.043064 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.18 0.07 ...... Frame ( 3) shift: -0.36 0.14 ...... Frame ( 4) shift: -0.54 0.21 ...... Frame ( 5) shift: -0.72 0.27 ...... Frame ( 6) shift: -0.80 0.33 ...... Frame ( 7) shift: -0.77 0.39 ...... Frame ( 8) shift: -0.74 0.44 ...... Frame ( 9) shift: -0.72 0.48 ...... Frame ( 10) shift: -0.72 0.52 ...... Frame ( 11) shift: -0.72 0.55 ...... Frame ( 12) shift: -0.71 0.57 ...... Frame ( 13) shift: -0.70 0.58 ...... Frame ( 14) shift: -0.70 0.59 ...... Frame ( 15) shift: -0.70 0.58 ...... Frame ( 16) shift: -0.73 0.57 ...... Frame ( 17) shift: -0.75 0.55 ...... Frame ( 18) shift: -0.75 0.56 ...... Frame ( 19) shift: -0.73 0.60 ...... Frame ( 20) shift: -0.71 0.64 ...... Frame ( 21) shift: -0.70 0.64 ...... Frame ( 22) shift: -0.71 0.59 ...... Frame ( 23) shift: -0.71 0.54 ...... Frame ( 24) shift: -0.70 0.51 ...... Frame ( 25) shift: -0.68 0.50 ...... Frame ( 26) shift: -0.66 0.49 ...... Frame ( 27) shift: -0.68 0.46 ...... Frame ( 28) shift: -0.75 0.41 ...... Frame ( 29) shift: -0.82 0.35 ...... Frame ( 30) shift: -0.86 0.34 ...... Frame ( 31) shift: -0.88 0.38 ...... Frame ( 32) shift: -0.90 0.42 ...... Frame ( 33) shift: -0.88 0.42 ...... Frame ( 34) shift: -0.83 0.38 ...... Frame ( 35) shift: -0.78 0.34 ...... Frame ( 36) shift: -0.78 0.32 ...... Frame ( 37) shift: -0.82 0.33 ...... Frame ( 38) shift: -0.86 0.33 ...... Frame ( 39) shift: -0.90 0.34 ...... Frame ( 40) shift: -0.94 0.35 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.032376 Iteration 2 Error: 0.193188 Iteration 3 Error: 0.059344 Iteration 4 Error: 0.017019 Align patch 2 23 left Iteration 1 Error: 1.023819 Iteration 2 Error: 0.156067 Iteration 3 Error: 0.038437 Align patch 3 22 left Iteration 1 Error: 0.809182 Iteration 2 Error: 0.173397 Iteration 3 Error: 0.041501 Align patch 4 21 left Iteration 1 Error: 0.863632 Iteration 2 Error: 0.133013 Iteration 3 Error: 0.029118 Align patch 5 20 left Iteration 1 Error: 0.598293 Iteration 2 Error: 0.104515 Iteration 3 Error: 0.027201 Align patch 6 19 left Iteration 1 Error: 1.110672 Iteration 2 Error: 0.220222 Iteration 3 Error: 0.050021 Iteration 4 Error: 0.028981 Align patch 7 18 left Iteration 1 Error: 0.962806 Iteration 2 Error: 0.235304 Iteration 3 Error: 0.047107 Align patch 8 17 left Iteration 1 Error: 0.718590 Iteration 2 Error: 0.079658 Iteration 3 Error: 0.021939 Align patch 9 16 left Iteration 1 Error: 1.140279 Iteration 2 Error: 0.187310 Iteration 3 Error: 0.055047 Iteration 4 Error: 0.017138 Align patch 10 15 left Iteration 1 Error: 0.803812 Iteration 2 Error: 0.127858 Iteration 3 Error: 0.023597 Align patch 11 14 left Iteration 1 Error: 0.988882 Iteration 2 Error: 0.211833 Iteration 3 Error: 0.047598 Align patch 12 13 left Iteration 1 Error: 1.247640 Iteration 2 Error: 0.222417 Iteration 3 Error: 0.072528 Iteration 4 Error: 0.032259 Align patch 13 12 left Iteration 1 Error: 1.345784 Iteration 2 Error: 0.244974 Iteration 3 Error: 0.075575 Iteration 4 Error: 0.025627 Align patch 14 11 left Iteration 1 Error: 0.561833 Iteration 2 Error: 0.147192 Iteration 3 Error: 0.039712 Align patch 15 10 left Iteration 1 Error: 0.658391 Iteration 2 Error: 0.116123 Iteration 3 Error: 0.025404 Align patch 16 9 left Iteration 1 Error: 1.026217 Iteration 2 Error: 0.164462 Iteration 3 Error: 0.053929 Iteration 4 Error: 0.026507 Align patch 17 8 left Iteration 1 Error: 0.777559 Iteration 2 Error: 0.181603 Iteration 3 Error: 0.078636 Iteration 4 Error: 0.014038 Align patch 18 7 left Iteration 1 Error: 1.241596 Iteration 2 Error: 0.119358 Iteration 3 Error: 0.020041 Align patch 19 6 left Iteration 1 Error: 0.861963 Iteration 2 Error: 0.108262 Iteration 3 Error: 0.030010 Align patch 20 5 left Iteration 1 Error: 1.073628 Iteration 2 Error: 0.126299 Iteration 3 Error: 0.035628 Align patch 21 4 left Iteration 1 Error: 1.318523 Iteration 2 Error: 0.233831 Iteration 3 Error: 0.058415 Iteration 4 Error: 0.020627 Align patch 22 3 left Iteration 1 Error: 0.936325 Iteration 2 Error: 0.137420 Iteration 3 Error: 0.053472 Iteration 4 Error: 0.021097 Align patch 23 2 left Iteration 1 Error: 0.954204 Iteration 2 Error: 0.186757 Iteration 3 Error: 0.044559 Align patch 24 1 left Iteration 1 Error: 1.242622 Iteration 2 Error: 0.198939 Iteration 3 Error: 0.038511 Align patch 25 0 left Iteration 1 Error: 0.895245 Iteration 2 Error: 0.100549 Iteration 3 Error: 0.023810 3D Fitting completed. Patch alignment time: 11.88(sec) Local motion has been corrected. Process thread exits. Computational time: 35.226303 sec Total time: 42.907036 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00010hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00010hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.764270s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00010hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.264267s ........................................ >>>>>>TIME<<<<<< FFT: 1.125867s Defocus_U Defocus_V Angle CCC 14349.61 15142.58 3.85 0.053830 Final Values Defocus_U Defocus_V Angle CCC 14346.48 15145.71 4.48 0.094305 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00010hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00010hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.997e-02 CC threshold: 0.734 Mean Std: 47.56 7.78 Num Hot pixels: 178 Hot pixel threshold: 94.27 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.700905 Iteration 2 Error: 0.212062 Iteration 3 Error: 0.067351 Iteration 4 Error: 0.020839 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.15 0.14 ...... Frame ( 3) shift: -0.30 0.28 ...... Frame ( 4) shift: -0.46 0.42 ...... Frame ( 5) shift: -0.61 0.56 ...... Frame ( 6) shift: -0.71 0.68 ...... Frame ( 7) shift: -0.77 0.79 ...... Frame ( 8) shift: -0.83 0.91 ...... Frame ( 9) shift: -0.86 1.04 ...... Frame ( 10) shift: -0.86 1.20 ...... Frame ( 11) shift: -0.86 1.36 ...... Frame ( 12) shift: -0.86 1.52 ...... Frame ( 13) shift: -0.86 1.67 ...... Frame ( 14) shift: -0.85 1.82 ...... Frame ( 15) shift: -0.87 1.93 ...... Frame ( 16) shift: -0.92 2.00 ...... Frame ( 17) shift: -0.97 2.07 ...... Frame ( 18) shift: -0.98 2.11 ...... Frame ( 19) shift: -0.96 2.12 ...... Frame ( 20) shift: -0.93 2.13 ...... Frame ( 21) shift: -0.93 2.17 ...... Frame ( 22) shift: -0.96 2.24 ...... Frame ( 23) shift: -0.99 2.31 ...... Frame ( 24) shift: -1.00 2.36 ...... Frame ( 25) shift: -0.99 2.37 ...... Frame ( 26) shift: -0.99 2.39 ...... Frame ( 27) shift: -1.03 2.41 ...... Frame ( 28) shift: -1.13 2.42 ...... Frame ( 29) shift: -1.22 2.44 ...... Frame ( 30) shift: -1.30 2.46 ...... Frame ( 31) shift: -1.38 2.50 ...... Frame ( 32) shift: -1.45 2.53 ...... Frame ( 33) shift: -1.48 2.56 ...... Frame ( 34) shift: -1.46 2.60 ...... Frame ( 35) shift: -1.45 2.64 ...... Frame ( 36) shift: -1.45 2.66 ...... Frame ( 37) shift: -1.48 2.67 ...... Frame ( 38) shift: -1.52 2.68 ...... Frame ( 39) shift: -1.55 2.69 ...... Frame ( 40) shift: -1.58 2.70 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.299460 Iteration 2 Error: 0.248306 Iteration 3 Error: 0.075597 Iteration 4 Error: 0.019042 Align patch 2 23 left Iteration 1 Error: 0.777858 Iteration 2 Error: 0.167607 Iteration 3 Error: 0.098267 Iteration 4 Error: 0.030410 Align patch 3 22 left Iteration 1 Error: 2.591193 Iteration 2 Error: 0.301466 Iteration 3 Error: 0.068359 Iteration 4 Error: 0.024078 Align patch 4 21 left Iteration 1 Error: 0.888684 Iteration 2 Error: 0.162528 Iteration 3 Error: 0.036393 Align patch 5 20 left Iteration 1 Error: 0.720986 Iteration 2 Error: 0.134765 Iteration 3 Error: 0.028192 Align patch 6 19 left Iteration 1 Error: 2.422380 Iteration 2 Error: 1.333485 Iteration 3 Error: 0.255748 Iteration 4 Error: 0.131496 Iteration 5 Error: 0.055918 Align patch 6 19 left Iteration 1 Error: 2.155123 Iteration 2 Error: 0.217927 Iteration 3 Error: 0.074889 Iteration 4 Error: 0.026583 Align patch 7 18 left Iteration 1 Error: 1.377256 Iteration 2 Error: 0.349954 Iteration 3 Error: 0.090504 Iteration 4 Error: 0.035132 Align patch 8 17 left Iteration 1 Error: 2.029966 Iteration 2 Error: 0.409929 Iteration 3 Error: 0.103508 Iteration 4 Error: 0.033340 Align patch 9 16 left Iteration 1 Error: 0.887781 Iteration 2 Error: 0.166150 Iteration 3 Error: 0.036382 Align patch 10 15 left Iteration 1 Error: 1.017520 Iteration 2 Error: 0.155281 Iteration 3 Error: 0.029630 Align patch 11 14 left Iteration 1 Error: 1.369677 Iteration 2 Error: 0.324155 Iteration 3 Error: 0.090698 Iteration 4 Error: 0.053637 Iteration 5 Error: 0.022666 Align patch 12 13 left Iteration 1 Error: 0.883293 Iteration 2 Error: 0.135265 Iteration 3 Error: 0.040590 Align patch 13 12 left Iteration 1 Error: 3.469202 Iteration 2 Error: 0.514944 Iteration 3 Error: 0.072501 Iteration 4 Error: 0.012937 Align patch 14 11 left Iteration 1 Error: 1.669624 Iteration 2 Error: 0.181650 Iteration 3 Error: 0.029084 Align patch 15 10 left Iteration 1 Error: 0.970114 Iteration 2 Error: 0.217450 Iteration 3 Error: 0.036728 Align patch 16 9 left Iteration 1 Error: 1.408844 Iteration 2 Error: 0.371311 Iteration 3 Error: 0.112531 Iteration 4 Error: 0.031942 Align patch 17 8 left Iteration 1 Error: 1.098781 Iteration 2 Error: 0.279331 Iteration 3 Error: 0.082503 Iteration 4 Error: 0.033794 Align patch 18 7 left Iteration 1 Error: 5.523191 Iteration 2 Error: 1.182773 Iteration 3 Error: 0.733436 Iteration 4 Error: 0.316749 Iteration 5 Error: 0.271488 Align patch 18 7 left Iteration 1 Error: 3.903429 Iteration 2 Error: 0.586751 Iteration 3 Error: 0.141496 Iteration 4 Error: 0.036688 Align patch 19 6 left Iteration 1 Error: 0.916715 Iteration 2 Error: 0.226750 Iteration 3 Error: 0.085805 Iteration 4 Error: 0.045709 Align patch 20 5 left Iteration 1 Error: 1.339005 Iteration 2 Error: 0.218301 Iteration 3 Error: 0.036834 Align patch 21 4 left Iteration 1 Error: 1.612131 Iteration 2 Error: 0.329832 Iteration 3 Error: 0.068289 Iteration 4 Error: 0.021495 Align patch 22 3 left Iteration 1 Error: 1.338830 Iteration 2 Error: 0.266000 Iteration 3 Error: 0.071554 Iteration 4 Error: 0.028956 Align patch 23 2 left Iteration 1 Error: 1.919156 Iteration 2 Error: 0.198824 Iteration 3 Error: 0.056443 Iteration 4 Error: 0.026720 Align patch 24 1 left Iteration 1 Error: 1.722631 Iteration 2 Error: 0.270466 Iteration 3 Error: 0.041081 Align patch 25 0 left Iteration 1 Error: 1.961610 Iteration 2 Error: 0.212460 Iteration 3 Error: 0.043523 3D Fitting completed. Patch alignment time: 13.23(sec) Local motion has been corrected. Process thread exits. Computational time: 27.770744 sec Total time: 35.634117 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00010hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00010hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.581443s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00010hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.526896s ........................................ >>>>>>TIME<<<<<< FFT: 0.927486s Defocus_U Defocus_V Angle CCC 15544.98 14798.81 86.30 0.045655 Final Values Defocus_U Defocus_V Angle CCC 15546.54 14819.13 86.93 0.079424 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00011hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00011hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.995e-02 CC threshold: 0.734 Mean Std: 46.86 7.64 Num Hot pixels: 184 Hot pixel threshold: 92.71 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.706441 Iteration 2 Error: 0.123690 Iteration 3 Error: 0.034095 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.16 0.23 ...... Frame ( 3) shift: -0.31 0.46 ...... Frame ( 4) shift: -0.47 0.70 ...... Frame ( 5) shift: -0.63 0.93 ...... Frame ( 6) shift: -0.66 1.08 ...... Frame ( 7) shift: -0.55 1.16 ...... Frame ( 8) shift: -0.45 1.24 ...... Frame ( 9) shift: -0.38 1.28 ...... Frame ( 10) shift: -0.34 1.28 ...... Frame ( 11) shift: -0.31 1.29 ...... Frame ( 12) shift: -0.24 1.27 ...... Frame ( 13) shift: -0.15 1.22 ...... Frame ( 14) shift: -0.07 1.18 ...... Frame ( 15) shift: -0.01 1.09 ...... Frame ( 16) shift: 0.02 0.96 ...... Frame ( 17) shift: 0.05 0.83 ...... Frame ( 18) shift: 0.06 0.72 ...... Frame ( 19) shift: 0.07 0.63 ...... Frame ( 20) shift: 0.08 0.53 ...... Frame ( 21) shift: 0.10 0.48 ...... Frame ( 22) shift: 0.13 0.47 ...... Frame ( 23) shift: 0.17 0.47 ...... Frame ( 24) shift: 0.20 0.42 ...... Frame ( 25) shift: 0.22 0.34 ...... Frame ( 26) shift: 0.24 0.26 ...... Frame ( 27) shift: 0.24 0.22 ...... Frame ( 28) shift: 0.21 0.23 ...... Frame ( 29) shift: 0.19 0.23 ...... Frame ( 30) shift: 0.20 0.23 ...... Frame ( 31) shift: 0.26 0.20 ...... Frame ( 32) shift: 0.32 0.18 ...... Frame ( 33) shift: 0.33 0.13 ...... Frame ( 34) shift: 0.29 0.07 ...... Frame ( 35) shift: 0.25 -0.00 ...... Frame ( 36) shift: 0.23 0.00 ...... Frame ( 37) shift: 0.23 0.07 ...... Frame ( 38) shift: 0.23 0.14 ...... Frame ( 39) shift: 0.22 0.21 ...... Frame ( 40) shift: 0.22 0.28 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.823500 Iteration 2 Error: 1.055773 Iteration 3 Error: 0.674258 Iteration 4 Error: 0.355546 Iteration 5 Error: 0.222450 Align patch 1 24 left Iteration 1 Error: 2.595802 Iteration 2 Error: 0.664659 Iteration 3 Error: 0.210994 Iteration 4 Error: 0.085545 Iteration 5 Error: 0.032816 Align patch 2 23 left Iteration 1 Error: 1.619722 Iteration 2 Error: 0.852529 Iteration 3 Error: 0.518136 Iteration 4 Error: 0.387615 Iteration 5 Error: 0.220816 Align patch 2 23 left Iteration 1 Error: 2.636472 Iteration 2 Error: 0.589013 Iteration 3 Error: 0.124738 Iteration 4 Error: 0.034218 Align patch 3 22 left Iteration 1 Error: 1.598961 Iteration 2 Error: 0.435808 Iteration 3 Error: 0.182416 Iteration 4 Error: 0.081098 Iteration 5 Error: 0.056563 Align patch 3 22 left Iteration 1 Error: 1.170954 Iteration 2 Error: 0.263814 Iteration 3 Error: 0.070730 Iteration 4 Error: 0.023332 Align patch 4 21 left Iteration 1 Error: 1.156837 Iteration 2 Error: 0.151508 Iteration 3 Error: 0.044167 Align patch 5 20 left Iteration 1 Error: 0.900085 Iteration 2 Error: 0.208674 Iteration 3 Error: 0.045774 Align patch 6 19 left Iteration 1 Error: 1.856081 Iteration 2 Error: 1.187561 Iteration 3 Error: 0.659340 Iteration 4 Error: 0.571063 Iteration 5 Error: 0.401241 Align patch 6 19 left Iteration 1 Error: 2.153738 Iteration 2 Error: 0.715086 Iteration 3 Error: 0.211577 Iteration 4 Error: 0.104684 Iteration 5 Error: 0.021564 Align patch 7 18 left Iteration 1 Error: 1.489212 Iteration 2 Error: 0.288021 Iteration 3 Error: 0.071279 Iteration 4 Error: 0.028342 Align patch 8 17 left Iteration 1 Error: 0.953186 Iteration 2 Error: 0.163581 Iteration 3 Error: 0.037008 Align patch 9 16 left Iteration 1 Error: 0.744841 Iteration 2 Error: 0.195972 Iteration 3 Error: 0.059853 Iteration 4 Error: 0.028714 Align patch 10 15 left Iteration 1 Error: 0.858434 Iteration 2 Error: 0.190955 Iteration 3 Error: 0.053496 Iteration 4 Error: 0.016805 Align patch 11 14 left Iteration 1 Error: 1.417506 Iteration 2 Error: 0.416439 Iteration 3 Error: 0.335157 Iteration 4 Error: 0.199638 Iteration 5 Error: 0.124468 Align patch 11 14 left Iteration 1 Error: 1.965986 Iteration 2 Error: 0.630412 Iteration 3 Error: 0.177246 Iteration 4 Error: 0.054067 Iteration 5 Error: 0.021996 Align patch 12 13 left Iteration 1 Error: 1.086152 Iteration 2 Error: 0.211290 Iteration 3 Error: 0.061415 Iteration 4 Error: 0.018076 Align patch 13 12 left Iteration 1 Error: 0.942125 Iteration 2 Error: 0.106162 Iteration 3 Error: 0.028702 Align patch 14 11 left Iteration 1 Error: 0.753410 Iteration 2 Error: 0.118816 Iteration 3 Error: 0.041074 Align patch 15 10 left Iteration 1 Error: 1.003123 Iteration 2 Error: 0.158763 Iteration 3 Error: 0.031092 Align patch 16 9 left Iteration 1 Error: 0.886184 Iteration 2 Error: 0.276272 Iteration 3 Error: 0.131461 Iteration 4 Error: 0.085232 Iteration 5 Error: 0.057139 Align patch 16 9 left Iteration 1 Error: 1.498676 Iteration 2 Error: 0.406745 Iteration 3 Error: 0.108464 Iteration 4 Error: 0.059118 Iteration 5 Error: 0.029585 Align patch 17 8 left Iteration 1 Error: 0.936471 Iteration 2 Error: 0.197516 Iteration 3 Error: 0.055527 Iteration 4 Error: 0.015490 Align patch 18 7 left Iteration 1 Error: 1.107157 Iteration 2 Error: 0.116067 Iteration 3 Error: 0.027569 Align patch 19 6 left Iteration 1 Error: 0.847053 Iteration 2 Error: 0.217179 Iteration 3 Error: 0.054596 Iteration 4 Error: 0.020975 Align patch 20 5 left Iteration 1 Error: 0.791217 Iteration 2 Error: 0.126807 Iteration 3 Error: 0.026833 Align patch 21 4 left Iteration 1 Error: 1.589962 Iteration 2 Error: 0.400059 Iteration 3 Error: 0.165297 Iteration 4 Error: 0.134576 Iteration 5 Error: 0.058232 Align patch 21 4 left Iteration 1 Error: 1.308519 Iteration 2 Error: 0.353310 Iteration 3 Error: 0.082795 Iteration 4 Error: 0.034142 Align patch 22 3 left Iteration 1 Error: 0.895801 Iteration 2 Error: 0.139902 Iteration 3 Error: 0.050080 Iteration 4 Error: 0.019010 Align patch 23 2 left Iteration 1 Error: 1.024121 Iteration 2 Error: 0.161750 Iteration 3 Error: 0.046231 Align patch 24 1 left Iteration 1 Error: 1.038273 Iteration 2 Error: 0.194052 Iteration 3 Error: 0.030931 Align patch 25 0 left Iteration 1 Error: 0.899184 Iteration 2 Error: 0.214176 Iteration 3 Error: 0.038544 3D Fitting completed. Patch alignment time: 17.71(sec) Local motion has been corrected. Process thread exits. Computational time: 28.058064 sec Total time: 34.594280 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00011hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00011hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.552089s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00011hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.617226s ........................................ >>>>>>TIME<<<<<< FFT: 1.113769s Defocus_U Defocus_V Angle CCC 8921.88 9710.94 14.86 0.040408 Final Values Defocus_U Defocus_V Angle CCC 8928.13 9717.19 14.24 0.079433 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00011hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00011hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 47.10 7.83 Num Hot pixels: 168 Hot pixel threshold: 94.05 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.169109 Iteration 2 Error: 0.093437 Iteration 3 Error: 0.016471 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.18 0.16 ...... Frame ( 3) shift: -0.37 0.31 ...... Frame ( 4) shift: -0.55 0.47 ...... Frame ( 5) shift: -0.73 0.63 ...... Frame ( 6) shift: -0.79 0.78 ...... Frame ( 7) shift: -0.71 0.94 ...... Frame ( 8) shift: -0.63 1.09 ...... Frame ( 9) shift: -0.54 1.18 ...... Frame ( 10) shift: -0.45 1.19 ...... Frame ( 11) shift: -0.36 1.20 ...... Frame ( 12) shift: -0.35 1.26 ...... Frame ( 13) shift: -0.40 1.38 ...... Frame ( 14) shift: -0.45 1.50 ...... Frame ( 15) shift: -0.43 1.57 ...... Frame ( 16) shift: -0.35 1.60 ...... Frame ( 17) shift: -0.27 1.62 ...... Frame ( 18) shift: -0.22 1.62 ...... Frame ( 19) shift: -0.20 1.59 ...... Frame ( 20) shift: -0.18 1.57 ...... Frame ( 21) shift: -0.15 1.55 ...... Frame ( 22) shift: -0.13 1.55 ...... Frame ( 23) shift: -0.10 1.54 ...... Frame ( 24) shift: -0.08 1.52 ...... Frame ( 25) shift: -0.07 1.50 ...... Frame ( 26) shift: -0.06 1.47 ...... Frame ( 27) shift: -0.03 1.47 ...... Frame ( 28) shift: 0.01 1.51 ...... Frame ( 29) shift: 0.05 1.55 ...... Frame ( 30) shift: 0.05 1.57 ...... Frame ( 31) shift: 0.03 1.59 ...... Frame ( 32) shift: 0.00 1.60 ...... Frame ( 33) shift: 0.00 1.62 ...... Frame ( 34) shift: 0.03 1.65 ...... Frame ( 35) shift: 0.06 1.68 ...... Frame ( 36) shift: 0.07 1.71 ...... Frame ( 37) shift: 0.06 1.74 ...... Frame ( 38) shift: 0.06 1.78 ...... Frame ( 39) shift: 0.05 1.81 ...... Frame ( 40) shift: 0.04 1.85 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.039482 Iteration 2 Error: 0.210904 Iteration 3 Error: 0.102425 Iteration 4 Error: 0.038374 Align patch 2 23 left Iteration 1 Error: 1.732249 Iteration 2 Error: 0.253743 Iteration 3 Error: 0.054947 Iteration 4 Error: 0.020535 Align patch 3 22 left Iteration 1 Error: 2.425032 Iteration 2 Error: 0.544592 Iteration 3 Error: 0.212006 Iteration 4 Error: 0.068643 Iteration 5 Error: 0.067946 Align patch 3 22 left Iteration 1 Error: 2.579416 Iteration 2 Error: 0.390415 Iteration 3 Error: 0.139972 Iteration 4 Error: 0.040026 Align patch 4 21 left Iteration 1 Error: 0.531229 Iteration 2 Error: 0.100737 Iteration 3 Error: 0.021292 Align patch 5 20 left Iteration 1 Error: 0.945559 Iteration 2 Error: 0.088433 Iteration 3 Error: 0.026115 Align patch 6 19 left Iteration 1 Error: 1.160157 Iteration 2 Error: 0.234973 Iteration 3 Error: 0.072109 Iteration 4 Error: 0.042979 Align patch 7 18 left Iteration 1 Error: 0.723249 Iteration 2 Error: 0.125588 Iteration 3 Error: 0.024878 Align patch 8 17 left Iteration 1 Error: 0.864558 Iteration 2 Error: 0.179732 Iteration 3 Error: 0.044439 Align patch 9 16 left Iteration 1 Error: 0.933310 Iteration 2 Error: 0.085464 Iteration 3 Error: 0.017724 Align patch 10 15 left Iteration 1 Error: 0.539110 Iteration 2 Error: 0.082011 Iteration 3 Error: 0.016293 Align patch 11 14 left Iteration 1 Error: 0.953324 Iteration 2 Error: 0.217850 Iteration 3 Error: 0.073485 Iteration 4 Error: 0.039063 Align patch 12 13 left Iteration 1 Error: 0.886250 Iteration 2 Error: 0.146382 Iteration 3 Error: 0.026097 Align patch 13 12 left Iteration 1 Error: 0.643565 Iteration 2 Error: 0.118939 Iteration 3 Error: 0.026279 Align patch 14 11 left Iteration 1 Error: 0.405986 Iteration 2 Error: 0.064005 Iteration 3 Error: 0.015351 Align patch 15 10 left Iteration 1 Error: 0.468228 Iteration 2 Error: 0.070411 Iteration 3 Error: 0.019762 Align patch 16 9 left Iteration 1 Error: 0.921588 Iteration 2 Error: 0.219532 Iteration 3 Error: 0.052532 Iteration 4 Error: 0.023713 Align patch 17 8 left Iteration 1 Error: 1.025527 Iteration 2 Error: 0.307776 Iteration 3 Error: 0.058784 Iteration 4 Error: 0.021267 Align patch 18 7 left Iteration 1 Error: 1.198812 Iteration 2 Error: 0.244929 Iteration 3 Error: 0.065504 Iteration 4 Error: 0.022318 Align patch 19 6 left Iteration 1 Error: 0.862502 Iteration 2 Error: 0.182349 Iteration 3 Error: 0.046425 Align patch 20 5 left Iteration 1 Error: 0.778440 Iteration 2 Error: 0.094462 Iteration 3 Error: 0.015427 Align patch 21 4 left Iteration 1 Error: 1.521944 Iteration 2 Error: 0.199239 Iteration 3 Error: 0.032765 Align patch 22 3 left Iteration 1 Error: 1.501710 Iteration 2 Error: 0.221426 Iteration 3 Error: 0.086623 Iteration 4 Error: 0.021860 Align patch 23 2 left Iteration 1 Error: 1.479998 Iteration 2 Error: 0.155779 Iteration 3 Error: 0.037520 Align patch 24 1 left Iteration 1 Error: 0.729313 Iteration 2 Error: 0.062832 Iteration 3 Error: 0.029240 Align patch 25 0 left Iteration 1 Error: 0.612735 Iteration 2 Error: 0.117716 Iteration 3 Error: 0.016561 3D Fitting completed. Patch alignment time: 12.30(sec) Local motion has been corrected. Process thread exits. Computational time: 24.019564 sec Total time: 30.606283 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00011hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00011hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.717165s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00011hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.341450s ........................................ >>>>>>TIME<<<<<< FFT: 0.942100s Defocus_U Defocus_V Angle CCC 9267.58 9767.58 2.72 0.043830 Final Values Defocus_U Defocus_V Angle CCC 9273.84 9776.97 3.67 0.084585 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00011hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00011hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.998e-02 CC threshold: 0.734 Mean Std: 47.66 7.72 Num Hot pixels: 174 Hot pixel threshold: 93.96 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.458741 Iteration 2 Error: 0.223802 Iteration 3 Error: 0.043129 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.23 0.11 ...... Frame ( 3) shift: -0.45 0.21 ...... Frame ( 4) shift: -0.68 0.32 ...... Frame ( 5) shift: -0.91 0.43 ...... Frame ( 6) shift: -0.98 0.57 ...... Frame ( 7) shift: -0.90 0.74 ...... Frame ( 8) shift: -0.81 0.90 ...... Frame ( 9) shift: -0.73 1.05 ...... Frame ( 10) shift: -0.65 1.18 ...... Frame ( 11) shift: -0.57 1.31 ...... Frame ( 12) shift: -0.45 1.46 ...... Frame ( 13) shift: -0.30 1.63 ...... Frame ( 14) shift: -0.15 1.80 ...... Frame ( 15) shift: -0.05 1.92 ...... Frame ( 16) shift: -0.01 1.99 ...... Frame ( 17) shift: 0.04 2.06 ...... Frame ( 18) shift: 0.06 2.11 ...... Frame ( 19) shift: 0.04 2.14 ...... Frame ( 20) shift: 0.03 2.17 ...... Frame ( 21) shift: 0.01 2.17 ...... Frame ( 22) shift: -0.02 2.13 ...... Frame ( 23) shift: -0.05 2.10 ...... Frame ( 24) shift: -0.08 2.06 ...... Frame ( 25) shift: -0.12 2.02 ...... Frame ( 26) shift: -0.16 1.97 ...... Frame ( 27) shift: -0.20 1.98 ...... Frame ( 28) shift: -0.25 2.04 ...... Frame ( 29) shift: -0.30 2.10 ...... Frame ( 30) shift: -0.33 2.15 ...... Frame ( 31) shift: -0.33 2.17 ...... Frame ( 32) shift: -0.33 2.20 ...... Frame ( 33) shift: -0.34 2.18 ...... Frame ( 34) shift: -0.35 2.11 ...... Frame ( 35) shift: -0.35 2.04 ...... Frame ( 36) shift: -0.34 2.00 ...... Frame ( 37) shift: -0.30 1.97 ...... Frame ( 38) shift: -0.26 1.93 ...... Frame ( 39) shift: -0.22 1.90 ...... Frame ( 40) shift: -0.19 1.87 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.252196 Iteration 2 Error: 0.204660 Iteration 3 Error: 0.081643 Iteration 4 Error: 0.020703 Align patch 2 23 left Iteration 1 Error: 1.689091 Iteration 2 Error: 0.291533 Iteration 3 Error: 0.085970 Iteration 4 Error: 0.037053 Align patch 3 22 left Iteration 1 Error: 0.780662 Iteration 2 Error: 0.184847 Iteration 3 Error: 0.033457 Align patch 4 21 left Iteration 1 Error: 0.863858 Iteration 2 Error: 0.144750 Iteration 3 Error: 0.037232 Align patch 5 20 left Iteration 1 Error: 0.603322 Iteration 2 Error: 0.104025 Iteration 3 Error: 0.021939 Align patch 6 19 left Iteration 1 Error: 0.731949 Iteration 2 Error: 0.265626 Iteration 3 Error: 0.081669 Iteration 4 Error: 0.045035 Align patch 7 18 left Iteration 1 Error: 1.631014 Iteration 2 Error: 0.210125 Iteration 3 Error: 0.069367 Iteration 4 Error: 0.021463 Align patch 8 17 left Iteration 1 Error: 0.992781 Iteration 2 Error: 0.115698 Iteration 3 Error: 0.029272 Align patch 9 16 left Iteration 1 Error: 0.571969 Iteration 2 Error: 0.111188 Iteration 3 Error: 0.038625 Align patch 10 15 left Iteration 1 Error: 0.593938 Iteration 2 Error: 0.083750 Iteration 3 Error: 0.028134 Align patch 11 14 left Iteration 1 Error: 0.895905 Iteration 2 Error: 0.166024 Iteration 3 Error: 0.034196 Align patch 12 13 left Iteration 1 Error: 1.077244 Iteration 2 Error: 0.340071 Iteration 3 Error: 0.091101 Iteration 4 Error: 0.039071 Align patch 13 12 left Iteration 1 Error: 1.027654 Iteration 2 Error: 0.221881 Iteration 3 Error: 0.104665 Iteration 4 Error: 0.030145 Align patch 14 11 left Iteration 1 Error: 0.763922 Iteration 2 Error: 0.108108 Iteration 3 Error: 0.027570 Align patch 15 10 left Iteration 1 Error: 0.753567 Iteration 2 Error: 0.101668 Iteration 3 Error: 0.021957 Align patch 16 9 left Iteration 1 Error: 1.440543 Iteration 2 Error: 0.230983 Iteration 3 Error: 0.065696 Iteration 4 Error: 0.021826 Align patch 17 8 left Iteration 1 Error: 0.660509 Iteration 2 Error: 0.223114 Iteration 3 Error: 0.081012 Iteration 4 Error: 0.029684 Align patch 18 7 left Iteration 1 Error: 0.987049 Iteration 2 Error: 0.173012 Iteration 3 Error: 0.060154 Iteration 4 Error: 0.023617 Align patch 19 6 left Iteration 1 Error: 0.945356 Iteration 2 Error: 0.196357 Iteration 3 Error: 0.053878 Iteration 4 Error: 0.019999 Align patch 20 5 left Iteration 1 Error: 0.805936 Iteration 2 Error: 0.099415 Iteration 3 Error: 0.024075 Align patch 21 4 left Iteration 1 Error: 1.445532 Iteration 2 Error: 0.289150 Iteration 3 Error: 0.118187 Iteration 4 Error: 0.054846 Iteration 5 Error: 0.018154 Align patch 22 3 left Iteration 1 Error: 0.675602 Iteration 2 Error: 0.118391 Iteration 3 Error: 0.036700 Align patch 23 2 left Iteration 1 Error: 0.736070 Iteration 2 Error: 0.208703 Iteration 3 Error: 0.063097 Iteration 4 Error: 0.027237 Align patch 24 1 left Iteration 1 Error: 0.789317 Iteration 2 Error: 0.077522 Iteration 3 Error: 0.018647 Align patch 25 0 left Iteration 1 Error: 0.770889 Iteration 2 Error: 0.096134 Iteration 3 Error: 0.021075 3D Fitting completed. Patch alignment time: 12.12(sec) Local motion has been corrected. Process thread exits. Computational time: 23.675859 sec Total time: 30.355055 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00011hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00011hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.589120s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00011hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.278308s ........................................ >>>>>>TIME<<<<<< FFT: 0.928783s Defocus_U Defocus_V Angle CCC 14976.56 15835.94 5.53 0.054192 Final Values Defocus_U Defocus_V Angle CCC 14973.44 15832.81 4.91 0.093816 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00011hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00011hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 47.68 7.76 Num Hot pixels: 184 Hot pixel threshold: 94.21 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.061801 Iteration 2 Error: 0.125947 Iteration 3 Error: 0.030748 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.15 0.13 ...... Frame ( 3) shift: -0.29 0.27 ...... Frame ( 4) shift: -0.44 0.40 ...... Frame ( 5) shift: -0.58 0.53 ...... Frame ( 6) shift: -0.61 0.67 ...... Frame ( 7) shift: -0.52 0.82 ...... Frame ( 8) shift: -0.42 0.96 ...... Frame ( 9) shift: -0.35 1.03 ...... Frame ( 10) shift: -0.30 1.03 ...... Frame ( 11) shift: -0.24 1.02 ...... Frame ( 12) shift: -0.19 1.06 ...... Frame ( 13) shift: -0.14 1.14 ...... Frame ( 14) shift: -0.09 1.23 ...... Frame ( 15) shift: -0.04 1.30 ...... Frame ( 16) shift: 0.02 1.35 ...... Frame ( 17) shift: 0.07 1.40 ...... Frame ( 18) shift: 0.07 1.45 ...... Frame ( 19) shift: 0.02 1.49 ...... Frame ( 20) shift: -0.04 1.54 ...... Frame ( 21) shift: -0.05 1.58 ...... Frame ( 22) shift: -0.02 1.61 ...... Frame ( 23) shift: 0.01 1.65 ...... Frame ( 24) shift: 0.03 1.63 ...... Frame ( 25) shift: 0.03 1.55 ...... Frame ( 26) shift: 0.04 1.48 ...... Frame ( 27) shift: 0.02 1.48 ...... Frame ( 28) shift: -0.01 1.54 ...... Frame ( 29) shift: -0.04 1.61 ...... Frame ( 30) shift: -0.06 1.66 ...... Frame ( 31) shift: -0.08 1.71 ...... Frame ( 32) shift: -0.10 1.75 ...... Frame ( 33) shift: -0.04 1.78 ...... Frame ( 34) shift: 0.09 1.80 ...... Frame ( 35) shift: 0.23 1.81 ...... Frame ( 36) shift: 0.26 1.81 ...... Frame ( 37) shift: 0.18 1.81 ...... Frame ( 38) shift: 0.10 1.81 ...... Frame ( 39) shift: 0.03 1.82 ...... Frame ( 40) shift: -0.05 1.82 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.824053 Iteration 2 Error: 0.128017 Iteration 3 Error: 0.046237 Align patch 2 23 left Iteration 1 Error: 0.677467 Iteration 2 Error: 0.227679 Iteration 3 Error: 0.068924 Iteration 4 Error: 0.031570 Align patch 3 22 left Iteration 1 Error: 0.728480 Iteration 2 Error: 0.168043 Iteration 3 Error: 0.030227 Align patch 4 21 left Iteration 1 Error: 0.712759 Iteration 2 Error: 0.115091 Iteration 3 Error: 0.031530 Align patch 5 20 left Iteration 1 Error: 0.519034 Iteration 2 Error: 0.109348 Iteration 3 Error: 0.025296 Align patch 6 19 left Iteration 1 Error: 0.982545 Iteration 2 Error: 0.295377 Iteration 3 Error: 0.086359 Iteration 4 Error: 0.029838 Align patch 7 18 left Iteration 1 Error: 1.103530 Iteration 2 Error: 0.174723 Iteration 3 Error: 0.033438 Align patch 8 17 left Iteration 1 Error: 0.937628 Iteration 2 Error: 0.220413 Iteration 3 Error: 0.103154 Iteration 4 Error: 0.031293 Align patch 9 16 left Iteration 1 Error: 0.621828 Iteration 2 Error: 0.220890 Iteration 3 Error: 0.080643 Iteration 4 Error: 0.054585 Iteration 5 Error: 0.025362 Align patch 10 15 left Iteration 1 Error: 0.719924 Iteration 2 Error: 0.115574 Iteration 3 Error: 0.021400 Align patch 11 14 left Iteration 1 Error: 0.736483 Iteration 2 Error: 0.089073 Iteration 3 Error: 0.024547 Align patch 12 13 left Iteration 1 Error: 1.267900 Iteration 2 Error: 0.226159 Iteration 3 Error: 0.088400 Iteration 4 Error: 0.058479 Iteration 5 Error: 0.035504 Align patch 13 12 left Iteration 1 Error: 0.524182 Iteration 2 Error: 0.122029 Iteration 3 Error: 0.045319 Align patch 14 11 left Iteration 1 Error: 0.929705 Iteration 2 Error: 0.152288 Iteration 3 Error: 0.037528 Align patch 15 10 left Iteration 1 Error: 0.646899 Iteration 2 Error: 0.143621 Iteration 3 Error: 0.065481 Iteration 4 Error: 0.027643 Align patch 16 9 left Iteration 1 Error: 1.019704 Iteration 2 Error: 0.248531 Iteration 3 Error: 0.091443 Iteration 4 Error: 0.024615 Align patch 17 8 left Iteration 1 Error: 1.217817 Iteration 2 Error: 0.254511 Iteration 3 Error: 0.053077 Iteration 4 Error: 0.017719 Align patch 18 7 left Iteration 1 Error: 1.038284 Iteration 2 Error: 0.159354 Iteration 3 Error: 0.037754 Align patch 19 6 left Iteration 1 Error: 0.664764 Iteration 2 Error: 0.121317 Iteration 3 Error: 0.029980 Align patch 20 5 left Iteration 1 Error: 0.805204 Iteration 2 Error: 0.102478 Iteration 3 Error: 0.026184 Align patch 21 4 left Iteration 1 Error: 0.993989 Iteration 2 Error: 0.246921 Iteration 3 Error: 0.068532 Iteration 4 Error: 0.024077 Align patch 22 3 left Iteration 1 Error: 0.820909 Iteration 2 Error: 0.148437 Iteration 3 Error: 0.043701 Align patch 23 2 left Iteration 1 Error: 0.853903 Iteration 2 Error: 0.129948 Iteration 3 Error: 0.024714 Align patch 24 1 left Iteration 1 Error: 0.760435 Iteration 2 Error: 0.099760 Iteration 3 Error: 0.019195 Align patch 25 0 left Iteration 1 Error: 0.786256 Iteration 2 Error: 0.110598 Iteration 3 Error: 0.034983 3D Fitting completed. Patch alignment time: 11.79(sec) Local motion has been corrected. Process thread exits. Computational time: 23.968004 sec Total time: 31.832933 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00011hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00011hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.686162s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00011hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.832374s ........................................ >>>>>>TIME<<<<<< FFT: 1.105733s Defocus_U Defocus_V Angle CCC 10918.67 10304.06 84.65 0.046108 Final Values Defocus_U Defocus_V Angle CCC 10931.17 10316.57 84.65 0.087639 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00012hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00012hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.999e-02 CC threshold: 0.734 Mean Std: 45.90 7.78 Num Hot pixels: 177 Hot pixel threshold: 92.55 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.394639 Iteration 2 Error: 0.235204 Iteration 3 Error: 0.073299 Iteration 4 Error: 0.015209 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.22 -0.04 ...... Frame ( 3) shift: -0.44 -0.09 ...... Frame ( 4) shift: -0.65 -0.13 ...... Frame ( 5) shift: -0.87 -0.18 ...... Frame ( 6) shift: -0.96 -0.11 ...... Frame ( 7) shift: -0.92 0.06 ...... Frame ( 8) shift: -0.88 0.23 ...... Frame ( 9) shift: -0.80 0.37 ...... Frame ( 10) shift: -0.66 0.47 ...... Frame ( 11) shift: -0.52 0.56 ...... Frame ( 12) shift: -0.45 0.67 ...... Frame ( 13) shift: -0.46 0.79 ...... Frame ( 14) shift: -0.47 0.91 ...... Frame ( 15) shift: -0.47 1.02 ...... Frame ( 16) shift: -0.46 1.13 ...... Frame ( 17) shift: -0.46 1.23 ...... Frame ( 18) shift: -0.41 1.29 ...... Frame ( 19) shift: -0.33 1.31 ...... Frame ( 20) shift: -0.24 1.33 ...... Frame ( 21) shift: -0.20 1.37 ...... Frame ( 22) shift: -0.21 1.43 ...... Frame ( 23) shift: -0.22 1.49 ...... Frame ( 24) shift: -0.21 1.56 ...... Frame ( 25) shift: -0.17 1.64 ...... Frame ( 26) shift: -0.14 1.72 ...... Frame ( 27) shift: -0.12 1.77 ...... Frame ( 28) shift: -0.12 1.80 ...... Frame ( 29) shift: -0.11 1.84 ...... Frame ( 30) shift: -0.06 1.87 ...... Frame ( 31) shift: 0.03 1.90 ...... Frame ( 32) shift: 0.12 1.94 ...... Frame ( 33) shift: 0.17 2.00 ...... Frame ( 34) shift: 0.18 2.09 ...... Frame ( 35) shift: 0.19 2.19 ...... Frame ( 36) shift: 0.23 2.26 ...... Frame ( 37) shift: 0.29 2.29 ...... Frame ( 38) shift: 0.36 2.33 ...... Frame ( 39) shift: 0.42 2.36 ...... Frame ( 40) shift: 0.49 2.40 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.269576 Iteration 2 Error: 0.343041 Iteration 3 Error: 0.114624 Iteration 4 Error: 0.043826 Align patch 2 23 left Iteration 1 Error: 1.025248 Iteration 2 Error: 0.175686 Iteration 3 Error: 0.069226 Iteration 4 Error: 0.028737 Align patch 3 22 left Iteration 1 Error: 1.789263 Iteration 2 Error: 0.389901 Iteration 3 Error: 0.180534 Iteration 4 Error: 0.067235 Iteration 5 Error: 0.031641 Align patch 4 21 left Iteration 1 Error: 0.820338 Iteration 2 Error: 0.149037 Iteration 3 Error: 0.074335 Iteration 4 Error: 0.019737 Align patch 5 20 left Iteration 1 Error: 0.483133 Iteration 2 Error: 0.106457 Iteration 3 Error: 0.034657 Align patch 6 19 left Iteration 1 Error: 2.159225 Iteration 2 Error: 0.239932 Iteration 3 Error: 0.083375 Iteration 4 Error: 0.043276 Align patch 7 18 left Iteration 1 Error: 1.012741 Iteration 2 Error: 0.131227 Iteration 3 Error: 0.047831 Align patch 8 17 left Iteration 1 Error: 0.750625 Iteration 2 Error: 0.169980 Iteration 3 Error: 0.046319 Align patch 9 16 left Iteration 1 Error: 0.693395 Iteration 2 Error: 0.114814 Iteration 3 Error: 0.035274 Align patch 10 15 left Iteration 1 Error: 0.781456 Iteration 2 Error: 0.157055 Iteration 3 Error: 0.035288 Align patch 11 14 left Iteration 1 Error: 1.051959 Iteration 2 Error: 0.168125 Iteration 3 Error: 0.057222 Iteration 4 Error: 0.021520 Align patch 12 13 left Iteration 1 Error: 1.623715 Iteration 2 Error: 0.259559 Iteration 3 Error: 0.107666 Iteration 4 Error: 0.048353 Align patch 13 12 left Iteration 1 Error: 1.153695 Iteration 2 Error: 0.248325 Iteration 3 Error: 0.051648 Iteration 4 Error: 0.023207 Align patch 14 11 left Iteration 1 Error: 0.887229 Iteration 2 Error: 0.107336 Iteration 3 Error: 0.027192 Align patch 15 10 left Iteration 1 Error: 0.867645 Iteration 2 Error: 0.073135 Iteration 3 Error: 0.013727 Align patch 16 9 left Iteration 1 Error: 1.081317 Iteration 2 Error: 0.136465 Iteration 3 Error: 0.033966 Align patch 17 8 left Iteration 1 Error: 0.699964 Iteration 2 Error: 0.146810 Iteration 3 Error: 0.044808 Align patch 18 7 left Iteration 1 Error: 1.085845 Iteration 2 Error: 0.429662 Iteration 3 Error: 0.144702 Iteration 4 Error: 0.063777 Iteration 5 Error: 0.016705 Align patch 19 6 left Iteration 1 Error: 0.881115 Iteration 2 Error: 0.168223 Iteration 3 Error: 0.038208 Align patch 20 5 left Iteration 1 Error: 0.655123 Iteration 2 Error: 0.090598 Iteration 3 Error: 0.027102 Align patch 21 4 left Iteration 1 Error: 0.950140 Iteration 2 Error: 0.296266 Iteration 3 Error: 0.090064 Iteration 4 Error: 0.043235 Align patch 22 3 left Iteration 1 Error: 0.961240 Iteration 2 Error: 0.222804 Iteration 3 Error: 0.078627 Iteration 4 Error: 0.036077 Align patch 23 2 left Iteration 1 Error: 1.287602 Iteration 2 Error: 0.189869 Iteration 3 Error: 0.052076 Iteration 4 Error: 0.018654 Align patch 24 1 left Iteration 1 Error: 0.834209 Iteration 2 Error: 0.204704 Iteration 3 Error: 0.065443 Iteration 4 Error: 0.024382 Align patch 25 0 left Iteration 1 Error: 1.513817 Iteration 2 Error: 0.111359 Iteration 3 Error: 0.015477 3D Fitting completed. Patch alignment time: 12.31(sec) Local motion has been corrected. Process thread exits. Computational time: 24.593100 sec Total time: 32.562309 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00012hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00012hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.652396s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00012hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.365803s ........................................ >>>>>>TIME<<<<<< FFT: 1.045599s Defocus_U Defocus_V Angle CCC 8658.21 9486.33 10.48 0.037285 Final Values Defocus_U Defocus_V Angle CCC 8658.21 9489.46 10.79 0.080034 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00012hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00012hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.001e-01 CC threshold: 0.735 Mean Std: 46.49 7.77 Num Hot pixels: 171 Hot pixel threshold: 93.10 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.457454 Iteration 2 Error: 0.192896 Iteration 3 Error: 0.034086 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.29 0.09 ...... Frame ( 3) shift: -0.58 0.18 ...... Frame ( 4) shift: -0.87 0.27 ...... Frame ( 5) shift: -1.16 0.36 ...... Frame ( 6) shift: -1.24 0.47 ...... Frame ( 7) shift: -1.10 0.62 ...... Frame ( 8) shift: -0.96 0.76 ...... Frame ( 9) shift: -0.84 0.91 ...... Frame ( 10) shift: -0.72 1.07 ...... Frame ( 11) shift: -0.61 1.22 ...... Frame ( 12) shift: -0.56 1.34 ...... Frame ( 13) shift: -0.57 1.43 ...... Frame ( 14) shift: -0.58 1.52 ...... Frame ( 15) shift: -0.54 1.60 ...... Frame ( 16) shift: -0.46 1.68 ...... Frame ( 17) shift: -0.38 1.75 ...... Frame ( 18) shift: -0.30 1.82 ...... Frame ( 19) shift: -0.23 1.89 ...... Frame ( 20) shift: -0.16 1.95 ...... Frame ( 21) shift: -0.12 2.01 ...... Frame ( 22) shift: -0.12 2.05 ...... Frame ( 23) shift: -0.13 2.09 ...... Frame ( 24) shift: -0.15 2.13 ...... Frame ( 25) shift: -0.19 2.17 ...... Frame ( 26) shift: -0.24 2.22 ...... Frame ( 27) shift: -0.27 2.23 ...... Frame ( 28) shift: -0.29 2.19 ...... Frame ( 29) shift: -0.32 2.16 ...... Frame ( 30) shift: -0.33 2.16 ...... Frame ( 31) shift: -0.34 2.20 ...... Frame ( 32) shift: -0.35 2.24 ...... Frame ( 33) shift: -0.35 2.27 ...... Frame ( 34) shift: -0.34 2.30 ...... Frame ( 35) shift: -0.34 2.32 ...... Frame ( 36) shift: -0.33 2.34 ...... Frame ( 37) shift: -0.32 2.34 ...... Frame ( 38) shift: -0.32 2.35 ...... Frame ( 39) shift: -0.31 2.36 ...... Frame ( 40) shift: -0.30 2.36 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.946309 Iteration 2 Error: 0.216804 Iteration 3 Error: 0.052566 Iteration 4 Error: 0.021501 Align patch 2 23 left Iteration 1 Error: 0.915699 Iteration 2 Error: 0.156087 Iteration 3 Error: 0.067350 Iteration 4 Error: 0.021095 Align patch 3 22 left Iteration 1 Error: 0.706501 Iteration 2 Error: 0.117330 Iteration 3 Error: 0.023008 Align patch 4 21 left Iteration 1 Error: 0.516856 Iteration 2 Error: 0.068939 Iteration 3 Error: 0.013024 Align patch 5 20 left Iteration 1 Error: 0.862870 Iteration 2 Error: 0.122630 Iteration 3 Error: 0.019412 Align patch 6 19 left Iteration 1 Error: 1.760564 Iteration 2 Error: 0.312954 Iteration 3 Error: 0.063755 Iteration 4 Error: 0.018701 Align patch 7 18 left Iteration 1 Error: 1.359862 Iteration 2 Error: 0.233141 Iteration 3 Error: 0.080191 Iteration 4 Error: 0.024604 Align patch 8 17 left Iteration 1 Error: 1.092059 Iteration 2 Error: 0.222436 Iteration 3 Error: 0.050257 Iteration 4 Error: 0.025100 Align patch 9 16 left Iteration 1 Error: 0.557336 Iteration 2 Error: 0.093168 Iteration 3 Error: 0.025477 Align patch 10 15 left Iteration 1 Error: 0.496173 Iteration 2 Error: 0.081088 Iteration 3 Error: 0.014193 Align patch 11 14 left Iteration 1 Error: 1.770269 Iteration 2 Error: 0.435082 Iteration 3 Error: 0.073228 Iteration 4 Error: 0.018305 Align patch 12 13 left Iteration 1 Error: 1.418977 Iteration 2 Error: 0.206666 Iteration 3 Error: 0.052720 Iteration 4 Error: 0.034762 Align patch 13 12 left Iteration 1 Error: 1.856479 Iteration 2 Error: 0.212708 Iteration 3 Error: 0.048039 Align patch 14 11 left Iteration 1 Error: 0.713990 Iteration 2 Error: 0.142925 Iteration 3 Error: 0.035040 Align patch 15 10 left Iteration 1 Error: 0.479905 Iteration 2 Error: 0.058776 Iteration 3 Error: 0.011852 Align patch 16 9 left Iteration 1 Error: 0.924903 Iteration 2 Error: 0.170239 Iteration 3 Error: 0.060027 Iteration 4 Error: 0.022936 Align patch 17 8 left Iteration 1 Error: 1.127379 Iteration 2 Error: 0.179815 Iteration 3 Error: 0.057161 Iteration 4 Error: 0.013465 Align patch 18 7 left Iteration 1 Error: 0.884886 Iteration 2 Error: 0.189790 Iteration 3 Error: 0.045835 Align patch 19 6 left Iteration 1 Error: 0.717979 Iteration 2 Error: 0.094298 Iteration 3 Error: 0.036933 Align patch 20 5 left Iteration 1 Error: 0.483320 Iteration 2 Error: 0.083666 Iteration 3 Error: 0.017603 Align patch 21 4 left Iteration 1 Error: 1.583076 Iteration 2 Error: 0.271957 Iteration 3 Error: 0.080493 Iteration 4 Error: 0.029136 Align patch 22 3 left Iteration 1 Error: 0.801318 Iteration 2 Error: 0.143192 Iteration 3 Error: 0.031637 Align patch 23 2 left Iteration 1 Error: 1.339175 Iteration 2 Error: 0.147005 Iteration 3 Error: 0.045537 Align patch 24 1 left Iteration 1 Error: 0.830507 Iteration 2 Error: 0.220297 Iteration 3 Error: 0.036947 Align patch 25 0 left Iteration 1 Error: 0.687681 Iteration 2 Error: 0.074913 Iteration 3 Error: 0.013490 3D Fitting completed. Patch alignment time: 11.72(sec) Local motion has been corrected. Process thread exits. Computational time: 22.714258 sec Total time: 29.656338 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00012hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00012hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.898244s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00012hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.686247s ........................................ >>>>>>TIME<<<<<< FFT: 1.001719s Defocus_U Defocus_V Angle CCC 11859.37 12429.70 0.00 0.050939 Final Values Defocus_U Defocus_V Angle CCC 11870.30 12434.39 0.00 0.093713 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00012hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00012hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.997e-02 CC threshold: 0.734 Mean Std: 47.46 7.67 Num Hot pixels: 180 Hot pixel threshold: 93.46 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.088293 Iteration 2 Error: 0.135943 Iteration 3 Error: 0.035229 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.26 0.05 ...... Frame ( 3) shift: -0.53 0.10 ...... Frame ( 4) shift: -0.79 0.16 ...... Frame ( 5) shift: -1.05 0.21 ...... Frame ( 6) shift: -1.12 0.30 ...... Frame ( 7) shift: -1.00 0.45 ...... Frame ( 8) shift: -0.88 0.59 ...... Frame ( 9) shift: -0.79 0.69 ...... Frame ( 10) shift: -0.73 0.75 ...... Frame ( 11) shift: -0.67 0.81 ...... Frame ( 12) shift: -0.65 0.89 ...... Frame ( 13) shift: -0.67 0.99 ...... Frame ( 14) shift: -0.68 1.08 ...... Frame ( 15) shift: -0.66 1.14 ...... Frame ( 16) shift: -0.60 1.17 ...... Frame ( 17) shift: -0.54 1.20 ...... Frame ( 18) shift: -0.51 1.25 ...... Frame ( 19) shift: -0.49 1.32 ...... Frame ( 20) shift: -0.48 1.39 ...... Frame ( 21) shift: -0.49 1.46 ...... Frame ( 22) shift: -0.53 1.52 ...... Frame ( 23) shift: -0.56 1.58 ...... Frame ( 24) shift: -0.57 1.64 ...... Frame ( 25) shift: -0.55 1.72 ...... Frame ( 26) shift: -0.54 1.80 ...... Frame ( 27) shift: -0.53 1.86 ...... Frame ( 28) shift: -0.52 1.89 ...... Frame ( 29) shift: -0.52 1.92 ...... Frame ( 30) shift: -0.50 1.92 ...... Frame ( 31) shift: -0.47 1.88 ...... Frame ( 32) shift: -0.44 1.84 ...... Frame ( 33) shift: -0.40 1.81 ...... Frame ( 34) shift: -0.36 1.80 ...... Frame ( 35) shift: -0.31 1.79 ...... Frame ( 36) shift: -0.29 1.77 ...... Frame ( 37) shift: -0.28 1.74 ...... Frame ( 38) shift: -0.27 1.71 ...... Frame ( 39) shift: -0.26 1.67 ...... Frame ( 40) shift: -0.24 1.64 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.825766 Iteration 2 Error: 0.108741 Iteration 3 Error: 0.032253 Align patch 2 23 left Iteration 1 Error: 0.574839 Iteration 2 Error: 0.141900 Iteration 3 Error: 0.055535 Iteration 4 Error: 0.039808 Align patch 3 22 left Iteration 1 Error: 1.258535 Iteration 2 Error: 0.566164 Iteration 3 Error: 0.236393 Iteration 4 Error: 0.179613 Iteration 5 Error: 0.068588 Align patch 3 22 left Iteration 1 Error: 1.957479 Iteration 2 Error: 0.265148 Iteration 3 Error: 0.059179 Iteration 4 Error: 0.024347 Align patch 4 21 left Iteration 1 Error: 1.014563 Iteration 2 Error: 0.273257 Iteration 3 Error: 0.068053 Iteration 4 Error: 0.038858 Align patch 5 20 left Iteration 1 Error: 0.835210 Iteration 2 Error: 0.109521 Iteration 3 Error: 0.036286 Align patch 6 19 left Iteration 1 Error: 1.103440 Iteration 2 Error: 0.172151 Iteration 3 Error: 0.048585 Align patch 7 18 left Iteration 1 Error: 1.054723 Iteration 2 Error: 0.211334 Iteration 3 Error: 0.046854 Align patch 8 17 left Iteration 1 Error: 0.900370 Iteration 2 Error: 0.161837 Iteration 3 Error: 0.026978 Align patch 9 16 left Iteration 1 Error: 0.745769 Iteration 2 Error: 0.213563 Iteration 3 Error: 0.044710 Align patch 10 15 left Iteration 1 Error: 0.644267 Iteration 2 Error: 0.148673 Iteration 3 Error: 0.035133 Align patch 11 14 left Iteration 1 Error: 0.990902 Iteration 2 Error: 0.195456 Iteration 3 Error: 0.074539 Iteration 4 Error: 0.039331 Align patch 12 13 left Iteration 1 Error: 0.974931 Iteration 2 Error: 0.162754 Iteration 3 Error: 0.052024 Iteration 4 Error: 0.017591 Align patch 13 12 left Iteration 1 Error: 1.180519 Iteration 2 Error: 0.220544 Iteration 3 Error: 0.059277 Iteration 4 Error: 0.016606 Align patch 14 11 left Iteration 1 Error: 1.222686 Iteration 2 Error: 0.175544 Iteration 3 Error: 0.035065 Align patch 15 10 left Iteration 1 Error: 0.691870 Iteration 2 Error: 0.110433 Iteration 3 Error: 0.022008 Align patch 16 9 left Iteration 1 Error: 0.793585 Iteration 2 Error: 0.173341 Iteration 3 Error: 0.058826 Iteration 4 Error: 0.016934 Align patch 17 8 left Iteration 1 Error: 0.969497 Iteration 2 Error: 0.138624 Iteration 3 Error: 0.028084 Align patch 18 7 left Iteration 1 Error: 1.036143 Iteration 2 Error: 0.132357 Iteration 3 Error: 0.026273 Align patch 19 6 left Iteration 1 Error: 1.205157 Iteration 2 Error: 0.158964 Iteration 3 Error: 0.040489 Align patch 20 5 left Iteration 1 Error: 1.036960 Iteration 2 Error: 0.133774 Iteration 3 Error: 0.013611 Align patch 21 4 left Iteration 1 Error: 1.456661 Iteration 2 Error: 0.306949 Iteration 3 Error: 0.090936 Iteration 4 Error: 0.033983 Align patch 22 3 left Iteration 1 Error: 1.067253 Iteration 2 Error: 0.200709 Iteration 3 Error: 0.040764 Align patch 23 2 left Iteration 1 Error: 0.665453 Iteration 2 Error: 0.115046 Iteration 3 Error: 0.033586 Align patch 24 1 left Iteration 1 Error: 0.786913 Iteration 2 Error: 0.191525 Iteration 3 Error: 0.044973 Align patch 25 0 left Iteration 1 Error: 1.004238 Iteration 2 Error: 0.222144 Iteration 3 Error: 0.045123 3D Fitting completed. Patch alignment time: 12.34(sec) Local motion has been corrected. Process thread exits. Computational time: 24.076561 sec Total time: 31.930927 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00012hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00012hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.830664s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00012hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.216496s ........................................ >>>>>>TIME<<<<<< FFT: 1.290950s Defocus_U Defocus_V Angle CCC 11021.48 11904.30 6.92 0.045348 Final Values Defocus_U Defocus_V Angle CCC 11041.82 11924.63 6.29 0.084174 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00012hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00012hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.998e-02 CC threshold: 0.734 Mean Std: 47.74 7.66 Num Hot pixels: 199 Hot pixel threshold: 93.70 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.177501 Iteration 2 Error: 0.120036 Iteration 3 Error: 0.027681 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.28 0.15 ...... Frame ( 3) shift: -0.55 0.31 ...... Frame ( 4) shift: -0.83 0.46 ...... Frame ( 5) shift: -1.11 0.61 ...... Frame ( 6) shift: -1.23 0.72 ...... Frame ( 7) shift: -1.19 0.78 ...... Frame ( 8) shift: -1.16 0.84 ...... Frame ( 9) shift: -1.11 0.91 ...... Frame ( 10) shift: -1.06 1.00 ...... Frame ( 11) shift: -1.02 1.10 ...... Frame ( 12) shift: -0.95 1.17 ...... Frame ( 13) shift: -0.86 1.22 ...... Frame ( 14) shift: -0.78 1.27 ...... Frame ( 15) shift: -0.74 1.35 ...... Frame ( 16) shift: -0.75 1.47 ...... Frame ( 17) shift: -0.77 1.59 ...... Frame ( 18) shift: -0.77 1.67 ...... Frame ( 19) shift: -0.77 1.70 ...... Frame ( 20) shift: -0.77 1.73 ...... Frame ( 21) shift: -0.78 1.74 ...... Frame ( 22) shift: -0.80 1.74 ...... Frame ( 23) shift: -0.82 1.74 ...... Frame ( 24) shift: -0.82 1.73 ...... Frame ( 25) shift: -0.81 1.70 ...... Frame ( 26) shift: -0.80 1.67 ...... Frame ( 27) shift: -0.79 1.66 ...... Frame ( 28) shift: -0.78 1.67 ...... Frame ( 29) shift: -0.77 1.68 ...... Frame ( 30) shift: -0.76 1.72 ...... Frame ( 31) shift: -0.74 1.80 ...... Frame ( 32) shift: -0.73 1.89 ...... Frame ( 33) shift: -0.72 1.90 ...... Frame ( 34) shift: -0.71 1.84 ...... Frame ( 35) shift: -0.71 1.78 ...... Frame ( 36) shift: -0.69 1.77 ...... Frame ( 37) shift: -0.67 1.80 ...... Frame ( 38) shift: -0.64 1.84 ...... Frame ( 39) shift: -0.62 1.87 ...... Frame ( 40) shift: -0.59 1.91 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.143379 Iteration 2 Error: 0.150811 Iteration 3 Error: 0.044567 Align patch 2 23 left Iteration 1 Error: 0.694614 Iteration 2 Error: 0.204075 Iteration 3 Error: 0.084194 Iteration 4 Error: 0.027967 Align patch 3 22 left Iteration 1 Error: 0.942883 Iteration 2 Error: 0.271882 Iteration 3 Error: 0.093805 Iteration 4 Error: 0.044532 Align patch 4 21 left Iteration 1 Error: 0.730406 Iteration 2 Error: 0.097641 Iteration 3 Error: 0.032340 Align patch 5 20 left Iteration 1 Error: 0.904915 Iteration 2 Error: 0.102908 Iteration 3 Error: 0.023133 Align patch 6 19 left Iteration 1 Error: 1.213537 Iteration 2 Error: 0.150602 Iteration 3 Error: 0.045075 Align patch 7 18 left Iteration 1 Error: 1.107879 Iteration 2 Error: 0.275621 Iteration 3 Error: 0.079763 Iteration 4 Error: 0.058807 Iteration 5 Error: 0.019159 Align patch 8 17 left Iteration 1 Error: 1.313713 Iteration 2 Error: 0.207159 Iteration 3 Error: 0.043702 Align patch 9 16 left Iteration 1 Error: 0.505683 Iteration 2 Error: 0.081953 Iteration 3 Error: 0.014747 Align patch 10 15 left Iteration 1 Error: 0.872691 Iteration 2 Error: 0.125440 Iteration 3 Error: 0.030847 Align patch 11 14 left Iteration 1 Error: 0.618285 Iteration 2 Error: 0.115823 Iteration 3 Error: 0.021790 Align patch 12 13 left Iteration 1 Error: 0.804517 Iteration 2 Error: 0.251118 Iteration 3 Error: 0.037601 Align patch 13 12 left Iteration 1 Error: 0.789823 Iteration 2 Error: 0.125266 Iteration 3 Error: 0.029013 Align patch 14 11 left Iteration 1 Error: 0.959690 Iteration 2 Error: 0.161459 Iteration 3 Error: 0.037583 Align patch 15 10 left Iteration 1 Error: 0.879499 Iteration 2 Error: 0.154183 Iteration 3 Error: 0.052564 Iteration 4 Error: 0.018905 Align patch 16 9 left Iteration 1 Error: 0.693889 Iteration 2 Error: 0.141735 Iteration 3 Error: 0.037787 Align patch 17 8 left Iteration 1 Error: 0.907840 Iteration 2 Error: 0.266194 Iteration 3 Error: 0.045395 Align patch 18 7 left Iteration 1 Error: 0.687267 Iteration 2 Error: 0.137910 Iteration 3 Error: 0.035867 Align patch 19 6 left Iteration 1 Error: 1.021082 Iteration 2 Error: 0.134524 Iteration 3 Error: 0.033021 Align patch 20 5 left Iteration 1 Error: 0.724267 Iteration 2 Error: 0.106352 Iteration 3 Error: 0.015081 Align patch 21 4 left Iteration 1 Error: 0.873061 Iteration 2 Error: 0.172035 Iteration 3 Error: 0.040259 Align patch 22 3 left Iteration 1 Error: 0.673527 Iteration 2 Error: 0.168141 Iteration 3 Error: 0.049887 Align patch 23 2 left Iteration 1 Error: 0.753212 Iteration 2 Error: 0.261512 Iteration 3 Error: 0.088208 Iteration 4 Error: 0.028083 Align patch 24 1 left Iteration 1 Error: 0.781633 Iteration 2 Error: 0.132759 Iteration 3 Error: 0.029784 Align patch 25 0 left Iteration 1 Error: 1.107940 Iteration 2 Error: 0.082516 Iteration 3 Error: 0.018580 3D Fitting completed. Patch alignment time: 11.27(sec) Local motion has been corrected. Process thread exits. Computational time: 22.839397 sec Total time: 30.399263 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00012hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00012hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.695938s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00012hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.395212s ........................................ >>>>>>TIME<<<<<< FFT: 1.101739s Defocus_U Defocus_V Angle CCC 12130.92 11462.94 86.32 0.048087 Final Values Defocus_U Defocus_V Angle CCC 12143.44 11481.71 85.70 0.087925 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00013hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00013hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 46.48 7.76 Num Hot pixels: 159 Hot pixel threshold: 93.02 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.495881 Iteration 2 Error: 0.125505 Iteration 3 Error: 0.025086 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.31 0.14 ...... Frame ( 3) shift: -0.62 0.28 ...... Frame ( 4) shift: -0.93 0.42 ...... Frame ( 5) shift: -1.24 0.56 ...... Frame ( 6) shift: -1.37 0.72 ...... Frame ( 7) shift: -1.34 0.92 ...... Frame ( 8) shift: -1.31 1.12 ...... Frame ( 9) shift: -1.26 1.26 ...... Frame ( 10) shift: -1.19 1.34 ...... Frame ( 11) shift: -1.12 1.43 ...... Frame ( 12) shift: -1.09 1.51 ...... Frame ( 13) shift: -1.09 1.59 ...... Frame ( 14) shift: -1.09 1.68 ...... Frame ( 15) shift: -1.05 1.76 ...... Frame ( 16) shift: -0.96 1.84 ...... Frame ( 17) shift: -0.88 1.91 ...... Frame ( 18) shift: -0.85 1.96 ...... Frame ( 19) shift: -0.88 1.96 ...... Frame ( 20) shift: -0.90 1.97 ...... Frame ( 21) shift: -0.89 1.99 ...... Frame ( 22) shift: -0.82 2.01 ...... Frame ( 23) shift: -0.76 2.04 ...... Frame ( 24) shift: -0.69 2.06 ...... Frame ( 25) shift: -0.61 2.09 ...... Frame ( 26) shift: -0.52 2.11 ...... Frame ( 27) shift: -0.50 2.12 ...... Frame ( 28) shift: -0.53 2.10 ...... Frame ( 29) shift: -0.57 2.09 ...... Frame ( 30) shift: -0.58 2.10 ...... Frame ( 31) shift: -0.56 2.12 ...... Frame ( 32) shift: -0.54 2.14 ...... Frame ( 33) shift: -0.49 2.10 ...... Frame ( 34) shift: -0.42 2.02 ...... Frame ( 35) shift: -0.34 1.93 ...... Frame ( 36) shift: -0.31 1.93 ...... Frame ( 37) shift: -0.30 2.00 ...... Frame ( 38) shift: -0.30 2.08 ...... Frame ( 39) shift: -0.30 2.16 ...... Frame ( 40) shift: -0.29 2.23 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.704913 Iteration 2 Error: 0.142455 Iteration 3 Error: 0.068213 Iteration 4 Error: 0.030688 Align patch 2 23 left Iteration 1 Error: 2.104410 Iteration 2 Error: 0.256537 Iteration 3 Error: 0.046941 Align patch 3 22 left Iteration 1 Error: 2.074283 Iteration 2 Error: 0.265574 Iteration 3 Error: 0.073801 Iteration 4 Error: 0.026566 Align patch 4 21 left Iteration 1 Error: 0.734285 Iteration 2 Error: 0.125055 Iteration 3 Error: 0.036530 Align patch 5 20 left Iteration 1 Error: 0.809170 Iteration 2 Error: 0.130802 Iteration 3 Error: 0.020861 Align patch 6 19 left Iteration 1 Error: 1.279377 Iteration 2 Error: 0.326262 Iteration 3 Error: 0.078421 Iteration 4 Error: 0.025542 Align patch 7 18 left Iteration 1 Error: 1.958667 Iteration 2 Error: 0.331133 Iteration 3 Error: 0.140420 Iteration 4 Error: 0.036329 Align patch 8 17 left Iteration 1 Error: 0.667980 Iteration 2 Error: 0.156324 Iteration 3 Error: 0.036442 Align patch 9 16 left Iteration 1 Error: 0.813971 Iteration 2 Error: 0.166253 Iteration 3 Error: 0.037586 Align patch 10 15 left Iteration 1 Error: 0.663256 Iteration 2 Error: 0.125346 Iteration 3 Error: 0.022077 Align patch 11 14 left Iteration 1 Error: 1.057954 Iteration 2 Error: 0.239799 Iteration 3 Error: 0.067836 Iteration 4 Error: 0.028333 Align patch 12 13 left Iteration 1 Error: 0.797390 Iteration 2 Error: 0.177416 Iteration 3 Error: 0.055314 Iteration 4 Error: 0.023339 Align patch 13 12 left Iteration 1 Error: 0.911367 Iteration 2 Error: 0.241631 Iteration 3 Error: 0.053298 Iteration 4 Error: 0.023416 Align patch 14 11 left Iteration 1 Error: 0.825070 Iteration 2 Error: 0.116824 Iteration 3 Error: 0.026761 Align patch 15 10 left Iteration 1 Error: 0.813934 Iteration 2 Error: 0.151123 Iteration 3 Error: 0.027939 Align patch 16 9 left Iteration 1 Error: 1.322793 Iteration 2 Error: 0.202020 Iteration 3 Error: 0.066329 Iteration 4 Error: 0.024938 Align patch 17 8 left Iteration 1 Error: 0.930082 Iteration 2 Error: 0.229695 Iteration 3 Error: 0.055812 Iteration 4 Error: 0.023449 Align patch 18 7 left Iteration 1 Error: 0.737536 Iteration 2 Error: 0.091513 Iteration 3 Error: 0.037725 Align patch 19 6 left Iteration 1 Error: 0.723509 Iteration 2 Error: 0.116548 Iteration 3 Error: 0.017718 Align patch 20 5 left Iteration 1 Error: 0.539062 Iteration 2 Error: 0.105881 Iteration 3 Error: 0.029573 Align patch 21 4 left Iteration 1 Error: 1.140003 Iteration 2 Error: 0.219692 Iteration 3 Error: 0.043189 Align patch 22 3 left Iteration 1 Error: 0.842919 Iteration 2 Error: 0.146184 Iteration 3 Error: 0.050573 Iteration 4 Error: 0.014509 Align patch 23 2 left Iteration 1 Error: 0.797283 Iteration 2 Error: 0.106146 Iteration 3 Error: 0.023682 Align patch 24 1 left Iteration 1 Error: 1.210060 Iteration 2 Error: 0.133870 Iteration 3 Error: 0.026546 Align patch 25 0 left Iteration 1 Error: 0.957666 Iteration 2 Error: 0.121545 Iteration 3 Error: 0.050961 Iteration 4 Error: 0.013669 3D Fitting completed. Patch alignment time: 12.33(sec) Local motion has been corrected. Process thread exits. Computational time: 21.434069 sec Total time: 30.317984 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00013hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00013hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.718264s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00013hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.714575s ........................................ >>>>>>TIME<<<<<< FFT: 0.920296s Defocus_U Defocus_V Angle CCC 12703.13 13527.35 11.36 0.048727 Final Values Defocus_U Defocus_V Angle CCC 12703.12 13543.02 11.99 0.087604 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00013hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00013hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.999e-02 CC threshold: 0.734 Mean Std: 46.63 7.76 Num Hot pixels: 188 Hot pixel threshold: 93.17 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.081212 Iteration 2 Error: 0.176620 Iteration 3 Error: 0.041864 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.25 0.12 ...... Frame ( 3) shift: -0.51 0.24 ...... Frame ( 4) shift: -0.76 0.36 ...... Frame ( 5) shift: -1.01 0.47 ...... Frame ( 6) shift: -1.15 0.57 ...... Frame ( 7) shift: -1.17 0.64 ...... Frame ( 8) shift: -1.19 0.72 ...... Frame ( 9) shift: -1.20 0.79 ...... Frame ( 10) shift: -1.19 0.86 ...... Frame ( 11) shift: -1.18 0.93 ...... Frame ( 12) shift: -1.15 0.94 ...... Frame ( 13) shift: -1.11 0.90 ...... Frame ( 14) shift: -1.06 0.86 ...... Frame ( 15) shift: -1.01 0.88 ...... Frame ( 16) shift: -0.94 0.95 ...... Frame ( 17) shift: -0.88 1.03 ...... Frame ( 18) shift: -0.84 1.15 ...... Frame ( 19) shift: -0.83 1.30 ...... Frame ( 20) shift: -0.82 1.45 ...... Frame ( 21) shift: -0.78 1.53 ...... Frame ( 22) shift: -0.72 1.56 ...... Frame ( 23) shift: -0.65 1.59 ...... Frame ( 24) shift: -0.60 1.62 ...... Frame ( 25) shift: -0.56 1.66 ...... Frame ( 26) shift: -0.51 1.70 ...... Frame ( 27) shift: -0.48 1.73 ...... Frame ( 28) shift: -0.47 1.77 ...... Frame ( 29) shift: -0.45 1.80 ...... Frame ( 30) shift: -0.44 1.84 ...... Frame ( 31) shift: -0.44 1.91 ...... Frame ( 32) shift: -0.44 1.97 ...... Frame ( 33) shift: -0.41 2.00 ...... Frame ( 34) shift: -0.35 2.01 ...... Frame ( 35) shift: -0.28 2.01 ...... Frame ( 36) shift: -0.23 2.02 ...... Frame ( 37) shift: -0.21 2.02 ...... Frame ( 38) shift: -0.18 2.02 ...... Frame ( 39) shift: -0.16 2.03 ...... Frame ( 40) shift: -0.13 2.03 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.053979 Iteration 2 Error: 0.206016 Iteration 3 Error: 0.119961 Iteration 4 Error: 0.072312 Iteration 5 Error: 0.029447 Align patch 2 23 left Iteration 1 Error: 1.109831 Iteration 2 Error: 0.184889 Iteration 3 Error: 0.047347 Align patch 3 22 left Iteration 1 Error: 0.886979 Iteration 2 Error: 0.117333 Iteration 3 Error: 0.054270 Iteration 4 Error: 0.014175 Align patch 4 21 left Iteration 1 Error: 0.699126 Iteration 2 Error: 0.129646 Iteration 3 Error: 0.026582 Align patch 5 20 left Iteration 1 Error: 0.662597 Iteration 2 Error: 0.109788 Iteration 3 Error: 0.019398 Align patch 6 19 left Iteration 1 Error: 1.181878 Iteration 2 Error: 0.343672 Iteration 3 Error: 0.185073 Iteration 4 Error: 0.119765 Iteration 5 Error: 0.075702 Align patch 6 19 left Iteration 1 Error: 2.823031 Iteration 2 Error: 0.377583 Iteration 3 Error: 0.130283 Iteration 4 Error: 0.044724 Align patch 7 18 left Iteration 1 Error: 2.172932 Iteration 2 Error: 0.301656 Iteration 3 Error: 0.227733 Iteration 4 Error: 0.079433 Iteration 5 Error: 0.069257 Align patch 7 18 left Iteration 1 Error: 2.582290 Iteration 2 Error: 0.216002 Iteration 3 Error: 0.043167 Align patch 8 17 left Iteration 1 Error: 0.662707 Iteration 2 Error: 0.128942 Iteration 3 Error: 0.065845 Iteration 4 Error: 0.022263 Align patch 9 16 left Iteration 1 Error: 0.822682 Iteration 2 Error: 0.074963 Iteration 3 Error: 0.029548 Align patch 10 15 left Iteration 1 Error: 0.548695 Iteration 2 Error: 0.074376 Iteration 3 Error: 0.020483 Align patch 11 14 left Iteration 1 Error: 0.768176 Iteration 2 Error: 0.123459 Iteration 3 Error: 0.026649 Align patch 12 13 left Iteration 1 Error: 1.031978 Iteration 2 Error: 0.162971 Iteration 3 Error: 0.034175 Align patch 13 12 left Iteration 1 Error: 0.599612 Iteration 2 Error: 0.211259 Iteration 3 Error: 0.093219 Iteration 4 Error: 0.026542 Align patch 14 11 left Iteration 1 Error: 1.517385 Iteration 2 Error: 0.262419 Iteration 3 Error: 0.045205 Align patch 15 10 left Iteration 1 Error: 0.662828 Iteration 2 Error: 0.144319 Iteration 3 Error: 0.029328 Align patch 16 9 left Iteration 1 Error: 0.973636 Iteration 2 Error: 0.192199 Iteration 3 Error: 0.072894 Iteration 4 Error: 0.035793 Align patch 17 8 left Iteration 1 Error: 1.099771 Iteration 2 Error: 0.281149 Iteration 3 Error: 0.064905 Iteration 4 Error: 0.039843 Align patch 18 7 left Iteration 1 Error: 0.803514 Iteration 2 Error: 0.196691 Iteration 3 Error: 0.064879 Iteration 4 Error: 0.024566 Align patch 19 6 left Iteration 1 Error: 0.561789 Iteration 2 Error: 0.072526 Iteration 3 Error: 0.016059 Align patch 20 5 left Iteration 1 Error: 0.552795 Iteration 2 Error: 0.048406 Align patch 21 4 left Iteration 1 Error: 1.465370 Iteration 2 Error: 0.194610 Iteration 3 Error: 0.060825 Iteration 4 Error: 0.021057 Align patch 22 3 left Iteration 1 Error: 1.209351 Iteration 2 Error: 0.193834 Iteration 3 Error: 0.032757 Align patch 23 2 left Iteration 1 Error: 1.015051 Iteration 2 Error: 0.175736 Iteration 3 Error: 0.049414 Align patch 24 1 left Iteration 1 Error: 1.038249 Iteration 2 Error: 0.100130 Iteration 3 Error: 0.019354 Align patch 25 0 left Iteration 1 Error: 0.972774 Iteration 2 Error: 0.070836 Iteration 3 Error: 0.015212 3D Fitting completed. Patch alignment time: 13.22(sec) Local motion has been corrected. Process thread exits. Computational time: 25.369883 sec Total time: 35.930332 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00013hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00013hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.612963s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00013hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.728433s ........................................ >>>>>>TIME<<<<<< FFT: 0.910098s Defocus_U Defocus_V Angle CCC 13164.05 13617.20 0.21 0.054535 Final Values Defocus_U Defocus_V Angle CCC 13146.87 13643.79 1.47 0.094302 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00013hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00013hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 1.000e-01 CC threshold: 0.734 Mean Std: 47.44 7.74 Num Hot pixels: 192 Hot pixel threshold: 93.87 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.885445 Iteration 2 Error: 0.072794 Iteration 3 Error: 0.016830 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.34 0.00 ...... Frame ( 3) shift: -0.67 0.00 ...... Frame ( 4) shift: -1.01 0.00 ...... Frame ( 5) shift: -1.35 0.01 ...... Frame ( 6) shift: -1.47 0.04 ...... Frame ( 7) shift: -1.38 0.11 ...... Frame ( 8) shift: -1.29 0.17 ...... Frame ( 9) shift: -1.25 0.26 ...... Frame ( 10) shift: -1.26 0.37 ...... Frame ( 11) shift: -1.27 0.49 ...... Frame ( 12) shift: -1.28 0.57 ...... Frame ( 13) shift: -1.29 0.63 ...... Frame ( 14) shift: -1.29 0.69 ...... Frame ( 15) shift: -1.28 0.72 ...... Frame ( 16) shift: -1.26 0.71 ...... Frame ( 17) shift: -1.24 0.71 ...... Frame ( 18) shift: -1.21 0.75 ...... Frame ( 19) shift: -1.19 0.83 ...... Frame ( 20) shift: -1.16 0.92 ...... Frame ( 21) shift: -1.13 0.98 ...... Frame ( 22) shift: -1.09 1.00 ...... Frame ( 23) shift: -1.04 1.02 ...... Frame ( 24) shift: -1.02 1.01 ...... Frame ( 25) shift: -1.01 0.98 ...... Frame ( 26) shift: -1.00 0.96 ...... Frame ( 27) shift: -1.02 0.93 ...... Frame ( 28) shift: -1.07 0.91 ...... Frame ( 29) shift: -1.12 0.89 ...... Frame ( 30) shift: -1.16 0.89 ...... Frame ( 31) shift: -1.19 0.90 ...... Frame ( 32) shift: -1.22 0.91 ...... Frame ( 33) shift: -1.21 0.89 ...... Frame ( 34) shift: -1.16 0.84 ...... Frame ( 35) shift: -1.11 0.78 ...... Frame ( 36) shift: -1.07 0.75 ...... Frame ( 37) shift: -1.03 0.72 ...... Frame ( 38) shift: -0.99 0.70 ...... Frame ( 39) shift: -0.95 0.67 ...... Frame ( 40) shift: -0.91 0.65 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.831448 Iteration 2 Error: 0.119665 Iteration 3 Error: 0.026690 Align patch 2 23 left Iteration 1 Error: 0.915965 Iteration 2 Error: 0.272981 Iteration 3 Error: 0.057185 Iteration 4 Error: 0.017740 Align patch 3 22 left Iteration 1 Error: 0.560924 Iteration 2 Error: 0.091918 Iteration 3 Error: 0.026555 Align patch 4 21 left Iteration 1 Error: 0.759322 Iteration 2 Error: 0.149163 Iteration 3 Error: 0.031992 Align patch 5 20 left Iteration 1 Error: 0.759633 Iteration 2 Error: 0.112190 Iteration 3 Error: 0.023574 Align patch 6 19 left Iteration 1 Error: 3.784703 Iteration 2 Error: 0.815851 Iteration 3 Error: 0.493479 Iteration 4 Error: 0.344356 Iteration 5 Error: 0.206023 Align patch 6 19 left Iteration 1 Error: 1.913283 Iteration 2 Error: 0.136318 Iteration 3 Error: 0.050443 Iteration 4 Error: 0.032682 Align patch 7 18 left Iteration 1 Error: 2.077647 Iteration 2 Error: 0.313465 Iteration 3 Error: 0.090483 Iteration 4 Error: 0.034053 Align patch 8 17 left Iteration 1 Error: 0.617588 Iteration 2 Error: 0.126573 Iteration 3 Error: 0.033341 Align patch 9 16 left Iteration 1 Error: 0.738283 Iteration 2 Error: 0.124568 Iteration 3 Error: 0.024045 Align patch 10 15 left Iteration 1 Error: 0.730092 Iteration 2 Error: 0.085703 Iteration 3 Error: 0.015182 Align patch 11 14 left Iteration 1 Error: 1.456951 Iteration 2 Error: 0.293821 Iteration 3 Error: 0.080402 Iteration 4 Error: 0.027705 Align patch 12 13 left Iteration 1 Error: 1.853187 Iteration 2 Error: 0.199947 Iteration 3 Error: 0.035332 Align patch 13 12 left Iteration 1 Error: 1.250567 Iteration 2 Error: 0.157440 Iteration 3 Error: 0.042547 Align patch 14 11 left Iteration 1 Error: 0.629034 Iteration 2 Error: 0.113589 Iteration 3 Error: 0.028003 Align patch 15 10 left Iteration 1 Error: 0.391254 Iteration 2 Error: 0.058505 Iteration 3 Error: 0.016096 Align patch 16 9 left Iteration 1 Error: 1.114882 Iteration 2 Error: 0.230007 Iteration 3 Error: 0.077017 Iteration 4 Error: 0.018822 Align patch 17 8 left Iteration 1 Error: 0.663002 Iteration 2 Error: 0.166437 Iteration 3 Error: 0.051300 Iteration 4 Error: 0.017576 Align patch 18 7 left Iteration 1 Error: 0.729078 Iteration 2 Error: 0.088844 Iteration 3 Error: 0.031202 Align patch 19 6 left Iteration 1 Error: 0.545818 Iteration 2 Error: 0.122904 Iteration 3 Error: 0.027432 Align patch 20 5 left Iteration 1 Error: 0.581086 Iteration 2 Error: 0.098671 Iteration 3 Error: 0.013869 Align patch 21 4 left Iteration 1 Error: 1.520346 Iteration 2 Error: 0.377685 Iteration 3 Error: 0.078809 Iteration 4 Error: 0.035839 Align patch 22 3 left Iteration 1 Error: 0.948846 Iteration 2 Error: 0.224851 Iteration 3 Error: 0.048724 Align patch 23 2 left Iteration 1 Error: 0.880009 Iteration 2 Error: 0.136605 Iteration 3 Error: 0.030393 Align patch 24 1 left Iteration 1 Error: 0.783715 Iteration 2 Error: 0.113886 Iteration 3 Error: 0.030162 Align patch 25 0 left Iteration 1 Error: 0.776766 Iteration 2 Error: 0.059409 Iteration 3 Error: 0.009464 3D Fitting completed. Patch alignment time: 12.54(sec) Local motion has been corrected. Process thread exits. Computational time: 24.843756 sec Total time: 32.276955 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00013hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00013hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.720941s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00013hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.556342s ........................................ >>>>>>TIME<<<<<< FFT: 1.051691s Defocus_U Defocus_V Angle CCC 11371.12 12312.60 6.95 0.048514 Final Values Defocus_U Defocus_V Angle CCC 11369.55 12323.54 6.64 0.087092 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00013hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00013hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.989e-02 CC threshold: 0.734 Mean Std: 47.40 7.75 Num Hot pixels: 185 Hot pixel threshold: 93.93 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.084929 Iteration 2 Error: 0.549775 Iteration 3 Error: 0.237604 Iteration 4 Error: 0.077393 Iteration 5 Error: 0.041978 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.15 0.19 ...... Frame ( 3) shift: -0.30 0.37 ...... Frame ( 4) shift: -0.45 0.56 ...... Frame ( 5) shift: -0.60 0.74 ...... Frame ( 6) shift: -0.65 0.95 ...... Frame ( 7) shift: -0.59 1.17 ...... Frame ( 8) shift: -0.54 1.39 ...... Frame ( 9) shift: -0.45 1.63 ...... Frame ( 10) shift: -0.32 1.89 ...... Frame ( 11) shift: -0.19 2.15 ...... Frame ( 12) shift: -0.15 2.35 ...... Frame ( 13) shift: -0.21 2.48 ...... Frame ( 14) shift: -0.26 2.62 ...... Frame ( 15) shift: -0.29 2.75 ...... Frame ( 16) shift: -0.30 2.89 ...... Frame ( 17) shift: -0.30 3.02 ...... Frame ( 18) shift: -0.33 3.15 ...... Frame ( 19) shift: -0.38 3.28 ...... Frame ( 20) shift: -0.42 3.42 ...... Frame ( 21) shift: -0.44 3.54 ...... Frame ( 22) shift: -0.44 3.64 ...... Frame ( 23) shift: -0.44 3.74 ...... Frame ( 24) shift: -0.46 3.86 ...... Frame ( 25) shift: -0.49 3.98 ...... Frame ( 26) shift: -0.53 4.10 ...... Frame ( 27) shift: -0.58 4.22 ...... Frame ( 28) shift: -0.63 4.32 ...... Frame ( 29) shift: -0.68 4.43 ...... Frame ( 30) shift: -0.72 4.49 ...... Frame ( 31) shift: -0.75 4.52 ...... Frame ( 32) shift: -0.78 4.55 ...... Frame ( 33) shift: -0.74 4.60 ...... Frame ( 34) shift: -0.65 4.66 ...... Frame ( 35) shift: -0.56 4.73 ...... Frame ( 36) shift: -0.55 4.74 ...... Frame ( 37) shift: -0.64 4.70 ...... Frame ( 38) shift: -0.72 4.66 ...... Frame ( 39) shift: -0.81 4.61 ...... Frame ( 40) shift: -0.89 4.57 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.342615 Iteration 2 Error: 0.338983 Iteration 3 Error: 0.061160 Iteration 4 Error: 0.013707 Align patch 2 23 left Iteration 1 Error: 2.841499 Iteration 2 Error: 0.347151 Iteration 3 Error: 0.163019 Iteration 4 Error: 0.049825 Align patch 3 22 left Iteration 1 Error: 1.784321 Iteration 2 Error: 0.507316 Iteration 3 Error: 0.268438 Iteration 4 Error: 0.075927 Iteration 5 Error: 0.033345 Align patch 4 21 left Iteration 1 Error: 2.135712 Iteration 2 Error: 0.339009 Iteration 3 Error: 0.074788 Iteration 4 Error: 0.031455 Align patch 5 20 left Iteration 1 Error: 4.392569 Iteration 2 Error: 0.837952 Iteration 3 Error: 0.238027 Iteration 4 Error: 0.073421 Iteration 5 Error: 0.022355 Align patch 6 19 left Iteration 1 Error: 1.593104 Iteration 2 Error: 0.669740 Iteration 3 Error: 0.121282 Iteration 4 Error: 0.072068 Iteration 5 Error: 0.013819 Align patch 7 18 left Iteration 1 Error: 1.617511 Iteration 2 Error: 0.263387 Iteration 3 Error: 0.071009 Iteration 4 Error: 0.018757 Align patch 8 17 left Iteration 1 Error: 1.444149 Iteration 2 Error: 0.362156 Iteration 3 Error: 0.100526 Iteration 4 Error: 0.029839 Align patch 9 16 left Iteration 1 Error: 2.614907 Iteration 2 Error: 1.526802 Iteration 3 Error: 0.508082 Iteration 4 Error: 0.387094 Iteration 5 Error: 0.197404 Align patch 9 16 left Iteration 1 Error: 2.446244 Iteration 2 Error: 0.825051 Iteration 3 Error: 0.307417 Iteration 4 Error: 0.115149 Iteration 5 Error: 0.047627 Align patch 10 15 left Iteration 1 Error: 2.516451 Iteration 2 Error: 1.798184 Iteration 3 Error: 0.973963 Iteration 4 Error: 0.614407 Iteration 5 Error: 0.500723 Align patch 10 15 left Iteration 1 Error: 2.954910 Iteration 2 Error: 0.774418 Iteration 3 Error: 0.261137 Iteration 4 Error: 0.086288 Iteration 5 Error: 0.030848 Align patch 11 14 left Iteration 1 Error: 1.691335 Iteration 2 Error: 0.578828 Iteration 3 Error: 0.091571 Iteration 4 Error: 0.055452 Iteration 5 Error: 0.025828 Align patch 12 13 left Iteration 1 Error: 1.502545 Iteration 2 Error: 0.471491 Iteration 3 Error: 0.192546 Iteration 4 Error: 0.115623 Iteration 5 Error: 0.028353 Align patch 13 12 left Iteration 1 Error: 1.880681 Iteration 2 Error: 0.564963 Iteration 3 Error: 0.115318 Iteration 4 Error: 0.049380 Align patch 14 11 left Iteration 1 Error: 2.029765 Iteration 2 Error: 0.836904 Iteration 3 Error: 0.322884 Iteration 4 Error: 0.126256 Iteration 5 Error: 0.062449 Align patch 14 11 left Iteration 1 Error: 3.077144 Iteration 2 Error: 0.742419 Iteration 3 Error: 0.175031 Iteration 4 Error: 0.060992 Iteration 5 Error: 0.020004 Align patch 15 10 left Iteration 1 Error: 4.153328 Iteration 2 Error: 1.536920 Iteration 3 Error: 0.495645 Iteration 4 Error: 0.239800 Iteration 5 Error: 0.091722 Align patch 15 10 left Iteration 1 Error: 4.124445 Iteration 2 Error: 0.981209 Iteration 3 Error: 0.306119 Iteration 4 Error: 0.078378 Iteration 5 Error: 0.027282 Align patch 16 9 left Iteration 1 Error: 1.852857 Iteration 2 Error: 0.632983 Iteration 3 Error: 0.120369 Iteration 4 Error: 0.065056 Iteration 5 Error: 0.029672 Align patch 17 8 left Iteration 1 Error: 0.959948 Iteration 2 Error: 0.326980 Iteration 3 Error: 0.149220 Iteration 4 Error: 0.063205 Iteration 5 Error: 0.041444 Align patch 18 7 left Iteration 1 Error: 1.179184 Iteration 2 Error: 0.447304 Iteration 3 Error: 0.247462 Iteration 4 Error: 0.172534 Iteration 5 Error: 0.084147 Align patch 18 7 left Iteration 1 Error: 0.731534 Iteration 2 Error: 0.192486 Iteration 3 Error: 0.054101 Iteration 4 Error: 0.032846 Align patch 19 6 left Iteration 1 Error: 1.261590 Iteration 2 Error: 0.504682 Iteration 3 Error: 0.228493 Iteration 4 Error: 0.078772 Iteration 5 Error: 0.036741 Align patch 20 5 left Iteration 1 Error: 1.935835 Iteration 2 Error: 0.557698 Iteration 3 Error: 0.297251 Iteration 4 Error: 0.147051 Iteration 5 Error: 0.109493 Align patch 20 5 left Iteration 1 Error: 2.202106 Iteration 2 Error: 0.344750 Iteration 3 Error: 0.098635 Iteration 4 Error: 0.041986 Align patch 21 4 left Iteration 1 Error: 1.358144 Iteration 2 Error: 0.402903 Iteration 3 Error: 0.115911 Iteration 4 Error: 0.041381 Align patch 22 3 left Iteration 1 Error: 1.735875 Iteration 2 Error: 0.282651 Iteration 3 Error: 0.125231 Iteration 4 Error: 0.036370 Align patch 23 2 left Iteration 1 Error: 0.999015 Iteration 2 Error: 0.172545 Iteration 3 Error: 0.061221 Iteration 4 Error: 0.026212 Align patch 24 1 left Iteration 1 Error: 1.222111 Iteration 2 Error: 0.228795 Iteration 3 Error: 0.044565 Align patch 25 0 left Iteration 1 Error: 1.504873 Iteration 2 Error: 0.191091 Iteration 3 Error: 0.037500 3D Fitting completed. Patch alignment time: 17.26(sec) Local motion has been corrected. Process thread exits. Computational time: 30.477915 sec Total time: 37.755077 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00013hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00013hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.658067s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00013hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.597290s ........................................ >>>>>>TIME<<<<<< FFT: 0.943492s Defocus_U Defocus_V Angle CCC 13293.04 12648.37 81.60 0.051496 Final Values Defocus_U Defocus_V Angle CCC 13296.15 12635.89 80.66 0.092832 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00014hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00014hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.998e-02 CC threshold: 0.734 Mean Std: 47.38 7.74 Num Hot pixels: 185 Hot pixel threshold: 93.81 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.950458 Iteration 2 Error: 0.120308 Iteration 3 Error: 0.031879 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.24 0.13 ...... Frame ( 3) shift: -0.49 0.26 ...... Frame ( 4) shift: -0.73 0.39 ...... Frame ( 5) shift: -0.97 0.52 ...... Frame ( 6) shift: -1.09 0.61 ...... Frame ( 7) shift: -1.07 0.65 ...... Frame ( 8) shift: -1.06 0.70 ...... Frame ( 9) shift: -1.03 0.75 ...... Frame ( 10) shift: -0.99 0.81 ...... Frame ( 11) shift: -0.94 0.87 ...... Frame ( 12) shift: -0.93 0.91 ...... Frame ( 13) shift: -0.95 0.93 ...... Frame ( 14) shift: -0.98 0.94 ...... Frame ( 15) shift: -0.97 0.98 ...... Frame ( 16) shift: -0.94 1.04 ...... Frame ( 17) shift: -0.90 1.10 ...... Frame ( 18) shift: -0.86 1.13 ...... Frame ( 19) shift: -0.82 1.12 ...... Frame ( 20) shift: -0.78 1.12 ...... Frame ( 21) shift: -0.75 1.17 ...... Frame ( 22) shift: -0.74 1.29 ...... Frame ( 23) shift: -0.73 1.40 ...... Frame ( 24) shift: -0.72 1.42 ...... Frame ( 25) shift: -0.72 1.34 ...... Frame ( 26) shift: -0.72 1.27 ...... Frame ( 27) shift: -0.69 1.25 ...... Frame ( 28) shift: -0.65 1.28 ...... Frame ( 29) shift: -0.61 1.32 ...... Frame ( 30) shift: -0.54 1.37 ...... Frame ( 31) shift: -0.47 1.42 ...... Frame ( 32) shift: -0.39 1.48 ...... Frame ( 33) shift: -0.36 1.56 ...... Frame ( 34) shift: -0.37 1.66 ...... Frame ( 35) shift: -0.39 1.76 ...... Frame ( 36) shift: -0.36 1.82 ...... Frame ( 37) shift: -0.29 1.85 ...... Frame ( 38) shift: -0.22 1.87 ...... Frame ( 39) shift: -0.15 1.90 ...... Frame ( 40) shift: -0.08 1.92 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.682250 Iteration 2 Error: 0.132684 Iteration 3 Error: 0.038920 Align patch 2 23 left Iteration 1 Error: 0.831962 Iteration 2 Error: 0.269540 Iteration 3 Error: 0.092614 Iteration 4 Error: 0.031542 Align patch 3 22 left Iteration 1 Error: 0.808066 Iteration 2 Error: 0.218721 Iteration 3 Error: 0.062390 Iteration 4 Error: 0.028796 Align patch 4 21 left Iteration 1 Error: 0.901653 Iteration 2 Error: 0.137509 Iteration 3 Error: 0.029266 Align patch 5 20 left Iteration 1 Error: 0.661204 Iteration 2 Error: 0.083049 Iteration 3 Error: 0.026066 Align patch 6 19 left Iteration 1 Error: 0.798326 Iteration 2 Error: 0.171861 Iteration 3 Error: 0.074914 Iteration 4 Error: 0.029941 Align patch 7 18 left Iteration 1 Error: 1.051382 Iteration 2 Error: 0.181721 Iteration 3 Error: 0.068879 Iteration 4 Error: 0.022490 Align patch 8 17 left Iteration 1 Error: 0.855990 Iteration 2 Error: 0.176413 Iteration 3 Error: 0.033635 Align patch 9 16 left Iteration 1 Error: 0.852108 Iteration 2 Error: 0.155362 Iteration 3 Error: 0.040422 Align patch 10 15 left Iteration 1 Error: 0.511852 Iteration 2 Error: 0.101574 Iteration 3 Error: 0.030018 Align patch 11 14 left Iteration 1 Error: 0.733895 Iteration 2 Error: 0.202214 Iteration 3 Error: 0.056279 Iteration 4 Error: 0.022180 Align patch 12 13 left Iteration 1 Error: 0.725662 Iteration 2 Error: 0.139828 Iteration 3 Error: 0.031834 Align patch 13 12 left Iteration 1 Error: 0.747582 Iteration 2 Error: 0.095574 Iteration 3 Error: 0.026039 Align patch 14 11 left Iteration 1 Error: 0.655317 Iteration 2 Error: 0.117144 Iteration 3 Error: 0.032431 Align patch 15 10 left Iteration 1 Error: 0.853039 Iteration 2 Error: 0.103688 Iteration 3 Error: 0.031465 Align patch 16 9 left Iteration 1 Error: 1.079152 Iteration 2 Error: 0.225729 Iteration 3 Error: 0.067793 Iteration 4 Error: 0.045785 Align patch 17 8 left Iteration 1 Error: 1.831082 Iteration 2 Error: 0.227702 Iteration 3 Error: 0.070068 Iteration 4 Error: 0.023227 Align patch 18 7 left Iteration 1 Error: 1.084142 Iteration 2 Error: 0.187185 Iteration 3 Error: 0.036622 Align patch 19 6 left Iteration 1 Error: 0.936831 Iteration 2 Error: 0.161517 Iteration 3 Error: 0.044733 Align patch 20 5 left Iteration 1 Error: 0.757233 Iteration 2 Error: 0.140174 Iteration 3 Error: 0.029134 Align patch 21 4 left Iteration 1 Error: 1.260347 Iteration 2 Error: 0.261813 Iteration 3 Error: 0.044481 Align patch 22 3 left Iteration 1 Error: 0.653482 Iteration 2 Error: 0.095966 Iteration 3 Error: 0.025445 Align patch 23 2 left Iteration 1 Error: 0.755847 Iteration 2 Error: 0.122995 Iteration 3 Error: 0.026542 Align patch 24 1 left Iteration 1 Error: 0.651758 Iteration 2 Error: 0.107322 Iteration 3 Error: 0.022193 Align patch 25 0 left Iteration 1 Error: 0.476703 Iteration 2 Error: 0.074550 Iteration 3 Error: 0.015876 3D Fitting completed. Patch alignment time: 11.89(sec) Local motion has been corrected. Process thread exits. Computational time: 23.842964 sec Total time: 31.158560 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00014hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00014hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.566954s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00014hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.574288s ........................................ >>>>>>TIME<<<<<< FFT: 0.942209s Defocus_U Defocus_V Angle CCC 12160.16 13074.22 12.46 0.050946 Final Values Defocus_U Defocus_V Angle CCC 12172.66 13077.37 12.78 0.094104 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00014hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00014hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.999e-02 CC threshold: 0.734 Mean Std: 47.29 7.79 Num Hot pixels: 176 Hot pixel threshold: 94.02 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.778141 Iteration 2 Error: 0.146294 Iteration 3 Error: 0.060574 Iteration 4 Error: 0.020075 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.22 0.07 ...... Frame ( 3) shift: -0.44 0.14 ...... Frame ( 4) shift: -0.66 0.22 ...... Frame ( 5) shift: -0.88 0.29 ...... Frame ( 6) shift: -0.97 0.47 ...... Frame ( 7) shift: -0.95 0.76 ...... Frame ( 8) shift: -0.92 1.04 ...... Frame ( 9) shift: -0.90 1.26 ...... Frame ( 10) shift: -0.87 1.41 ...... Frame ( 11) shift: -0.85 1.56 ...... Frame ( 12) shift: -0.85 1.69 ...... Frame ( 13) shift: -0.88 1.81 ...... Frame ( 14) shift: -0.91 1.92 ...... Frame ( 15) shift: -0.91 1.99 ...... Frame ( 16) shift: -0.89 2.02 ...... Frame ( 17) shift: -0.86 2.05 ...... Frame ( 18) shift: -0.84 2.10 ...... Frame ( 19) shift: -0.81 2.16 ...... Frame ( 20) shift: -0.78 2.23 ...... Frame ( 21) shift: -0.77 2.27 ...... Frame ( 22) shift: -0.78 2.26 ...... Frame ( 23) shift: -0.80 2.25 ...... Frame ( 24) shift: -0.80 2.27 ...... Frame ( 25) shift: -0.80 2.32 ...... Frame ( 26) shift: -0.80 2.36 ...... Frame ( 27) shift: -0.81 2.39 ...... Frame ( 28) shift: -0.83 2.42 ...... Frame ( 29) shift: -0.84 2.45 ...... Frame ( 30) shift: -0.82 2.47 ...... Frame ( 31) shift: -0.75 2.49 ...... Frame ( 32) shift: -0.68 2.52 ...... Frame ( 33) shift: -0.66 2.54 ...... Frame ( 34) shift: -0.70 2.56 ...... Frame ( 35) shift: -0.73 2.59 ...... Frame ( 36) shift: -0.74 2.59 ...... Frame ( 37) shift: -0.72 2.57 ...... Frame ( 38) shift: -0.70 2.55 ...... Frame ( 39) shift: -0.68 2.53 ...... Frame ( 40) shift: -0.66 2.52 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 4.547789 Iteration 2 Error: 0.893797 Iteration 3 Error: 0.748817 Iteration 4 Error: 0.328755 Iteration 5 Error: 0.170184 Align patch 1 24 left Iteration 1 Error: 2.413540 Iteration 2 Error: 0.130608 Iteration 3 Error: 0.037364 Align patch 2 23 left Iteration 1 Error: 0.921069 Iteration 2 Error: 0.184125 Iteration 3 Error: 0.040948 Align patch 3 22 left Iteration 1 Error: 1.836606 Iteration 2 Error: 0.250025 Iteration 3 Error: 0.088313 Iteration 4 Error: 0.017343 Align patch 4 21 left Iteration 1 Error: 0.802967 Iteration 2 Error: 0.227122 Iteration 3 Error: 0.073956 Iteration 4 Error: 0.019292 Align patch 5 20 left Iteration 1 Error: 0.831821 Iteration 2 Error: 0.117201 Iteration 3 Error: 0.025270 Align patch 6 19 left Iteration 1 Error: 1.072348 Iteration 2 Error: 0.614226 Iteration 3 Error: 0.240918 Iteration 4 Error: 0.308470 Iteration 5 Error: 0.143327 Align patch 6 19 left Iteration 1 Error: 1.713509 Iteration 2 Error: 0.233147 Iteration 3 Error: 0.051521 Iteration 4 Error: 0.029567 Align patch 7 18 left Iteration 1 Error: 0.691873 Iteration 2 Error: 0.128075 Iteration 3 Error: 0.038965 Align patch 8 17 left Iteration 1 Error: 2.426053 Iteration 2 Error: 0.200065 Iteration 3 Error: 0.055664 Iteration 4 Error: 0.024875 Align patch 9 16 left Iteration 1 Error: 0.578987 Iteration 2 Error: 0.086281 Iteration 3 Error: 0.026590 Align patch 10 15 left Iteration 1 Error: 0.822869 Iteration 2 Error: 0.101909 Iteration 3 Error: 0.025458 Align patch 11 14 left Iteration 1 Error: 0.962932 Iteration 2 Error: 0.366657 Iteration 3 Error: 0.118180 Iteration 4 Error: 0.148954 Iteration 5 Error: 0.092997 Align patch 11 14 left Iteration 1 Error: 2.020818 Iteration 2 Error: 0.157945 Iteration 3 Error: 0.043456 Align patch 12 13 left Iteration 1 Error: 0.838584 Iteration 2 Error: 0.169538 Iteration 3 Error: 0.048069 Align patch 13 12 left Iteration 1 Error: 0.756844 Iteration 2 Error: 0.181956 Iteration 3 Error: 0.068098 Iteration 4 Error: 0.015805 Align patch 14 11 left Iteration 1 Error: 0.657289 Iteration 2 Error: 0.135070 Iteration 3 Error: 0.036413 Align patch 15 10 left Iteration 1 Error: 1.049282 Iteration 2 Error: 0.116244 Iteration 3 Error: 0.020450 Align patch 16 9 left Iteration 1 Error: 1.346948 Iteration 2 Error: 0.167019 Iteration 3 Error: 0.034339 Align patch 17 8 left Iteration 1 Error: 0.916806 Iteration 2 Error: 0.314870 Iteration 3 Error: 0.079550 Iteration 4 Error: 0.040491 Align patch 18 7 left Iteration 1 Error: 1.248960 Iteration 2 Error: 0.189914 Iteration 3 Error: 0.040443 Align patch 19 6 left Iteration 1 Error: 0.835195 Iteration 2 Error: 0.114570 Iteration 3 Error: 0.036933 Align patch 20 5 left Iteration 1 Error: 0.681067 Iteration 2 Error: 0.077652 Iteration 3 Error: 0.018068 Align patch 21 4 left Iteration 1 Error: 1.066541 Iteration 2 Error: 0.185292 Iteration 3 Error: 0.080876 Iteration 4 Error: 0.027285 Align patch 22 3 left Iteration 1 Error: 1.240633 Iteration 2 Error: 0.149570 Iteration 3 Error: 0.046997 Align patch 23 2 left Iteration 1 Error: 0.760563 Iteration 2 Error: 0.197152 Iteration 3 Error: 0.053027 Iteration 4 Error: 0.019890 Align patch 24 1 left Iteration 1 Error: 0.745194 Iteration 2 Error: 0.105692 Iteration 3 Error: 0.030858 Align patch 25 0 left Iteration 1 Error: 0.431171 Iteration 2 Error: 0.028349 3D Fitting completed. Patch alignment time: 13.56(sec) Local motion has been corrected. Process thread exits. Computational time: 30.596653 sec Total time: 38.407379 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00014hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00014hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.648673s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00014hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 4.609276s ........................................ >>>>>>TIME<<<<<< FFT: 1.088890s Defocus_U Defocus_V Angle CCC 10691.38 11265.65 3.28 0.047275 Final Values Defocus_U Defocus_V Angle CCC 10699.21 11304.80 3.60 0.087434 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00014hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00014hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 48.36 7.63 Num Hot pixels: 191 Hot pixel threshold: 94.15 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.995767 Iteration 2 Error: 0.041236 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.30 0.17 ...... Frame ( 3) shift: -0.59 0.34 ...... Frame ( 4) shift: -0.89 0.50 ...... Frame ( 5) shift: -1.19 0.67 ...... Frame ( 6) shift: -1.33 0.75 ...... Frame ( 7) shift: -1.32 0.74 ...... Frame ( 8) shift: -1.31 0.73 ...... Frame ( 9) shift: -1.32 0.73 ...... Frame ( 10) shift: -1.35 0.74 ...... Frame ( 11) shift: -1.38 0.75 ...... Frame ( 12) shift: -1.39 0.77 ...... Frame ( 13) shift: -1.40 0.78 ...... Frame ( 14) shift: -1.40 0.79 ...... Frame ( 15) shift: -1.41 0.79 ...... Frame ( 16) shift: -1.41 0.78 ...... Frame ( 17) shift: -1.41 0.77 ...... Frame ( 18) shift: -1.41 0.73 ...... Frame ( 19) shift: -1.41 0.67 ...... Frame ( 20) shift: -1.40 0.61 ...... Frame ( 21) shift: -1.40 0.61 ...... Frame ( 22) shift: -1.39 0.67 ...... Frame ( 23) shift: -1.38 0.73 ...... Frame ( 24) shift: -1.38 0.74 ...... Frame ( 25) shift: -1.37 0.69 ...... Frame ( 26) shift: -1.36 0.65 ...... Frame ( 27) shift: -1.35 0.61 ...... Frame ( 28) shift: -1.33 0.58 ...... Frame ( 29) shift: -1.31 0.54 ...... Frame ( 30) shift: -1.32 0.56 ...... Frame ( 31) shift: -1.36 0.62 ...... Frame ( 32) shift: -1.40 0.67 ...... Frame ( 33) shift: -1.41 0.72 ...... Frame ( 34) shift: -1.39 0.75 ...... Frame ( 35) shift: -1.36 0.78 ...... Frame ( 36) shift: -1.34 0.81 ...... Frame ( 37) shift: -1.32 0.84 ...... Frame ( 38) shift: -1.30 0.87 ...... Frame ( 39) shift: -1.28 0.90 ...... Frame ( 40) shift: -1.25 0.94 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.770134 Iteration 2 Error: 0.121490 Iteration 3 Error: 0.029020 Align patch 2 23 left Iteration 1 Error: 0.971569 Iteration 2 Error: 0.233727 Iteration 3 Error: 0.038427 Align patch 3 22 left Iteration 1 Error: 0.816564 Iteration 2 Error: 0.161855 Iteration 3 Error: 0.066406 Iteration 4 Error: 0.022768 Align patch 4 21 left Iteration 1 Error: 0.716210 Iteration 2 Error: 0.113159 Iteration 3 Error: 0.017877 Align patch 5 20 left Iteration 1 Error: 0.702274 Iteration 2 Error: 0.106389 Iteration 3 Error: 0.017335 Align patch 6 19 left Iteration 1 Error: 0.980634 Iteration 2 Error: 0.206496 Iteration 3 Error: 0.038024 Align patch 7 18 left Iteration 1 Error: 0.634559 Iteration 2 Error: 0.138338 Iteration 3 Error: 0.040567 Align patch 8 17 left Iteration 1 Error: 0.833989 Iteration 2 Error: 0.129664 Iteration 3 Error: 0.046020 Align patch 9 16 left Iteration 1 Error: 1.343396 Iteration 2 Error: 0.195757 Iteration 3 Error: 0.056515 Iteration 4 Error: 0.014341 Align patch 10 15 left Iteration 1 Error: 0.788660 Iteration 2 Error: 0.095948 Iteration 3 Error: 0.026303 Align patch 11 14 left Iteration 1 Error: 1.375000 Iteration 2 Error: 0.179855 Iteration 3 Error: 0.053748 Iteration 4 Error: 0.014763 Align patch 12 13 left Iteration 1 Error: 1.478883 Iteration 2 Error: 0.216300 Iteration 3 Error: 0.059427 Iteration 4 Error: 0.021826 Align patch 13 12 left Iteration 1 Error: 0.707372 Iteration 2 Error: 0.149806 Iteration 3 Error: 0.042059 Align patch 14 11 left Iteration 1 Error: 0.897984 Iteration 2 Error: 0.126591 Iteration 3 Error: 0.044908 Align patch 15 10 left Iteration 1 Error: 0.644460 Iteration 2 Error: 0.130751 Iteration 3 Error: 0.025254 Align patch 16 9 left Iteration 1 Error: 1.696650 Iteration 2 Error: 0.137492 Iteration 3 Error: 0.045898 Align patch 17 8 left Iteration 1 Error: 0.806904 Iteration 2 Error: 0.140821 Iteration 3 Error: 0.030409 Align patch 18 7 left Iteration 1 Error: 1.112139 Iteration 2 Error: 0.183565 Iteration 3 Error: 0.095153 Iteration 4 Error: 0.028625 Align patch 19 6 left Iteration 1 Error: 0.662047 Iteration 2 Error: 0.264739 Iteration 3 Error: 0.092925 Iteration 4 Error: 0.060724 Iteration 5 Error: 0.031803 Align patch 20 5 left Iteration 1 Error: 0.963955 Iteration 2 Error: 0.155019 Iteration 3 Error: 0.050853 Iteration 4 Error: 0.024937 Align patch 21 4 left Iteration 1 Error: 1.552770 Iteration 2 Error: 0.160702 Iteration 3 Error: 0.047790 Align patch 22 3 left Iteration 1 Error: 1.147071 Iteration 2 Error: 0.283785 Iteration 3 Error: 0.057961 Iteration 4 Error: 0.038483 Align patch 23 2 left Iteration 1 Error: 0.743934 Iteration 2 Error: 0.203115 Iteration 3 Error: 0.046324 Align patch 24 1 left Iteration 1 Error: 0.674300 Iteration 2 Error: 0.101577 Iteration 3 Error: 0.029447 Align patch 25 0 left Iteration 1 Error: 0.956887 Iteration 2 Error: 0.103647 Iteration 3 Error: 0.021623 3D Fitting completed. Patch alignment time: 11.97(sec) Local motion has been corrected. Process thread exits. Computational time: 25.141315 sec Total time: 31.850267 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00014hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00014hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.464643s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00014hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.413472s ........................................ >>>>>>TIME<<<<<< FFT: 0.949144s Defocus_U Defocus_V Angle CCC 11298.79 12248.09 7.53 0.045946 Final Values Defocus_U Defocus_V Angle CCC 11311.29 12254.34 7.53 0.086353 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00014hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00014hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 47.12 7.80 Num Hot pixels: 177 Hot pixel threshold: 93.90 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.429684 Iteration 2 Error: 0.114365 Iteration 3 Error: 0.023873 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.36 0.13 ...... Frame ( 3) shift: -0.71 0.27 ...... Frame ( 4) shift: -1.07 0.40 ...... Frame ( 5) shift: -1.42 0.53 ...... Frame ( 6) shift: -1.63 0.66 ...... Frame ( 7) shift: -1.68 0.78 ...... Frame ( 8) shift: -1.72 0.91 ...... Frame ( 9) shift: -1.76 0.96 ...... Frame ( 10) shift: -1.77 0.95 ...... Frame ( 11) shift: -1.78 0.94 ...... Frame ( 12) shift: -1.81 0.94 ...... Frame ( 13) shift: -1.86 0.97 ...... Frame ( 14) shift: -1.91 0.99 ...... Frame ( 15) shift: -1.94 1.03 ...... Frame ( 16) shift: -1.97 1.08 ...... Frame ( 17) shift: -1.99 1.14 ...... Frame ( 18) shift: -2.02 1.16 ...... Frame ( 19) shift: -2.06 1.15 ...... Frame ( 20) shift: -2.09 1.14 ...... Frame ( 21) shift: -2.06 1.11 ...... Frame ( 22) shift: -1.97 1.05 ...... Frame ( 23) shift: -1.87 0.99 ...... Frame ( 24) shift: -1.83 0.98 ...... Frame ( 25) shift: -1.83 1.02 ...... Frame ( 26) shift: -1.83 1.05 ...... Frame ( 27) shift: -1.81 1.07 ...... Frame ( 28) shift: -1.78 1.08 ...... Frame ( 29) shift: -1.75 1.08 ...... Frame ( 30) shift: -1.73 1.07 ...... Frame ( 31) shift: -1.72 1.04 ...... Frame ( 32) shift: -1.71 1.02 ...... Frame ( 33) shift: -1.72 1.01 ...... Frame ( 34) shift: -1.74 1.04 ...... Frame ( 35) shift: -1.76 1.06 ...... Frame ( 36) shift: -1.77 1.09 ...... Frame ( 37) shift: -1.77 1.13 ...... Frame ( 38) shift: -1.77 1.16 ...... Frame ( 39) shift: -1.77 1.20 ...... Frame ( 40) shift: -1.77 1.24 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.841318 Iteration 2 Error: 0.356297 Iteration 3 Error: 0.142320 Iteration 4 Error: 0.041621 Align patch 2 23 left Iteration 1 Error: 0.617107 Iteration 2 Error: 0.112022 Iteration 3 Error: 0.033187 Align patch 3 22 left Iteration 1 Error: 0.757356 Iteration 2 Error: 0.174149 Iteration 3 Error: 0.041858 Align patch 4 21 left Iteration 1 Error: 0.690630 Iteration 2 Error: 0.158708 Iteration 3 Error: 0.046931 Align patch 5 20 left Iteration 1 Error: 0.577583 Iteration 2 Error: 0.143187 Iteration 3 Error: 0.019464 Align patch 6 19 left Iteration 1 Error: 1.136007 Iteration 2 Error: 0.592532 Iteration 3 Error: 0.292138 Iteration 4 Error: 0.198870 Iteration 5 Error: 0.130388 Align patch 6 19 left Iteration 1 Error: 2.149981 Iteration 2 Error: 0.198397 Iteration 3 Error: 0.042348 Align patch 7 18 left Iteration 1 Error: 0.686726 Iteration 2 Error: 0.176446 Iteration 3 Error: 0.068146 Iteration 4 Error: 0.034782 Align patch 8 17 left Iteration 1 Error: 1.183362 Iteration 2 Error: 0.256421 Iteration 3 Error: 0.055415 Iteration 4 Error: 0.016405 Align patch 9 16 left Iteration 1 Error: 0.698930 Iteration 2 Error: 0.133500 Iteration 3 Error: 0.032015 Align patch 10 15 left Iteration 1 Error: 0.685121 Iteration 2 Error: 0.131502 Iteration 3 Error: 0.031613 Align patch 11 14 left Iteration 1 Error: 0.988665 Iteration 2 Error: 0.309447 Iteration 3 Error: 0.153861 Iteration 4 Error: 0.080233 Iteration 5 Error: 0.039420 Align patch 12 13 left Iteration 1 Error: 0.807134 Iteration 2 Error: 0.145429 Iteration 3 Error: 0.047671 Align patch 13 12 left Iteration 1 Error: 0.668287 Iteration 2 Error: 0.166758 Iteration 3 Error: 0.057192 Iteration 4 Error: 0.026320 Align patch 14 11 left Iteration 1 Error: 0.929966 Iteration 2 Error: 0.148082 Iteration 3 Error: 0.066670 Iteration 4 Error: 0.024119 Align patch 15 10 left Iteration 1 Error: 0.499717 Iteration 2 Error: 0.151349 Iteration 3 Error: 0.035035 Align patch 16 9 left Iteration 1 Error: 0.897846 Iteration 2 Error: 0.242960 Iteration 3 Error: 0.109686 Iteration 4 Error: 0.047897 Align patch 17 8 left Iteration 1 Error: 0.927378 Iteration 2 Error: 0.185791 Iteration 3 Error: 0.072570 Iteration 4 Error: 0.028843 Align patch 18 7 left Iteration 1 Error: 0.879658 Iteration 2 Error: 0.162520 Iteration 3 Error: 0.064031 Iteration 4 Error: 0.028592 Align patch 19 6 left Iteration 1 Error: 0.676423 Iteration 2 Error: 0.116471 Iteration 3 Error: 0.045924 Align patch 20 5 left Iteration 1 Error: 0.950284 Iteration 2 Error: 0.104774 Iteration 3 Error: 0.031175 Align patch 21 4 left Iteration 1 Error: 0.877335 Iteration 2 Error: 0.259909 Iteration 3 Error: 0.073731 Iteration 4 Error: 0.019806 Align patch 22 3 left Iteration 1 Error: 1.078375 Iteration 2 Error: 0.241604 Iteration 3 Error: 0.043629 Align patch 23 2 left Iteration 1 Error: 1.141455 Iteration 2 Error: 0.125203 Iteration 3 Error: 0.026593 Align patch 24 1 left Iteration 1 Error: 1.256956 Iteration 2 Error: 0.101106 Iteration 3 Error: 0.019433 Align patch 25 0 left Iteration 1 Error: 0.694541 Iteration 2 Error: 0.104752 Iteration 3 Error: 0.022488 3D Fitting completed. Patch alignment time: 12.12(sec) Local motion has been corrected. Process thread exits. Computational time: 24.188105 sec Total time: 31.682402 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00014hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00014hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.766456s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00014hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 5.284785s ........................................ >>>>>>TIME<<<<<< FFT: 1.126434s Defocus_U Defocus_V Angle CCC 13248.04 12615.23 84.38 0.051507 Final Values Defocus_U Defocus_V Angle CCC 13266.79 12615.23 84.38 0.092519 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00015hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00015hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.993e-02 CC threshold: 0.734 Mean Std: 47.02 7.72 Num Hot pixels: 174 Hot pixel threshold: 93.34 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.892579 Iteration 2 Error: 0.092589 Iteration 3 Error: 0.017327 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.10 0.17 ...... Frame ( 3) shift: -0.19 0.34 ...... Frame ( 4) shift: -0.29 0.51 ...... Frame ( 5) shift: -0.39 0.68 ...... Frame ( 6) shift: -0.34 0.81 ...... Frame ( 7) shift: -0.16 0.88 ...... Frame ( 8) shift: 0.02 0.95 ...... Frame ( 9) shift: 0.15 1.01 ...... Frame ( 10) shift: 0.23 1.05 ...... Frame ( 11) shift: 0.31 1.09 ...... Frame ( 12) shift: 0.41 1.13 ...... Frame ( 13) shift: 0.53 1.18 ...... Frame ( 14) shift: 0.64 1.22 ...... Frame ( 15) shift: 0.70 1.23 ...... Frame ( 16) shift: 0.70 1.20 ...... Frame ( 17) shift: 0.70 1.17 ...... Frame ( 18) shift: 0.72 1.15 ...... Frame ( 19) shift: 0.76 1.12 ...... Frame ( 20) shift: 0.80 1.10 ...... Frame ( 21) shift: 0.81 1.08 ...... Frame ( 22) shift: 0.78 1.05 ...... Frame ( 23) shift: 0.76 1.03 ...... Frame ( 24) shift: 0.74 0.98 ...... Frame ( 25) shift: 0.73 0.92 ...... Frame ( 26) shift: 0.71 0.85 ...... Frame ( 27) shift: 0.72 0.86 ...... Frame ( 28) shift: 0.74 0.95 ...... Frame ( 29) shift: 0.76 1.05 ...... Frame ( 30) shift: 0.77 1.08 ...... Frame ( 31) shift: 0.77 1.03 ...... Frame ( 32) shift: 0.76 0.99 ...... Frame ( 33) shift: 0.72 0.97 ...... Frame ( 34) shift: 0.64 0.97 ...... Frame ( 35) shift: 0.56 0.96 ...... Frame ( 36) shift: 0.54 0.94 ...... Frame ( 37) shift: 0.59 0.91 ...... Frame ( 38) shift: 0.65 0.88 ...... Frame ( 39) shift: 0.70 0.85 ...... Frame ( 40) shift: 0.75 0.81 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.978106 Iteration 2 Error: 2.179208 Iteration 3 Error: 1.110924 Iteration 4 Error: 0.849315 Iteration 5 Error: 0.666416 Align patch 1 24 left Iteration 1 Error: 4.767229 Iteration 2 Error: 1.763965 Iteration 3 Error: 1.142299 Iteration 4 Error: 1.055591 Iteration 5 Error: 0.904506 Align patch 2 23 left Iteration 1 Error: 0.890623 Iteration 2 Error: 0.243137 Iteration 3 Error: 0.064837 Iteration 4 Error: 0.026531 Align patch 3 22 left Iteration 1 Error: 1.284856 Iteration 2 Error: 0.272670 Iteration 3 Error: 0.049400 Align patch 4 21 left Iteration 1 Error: 1.675292 Iteration 2 Error: 0.569096 Iteration 3 Error: 0.124771 Iteration 4 Error: 0.064456 Iteration 5 Error: 0.014808 Align patch 5 20 left Iteration 1 Error: 1.629696 Iteration 2 Error: 0.361316 Iteration 3 Error: 0.084845 Iteration 4 Error: 0.029587 Align patch 6 19 left Iteration 1 Error: 2.560080 Iteration 2 Error: 0.590666 Iteration 3 Error: 0.388441 Iteration 4 Error: 0.240488 Iteration 5 Error: 0.142624 Align patch 6 19 left Iteration 1 Error: 5.239488 Iteration 2 Error: 2.047340 Iteration 3 Error: 1.457626 Iteration 4 Error: 1.134449 Iteration 5 Error: 0.869791 Align patch 7 18 left Iteration 1 Error: 2.837783 Iteration 2 Error: 2.884262 Iteration 3 Error: 0.849818 Iteration 4 Error: 0.502445 Iteration 5 Error: 0.375067 Align patch 7 18 left Iteration 1 Error: 2.595555 Iteration 2 Error: 0.730058 Iteration 3 Error: 0.375143 Iteration 4 Error: 0.229349 Iteration 5 Error: 0.156444 Align patch 8 17 left Iteration 1 Error: 1.076505 Iteration 2 Error: 0.151474 Iteration 3 Error: 0.042808 Align patch 9 16 left Iteration 1 Error: 0.913864 Iteration 2 Error: 0.230822 Iteration 3 Error: 0.057330 Iteration 4 Error: 0.019858 Align patch 10 15 left Iteration 1 Error: 0.904836 Iteration 2 Error: 0.134546 Iteration 3 Error: 0.038155 Align patch 11 14 left Iteration 1 Error: 1.997223 Iteration 2 Error: 0.612691 Iteration 3 Error: 0.364190 Iteration 4 Error: 0.191178 Iteration 5 Error: 0.112448 Align patch 11 14 left Iteration 1 Error: 4.060860 Iteration 2 Error: 0.901158 Iteration 3 Error: 0.469488 Iteration 4 Error: 0.222476 Iteration 5 Error: 0.135885 Align patch 12 13 left Iteration 1 Error: 1.861696 Iteration 2 Error: 0.802075 Iteration 3 Error: 0.355240 Iteration 4 Error: 0.221035 Iteration 5 Error: 0.175268 Align patch 12 13 left Iteration 1 Error: 2.716203 Iteration 2 Error: 0.678609 Iteration 3 Error: 0.284922 Iteration 4 Error: 0.159475 Iteration 5 Error: 0.061428 Align patch 13 12 left Iteration 1 Error: 3.351748 Iteration 2 Error: 0.502649 Iteration 3 Error: 0.217725 Iteration 4 Error: 0.101874 Iteration 5 Error: 0.026120 Align patch 14 11 left Iteration 1 Error: 2.020236 Iteration 2 Error: 0.506627 Iteration 3 Error: 0.350456 Iteration 4 Error: 0.177244 Iteration 5 Error: 0.111390 Align patch 14 11 left Iteration 1 Error: 1.656184 Iteration 2 Error: 0.257260 Iteration 3 Error: 0.050410 Iteration 4 Error: 0.020176 Align patch 15 10 left Iteration 1 Error: 0.632446 Iteration 2 Error: 0.093624 Iteration 3 Error: 0.014857 Align patch 16 9 left Iteration 1 Error: 4.480611 Iteration 2 Error: 1.168154 Iteration 3 Error: 0.661714 Iteration 4 Error: 0.555496 Iteration 5 Error: 0.448157 Align patch 16 9 left Iteration 1 Error: 3.717601 Iteration 2 Error: 1.230859 Iteration 3 Error: 0.564099 Iteration 4 Error: 0.310388 Iteration 5 Error: 0.180042 Align patch 17 8 left Iteration 1 Error: 2.043742 Iteration 2 Error: 0.786150 Iteration 3 Error: 0.614665 Iteration 4 Error: 0.601875 Iteration 5 Error: 0.628044 Align patch 17 8 left Iteration 1 Error: 3.692433 Iteration 2 Error: 1.364016 Iteration 3 Error: 0.624995 Iteration 4 Error: 0.373113 Iteration 5 Error: 0.233295 Align patch 18 7 left Iteration 1 Error: 0.617488 Iteration 2 Error: 0.196791 Iteration 3 Error: 0.042311 Align patch 19 6 left Iteration 1 Error: 0.831323 Iteration 2 Error: 0.115353 Iteration 3 Error: 0.026890 Align patch 20 5 left Iteration 1 Error: 0.875648 Iteration 2 Error: 0.139698 Iteration 3 Error: 0.028360 Align patch 21 4 left Iteration 1 Error: 1.256661 Iteration 2 Error: 0.516568 Iteration 3 Error: 0.332752 Iteration 4 Error: 0.311628 Iteration 5 Error: 0.305667 Align patch 21 4 left Iteration 1 Error: 2.382245 Iteration 2 Error: 0.996971 Iteration 3 Error: 0.389742 Iteration 4 Error: 0.236441 Iteration 5 Error: 0.122207 Align patch 22 3 left Iteration 1 Error: 1.123252 Iteration 2 Error: 0.648768 Iteration 3 Error: 0.420804 Iteration 4 Error: 0.262113 Iteration 5 Error: 0.164828 Align patch 22 3 left Iteration 1 Error: 2.442374 Iteration 2 Error: 0.878934 Iteration 3 Error: 0.407512 Iteration 4 Error: 0.240451 Iteration 5 Error: 0.112985 Align patch 23 2 left Iteration 1 Error: 2.309917 Iteration 2 Error: 0.317936 Iteration 3 Error: 0.111279 Iteration 4 Error: 0.039826 Align patch 24 1 left Iteration 1 Error: 1.070759 Iteration 2 Error: 0.149318 Iteration 3 Error: 0.027108 Align patch 25 0 left Iteration 1 Error: 0.673559 Iteration 2 Error: 0.102920 Iteration 3 Error: 0.022102 3D Fitting completed. Patch alignment time: 19.52(sec) Local motion has been corrected. Process thread exits. Computational time: 31.643766 sec Total time: 39.240452 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00015hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00015hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.580835s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00015hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.431709s ........................................ >>>>>>TIME<<<<<< FFT: 1.011645s Defocus_U Defocus_V Angle CCC 12126.95 12939.45 10.97 0.041328 Final Values Defocus_U Defocus_V Angle CCC 12134.77 12931.64 10.97 0.074287 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00015hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00015hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 47.05 7.87 Num Hot pixels: 175 Hot pixel threshold: 94.25 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.359181 Iteration 2 Error: 0.142065 Iteration 3 Error: 0.026968 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.17 0.22 ...... Frame ( 3) shift: -0.34 0.44 ...... Frame ( 4) shift: -0.51 0.66 ...... Frame ( 5) shift: -0.67 0.88 ...... Frame ( 6) shift: -0.72 1.05 ...... Frame ( 7) shift: -0.65 1.18 ...... Frame ( 8) shift: -0.58 1.32 ...... Frame ( 9) shift: -0.49 1.41 ...... Frame ( 10) shift: -0.39 1.47 ...... Frame ( 11) shift: -0.28 1.53 ...... Frame ( 12) shift: -0.20 1.56 ...... Frame ( 13) shift: -0.14 1.58 ...... Frame ( 14) shift: -0.08 1.60 ...... Frame ( 15) shift: -0.07 1.64 ...... Frame ( 16) shift: -0.10 1.69 ...... Frame ( 17) shift: -0.12 1.74 ...... Frame ( 18) shift: -0.15 1.79 ...... Frame ( 19) shift: -0.16 1.84 ...... Frame ( 20) shift: -0.18 1.89 ...... Frame ( 21) shift: -0.19 1.92 ...... Frame ( 22) shift: -0.20 1.94 ...... Frame ( 23) shift: -0.21 1.96 ...... Frame ( 24) shift: -0.23 1.99 ...... Frame ( 25) shift: -0.26 2.03 ...... Frame ( 26) shift: -0.30 2.06 ...... Frame ( 27) shift: -0.30 2.05 ...... Frame ( 28) shift: -0.26 2.00 ...... Frame ( 29) shift: -0.22 1.95 ...... Frame ( 30) shift: -0.22 1.94 ...... Frame ( 31) shift: -0.26 1.98 ...... Frame ( 32) shift: -0.30 2.01 ...... Frame ( 33) shift: -0.30 2.02 ...... Frame ( 34) shift: -0.28 2.01 ...... Frame ( 35) shift: -0.25 1.99 ...... Frame ( 36) shift: -0.25 2.01 ...... Frame ( 37) shift: -0.26 2.05 ...... Frame ( 38) shift: -0.28 2.09 ...... Frame ( 39) shift: -0.30 2.13 ...... Frame ( 40) shift: -0.32 2.18 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.774347 Iteration 2 Error: 0.355696 Iteration 3 Error: 0.190508 Iteration 4 Error: 0.098285 Iteration 5 Error: 0.045880 Align patch 2 23 left Iteration 1 Error: 1.494071 Iteration 2 Error: 0.206950 Iteration 3 Error: 0.050273 Iteration 4 Error: 0.024008 Align patch 3 22 left Iteration 1 Error: 1.136186 Iteration 2 Error: 0.180304 Iteration 3 Error: 0.066223 Iteration 4 Error: 0.019363 Align patch 4 21 left Iteration 1 Error: 0.556195 Iteration 2 Error: 0.096457 Iteration 3 Error: 0.015304 Align patch 5 20 left Iteration 1 Error: 0.802747 Iteration 2 Error: 0.180888 Iteration 3 Error: 0.045259 Align patch 6 19 left Iteration 1 Error: 1.817864 Iteration 2 Error: 0.256054 Iteration 3 Error: 0.069914 Iteration 4 Error: 0.026129 Align patch 7 18 left Iteration 1 Error: 1.619469 Iteration 2 Error: 0.127189 Iteration 3 Error: 0.065004 Iteration 4 Error: 0.019299 Align patch 8 17 left Iteration 1 Error: 0.841716 Iteration 2 Error: 0.194469 Iteration 3 Error: 0.049834 Align patch 9 16 left Iteration 1 Error: 0.698184 Iteration 2 Error: 0.128630 Iteration 3 Error: 0.033234 Align patch 10 15 left Iteration 1 Error: 0.468236 Iteration 2 Error: 0.065425 Iteration 3 Error: 0.016035 Align patch 11 14 left Iteration 1 Error: 1.005879 Iteration 2 Error: 0.267881 Iteration 3 Error: 0.043116 Align patch 12 13 left Iteration 1 Error: 0.784449 Iteration 2 Error: 0.106487 Iteration 3 Error: 0.031723 Align patch 13 12 left Iteration 1 Error: 0.815228 Iteration 2 Error: 0.170172 Iteration 3 Error: 0.040781 Align patch 14 11 left Iteration 1 Error: 0.642469 Iteration 2 Error: 0.144469 Iteration 3 Error: 0.027535 Align patch 15 10 left Iteration 1 Error: 0.758677 Iteration 2 Error: 0.163975 Iteration 3 Error: 0.030568 Align patch 16 9 left Iteration 1 Error: 0.849778 Iteration 2 Error: 0.101942 Iteration 3 Error: 0.033121 Align patch 17 8 left Iteration 1 Error: 0.936308 Iteration 2 Error: 0.087687 Iteration 3 Error: 0.033240 Align patch 18 7 left Iteration 1 Error: 1.421774 Iteration 2 Error: 0.217196 Iteration 3 Error: 0.072177 Iteration 4 Error: 0.026676 Align patch 19 6 left Iteration 1 Error: 0.557862 Iteration 2 Error: 0.105674 Iteration 3 Error: 0.020284 Align patch 20 5 left Iteration 1 Error: 0.558309 Iteration 2 Error: 0.051309 Iteration 3 Error: 0.009901 Align patch 21 4 left Iteration 1 Error: 0.754221 Iteration 2 Error: 0.144222 Iteration 3 Error: 0.049374 Align patch 22 3 left Iteration 1 Error: 0.599181 Iteration 2 Error: 0.159443 Iteration 3 Error: 0.042416 Align patch 23 2 left Iteration 1 Error: 1.326897 Iteration 2 Error: 0.267710 Iteration 3 Error: 0.080598 Iteration 4 Error: 0.030206 Align patch 24 1 left Iteration 1 Error: 0.725085 Iteration 2 Error: 0.078091 Iteration 3 Error: 0.026102 Align patch 25 0 left Iteration 1 Error: 0.686865 Iteration 2 Error: 0.070519 Iteration 3 Error: 0.008352 3D Fitting completed. Patch alignment time: 12.59(sec) Local motion has been corrected. Process thread exits. Computational time: 24.158907 sec Total time: 36.377254 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00015hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00015hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.549469s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00015hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.220231s ........................................ >>>>>>TIME<<<<<< FFT: 0.906158s Defocus_U Defocus_V Angle CCC 8427.77 8943.39 0.23 0.035975 Final Values Defocus_U Defocus_V Angle CCC 8421.52 8965.29 0.54 0.076469 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00015hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00015hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 9.997e-02 CC threshold: 0.734 Mean Std: 47.84 7.69 Num Hot pixels: 201 Hot pixel threshold: 93.98 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.110816 Iteration 2 Error: 0.073980 Iteration 3 Error: 0.022209 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.24 0.12 ...... Frame ( 3) shift: -0.49 0.24 ...... Frame ( 4) shift: -0.73 0.35 ...... Frame ( 5) shift: -0.97 0.47 ...... Frame ( 6) shift: -1.07 0.60 ...... Frame ( 7) shift: -1.03 0.74 ...... Frame ( 8) shift: -0.98 0.88 ...... Frame ( 9) shift: -0.94 0.99 ...... Frame ( 10) shift: -0.92 1.07 ...... Frame ( 11) shift: -0.90 1.15 ...... Frame ( 12) shift: -0.85 1.21 ...... Frame ( 13) shift: -0.77 1.24 ...... Frame ( 14) shift: -0.70 1.27 ...... Frame ( 15) shift: -0.67 1.31 ...... Frame ( 16) shift: -0.67 1.38 ...... Frame ( 17) shift: -0.67 1.45 ...... Frame ( 18) shift: -0.67 1.48 ...... Frame ( 19) shift: -0.65 1.47 ...... Frame ( 20) shift: -0.63 1.47 ...... Frame ( 21) shift: -0.62 1.48 ...... Frame ( 22) shift: -0.61 1.52 ...... Frame ( 23) shift: -0.60 1.55 ...... Frame ( 24) shift: -0.63 1.56 ...... Frame ( 25) shift: -0.71 1.53 ...... Frame ( 26) shift: -0.79 1.51 ...... Frame ( 27) shift: -0.82 1.49 ...... Frame ( 28) shift: -0.82 1.50 ...... Frame ( 29) shift: -0.81 1.50 ...... Frame ( 30) shift: -0.84 1.50 ...... Frame ( 31) shift: -0.89 1.51 ...... Frame ( 32) shift: -0.94 1.52 ...... Frame ( 33) shift: -0.95 1.48 ...... Frame ( 34) shift: -0.90 1.41 ...... Frame ( 35) shift: -0.86 1.34 ...... Frame ( 36) shift: -0.86 1.32 ...... Frame ( 37) shift: -0.90 1.37 ...... Frame ( 38) shift: -0.95 1.42 ...... Frame ( 39) shift: -0.99 1.47 ...... Frame ( 40) shift: -1.04 1.52 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.798382 Iteration 2 Error: 0.215216 Iteration 3 Error: 0.067621 Iteration 4 Error: 0.030982 Align patch 2 23 left Iteration 1 Error: 1.484509 Iteration 2 Error: 0.249988 Iteration 3 Error: 0.091234 Iteration 4 Error: 0.018159 Align patch 3 22 left Iteration 1 Error: 1.597030 Iteration 2 Error: 0.166934 Iteration 3 Error: 0.051628 Iteration 4 Error: 0.016019 Align patch 4 21 left Iteration 1 Error: 0.609039 Iteration 2 Error: 0.127061 Iteration 3 Error: 0.032088 Align patch 5 20 left Iteration 1 Error: 0.495576 Iteration 2 Error: 0.097736 Iteration 3 Error: 0.013664 Align patch 6 19 left Iteration 1 Error: 0.726313 Iteration 2 Error: 0.121767 Iteration 3 Error: 0.035801 Align patch 7 18 left Iteration 1 Error: 1.348720 Iteration 2 Error: 0.288772 Iteration 3 Error: 0.093577 Iteration 4 Error: 0.054417 Iteration 5 Error: 0.037426 Align patch 8 17 left Iteration 1 Error: 0.766125 Iteration 2 Error: 0.115054 Iteration 3 Error: 0.020139 Align patch 9 16 left Iteration 1 Error: 1.145364 Iteration 2 Error: 0.162962 Iteration 3 Error: 0.036013 Align patch 10 15 left Iteration 1 Error: 0.837489 Iteration 2 Error: 0.163346 Iteration 3 Error: 0.062061 Iteration 4 Error: 0.015509 Align patch 11 14 left Iteration 1 Error: 0.886217 Iteration 2 Error: 0.116153 Iteration 3 Error: 0.022159 Align patch 12 13 left Iteration 1 Error: 1.135866 Iteration 2 Error: 0.280596 Iteration 3 Error: 0.100581 Iteration 4 Error: 0.036656 Align patch 13 12 left Iteration 1 Error: 0.780142 Iteration 2 Error: 0.174255 Iteration 3 Error: 0.061953 Iteration 4 Error: 0.018776 Align patch 14 11 left Iteration 1 Error: 0.629776 Iteration 2 Error: 0.160819 Iteration 3 Error: 0.050810 Iteration 4 Error: 0.017154 Align patch 15 10 left Iteration 1 Error: 0.937046 Iteration 2 Error: 0.194277 Iteration 3 Error: 0.047920 Align patch 16 9 left Iteration 1 Error: 0.774970 Iteration 2 Error: 0.174041 Iteration 3 Error: 0.038595 Align patch 17 8 left Iteration 1 Error: 0.784205 Iteration 2 Error: 0.136310 Iteration 3 Error: 0.047564 Align patch 18 7 left Iteration 1 Error: 0.693425 Iteration 2 Error: 0.142317 Iteration 3 Error: 0.030485 Align patch 19 6 left Iteration 1 Error: 0.687559 Iteration 2 Error: 0.136327 Iteration 3 Error: 0.027301 Align patch 20 5 left Iteration 1 Error: 0.649429 Iteration 2 Error: 0.081971 Iteration 3 Error: 0.031658 Align patch 21 4 left Iteration 1 Error: 1.139672 Iteration 2 Error: 0.148519 Iteration 3 Error: 0.031202 Align patch 22 3 left Iteration 1 Error: 1.115750 Iteration 2 Error: 0.183667 Iteration 3 Error: 0.037919 Align patch 23 2 left Iteration 1 Error: 1.102595 Iteration 2 Error: 0.203981 Iteration 3 Error: 0.045673 Align patch 24 1 left Iteration 1 Error: 1.015475 Iteration 2 Error: 0.093676 Iteration 3 Error: 0.023101 Align patch 25 0 left Iteration 1 Error: 0.501345 Iteration 2 Error: 0.091605 Iteration 3 Error: 0.020646 3D Fitting completed. Patch alignment time: 11.47(sec) Local motion has been corrected. Process thread exits. Computational time: 21.195488 sec Total time: 28.871389 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00015hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00015hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.551666s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00015hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.368437s ........................................ >>>>>>TIME<<<<<< FFT: 0.975163s Defocus_U Defocus_V Angle CCC 11019.53 11855.47 7.84 0.044853 Final Values Defocus_U Defocus_V Angle CCC 11038.28 11855.47 9.10 0.083351 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00015hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00015hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.001e-01 CC threshold: 0.735 Mean Std: 47.27 7.79 Num Hot pixels: 191 Hot pixel threshold: 94.00 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.989807 Iteration 2 Error: 0.092408 Iteration 3 Error: 0.018085 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.23 0.00 ...... Frame ( 3) shift: -0.45 0.00 ...... Frame ( 4) shift: -0.68 0.00 ...... Frame ( 5) shift: -0.90 0.00 ...... Frame ( 6) shift: -0.96 0.08 ...... Frame ( 7) shift: -0.86 0.25 ...... Frame ( 8) shift: -0.76 0.41 ...... Frame ( 9) shift: -0.69 0.54 ...... Frame ( 10) shift: -0.64 0.64 ...... Frame ( 11) shift: -0.59 0.75 ...... Frame ( 12) shift: -0.53 0.82 ...... Frame ( 13) shift: -0.45 0.86 ...... Frame ( 14) shift: -0.37 0.89 ...... Frame ( 15) shift: -0.31 0.91 ...... Frame ( 16) shift: -0.27 0.90 ...... Frame ( 17) shift: -0.22 0.89 ...... Frame ( 18) shift: -0.17 0.89 ...... Frame ( 19) shift: -0.13 0.88 ...... Frame ( 20) shift: -0.09 0.87 ...... Frame ( 21) shift: -0.07 0.88 ...... Frame ( 22) shift: -0.08 0.91 ...... Frame ( 23) shift: -0.08 0.94 ...... Frame ( 24) shift: -0.08 0.97 ...... Frame ( 25) shift: -0.07 1.01 ...... Frame ( 26) shift: -0.06 1.04 ...... Frame ( 27) shift: -0.05 1.07 ...... Frame ( 28) shift: -0.05 1.09 ...... Frame ( 29) shift: -0.05 1.10 ...... Frame ( 30) shift: -0.05 1.10 ...... Frame ( 31) shift: -0.05 1.08 ...... Frame ( 32) shift: -0.06 1.06 ...... Frame ( 33) shift: -0.05 1.01 ...... Frame ( 34) shift: -0.05 0.92 ...... Frame ( 35) shift: -0.04 0.84 ...... Frame ( 36) shift: -0.03 0.83 ...... Frame ( 37) shift: -0.00 0.89 ...... Frame ( 38) shift: 0.02 0.95 ...... Frame ( 39) shift: 0.05 1.01 ...... Frame ( 40) shift: 0.08 1.07 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.862979 Iteration 2 Error: 0.140718 Iteration 3 Error: 0.027735 Align patch 2 23 left Iteration 1 Error: 1.333529 Iteration 2 Error: 0.173818 Iteration 3 Error: 0.072776 Iteration 4 Error: 0.029931 Align patch 3 22 left Iteration 1 Error: 0.875348 Iteration 2 Error: 0.184907 Iteration 3 Error: 0.061221 Iteration 4 Error: 0.015551 Align patch 4 21 left Iteration 1 Error: 1.295743 Iteration 2 Error: 0.166555 Iteration 3 Error: 0.059049 Iteration 4 Error: 0.018341 Align patch 5 20 left Iteration 1 Error: 0.661048 Iteration 2 Error: 0.086839 Iteration 3 Error: 0.033971 Align patch 6 19 left Iteration 1 Error: 0.896262 Iteration 2 Error: 0.137873 Iteration 3 Error: 0.038725 Align patch 7 18 left Iteration 1 Error: 1.181087 Iteration 2 Error: 0.500418 Iteration 3 Error: 0.108662 Iteration 4 Error: 0.073048 Iteration 5 Error: 0.015679 Align patch 8 17 left Iteration 1 Error: 0.823419 Iteration 2 Error: 0.255750 Iteration 3 Error: 0.065920 Iteration 4 Error: 0.032161 Align patch 9 16 left Iteration 1 Error: 1.441809 Iteration 2 Error: 0.168372 Iteration 3 Error: 0.049831 Align patch 10 15 left Iteration 1 Error: 0.705347 Iteration 2 Error: 0.239895 Iteration 3 Error: 0.038195 Align patch 11 14 left Iteration 1 Error: 1.117474 Iteration 2 Error: 0.181092 Iteration 3 Error: 0.052232 Iteration 4 Error: 0.028248 Align patch 12 13 left Iteration 1 Error: 1.137688 Iteration 2 Error: 0.244315 Iteration 3 Error: 0.057606 Iteration 4 Error: 0.027792 Align patch 13 12 left Iteration 1 Error: 0.909118 Iteration 2 Error: 0.103764 Iteration 3 Error: 0.026135 Align patch 14 11 left Iteration 1 Error: 0.723987 Iteration 2 Error: 0.128310 Iteration 3 Error: 0.033941 Align patch 15 10 left Iteration 1 Error: 0.899419 Iteration 2 Error: 0.117135 Iteration 3 Error: 0.027973 Align patch 16 9 left Iteration 1 Error: 1.158585 Iteration 2 Error: 0.166872 Iteration 3 Error: 0.042891 Align patch 17 8 left Iteration 1 Error: 1.149451 Iteration 2 Error: 0.162787 Iteration 3 Error: 0.044591 Align patch 18 7 left Iteration 1 Error: 0.728751 Iteration 2 Error: 0.084868 Iteration 3 Error: 0.020015 Align patch 19 6 left Iteration 1 Error: 0.623638 Iteration 2 Error: 0.124550 Iteration 3 Error: 0.034341 Align patch 20 5 left Iteration 1 Error: 1.371286 Iteration 2 Error: 0.146617 Iteration 3 Error: 0.027565 Align patch 21 4 left Iteration 1 Error: 1.260737 Iteration 2 Error: 0.136043 Iteration 3 Error: 0.033986 Align patch 22 3 left Iteration 1 Error: 0.945740 Iteration 2 Error: 0.133702 Iteration 3 Error: 0.035880 Align patch 23 2 left Iteration 1 Error: 1.191764 Iteration 2 Error: 0.136040 Iteration 3 Error: 0.032133 Align patch 24 1 left Iteration 1 Error: 0.836565 Iteration 2 Error: 0.175931 Iteration 3 Error: 0.033266 Align patch 25 0 left Iteration 1 Error: 1.889646 Iteration 2 Error: 0.124387 Iteration 3 Error: 0.008900 3D Fitting completed. Patch alignment time: 11.62(sec) Local motion has been corrected. Process thread exits. Computational time: 21.417543 sec Total time: 27.666904 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00015hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00015hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.550462s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00015hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.303464s ........................................ >>>>>>TIME<<<<<< FFT: 0.936940s Defocus_U Defocus_V Angle CCC 10673.88 10017.53 85.76 0.047800 Final Values Defocus_U Defocus_V Angle CCC 10675.47 10031.62 85.13 0.089053 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00016hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00016hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.990e-02 CC threshold: 0.734 Mean Std: 47.09 7.57 Num Hot pixels: 209 Hot pixel threshold: 92.48 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.569831 Iteration 2 Error: 0.417056 Iteration 3 Error: 0.194483 Iteration 4 Error: 0.088263 Iteration 5 Error: 0.036015 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.36 -0.08 ...... Frame ( 3) shift: -0.73 -0.16 ...... Frame ( 4) shift: -1.09 -0.24 ...... Frame ( 5) shift: -1.46 -0.32 ...... Frame ( 6) shift: -1.61 -0.31 ...... Frame ( 7) shift: -1.55 -0.21 ...... Frame ( 8) shift: -1.49 -0.11 ...... Frame ( 9) shift: -1.49 0.01 ...... Frame ( 10) shift: -1.54 0.16 ...... Frame ( 11) shift: -1.60 0.32 ...... Frame ( 12) shift: -1.63 0.49 ...... Frame ( 13) shift: -1.62 0.69 ...... Frame ( 14) shift: -1.61 0.88 ...... Frame ( 15) shift: -1.58 1.07 ...... Frame ( 16) shift: -1.52 1.24 ...... Frame ( 17) shift: -1.47 1.41 ...... Frame ( 18) shift: -1.45 1.59 ...... Frame ( 19) shift: -1.47 1.78 ...... Frame ( 20) shift: -1.49 1.97 ...... Frame ( 21) shift: -1.47 2.14 ...... Frame ( 22) shift: -1.41 2.27 ...... Frame ( 23) shift: -1.35 2.41 ...... Frame ( 24) shift: -1.37 2.54 ...... Frame ( 25) shift: -1.46 2.68 ...... Frame ( 26) shift: -1.56 2.82 ...... Frame ( 27) shift: -1.63 2.90 ...... Frame ( 28) shift: -1.68 2.93 ...... Frame ( 29) shift: -1.72 2.96 ...... Frame ( 30) shift: -1.75 3.02 ...... Frame ( 31) shift: -1.76 3.12 ...... Frame ( 32) shift: -1.77 3.21 ...... Frame ( 33) shift: -1.77 3.28 ...... Frame ( 34) shift: -1.75 3.32 ...... Frame ( 35) shift: -1.73 3.35 ...... Frame ( 36) shift: -1.70 3.42 ...... Frame ( 37) shift: -1.65 3.50 ...... Frame ( 38) shift: -1.60 3.59 ...... Frame ( 39) shift: -1.55 3.67 ...... Frame ( 40) shift: -1.50 3.76 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 3.553916 Iteration 2 Error: 0.781364 Iteration 3 Error: 0.222040 Iteration 4 Error: 0.180156 Iteration 5 Error: 0.107859 Align patch 1 24 left Iteration 1 Error: 2.484101 Iteration 2 Error: 0.428185 Iteration 3 Error: 0.195851 Iteration 4 Error: 0.049558 Align patch 2 23 left Iteration 1 Error: 2.496766 Iteration 2 Error: 0.308945 Iteration 3 Error: 0.228422 Iteration 4 Error: 0.060074 Iteration 5 Error: 0.049173 Align patch 3 22 left Iteration 1 Error: 1.773252 Iteration 2 Error: 0.311718 Iteration 3 Error: 0.101504 Iteration 4 Error: 0.027947 Align patch 4 21 left Iteration 1 Error: 1.004824 Iteration 2 Error: 0.341163 Iteration 3 Error: 0.118636 Iteration 4 Error: 0.073908 Iteration 5 Error: 0.025897 Align patch 5 20 left Iteration 1 Error: 0.663826 Iteration 2 Error: 0.188014 Iteration 3 Error: 0.041797 Align patch 6 19 left Iteration 1 Error: 3.126074 Iteration 2 Error: 1.035639 Iteration 3 Error: 0.385115 Iteration 4 Error: 0.330889 Iteration 5 Error: 0.176913 Align patch 6 19 left Iteration 1 Error: 2.896653 Iteration 2 Error: 0.562878 Iteration 3 Error: 0.168616 Iteration 4 Error: 0.059588 Iteration 5 Error: 0.031235 Align patch 7 18 left Iteration 1 Error: 1.204075 Iteration 2 Error: 0.745819 Iteration 3 Error: 0.216682 Iteration 4 Error: 0.167800 Iteration 5 Error: 0.083634 Align patch 7 18 left Iteration 1 Error: 2.124149 Iteration 2 Error: 0.410645 Iteration 3 Error: 0.136418 Iteration 4 Error: 0.037661 Align patch 8 17 left Iteration 1 Error: 1.800388 Iteration 2 Error: 0.438962 Iteration 3 Error: 0.235217 Iteration 4 Error: 0.112630 Iteration 5 Error: 0.061090 Align patch 8 17 left Iteration 1 Error: 1.810241 Iteration 2 Error: 0.296388 Iteration 3 Error: 0.056612 Iteration 4 Error: 0.025532 Align patch 9 16 left Iteration 1 Error: 1.373038 Iteration 2 Error: 0.274933 Iteration 3 Error: 0.060940 Iteration 4 Error: 0.019718 Align patch 10 15 left Iteration 1 Error: 0.680858 Iteration 2 Error: 0.165176 Iteration 3 Error: 0.039305 Align patch 11 14 left Iteration 1 Error: 2.891769 Iteration 2 Error: 2.331372 Iteration 3 Error: 1.030595 Iteration 4 Error: 0.524691 Iteration 5 Error: 0.321010 Align patch 11 14 left Iteration 1 Error: 2.957871 Iteration 2 Error: 0.952434 Iteration 3 Error: 0.293384 Iteration 4 Error: 0.096661 Iteration 5 Error: 0.072412 Align patch 12 13 left Iteration 1 Error: 2.272028 Iteration 2 Error: 0.783432 Iteration 3 Error: 0.656555 Iteration 4 Error: 0.581767 Iteration 5 Error: 0.586857 Align patch 12 13 left Iteration 1 Error: 2.645220 Iteration 2 Error: 0.699360 Iteration 3 Error: 0.199210 Iteration 4 Error: 0.082167 Iteration 5 Error: 0.044109 Align patch 13 12 left Iteration 1 Error: 1.435605 Iteration 2 Error: 0.473772 Iteration 3 Error: 0.226725 Iteration 4 Error: 0.120324 Iteration 5 Error: 0.040588 Align patch 14 11 left Iteration 1 Error: 0.772580 Iteration 2 Error: 0.156625 Iteration 3 Error: 0.056245 Iteration 4 Error: 0.030765 Align patch 15 10 left Iteration 1 Error: 1.018028 Iteration 2 Error: 0.215240 Iteration 3 Error: 0.075974 Iteration 4 Error: 0.033712 Align patch 16 9 left Iteration 1 Error: 4.611799 Iteration 2 Error: 3.076481 Iteration 3 Error: 2.410443 Iteration 4 Error: 0.573566 Iteration 5 Error: 0.246204 Align patch 16 9 left Iteration 1 Error: 3.581750 Iteration 2 Error: 1.200613 Iteration 3 Error: 0.519282 Iteration 4 Error: 0.209112 Iteration 5 Error: 0.076607 Align patch 17 8 left Iteration 1 Error: 2.023850 Iteration 2 Error: 1.055637 Iteration 3 Error: 0.844831 Iteration 4 Error: 0.534491 Iteration 5 Error: 0.413072 Align patch 17 8 left Iteration 1 Error: 2.808915 Iteration 2 Error: 0.747706 Iteration 3 Error: 0.289819 Iteration 4 Error: 0.116681 Iteration 5 Error: 0.065750 Align patch 18 7 left Iteration 1 Error: 1.368900 Iteration 2 Error: 0.516451 Iteration 3 Error: 0.290495 Iteration 4 Error: 0.237481 Iteration 5 Error: 0.100867 Align patch 18 7 left Iteration 1 Error: 1.401675 Iteration 2 Error: 0.320323 Iteration 3 Error: 0.117904 Iteration 4 Error: 0.044403 Align patch 19 6 left Iteration 1 Error: 0.846127 Iteration 2 Error: 0.139313 Iteration 3 Error: 0.032578 Align patch 20 5 left Iteration 1 Error: 0.984551 Iteration 2 Error: 0.096419 Iteration 3 Error: 0.021976 Align patch 21 4 left Iteration 1 Error: 4.610803 Iteration 2 Error: 1.626681 Iteration 3 Error: 0.786011 Iteration 4 Error: 0.690862 Iteration 5 Error: 0.734803 Align patch 21 4 left Iteration 1 Error: 2.622661 Iteration 2 Error: 0.757622 Iteration 3 Error: 0.519109 Iteration 4 Error: 0.266034 Iteration 5 Error: 0.158908 Align patch 22 3 left Iteration 1 Error: 1.215590 Iteration 2 Error: 0.814993 Iteration 3 Error: 0.374155 Iteration 4 Error: 0.273610 Iteration 5 Error: 0.248476 Align patch 22 3 left Iteration 1 Error: 1.971901 Iteration 2 Error: 0.625580 Iteration 3 Error: 0.287916 Iteration 4 Error: 0.131177 Iteration 5 Error: 0.124139 Align patch 23 2 left Iteration 1 Error: 1.151649 Iteration 2 Error: 0.490023 Iteration 3 Error: 0.264617 Iteration 4 Error: 0.134167 Iteration 5 Error: 0.090020 Align patch 23 2 left Iteration 1 Error: 1.035046 Iteration 2 Error: 0.232906 Iteration 3 Error: 0.081024 Iteration 4 Error: 0.019574 Align patch 24 1 left Iteration 1 Error: 0.786279 Iteration 2 Error: 0.237017 Iteration 3 Error: 0.076352 Iteration 4 Error: 0.028124 Align patch 25 0 left Iteration 1 Error: 1.661420 Iteration 2 Error: 0.255579 Iteration 3 Error: 0.041806 3D Fitting completed. Patch alignment time: 21.86(sec) Local motion has been corrected. Process thread exits. Computational time: 33.050404 sec Total time: 40.504749 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00016hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00016hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.557560s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00016hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.497190s ........................................ >>>>>>TIME<<<<<< FFT: 1.076184s Defocus_U Defocus_V Angle CCC 9263.70 10095.73 12.88 0.048299 Final Values Defocus_U Defocus_V Angle CCC 9249.63 10112.94 11.94 0.096284 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00016hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00016hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.997e-02 CC threshold: 0.734 Mean Std: 47.19 7.77 Num Hot pixels: 173 Hot pixel threshold: 93.79 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.244237 Iteration 2 Error: 0.218200 Iteration 3 Error: 0.052750 Iteration 4 Error: 0.026991 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.25 -0.04 ...... Frame ( 3) shift: -0.49 -0.09 ...... Frame ( 4) shift: -0.74 -0.13 ...... Frame ( 5) shift: -0.99 -0.17 ...... Frame ( 6) shift: -1.10 -0.11 ...... Frame ( 7) shift: -1.07 0.07 ...... Frame ( 8) shift: -1.04 0.25 ...... Frame ( 9) shift: -0.98 0.39 ...... Frame ( 10) shift: -0.90 0.51 ...... Frame ( 11) shift: -0.82 0.62 ...... Frame ( 12) shift: -0.73 0.73 ...... Frame ( 13) shift: -0.62 0.84 ...... Frame ( 14) shift: -0.52 0.94 ...... Frame ( 15) shift: -0.46 0.98 ...... Frame ( 16) shift: -0.44 0.97 ...... Frame ( 17) shift: -0.43 0.95 ...... Frame ( 18) shift: -0.41 0.97 ...... Frame ( 19) shift: -0.39 1.04 ...... Frame ( 20) shift: -0.37 1.10 ...... Frame ( 21) shift: -0.36 1.18 ...... Frame ( 22) shift: -0.37 1.26 ...... Frame ( 23) shift: -0.37 1.35 ...... Frame ( 24) shift: -0.33 1.42 ...... Frame ( 25) shift: -0.24 1.50 ...... Frame ( 26) shift: -0.15 1.57 ...... Frame ( 27) shift: -0.13 1.61 ...... Frame ( 28) shift: -0.19 1.63 ...... Frame ( 29) shift: -0.25 1.64 ...... Frame ( 30) shift: -0.29 1.65 ...... Frame ( 31) shift: -0.31 1.67 ...... Frame ( 32) shift: -0.33 1.68 ...... Frame ( 33) shift: -0.33 1.74 ...... Frame ( 34) shift: -0.29 1.87 ...... Frame ( 35) shift: -0.26 1.99 ...... Frame ( 36) shift: -0.24 2.04 ...... Frame ( 37) shift: -0.24 2.01 ...... Frame ( 38) shift: -0.24 1.98 ...... Frame ( 39) shift: -0.25 1.94 ...... Frame ( 40) shift: -0.25 1.91 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.704537 Iteration 2 Error: 0.281796 Iteration 3 Error: 0.093914 Iteration 4 Error: 0.026170 Align patch 2 23 left Iteration 1 Error: 1.437406 Iteration 2 Error: 0.162647 Iteration 3 Error: 0.055275 Iteration 4 Error: 0.020996 Align patch 3 22 left Iteration 1 Error: 2.111155 Iteration 2 Error: 0.336389 Iteration 3 Error: 0.115026 Iteration 4 Error: 0.045876 Align patch 4 21 left Iteration 1 Error: 0.552926 Iteration 2 Error: 0.122384 Iteration 3 Error: 0.051297 Iteration 4 Error: 0.029557 Align patch 5 20 left Iteration 1 Error: 0.557036 Iteration 2 Error: 0.108992 Iteration 3 Error: 0.026255 Align patch 6 19 left Iteration 1 Error: 1.143342 Iteration 2 Error: 0.185623 Iteration 3 Error: 0.055916 Iteration 4 Error: 0.028718 Align patch 7 18 left Iteration 1 Error: 0.844830 Iteration 2 Error: 0.145912 Iteration 3 Error: 0.033172 Align patch 8 17 left Iteration 1 Error: 0.860261 Iteration 2 Error: 0.216736 Iteration 3 Error: 0.040579 Align patch 9 16 left Iteration 1 Error: 0.742274 Iteration 2 Error: 0.109924 Iteration 3 Error: 0.029661 Align patch 10 15 left Iteration 1 Error: 0.766507 Iteration 2 Error: 0.164165 Iteration 3 Error: 0.072003 Iteration 4 Error: 0.031859 Align patch 11 14 left Iteration 1 Error: 1.590499 Iteration 2 Error: 0.454585 Iteration 3 Error: 0.121838 Iteration 4 Error: 0.079762 Iteration 5 Error: 0.032298 Align patch 12 13 left Iteration 1 Error: 0.953833 Iteration 2 Error: 0.307436 Iteration 3 Error: 0.078794 Iteration 4 Error: 0.031225 Align patch 13 12 left Iteration 1 Error: 1.209296 Iteration 2 Error: 0.149212 Iteration 3 Error: 0.023886 Align patch 14 11 left Iteration 1 Error: 0.735458 Iteration 2 Error: 0.130203 Iteration 3 Error: 0.049318 Align patch 15 10 left Iteration 1 Error: 0.784656 Iteration 2 Error: 0.099541 Iteration 3 Error: 0.027744 Align patch 16 9 left Iteration 1 Error: 1.039572 Iteration 2 Error: 0.142912 Iteration 3 Error: 0.029004 Align patch 17 8 left Iteration 1 Error: 1.207488 Iteration 2 Error: 0.123891 Iteration 3 Error: 0.065970 Iteration 4 Error: 0.019248 Align patch 18 7 left Iteration 1 Error: 0.815708 Iteration 2 Error: 0.108506 Iteration 3 Error: 0.028344 Align patch 19 6 left Iteration 1 Error: 0.682929 Iteration 2 Error: 0.111789 Iteration 3 Error: 0.016999 Align patch 20 5 left Iteration 1 Error: 0.749128 Iteration 2 Error: 0.095463 Iteration 3 Error: 0.021097 Align patch 21 4 left Iteration 1 Error: 1.161801 Iteration 2 Error: 0.271214 Iteration 3 Error: 0.063746 Iteration 4 Error: 0.022593 Align patch 22 3 left Iteration 1 Error: 0.907463 Iteration 2 Error: 0.200859 Iteration 3 Error: 0.052548 Iteration 4 Error: 0.024881 Align patch 23 2 left Iteration 1 Error: 0.860557 Iteration 2 Error: 0.119437 Iteration 3 Error: 0.033951 Align patch 24 1 left Iteration 1 Error: 0.798583 Iteration 2 Error: 0.115343 Iteration 3 Error: 0.026981 Align patch 25 0 left Iteration 1 Error: 0.753358 Iteration 2 Error: 0.170723 Iteration 3 Error: 0.055637 Iteration 4 Error: 0.020138 3D Fitting completed. Patch alignment time: 11.91(sec) Local motion has been corrected. Process thread exits. Computational time: 22.030376 sec Total time: 28.694580 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00016hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00016hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.646616s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00016hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.979516s ........................................ >>>>>>TIME<<<<<< FFT: 0.928418s Defocus_U Defocus_V Angle CCC 9875.00 9421.88 87.60 0.038297 Final Values Defocus_U Defocus_V Angle CCC 9887.51 9425.06 86.66 0.077407 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00016hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00016hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 46.60 7.67 Num Hot pixels: 170 Hot pixel threshold: 92.60 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.138129 Iteration 2 Error: 0.083914 Iteration 3 Error: 0.023366 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.38 -0.05 ...... Frame ( 3) shift: -0.75 -0.09 ...... Frame ( 4) shift: -1.13 -0.14 ...... Frame ( 5) shift: -1.51 -0.18 ...... Frame ( 6) shift: -1.72 -0.17 ...... Frame ( 7) shift: -1.77 -0.10 ...... Frame ( 8) shift: -1.82 -0.02 ...... Frame ( 9) shift: -1.83 0.03 ...... Frame ( 10) shift: -1.81 0.07 ...... Frame ( 11) shift: -1.79 0.10 ...... Frame ( 12) shift: -1.75 0.17 ...... Frame ( 13) shift: -1.68 0.27 ...... Frame ( 14) shift: -1.62 0.38 ...... Frame ( 15) shift: -1.59 0.46 ...... Frame ( 16) shift: -1.60 0.52 ...... Frame ( 17) shift: -1.61 0.58 ...... Frame ( 18) shift: -1.62 0.63 ...... Frame ( 19) shift: -1.63 0.68 ...... Frame ( 20) shift: -1.64 0.73 ...... Frame ( 21) shift: -1.63 0.79 ...... Frame ( 22) shift: -1.60 0.84 ...... Frame ( 23) shift: -1.57 0.90 ...... Frame ( 24) shift: -1.54 0.92 ...... Frame ( 25) shift: -1.51 0.89 ...... Frame ( 26) shift: -1.48 0.85 ...... Frame ( 27) shift: -1.50 0.84 ...... Frame ( 28) shift: -1.57 0.83 ...... Frame ( 29) shift: -1.64 0.83 ...... Frame ( 30) shift: -1.65 0.82 ...... Frame ( 31) shift: -1.59 0.80 ...... Frame ( 32) shift: -1.52 0.78 ...... Frame ( 33) shift: -1.52 0.77 ...... Frame ( 34) shift: -1.56 0.78 ...... Frame ( 35) shift: -1.61 0.78 ...... Frame ( 36) shift: -1.63 0.80 ...... Frame ( 37) shift: -1.62 0.82 ...... Frame ( 38) shift: -1.62 0.85 ...... Frame ( 39) shift: -1.61 0.88 ...... Frame ( 40) shift: -1.61 0.90 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.902448 Iteration 2 Error: 0.326743 Iteration 3 Error: 0.087800 Iteration 4 Error: 0.020573 Align patch 2 23 left Iteration 1 Error: 0.837795 Iteration 2 Error: 0.183571 Iteration 3 Error: 0.083200 Iteration 4 Error: 0.058321 Iteration 5 Error: 0.037652 Align patch 3 22 left Iteration 1 Error: 0.578097 Iteration 2 Error: 0.166129 Iteration 3 Error: 0.065012 Iteration 4 Error: 0.026537 Align patch 4 21 left Iteration 1 Error: 1.435117 Iteration 2 Error: 0.211105 Iteration 3 Error: 0.048401 Align patch 5 20 left Iteration 1 Error: 0.547611 Iteration 2 Error: 0.165782 Iteration 3 Error: 0.047982 Align patch 6 19 left Iteration 1 Error: 1.193768 Iteration 2 Error: 0.161714 Iteration 3 Error: 0.038447 Align patch 7 18 left Iteration 1 Error: 0.864801 Iteration 2 Error: 0.116692 Iteration 3 Error: 0.063126 Iteration 4 Error: 0.018029 Align patch 8 17 left Iteration 1 Error: 0.820011 Iteration 2 Error: 0.166236 Iteration 3 Error: 0.043014 Align patch 9 16 left Iteration 1 Error: 0.711134 Iteration 2 Error: 0.146713 Iteration 3 Error: 0.024904 Align patch 10 15 left Iteration 1 Error: 0.713182 Iteration 2 Error: 0.089680 Iteration 3 Error: 0.026089 Align patch 11 14 left Iteration 1 Error: 0.801931 Iteration 2 Error: 0.116610 Iteration 3 Error: 0.027857 Align patch 12 13 left Iteration 1 Error: 0.691608 Iteration 2 Error: 0.128438 Iteration 3 Error: 0.041869 Align patch 13 12 left Iteration 1 Error: 0.676144 Iteration 2 Error: 0.179080 Iteration 3 Error: 0.046898 Align patch 14 11 left Iteration 1 Error: 0.563924 Iteration 2 Error: 0.128976 Iteration 3 Error: 0.027715 Align patch 15 10 left Iteration 1 Error: 0.621964 Iteration 2 Error: 0.090193 Iteration 3 Error: 0.017543 Align patch 16 9 left Iteration 1 Error: 1.098196 Iteration 2 Error: 0.132770 Iteration 3 Error: 0.035319 Align patch 17 8 left Iteration 1 Error: 0.781440 Iteration 2 Error: 0.158135 Iteration 3 Error: 0.050508 Iteration 4 Error: 0.022047 Align patch 18 7 left Iteration 1 Error: 0.900781 Iteration 2 Error: 0.094717 Iteration 3 Error: 0.018004 Align patch 19 6 left Iteration 1 Error: 0.547854 Iteration 2 Error: 0.071484 Iteration 3 Error: 0.018792 Align patch 20 5 left Iteration 1 Error: 0.306694 Iteration 2 Error: 0.041046 Align patch 21 4 left Iteration 1 Error: 0.831453 Iteration 2 Error: 0.092265 Iteration 3 Error: 0.016851 Align patch 22 3 left Iteration 1 Error: 0.943318 Iteration 2 Error: 0.176048 Iteration 3 Error: 0.022062 Align patch 23 2 left Iteration 1 Error: 0.943127 Iteration 2 Error: 0.161410 Iteration 3 Error: 0.034066 Align patch 24 1 left Iteration 1 Error: 0.585434 Iteration 2 Error: 0.103068 Iteration 3 Error: 0.040030 Align patch 25 0 left Iteration 1 Error: 0.535456 Iteration 2 Error: 0.074900 Iteration 3 Error: 0.016791 3D Fitting completed. Patch alignment time: 11.29(sec) Local motion has been corrected. Process thread exits. Computational time: 22.006844 sec Total time: 29.442139 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00016hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00016hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.615246s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00016hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.638511s ........................................ >>>>>>TIME<<<<<< FFT: 0.911121s Defocus_U Defocus_V Angle CCC 10695.32 11468.76 5.14 0.051258 Final Values Defocus_U Defocus_V Angle CCC 10696.89 11476.58 4.83 0.095895 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00016hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00016hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 9.998e-02 CC threshold: 0.734 Mean Std: 47.12 7.74 Num Hot pixels: 177 Hot pixel threshold: 93.54 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.931529 Iteration 2 Error: 0.092756 Iteration 3 Error: 0.018980 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.34 -0.00 ...... Frame ( 3) shift: -0.68 -0.01 ...... Frame ( 4) shift: -1.02 -0.01 ...... Frame ( 5) shift: -1.36 -0.01 ...... Frame ( 6) shift: -1.51 0.04 ...... Frame ( 7) shift: -1.48 0.13 ...... Frame ( 8) shift: -1.44 0.23 ...... Frame ( 9) shift: -1.41 0.36 ...... Frame ( 10) shift: -1.37 0.52 ...... Frame ( 11) shift: -1.33 0.68 ...... Frame ( 12) shift: -1.28 0.77 ...... Frame ( 13) shift: -1.22 0.80 ...... Frame ( 14) shift: -1.15 0.82 ...... Frame ( 15) shift: -1.11 0.85 ...... Frame ( 16) shift: -1.10 0.87 ...... Frame ( 17) shift: -1.08 0.90 ...... Frame ( 18) shift: -1.09 0.90 ...... Frame ( 19) shift: -1.13 0.88 ...... Frame ( 20) shift: -1.16 0.86 ...... Frame ( 21) shift: -1.18 0.88 ...... Frame ( 22) shift: -1.19 0.95 ...... Frame ( 23) shift: -1.20 1.02 ...... Frame ( 24) shift: -1.16 1.05 ...... Frame ( 25) shift: -1.06 1.05 ...... Frame ( 26) shift: -0.97 1.05 ...... Frame ( 27) shift: -0.94 1.06 ...... Frame ( 28) shift: -0.98 1.08 ...... Frame ( 29) shift: -1.02 1.10 ...... Frame ( 30) shift: -1.02 1.10 ...... Frame ( 31) shift: -0.98 1.07 ...... Frame ( 32) shift: -0.93 1.05 ...... Frame ( 33) shift: -0.91 1.03 ...... Frame ( 34) shift: -0.89 1.02 ...... Frame ( 35) shift: -0.87 1.01 ...... Frame ( 36) shift: -0.86 1.01 ...... Frame ( 37) shift: -0.86 1.00 ...... Frame ( 38) shift: -0.86 1.00 ...... Frame ( 39) shift: -0.85 0.99 ...... Frame ( 40) shift: -0.85 0.99 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.453444 Iteration 2 Error: 0.315325 Iteration 3 Error: 0.117230 Iteration 4 Error: 0.041597 Align patch 2 23 left Iteration 1 Error: 2.592555 Iteration 2 Error: 0.265711 Iteration 3 Error: 0.164809 Iteration 4 Error: 0.033020 Align patch 3 22 left Iteration 1 Error: 0.814220 Iteration 2 Error: 0.118501 Iteration 3 Error: 0.052561 Iteration 4 Error: 0.022153 Align patch 4 21 left Iteration 1 Error: 0.827129 Iteration 2 Error: 0.167186 Iteration 3 Error: 0.042340 Align patch 5 20 left Iteration 1 Error: 0.996127 Iteration 2 Error: 0.156159 Iteration 3 Error: 0.051816 Iteration 4 Error: 0.020145 Align patch 6 19 left Iteration 1 Error: 0.872470 Iteration 2 Error: 0.107875 Iteration 3 Error: 0.040036 Align patch 7 18 left Iteration 1 Error: 1.293343 Iteration 2 Error: 0.232762 Iteration 3 Error: 0.085030 Iteration 4 Error: 0.029713 Align patch 8 17 left Iteration 1 Error: 1.401957 Iteration 2 Error: 0.249284 Iteration 3 Error: 0.045225 Align patch 9 16 left Iteration 1 Error: 0.761168 Iteration 2 Error: 0.129098 Iteration 3 Error: 0.029187 Align patch 10 15 left Iteration 1 Error: 0.614528 Iteration 2 Error: 0.100566 Iteration 3 Error: 0.030965 Align patch 11 14 left Iteration 1 Error: 0.668348 Iteration 2 Error: 0.156846 Iteration 3 Error: 0.035368 Align patch 12 13 left Iteration 1 Error: 0.582668 Iteration 2 Error: 0.076329 Iteration 3 Error: 0.020833 Align patch 13 12 left Iteration 1 Error: 0.554982 Iteration 2 Error: 0.098587 Iteration 3 Error: 0.034518 Align patch 14 11 left Iteration 1 Error: 0.818122 Iteration 2 Error: 0.145584 Iteration 3 Error: 0.035703 Align patch 15 10 left Iteration 1 Error: 0.715136 Iteration 2 Error: 0.202479 Iteration 3 Error: 0.049199 Align patch 16 9 left Iteration 1 Error: 1.244045 Iteration 2 Error: 0.145507 Iteration 3 Error: 0.033257 Align patch 17 8 left Iteration 1 Error: 1.004696 Iteration 2 Error: 0.217476 Iteration 3 Error: 0.049077 Align patch 18 7 left Iteration 1 Error: 1.030080 Iteration 2 Error: 0.136333 Iteration 3 Error: 0.023789 Align patch 19 6 left Iteration 1 Error: 0.862013 Iteration 2 Error: 0.112514 Iteration 3 Error: 0.029273 Align patch 20 5 left Iteration 1 Error: 0.689186 Iteration 2 Error: 0.126748 Iteration 3 Error: 0.039288 Align patch 21 4 left Iteration 1 Error: 1.145683 Iteration 2 Error: 0.276358 Iteration 3 Error: 0.057294 Iteration 4 Error: 0.015598 Align patch 22 3 left Iteration 1 Error: 1.083580 Iteration 2 Error: 0.144830 Iteration 3 Error: 0.039742 Align patch 23 2 left Iteration 1 Error: 1.363349 Iteration 2 Error: 0.171081 Iteration 3 Error: 0.042819 Align patch 24 1 left Iteration 1 Error: 0.828968 Iteration 2 Error: 0.170815 Iteration 3 Error: 0.041772 Align patch 25 0 left Iteration 1 Error: 0.492331 Iteration 2 Error: 0.058413 Iteration 3 Error: 0.014999 3D Fitting completed. Patch alignment time: 11.33(sec) Local motion has been corrected. Process thread exits. Computational time: 23.782015 sec Total time: 32.191532 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00016hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00016hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.604017s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00016hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.352220s ........................................ >>>>>>TIME<<<<<< FFT: 1.029003s Defocus_U Defocus_V Angle CCC 10871.12 10218.73 82.77 0.048453 Final Values Defocus_U Defocus_V Angle CCC 10886.74 10240.63 83.09 0.090095 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00017hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00017hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.997e-02 CC threshold: 0.734 Mean Std: 45.90 7.76 Num Hot pixels: 174 Hot pixel threshold: 92.46 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.555607 Iteration 2 Error: 0.135507 Iteration 3 Error: 0.038556 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.35 0.12 ...... Frame ( 3) shift: -0.69 0.25 ...... Frame ( 4) shift: -1.04 0.37 ...... Frame ( 5) shift: -1.38 0.49 ...... Frame ( 6) shift: -1.54 0.62 ...... Frame ( 7) shift: -1.53 0.75 ...... Frame ( 8) shift: -1.51 0.88 ...... Frame ( 9) shift: -1.49 0.99 ...... Frame ( 10) shift: -1.45 1.09 ...... Frame ( 11) shift: -1.41 1.19 ...... Frame ( 12) shift: -1.35 1.31 ...... Frame ( 13) shift: -1.27 1.44 ...... Frame ( 14) shift: -1.18 1.57 ...... Frame ( 15) shift: -1.15 1.68 ...... Frame ( 16) shift: -1.16 1.77 ...... Frame ( 17) shift: -1.18 1.86 ...... Frame ( 18) shift: -1.19 1.91 ...... Frame ( 19) shift: -1.20 1.91 ...... Frame ( 20) shift: -1.22 1.92 ...... Frame ( 21) shift: -1.21 1.94 ...... Frame ( 22) shift: -1.18 1.96 ...... Frame ( 23) shift: -1.16 1.99 ...... Frame ( 24) shift: -1.12 2.01 ...... Frame ( 25) shift: -1.08 2.01 ...... Frame ( 26) shift: -1.04 2.01 ...... Frame ( 27) shift: -1.05 2.04 ...... Frame ( 28) shift: -1.10 2.10 ...... Frame ( 29) shift: -1.15 2.16 ...... Frame ( 30) shift: -1.16 2.16 ...... Frame ( 31) shift: -1.15 2.11 ...... Frame ( 32) shift: -1.14 2.05 ...... Frame ( 33) shift: -1.13 2.04 ...... Frame ( 34) shift: -1.14 2.07 ...... Frame ( 35) shift: -1.14 2.09 ...... Frame ( 36) shift: -1.15 2.11 ...... Frame ( 37) shift: -1.16 2.13 ...... Frame ( 38) shift: -1.17 2.14 ...... Frame ( 39) shift: -1.19 2.15 ...... Frame ( 40) shift: -1.20 2.16 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.142156 Iteration 2 Error: 0.323022 Iteration 3 Error: 0.059943 Iteration 4 Error: 0.022742 Align patch 2 23 left Iteration 1 Error: 0.909471 Iteration 2 Error: 0.172773 Iteration 3 Error: 0.096938 Iteration 4 Error: 0.038530 Align patch 3 22 left Iteration 1 Error: 0.868397 Iteration 2 Error: 0.206934 Iteration 3 Error: 0.058681 Iteration 4 Error: 0.020601 Align patch 4 21 left Iteration 1 Error: 0.652412 Iteration 2 Error: 0.177728 Iteration 3 Error: 0.045435 Align patch 5 20 left Iteration 1 Error: 0.936858 Iteration 2 Error: 0.127354 Iteration 3 Error: 0.022597 Align patch 6 19 left Iteration 1 Error: 0.856729 Iteration 2 Error: 0.112231 Iteration 3 Error: 0.033035 Align patch 7 18 left Iteration 1 Error: 1.689618 Iteration 2 Error: 0.405035 Iteration 3 Error: 0.091377 Iteration 4 Error: 0.043628 Align patch 8 17 left Iteration 1 Error: 1.082649 Iteration 2 Error: 0.261804 Iteration 3 Error: 0.062897 Iteration 4 Error: 0.020602 Align patch 9 16 left Iteration 1 Error: 0.603044 Iteration 2 Error: 0.106459 Iteration 3 Error: 0.028160 Align patch 10 15 left Iteration 1 Error: 0.503878 Iteration 2 Error: 0.084980 Iteration 3 Error: 0.027121 Align patch 11 14 left Iteration 1 Error: 0.798969 Iteration 2 Error: 0.128624 Iteration 3 Error: 0.026013 Align patch 12 13 left Iteration 1 Error: 0.686360 Iteration 2 Error: 0.179720 Iteration 3 Error: 0.026386 Align patch 13 12 left Iteration 1 Error: 0.778254 Iteration 2 Error: 0.146555 Iteration 3 Error: 0.060543 Iteration 4 Error: 0.020806 Align patch 14 11 left Iteration 1 Error: 1.034775 Iteration 2 Error: 0.108480 Iteration 3 Error: 0.029896 Align patch 15 10 left Iteration 1 Error: 0.752156 Iteration 2 Error: 0.067746 Iteration 3 Error: 0.016221 Align patch 16 9 left Iteration 1 Error: 0.739571 Iteration 2 Error: 0.154594 Iteration 3 Error: 0.036332 Align patch 17 8 left Iteration 1 Error: 0.826143 Iteration 2 Error: 0.179129 Iteration 3 Error: 0.036302 Align patch 18 7 left Iteration 1 Error: 0.789828 Iteration 2 Error: 0.185690 Iteration 3 Error: 0.037850 Align patch 19 6 left Iteration 1 Error: 0.668010 Iteration 2 Error: 0.091108 Iteration 3 Error: 0.031945 Align patch 20 5 left Iteration 1 Error: 0.746071 Iteration 2 Error: 0.106628 Iteration 3 Error: 0.033584 Align patch 21 4 left Iteration 1 Error: 0.746481 Iteration 2 Error: 0.123766 Iteration 3 Error: 0.029796 Align patch 22 3 left Iteration 1 Error: 0.944228 Iteration 2 Error: 0.161697 Iteration 3 Error: 0.045781 Align patch 23 2 left Iteration 1 Error: 0.863793 Iteration 2 Error: 0.120083 Iteration 3 Error: 0.030210 Align patch 24 1 left Iteration 1 Error: 0.718454 Iteration 2 Error: 0.109232 Iteration 3 Error: 0.029245 Align patch 25 0 left Iteration 1 Error: 1.067548 Iteration 2 Error: 0.120831 Iteration 3 Error: 0.025268 3D Fitting completed. Patch alignment time: 11.84(sec) Local motion has been corrected. Process thread exits. Computational time: 23.352673 sec Total time: 30.806917 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00017hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00017hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.602691s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00017hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.002532s ........................................ >>>>>>TIME<<<<<< FFT: 1.033454s Defocus_U Defocus_V Angle CCC 9826.18 10673.84 12.82 0.044844 Final Values Defocus_U Defocus_V Angle CCC 9827.74 10681.65 13.13 0.084817 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00017hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00017hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.986e-02 CC threshold: 0.733 Mean Std: 44.88 7.61 Num Hot pixels: 168 Hot pixel threshold: 90.54 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.904937 Iteration 2 Error: 0.611779 Iteration 3 Error: 0.282353 Iteration 4 Error: 0.156903 Iteration 5 Error: 0.071195 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.25 -0.01 ...... Frame ( 3) shift: -0.50 -0.02 ...... Frame ( 4) shift: -0.76 -0.03 ...... Frame ( 5) shift: -1.01 -0.05 ...... Frame ( 6) shift: -1.13 0.07 ...... Frame ( 7) shift: -1.14 0.32 ...... Frame ( 8) shift: -1.14 0.57 ...... Frame ( 9) shift: -1.14 0.81 ...... Frame ( 10) shift: -1.16 1.06 ...... Frame ( 11) shift: -1.18 1.30 ...... Frame ( 12) shift: -1.18 1.53 ...... Frame ( 13) shift: -1.17 1.74 ...... Frame ( 14) shift: -1.17 1.95 ...... Frame ( 15) shift: -1.16 2.15 ...... Frame ( 16) shift: -1.16 2.32 ...... Frame ( 17) shift: -1.16 2.49 ...... Frame ( 18) shift: -1.14 2.66 ...... Frame ( 19) shift: -1.11 2.81 ...... Frame ( 20) shift: -1.08 2.96 ...... Frame ( 21) shift: -1.07 3.10 ...... Frame ( 22) shift: -1.08 3.24 ...... Frame ( 23) shift: -1.09 3.38 ...... Frame ( 24) shift: -1.09 3.52 ...... Frame ( 25) shift: -1.07 3.64 ...... Frame ( 26) shift: -1.06 3.77 ...... Frame ( 27) shift: -1.08 3.85 ...... Frame ( 28) shift: -1.16 3.89 ...... Frame ( 29) shift: -1.23 3.93 ...... Frame ( 30) shift: -1.27 4.02 ...... Frame ( 31) shift: -1.28 4.16 ...... Frame ( 32) shift: -1.30 4.31 ...... Frame ( 33) shift: -1.26 4.34 ...... Frame ( 34) shift: -1.17 4.26 ...... Frame ( 35) shift: -1.08 4.19 ...... Frame ( 36) shift: -1.01 4.17 ...... Frame ( 37) shift: -0.98 4.19 ...... Frame ( 38) shift: -0.94 4.22 ...... Frame ( 39) shift: -0.90 4.25 ...... Frame ( 40) shift: -0.86 4.28 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 4.705312 Iteration 2 Error: 0.742064 Iteration 3 Error: 0.323225 Iteration 4 Error: 0.084815 Iteration 5 Error: 0.046839 Align patch 2 23 left Iteration 1 Error: 3.769530 Iteration 2 Error: 0.734275 Iteration 3 Error: 0.310996 Iteration 4 Error: 0.123058 Iteration 5 Error: 0.043485 Align patch 3 22 left Iteration 1 Error: 0.998484 Iteration 2 Error: 0.208738 Iteration 3 Error: 0.086921 Iteration 4 Error: 0.041785 Align patch 4 21 left Iteration 1 Error: 0.716325 Iteration 2 Error: 0.150842 Iteration 3 Error: 0.045131 Align patch 5 20 left Iteration 1 Error: 1.915097 Iteration 2 Error: 0.266748 Iteration 3 Error: 0.064772 Iteration 4 Error: 0.016931 Align patch 6 19 left Iteration 1 Error: 5.773241 Iteration 2 Error: 0.968082 Iteration 3 Error: 0.364023 Iteration 4 Error: 0.202920 Iteration 5 Error: 0.085988 Align patch 6 19 left Iteration 1 Error: 3.544788 Iteration 2 Error: 0.561216 Iteration 3 Error: 0.158137 Iteration 4 Error: 0.056624 Iteration 5 Error: 0.024742 Align patch 7 18 left Iteration 1 Error: 3.414770 Iteration 2 Error: 1.527521 Iteration 3 Error: 0.997977 Iteration 4 Error: 0.418837 Iteration 5 Error: 0.208269 Align patch 7 18 left Iteration 1 Error: 2.772269 Iteration 2 Error: 0.519429 Iteration 3 Error: 0.163917 Iteration 4 Error: 0.079953 Iteration 5 Error: 0.026298 Align patch 8 17 left Iteration 1 Error: 1.712148 Iteration 2 Error: 0.271391 Iteration 3 Error: 0.134960 Iteration 4 Error: 0.048119 Align patch 9 16 left Iteration 1 Error: 1.166967 Iteration 2 Error: 0.410741 Iteration 3 Error: 0.087919 Iteration 4 Error: 0.038908 Align patch 10 15 left Iteration 1 Error: 1.264387 Iteration 2 Error: 0.364781 Iteration 3 Error: 0.074706 Iteration 4 Error: 0.035714 Align patch 11 14 left Iteration 1 Error: 2.998718 Iteration 2 Error: 2.773903 Iteration 3 Error: 0.992514 Iteration 4 Error: 1.280699 Iteration 5 Error: 0.828211 Align patch 11 14 left Iteration 1 Error: 2.970647 Iteration 2 Error: 1.022801 Iteration 3 Error: 0.239330 Iteration 4 Error: 0.066618 Iteration 5 Error: 0.021299 Align patch 12 13 left Iteration 1 Error: 2.002063 Iteration 2 Error: 0.857242 Iteration 3 Error: 0.446268 Iteration 4 Error: 0.311041 Iteration 5 Error: 0.239259 Align patch 12 13 left Iteration 1 Error: 1.945697 Iteration 2 Error: 0.547693 Iteration 3 Error: 0.182113 Iteration 4 Error: 0.059345 Iteration 5 Error: 0.038337 Align patch 13 12 left Iteration 1 Error: 1.203063 Iteration 2 Error: 0.559997 Iteration 3 Error: 0.273492 Iteration 4 Error: 0.214209 Iteration 5 Error: 0.141187 Align patch 13 12 left Iteration 1 Error: 1.110781 Iteration 2 Error: 0.211950 Iteration 3 Error: 0.066023 Iteration 4 Error: 0.025480 Align patch 14 11 left Iteration 1 Error: 1.079989 Iteration 2 Error: 0.287740 Iteration 3 Error: 0.131581 Iteration 4 Error: 0.044149 Align patch 15 10 left Iteration 1 Error: 1.060388 Iteration 2 Error: 0.286353 Iteration 3 Error: 0.110310 Iteration 4 Error: 0.049504 Align patch 16 9 left Iteration 1 Error: 5.930925 Iteration 2 Error: 3.485311 Iteration 3 Error: 0.878777 Iteration 4 Error: 0.392600 Iteration 5 Error: 0.197536 Align patch 16 9 left Iteration 1 Error: 3.980796 Iteration 2 Error: 1.299082 Iteration 3 Error: 0.444809 Iteration 4 Error: 0.130891 Iteration 5 Error: 0.082111 Align patch 17 8 left Iteration 1 Error: 3.421092 Iteration 2 Error: 1.361823 Iteration 3 Error: 0.391752 Iteration 4 Error: 0.242478 Iteration 5 Error: 0.109971 Align patch 17 8 left Iteration 1 Error: 2.793147 Iteration 2 Error: 0.875365 Iteration 3 Error: 0.362242 Iteration 4 Error: 0.093284 Iteration 5 Error: 0.066560 Align patch 18 7 left Iteration 1 Error: 1.574141 Iteration 2 Error: 0.543734 Iteration 3 Error: 0.197211 Iteration 4 Error: 0.109984 Iteration 5 Error: 0.057929 Align patch 18 7 left Iteration 1 Error: 1.837688 Iteration 2 Error: 0.374534 Iteration 3 Error: 0.083562 Iteration 4 Error: 0.028369 Align patch 19 6 left Iteration 1 Error: 0.741577 Iteration 2 Error: 0.215805 Iteration 3 Error: 0.079839 Iteration 4 Error: 0.040610 Align patch 20 5 left Iteration 1 Error: 0.634364 Iteration 2 Error: 0.190608 Iteration 3 Error: 0.047123 Align patch 21 4 left Iteration 1 Error: 7.536421 Iteration 2 Error: 8.615992 Iteration 3 Error: 3.467396 Iteration 4 Error: 0.717343 Iteration 5 Error: 0.602155 Align patch 21 4 left Iteration 1 Error: 3.990602 Iteration 2 Error: 2.025271 Iteration 3 Error: 0.586902 Iteration 4 Error: 0.198827 Iteration 5 Error: 0.073535 Align patch 22 3 left Iteration 1 Error: 4.902975 Iteration 2 Error: 3.989123 Iteration 3 Error: 1.122942 Iteration 4 Error: 0.983006 Iteration 5 Error: 0.423119 Align patch 22 3 left Iteration 1 Error: 3.233060 Iteration 2 Error: 1.204393 Iteration 3 Error: 0.408350 Iteration 4 Error: 0.208988 Iteration 5 Error: 0.111866 Align patch 23 2 left Iteration 1 Error: 2.538075 Iteration 2 Error: 0.839206 Iteration 3 Error: 0.527595 Iteration 4 Error: 0.285137 Iteration 5 Error: 0.172322 Align patch 23 2 left Iteration 1 Error: 2.200331 Iteration 2 Error: 0.498475 Iteration 3 Error: 0.130723 Iteration 4 Error: 0.048229 Align patch 24 1 left Iteration 1 Error: 1.000871 Iteration 2 Error: 0.283865 Iteration 3 Error: 0.117934 Iteration 4 Error: 0.057502 Iteration 5 Error: 0.038995 Align patch 25 0 left Iteration 1 Error: 0.915996 Iteration 2 Error: 0.160114 Iteration 3 Error: 0.063368 Iteration 4 Error: 0.018400 3D Fitting completed. Patch alignment time: 20.73(sec) Local motion has been corrected. Process thread exits. Computational time: 33.046207 sec Total time: 42.766552 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00017hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00017hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.585450s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00017hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.286518s ........................................ >>>>>>TIME<<<<<< FFT: 0.940205s Defocus_U Defocus_V Angle CCC 11611.31 12138.69 5.23 0.047651 Final Values Defocus_U Defocus_V Angle CCC 11620.67 12154.33 4.91 0.089478 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00017hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00017hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.999e-02 CC threshold: 0.734 Mean Std: 47.04 7.64 Num Hot pixels: 186 Hot pixel threshold: 92.90 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.860659 Iteration 2 Error: 0.145829 Iteration 3 Error: 0.030083 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.39 0.05 ...... Frame ( 3) shift: -0.79 0.11 ...... Frame ( 4) shift: -1.18 0.16 ...... Frame ( 5) shift: -1.57 0.22 ...... Frame ( 6) shift: -1.75 0.31 ...... Frame ( 7) shift: -1.72 0.44 ...... Frame ( 8) shift: -1.69 0.58 ...... Frame ( 9) shift: -1.65 0.66 ...... Frame ( 10) shift: -1.60 0.69 ...... Frame ( 11) shift: -1.56 0.72 ...... Frame ( 12) shift: -1.52 0.76 ...... Frame ( 13) shift: -1.50 0.81 ...... Frame ( 14) shift: -1.47 0.86 ...... Frame ( 15) shift: -1.45 0.89 ...... Frame ( 16) shift: -1.44 0.89 ...... Frame ( 17) shift: -1.43 0.90 ...... Frame ( 18) shift: -1.38 0.89 ...... Frame ( 19) shift: -1.30 0.87 ...... Frame ( 20) shift: -1.22 0.85 ...... Frame ( 21) shift: -1.16 0.83 ...... Frame ( 22) shift: -1.13 0.80 ...... Frame ( 23) shift: -1.10 0.77 ...... Frame ( 24) shift: -1.06 0.79 ...... Frame ( 25) shift: -1.00 0.84 ...... Frame ( 26) shift: -0.94 0.90 ...... Frame ( 27) shift: -0.88 0.95 ...... Frame ( 28) shift: -0.83 1.00 ...... Frame ( 29) shift: -0.78 1.04 ...... Frame ( 30) shift: -0.74 1.06 ...... Frame ( 31) shift: -0.72 1.04 ...... Frame ( 32) shift: -0.69 1.03 ...... Frame ( 33) shift: -0.68 1.04 ...... Frame ( 34) shift: -0.68 1.08 ...... Frame ( 35) shift: -0.67 1.12 ...... Frame ( 36) shift: -0.65 1.14 ...... Frame ( 37) shift: -0.62 1.13 ...... Frame ( 38) shift: -0.59 1.13 ...... Frame ( 39) shift: -0.56 1.12 ...... Frame ( 40) shift: -0.53 1.11 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.198491 Iteration 2 Error: 0.134506 Iteration 3 Error: 0.038449 Align patch 2 23 left Iteration 1 Error: 1.176044 Iteration 2 Error: 0.193612 Iteration 3 Error: 0.033916 Align patch 3 22 left Iteration 1 Error: 0.608625 Iteration 2 Error: 0.142131 Iteration 3 Error: 0.043449 Align patch 4 21 left Iteration 1 Error: 1.027687 Iteration 2 Error: 0.130326 Iteration 3 Error: 0.029707 Align patch 5 20 left Iteration 1 Error: 0.700370 Iteration 2 Error: 0.113839 Iteration 3 Error: 0.022594 Align patch 6 19 left Iteration 1 Error: 1.788294 Iteration 2 Error: 0.232406 Iteration 3 Error: 0.098359 Iteration 4 Error: 0.045517 Align patch 7 18 left Iteration 1 Error: 0.962978 Iteration 2 Error: 0.212559 Iteration 3 Error: 0.065009 Iteration 4 Error: 0.029202 Align patch 8 17 left Iteration 1 Error: 0.518386 Iteration 2 Error: 0.100696 Iteration 3 Error: 0.025194 Align patch 9 16 left Iteration 1 Error: 0.909899 Iteration 2 Error: 0.191598 Iteration 3 Error: 0.058344 Iteration 4 Error: 0.020320 Align patch 10 15 left Iteration 1 Error: 0.897442 Iteration 2 Error: 0.184481 Iteration 3 Error: 0.059060 Iteration 4 Error: 0.012599 Align patch 11 14 left Iteration 1 Error: 0.977709 Iteration 2 Error: 0.202674 Iteration 3 Error: 0.071669 Iteration 4 Error: 0.031801 Align patch 12 13 left Iteration 1 Error: 0.947081 Iteration 2 Error: 0.108388 Iteration 3 Error: 0.040414 Align patch 13 12 left Iteration 1 Error: 1.237083 Iteration 2 Error: 0.284800 Iteration 3 Error: 0.080496 Iteration 4 Error: 0.035129 Align patch 14 11 left Iteration 1 Error: 1.276472 Iteration 2 Error: 0.153365 Iteration 3 Error: 0.035499 Align patch 15 10 left Iteration 1 Error: 0.829484 Iteration 2 Error: 0.128491 Iteration 3 Error: 0.034696 Align patch 16 9 left Iteration 1 Error: 0.812613 Iteration 2 Error: 0.143745 Iteration 3 Error: 0.050201 Iteration 4 Error: 0.014408 Align patch 17 8 left Iteration 1 Error: 0.665097 Iteration 2 Error: 0.088370 Iteration 3 Error: 0.030449 Align patch 18 7 left Iteration 1 Error: 0.680550 Iteration 2 Error: 0.082665 Iteration 3 Error: 0.023011 Align patch 19 6 left Iteration 1 Error: 0.605844 Iteration 2 Error: 0.090380 Iteration 3 Error: 0.020545 Align patch 20 5 left Iteration 1 Error: 1.085993 Iteration 2 Error: 0.097478 Iteration 3 Error: 0.011925 Align patch 21 4 left Iteration 1 Error: 0.837066 Iteration 2 Error: 0.140974 Iteration 3 Error: 0.036397 Align patch 22 3 left Iteration 1 Error: 0.974995 Iteration 2 Error: 0.148493 Iteration 3 Error: 0.037547 Align patch 23 2 left Iteration 1 Error: 1.324056 Iteration 2 Error: 0.102694 Iteration 3 Error: 0.024816 Align patch 24 1 left Iteration 1 Error: 0.873277 Iteration 2 Error: 0.128723 Iteration 3 Error: 0.030443 Align patch 25 0 left Iteration 1 Error: 0.623633 Iteration 2 Error: 0.094008 Iteration 3 Error: 0.015844 3D Fitting completed. Patch alignment time: 12.58(sec) Local motion has been corrected. Process thread exits. Computational time: 24.008461 sec Total time: 32.283180 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00017hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00017hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.563325s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00017hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.658799s ........................................ >>>>>>TIME<<<<<< FFT: 1.101452s Defocus_U Defocus_V Angle CCC 13576.17 14435.55 5.53 0.057388 Final Values Defocus_U Defocus_V Angle CCC 13582.42 14429.30 5.53 0.097948 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00017hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00017hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.001e-01 CC threshold: 0.735 Mean Std: 44.89 7.52 Num Hot pixels: 196 Hot pixel threshold: 90.00 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.028067 Iteration 2 Error: 0.113166 Iteration 3 Error: 0.018599 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.20 0.07 ...... Frame ( 3) shift: -0.41 0.14 ...... Frame ( 4) shift: -0.61 0.22 ...... Frame ( 5) shift: -0.82 0.29 ...... Frame ( 6) shift: -0.91 0.35 ...... Frame ( 7) shift: -0.90 0.39 ...... Frame ( 8) shift: -0.88 0.43 ...... Frame ( 9) shift: -0.89 0.51 ...... Frame ( 10) shift: -0.94 0.63 ...... Frame ( 11) shift: -0.98 0.75 ...... Frame ( 12) shift: -1.00 0.85 ...... Frame ( 13) shift: -1.00 0.94 ...... Frame ( 14) shift: -0.99 1.02 ...... Frame ( 15) shift: -1.00 1.11 ...... Frame ( 16) shift: -1.02 1.20 ...... Frame ( 17) shift: -1.04 1.29 ...... Frame ( 18) shift: -1.05 1.32 ...... Frame ( 19) shift: -1.06 1.30 ...... Frame ( 20) shift: -1.06 1.27 ...... Frame ( 21) shift: -1.05 1.26 ...... Frame ( 22) shift: -1.02 1.28 ...... Frame ( 23) shift: -1.00 1.30 ...... Frame ( 24) shift: -1.00 1.29 ...... Frame ( 25) shift: -1.03 1.27 ...... Frame ( 26) shift: -1.05 1.24 ...... Frame ( 27) shift: -1.08 1.24 ...... Frame ( 28) shift: -1.12 1.25 ...... Frame ( 29) shift: -1.16 1.27 ...... Frame ( 30) shift: -1.19 1.28 ...... Frame ( 31) shift: -1.22 1.30 ...... Frame ( 32) shift: -1.25 1.32 ...... Frame ( 33) shift: -1.24 1.34 ...... Frame ( 34) shift: -1.20 1.37 ...... Frame ( 35) shift: -1.16 1.40 ...... Frame ( 36) shift: -1.15 1.41 ...... Frame ( 37) shift: -1.15 1.39 ...... Frame ( 38) shift: -1.15 1.38 ...... Frame ( 39) shift: -1.16 1.36 ...... Frame ( 40) shift: -1.16 1.35 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.254554 Iteration 2 Error: 0.247716 Iteration 3 Error: 0.049262 Align patch 2 23 left Iteration 1 Error: 3.173098 Iteration 2 Error: 0.298842 Iteration 3 Error: 0.093301 Iteration 4 Error: 0.029473 Align patch 3 22 left Iteration 1 Error: 0.750372 Iteration 2 Error: 0.173601 Iteration 3 Error: 0.116884 Iteration 4 Error: 0.040390 Align patch 4 21 left Iteration 1 Error: 0.767019 Iteration 2 Error: 0.113158 Iteration 3 Error: 0.027231 Align patch 5 20 left Iteration 1 Error: 0.765807 Iteration 2 Error: 0.196666 Iteration 3 Error: 0.028781 Align patch 6 19 left Iteration 1 Error: 1.227469 Iteration 2 Error: 0.236043 Iteration 3 Error: 0.067209 Iteration 4 Error: 0.041020 Align patch 7 18 left Iteration 1 Error: 1.547895 Iteration 2 Error: 0.180190 Iteration 3 Error: 0.050915 Iteration 4 Error: 0.036038 Align patch 8 17 left Iteration 1 Error: 0.613433 Iteration 2 Error: 0.177078 Iteration 3 Error: 0.084787 Iteration 4 Error: 0.045240 Align patch 9 16 left Iteration 1 Error: 1.078513 Iteration 2 Error: 0.143040 Iteration 3 Error: 0.034665 Align patch 10 15 left Iteration 1 Error: 0.796965 Iteration 2 Error: 0.103290 Iteration 3 Error: 0.041796 Align patch 11 14 left Iteration 1 Error: 0.985938 Iteration 2 Error: 0.119260 Iteration 3 Error: 0.022792 Align patch 12 13 left Iteration 1 Error: 0.997639 Iteration 2 Error: 0.122443 Iteration 3 Error: 0.033390 Align patch 13 12 left Iteration 1 Error: 1.284611 Iteration 2 Error: 0.142546 Iteration 3 Error: 0.044532 Align patch 14 11 left Iteration 1 Error: 0.754348 Iteration 2 Error: 0.109402 Iteration 3 Error: 0.039954 Align patch 15 10 left Iteration 1 Error: 0.770453 Iteration 2 Error: 0.088572 Iteration 3 Error: 0.022444 Align patch 16 9 left Iteration 1 Error: 0.720805 Iteration 2 Error: 0.219777 Iteration 3 Error: 0.045375 Align patch 17 8 left Iteration 1 Error: 1.251610 Iteration 2 Error: 0.207464 Iteration 3 Error: 0.086080 Iteration 4 Error: 0.030911 Align patch 18 7 left Iteration 1 Error: 1.342526 Iteration 2 Error: 0.188799 Iteration 3 Error: 0.091423 Iteration 4 Error: 0.021354 Align patch 19 6 left Iteration 1 Error: 0.611689 Iteration 2 Error: 0.127289 Iteration 3 Error: 0.031114 Align patch 20 5 left Iteration 1 Error: 1.116160 Iteration 2 Error: 0.340973 Iteration 3 Error: 0.059447 Iteration 4 Error: 0.021103 Align patch 21 4 left Iteration 1 Error: 0.969648 Iteration 2 Error: 0.164153 Iteration 3 Error: 0.025790 Align patch 22 3 left Iteration 1 Error: 0.678814 Iteration 2 Error: 0.118632 Iteration 3 Error: 0.027369 Align patch 23 2 left Iteration 1 Error: 1.481144 Iteration 2 Error: 0.173775 Iteration 3 Error: 0.075496 Iteration 4 Error: 0.023853 Align patch 24 1 left Iteration 1 Error: 1.429574 Iteration 2 Error: 0.153816 Iteration 3 Error: 0.049824 Align patch 25 0 left Iteration 1 Error: 1.132801 Iteration 2 Error: 0.252281 Iteration 3 Error: 0.063597 Iteration 4 Error: 0.038411 3D Fitting completed. Patch alignment time: 11.77(sec) Local motion has been corrected. Process thread exits. Computational time: 21.562746 sec Total time: 28.868298 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00017hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00017hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.463896s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00017hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.522345s ........................................ >>>>>>TIME<<<<<< FFT: 0.893768s Defocus_U Defocus_V Angle CCC 11046.99 11502.53 9.89 0.042585 Final Values Defocus_U Defocus_V Angle CCC 11618.29 10972.06 85.34 0.081970 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00018hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00018hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 1.000e-01 CC threshold: 0.734 Mean Std: 46.49 7.88 Num Hot pixels: 168 Hot pixel threshold: 93.77 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.785864 Iteration 2 Error: 0.080361 Iteration 3 Error: 0.025806 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.28 0.03 ...... Frame ( 3) shift: -0.56 0.05 ...... Frame ( 4) shift: -0.83 0.08 ...... Frame ( 5) shift: -1.11 0.10 ...... Frame ( 6) shift: -1.25 0.15 ...... Frame ( 7) shift: -1.24 0.22 ...... Frame ( 8) shift: -1.24 0.28 ...... Frame ( 9) shift: -1.22 0.34 ...... Frame ( 10) shift: -1.17 0.37 ...... Frame ( 11) shift: -1.13 0.41 ...... Frame ( 12) shift: -1.12 0.46 ...... Frame ( 13) shift: -1.15 0.52 ...... Frame ( 14) shift: -1.17 0.58 ...... Frame ( 15) shift: -1.17 0.59 ...... Frame ( 16) shift: -1.15 0.56 ...... Frame ( 17) shift: -1.12 0.53 ...... Frame ( 18) shift: -1.09 0.55 ...... Frame ( 19) shift: -1.05 0.62 ...... Frame ( 20) shift: -1.01 0.68 ...... Frame ( 21) shift: -0.97 0.73 ...... Frame ( 22) shift: -0.94 0.77 ...... Frame ( 23) shift: -0.91 0.81 ...... Frame ( 24) shift: -0.92 0.84 ...... Frame ( 25) shift: -0.97 0.84 ...... Frame ( 26) shift: -1.02 0.84 ...... Frame ( 27) shift: -1.02 0.87 ...... Frame ( 28) shift: -0.96 0.94 ...... Frame ( 29) shift: -0.90 1.00 ...... Frame ( 30) shift: -0.87 1.04 ...... Frame ( 31) shift: -0.87 1.05 ...... Frame ( 32) shift: -0.87 1.06 ...... Frame ( 33) shift: -0.85 1.07 ...... Frame ( 34) shift: -0.79 1.07 ...... Frame ( 35) shift: -0.74 1.08 ...... Frame ( 36) shift: -0.70 1.06 ...... Frame ( 37) shift: -0.66 1.02 ...... Frame ( 38) shift: -0.62 0.97 ...... Frame ( 39) shift: -0.58 0.93 ...... Frame ( 40) shift: -0.54 0.88 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.685123 Iteration 2 Error: 0.437679 Iteration 3 Error: 0.129019 Iteration 4 Error: 0.035610 Align patch 2 23 left Iteration 1 Error: 1.258664 Iteration 2 Error: 0.164902 Iteration 3 Error: 0.039184 Align patch 3 22 left Iteration 1 Error: 1.288819 Iteration 2 Error: 0.251770 Iteration 3 Error: 0.045043 Align patch 4 21 left Iteration 1 Error: 0.765853 Iteration 2 Error: 0.114573 Iteration 3 Error: 0.021059 Align patch 5 20 left Iteration 1 Error: 0.930013 Iteration 2 Error: 0.171379 Iteration 3 Error: 0.030832 Align patch 6 19 left Iteration 1 Error: 0.729302 Iteration 2 Error: 0.178559 Iteration 3 Error: 0.032209 Align patch 7 18 left Iteration 1 Error: 0.836227 Iteration 2 Error: 0.169282 Iteration 3 Error: 0.054302 Iteration 4 Error: 0.022160 Align patch 8 17 left Iteration 1 Error: 0.763265 Iteration 2 Error: 0.206863 Iteration 3 Error: 0.041245 Align patch 9 16 left Iteration 1 Error: 0.664249 Iteration 2 Error: 0.111534 Iteration 3 Error: 0.023124 Align patch 10 15 left Iteration 1 Error: 0.832082 Iteration 2 Error: 0.176516 Iteration 3 Error: 0.041870 Align patch 11 14 left Iteration 1 Error: 1.041190 Iteration 2 Error: 0.157442 Iteration 3 Error: 0.039071 Align patch 12 13 left Iteration 1 Error: 0.973993 Iteration 2 Error: 0.157115 Iteration 3 Error: 0.050497 Iteration 4 Error: 0.017822 Align patch 13 12 left Iteration 1 Error: 0.825782 Iteration 2 Error: 0.143177 Iteration 3 Error: 0.039373 Align patch 14 11 left Iteration 1 Error: 0.936923 Iteration 2 Error: 0.145846 Iteration 3 Error: 0.056200 Iteration 4 Error: 0.022239 Align patch 15 10 left Iteration 1 Error: 0.753867 Iteration 2 Error: 0.172958 Iteration 3 Error: 0.048320 Align patch 16 9 left Iteration 1 Error: 1.001732 Iteration 2 Error: 0.106424 Iteration 3 Error: 0.032952 Align patch 17 8 left Iteration 1 Error: 1.236268 Iteration 2 Error: 0.184357 Iteration 3 Error: 0.043485 Align patch 18 7 left Iteration 1 Error: 0.649070 Iteration 2 Error: 0.102719 Iteration 3 Error: 0.027902 Align patch 19 6 left Iteration 1 Error: 0.496067 Iteration 2 Error: 0.078467 Iteration 3 Error: 0.019841 Align patch 20 5 left Iteration 1 Error: 0.459881 Iteration 2 Error: 0.127220 Iteration 3 Error: 0.027420 Align patch 21 4 left Iteration 1 Error: 1.147061 Iteration 2 Error: 0.202875 Iteration 3 Error: 0.049909 Align patch 22 3 left Iteration 1 Error: 0.884482 Iteration 2 Error: 0.222588 Iteration 3 Error: 0.073159 Iteration 4 Error: 0.032514 Align patch 23 2 left Iteration 1 Error: 0.916410 Iteration 2 Error: 0.145564 Iteration 3 Error: 0.023844 Align patch 24 1 left Iteration 1 Error: 0.970613 Iteration 2 Error: 0.113440 Iteration 3 Error: 0.041023 Align patch 25 0 left Iteration 1 Error: 0.566393 Iteration 2 Error: 0.088557 Iteration 3 Error: 0.021298 3D Fitting completed. Patch alignment time: 11.77(sec) Local motion has been corrected. Process thread exits. Computational time: 23.423029 sec Total time: 31.058722 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00018hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00018hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.463631s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00018hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.617218s ........................................ >>>>>>TIME<<<<<< FFT: 1.049830s Defocus_U Defocus_V Angle CCC 8494.14 9302.73 13.80 0.040413 Final Values Defocus_U Defocus_V Angle CCC 8483.20 9301.18 12.86 0.082973 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00018hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00018hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.997e-02 CC threshold: 0.734 Mean Std: 46.06 7.83 Num Hot pixels: 180 Hot pixel threshold: 93.06 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.289194 Iteration 2 Error: 0.199104 Iteration 3 Error: 0.047379 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.25 0.04 ...... Frame ( 3) shift: -0.49 0.08 ...... Frame ( 4) shift: -0.74 0.12 ...... Frame ( 5) shift: -0.98 0.15 ...... Frame ( 6) shift: -1.16 0.26 ...... Frame ( 7) shift: -1.28 0.43 ...... Frame ( 8) shift: -1.39 0.60 ...... Frame ( 9) shift: -1.44 0.71 ...... Frame ( 10) shift: -1.42 0.76 ...... Frame ( 11) shift: -1.41 0.82 ...... Frame ( 12) shift: -1.39 0.89 ...... Frame ( 13) shift: -1.37 0.98 ...... Frame ( 14) shift: -1.36 1.07 ...... Frame ( 15) shift: -1.30 1.15 ...... Frame ( 16) shift: -1.22 1.23 ...... Frame ( 17) shift: -1.13 1.31 ...... Frame ( 18) shift: -1.07 1.39 ...... Frame ( 19) shift: -1.03 1.48 ...... Frame ( 20) shift: -1.00 1.57 ...... Frame ( 21) shift: -0.98 1.60 ...... Frame ( 22) shift: -0.97 1.58 ...... Frame ( 23) shift: -0.97 1.55 ...... Frame ( 24) shift: -0.97 1.55 ...... Frame ( 25) shift: -0.96 1.57 ...... Frame ( 26) shift: -0.96 1.60 ...... Frame ( 27) shift: -0.95 1.67 ...... Frame ( 28) shift: -0.93 1.78 ...... Frame ( 29) shift: -0.91 1.90 ...... Frame ( 30) shift: -0.89 1.96 ...... Frame ( 31) shift: -0.88 1.98 ...... Frame ( 32) shift: -0.86 1.99 ...... Frame ( 33) shift: -0.82 2.01 ...... Frame ( 34) shift: -0.77 2.03 ...... Frame ( 35) shift: -0.72 2.06 ...... Frame ( 36) shift: -0.69 2.09 ...... Frame ( 37) shift: -0.70 2.15 ...... Frame ( 38) shift: -0.70 2.20 ...... Frame ( 39) shift: -0.70 2.25 ...... Frame ( 40) shift: -0.70 2.31 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.027982 Iteration 2 Error: 0.229401 Iteration 3 Error: 0.074681 Iteration 4 Error: 0.033169 Align patch 2 23 left Iteration 1 Error: 1.080918 Iteration 2 Error: 0.214768 Iteration 3 Error: 0.105687 Iteration 4 Error: 0.034872 Align patch 3 22 left Iteration 1 Error: 1.303375 Iteration 2 Error: 0.145550 Iteration 3 Error: 0.042232 Align patch 4 21 left Iteration 1 Error: 0.848765 Iteration 2 Error: 0.142865 Iteration 3 Error: 0.024700 Align patch 5 20 left Iteration 1 Error: 1.104122 Iteration 2 Error: 0.167314 Iteration 3 Error: 0.029726 Align patch 6 19 left Iteration 1 Error: 0.871381 Iteration 2 Error: 0.160424 Iteration 3 Error: 0.066120 Iteration 4 Error: 0.037453 Align patch 7 18 left Iteration 1 Error: 1.508814 Iteration 2 Error: 0.501238 Iteration 3 Error: 0.194233 Iteration 4 Error: 0.138811 Iteration 5 Error: 0.053792 Align patch 7 18 left Iteration 1 Error: 1.484895 Iteration 2 Error: 0.117003 Iteration 3 Error: 0.029464 Align patch 8 17 left Iteration 1 Error: 0.918972 Iteration 2 Error: 0.226299 Iteration 3 Error: 0.063536 Iteration 4 Error: 0.024504 Align patch 9 16 left Iteration 1 Error: 0.565136 Iteration 2 Error: 0.083929 Iteration 3 Error: 0.020921 Align patch 10 15 left Iteration 1 Error: 0.973535 Iteration 2 Error: 0.102349 Iteration 3 Error: 0.035835 Align patch 11 14 left Iteration 1 Error: 0.950229 Iteration 2 Error: 0.285512 Iteration 3 Error: 0.058824 Iteration 4 Error: 0.031916 Align patch 12 13 left Iteration 1 Error: 0.918864 Iteration 2 Error: 0.264493 Iteration 3 Error: 0.108597 Iteration 4 Error: 0.060590 Iteration 5 Error: 0.054887 Align patch 12 13 left Iteration 1 Error: 1.659353 Iteration 2 Error: 0.159537 Iteration 3 Error: 0.034527 Align patch 13 12 left Iteration 1 Error: 0.765071 Iteration 2 Error: 0.200024 Iteration 3 Error: 0.043541 Align patch 14 11 left Iteration 1 Error: 0.718172 Iteration 2 Error: 0.091294 Iteration 3 Error: 0.025576 Align patch 15 10 left Iteration 1 Error: 0.763795 Iteration 2 Error: 0.199052 Iteration 3 Error: 0.045295 Align patch 16 9 left Iteration 1 Error: 0.747963 Iteration 2 Error: 0.150839 Iteration 3 Error: 0.068640 Iteration 4 Error: 0.041714 Align patch 17 8 left Iteration 1 Error: 0.946123 Iteration 2 Error: 0.164918 Iteration 3 Error: 0.051304 Iteration 4 Error: 0.013584 Align patch 18 7 left Iteration 1 Error: 0.762108 Iteration 2 Error: 0.152004 Iteration 3 Error: 0.048927 Align patch 19 6 left Iteration 1 Error: 0.455507 Iteration 2 Error: 0.062849 Iteration 3 Error: 0.015610 Align patch 20 5 left Iteration 1 Error: 0.686927 Iteration 2 Error: 0.121198 Iteration 3 Error: 0.029658 Align patch 21 4 left Iteration 1 Error: 1.320752 Iteration 2 Error: 0.201712 Iteration 3 Error: 0.039555 Align patch 22 3 left Iteration 1 Error: 0.939951 Iteration 2 Error: 0.136060 Iteration 3 Error: 0.023616 Align patch 23 2 left Iteration 1 Error: 0.837717 Iteration 2 Error: 0.144697 Iteration 3 Error: 0.027109 Align patch 24 1 left Iteration 1 Error: 0.620336 Iteration 2 Error: 0.078127 Iteration 3 Error: 0.016884 Align patch 25 0 left Iteration 1 Error: 0.714839 Iteration 2 Error: 0.099210 Iteration 3 Error: 0.024329 3D Fitting completed. Patch alignment time: 12.90(sec) Local motion has been corrected. Process thread exits. Computational time: 24.765991 sec Total time: 32.203293 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00018hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00018hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.647974s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00018hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.781455s ........................................ >>>>>>TIME<<<<<< FFT: 0.925224s Defocus_U Defocus_V Angle CCC 12136.72 11652.34 87.52 0.044554 Final Values Defocus_U Defocus_V Angle CCC 12172.66 11672.67 85.98 0.080500 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00018hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00018hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 47.22 7.68 Num Hot pixels: 179 Hot pixel threshold: 93.29 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.371011 Iteration 2 Error: 0.068850 Iteration 3 Error: 0.014367 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.36 0.06 ...... Frame ( 3) shift: -0.71 0.12 ...... Frame ( 4) shift: -1.07 0.18 ...... Frame ( 5) shift: -1.42 0.24 ...... Frame ( 6) shift: -1.63 0.26 ...... Frame ( 7) shift: -1.68 0.23 ...... Frame ( 8) shift: -1.74 0.20 ...... Frame ( 9) shift: -1.78 0.21 ...... Frame ( 10) shift: -1.80 0.27 ...... Frame ( 11) shift: -1.82 0.32 ...... Frame ( 12) shift: -1.83 0.36 ...... Frame ( 13) shift: -1.81 0.39 ...... Frame ( 14) shift: -1.79 0.42 ...... Frame ( 15) shift: -1.81 0.40 ...... Frame ( 16) shift: -1.85 0.35 ...... Frame ( 17) shift: -1.89 0.30 ...... Frame ( 18) shift: -1.94 0.29 ...... Frame ( 19) shift: -2.00 0.33 ...... Frame ( 20) shift: -2.06 0.36 ...... Frame ( 21) shift: -2.08 0.35 ...... Frame ( 22) shift: -2.06 0.29 ...... Frame ( 23) shift: -2.05 0.23 ...... Frame ( 24) shift: -2.00 0.24 ...... Frame ( 25) shift: -1.91 0.31 ...... Frame ( 26) shift: -1.83 0.39 ...... Frame ( 27) shift: -1.84 0.40 ...... Frame ( 28) shift: -1.95 0.35 ...... Frame ( 29) shift: -2.06 0.29 ...... Frame ( 30) shift: -2.11 0.29 ...... Frame ( 31) shift: -2.11 0.34 ...... Frame ( 32) shift: -2.11 0.39 ...... Frame ( 33) shift: -2.09 0.42 ...... Frame ( 34) shift: -2.04 0.42 ...... Frame ( 35) shift: -1.99 0.43 ...... Frame ( 36) shift: -1.97 0.46 ...... Frame ( 37) shift: -2.00 0.51 ...... Frame ( 38) shift: -2.03 0.57 ...... Frame ( 39) shift: -2.06 0.62 ...... Frame ( 40) shift: -2.09 0.68 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.662005 Iteration 2 Error: 0.447471 Iteration 3 Error: 0.183486 Iteration 4 Error: 0.069178 Iteration 5 Error: 0.024527 Align patch 2 23 left Iteration 1 Error: 0.790619 Iteration 2 Error: 0.135895 Iteration 3 Error: 0.038512 Align patch 3 22 left Iteration 1 Error: 1.078231 Iteration 2 Error: 0.153466 Iteration 3 Error: 0.030770 Align patch 4 21 left Iteration 1 Error: 0.513958 Iteration 2 Error: 0.111618 Iteration 3 Error: 0.019805 Align patch 5 20 left Iteration 1 Error: 0.725363 Iteration 2 Error: 0.147140 Iteration 3 Error: 0.036586 Align patch 6 19 left Iteration 1 Error: 1.212044 Iteration 2 Error: 0.192143 Iteration 3 Error: 0.029710 Align patch 7 18 left Iteration 1 Error: 1.028131 Iteration 2 Error: 0.207620 Iteration 3 Error: 0.049047 Align patch 8 17 left Iteration 1 Error: 0.761550 Iteration 2 Error: 0.113811 Iteration 3 Error: 0.037415 Align patch 9 16 left Iteration 1 Error: 0.741024 Iteration 2 Error: 0.118431 Iteration 3 Error: 0.028158 Align patch 10 15 left Iteration 1 Error: 0.678861 Iteration 2 Error: 0.162303 Iteration 3 Error: 0.032432 Align patch 11 14 left Iteration 1 Error: 0.845659 Iteration 2 Error: 0.193475 Iteration 3 Error: 0.064974 Iteration 4 Error: 0.012749 Align patch 12 13 left Iteration 1 Error: 1.635143 Iteration 2 Error: 0.336491 Iteration 3 Error: 0.187884 Iteration 4 Error: 0.038057 Align patch 13 12 left Iteration 1 Error: 0.732170 Iteration 2 Error: 0.091036 Iteration 3 Error: 0.023543 Align patch 14 11 left Iteration 1 Error: 0.790251 Iteration 2 Error: 0.118592 Iteration 3 Error: 0.022128 Align patch 15 10 left Iteration 1 Error: 0.980181 Iteration 2 Error: 0.118031 Iteration 3 Error: 0.038352 Align patch 16 9 left Iteration 1 Error: 0.934589 Iteration 2 Error: 0.193120 Iteration 3 Error: 0.064314 Iteration 4 Error: 0.013568 Align patch 17 8 left Iteration 1 Error: 1.068895 Iteration 2 Error: 0.148959 Iteration 3 Error: 0.032940 Align patch 18 7 left Iteration 1 Error: 0.568850 Iteration 2 Error: 0.086485 Iteration 3 Error: 0.016725 Align patch 19 6 left Iteration 1 Error: 0.727922 Iteration 2 Error: 0.080743 Iteration 3 Error: 0.014991 Align patch 20 5 left Iteration 1 Error: 0.602066 Iteration 2 Error: 0.089496 Iteration 3 Error: 0.020881 Align patch 21 4 left Iteration 1 Error: 1.554665 Iteration 2 Error: 0.256345 Iteration 3 Error: 0.080522 Iteration 4 Error: 0.067494 Iteration 5 Error: 0.037257 Align patch 22 3 left Iteration 1 Error: 1.484666 Iteration 2 Error: 0.101257 Iteration 3 Error: 0.042909 Align patch 23 2 left Iteration 1 Error: 0.629334 Iteration 2 Error: 0.124435 Iteration 3 Error: 0.037607 Align patch 24 1 left Iteration 1 Error: 0.783654 Iteration 2 Error: 0.118407 Iteration 3 Error: 0.017601 Align patch 25 0 left Iteration 1 Error: 0.465391 Iteration 2 Error: 0.059917 Iteration 3 Error: 0.015810 3D Fitting completed. Patch alignment time: 11.37(sec) Local motion has been corrected. Process thread exits. Computational time: 22.625538 sec Total time: 29.432928 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00018hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00018hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.590924s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00018hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.449101s ........................................ >>>>>>TIME<<<<<< FFT: 0.959275s Defocus_U Defocus_V Angle CCC 12451.17 13357.42 4.86 0.050658 Final Values Defocus_U Defocus_V Angle CCC 12458.99 13352.74 4.86 0.092322 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00018hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00018hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 1.000e-01 CC threshold: 0.734 Mean Std: 46.84 7.70 Num Hot pixels: 177 Hot pixel threshold: 93.06 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.303203 Iteration 2 Error: 0.137223 Iteration 3 Error: 0.033550 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.22 0.21 ...... Frame ( 3) shift: -0.44 0.41 ...... Frame ( 4) shift: -0.67 0.62 ...... Frame ( 5) shift: -0.89 0.83 ...... Frame ( 6) shift: -0.96 0.96 ...... Frame ( 7) shift: -0.87 1.03 ...... Frame ( 8) shift: -0.78 1.09 ...... Frame ( 9) shift: -0.70 1.18 ...... Frame ( 10) shift: -0.61 1.30 ...... Frame ( 11) shift: -0.53 1.42 ...... Frame ( 12) shift: -0.52 1.47 ...... Frame ( 13) shift: -0.59 1.47 ...... Frame ( 14) shift: -0.65 1.46 ...... Frame ( 15) shift: -0.64 1.52 ...... Frame ( 16) shift: -0.55 1.63 ...... Frame ( 17) shift: -0.46 1.75 ...... Frame ( 18) shift: -0.42 1.83 ...... Frame ( 19) shift: -0.41 1.86 ...... Frame ( 20) shift: -0.40 1.89 ...... Frame ( 21) shift: -0.36 1.94 ...... Frame ( 22) shift: -0.29 2.00 ...... Frame ( 23) shift: -0.21 2.07 ...... Frame ( 24) shift: -0.19 2.09 ...... Frame ( 25) shift: -0.22 2.06 ...... Frame ( 26) shift: -0.25 2.04 ...... Frame ( 27) shift: -0.22 2.02 ...... Frame ( 28) shift: -0.12 2.01 ...... Frame ( 29) shift: -0.02 1.99 ...... Frame ( 30) shift: 0.03 1.97 ...... Frame ( 31) shift: 0.04 1.95 ...... Frame ( 32) shift: 0.05 1.92 ...... Frame ( 33) shift: 0.04 1.95 ...... Frame ( 34) shift: -0.00 2.05 ...... Frame ( 35) shift: -0.05 2.14 ...... Frame ( 36) shift: -0.03 2.15 ...... Frame ( 37) shift: 0.05 2.07 ...... Frame ( 38) shift: 0.13 2.00 ...... Frame ( 39) shift: 0.21 1.93 ...... Frame ( 40) shift: 0.29 1.85 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.984501 Iteration 2 Error: 0.252183 Iteration 3 Error: 0.054052 Iteration 4 Error: 0.016358 Align patch 2 23 left Iteration 1 Error: 0.840061 Iteration 2 Error: 0.239737 Iteration 3 Error: 0.082298 Iteration 4 Error: 0.028805 Align patch 3 22 left Iteration 1 Error: 0.709565 Iteration 2 Error: 0.147146 Iteration 3 Error: 0.026061 Align patch 4 21 left Iteration 1 Error: 0.777808 Iteration 2 Error: 0.136945 Iteration 3 Error: 0.032416 Align patch 5 20 left Iteration 1 Error: 0.765257 Iteration 2 Error: 0.144878 Iteration 3 Error: 0.022857 Align patch 6 19 left Iteration 1 Error: 2.185444 Iteration 2 Error: 0.234798 Iteration 3 Error: 0.105881 Iteration 4 Error: 0.037227 Align patch 7 18 left Iteration 1 Error: 1.447805 Iteration 2 Error: 0.196843 Iteration 3 Error: 0.095750 Iteration 4 Error: 0.048247 Align patch 8 17 left Iteration 1 Error: 0.713413 Iteration 2 Error: 0.229366 Iteration 3 Error: 0.057883 Iteration 4 Error: 0.040853 Align patch 9 16 left Iteration 1 Error: 0.927610 Iteration 2 Error: 0.182863 Iteration 3 Error: 0.034318 Align patch 10 15 left Iteration 1 Error: 0.635193 Iteration 2 Error: 0.090596 Iteration 3 Error: 0.023476 Align patch 11 14 left Iteration 1 Error: 0.974757 Iteration 2 Error: 0.255474 Iteration 3 Error: 0.123708 Iteration 4 Error: 0.049921 Align patch 12 13 left Iteration 1 Error: 0.862953 Iteration 2 Error: 0.112944 Iteration 3 Error: 0.037834 Align patch 13 12 left Iteration 1 Error: 0.697302 Iteration 2 Error: 0.158718 Iteration 3 Error: 0.069459 Iteration 4 Error: 0.034324 Align patch 14 11 left Iteration 1 Error: 0.781862 Iteration 2 Error: 0.165575 Iteration 3 Error: 0.033855 Align patch 15 10 left Iteration 1 Error: 0.762310 Iteration 2 Error: 0.107140 Iteration 3 Error: 0.024026 Align patch 16 9 left Iteration 1 Error: 0.848536 Iteration 2 Error: 0.224739 Iteration 3 Error: 0.117137 Iteration 4 Error: 0.047698 Align patch 17 8 left Iteration 1 Error: 0.823345 Iteration 2 Error: 0.153352 Iteration 3 Error: 0.043352 Align patch 18 7 left Iteration 1 Error: 0.949931 Iteration 2 Error: 0.124601 Iteration 3 Error: 0.037404 Align patch 19 6 left Iteration 1 Error: 0.913694 Iteration 2 Error: 0.164415 Iteration 3 Error: 0.031248 Align patch 20 5 left Iteration 1 Error: 0.894542 Iteration 2 Error: 0.163226 Iteration 3 Error: 0.039200 Align patch 21 4 left Iteration 1 Error: 1.063248 Iteration 2 Error: 0.215772 Iteration 3 Error: 0.063392 Iteration 4 Error: 0.027863 Align patch 22 3 left Iteration 1 Error: 0.990732 Iteration 2 Error: 0.211229 Iteration 3 Error: 0.031463 Align patch 23 2 left Iteration 1 Error: 1.356374 Iteration 2 Error: 0.210491 Iteration 3 Error: 0.064981 Iteration 4 Error: 0.019443 Align patch 24 1 left Iteration 1 Error: 1.016008 Iteration 2 Error: 0.183911 Iteration 3 Error: 0.038177 Align patch 25 0 left Iteration 1 Error: 0.739201 Iteration 2 Error: 0.118030 Iteration 3 Error: 0.025037 3D Fitting completed. Patch alignment time: 11.48(sec) Local motion has been corrected. Process thread exits. Computational time: 24.058817 sec Total time: 31.991222 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00018hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00018hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.862068s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00018hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.177772s ........................................ >>>>>>TIME<<<<<< FFT: 0.980842s Defocus_U Defocus_V Angle CCC 12504.99 11901.33 85.99 0.054321 Final Values Defocus_U Defocus_V Angle CCC 12512.80 11909.14 85.37 0.099161 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00019hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00019hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.997e-02 CC threshold: 0.734 Mean Std: 47.80 7.70 Num Hot pixels: 208 Hot pixel threshold: 94.02 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.466853 Iteration 2 Error: 0.210772 Iteration 3 Error: 0.069269 Iteration 4 Error: 0.031520 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.19 0.17 ...... Frame ( 3) shift: -0.37 0.34 ...... Frame ( 4) shift: -0.56 0.51 ...... Frame ( 5) shift: -0.74 0.67 ...... Frame ( 6) shift: -0.80 0.83 ...... Frame ( 7) shift: -0.72 0.98 ...... Frame ( 8) shift: -0.65 1.13 ...... Frame ( 9) shift: -0.56 1.27 ...... Frame ( 10) shift: -0.44 1.40 ...... Frame ( 11) shift: -0.32 1.53 ...... Frame ( 12) shift: -0.24 1.66 ...... Frame ( 13) shift: -0.20 1.77 ...... Frame ( 14) shift: -0.16 1.89 ...... Frame ( 15) shift: -0.11 2.00 ...... Frame ( 16) shift: -0.04 2.12 ...... Frame ( 17) shift: 0.02 2.24 ...... Frame ( 18) shift: 0.05 2.30 ...... Frame ( 19) shift: 0.04 2.30 ...... Frame ( 20) shift: 0.04 2.31 ...... Frame ( 21) shift: 0.04 2.28 ...... Frame ( 22) shift: 0.04 2.23 ...... Frame ( 23) shift: 0.04 2.18 ...... Frame ( 24) shift: 0.03 2.16 ...... Frame ( 25) shift: 0.00 2.19 ...... Frame ( 26) shift: -0.02 2.21 ...... Frame ( 27) shift: -0.01 2.21 ...... Frame ( 28) shift: 0.05 2.19 ...... Frame ( 29) shift: 0.10 2.16 ...... Frame ( 30) shift: 0.12 2.17 ...... Frame ( 31) shift: 0.11 2.20 ...... Frame ( 32) shift: 0.09 2.23 ...... Frame ( 33) shift: 0.12 2.25 ...... Frame ( 34) shift: 0.18 2.26 ...... Frame ( 35) shift: 0.23 2.27 ...... Frame ( 36) shift: 0.26 2.28 ...... Frame ( 37) shift: 0.24 2.30 ...... Frame ( 38) shift: 0.23 2.33 ...... Frame ( 39) shift: 0.21 2.35 ...... Frame ( 40) shift: 0.20 2.37 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.681438 Iteration 2 Error: 0.721819 Iteration 3 Error: 0.258291 Iteration 4 Error: 0.144072 Iteration 5 Error: 0.066920 Align patch 1 24 left Iteration 1 Error: 2.355102 Iteration 2 Error: 0.127111 Iteration 3 Error: 0.032682 Align patch 2 23 left Iteration 1 Error: 4.410032 Iteration 2 Error: 0.588439 Iteration 3 Error: 0.198028 Iteration 4 Error: 0.086605 Iteration 5 Error: 0.024322 Align patch 3 22 left Iteration 1 Error: 1.789631 Iteration 2 Error: 0.360961 Iteration 3 Error: 0.353808 Iteration 4 Error: 0.084739 Iteration 5 Error: 0.091949 Align patch 3 22 left Iteration 1 Error: 1.414514 Iteration 2 Error: 0.180927 Iteration 3 Error: 0.055708 Iteration 4 Error: 0.022874 Align patch 4 21 left Iteration 1 Error: 0.923539 Iteration 2 Error: 0.262289 Iteration 3 Error: 0.099387 Iteration 4 Error: 0.037589 Align patch 5 20 left Iteration 1 Error: 0.776173 Iteration 2 Error: 0.118139 Iteration 3 Error: 0.027123 Align patch 6 19 left Iteration 1 Error: 0.732281 Iteration 2 Error: 0.265369 Iteration 3 Error: 0.041417 Align patch 7 18 left Iteration 1 Error: 0.797808 Iteration 2 Error: 0.135027 Iteration 3 Error: 0.036567 Align patch 8 17 left Iteration 1 Error: 1.190539 Iteration 2 Error: 0.147332 Iteration 3 Error: 0.038669 Align patch 9 16 left Iteration 1 Error: 1.072770 Iteration 2 Error: 0.189773 Iteration 3 Error: 0.053674 Iteration 4 Error: 0.027908 Align patch 10 15 left Iteration 1 Error: 0.666681 Iteration 2 Error: 0.111772 Iteration 3 Error: 0.030602 Align patch 11 14 left Iteration 1 Error: 1.181927 Iteration 2 Error: 0.253732 Iteration 3 Error: 0.069719 Iteration 4 Error: 0.022859 Align patch 12 13 left Iteration 1 Error: 0.838198 Iteration 2 Error: 0.270366 Iteration 3 Error: 0.055329 Iteration 4 Error: 0.014502 Align patch 13 12 left Iteration 1 Error: 0.836317 Iteration 2 Error: 0.152778 Iteration 3 Error: 0.041563 Align patch 14 11 left Iteration 1 Error: 1.120358 Iteration 2 Error: 0.235232 Iteration 3 Error: 0.089964 Iteration 4 Error: 0.029218 Align patch 15 10 left Iteration 1 Error: 0.622264 Iteration 2 Error: 0.163982 Iteration 3 Error: 0.058565 Iteration 4 Error: 0.017375 Align patch 16 9 left Iteration 1 Error: 0.917703 Iteration 2 Error: 0.184447 Iteration 3 Error: 0.059969 Iteration 4 Error: 0.022247 Align patch 17 8 left Iteration 1 Error: 0.639047 Iteration 2 Error: 0.150686 Iteration 3 Error: 0.046821 Align patch 18 7 left Iteration 1 Error: 0.726293 Iteration 2 Error: 0.194436 Iteration 3 Error: 0.078796 Iteration 4 Error: 0.028971 Align patch 19 6 left Iteration 1 Error: 0.690804 Iteration 2 Error: 0.098079 Iteration 3 Error: 0.025170 Align patch 20 5 left Iteration 1 Error: 0.650552 Iteration 2 Error: 0.119598 Iteration 3 Error: 0.035733 Align patch 21 4 left Iteration 1 Error: 0.963598 Iteration 2 Error: 0.258748 Iteration 3 Error: 0.071609 Iteration 4 Error: 0.030982 Align patch 22 3 left Iteration 1 Error: 0.946908 Iteration 2 Error: 0.226688 Iteration 3 Error: 0.085890 Iteration 4 Error: 0.032347 Align patch 23 2 left Iteration 1 Error: 0.973749 Iteration 2 Error: 0.138337 Iteration 3 Error: 0.033715 Align patch 24 1 left Iteration 1 Error: 2.121551 Iteration 2 Error: 0.179559 Iteration 3 Error: 0.035376 Align patch 25 0 left Iteration 1 Error: 0.567403 Iteration 2 Error: 0.079803 Iteration 3 Error: 0.021894 3D Fitting completed. Patch alignment time: 13.75(sec) Local motion has been corrected. Process thread exits. Computational time: 26.016357 sec Total time: 32.517658 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00019hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00019hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.613444s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00019hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.612426s ........................................ >>>>>>TIME<<<<<< FFT: 0.993336s Defocus_U Defocus_V Angle CCC 8667.98 9468.76 13.87 0.038197 Final Values Defocus_U Defocus_V Angle CCC 8671.08 9475.04 13.56 0.078660 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00019hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00019hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.001e-01 CC threshold: 0.735 Mean Std: 46.13 8.21 Num Hot pixels: 142 Hot pixel threshold: 95.41 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.617464 Iteration 2 Error: 0.099244 Iteration 3 Error: 0.019788 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.16 -0.00 ...... Frame ( 3) shift: -0.32 -0.01 ...... Frame ( 4) shift: -0.48 -0.01 ...... Frame ( 5) shift: -0.64 -0.01 ...... Frame ( 6) shift: -0.70 0.02 ...... Frame ( 7) shift: -0.67 0.08 ...... Frame ( 8) shift: -0.65 0.15 ...... Frame ( 9) shift: -0.58 0.20 ...... Frame ( 10) shift: -0.48 0.23 ...... Frame ( 11) shift: -0.39 0.26 ...... Frame ( 12) shift: -0.34 0.32 ...... Frame ( 13) shift: -0.35 0.38 ...... Frame ( 14) shift: -0.36 0.45 ...... Frame ( 15) shift: -0.36 0.49 ...... Frame ( 16) shift: -0.36 0.50 ...... Frame ( 17) shift: -0.35 0.50 ...... Frame ( 18) shift: -0.38 0.52 ...... Frame ( 19) shift: -0.43 0.55 ...... Frame ( 20) shift: -0.48 0.58 ...... Frame ( 21) shift: -0.51 0.60 ...... Frame ( 22) shift: -0.52 0.63 ...... Frame ( 23) shift: -0.53 0.65 ...... Frame ( 24) shift: -0.53 0.66 ...... Frame ( 25) shift: -0.51 0.65 ...... Frame ( 26) shift: -0.50 0.64 ...... Frame ( 27) shift: -0.49 0.68 ...... Frame ( 28) shift: -0.46 0.75 ...... Frame ( 29) shift: -0.43 0.83 ...... Frame ( 30) shift: -0.40 0.87 ...... Frame ( 31) shift: -0.38 0.89 ...... Frame ( 32) shift: -0.35 0.90 ...... Frame ( 33) shift: -0.37 0.92 ...... Frame ( 34) shift: -0.42 0.94 ...... Frame ( 35) shift: -0.48 0.96 ...... Frame ( 36) shift: -0.52 1.00 ...... Frame ( 37) shift: -0.55 1.06 ...... Frame ( 38) shift: -0.58 1.12 ...... Frame ( 39) shift: -0.61 1.18 ...... Frame ( 40) shift: -0.64 1.24 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.089646 Iteration 2 Error: 0.172118 Iteration 3 Error: 0.046459 Align patch 2 23 left Iteration 1 Error: 1.412863 Iteration 2 Error: 0.188853 Iteration 3 Error: 0.071372 Iteration 4 Error: 0.021034 Align patch 3 22 left Iteration 1 Error: 1.106354 Iteration 2 Error: 0.124667 Iteration 3 Error: 0.032812 Align patch 4 21 left Iteration 1 Error: 0.610788 Iteration 2 Error: 0.142245 Iteration 3 Error: 0.040558 Align patch 5 20 left Iteration 1 Error: 0.846441 Iteration 2 Error: 0.101760 Iteration 3 Error: 0.010738 Align patch 6 19 left Iteration 1 Error: 1.622540 Iteration 2 Error: 0.228748 Iteration 3 Error: 0.100035 Iteration 4 Error: 0.051205 Iteration 5 Error: 0.015568 Align patch 7 18 left Iteration 1 Error: 0.743553 Iteration 2 Error: 0.192266 Iteration 3 Error: 0.054087 Iteration 4 Error: 0.021787 Align patch 8 17 left Iteration 1 Error: 0.946547 Iteration 2 Error: 0.129614 Iteration 3 Error: 0.037806 Align patch 9 16 left Iteration 1 Error: 0.734987 Iteration 2 Error: 0.077978 Iteration 3 Error: 0.022265 Align patch 10 15 left Iteration 1 Error: 0.385547 Iteration 2 Error: 0.070064 Iteration 3 Error: 0.018107 Align patch 11 14 left Iteration 1 Error: 1.048387 Iteration 2 Error: 0.207896 Iteration 3 Error: 0.065907 Iteration 4 Error: 0.021132 Align patch 12 13 left Iteration 1 Error: 0.565216 Iteration 2 Error: 0.101994 Iteration 3 Error: 0.024704 Align patch 13 12 left Iteration 1 Error: 0.869687 Iteration 2 Error: 0.162291 Iteration 3 Error: 0.053855 Iteration 4 Error: 0.033504 Align patch 14 11 left Iteration 1 Error: 0.554943 Iteration 2 Error: 0.111897 Iteration 3 Error: 0.029133 Align patch 15 10 left Iteration 1 Error: 0.628377 Iteration 2 Error: 0.099710 Iteration 3 Error: 0.021973 Align patch 16 9 left Iteration 1 Error: 0.898505 Iteration 2 Error: 0.157331 Iteration 3 Error: 0.064733 Iteration 4 Error: 0.038518 Align patch 17 8 left Iteration 1 Error: 0.707115 Iteration 2 Error: 0.127570 Iteration 3 Error: 0.032394 Align patch 18 7 left Iteration 1 Error: 0.595674 Iteration 2 Error: 0.123651 Iteration 3 Error: 0.031812 Align patch 19 6 left Iteration 1 Error: 0.642177 Iteration 2 Error: 0.150648 Iteration 3 Error: 0.033907 Align patch 20 5 left Iteration 1 Error: 0.986983 Iteration 2 Error: 0.182591 Iteration 3 Error: 0.026406 Align patch 21 4 left Iteration 1 Error: 0.709392 Iteration 2 Error: 0.094448 Iteration 3 Error: 0.032584 Align patch 22 3 left Iteration 1 Error: 0.729675 Iteration 2 Error: 0.159312 Iteration 3 Error: 0.035969 Align patch 23 2 left Iteration 1 Error: 0.810280 Iteration 2 Error: 0.100298 Iteration 3 Error: 0.035178 Align patch 24 1 left Iteration 1 Error: 0.797196 Iteration 2 Error: 0.225168 Iteration 3 Error: 0.051893 Iteration 4 Error: 0.010623 Align patch 25 0 left Iteration 1 Error: 0.524639 Iteration 2 Error: 0.080393 Iteration 3 Error: 0.018173 3D Fitting completed. Patch alignment time: 11.42(sec) Local motion has been corrected. Process thread exits. Computational time: 26.155056 sec Total time: 34.451736 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00019hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00019hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.761280s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00019hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.517631s ........................................ >>>>>>TIME<<<<<< FFT: 0.977456s Defocus_U Defocus_V Angle CCC 10257.61 10687.71 0.98 0.045725 Final Values Defocus_U Defocus_V Angle CCC 10256.04 10692.40 2.86 0.083485 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00019hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00019hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.994e-02 CC threshold: 0.734 Mean Std: 46.83 7.75 Num Hot pixels: 183 Hot pixel threshold: 93.35 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.696787 Iteration 2 Error: 0.272815 Iteration 3 Error: 0.088331 Iteration 4 Error: 0.017753 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.45 -0.08 ...... Frame ( 3) shift: -0.90 -0.17 ...... Frame ( 4) shift: -1.36 -0.25 ...... Frame ( 5) shift: -1.81 -0.33 ...... Frame ( 6) shift: -1.98 -0.30 ...... Frame ( 7) shift: -1.86 -0.17 ...... Frame ( 8) shift: -1.75 -0.03 ...... Frame ( 9) shift: -1.65 0.16 ...... Frame ( 10) shift: -1.57 0.41 ...... Frame ( 11) shift: -1.50 0.65 ...... Frame ( 12) shift: -1.43 0.86 ...... Frame ( 13) shift: -1.37 1.02 ...... Frame ( 14) shift: -1.31 1.19 ...... Frame ( 15) shift: -1.25 1.32 ...... Frame ( 16) shift: -1.20 1.42 ...... Frame ( 17) shift: -1.15 1.53 ...... Frame ( 18) shift: -1.12 1.58 ...... Frame ( 19) shift: -1.11 1.59 ...... Frame ( 20) shift: -1.10 1.59 ...... Frame ( 21) shift: -1.08 1.62 ...... Frame ( 22) shift: -1.03 1.67 ...... Frame ( 23) shift: -0.98 1.72 ...... Frame ( 24) shift: -0.96 1.80 ...... Frame ( 25) shift: -0.96 1.89 ...... Frame ( 26) shift: -0.96 1.98 ...... Frame ( 27) shift: -0.93 2.03 ...... Frame ( 28) shift: -0.87 2.03 ...... Frame ( 29) shift: -0.80 2.04 ...... Frame ( 30) shift: -0.78 2.03 ...... Frame ( 31) shift: -0.79 2.03 ...... Frame ( 32) shift: -0.81 2.02 ...... Frame ( 33) shift: -0.83 2.00 ...... Frame ( 34) shift: -0.85 1.98 ...... Frame ( 35) shift: -0.88 1.95 ...... Frame ( 36) shift: -0.88 1.98 ...... Frame ( 37) shift: -0.84 2.07 ...... Frame ( 38) shift: -0.79 2.15 ...... Frame ( 39) shift: -0.75 2.24 ...... Frame ( 40) shift: -0.71 2.33 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.557225 Iteration 2 Error: 0.348921 Iteration 3 Error: 0.126987 Iteration 4 Error: 0.052658 Iteration 5 Error: 0.021654 Align patch 2 23 left Iteration 1 Error: 2.880420 Iteration 2 Error: 0.456560 Iteration 3 Error: 0.147992 Iteration 4 Error: 0.076000 Iteration 5 Error: 0.031163 Align patch 3 22 left Iteration 1 Error: 2.123118 Iteration 2 Error: 0.367890 Iteration 3 Error: 0.132615 Iteration 4 Error: 0.057391 Iteration 5 Error: 0.027746 Align patch 4 21 left Iteration 1 Error: 0.933976 Iteration 2 Error: 0.243668 Iteration 3 Error: 0.069024 Iteration 4 Error: 0.034929 Align patch 5 20 left Iteration 1 Error: 0.596732 Iteration 2 Error: 0.128378 Iteration 3 Error: 0.022304 Align patch 6 19 left Iteration 1 Error: 1.845657 Iteration 2 Error: 0.607992 Iteration 3 Error: 0.167690 Iteration 4 Error: 0.053808 Iteration 5 Error: 0.024621 Align patch 7 18 left Iteration 1 Error: 2.457565 Iteration 2 Error: 0.281958 Iteration 3 Error: 0.121186 Iteration 4 Error: 0.034860 Align patch 8 17 left Iteration 1 Error: 3.356216 Iteration 2 Error: 0.874745 Iteration 3 Error: 0.166036 Iteration 4 Error: 0.089009 Iteration 5 Error: 0.015492 Align patch 9 16 left Iteration 1 Error: 1.097989 Iteration 2 Error: 0.314663 Iteration 3 Error: 0.161357 Iteration 4 Error: 0.068026 Iteration 5 Error: 0.035945 Align patch 10 15 left Iteration 1 Error: 0.904513 Iteration 2 Error: 0.091861 Iteration 3 Error: 0.028685 Align patch 11 14 left Iteration 1 Error: 1.110657 Iteration 2 Error: 0.209846 Iteration 3 Error: 0.075888 Iteration 4 Error: 0.026791 Align patch 12 13 left Iteration 1 Error: 0.958187 Iteration 2 Error: 0.220631 Iteration 3 Error: 0.049523 Align patch 13 12 left Iteration 1 Error: 1.171800 Iteration 2 Error: 0.129828 Iteration 3 Error: 0.040927 Align patch 14 11 left Iteration 1 Error: 1.165428 Iteration 2 Error: 0.191743 Iteration 3 Error: 0.073295 Iteration 4 Error: 0.026549 Align patch 15 10 left Iteration 1 Error: 0.591312 Iteration 2 Error: 0.148966 Iteration 3 Error: 0.022423 Align patch 16 9 left Iteration 1 Error: 1.632822 Iteration 2 Error: 0.358353 Iteration 3 Error: 0.103683 Iteration 4 Error: 0.034547 Align patch 17 8 left Iteration 1 Error: 1.159851 Iteration 2 Error: 0.387987 Iteration 3 Error: 0.271571 Iteration 4 Error: 0.129754 Iteration 5 Error: 0.082524 Align patch 17 8 left Iteration 1 Error: 1.532140 Iteration 2 Error: 0.214736 Iteration 3 Error: 0.067173 Iteration 4 Error: 0.028252 Align patch 18 7 left Iteration 1 Error: 0.761087 Iteration 2 Error: 0.184872 Iteration 3 Error: 0.026959 Align patch 19 6 left Iteration 1 Error: 0.898136 Iteration 2 Error: 0.081916 Iteration 3 Error: 0.026992 Align patch 20 5 left Iteration 1 Error: 0.509375 Iteration 2 Error: 0.082125 Iteration 3 Error: 0.022989 Align patch 21 4 left Iteration 1 Error: 0.867009 Iteration 2 Error: 0.131337 Iteration 3 Error: 0.042296 Align patch 22 3 left Iteration 1 Error: 0.888020 Iteration 2 Error: 0.244515 Iteration 3 Error: 0.079963 Iteration 4 Error: 0.037530 Align patch 23 2 left Iteration 1 Error: 0.927682 Iteration 2 Error: 0.123231 Iteration 3 Error: 0.031590 Align patch 24 1 left Iteration 1 Error: 0.772014 Iteration 2 Error: 0.069074 Iteration 3 Error: 0.013740 Align patch 25 0 left Iteration 1 Error: 1.112067 Iteration 2 Error: 0.230158 Iteration 3 Error: 0.056243 Iteration 4 Error: 0.010722 3D Fitting completed. Patch alignment time: 13.90(sec) Local motion has been corrected. Process thread exits. Computational time: 28.375977 sec Total time: 35.829163 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00019hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00019hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.670729s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00019hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.993027s ........................................ >>>>>>TIME<<<<<< FFT: 0.912579s Defocus_U Defocus_V Angle CCC 14601.56 15390.62 3.02 0.052319 Final Values Defocus_U Defocus_V Angle CCC 14606.25 15420.34 4.30 0.088071 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00019hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00019hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 1.000e-01 CC threshold: 0.734 Mean Std: 46.49 7.75 Num Hot pixels: 183 Hot pixel threshold: 93.00 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.087544 Iteration 2 Error: 0.050603 Iteration 3 Error: 0.020731 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.36 -0.07 ...... Frame ( 3) shift: -0.72 -0.15 ...... Frame ( 4) shift: -1.07 -0.22 ...... Frame ( 5) shift: -1.43 -0.29 ...... Frame ( 6) shift: -1.52 -0.24 ...... Frame ( 7) shift: -1.36 -0.06 ...... Frame ( 8) shift: -1.19 0.12 ...... Frame ( 9) shift: -1.06 0.30 ...... Frame ( 10) shift: -0.97 0.48 ...... Frame ( 11) shift: -0.88 0.65 ...... Frame ( 12) shift: -0.79 0.74 ...... Frame ( 13) shift: -0.70 0.72 ...... Frame ( 14) shift: -0.61 0.71 ...... Frame ( 15) shift: -0.53 0.70 ...... Frame ( 16) shift: -0.47 0.69 ...... Frame ( 17) shift: -0.40 0.68 ...... Frame ( 18) shift: -0.39 0.68 ...... Frame ( 19) shift: -0.44 0.68 ...... Frame ( 20) shift: -0.49 0.68 ...... Frame ( 21) shift: -0.50 0.67 ...... Frame ( 22) shift: -0.48 0.64 ...... Frame ( 23) shift: -0.46 0.61 ...... Frame ( 24) shift: -0.47 0.55 ...... Frame ( 25) shift: -0.49 0.45 ...... Frame ( 26) shift: -0.51 0.36 ...... Frame ( 27) shift: -0.55 0.28 ...... Frame ( 28) shift: -0.60 0.22 ...... Frame ( 29) shift: -0.65 0.16 ...... Frame ( 30) shift: -0.66 0.11 ...... Frame ( 31) shift: -0.63 0.08 ...... Frame ( 32) shift: -0.60 0.05 ...... Frame ( 33) shift: -0.60 0.02 ...... Frame ( 34) shift: -0.63 -0.01 ...... Frame ( 35) shift: -0.66 -0.04 ...... Frame ( 36) shift: -0.68 -0.05 ...... Frame ( 37) shift: -0.70 -0.04 ...... Frame ( 38) shift: -0.71 -0.03 ...... Frame ( 39) shift: -0.73 -0.02 ...... Frame ( 40) shift: -0.75 -0.01 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.920739 Iteration 2 Error: 0.157299 Iteration 3 Error: 0.029830 Align patch 2 23 left Iteration 1 Error: 0.834325 Iteration 2 Error: 0.214875 Iteration 3 Error: 0.043061 Align patch 3 22 left Iteration 1 Error: 0.706967 Iteration 2 Error: 0.211647 Iteration 3 Error: 0.047464 Align patch 4 21 left Iteration 1 Error: 1.057383 Iteration 2 Error: 0.106406 Iteration 3 Error: 0.024215 Align patch 5 20 left Iteration 1 Error: 0.683397 Iteration 2 Error: 0.089163 Iteration 3 Error: 0.029290 Align patch 6 19 left Iteration 1 Error: 0.639015 Iteration 2 Error: 0.099527 Iteration 3 Error: 0.041502 Align patch 7 18 left Iteration 1 Error: 0.730027 Iteration 2 Error: 0.167385 Iteration 3 Error: 0.046704 Align patch 8 17 left Iteration 1 Error: 1.061129 Iteration 2 Error: 0.136566 Iteration 3 Error: 0.034328 Align patch 9 16 left Iteration 1 Error: 1.080573 Iteration 2 Error: 0.125789 Iteration 3 Error: 0.039773 Align patch 10 15 left Iteration 1 Error: 0.409454 Iteration 2 Error: 0.072318 Iteration 3 Error: 0.013579 Align patch 11 14 left Iteration 1 Error: 0.911656 Iteration 2 Error: 0.116485 Iteration 3 Error: 0.039702 Align patch 12 13 left Iteration 1 Error: 0.814890 Iteration 2 Error: 0.152750 Iteration 3 Error: 0.041480 Align patch 13 12 left Iteration 1 Error: 0.911400 Iteration 2 Error: 0.273599 Iteration 3 Error: 0.086712 Iteration 4 Error: 0.018837 Align patch 14 11 left Iteration 1 Error: 0.852241 Iteration 2 Error: 0.075406 Iteration 3 Error: 0.020657 Align patch 15 10 left Iteration 1 Error: 0.642637 Iteration 2 Error: 0.088837 Iteration 3 Error: 0.011694 Align patch 16 9 left Iteration 1 Error: 1.196014 Iteration 2 Error: 0.169021 Iteration 3 Error: 0.051526 Iteration 4 Error: 0.021348 Align patch 17 8 left Iteration 1 Error: 1.610343 Iteration 2 Error: 0.226842 Iteration 3 Error: 0.045136 Align patch 18 7 left Iteration 1 Error: 1.117433 Iteration 2 Error: 0.078248 Iteration 3 Error: 0.019666 Align patch 19 6 left Iteration 1 Error: 1.048914 Iteration 2 Error: 0.110130 Iteration 3 Error: 0.028314 Align patch 20 5 left Iteration 1 Error: 0.706157 Iteration 2 Error: 0.100424 Iteration 3 Error: 0.019234 Align patch 21 4 left Iteration 1 Error: 1.360097 Iteration 2 Error: 0.223923 Iteration 3 Error: 0.072984 Iteration 4 Error: 0.019522 Align patch 22 3 left Iteration 1 Error: 1.444069 Iteration 2 Error: 0.207691 Iteration 3 Error: 0.046679 Align patch 23 2 left Iteration 1 Error: 1.080538 Iteration 2 Error: 0.119632 Iteration 3 Error: 0.034065 Align patch 24 1 left Iteration 1 Error: 0.473811 Iteration 2 Error: 0.059907 Iteration 3 Error: 0.015144 Align patch 25 0 left Iteration 1 Error: 0.823166 Iteration 2 Error: 0.112536 Iteration 3 Error: 0.028034 3D Fitting completed. Patch alignment time: 11.86(sec) Local motion has been corrected. Process thread exits. Computational time: 23.018791 sec Total time: 29.901505 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00019hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00019hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.696963s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00019hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.907856s ........................................ >>>>>>TIME<<<<<< FFT: 0.920615s Defocus_U Defocus_V Angle CCC 14375.02 13820.32 81.96 0.054654 Final Values Defocus_U Defocus_V Angle CCC 14381.27 13807.82 82.90 0.092782 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00020hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00020hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.342e-01 9.983e-02 CC threshold: 0.733 Mean Std: 45.49 7.62 Num Hot pixels: 189 Hot pixel threshold: 91.21 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.003445 Iteration 2 Error: 0.639200 Iteration 3 Error: 0.455110 Iteration 4 Error: 0.285329 Iteration 5 Error: 0.215720 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.30 -0.00 ...... Frame ( 3) shift: -0.59 -0.00 ...... Frame ( 4) shift: -0.89 -0.00 ...... Frame ( 5) shift: -1.18 -0.00 ...... Frame ( 6) shift: -1.35 0.02 ...... Frame ( 7) shift: -1.39 0.08 ...... Frame ( 8) shift: -1.43 0.14 ...... Frame ( 9) shift: -1.48 0.30 ...... Frame ( 10) shift: -1.55 0.56 ...... Frame ( 11) shift: -1.61 0.83 ...... Frame ( 12) shift: -1.72 1.09 ...... Frame ( 13) shift: -1.88 1.35 ...... Frame ( 14) shift: -2.03 1.61 ...... Frame ( 15) shift: -2.19 1.82 ...... Frame ( 16) shift: -2.33 1.97 ...... Frame ( 17) shift: -2.48 2.13 ...... Frame ( 18) shift: -2.63 2.29 ...... Frame ( 19) shift: -2.78 2.47 ...... Frame ( 20) shift: -2.92 2.65 ...... Frame ( 21) shift: -3.01 2.81 ...... Frame ( 22) shift: -3.05 2.95 ...... Frame ( 23) shift: -3.08 3.09 ...... Frame ( 24) shift: -3.12 3.22 ...... Frame ( 25) shift: -3.18 3.35 ...... Frame ( 26) shift: -3.24 3.48 ...... Frame ( 27) shift: -3.30 3.62 ...... Frame ( 28) shift: -3.36 3.77 ...... Frame ( 29) shift: -3.42 3.92 ...... Frame ( 30) shift: -3.48 4.03 ...... Frame ( 31) shift: -3.55 4.12 ...... Frame ( 32) shift: -3.62 4.21 ...... Frame ( 33) shift: -3.69 4.31 ...... Frame ( 34) shift: -3.78 4.43 ...... Frame ( 35) shift: -3.86 4.55 ...... Frame ( 36) shift: -3.91 4.67 ...... Frame ( 37) shift: -3.93 4.77 ...... Frame ( 38) shift: -3.95 4.88 ...... Frame ( 39) shift: -3.97 4.99 ...... Frame ( 40) shift: -3.99 5.10 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.180543 Iteration 2 Error: 0.255209 Iteration 3 Error: 0.131855 Iteration 4 Error: 0.047923 Align patch 2 23 left Iteration 1 Error: 1.814319 Iteration 2 Error: 0.672068 Iteration 3 Error: 0.131540 Iteration 4 Error: 0.060236 Iteration 5 Error: 0.045857 Align patch 3 22 left Iteration 1 Error: 0.654280 Iteration 2 Error: 0.211682 Iteration 3 Error: 0.111765 Iteration 4 Error: 0.067433 Iteration 5 Error: 0.057433 Align patch 3 22 left Iteration 1 Error: 1.464141 Iteration 2 Error: 0.446813 Iteration 3 Error: 0.183409 Iteration 4 Error: 0.061971 Iteration 5 Error: 0.030370 Align patch 4 21 left Iteration 1 Error: 1.441170 Iteration 2 Error: 0.525581 Iteration 3 Error: 0.191014 Iteration 4 Error: 0.127125 Iteration 5 Error: 0.061571 Align patch 4 21 left Iteration 1 Error: 1.982934 Iteration 2 Error: 0.545977 Iteration 3 Error: 0.219725 Iteration 4 Error: 0.083583 Iteration 5 Error: 0.034377 Align patch 5 20 left Iteration 1 Error: 3.483146 Iteration 2 Error: 2.715257 Iteration 3 Error: 1.060339 Iteration 4 Error: 0.652836 Iteration 5 Error: 0.454036 Align patch 5 20 left Iteration 1 Error: 3.063641 Iteration 2 Error: 1.435673 Iteration 3 Error: 0.764218 Iteration 4 Error: 0.405141 Iteration 5 Error: 0.218632 Align patch 6 19 left Iteration 1 Error: 2.125914 Iteration 2 Error: 0.288694 Iteration 3 Error: 0.142815 Iteration 4 Error: 0.062697 Iteration 5 Error: 0.028266 Align patch 7 18 left Iteration 1 Error: 2.130338 Iteration 2 Error: 0.510233 Iteration 3 Error: 0.322529 Iteration 4 Error: 0.163718 Iteration 5 Error: 0.098630 Align patch 7 18 left Iteration 1 Error: 2.180606 Iteration 2 Error: 0.460236 Iteration 3 Error: 0.165182 Iteration 4 Error: 0.086718 Iteration 5 Error: 0.041807 Align patch 8 17 left Iteration 1 Error: 4.487227 Iteration 2 Error: 1.427734 Iteration 3 Error: 0.336743 Iteration 4 Error: 0.154214 Iteration 5 Error: 0.076151 Align patch 8 17 left Iteration 1 Error: 2.974656 Iteration 2 Error: 0.689008 Iteration 3 Error: 0.161213 Iteration 4 Error: 0.067282 Iteration 5 Error: 0.029655 Align patch 9 16 left Iteration 1 Error: 4.930771 Iteration 2 Error: 2.390764 Iteration 3 Error: 0.538946 Iteration 4 Error: 0.279108 Iteration 5 Error: 0.103476 Align patch 9 16 left Iteration 1 Error: 3.313306 Iteration 2 Error: 0.986476 Iteration 3 Error: 0.307741 Iteration 4 Error: 0.136199 Iteration 5 Error: 0.066545 Align patch 10 15 left Iteration 1 Error: 3.387481 Iteration 2 Error: 2.256626 Iteration 3 Error: 1.024327 Iteration 4 Error: 0.777975 Iteration 5 Error: 0.539039 Align patch 10 15 left Iteration 1 Error: 3.140657 Iteration 2 Error: 1.530430 Iteration 3 Error: 0.860389 Iteration 4 Error: 0.479523 Iteration 5 Error: 0.238718 Align patch 11 14 left Iteration 1 Error: 2.420168 Iteration 2 Error: 0.609247 Iteration 3 Error: 0.210032 Iteration 4 Error: 0.110094 Iteration 5 Error: 0.046469 Align patch 12 13 left Iteration 1 Error: 2.710130 Iteration 2 Error: 0.546173 Iteration 3 Error: 0.337089 Iteration 4 Error: 0.210629 Iteration 5 Error: 0.147663 Align patch 12 13 left Iteration 1 Error: 2.414914 Iteration 2 Error: 0.529626 Iteration 3 Error: 0.209884 Iteration 4 Error: 0.083080 Iteration 5 Error: 0.023163 Align patch 13 12 left Iteration 1 Error: 2.640097 Iteration 2 Error: 1.076353 Iteration 3 Error: 0.686743 Iteration 4 Error: 0.397171 Iteration 5 Error: 0.246823 Align patch 13 12 left Iteration 1 Error: 2.476612 Iteration 2 Error: 0.805183 Iteration 3 Error: 0.219262 Iteration 4 Error: 0.109133 Iteration 5 Error: 0.062874 Align patch 14 11 left Iteration 1 Error: 3.441976 Iteration 2 Error: 1.995873 Iteration 3 Error: 0.544315 Iteration 4 Error: 0.205496 Iteration 5 Error: 0.095892 Align patch 14 11 left Iteration 1 Error: 3.479236 Iteration 2 Error: 1.105408 Iteration 3 Error: 0.334446 Iteration 4 Error: 0.141148 Iteration 5 Error: 0.049525 Align patch 15 10 left Iteration 1 Error: 1.820673 Iteration 2 Error: 0.859260 Iteration 3 Error: 0.809019 Iteration 4 Error: 0.729291 Iteration 5 Error: 0.561114 Align patch 15 10 left Iteration 1 Error: 2.394055 Iteration 2 Error: 0.980461 Iteration 3 Error: 0.434763 Iteration 4 Error: 0.216364 Iteration 5 Error: 0.105413 Align patch 16 9 left Iteration 1 Error: 1.251804 Iteration 2 Error: 0.295009 Iteration 3 Error: 0.160267 Iteration 4 Error: 0.066192 Iteration 5 Error: 0.029469 Align patch 17 8 left Iteration 1 Error: 1.844759 Iteration 2 Error: 0.472390 Iteration 3 Error: 0.190976 Iteration 4 Error: 0.111168 Iteration 5 Error: 0.063628 Align patch 17 8 left Iteration 1 Error: 1.681191 Iteration 2 Error: 0.450401 Iteration 3 Error: 0.149383 Iteration 4 Error: 0.043869 Align patch 18 7 left Iteration 1 Error: 2.692680 Iteration 2 Error: 0.622655 Iteration 3 Error: 0.505188 Iteration 4 Error: 0.196556 Iteration 5 Error: 0.116707 Align patch 18 7 left Iteration 1 Error: 1.257304 Iteration 2 Error: 0.376130 Iteration 3 Error: 0.089862 Iteration 4 Error: 0.041444 Align patch 19 6 left Iteration 1 Error: 1.398580 Iteration 2 Error: 0.383868 Iteration 3 Error: 0.301565 Iteration 4 Error: 0.167871 Iteration 5 Error: 0.119068 Align patch 19 6 left Iteration 1 Error: 1.445539 Iteration 2 Error: 0.308463 Iteration 3 Error: 0.090186 Iteration 4 Error: 0.035810 Align patch 20 5 left Iteration 1 Error: 0.912266 Iteration 2 Error: 0.227189 Iteration 3 Error: 0.096851 Iteration 4 Error: 0.053448 Iteration 5 Error: 0.028246 Align patch 21 4 left Iteration 1 Error: 1.161758 Iteration 2 Error: 0.398820 Iteration 3 Error: 0.184013 Iteration 4 Error: 0.056686 Iteration 5 Error: 0.035057 Align patch 22 3 left Iteration 1 Error: 1.610583 Iteration 2 Error: 0.314731 Iteration 3 Error: 0.116556 Iteration 4 Error: 0.061260 Iteration 5 Error: 0.023718 Align patch 23 2 left Iteration 1 Error: 1.072093 Iteration 2 Error: 0.185385 Iteration 3 Error: 0.060584 Iteration 4 Error: 0.022154 Align patch 24 1 left Iteration 1 Error: 1.339404 Iteration 2 Error: 0.403091 Iteration 3 Error: 0.139199 Iteration 4 Error: 0.074686 Iteration 5 Error: 0.025803 Align patch 25 0 left Iteration 1 Error: 2.112760 Iteration 2 Error: 0.553844 Iteration 3 Error: 0.102242 Iteration 4 Error: 0.032756 3D Fitting completed. Patch alignment time: 24.72(sec) Local motion has been corrected. Process thread exits. Computational time: 35.328598 sec Total time: 42.468910 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00020hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00020hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.505898s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00020hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.742982s ........................................ >>>>>>TIME<<<<<< FFT: 0.893077s Defocus_U Defocus_V Angle CCC 9470.70 10259.77 13.03 0.051689 Final Values Defocus_U Defocus_V Angle CCC 9462.88 10280.09 13.97 0.103872 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00020hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00020hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.998e-02 CC threshold: 0.734 Mean Std: 45.65 7.78 Num Hot pixels: 175 Hot pixel threshold: 92.30 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.603430 Iteration 2 Error: 0.150011 Iteration 3 Error: 0.041872 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.32 0.11 ...... Frame ( 3) shift: -0.64 0.22 ...... Frame ( 4) shift: -0.96 0.33 ...... Frame ( 5) shift: -1.28 0.44 ...... Frame ( 6) shift: -1.41 0.59 ...... Frame ( 7) shift: -1.37 0.77 ...... Frame ( 8) shift: -1.32 0.96 ...... Frame ( 9) shift: -1.25 1.13 ...... Frame ( 10) shift: -1.18 1.27 ...... Frame ( 11) shift: -1.10 1.41 ...... Frame ( 12) shift: -1.05 1.53 ...... Frame ( 13) shift: -1.02 1.63 ...... Frame ( 14) shift: -0.99 1.72 ...... Frame ( 15) shift: -0.97 1.80 ...... Frame ( 16) shift: -0.96 1.86 ...... Frame ( 17) shift: -0.95 1.92 ...... Frame ( 18) shift: -0.97 1.95 ...... Frame ( 19) shift: -1.00 1.96 ...... Frame ( 20) shift: -1.04 1.96 ...... Frame ( 21) shift: -1.07 2.01 ...... Frame ( 22) shift: -1.08 2.10 ...... Frame ( 23) shift: -1.09 2.19 ...... Frame ( 24) shift: -1.09 2.24 ...... Frame ( 25) shift: -1.07 2.26 ...... Frame ( 26) shift: -1.05 2.28 ...... Frame ( 27) shift: -1.02 2.25 ...... Frame ( 28) shift: -0.99 2.18 ...... Frame ( 29) shift: -0.95 2.10 ...... Frame ( 30) shift: -0.93 2.11 ...... Frame ( 31) shift: -0.91 2.19 ...... Frame ( 32) shift: -0.89 2.27 ...... Frame ( 33) shift: -0.86 2.36 ...... Frame ( 34) shift: -0.82 2.48 ...... Frame ( 35) shift: -0.78 2.59 ...... Frame ( 36) shift: -0.74 2.63 ...... Frame ( 37) shift: -0.71 2.58 ...... Frame ( 38) shift: -0.68 2.53 ...... Frame ( 39) shift: -0.64 2.49 ...... Frame ( 40) shift: -0.61 2.44 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.251843 Iteration 2 Error: 0.321613 Iteration 3 Error: 0.250297 Iteration 4 Error: 0.183722 Iteration 5 Error: 0.121155 Align patch 1 24 left Iteration 1 Error: 1.410471 Iteration 2 Error: 0.118693 Iteration 3 Error: 0.034397 Align patch 2 23 left Iteration 1 Error: 0.912917 Iteration 2 Error: 0.127886 Iteration 3 Error: 0.040367 Align patch 3 22 left Iteration 1 Error: 0.829797 Iteration 2 Error: 0.133430 Iteration 3 Error: 0.036564 Align patch 4 21 left Iteration 1 Error: 0.683688 Iteration 2 Error: 0.242831 Iteration 3 Error: 0.087214 Iteration 4 Error: 0.037127 Align patch 5 20 left Iteration 1 Error: 0.817533 Iteration 2 Error: 0.112337 Iteration 3 Error: 0.024623 Align patch 6 19 left Iteration 1 Error: 1.112779 Iteration 2 Error: 0.221596 Iteration 3 Error: 0.031651 Align patch 7 18 left Iteration 1 Error: 0.675531 Iteration 2 Error: 0.168835 Iteration 3 Error: 0.066747 Iteration 4 Error: 0.027484 Align patch 8 17 left Iteration 1 Error: 0.682366 Iteration 2 Error: 0.176647 Iteration 3 Error: 0.058554 Iteration 4 Error: 0.029108 Align patch 9 16 left Iteration 1 Error: 1.361401 Iteration 2 Error: 0.095160 Iteration 3 Error: 0.025986 Align patch 10 15 left Iteration 1 Error: 0.714760 Iteration 2 Error: 0.188619 Iteration 3 Error: 0.059955 Iteration 4 Error: 0.019165 Align patch 11 14 left Iteration 1 Error: 0.872684 Iteration 2 Error: 0.214483 Iteration 3 Error: 0.084288 Iteration 4 Error: 0.031064 Align patch 12 13 left Iteration 1 Error: 1.197562 Iteration 2 Error: 0.222718 Iteration 3 Error: 0.110299 Iteration 4 Error: 0.020775 Align patch 13 12 left Iteration 1 Error: 0.865581 Iteration 2 Error: 0.190505 Iteration 3 Error: 0.108301 Iteration 4 Error: 0.031072 Align patch 14 11 left Iteration 1 Error: 0.876539 Iteration 2 Error: 0.127727 Iteration 3 Error: 0.034015 Align patch 15 10 left Iteration 1 Error: 0.879394 Iteration 2 Error: 0.166333 Iteration 3 Error: 0.029570 Align patch 16 9 left Iteration 1 Error: 1.679005 Iteration 2 Error: 0.258052 Iteration 3 Error: 0.144537 Iteration 4 Error: 0.057470 Iteration 5 Error: 0.020983 Align patch 17 8 left Iteration 1 Error: 1.152311 Iteration 2 Error: 0.296086 Iteration 3 Error: 0.071262 Iteration 4 Error: 0.032269 Align patch 18 7 left Iteration 1 Error: 1.405235 Iteration 2 Error: 0.228413 Iteration 3 Error: 0.063153 Iteration 4 Error: 0.025450 Align patch 19 6 left Iteration 1 Error: 0.500406 Iteration 2 Error: 0.097032 Iteration 3 Error: 0.022758 Align patch 20 5 left Iteration 1 Error: 0.675913 Iteration 2 Error: 0.079691 Iteration 3 Error: 0.026762 Align patch 21 4 left Iteration 1 Error: 0.687114 Iteration 2 Error: 0.189543 Iteration 3 Error: 0.043599 Align patch 22 3 left Iteration 1 Error: 0.998316 Iteration 2 Error: 0.218842 Iteration 3 Error: 0.050498 Iteration 4 Error: 0.024375 Align patch 23 2 left Iteration 1 Error: 0.651182 Iteration 2 Error: 0.112840 Iteration 3 Error: 0.034373 Align patch 24 1 left Iteration 1 Error: 0.858213 Iteration 2 Error: 0.125846 Iteration 3 Error: 0.033920 Align patch 25 0 left Iteration 1 Error: 0.751741 Iteration 2 Error: 0.133328 Iteration 3 Error: 0.021800 3D Fitting completed. Patch alignment time: 13.11(sec) Local motion has been corrected. Process thread exits. Computational time: 23.590603 sec Total time: 30.371426 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00020hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00020hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.714720s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00020hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.609966s ........................................ >>>>>>TIME<<<<<< FFT: 0.973517s Defocus_U Defocus_V Angle CCC 10393.46 10859.40 0.60 0.045829 Final Values Defocus_U Defocus_V Angle CCC 10405.96 10887.56 0.92 0.084273 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00006sq_v01_00020hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00020hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.001e-01 CC threshold: 0.735 Mean Std: 43.86 8.00 Num Hot pixels: 151 Hot pixel threshold: 91.85 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.917589 Iteration 2 Error: 0.095291 Iteration 3 Error: 0.017990 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.27 -0.00 ...... Frame ( 3) shift: -0.54 -0.00 ...... Frame ( 4) shift: -0.81 -0.00 ...... Frame ( 5) shift: -1.09 -0.00 ...... Frame ( 6) shift: -1.19 0.05 ...... Frame ( 7) shift: -1.14 0.16 ...... Frame ( 8) shift: -1.09 0.28 ...... Frame ( 9) shift: -1.03 0.40 ...... Frame ( 10) shift: -0.98 0.52 ...... Frame ( 11) shift: -0.93 0.65 ...... Frame ( 12) shift: -0.86 0.73 ...... Frame ( 13) shift: -0.76 0.77 ...... Frame ( 14) shift: -0.66 0.80 ...... Frame ( 15) shift: -0.60 0.84 ...... Frame ( 16) shift: -0.58 0.89 ...... Frame ( 17) shift: -0.56 0.93 ...... Frame ( 18) shift: -0.54 0.94 ...... Frame ( 19) shift: -0.53 0.90 ...... Frame ( 20) shift: -0.52 0.87 ...... Frame ( 21) shift: -0.49 0.85 ...... Frame ( 22) shift: -0.45 0.85 ...... Frame ( 23) shift: -0.41 0.85 ...... Frame ( 24) shift: -0.37 0.84 ...... Frame ( 25) shift: -0.32 0.80 ...... Frame ( 26) shift: -0.27 0.76 ...... Frame ( 27) shift: -0.25 0.74 ...... Frame ( 28) shift: -0.25 0.75 ...... Frame ( 29) shift: -0.25 0.76 ...... Frame ( 30) shift: -0.24 0.76 ...... Frame ( 31) shift: -0.21 0.75 ...... Frame ( 32) shift: -0.19 0.75 ...... Frame ( 33) shift: -0.17 0.75 ...... Frame ( 34) shift: -0.15 0.74 ...... Frame ( 35) shift: -0.13 0.74 ...... Frame ( 36) shift: -0.11 0.72 ...... Frame ( 37) shift: -0.10 0.67 ...... Frame ( 38) shift: -0.09 0.62 ...... Frame ( 39) shift: -0.07 0.58 ...... Frame ( 40) shift: -0.06 0.53 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 3.876885 Iteration 2 Error: 0.280436 Iteration 3 Error: 0.083774 Iteration 4 Error: 0.023758 Align patch 2 23 left Iteration 1 Error: 1.793972 Iteration 2 Error: 0.171681 Iteration 3 Error: 0.053081 Iteration 4 Error: 0.017399 Align patch 3 22 left Iteration 1 Error: 1.518388 Iteration 2 Error: 0.176109 Iteration 3 Error: 0.044253 Align patch 4 21 left Iteration 1 Error: 1.245722 Iteration 2 Error: 0.106797 Iteration 3 Error: 0.011692 Align patch 5 20 left Iteration 1 Error: 1.453083 Iteration 2 Error: 0.081151 Iteration 3 Error: 0.009543 Align patch 6 19 left Iteration 1 Error: 1.552326 Iteration 2 Error: 0.293046 Iteration 3 Error: 0.074393 Iteration 4 Error: 0.028723 Align patch 7 18 left Iteration 1 Error: 1.084740 Iteration 2 Error: 0.143780 Iteration 3 Error: 0.029097 Align patch 8 17 left Iteration 1 Error: 0.863773 Iteration 2 Error: 0.156678 Iteration 3 Error: 0.035960 Align patch 9 16 left Iteration 1 Error: 0.670748 Iteration 2 Error: 0.098648 Iteration 3 Error: 0.022335 Align patch 10 15 left Iteration 1 Error: 1.841760 Iteration 2 Error: 0.092222 Iteration 3 Error: 0.006259 Align patch 11 14 left Iteration 1 Error: 0.961055 Iteration 2 Error: 0.248944 Iteration 3 Error: 0.104873 Iteration 4 Error: 0.028275 Align patch 12 13 left Iteration 1 Error: 0.836787 Iteration 2 Error: 0.137771 Iteration 3 Error: 0.021986 Align patch 13 12 left Iteration 1 Error: 2.638495 Iteration 2 Error: 0.925597 Iteration 3 Error: 0.345851 Iteration 4 Error: 0.123060 Iteration 5 Error: 0.042648 Align patch 14 11 left Iteration 1 Error: 1.107580 Iteration 2 Error: 0.093564 Iteration 3 Error: 0.019141 Align patch 15 10 left Iteration 1 Error: 0.873504 Iteration 2 Error: 0.259297 Iteration 3 Error: 0.059252 Iteration 4 Error: 0.025175 Align patch 16 9 left Iteration 1 Error: 1.316636 Iteration 2 Error: 0.321379 Iteration 3 Error: 0.170551 Iteration 4 Error: 0.060812 Iteration 5 Error: 0.041345 Align patch 17 8 left Iteration 1 Error: 1.032972 Iteration 2 Error: 0.224341 Iteration 3 Error: 0.048353 Align patch 18 7 left Iteration 1 Error: 0.738072 Iteration 2 Error: 0.126224 Iteration 3 Error: 0.027285 Align patch 19 6 left Iteration 1 Error: 1.198000 Iteration 2 Error: 0.172529 Iteration 3 Error: 0.060091 Iteration 4 Error: 0.020352 Align patch 20 5 left Iteration 1 Error: 0.808310 Iteration 2 Error: 0.170000 Iteration 3 Error: 0.028331 Align patch 21 4 left Iteration 1 Error: 0.965696 Iteration 2 Error: 0.181836 Iteration 3 Error: 0.052862 Iteration 4 Error: 0.016868 Align patch 22 3 left Iteration 1 Error: 1.053163 Iteration 2 Error: 0.183374 Iteration 3 Error: 0.047557 Align patch 23 2 left Iteration 1 Error: 1.178026 Iteration 2 Error: 0.155913 Iteration 3 Error: 0.068341 Iteration 4 Error: 0.016529 Align patch 24 1 left Iteration 1 Error: 1.097834 Iteration 2 Error: 0.238701 Iteration 3 Error: 0.056329 Iteration 4 Error: 0.024664 Align patch 25 0 left Iteration 1 Error: 0.962762 Iteration 2 Error: 0.220107 Iteration 3 Error: 0.027544 3D Fitting completed. Patch alignment time: 12.59(sec) Local motion has been corrected. Process thread exits. Computational time: 23.751181 sec Total time: 30.182657 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00020hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00020hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.509162s Reading file: gc_18feb27f_CTD_g1_00012gr_00006sq_v01_00020hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.451371s ........................................ >>>>>>TIME<<<<<< FFT: 1.105146s Defocus_U Defocus_V Angle CCC 14826.18 14115.25 85.11 0.065162 Final Values Defocus_U Defocus_V Angle CCC 14830.88 14113.69 85.11 0.107474 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00007sq_v01_00002hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00002hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.319e-01 9.835e-02 CC threshold: 0.722 Mean Std: 39.53 6.82 Num Hot pixels: 174 Hot pixel threshold: 80.47 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.980494 Iteration 2 Error: 0.374400 Iteration 3 Error: 0.172185 Iteration 4 Error: 0.071789 Iteration 5 Error: 0.032540 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.22 -0.43 ...... Frame ( 3) shift: -0.44 -0.85 ...... Frame ( 4) shift: -0.66 -1.28 ...... Frame ( 5) shift: -0.89 -1.71 ...... Frame ( 6) shift: -1.07 -2.10 ...... Frame ( 7) shift: -1.21 -2.45 ...... Frame ( 8) shift: -1.36 -2.79 ...... Frame ( 9) shift: -1.46 -3.07 ...... Frame ( 10) shift: -1.53 -3.27 ...... Frame ( 11) shift: -1.60 -3.47 ...... Frame ( 12) shift: -1.70 -3.67 ...... Frame ( 13) shift: -1.84 -3.87 ...... Frame ( 14) shift: -1.98 -4.07 ...... Frame ( 15) shift: -2.04 -4.20 ...... Frame ( 16) shift: -2.04 -4.26 ...... Frame ( 17) shift: -2.04 -4.33 ...... Frame ( 18) shift: -2.05 -4.40 ...... Frame ( 19) shift: -2.06 -4.48 ...... Frame ( 20) shift: -2.08 -4.56 ...... Frame ( 21) shift: -2.10 -4.59 ...... Frame ( 22) shift: -2.13 -4.57 ...... Frame ( 23) shift: -2.17 -4.56 ...... Frame ( 24) shift: -2.15 -4.53 ...... Frame ( 25) shift: -2.10 -4.50 ...... Frame ( 26) shift: -2.04 -4.46 ...... Frame ( 27) shift: -1.97 -4.47 ...... Frame ( 28) shift: -1.89 -4.52 ...... Frame ( 29) shift: -1.81 -4.58 ...... Frame ( 30) shift: -1.77 -4.60 ...... Frame ( 31) shift: -1.80 -4.60 ...... Frame ( 32) shift: -1.82 -4.60 ...... Frame ( 33) shift: -1.82 -4.59 ...... Frame ( 34) shift: -1.79 -4.57 ...... Frame ( 35) shift: -1.77 -4.56 ...... Frame ( 36) shift: -1.75 -4.52 ...... Frame ( 37) shift: -1.72 -4.44 ...... Frame ( 38) shift: -1.70 -4.37 ...... Frame ( 39) shift: -1.68 -4.30 ...... Frame ( 40) shift: -1.66 -4.22 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 4.641487 Iteration 2 Error: 1.428859 Iteration 3 Error: 0.374896 Iteration 4 Error: 0.228068 Iteration 5 Error: 0.129926 Align patch 1 24 left Iteration 1 Error: 3.626236 Iteration 2 Error: 0.481168 Iteration 3 Error: 0.164573 Iteration 4 Error: 0.042327 Align patch 2 23 left Iteration 1 Error: 2.514670 Iteration 2 Error: 0.483270 Iteration 3 Error: 0.191968 Iteration 4 Error: 0.096814 Iteration 5 Error: 0.034946 Align patch 3 22 left Iteration 1 Error: 3.658900 Iteration 2 Error: 0.402377 Iteration 3 Error: 0.124992 Iteration 4 Error: 0.063690 Iteration 5 Error: 0.022906 Align patch 4 21 left Iteration 1 Error: 1.697665 Iteration 2 Error: 0.269772 Iteration 3 Error: 0.063677 Iteration 4 Error: 0.020379 Align patch 5 20 left Iteration 1 Error: 2.503304 Iteration 2 Error: 0.299547 Iteration 3 Error: 0.099288 Iteration 4 Error: 0.034638 Align patch 6 19 left Iteration 1 Error: 5.575919 Iteration 2 Error: 0.977153 Iteration 3 Error: 0.333291 Iteration 4 Error: 0.102889 Iteration 5 Error: 0.051484 Align patch 6 19 left Iteration 1 Error: 4.433440 Iteration 2 Error: 0.620220 Iteration 3 Error: 0.141074 Iteration 4 Error: 0.041934 Align patch 7 18 left Iteration 1 Error: 3.834273 Iteration 2 Error: 1.174355 Iteration 3 Error: 0.225105 Iteration 4 Error: 0.094243 Iteration 5 Error: 0.037414 Align patch 8 17 left Iteration 1 Error: 3.122138 Iteration 2 Error: 0.704096 Iteration 3 Error: 0.122953 Iteration 4 Error: 0.030874 Align patch 9 16 left Iteration 1 Error: 1.100003 Iteration 2 Error: 0.186442 Iteration 3 Error: 0.042189 Align patch 10 15 left Iteration 1 Error: 2.195266 Iteration 2 Error: 0.256644 Iteration 3 Error: 0.051754 Iteration 4 Error: 0.020576 Align patch 11 14 left Iteration 1 Error: 6.186969 Iteration 2 Error: 1.521237 Iteration 3 Error: 0.262321 Iteration 4 Error: 0.095935 Iteration 5 Error: 0.036043 Align patch 12 13 left Iteration 1 Error: 4.069423 Iteration 2 Error: 0.556322 Iteration 3 Error: 0.207261 Iteration 4 Error: 0.055266 Iteration 5 Error: 0.017081 Align patch 13 12 left Iteration 1 Error: 1.508003 Iteration 2 Error: 0.271705 Iteration 3 Error: 0.093720 Iteration 4 Error: 0.031978 Align patch 14 11 left Iteration 1 Error: 0.872792 Iteration 2 Error: 0.243009 Iteration 3 Error: 0.179887 Iteration 4 Error: 0.107401 Iteration 5 Error: 0.092109 Align patch 14 11 left Iteration 1 Error: 0.823191 Iteration 2 Error: 0.099408 Iteration 3 Error: 0.027988 Align patch 15 10 left Iteration 1 Error: 2.065304 Iteration 2 Error: 0.379874 Iteration 3 Error: 0.129980 Iteration 4 Error: 0.038573 Align patch 16 9 left Iteration 1 Error: 4.989638 Iteration 2 Error: 1.391017 Iteration 3 Error: 0.467849 Iteration 4 Error: 0.239745 Iteration 5 Error: 0.075644 Align patch 16 9 left Iteration 1 Error: 3.861088 Iteration 2 Error: 0.336106 Iteration 3 Error: 0.101763 Iteration 4 Error: 0.032199 Align patch 17 8 left Iteration 1 Error: 2.956839 Iteration 2 Error: 0.540030 Iteration 3 Error: 0.239649 Iteration 4 Error: 0.062048 Iteration 5 Error: 0.029150 Align patch 18 7 left Iteration 1 Error: 1.017608 Iteration 2 Error: 0.216696 Iteration 3 Error: 0.050124 Iteration 4 Error: 0.036409 Align patch 19 6 left Iteration 1 Error: 1.231443 Iteration 2 Error: 0.246219 Iteration 3 Error: 0.078495 Iteration 4 Error: 0.032523 Align patch 20 5 left Iteration 1 Error: 2.645471 Iteration 2 Error: 0.494232 Iteration 3 Error: 0.102002 Iteration 4 Error: 0.030359 Align patch 21 4 left Iteration 1 Error: 3.166652 Iteration 2 Error: 0.441217 Iteration 3 Error: 0.258940 Iteration 4 Error: 0.060694 Iteration 5 Error: 0.036614 Align patch 22 3 left Iteration 1 Error: 2.518073 Iteration 2 Error: 0.458072 Iteration 3 Error: 0.149563 Iteration 4 Error: 0.056409 Iteration 5 Error: 0.020926 Align patch 23 2 left Iteration 1 Error: 0.875134 Iteration 2 Error: 0.250014 Iteration 3 Error: 0.087066 Iteration 4 Error: 0.029183 Align patch 24 1 left Iteration 1 Error: 1.916188 Iteration 2 Error: 0.433607 Iteration 3 Error: 0.126576 Iteration 4 Error: 0.046370 Align patch 25 0 left Iteration 1 Error: 2.225762 Iteration 2 Error: 0.458847 Iteration 3 Error: 0.139585 Iteration 4 Error: 0.048278 3D Fitting completed. Patch alignment time: 15.98(sec) Local motion has been corrected. Process thread exits. Computational time: 26.699274 sec Total time: 33.628235 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00002hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00002hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.637584s Reading file: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00002hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.820315s ........................................ >>>>>>TIME<<<<<< FFT: 0.935481s Defocus_U Defocus_V Angle CCC 9488.30 8785.18 82.68 -0.017686 Final Values Defocus_U Defocus_V Angle CCC 9505.49 8761.74 82.37 -0.124709 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00007sq_v01_00003hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00003hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 9.999e-02 CC threshold: 0.734 Mean Std: 42.71 7.05 Num Hot pixels: 197 Hot pixel threshold: 85.01 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.868575 Iteration 2 Error: 0.152430 Iteration 3 Error: 0.039337 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.12 -0.08 ...... Frame ( 3) shift: -0.23 -0.15 ...... Frame ( 4) shift: -0.35 -0.23 ...... Frame ( 5) shift: -0.46 -0.30 ...... Frame ( 6) shift: -0.49 -0.33 ...... Frame ( 7) shift: -0.42 -0.31 ...... Frame ( 8) shift: -0.36 -0.29 ...... Frame ( 9) shift: -0.30 -0.28 ...... Frame ( 10) shift: -0.26 -0.29 ...... Frame ( 11) shift: -0.21 -0.29 ...... Frame ( 12) shift: -0.13 -0.34 ...... Frame ( 13) shift: -0.03 -0.45 ...... Frame ( 14) shift: 0.07 -0.56 ...... Frame ( 15) shift: 0.18 -0.58 ...... Frame ( 16) shift: 0.29 -0.53 ...... Frame ( 17) shift: 0.40 -0.48 ...... Frame ( 18) shift: 0.50 -0.44 ...... Frame ( 19) shift: 0.59 -0.40 ...... Frame ( 20) shift: 0.69 -0.36 ...... Frame ( 21) shift: 0.77 -0.32 ...... Frame ( 22) shift: 0.84 -0.28 ...... Frame ( 23) shift: 0.90 -0.24 ...... Frame ( 24) shift: 0.95 -0.22 ...... Frame ( 25) shift: 0.98 -0.21 ...... Frame ( 26) shift: 1.00 -0.21 ...... Frame ( 27) shift: 1.03 -0.20 ...... Frame ( 28) shift: 1.07 -0.19 ...... Frame ( 29) shift: 1.11 -0.17 ...... Frame ( 30) shift: 1.12 -0.15 ...... Frame ( 31) shift: 1.11 -0.12 ...... Frame ( 32) shift: 1.10 -0.10 ...... Frame ( 33) shift: 1.08 -0.08 ...... Frame ( 34) shift: 1.07 -0.07 ...... Frame ( 35) shift: 1.06 -0.05 ...... Frame ( 36) shift: 1.09 -0.01 ...... Frame ( 37) shift: 1.17 0.06 ...... Frame ( 38) shift: 1.24 0.12 ...... Frame ( 39) shift: 1.32 0.19 ...... Frame ( 40) shift: 1.40 0.26 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.742670 Iteration 2 Error: 0.182066 Iteration 3 Error: 0.032773 Align patch 2 23 left Iteration 1 Error: 0.679989 Iteration 2 Error: 0.119249 Iteration 3 Error: 0.040927 Align patch 3 22 left Iteration 1 Error: 0.968920 Iteration 2 Error: 0.220869 Iteration 3 Error: 0.058302 Iteration 4 Error: 0.021220 Align patch 4 21 left Iteration 1 Error: 1.364928 Iteration 2 Error: 0.249811 Iteration 3 Error: 0.061605 Iteration 4 Error: 0.036576 Align patch 5 20 left Iteration 1 Error: 0.901117 Iteration 2 Error: 0.190485 Iteration 3 Error: 0.044752 Align patch 6 19 left Iteration 1 Error: 0.670743 Iteration 2 Error: 0.121515 Iteration 3 Error: 0.049619 Align patch 7 18 left Iteration 1 Error: 0.922074 Iteration 2 Error: 0.142364 Iteration 3 Error: 0.032428 Align patch 8 17 left Iteration 1 Error: 0.588773 Iteration 2 Error: 0.178815 Iteration 3 Error: 0.044264 Align patch 9 16 left Iteration 1 Error: 0.949823 Iteration 2 Error: 0.126002 Iteration 3 Error: 0.028323 Align patch 10 15 left Iteration 1 Error: 1.208397 Iteration 2 Error: 0.201607 Iteration 3 Error: 0.039029 Align patch 11 14 left Iteration 1 Error: 0.899177 Iteration 2 Error: 0.211340 Iteration 3 Error: 0.056806 Iteration 4 Error: 0.013335 Align patch 12 13 left Iteration 1 Error: 0.720457 Iteration 2 Error: 0.089898 Iteration 3 Error: 0.026969 Align patch 13 12 left Iteration 1 Error: 0.679318 Iteration 2 Error: 0.141483 Iteration 3 Error: 0.032393 Align patch 14 11 left Iteration 1 Error: 0.910618 Iteration 2 Error: 0.129955 Iteration 3 Error: 0.032851 Align patch 15 10 left Iteration 1 Error: 0.912990 Iteration 2 Error: 0.140042 Iteration 3 Error: 0.028830 Align patch 16 9 left Iteration 1 Error: 0.761673 Iteration 2 Error: 0.120359 Iteration 3 Error: 0.019980 Align patch 17 8 left Iteration 1 Error: 0.896124 Iteration 2 Error: 0.127629 Iteration 3 Error: 0.037902 Align patch 18 7 left Iteration 1 Error: 0.560348 Iteration 2 Error: 0.165249 Iteration 3 Error: 0.050010 Iteration 4 Error: 0.013052 Align patch 19 6 left Iteration 1 Error: 0.736592 Iteration 2 Error: 0.109928 Iteration 3 Error: 0.036152 Align patch 20 5 left Iteration 1 Error: 0.735375 Iteration 2 Error: 0.164639 Iteration 3 Error: 0.070413 Iteration 4 Error: 0.032103 Align patch 21 4 left Iteration 1 Error: 0.819461 Iteration 2 Error: 0.168429 Iteration 3 Error: 0.054515 Iteration 4 Error: 0.023085 Align patch 22 3 left Iteration 1 Error: 0.936644 Iteration 2 Error: 0.139141 Iteration 3 Error: 0.034744 Align patch 23 2 left Iteration 1 Error: 0.648956 Iteration 2 Error: 0.127774 Iteration 3 Error: 0.021909 Align patch 24 1 left Iteration 1 Error: 0.844543 Iteration 2 Error: 0.139530 Iteration 3 Error: 0.019001 Align patch 25 0 left Iteration 1 Error: 1.008100 Iteration 2 Error: 0.161644 Iteration 3 Error: 0.037700 3D Fitting completed. Patch alignment time: 12.33(sec) Local motion has been corrected. Process thread exits. Computational time: 23.284229 sec Total time: 30.526773 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00003hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00003hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.811184s Reading file: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00003hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.657970s ........................................ >>>>>>TIME<<<<<< FFT: 1.087085s Defocus_U Defocus_V Angle CCC 10802.77 10216.82 84.61 0.043042 Final Values Defocus_U Defocus_V Angle CCC 10810.57 10230.89 84.61 0.078107 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00007sq_v01_00003hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00003hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.338e-01 9.960e-02 CC threshold: 0.731 Mean Std: 41.85 6.96 Num Hot pixels: 216 Hot pixel threshold: 83.61 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.793963 Iteration 2 Error: 0.337868 Iteration 3 Error: 0.089363 Iteration 4 Error: 0.020360 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.03 -0.44 ...... Frame ( 3) shift: -0.06 -0.88 ...... Frame ( 4) shift: -0.08 -1.32 ...... Frame ( 5) shift: -0.11 -1.76 ...... Frame ( 6) shift: -0.21 -2.13 ...... Frame ( 7) shift: -0.36 -2.44 ...... Frame ( 8) shift: -0.52 -2.75 ...... Frame ( 9) shift: -0.63 -3.00 ...... Frame ( 10) shift: -0.68 -3.20 ...... Frame ( 11) shift: -0.74 -3.39 ...... Frame ( 12) shift: -0.79 -3.55 ...... Frame ( 13) shift: -0.84 -3.68 ...... Frame ( 14) shift: -0.88 -3.81 ...... Frame ( 15) shift: -0.91 -3.93 ...... Frame ( 16) shift: -0.91 -4.05 ...... Frame ( 17) shift: -0.92 -4.18 ...... Frame ( 18) shift: -0.92 -4.25 ...... Frame ( 19) shift: -0.92 -4.27 ...... Frame ( 20) shift: -0.93 -4.29 ...... Frame ( 21) shift: -0.90 -4.30 ...... Frame ( 22) shift: -0.84 -4.31 ...... Frame ( 23) shift: -0.78 -4.32 ...... Frame ( 24) shift: -0.75 -4.34 ...... Frame ( 25) shift: -0.74 -4.37 ...... Frame ( 26) shift: -0.73 -4.40 ...... Frame ( 27) shift: -0.71 -4.46 ...... Frame ( 28) shift: -0.69 -4.55 ...... Frame ( 29) shift: -0.67 -4.65 ...... Frame ( 30) shift: -0.64 -4.70 ...... Frame ( 31) shift: -0.62 -4.72 ...... Frame ( 32) shift: -0.60 -4.74 ...... Frame ( 33) shift: -0.57 -4.70 ...... Frame ( 34) shift: -0.53 -4.60 ...... Frame ( 35) shift: -0.50 -4.50 ...... Frame ( 36) shift: -0.47 -4.47 ...... Frame ( 37) shift: -0.45 -4.49 ...... Frame ( 38) shift: -0.43 -4.52 ...... Frame ( 39) shift: -0.41 -4.55 ...... Frame ( 40) shift: -0.38 -4.57 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.962892 Iteration 2 Error: 0.338707 Iteration 3 Error: 0.083597 Iteration 4 Error: 0.023031 Align patch 2 23 left Iteration 1 Error: 1.175918 Iteration 2 Error: 0.159101 Iteration 3 Error: 0.042232 Align patch 3 22 left Iteration 1 Error: 0.998476 Iteration 2 Error: 0.151969 Iteration 3 Error: 0.058519 Iteration 4 Error: 0.019022 Align patch 4 21 left Iteration 1 Error: 1.824942 Iteration 2 Error: 0.173324 Iteration 3 Error: 0.049496 Align patch 5 20 left Iteration 1 Error: 2.429990 Iteration 2 Error: 0.429214 Iteration 3 Error: 0.069809 Iteration 4 Error: 0.027516 Align patch 6 19 left Iteration 1 Error: 1.037072 Iteration 2 Error: 0.182767 Iteration 3 Error: 0.076009 Iteration 4 Error: 0.037660 Align patch 7 18 left Iteration 1 Error: 0.861069 Iteration 2 Error: 0.171950 Iteration 3 Error: 0.056731 Iteration 4 Error: 0.018760 Align patch 8 17 left Iteration 1 Error: 0.759780 Iteration 2 Error: 0.234343 Iteration 3 Error: 0.061855 Iteration 4 Error: 0.027026 Align patch 9 16 left Iteration 1 Error: 0.890530 Iteration 2 Error: 0.147429 Iteration 3 Error: 0.032597 Align patch 10 15 left Iteration 1 Error: 1.025186 Iteration 2 Error: 0.172717 Iteration 3 Error: 0.044587 Align patch 11 14 left Iteration 1 Error: 2.013158 Iteration 2 Error: 0.228192 Iteration 3 Error: 0.067984 Iteration 4 Error: 0.030952 Align patch 12 13 left Iteration 1 Error: 1.894614 Iteration 2 Error: 0.361986 Iteration 3 Error: 0.113091 Iteration 4 Error: 0.074340 Iteration 5 Error: 0.019426 Align patch 13 12 left Iteration 1 Error: 1.254715 Iteration 2 Error: 0.230849 Iteration 3 Error: 0.116131 Iteration 4 Error: 0.026370 Align patch 14 11 left Iteration 1 Error: 1.158747 Iteration 2 Error: 0.194027 Iteration 3 Error: 0.065539 Iteration 4 Error: 0.018058 Align patch 15 10 left Iteration 1 Error: 0.994948 Iteration 2 Error: 0.165854 Iteration 3 Error: 0.053003 Iteration 4 Error: 0.013636 Align patch 16 9 left Iteration 1 Error: 3.252748 Iteration 2 Error: 0.568163 Iteration 3 Error: 0.218357 Iteration 4 Error: 0.140988 Iteration 5 Error: 0.051071 Align patch 16 9 left Iteration 1 Error: 3.151433 Iteration 2 Error: 0.309397 Iteration 3 Error: 0.053231 Iteration 4 Error: 0.015346 Align patch 17 8 left Iteration 1 Error: 2.821202 Iteration 2 Error: 0.385547 Iteration 3 Error: 0.121719 Iteration 4 Error: 0.038124 Align patch 18 7 left Iteration 1 Error: 1.051130 Iteration 2 Error: 0.258920 Iteration 3 Error: 0.144785 Iteration 4 Error: 0.075139 Iteration 5 Error: 0.043384 Align patch 19 6 left Iteration 1 Error: 0.651797 Iteration 2 Error: 0.139996 Iteration 3 Error: 0.026815 Align patch 20 5 left Iteration 1 Error: 1.311012 Iteration 2 Error: 0.248577 Iteration 3 Error: 0.044797 Align patch 21 4 left Iteration 1 Error: 3.941046 Iteration 2 Error: 0.751011 Iteration 3 Error: 0.192069 Iteration 4 Error: 0.105302 Iteration 5 Error: 0.028211 Align patch 22 3 left Iteration 1 Error: 2.319510 Iteration 2 Error: 0.952119 Iteration 3 Error: 0.441777 Iteration 4 Error: 0.355175 Iteration 5 Error: 0.155761 Align patch 22 3 left Iteration 1 Error: 2.434407 Iteration 2 Error: 0.240981 Iteration 3 Error: 0.064220 Iteration 4 Error: 0.031937 Align patch 23 2 left Iteration 1 Error: 0.884325 Iteration 2 Error: 0.125576 Iteration 3 Error: 0.034888 Align patch 24 1 left Iteration 1 Error: 0.685937 Iteration 2 Error: 0.195073 Iteration 3 Error: 0.043777 Align patch 25 0 left Iteration 1 Error: 1.876411 Iteration 2 Error: 0.214933 Iteration 3 Error: 0.046567 3D Fitting completed. Patch alignment time: 13.94(sec) Local motion has been corrected. Process thread exits. Computational time: 25.049562 sec Total time: 32.030159 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00003hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00003hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.607579s Reading file: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00003hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.629590s ........................................ >>>>>>TIME<<<<<< FFT: 0.983943s Defocus_U Defocus_V Angle CCC 14494.14 15357.42 8.80 0.036516 Final Values Defocus_U Defocus_V Angle CCC 14500.28 15391.99 8.49 0.035463 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00007sq_v01_00005hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00005hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.329e-01 9.903e-02 CC threshold: 0.727 Mean Std: 38.51 10.44 Num Hot pixels: 56 Hot pixel threshold: 101.16 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.557607 Iteration 2 Error: 0.265825 Iteration 3 Error: 0.050603 Iteration 4 Error: 0.019099 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.03 -0.04 ...... Frame ( 3) shift: 0.05 -0.08 ...... Frame ( 4) shift: 0.08 -0.12 ...... Frame ( 5) shift: 0.11 -0.16 ...... Frame ( 6) shift: 0.16 -0.18 ...... Frame ( 7) shift: 0.23 -0.18 ...... Frame ( 8) shift: 0.31 -0.18 ...... Frame ( 9) shift: 0.39 -0.21 ...... Frame ( 10) shift: 0.47 -0.25 ...... Frame ( 11) shift: 0.55 -0.29 ...... Frame ( 12) shift: 0.65 -0.34 ...... Frame ( 13) shift: 0.77 -0.39 ...... Frame ( 14) shift: 0.88 -0.45 ...... Frame ( 15) shift: 1.00 -0.46 ...... Frame ( 16) shift: 1.14 -0.44 ...... Frame ( 17) shift: 1.27 -0.42 ...... Frame ( 18) shift: 1.40 -0.37 ...... Frame ( 19) shift: 1.52 -0.30 ...... Frame ( 20) shift: 1.63 -0.23 ...... Frame ( 21) shift: 1.72 -0.18 ...... Frame ( 22) shift: 1.78 -0.17 ...... Frame ( 23) shift: 1.84 -0.16 ...... Frame ( 24) shift: 1.92 -0.12 ...... Frame ( 25) shift: 2.01 -0.04 ...... Frame ( 26) shift: 2.10 0.04 ...... Frame ( 27) shift: 2.20 0.08 ...... Frame ( 28) shift: 2.31 0.09 ...... Frame ( 29) shift: 2.41 0.09 ...... Frame ( 30) shift: 2.48 0.12 ...... Frame ( 31) shift: 2.51 0.16 ...... Frame ( 32) shift: 2.53 0.21 ...... Frame ( 33) shift: 2.58 0.23 ...... Frame ( 34) shift: 2.63 0.24 ...... Frame ( 35) shift: 2.68 0.26 ...... Frame ( 36) shift: 2.76 0.31 ...... Frame ( 37) shift: 2.86 0.42 ...... Frame ( 38) shift: 2.96 0.53 ...... Frame ( 39) shift: 3.06 0.64 ...... Frame ( 40) shift: 3.16 0.75 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 18.101494 Iteration 2 Error: 15.869758 Iteration 3 Error: 0.465505 Iteration 4 Error: 0.158926 Iteration 5 Error: 0.083482 Align patch 1 24 left Iteration 1 Error: 2.829988 Iteration 2 Error: 0.728474 Iteration 3 Error: 0.266016 Iteration 4 Error: 0.126924 Iteration 5 Error: 0.048350 Align patch 2 23 left Iteration 1 Error: 2.130246 Iteration 2 Error: 0.431235 Iteration 3 Error: 0.210986 Iteration 4 Error: 0.103445 Iteration 5 Error: 0.052289 Align patch 2 23 left Iteration 1 Error: 3.197187 Iteration 2 Error: 1.039635 Iteration 3 Error: 0.239589 Iteration 4 Error: 0.150729 Iteration 5 Error: 0.039638 Align patch 3 22 left Iteration 1 Error: 0.726692 Iteration 2 Error: 0.130896 Iteration 3 Error: 0.029466 Align patch 4 21 left Iteration 1 Error: 1.950333 Iteration 2 Error: 0.250354 Iteration 3 Error: 0.067251 Iteration 4 Error: 0.027045 Align patch 5 20 left Iteration 1 Error: 1.370500 Iteration 2 Error: 0.190235 Iteration 3 Error: 0.048717 Align patch 6 19 left Iteration 1 Error: 36.293686 Iteration 2 Error: 36.035206 Iteration 3 Error: 35.222919 Iteration 4 Error: 33.951767 Iteration 5 Error: 39.521687 Align patch 6 19 left Iteration 1 Error: 2.845102 Iteration 2 Error: 0.608833 Iteration 3 Error: 0.201179 Iteration 4 Error: 0.116995 Iteration 5 Error: 0.029035 Align patch 7 18 left Iteration 1 Error: 1.932105 Iteration 2 Error: 0.747090 Iteration 3 Error: 0.132281 Iteration 4 Error: 0.090275 Iteration 5 Error: 0.021168 Align patch 8 17 left Iteration 1 Error: 2.012147 Iteration 2 Error: 0.431893 Iteration 3 Error: 0.066191 Iteration 4 Error: 0.044157 Align patch 9 16 left Iteration 1 Error: 1.691756 Iteration 2 Error: 0.357477 Iteration 3 Error: 0.077289 Iteration 4 Error: 0.036207 Align patch 10 15 left Iteration 1 Error: 1.221561 Iteration 2 Error: 0.153303 Iteration 3 Error: 0.056509 Iteration 4 Error: 0.020551 Align patch 11 14 left Iteration 1 Error: 2.077809 Iteration 2 Error: 0.608394 Iteration 3 Error: 0.159553 Iteration 4 Error: 0.053729 Iteration 5 Error: 0.017670 Align patch 12 13 left Iteration 1 Error: 1.564355 Iteration 2 Error: 0.193368 Iteration 3 Error: 0.051957 Iteration 4 Error: 0.014825 Align patch 13 12 left Iteration 1 Error: 0.866909 Iteration 2 Error: 0.255891 Iteration 3 Error: 0.041726 Align patch 14 11 left Iteration 1 Error: 1.298209 Iteration 2 Error: 0.203615 Iteration 3 Error: 0.046691 Align patch 15 10 left Iteration 1 Error: 1.330786 Iteration 2 Error: 0.221278 Iteration 3 Error: 0.055482 Iteration 4 Error: 0.017821 Align patch 16 9 left Iteration 1 Error: 1.393500 Iteration 2 Error: 0.438994 Iteration 3 Error: 0.106385 Iteration 4 Error: 0.022183 Align patch 17 8 left Iteration 1 Error: 1.157317 Iteration 2 Error: 0.564686 Iteration 3 Error: 0.142336 Iteration 4 Error: 0.077703 Iteration 5 Error: 0.025124 Align patch 18 7 left Iteration 1 Error: 0.978239 Iteration 2 Error: 0.177750 Iteration 3 Error: 0.043358 Align patch 19 6 left Iteration 1 Error: 1.168853 Iteration 2 Error: 0.314087 Iteration 3 Error: 0.055525 Iteration 4 Error: 0.026408 Align patch 20 5 left Iteration 1 Error: 0.936149 Iteration 2 Error: 0.296463 Iteration 3 Error: 0.107010 Iteration 4 Error: 0.065989 Iteration 5 Error: 0.025589 Align patch 21 4 left Iteration 1 Error: 1.557531 Iteration 2 Error: 0.253186 Iteration 3 Error: 0.074928 Iteration 4 Error: 0.026388 Align patch 22 3 left Iteration 1 Error: 1.262424 Iteration 2 Error: 0.253309 Iteration 3 Error: 0.060004 Iteration 4 Error: 0.024721 Align patch 23 2 left Iteration 1 Error: 1.311559 Iteration 2 Error: 0.339552 Iteration 3 Error: 0.081201 Iteration 4 Error: 0.028716 Align patch 24 1 left Iteration 1 Error: 0.806199 Iteration 2 Error: 0.239049 Iteration 3 Error: 0.060853 Iteration 4 Error: 0.035394 Align patch 25 0 left Iteration 1 Error: 1.188863 Iteration 2 Error: 0.193349 Iteration 3 Error: 0.064659 Iteration 4 Error: 0.018711 3D Fitting completed. Patch alignment time: 14.80(sec) Local motion has been corrected. Process thread exits. Computational time: 28.284176 sec Total time: 35.850719 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00005hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00005hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.468507s Reading file: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00005hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.388055s ........................................ >>>>>>TIME<<<<<< FFT: 1.155218s Defocus_U Defocus_V Angle CCC 8162.12 9013.69 12.46 0.012617 Final Values Defocus_U Defocus_V Angle CCC 8159.00 9016.81 12.77 0.031847 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00007sq_v01_00005hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00005hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.001e-01 CC threshold: 0.735 Mean Std: 43.54 7.20 Num Hot pixels: 191 Hot pixel threshold: 86.77 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.570910 Iteration 2 Error: 0.101529 Iteration 3 Error: 0.021843 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.20 0.01 ...... Frame ( 3) shift: -0.40 0.03 ...... Frame ( 4) shift: -0.61 0.04 ...... Frame ( 5) shift: -0.81 0.05 ...... Frame ( 6) shift: -0.91 0.09 ...... Frame ( 7) shift: -0.90 0.15 ...... Frame ( 8) shift: -0.89 0.20 ...... Frame ( 9) shift: -0.85 0.22 ...... Frame ( 10) shift: -0.79 0.19 ...... Frame ( 11) shift: -0.74 0.16 ...... Frame ( 12) shift: -0.72 0.16 ...... Frame ( 13) shift: -0.75 0.18 ...... Frame ( 14) shift: -0.77 0.21 ...... Frame ( 15) shift: -0.76 0.22 ...... Frame ( 16) shift: -0.70 0.23 ...... Frame ( 17) shift: -0.65 0.23 ...... Frame ( 18) shift: -0.63 0.26 ...... Frame ( 19) shift: -0.63 0.32 ...... Frame ( 20) shift: -0.64 0.38 ...... Frame ( 21) shift: -0.61 0.42 ...... Frame ( 22) shift: -0.56 0.45 ...... Frame ( 23) shift: -0.51 0.48 ...... Frame ( 24) shift: -0.46 0.47 ...... Frame ( 25) shift: -0.41 0.43 ...... Frame ( 26) shift: -0.36 0.39 ...... Frame ( 27) shift: -0.29 0.41 ...... Frame ( 28) shift: -0.20 0.48 ...... Frame ( 29) shift: -0.10 0.56 ...... Frame ( 30) shift: -0.04 0.59 ...... Frame ( 31) shift: -0.00 0.57 ...... Frame ( 32) shift: 0.03 0.55 ...... Frame ( 33) shift: 0.08 0.54 ...... Frame ( 34) shift: 0.14 0.53 ...... Frame ( 35) shift: 0.19 0.52 ...... Frame ( 36) shift: 0.22 0.52 ...... Frame ( 37) shift: 0.21 0.53 ...... Frame ( 38) shift: 0.19 0.55 ...... Frame ( 39) shift: 0.18 0.56 ...... Frame ( 40) shift: 0.17 0.57 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.741096 Iteration 2 Error: 0.073143 Iteration 3 Error: 0.017662 Align patch 2 23 left Iteration 1 Error: 1.002133 Iteration 2 Error: 0.195883 Iteration 3 Error: 0.048060 Align patch 3 22 left Iteration 1 Error: 0.573821 Iteration 2 Error: 0.122249 Iteration 3 Error: 0.032408 Align patch 4 21 left Iteration 1 Error: 1.382305 Iteration 2 Error: 0.210113 Iteration 3 Error: 0.062139 Iteration 4 Error: 0.026221 Align patch 5 20 left Iteration 1 Error: 0.689579 Iteration 2 Error: 0.127733 Iteration 3 Error: 0.032113 Align patch 6 19 left Iteration 1 Error: 0.926576 Iteration 2 Error: 0.129846 Iteration 3 Error: 0.032291 Align patch 7 18 left Iteration 1 Error: 0.682471 Iteration 2 Error: 0.114200 Iteration 3 Error: 0.020335 Align patch 8 17 left Iteration 1 Error: 0.552598 Iteration 2 Error: 0.070762 Iteration 3 Error: 0.013740 Align patch 9 16 left Iteration 1 Error: 0.766316 Iteration 2 Error: 0.101092 Iteration 3 Error: 0.016678 Align patch 10 15 left Iteration 1 Error: 0.799109 Iteration 2 Error: 0.169035 Iteration 3 Error: 0.027281 Align patch 11 14 left Iteration 1 Error: 0.742258 Iteration 2 Error: 0.072901 Iteration 3 Error: 0.023136 Align patch 12 13 left Iteration 1 Error: 0.524284 Iteration 2 Error: 0.072939 Iteration 3 Error: 0.022160 Align patch 13 12 left Iteration 1 Error: 0.463665 Iteration 2 Error: 0.119299 Iteration 3 Error: 0.022040 Align patch 14 11 left Iteration 1 Error: 0.669214 Iteration 2 Error: 0.058379 Iteration 3 Error: 0.014674 Align patch 15 10 left Iteration 1 Error: 0.551410 Iteration 2 Error: 0.099951 Iteration 3 Error: 0.018425 Align patch 16 9 left Iteration 1 Error: 1.063416 Iteration 2 Error: 0.225781 Iteration 3 Error: 0.037137 Align patch 17 8 left Iteration 1 Error: 0.700695 Iteration 2 Error: 0.134518 Iteration 3 Error: 0.035265 Align patch 18 7 left Iteration 1 Error: 0.627919 Iteration 2 Error: 0.068701 Iteration 3 Error: 0.022261 Align patch 19 6 left Iteration 1 Error: 0.673069 Iteration 2 Error: 0.094443 Iteration 3 Error: 0.027665 Align patch 20 5 left Iteration 1 Error: 0.727507 Iteration 2 Error: 0.060314 Iteration 3 Error: 0.022106 Align patch 21 4 left Iteration 1 Error: 1.331415 Iteration 2 Error: 0.110590 Iteration 3 Error: 0.027371 Align patch 22 3 left Iteration 1 Error: 0.750416 Iteration 2 Error: 0.068148 Iteration 3 Error: 0.020438 Align patch 23 2 left Iteration 1 Error: 0.703582 Iteration 2 Error: 0.147877 Iteration 3 Error: 0.021347 Align patch 24 1 left Iteration 1 Error: 0.854600 Iteration 2 Error: 0.098132 Iteration 3 Error: 0.025828 Align patch 25 0 left Iteration 1 Error: 0.609548 Iteration 2 Error: 0.124786 Iteration 3 Error: 0.028907 3D Fitting completed. Patch alignment time: 11.28(sec) Local motion has been corrected. Process thread exits. Computational time: 23.775278 sec Total time: 32.782379 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00005hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00005hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.570554s Reading file: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00005hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.756314s ........................................ >>>>>>TIME<<<<<< FFT: 0.929483s Defocus_U Defocus_V Angle CCC 13390.65 12882.84 89.81 0.053111 Final Values Defocus_U Defocus_V Angle CCC 13392.22 12890.66 89.51 0.090929 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00007sq_v01_00005hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00005hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.995e-02 CC threshold: 0.734 Mean Std: 43.94 7.19 Num Hot pixels: 192 Hot pixel threshold: 87.05 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.235310 Iteration 2 Error: 0.262800 Iteration 3 Error: 0.078546 Iteration 4 Error: 0.026806 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.30 -0.07 ...... Frame ( 3) shift: -0.60 -0.15 ...... Frame ( 4) shift: -0.90 -0.22 ...... Frame ( 5) shift: -1.20 -0.29 ...... Frame ( 6) shift: -1.31 -0.34 ...... Frame ( 7) shift: -1.23 -0.35 ...... Frame ( 8) shift: -1.15 -0.36 ...... Frame ( 9) shift: -1.05 -0.31 ...... Frame ( 10) shift: -0.92 -0.20 ...... Frame ( 11) shift: -0.80 -0.08 ...... Frame ( 12) shift: -0.71 0.02 ...... Frame ( 13) shift: -0.68 0.10 ...... Frame ( 14) shift: -0.64 0.19 ...... Frame ( 15) shift: -0.57 0.27 ...... Frame ( 16) shift: -0.47 0.35 ...... Frame ( 17) shift: -0.38 0.43 ...... Frame ( 18) shift: -0.28 0.49 ...... Frame ( 19) shift: -0.18 0.53 ...... Frame ( 20) shift: -0.08 0.56 ...... Frame ( 21) shift: -0.02 0.59 ...... Frame ( 22) shift: 0.01 0.61 ...... Frame ( 23) shift: 0.03 0.63 ...... Frame ( 24) shift: 0.10 0.63 ...... Frame ( 25) shift: 0.21 0.63 ...... Frame ( 26) shift: 0.33 0.63 ...... Frame ( 27) shift: 0.41 0.67 ...... Frame ( 28) shift: 0.45 0.76 ...... Frame ( 29) shift: 0.48 0.84 ...... Frame ( 30) shift: 0.54 0.88 ...... Frame ( 31) shift: 0.63 0.88 ...... Frame ( 32) shift: 0.72 0.88 ...... Frame ( 33) shift: 0.78 0.94 ...... Frame ( 34) shift: 0.82 1.06 ...... Frame ( 35) shift: 0.85 1.18 ...... Frame ( 36) shift: 0.91 1.24 ...... Frame ( 37) shift: 0.99 1.25 ...... Frame ( 38) shift: 1.07 1.25 ...... Frame ( 39) shift: 1.16 1.25 ...... Frame ( 40) shift: 1.24 1.26 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.243673 Iteration 2 Error: 0.195052 Iteration 3 Error: 0.100603 Iteration 4 Error: 0.039749 Align patch 2 23 left Iteration 1 Error: 0.873732 Iteration 2 Error: 0.130407 Iteration 3 Error: 0.025581 Align patch 3 22 left Iteration 1 Error: 0.714105 Iteration 2 Error: 0.169714 Iteration 3 Error: 0.086014 Iteration 4 Error: 0.037101 Align patch 4 21 left Iteration 1 Error: 0.843259 Iteration 2 Error: 0.132272 Iteration 3 Error: 0.023909 Align patch 5 20 left Iteration 1 Error: 1.097501 Iteration 2 Error: 0.107090 Iteration 3 Error: 0.049086 Align patch 6 19 left Iteration 1 Error: 1.709651 Iteration 2 Error: 0.366530 Iteration 3 Error: 0.140094 Iteration 4 Error: 0.029884 Align patch 7 18 left Iteration 1 Error: 0.884841 Iteration 2 Error: 0.187421 Iteration 3 Error: 0.060809 Iteration 4 Error: 0.017629 Align patch 8 17 left Iteration 1 Error: 0.976471 Iteration 2 Error: 0.155558 Iteration 3 Error: 0.050905 Iteration 4 Error: 0.013642 Align patch 9 16 left Iteration 1 Error: 0.925833 Iteration 2 Error: 0.158501 Iteration 3 Error: 0.073395 Iteration 4 Error: 0.023242 Align patch 10 15 left Iteration 1 Error: 1.114105 Iteration 2 Error: 0.141213 Iteration 3 Error: 0.028416 Align patch 11 14 left Iteration 1 Error: 1.300571 Iteration 2 Error: 0.221653 Iteration 3 Error: 0.058149 Iteration 4 Error: 0.024114 Align patch 12 13 left Iteration 1 Error: 1.513919 Iteration 2 Error: 0.182044 Iteration 3 Error: 0.076275 Iteration 4 Error: 0.035981 Align patch 13 12 left Iteration 1 Error: 0.706562 Iteration 2 Error: 0.230296 Iteration 3 Error: 0.045943 Align patch 14 11 left Iteration 1 Error: 0.542838 Iteration 2 Error: 0.088712 Iteration 3 Error: 0.042923 Align patch 15 10 left Iteration 1 Error: 0.637298 Iteration 2 Error: 0.108933 Iteration 3 Error: 0.031503 Align patch 16 9 left Iteration 1 Error: 1.297628 Iteration 2 Error: 0.228162 Iteration 3 Error: 0.065968 Iteration 4 Error: 0.030913 Align patch 17 8 left Iteration 1 Error: 0.638071 Iteration 2 Error: 0.136687 Iteration 3 Error: 0.064640 Iteration 4 Error: 0.029220 Align patch 18 7 left Iteration 1 Error: 1.163643 Iteration 2 Error: 0.269443 Iteration 3 Error: 0.064570 Iteration 4 Error: 0.030745 Align patch 19 6 left Iteration 1 Error: 1.218498 Iteration 2 Error: 0.200140 Iteration 3 Error: 0.044582 Align patch 20 5 left Iteration 1 Error: 0.825409 Iteration 2 Error: 0.182441 Iteration 3 Error: 0.051217 Iteration 4 Error: 0.022994 Align patch 21 4 left Iteration 1 Error: 1.122993 Iteration 2 Error: 0.194247 Iteration 3 Error: 0.051908 Iteration 4 Error: 0.020892 Align patch 22 3 left Iteration 1 Error: 0.955256 Iteration 2 Error: 0.180098 Iteration 3 Error: 0.033872 Align patch 23 2 left Iteration 1 Error: 1.006962 Iteration 2 Error: 0.307546 Iteration 3 Error: 0.059220 Iteration 4 Error: 0.027998 Align patch 24 1 left Iteration 1 Error: 0.779670 Iteration 2 Error: 0.247048 Iteration 3 Error: 0.052017 Iteration 4 Error: 0.017406 Align patch 25 0 left Iteration 1 Error: 1.150577 Iteration 2 Error: 0.237168 Iteration 3 Error: 0.074481 Iteration 4 Error: 0.027491 3D Fitting completed. Patch alignment time: 12.48(sec) Local motion has been corrected. Process thread exits. Computational time: 26.557583 sec Total time: 34.143536 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00005hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00005hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.542313s Reading file: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00005hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.346668s ........................................ >>>>>>TIME<<<<<< FFT: 1.081459s Defocus_U Defocus_V Angle CCC 14849.59 15658.30 6.85 0.052092 Final Values Defocus_U Defocus_V Angle CCC 14840.21 15664.56 6.22 0.087320 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00007sq_v01_00005hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00005hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.992e-02 CC threshold: 0.734 Mean Std: 43.25 7.20 Num Hot pixels: 187 Hot pixel threshold: 86.46 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.657477 Iteration 2 Error: 0.117288 Iteration 3 Error: 0.024741 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.24 -0.13 ...... Frame ( 3) shift: -0.49 -0.27 ...... Frame ( 4) shift: -0.73 -0.40 ...... Frame ( 5) shift: -0.98 -0.53 ...... Frame ( 6) shift: -1.12 -0.60 ...... Frame ( 7) shift: -1.16 -0.60 ...... Frame ( 8) shift: -1.20 -0.60 ...... Frame ( 9) shift: -1.20 -0.55 ...... Frame ( 10) shift: -1.17 -0.45 ...... Frame ( 11) shift: -1.14 -0.35 ...... Frame ( 12) shift: -1.07 -0.29 ...... Frame ( 13) shift: -0.98 -0.29 ...... Frame ( 14) shift: -0.89 -0.29 ...... Frame ( 15) shift: -0.83 -0.27 ...... Frame ( 16) shift: -0.82 -0.22 ...... Frame ( 17) shift: -0.81 -0.17 ...... Frame ( 18) shift: -0.75 -0.16 ...... Frame ( 19) shift: -0.65 -0.19 ...... Frame ( 20) shift: -0.55 -0.21 ...... Frame ( 21) shift: -0.50 -0.21 ...... Frame ( 22) shift: -0.48 -0.17 ...... Frame ( 23) shift: -0.47 -0.14 ...... Frame ( 24) shift: -0.44 -0.10 ...... Frame ( 25) shift: -0.40 -0.06 ...... Frame ( 26) shift: -0.36 -0.02 ...... Frame ( 27) shift: -0.29 -0.01 ...... Frame ( 28) shift: -0.19 -0.02 ...... Frame ( 29) shift: -0.09 -0.04 ...... Frame ( 30) shift: -0.06 -0.02 ...... Frame ( 31) shift: -0.10 0.02 ...... Frame ( 32) shift: -0.14 0.06 ...... Frame ( 33) shift: -0.17 0.07 ...... Frame ( 34) shift: -0.18 0.05 ...... Frame ( 35) shift: -0.20 0.03 ...... Frame ( 36) shift: -0.20 0.02 ...... Frame ( 37) shift: -0.18 0.02 ...... Frame ( 38) shift: -0.17 0.01 ...... Frame ( 39) shift: -0.15 0.01 ...... Frame ( 40) shift: -0.14 0.00 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.021028 Iteration 2 Error: 0.220224 Iteration 3 Error: 0.076515 Iteration 4 Error: 0.028923 Align patch 2 23 left Iteration 1 Error: 1.490951 Iteration 2 Error: 0.418626 Iteration 3 Error: 0.103293 Iteration 4 Error: 0.046914 Align patch 3 22 left Iteration 1 Error: 1.038934 Iteration 2 Error: 0.201390 Iteration 3 Error: 0.054892 Iteration 4 Error: 0.020776 Align patch 4 21 left Iteration 1 Error: 0.595368 Iteration 2 Error: 0.160608 Iteration 3 Error: 0.052100 Iteration 4 Error: 0.022040 Align patch 5 20 left Iteration 1 Error: 0.992928 Iteration 2 Error: 0.142144 Iteration 3 Error: 0.032518 Align patch 6 19 left Iteration 1 Error: 1.021483 Iteration 2 Error: 0.130551 Iteration 3 Error: 0.049723 Align patch 7 18 left Iteration 1 Error: 1.216538 Iteration 2 Error: 0.196027 Iteration 3 Error: 0.070611 Iteration 4 Error: 0.017781 Align patch 8 17 left Iteration 1 Error: 0.724260 Iteration 2 Error: 0.099181 Iteration 3 Error: 0.040632 Align patch 9 16 left Iteration 1 Error: 0.705136 Iteration 2 Error: 0.084776 Iteration 3 Error: 0.028593 Align patch 10 15 left Iteration 1 Error: 0.864739 Iteration 2 Error: 0.138407 Iteration 3 Error: 0.041669 Align patch 11 14 left Iteration 1 Error: 0.796406 Iteration 2 Error: 0.192656 Iteration 3 Error: 0.078541 Iteration 4 Error: 0.033546 Align patch 12 13 left Iteration 1 Error: 0.699436 Iteration 2 Error: 0.166756 Iteration 3 Error: 0.037652 Align patch 13 12 left Iteration 1 Error: 0.564906 Iteration 2 Error: 0.123004 Iteration 3 Error: 0.023517 Align patch 14 11 left Iteration 1 Error: 0.547058 Iteration 2 Error: 0.097234 Iteration 3 Error: 0.026444 Align patch 15 10 left Iteration 1 Error: 1.067890 Iteration 2 Error: 0.155690 Iteration 3 Error: 0.041738 Align patch 16 9 left Iteration 1 Error: 0.776485 Iteration 2 Error: 0.104820 Iteration 3 Error: 0.031129 Align patch 17 8 left Iteration 1 Error: 0.587007 Iteration 2 Error: 0.162683 Iteration 3 Error: 0.041046 Align patch 18 7 left Iteration 1 Error: 0.864337 Iteration 2 Error: 0.121342 Iteration 3 Error: 0.038893 Align patch 19 6 left Iteration 1 Error: 0.776544 Iteration 2 Error: 0.142781 Iteration 3 Error: 0.029941 Align patch 20 5 left Iteration 1 Error: 0.844106 Iteration 2 Error: 0.182820 Iteration 3 Error: 0.061487 Iteration 4 Error: 0.017665 Align patch 21 4 left Iteration 1 Error: 1.350134 Iteration 2 Error: 0.179691 Iteration 3 Error: 0.088396 Iteration 4 Error: 0.024646 Align patch 22 3 left Iteration 1 Error: 0.732517 Iteration 2 Error: 0.122548 Iteration 3 Error: 0.031577 Align patch 23 2 left Iteration 1 Error: 0.899581 Iteration 2 Error: 0.175791 Iteration 3 Error: 0.066675 Iteration 4 Error: 0.018407 Align patch 24 1 left Iteration 1 Error: 0.534838 Iteration 2 Error: 0.067329 Iteration 3 Error: 0.033901 Align patch 25 0 left Iteration 1 Error: 0.820778 Iteration 2 Error: 0.175644 Iteration 3 Error: 0.050548 Iteration 4 Error: 0.015636 3D Fitting completed. Patch alignment time: 12.20(sec) Local motion has been corrected. Process thread exits. Computational time: 22.168692 sec Total time: 29.328890 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00005hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00005hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.489064s Reading file: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00005hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.236450s ........................................ >>>>>>TIME<<<<<< FFT: 1.047218s Defocus_U Defocus_V Angle CCC 13457.06 12757.84 83.21 0.043537 Final Values Defocus_U Defocus_V Angle CCC 13449.24 12771.92 83.21 0.076497 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00007sq_v01_00006hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00006hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.999e-02 CC threshold: 0.734 Mean Std: 41.88 6.96 Num Hot pixels: 188 Hot pixel threshold: 83.62 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.299779 Iteration 2 Error: 0.263651 Iteration 3 Error: 0.062793 Iteration 4 Error: 0.022990 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.14 -0.00 ...... Frame ( 3) shift: -0.27 -0.01 ...... Frame ( 4) shift: -0.41 -0.01 ...... Frame ( 5) shift: -0.55 -0.02 ...... Frame ( 6) shift: -0.57 -0.01 ...... Frame ( 7) shift: -0.47 0.03 ...... Frame ( 8) shift: -0.37 0.06 ...... Frame ( 9) shift: -0.29 0.13 ...... Frame ( 10) shift: -0.21 0.22 ...... Frame ( 11) shift: -0.13 0.32 ...... Frame ( 12) shift: -0.05 0.39 ...... Frame ( 13) shift: 0.04 0.43 ...... Frame ( 14) shift: 0.13 0.46 ...... Frame ( 15) shift: 0.18 0.55 ...... Frame ( 16) shift: 0.19 0.67 ...... Frame ( 17) shift: 0.20 0.80 ...... Frame ( 18) shift: 0.23 0.89 ...... Frame ( 19) shift: 0.29 0.94 ...... Frame ( 20) shift: 0.35 0.99 ...... Frame ( 21) shift: 0.42 1.02 ...... Frame ( 22) shift: 0.50 1.05 ...... Frame ( 23) shift: 0.57 1.08 ...... Frame ( 24) shift: 0.65 1.09 ...... Frame ( 25) shift: 0.74 1.10 ...... Frame ( 26) shift: 0.84 1.10 ...... Frame ( 27) shift: 0.87 1.10 ...... Frame ( 28) shift: 0.83 1.08 ...... Frame ( 29) shift: 0.80 1.06 ...... Frame ( 30) shift: 0.81 1.06 ...... Frame ( 31) shift: 0.88 1.06 ...... Frame ( 32) shift: 0.94 1.07 ...... Frame ( 33) shift: 1.04 1.15 ...... Frame ( 34) shift: 1.20 1.31 ...... Frame ( 35) shift: 1.35 1.48 ...... Frame ( 36) shift: 1.47 1.55 ...... Frame ( 37) shift: 1.55 1.52 ...... Frame ( 38) shift: 1.63 1.50 ...... Frame ( 39) shift: 1.72 1.48 ...... Frame ( 40) shift: 1.80 1.46 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.753303 Iteration 2 Error: 0.196160 Iteration 3 Error: 0.050425 Iteration 4 Error: 0.014868 Align patch 2 23 left Iteration 1 Error: 0.586464 Iteration 2 Error: 0.159286 Iteration 3 Error: 0.041210 Align patch 3 22 left Iteration 1 Error: 1.038740 Iteration 2 Error: 0.186070 Iteration 3 Error: 0.059165 Iteration 4 Error: 0.031194 Align patch 4 21 left Iteration 1 Error: 1.233319 Iteration 2 Error: 0.276450 Iteration 3 Error: 0.117634 Iteration 4 Error: 0.040569 Align patch 5 20 left Iteration 1 Error: 0.779262 Iteration 2 Error: 0.231383 Iteration 3 Error: 0.106629 Iteration 4 Error: 0.045843 Align patch 6 19 left Iteration 1 Error: 0.692596 Iteration 2 Error: 0.268858 Iteration 3 Error: 0.078826 Iteration 4 Error: 0.029941 Align patch 7 18 left Iteration 1 Error: 0.494326 Iteration 2 Error: 0.070694 Iteration 3 Error: 0.036584 Align patch 8 17 left Iteration 1 Error: 0.742155 Iteration 2 Error: 0.217756 Iteration 3 Error: 0.064352 Iteration 4 Error: 0.030362 Align patch 9 16 left Iteration 1 Error: 1.219342 Iteration 2 Error: 0.243604 Iteration 3 Error: 0.129836 Iteration 4 Error: 0.045896 Align patch 10 15 left Iteration 1 Error: 0.567816 Iteration 2 Error: 0.081478 Iteration 3 Error: 0.018349 Align patch 11 14 left Iteration 1 Error: 0.782255 Iteration 2 Error: 0.196394 Iteration 3 Error: 0.063285 Iteration 4 Error: 0.021614 Align patch 12 13 left Iteration 1 Error: 1.072117 Iteration 2 Error: 0.260590 Iteration 3 Error: 0.085471 Iteration 4 Error: 0.032308 Align patch 13 12 left Iteration 1 Error: 0.754137 Iteration 2 Error: 0.198731 Iteration 3 Error: 0.054270 Iteration 4 Error: 0.019369 Align patch 14 11 left Iteration 1 Error: 0.641374 Iteration 2 Error: 0.109939 Iteration 3 Error: 0.042796 Align patch 15 10 left Iteration 1 Error: 0.839061 Iteration 2 Error: 0.217573 Iteration 3 Error: 0.038527 Align patch 16 9 left Iteration 1 Error: 0.990934 Iteration 2 Error: 0.213769 Iteration 3 Error: 0.073835 Iteration 4 Error: 0.036290 Align patch 17 8 left Iteration 1 Error: 0.704685 Iteration 2 Error: 0.122936 Iteration 3 Error: 0.032318 Align patch 18 7 left Iteration 1 Error: 0.714656 Iteration 2 Error: 0.206990 Iteration 3 Error: 0.040709 Align patch 19 6 left Iteration 1 Error: 0.735606 Iteration 2 Error: 0.149961 Iteration 3 Error: 0.056654 Iteration 4 Error: 0.024545 Align patch 20 5 left Iteration 1 Error: 1.683834 Iteration 2 Error: 0.177766 Iteration 3 Error: 0.064979 Iteration 4 Error: 0.016917 Align patch 21 4 left Iteration 1 Error: 1.009330 Iteration 2 Error: 0.164825 Iteration 3 Error: 0.079118 Iteration 4 Error: 0.017059 Align patch 22 3 left Iteration 1 Error: 1.444895 Iteration 2 Error: 0.317926 Iteration 3 Error: 0.067377 Iteration 4 Error: 0.030855 Align patch 23 2 left Iteration 1 Error: 0.985364 Iteration 2 Error: 0.142690 Iteration 3 Error: 0.056291 Iteration 4 Error: 0.018702 Align patch 24 1 left Iteration 1 Error: 0.786550 Iteration 2 Error: 0.132387 Iteration 3 Error: 0.035613 Align patch 25 0 left Iteration 1 Error: 0.508955 Iteration 2 Error: 0.128642 Iteration 3 Error: 0.046216 3D Fitting completed. Patch alignment time: 12.45(sec) Local motion has been corrected. Process thread exits. Computational time: 23.749605 sec Total time: 30.259253 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00006hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00006hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.586198s Reading file: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00006hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.239375s ........................................ >>>>>>TIME<<<<<< FFT: 1.010903s Defocus_U Defocus_V Angle CCC 9546.90 10441.43 12.53 0.033700 Final Values Defocus_U Defocus_V Angle CCC 9543.73 10447.72 11.90 0.063018 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00007sq_v01_00006hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00006hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 1.000e-01 CC threshold: 0.734 Mean Std: 42.88 7.08 Num Hot pixels: 179 Hot pixel threshold: 85.37 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.712660 Iteration 2 Error: 0.170234 Iteration 3 Error: 0.044326 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.28 -0.00 ...... Frame ( 3) shift: -0.56 -0.00 ...... Frame ( 4) shift: -0.84 -0.00 ...... Frame ( 5) shift: -1.12 -0.00 ...... Frame ( 6) shift: -1.25 -0.03 ...... Frame ( 7) shift: -1.22 -0.08 ...... Frame ( 8) shift: -1.20 -0.14 ...... Frame ( 9) shift: -1.17 -0.15 ...... Frame ( 10) shift: -1.13 -0.12 ...... Frame ( 11) shift: -1.10 -0.10 ...... Frame ( 12) shift: -1.08 -0.01 ...... Frame ( 13) shift: -1.07 0.13 ...... Frame ( 14) shift: -1.05 0.27 ...... Frame ( 15) shift: -1.02 0.35 ...... Frame ( 16) shift: -0.97 0.35 ...... Frame ( 17) shift: -0.92 0.36 ...... Frame ( 18) shift: -0.91 0.37 ...... Frame ( 19) shift: -0.93 0.38 ...... Frame ( 20) shift: -0.96 0.39 ...... Frame ( 21) shift: -0.94 0.41 ...... Frame ( 22) shift: -0.87 0.43 ...... Frame ( 23) shift: -0.81 0.45 ...... Frame ( 24) shift: -0.78 0.48 ...... Frame ( 25) shift: -0.77 0.53 ...... Frame ( 26) shift: -0.77 0.58 ...... Frame ( 27) shift: -0.75 0.62 ...... Frame ( 28) shift: -0.73 0.65 ...... Frame ( 29) shift: -0.71 0.69 ...... Frame ( 30) shift: -0.66 0.75 ...... Frame ( 31) shift: -0.57 0.86 ...... Frame ( 32) shift: -0.49 0.96 ...... Frame ( 33) shift: -0.42 0.98 ...... Frame ( 34) shift: -0.36 0.91 ...... Frame ( 35) shift: -0.30 0.84 ...... Frame ( 36) shift: -0.26 0.84 ...... Frame ( 37) shift: -0.25 0.90 ...... Frame ( 38) shift: -0.23 0.96 ...... Frame ( 39) shift: -0.21 1.02 ...... Frame ( 40) shift: -0.20 1.09 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.910538 Iteration 2 Error: 0.184549 Iteration 3 Error: 0.061109 Iteration 4 Error: 0.019195 Align patch 2 23 left Iteration 1 Error: 0.637194 Iteration 2 Error: 0.117625 Iteration 3 Error: 0.031260 Align patch 3 22 left Iteration 1 Error: 0.801165 Iteration 2 Error: 0.164294 Iteration 3 Error: 0.027030 Align patch 4 21 left Iteration 1 Error: 0.826456 Iteration 2 Error: 0.131369 Iteration 3 Error: 0.041388 Align patch 5 20 left Iteration 1 Error: 0.891203 Iteration 2 Error: 0.199224 Iteration 3 Error: 0.054292 Iteration 4 Error: 0.020992 Align patch 6 19 left Iteration 1 Error: 0.828541 Iteration 2 Error: 0.208828 Iteration 3 Error: 0.133690 Iteration 4 Error: 0.042342 Align patch 7 18 left Iteration 1 Error: 0.509409 Iteration 2 Error: 0.075310 Iteration 3 Error: 0.022949 Align patch 8 17 left Iteration 1 Error: 0.691576 Iteration 2 Error: 0.115053 Iteration 3 Error: 0.035559 Align patch 9 16 left Iteration 1 Error: 1.788463 Iteration 2 Error: 0.210922 Iteration 3 Error: 0.076538 Iteration 4 Error: 0.021917 Align patch 10 15 left Iteration 1 Error: 1.050467 Iteration 2 Error: 0.146438 Iteration 3 Error: 0.058759 Iteration 4 Error: 0.017252 Align patch 11 14 left Iteration 1 Error: 0.755322 Iteration 2 Error: 0.164489 Iteration 3 Error: 0.022500 Align patch 12 13 left Iteration 1 Error: 0.893436 Iteration 2 Error: 0.158838 Iteration 3 Error: 0.035020 Align patch 13 12 left Iteration 1 Error: 0.593105 Iteration 2 Error: 0.119200 Iteration 3 Error: 0.023791 Align patch 14 11 left Iteration 1 Error: 0.655921 Iteration 2 Error: 0.100477 Iteration 3 Error: 0.020564 Align patch 15 10 left Iteration 1 Error: 0.555772 Iteration 2 Error: 0.092828 Iteration 3 Error: 0.031008 Align patch 16 9 left Iteration 1 Error: 1.305775 Iteration 2 Error: 0.262083 Iteration 3 Error: 0.061644 Iteration 4 Error: 0.020431 Align patch 17 8 left Iteration 1 Error: 0.624414 Iteration 2 Error: 0.090421 Iteration 3 Error: 0.027308 Align patch 18 7 left Iteration 1 Error: 0.452940 Iteration 2 Error: 0.125727 Iteration 3 Error: 0.028460 Align patch 19 6 left Iteration 1 Error: 0.961881 Iteration 2 Error: 0.155494 Iteration 3 Error: 0.037549 Align patch 20 5 left Iteration 1 Error: 0.580239 Iteration 2 Error: 0.116862 Iteration 3 Error: 0.038206 Align patch 21 4 left Iteration 1 Error: 0.785609 Iteration 2 Error: 0.195461 Iteration 3 Error: 0.067481 Iteration 4 Error: 0.019240 Align patch 22 3 left Iteration 1 Error: 0.850688 Iteration 2 Error: 0.171070 Iteration 3 Error: 0.041361 Align patch 23 2 left Iteration 1 Error: 0.550665 Iteration 2 Error: 0.081887 Iteration 3 Error: 0.021199 Align patch 24 1 left Iteration 1 Error: 0.567309 Iteration 2 Error: 0.103780 Iteration 3 Error: 0.026021 Align patch 25 0 left Iteration 1 Error: 0.704104 Iteration 2 Error: 0.128809 Iteration 3 Error: 0.035542 3D Fitting completed. Patch alignment time: 11.32(sec) Local motion has been corrected. Process thread exits. Computational time: 21.705086 sec Total time: 30.508039 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00006hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00006hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.516177s Reading file: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00006hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.836827s ........................................ >>>>>>TIME<<<<<< FFT: 1.120430s Defocus_U Defocus_V Angle CCC 13457.06 12941.43 89.95 0.043827 Final Values Defocus_U Defocus_V Angle CCC 12935.18 13472.69 0.90 0.076450 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00007sq_v01_00006hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00006hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 9.999e-02 CC threshold: 0.734 Mean Std: 42.56 7.01 Num Hot pixels: 197 Hot pixel threshold: 84.64 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.870114 Iteration 2 Error: 0.147142 Iteration 3 Error: 0.038354 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.13 -0.15 ...... Frame ( 3) shift: -0.26 -0.30 ...... Frame ( 4) shift: -0.39 -0.46 ...... Frame ( 5) shift: -0.51 -0.61 ...... Frame ( 6) shift: -0.56 -0.70 ...... Frame ( 7) shift: -0.53 -0.72 ...... Frame ( 8) shift: -0.50 -0.74 ...... Frame ( 9) shift: -0.43 -0.78 ...... Frame ( 10) shift: -0.34 -0.82 ...... Frame ( 11) shift: -0.25 -0.87 ...... Frame ( 12) shift: -0.16 -0.85 ...... Frame ( 13) shift: -0.06 -0.78 ...... Frame ( 14) shift: 0.03 -0.70 ...... Frame ( 15) shift: 0.09 -0.65 ...... Frame ( 16) shift: 0.12 -0.62 ...... Frame ( 17) shift: 0.15 -0.60 ...... Frame ( 18) shift: 0.20 -0.56 ...... Frame ( 19) shift: 0.28 -0.51 ...... Frame ( 20) shift: 0.35 -0.46 ...... Frame ( 21) shift: 0.40 -0.45 ...... Frame ( 22) shift: 0.43 -0.48 ...... Frame ( 23) shift: 0.46 -0.51 ...... Frame ( 24) shift: 0.51 -0.51 ...... Frame ( 25) shift: 0.56 -0.49 ...... Frame ( 26) shift: 0.62 -0.47 ...... Frame ( 27) shift: 0.68 -0.40 ...... Frame ( 28) shift: 0.73 -0.28 ...... Frame ( 29) shift: 0.79 -0.16 ...... Frame ( 30) shift: 0.83 -0.09 ...... Frame ( 31) shift: 0.87 -0.07 ...... Frame ( 32) shift: 0.90 -0.05 ...... Frame ( 33) shift: 0.93 -0.00 ...... Frame ( 34) shift: 0.95 0.08 ...... Frame ( 35) shift: 0.97 0.16 ...... Frame ( 36) shift: 0.98 0.21 ...... Frame ( 37) shift: 0.99 0.23 ...... Frame ( 38) shift: 1.00 0.26 ...... Frame ( 39) shift: 1.00 0.28 ...... Frame ( 40) shift: 1.01 0.31 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.389408 Iteration 2 Error: 0.142636 Iteration 3 Error: 0.046050 Align patch 2 23 left Iteration 1 Error: 1.178805 Iteration 2 Error: 0.227829 Iteration 3 Error: 0.051780 Iteration 4 Error: 0.019880 Align patch 3 22 left Iteration 1 Error: 0.733835 Iteration 2 Error: 0.117047 Iteration 3 Error: 0.035871 Align patch 4 21 left Iteration 1 Error: 0.933936 Iteration 2 Error: 0.234523 Iteration 3 Error: 0.068639 Iteration 4 Error: 0.026961 Align patch 5 20 left Iteration 1 Error: 0.719548 Iteration 2 Error: 0.161823 Iteration 3 Error: 0.052686 Iteration 4 Error: 0.018637 Align patch 6 19 left Iteration 1 Error: 1.062673 Iteration 2 Error: 0.157811 Iteration 3 Error: 0.055578 Iteration 4 Error: 0.013120 Align patch 7 18 left Iteration 1 Error: 0.975559 Iteration 2 Error: 0.157311 Iteration 3 Error: 0.049293 Align patch 8 17 left Iteration 1 Error: 0.804945 Iteration 2 Error: 0.120102 Iteration 3 Error: 0.026025 Align patch 9 16 left Iteration 1 Error: 0.762522 Iteration 2 Error: 0.168890 Iteration 3 Error: 0.067246 Iteration 4 Error: 0.026570 Align patch 10 15 left Iteration 1 Error: 0.798988 Iteration 2 Error: 0.115173 Iteration 3 Error: 0.035471 Align patch 11 14 left Iteration 1 Error: 0.673934 Iteration 2 Error: 0.065095 Iteration 3 Error: 0.012695 Align patch 12 13 left Iteration 1 Error: 0.749291 Iteration 2 Error: 0.185441 Iteration 3 Error: 0.026814 Align patch 13 12 left Iteration 1 Error: 0.650109 Iteration 2 Error: 0.087365 Iteration 3 Error: 0.023347 Align patch 14 11 left Iteration 1 Error: 0.913555 Iteration 2 Error: 0.066714 Iteration 3 Error: 0.022591 Align patch 15 10 left Iteration 1 Error: 0.961012 Iteration 2 Error: 0.231133 Iteration 3 Error: 0.044936 Align patch 16 9 left Iteration 1 Error: 0.903686 Iteration 2 Error: 0.155912 Iteration 3 Error: 0.041678 Align patch 17 8 left Iteration 1 Error: 0.446223 Iteration 2 Error: 0.079111 Iteration 3 Error: 0.032380 Align patch 18 7 left Iteration 1 Error: 0.716421 Iteration 2 Error: 0.158266 Iteration 3 Error: 0.039552 Align patch 19 6 left Iteration 1 Error: 1.285656 Iteration 2 Error: 0.225511 Iteration 3 Error: 0.083687 Iteration 4 Error: 0.042142 Align patch 20 5 left Iteration 1 Error: 0.723902 Iteration 2 Error: 0.150217 Iteration 3 Error: 0.050234 Iteration 4 Error: 0.011945 Align patch 21 4 left Iteration 1 Error: 1.213989 Iteration 2 Error: 0.158549 Iteration 3 Error: 0.032243 Align patch 22 3 left Iteration 1 Error: 0.642821 Iteration 2 Error: 0.087674 Iteration 3 Error: 0.027629 Align patch 23 2 left Iteration 1 Error: 0.654571 Iteration 2 Error: 0.140074 Iteration 3 Error: 0.044769 Align patch 24 1 left Iteration 1 Error: 0.913679 Iteration 2 Error: 0.168568 Iteration 3 Error: 0.040951 Align patch 25 0 left Iteration 1 Error: 1.012087 Iteration 2 Error: 0.122553 Iteration 3 Error: 0.028227 3D Fitting completed. Patch alignment time: 11.83(sec) Local motion has been corrected. Process thread exits. Computational time: 25.604019 sec Total time: 34.022781 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00006hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00006hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.556715s Reading file: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00006hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.501371s ........................................ >>>>>>TIME<<<<<< FFT: 0.946137s Defocus_U Defocus_V Angle CCC 11386.69 12296.98 5.76 0.038275 Final Values Defocus_U Defocus_V Angle CCC 11400.75 12314.17 6.39 0.070388 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00007sq_v01_00006hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00006hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.734 Mean Std: 42.69 7.05 Num Hot pixels: 193 Hot pixel threshold: 84.99 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.676289 Iteration 2 Error: 0.138957 Iteration 3 Error: 0.045124 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.20 -0.17 ...... Frame ( 3) shift: -0.39 -0.34 ...... Frame ( 4) shift: -0.59 -0.51 ...... Frame ( 5) shift: -0.78 -0.68 ...... Frame ( 6) shift: -0.86 -0.77 ...... Frame ( 7) shift: -0.82 -0.78 ...... Frame ( 8) shift: -0.78 -0.79 ...... Frame ( 9) shift: -0.74 -0.78 ...... Frame ( 10) shift: -0.71 -0.76 ...... Frame ( 11) shift: -0.68 -0.73 ...... Frame ( 12) shift: -0.62 -0.70 ...... Frame ( 13) shift: -0.55 -0.66 ...... Frame ( 14) shift: -0.47 -0.61 ...... Frame ( 15) shift: -0.43 -0.53 ...... Frame ( 16) shift: -0.43 -0.40 ...... Frame ( 17) shift: -0.43 -0.26 ...... Frame ( 18) shift: -0.43 -0.20 ...... Frame ( 19) shift: -0.45 -0.20 ...... Frame ( 20) shift: -0.47 -0.21 ...... Frame ( 21) shift: -0.46 -0.17 ...... Frame ( 22) shift: -0.42 -0.10 ...... Frame ( 23) shift: -0.39 -0.02 ...... Frame ( 24) shift: -0.34 0.05 ...... Frame ( 25) shift: -0.27 0.10 ...... Frame ( 26) shift: -0.20 0.15 ...... Frame ( 27) shift: -0.19 0.22 ...... Frame ( 28) shift: -0.24 0.31 ...... Frame ( 29) shift: -0.28 0.41 ...... Frame ( 30) shift: -0.28 0.46 ...... Frame ( 31) shift: -0.23 0.47 ...... Frame ( 32) shift: -0.17 0.47 ...... Frame ( 33) shift: -0.12 0.47 ...... Frame ( 34) shift: -0.08 0.44 ...... Frame ( 35) shift: -0.03 0.41 ...... Frame ( 36) shift: 0.02 0.41 ...... Frame ( 37) shift: 0.07 0.44 ...... Frame ( 38) shift: 0.13 0.46 ...... Frame ( 39) shift: 0.18 0.49 ...... Frame ( 40) shift: 0.23 0.51 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.576836 Iteration 2 Error: 0.251961 Iteration 3 Error: 0.052350 Iteration 4 Error: 0.015862 Align patch 2 23 left Iteration 1 Error: 1.011678 Iteration 2 Error: 0.210136 Iteration 3 Error: 0.058571 Iteration 4 Error: 0.036880 Align patch 3 22 left Iteration 1 Error: 0.856593 Iteration 2 Error: 0.171641 Iteration 3 Error: 0.069468 Iteration 4 Error: 0.030225 Align patch 4 21 left Iteration 1 Error: 0.859554 Iteration 2 Error: 0.180987 Iteration 3 Error: 0.039231 Align patch 5 20 left Iteration 1 Error: 0.912119 Iteration 2 Error: 0.121673 Iteration 3 Error: 0.015217 Align patch 6 19 left Iteration 1 Error: 1.299532 Iteration 2 Error: 0.173444 Iteration 3 Error: 0.039213 Align patch 7 18 left Iteration 1 Error: 0.771617 Iteration 2 Error: 0.170309 Iteration 3 Error: 0.051987 Iteration 4 Error: 0.026320 Align patch 8 17 left Iteration 1 Error: 0.895569 Iteration 2 Error: 0.277383 Iteration 3 Error: 0.071901 Iteration 4 Error: 0.028476 Align patch 9 16 left Iteration 1 Error: 0.721609 Iteration 2 Error: 0.179641 Iteration 3 Error: 0.035942 Align patch 10 15 left Iteration 1 Error: 0.983077 Iteration 2 Error: 0.259349 Iteration 3 Error: 0.063535 Iteration 4 Error: 0.018898 Align patch 11 14 left Iteration 1 Error: 1.543266 Iteration 2 Error: 0.117084 Iteration 3 Error: 0.038092 Align patch 12 13 left Iteration 1 Error: 0.899315 Iteration 2 Error: 0.175521 Iteration 3 Error: 0.090141 Iteration 4 Error: 0.026983 Align patch 13 12 left Iteration 1 Error: 0.749172 Iteration 2 Error: 0.100259 Iteration 3 Error: 0.030969 Align patch 14 11 left Iteration 1 Error: 0.675339 Iteration 2 Error: 0.147968 Iteration 3 Error: 0.030908 Align patch 15 10 left Iteration 1 Error: 0.860009 Iteration 2 Error: 0.205971 Iteration 3 Error: 0.065683 Iteration 4 Error: 0.018016 Align patch 16 9 left Iteration 1 Error: 0.849556 Iteration 2 Error: 0.161618 Iteration 3 Error: 0.045988 Align patch 17 8 left Iteration 1 Error: 0.728016 Iteration 2 Error: 0.143343 Iteration 3 Error: 0.033532 Align patch 18 7 left Iteration 1 Error: 0.901311 Iteration 2 Error: 0.197061 Iteration 3 Error: 0.069977 Iteration 4 Error: 0.017090 Align patch 19 6 left Iteration 1 Error: 0.766588 Iteration 2 Error: 0.128595 Iteration 3 Error: 0.032803 Align patch 20 5 left Iteration 1 Error: 1.001751 Iteration 2 Error: 0.168938 Iteration 3 Error: 0.054718 Iteration 4 Error: 0.017419 Align patch 21 4 left Iteration 1 Error: 1.213154 Iteration 2 Error: 0.181174 Iteration 3 Error: 0.038134 Align patch 22 3 left Iteration 1 Error: 0.730911 Iteration 2 Error: 0.196591 Iteration 3 Error: 0.064508 Iteration 4 Error: 0.026168 Align patch 23 2 left Iteration 1 Error: 0.695179 Iteration 2 Error: 0.263745 Iteration 3 Error: 0.056678 Iteration 4 Error: 0.032693 Align patch 24 1 left Iteration 1 Error: 0.927030 Iteration 2 Error: 0.135318 Iteration 3 Error: 0.029673 Align patch 25 0 left Iteration 1 Error: 1.112566 Iteration 2 Error: 0.219654 Iteration 3 Error: 0.036411 3D Fitting completed. Patch alignment time: 11.79(sec) Local motion has been corrected. Process thread exits. Computational time: 26.110193 sec Total time: 34.531235 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00006hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00006hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.515157s Reading file: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00006hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.872152s ........................................ >>>>>>TIME<<<<<< FFT: 0.980284s Defocus_U Defocus_V Angle CCC 13035.22 12367.22 87.81 0.043392 Final Values Defocus_U Defocus_V Angle CCC 13046.16 12381.29 87.50 0.076601 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00007sq_v01_00007hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00007hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.992e-02 CC threshold: 0.734 Mean Std: 41.64 7.02 Num Hot pixels: 199 Hot pixel threshold: 83.75 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.387257 Iteration 2 Error: 0.272342 Iteration 3 Error: 0.072177 Iteration 4 Error: 0.022778 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.16 -0.04 ...... Frame ( 3) shift: -0.32 -0.09 ...... Frame ( 4) shift: -0.47 -0.13 ...... Frame ( 5) shift: -0.63 -0.17 ...... Frame ( 6) shift: -0.69 -0.19 ...... Frame ( 7) shift: -0.64 -0.17 ...... Frame ( 8) shift: -0.59 -0.16 ...... Frame ( 9) shift: -0.56 -0.12 ...... Frame ( 10) shift: -0.54 -0.06 ...... Frame ( 11) shift: -0.52 -0.00 ...... Frame ( 12) shift: -0.51 0.05 ...... Frame ( 13) shift: -0.51 0.09 ...... Frame ( 14) shift: -0.52 0.12 ...... Frame ( 15) shift: -0.46 0.14 ...... Frame ( 16) shift: -0.35 0.13 ...... Frame ( 17) shift: -0.24 0.11 ...... Frame ( 18) shift: -0.19 0.16 ...... Frame ( 19) shift: -0.19 0.27 ...... Frame ( 20) shift: -0.20 0.39 ...... Frame ( 21) shift: -0.20 0.47 ...... Frame ( 22) shift: -0.19 0.54 ...... Frame ( 23) shift: -0.18 0.61 ...... Frame ( 24) shift: -0.13 0.70 ...... Frame ( 25) shift: -0.05 0.81 ...... Frame ( 26) shift: 0.03 0.92 ...... Frame ( 27) shift: 0.09 1.04 ...... Frame ( 28) shift: 0.14 1.17 ...... Frame ( 29) shift: 0.19 1.30 ...... Frame ( 30) shift: 0.22 1.43 ...... Frame ( 31) shift: 0.22 1.56 ...... Frame ( 32) shift: 0.23 1.69 ...... Frame ( 33) shift: 0.27 1.76 ...... Frame ( 34) shift: 0.35 1.77 ...... Frame ( 35) shift: 0.44 1.77 ...... Frame ( 36) shift: 0.48 1.82 ...... Frame ( 37) shift: 0.49 1.92 ...... Frame ( 38) shift: 0.49 2.03 ...... Frame ( 39) shift: 0.50 2.13 ...... Frame ( 40) shift: 0.51 2.23 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.681747 Iteration 2 Error: 0.282256 Iteration 3 Error: 0.105276 Iteration 4 Error: 0.054937 Iteration 5 Error: 0.021489 Align patch 2 23 left Iteration 1 Error: 1.039865 Iteration 2 Error: 0.137142 Iteration 3 Error: 0.037708 Align patch 3 22 left Iteration 1 Error: 0.864011 Iteration 2 Error: 0.171942 Iteration 3 Error: 0.048658 Align patch 4 21 left Iteration 1 Error: 1.507010 Iteration 2 Error: 0.261056 Iteration 3 Error: 0.088258 Iteration 4 Error: 0.044358 Align patch 5 20 left Iteration 1 Error: 0.853377 Iteration 2 Error: 0.273540 Iteration 3 Error: 0.067043 Iteration 4 Error: 0.039415 Align patch 6 19 left Iteration 1 Error: 0.857348 Iteration 2 Error: 0.195091 Iteration 3 Error: 0.066042 Iteration 4 Error: 0.025024 Align patch 7 18 left Iteration 1 Error: 0.985515 Iteration 2 Error: 0.158760 Iteration 3 Error: 0.053176 Iteration 4 Error: 0.044631 Align patch 8 17 left Iteration 1 Error: 0.760287 Iteration 2 Error: 0.186362 Iteration 3 Error: 0.034897 Align patch 9 16 left Iteration 1 Error: 0.781669 Iteration 2 Error: 0.161269 Iteration 3 Error: 0.073976 Iteration 4 Error: 0.038054 Align patch 10 15 left Iteration 1 Error: 0.647543 Iteration 2 Error: 0.112117 Iteration 3 Error: 0.023397 Align patch 11 14 left Iteration 1 Error: 0.721716 Iteration 2 Error: 0.131443 Iteration 3 Error: 0.037129 Align patch 12 13 left Iteration 1 Error: 0.646285 Iteration 2 Error: 0.098547 Iteration 3 Error: 0.025749 Align patch 13 12 left Iteration 1 Error: 0.614217 Iteration 2 Error: 0.162002 Iteration 3 Error: 0.039281 Align patch 14 11 left Iteration 1 Error: 1.197558 Iteration 2 Error: 0.232388 Iteration 3 Error: 0.057528 Iteration 4 Error: 0.027611 Align patch 15 10 left Iteration 1 Error: 1.086359 Iteration 2 Error: 0.221579 Iteration 3 Error: 0.064984 Iteration 4 Error: 0.026185 Align patch 16 9 left Iteration 1 Error: 1.254719 Iteration 2 Error: 0.158087 Iteration 3 Error: 0.027281 Align patch 17 8 left Iteration 1 Error: 0.814508 Iteration 2 Error: 0.166409 Iteration 3 Error: 0.035624 Align patch 18 7 left Iteration 1 Error: 0.896046 Iteration 2 Error: 0.126756 Iteration 3 Error: 0.029359 Align patch 19 6 left Iteration 1 Error: 0.876751 Iteration 2 Error: 0.178558 Iteration 3 Error: 0.067233 Iteration 4 Error: 0.021317 Align patch 20 5 left Iteration 1 Error: 0.846092 Iteration 2 Error: 0.107875 Iteration 3 Error: 0.026274 Align patch 21 4 left Iteration 1 Error: 1.029129 Iteration 2 Error: 0.244468 Iteration 3 Error: 0.053337 Iteration 4 Error: 0.024183 Align patch 22 3 left Iteration 1 Error: 0.858333 Iteration 2 Error: 0.202019 Iteration 3 Error: 0.097486 Iteration 4 Error: 0.028753 Align patch 23 2 left Iteration 1 Error: 0.812827 Iteration 2 Error: 0.208501 Iteration 3 Error: 0.049620 Align patch 24 1 left Iteration 1 Error: 1.568400 Iteration 2 Error: 0.417759 Iteration 3 Error: 0.129091 Iteration 4 Error: 0.065377 Iteration 5 Error: 0.024093 Align patch 25 0 left Iteration 1 Error: 0.859828 Iteration 2 Error: 0.154846 Iteration 3 Error: 0.038835 3D Fitting completed. Patch alignment time: 12.58(sec) Local motion has been corrected. Process thread exits. Computational time: 29.581381 sec Total time: 36.378307 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00007hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00007hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.476153s Reading file: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00007hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 4.714872s ........................................ >>>>>>TIME<<<<<< FFT: 1.298862s Defocus_U Defocus_V Angle CCC 10416.04 11255.93 11.86 0.035725 Final Values Defocus_U Defocus_V Angle CCC 10431.68 11274.69 12.18 0.064157 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00007sq_v01_00007hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00007hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 41.72 6.99 Num Hot pixels: 210 Hot pixel threshold: 83.67 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.539048 Iteration 2 Error: 0.095554 Iteration 3 Error: 0.022265 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.21 -0.06 ...... Frame ( 3) shift: -0.42 -0.11 ...... Frame ( 4) shift: -0.63 -0.17 ...... Frame ( 5) shift: -0.84 -0.23 ...... Frame ( 6) shift: -0.91 -0.26 ...... Frame ( 7) shift: -0.85 -0.27 ...... Frame ( 8) shift: -0.79 -0.27 ...... Frame ( 9) shift: -0.76 -0.24 ...... Frame ( 10) shift: -0.76 -0.16 ...... Frame ( 11) shift: -0.76 -0.09 ...... Frame ( 12) shift: -0.74 -0.03 ...... Frame ( 13) shift: -0.72 0.01 ...... Frame ( 14) shift: -0.70 0.05 ...... Frame ( 15) shift: -0.64 0.06 ...... Frame ( 16) shift: -0.56 0.05 ...... Frame ( 17) shift: -0.47 0.03 ...... Frame ( 18) shift: -0.46 0.07 ...... Frame ( 19) shift: -0.53 0.15 ...... Frame ( 20) shift: -0.59 0.23 ...... Frame ( 21) shift: -0.64 0.30 ...... Frame ( 22) shift: -0.66 0.36 ...... Frame ( 23) shift: -0.69 0.42 ...... Frame ( 24) shift: -0.66 0.45 ...... Frame ( 25) shift: -0.57 0.46 ...... Frame ( 26) shift: -0.49 0.47 ...... Frame ( 27) shift: -0.45 0.49 ...... Frame ( 28) shift: -0.44 0.53 ...... Frame ( 29) shift: -0.44 0.56 ...... Frame ( 30) shift: -0.43 0.57 ...... Frame ( 31) shift: -0.39 0.57 ...... Frame ( 32) shift: -0.36 0.56 ...... Frame ( 33) shift: -0.34 0.56 ...... Frame ( 34) shift: -0.31 0.59 ...... Frame ( 35) shift: -0.29 0.61 ...... Frame ( 36) shift: -0.28 0.62 ...... Frame ( 37) shift: -0.29 0.59 ...... Frame ( 38) shift: -0.30 0.57 ...... Frame ( 39) shift: -0.31 0.55 ...... Frame ( 40) shift: -0.31 0.53 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.758429 Iteration 2 Error: 0.127509 Iteration 3 Error: 0.047931 Align patch 2 23 left Iteration 1 Error: 0.687914 Iteration 2 Error: 0.147463 Iteration 3 Error: 0.036926 Align patch 3 22 left Iteration 1 Error: 0.782823 Iteration 2 Error: 0.113036 Iteration 3 Error: 0.034825 Align patch 4 21 left Iteration 1 Error: 0.763698 Iteration 2 Error: 0.098611 Iteration 3 Error: 0.024118 Align patch 5 20 left Iteration 1 Error: 0.860232 Iteration 2 Error: 0.112716 Iteration 3 Error: 0.029652 Align patch 6 19 left Iteration 1 Error: 1.203505 Iteration 2 Error: 0.223005 Iteration 3 Error: 0.071179 Iteration 4 Error: 0.032436 Align patch 7 18 left Iteration 1 Error: 0.902996 Iteration 2 Error: 0.241614 Iteration 3 Error: 0.069240 Iteration 4 Error: 0.017725 Align patch 8 17 left Iteration 1 Error: 0.792032 Iteration 2 Error: 0.122113 Iteration 3 Error: 0.056113 Iteration 4 Error: 0.017959 Align patch 9 16 left Iteration 1 Error: 0.499382 Iteration 2 Error: 0.096452 Iteration 3 Error: 0.027641 Align patch 10 15 left Iteration 1 Error: 0.867298 Iteration 2 Error: 0.129743 Iteration 3 Error: 0.035428 Align patch 11 14 left Iteration 1 Error: 0.591086 Iteration 2 Error: 0.112243 Iteration 3 Error: 0.030093 Align patch 12 13 left Iteration 1 Error: 0.616311 Iteration 2 Error: 0.126555 Iteration 3 Error: 0.028188 Align patch 13 12 left Iteration 1 Error: 0.697188 Iteration 2 Error: 0.108832 Iteration 3 Error: 0.020673 Align patch 14 11 left Iteration 1 Error: 0.662221 Iteration 2 Error: 0.119715 Iteration 3 Error: 0.011621 Align patch 15 10 left Iteration 1 Error: 0.630926 Iteration 2 Error: 0.098046 Iteration 3 Error: 0.018611 Align patch 16 9 left Iteration 1 Error: 0.718118 Iteration 2 Error: 0.121936 Iteration 3 Error: 0.019698 Align patch 17 8 left Iteration 1 Error: 0.504434 Iteration 2 Error: 0.108614 Iteration 3 Error: 0.029481 Align patch 18 7 left Iteration 1 Error: 0.672006 Iteration 2 Error: 0.108719 Iteration 3 Error: 0.029942 Align patch 19 6 left Iteration 1 Error: 0.589487 Iteration 2 Error: 0.073541 Iteration 3 Error: 0.016374 Align patch 20 5 left Iteration 1 Error: 0.501729 Iteration 2 Error: 0.058887 Iteration 3 Error: 0.010912 Align patch 21 4 left Iteration 1 Error: 1.113911 Iteration 2 Error: 0.201462 Iteration 3 Error: 0.036661 Align patch 22 3 left Iteration 1 Error: 0.858588 Iteration 2 Error: 0.108047 Iteration 3 Error: 0.030310 Align patch 23 2 left Iteration 1 Error: 0.690235 Iteration 2 Error: 0.098017 Iteration 3 Error: 0.018636 Align patch 24 1 left Iteration 1 Error: 0.623374 Iteration 2 Error: 0.148392 Iteration 3 Error: 0.054159 Iteration 4 Error: 0.020933 Align patch 25 0 left Iteration 1 Error: 0.607571 Iteration 2 Error: 0.106841 Iteration 3 Error: 0.023189 3D Fitting completed. Patch alignment time: 11.11(sec) Local motion has been corrected. Process thread exits. Computational time: 25.097729 sec Total time: 32.764683 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00007hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00007hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.475074s Reading file: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00007hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.898439s ........................................ >>>>>>TIME<<<<<< FFT: 1.054766s Defocus_U Defocus_V Angle CCC 8333.99 8814.46 5.22 0.027435 Final Values Defocus_U Defocus_V Angle CCC 8335.55 8825.40 4.59 0.060579 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00007sq_v01_00007hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00007hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 1.000e-01 CC threshold: 0.734 Mean Std: 41.40 6.95 Num Hot pixels: 206 Hot pixel threshold: 83.10 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.530136 Iteration 2 Error: 0.384575 Iteration 3 Error: 0.124694 Iteration 4 Error: 0.053149 Iteration 5 Error: 0.021142 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.10 -0.07 ...... Frame ( 3) shift: -0.20 -0.13 ...... Frame ( 4) shift: -0.29 -0.20 ...... Frame ( 5) shift: -0.39 -0.27 ...... Frame ( 6) shift: -0.45 -0.26 ...... Frame ( 7) shift: -0.46 -0.18 ...... Frame ( 8) shift: -0.48 -0.09 ...... Frame ( 9) shift: -0.46 0.00 ...... Frame ( 10) shift: -0.40 0.12 ...... Frame ( 11) shift: -0.34 0.23 ...... Frame ( 12) shift: -0.28 0.31 ...... Frame ( 13) shift: -0.21 0.36 ...... Frame ( 14) shift: -0.15 0.40 ...... Frame ( 15) shift: -0.11 0.48 ...... Frame ( 16) shift: -0.09 0.57 ...... Frame ( 17) shift: -0.08 0.67 ...... Frame ( 18) shift: -0.10 0.84 ...... Frame ( 19) shift: -0.14 1.10 ...... Frame ( 20) shift: -0.18 1.35 ...... Frame ( 21) shift: -0.15 1.56 ...... Frame ( 22) shift: -0.07 1.71 ...... Frame ( 23) shift: 0.02 1.87 ...... Frame ( 24) shift: 0.06 1.94 ...... Frame ( 25) shift: 0.05 1.93 ...... Frame ( 26) shift: 0.03 1.92 ...... Frame ( 27) shift: 0.04 1.95 ...... Frame ( 28) shift: 0.07 2.02 ...... Frame ( 29) shift: 0.09 2.09 ...... Frame ( 30) shift: 0.14 2.18 ...... Frame ( 31) shift: 0.22 2.28 ...... Frame ( 32) shift: 0.30 2.39 ...... Frame ( 33) shift: 0.38 2.46 ...... Frame ( 34) shift: 0.48 2.50 ...... Frame ( 35) shift: 0.57 2.54 ...... Frame ( 36) shift: 0.66 2.60 ...... Frame ( 37) shift: 0.76 2.69 ...... Frame ( 38) shift: 0.85 2.78 ...... Frame ( 39) shift: 0.95 2.87 ...... Frame ( 40) shift: 1.04 2.96 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.758051 Iteration 2 Error: 0.208104 Iteration 3 Error: 0.091424 Iteration 4 Error: 0.052341 Iteration 5 Error: 0.027857 Align patch 2 23 left Iteration 1 Error: 1.711130 Iteration 2 Error: 0.277564 Iteration 3 Error: 0.129876 Iteration 4 Error: 0.031802 Align patch 3 22 left Iteration 1 Error: 1.299935 Iteration 2 Error: 0.206852 Iteration 3 Error: 0.081560 Iteration 4 Error: 0.051465 Iteration 5 Error: 0.017667 Align patch 4 21 left Iteration 1 Error: 0.643104 Iteration 2 Error: 0.138491 Iteration 3 Error: 0.052705 Iteration 4 Error: 0.022040 Align patch 5 20 left Iteration 1 Error: 1.085623 Iteration 2 Error: 0.218273 Iteration 3 Error: 0.058587 Iteration 4 Error: 0.020893 Align patch 6 19 left Iteration 1 Error: 1.162417 Iteration 2 Error: 0.362615 Iteration 3 Error: 0.239455 Iteration 4 Error: 0.110277 Iteration 5 Error: 0.082718 Align patch 6 19 left Iteration 1 Error: 1.512672 Iteration 2 Error: 0.215680 Iteration 3 Error: 0.048961 Align patch 7 18 left Iteration 1 Error: 0.609848 Iteration 2 Error: 0.186924 Iteration 3 Error: 0.056631 Iteration 4 Error: 0.043751 Align patch 8 17 left Iteration 1 Error: 0.990975 Iteration 2 Error: 0.238931 Iteration 3 Error: 0.132363 Iteration 4 Error: 0.055768 Iteration 5 Error: 0.022668 Align patch 9 16 left Iteration 1 Error: 1.586851 Iteration 2 Error: 0.477689 Iteration 3 Error: 0.258189 Iteration 4 Error: 0.152198 Iteration 5 Error: 0.101642 Align patch 9 16 left Iteration 1 Error: 1.196153 Iteration 2 Error: 0.330017 Iteration 3 Error: 0.122655 Iteration 4 Error: 0.052620 Iteration 5 Error: 0.019171 Align patch 10 15 left Iteration 1 Error: 1.689437 Iteration 2 Error: 0.336523 Iteration 3 Error: 0.185946 Iteration 4 Error: 0.135096 Iteration 5 Error: 0.069628 Align patch 10 15 left Iteration 1 Error: 1.420441 Iteration 2 Error: 0.448364 Iteration 3 Error: 0.197463 Iteration 4 Error: 0.096807 Iteration 5 Error: 0.062663 Align patch 11 14 left Iteration 1 Error: 0.817702 Iteration 2 Error: 0.357431 Iteration 3 Error: 0.100533 Iteration 4 Error: 0.056114 Iteration 5 Error: 0.025205 Align patch 12 13 left Iteration 1 Error: 0.986548 Iteration 2 Error: 0.193673 Iteration 3 Error: 0.048643 Align patch 13 12 left Iteration 1 Error: 0.955277 Iteration 2 Error: 0.235321 Iteration 3 Error: 0.083437 Iteration 4 Error: 0.039455 Align patch 14 11 left Iteration 1 Error: 1.149554 Iteration 2 Error: 0.210739 Iteration 3 Error: 0.081666 Iteration 4 Error: 0.027285 Align patch 15 10 left Iteration 1 Error: 0.881340 Iteration 2 Error: 0.211330 Iteration 3 Error: 0.068292 Iteration 4 Error: 0.024869 Align patch 16 9 left Iteration 1 Error: 1.054922 Iteration 2 Error: 0.351153 Iteration 3 Error: 0.159455 Iteration 4 Error: 0.058085 Iteration 5 Error: 0.024663 Align patch 17 8 left Iteration 1 Error: 0.718070 Iteration 2 Error: 0.202863 Iteration 3 Error: 0.056761 Iteration 4 Error: 0.037697 Align patch 18 7 left Iteration 1 Error: 0.829766 Iteration 2 Error: 0.183082 Iteration 3 Error: 0.040891 Align patch 19 6 left Iteration 1 Error: 1.017577 Iteration 2 Error: 0.199289 Iteration 3 Error: 0.079941 Iteration 4 Error: 0.032010 Align patch 20 5 left Iteration 1 Error: 1.306011 Iteration 2 Error: 0.262098 Iteration 3 Error: 0.065740 Iteration 4 Error: 0.022059 Align patch 21 4 left Iteration 1 Error: 0.655012 Iteration 2 Error: 0.245734 Iteration 3 Error: 0.112750 Iteration 4 Error: 0.050428 Iteration 5 Error: 0.021764 Align patch 22 3 left Iteration 1 Error: 1.150699 Iteration 2 Error: 0.183581 Iteration 3 Error: 0.038189 Align patch 23 2 left Iteration 1 Error: 0.899242 Iteration 2 Error: 0.140073 Iteration 3 Error: 0.035115 Align patch 24 1 left Iteration 1 Error: 1.571177 Iteration 2 Error: 0.448932 Iteration 3 Error: 0.166270 Iteration 4 Error: 0.071383 Iteration 5 Error: 0.031226 Align patch 25 0 left Iteration 1 Error: 1.411385 Iteration 2 Error: 0.348491 Iteration 3 Error: 0.151757 Iteration 4 Error: 0.052655 Iteration 5 Error: 0.016558 3D Fitting completed. Patch alignment time: 15.47(sec) Local motion has been corrected. Process thread exits. Computational time: 28.865566 sec Total time: 36.692047 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00007hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00007hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.586595s Reading file: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00007hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.656070s ........................................ >>>>>>TIME<<<<<< FFT: 0.944717s Defocus_U Defocus_V Angle CCC 11029.32 11853.67 5.18 0.037186 Final Values Defocus_U Defocus_V Angle CCC 11055.91 11883.39 5.50 0.065795 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00007sq_v01_00007hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00007hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.999e-02 CC threshold: 0.734 Mean Std: 41.06 6.87 Num Hot pixels: 200 Hot pixel threshold: 82.26 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.936889 Iteration 2 Error: 0.173560 Iteration 3 Error: 0.038107 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.03 0.09 ...... Frame ( 3) shift: 0.07 0.18 ...... Frame ( 4) shift: 0.10 0.27 ...... Frame ( 5) shift: 0.14 0.36 ...... Frame ( 6) shift: 0.18 0.40 ...... Frame ( 7) shift: 0.22 0.39 ...... Frame ( 8) shift: 0.27 0.37 ...... Frame ( 9) shift: 0.31 0.41 ...... Frame ( 10) shift: 0.34 0.49 ...... Frame ( 11) shift: 0.38 0.57 ...... Frame ( 12) shift: 0.43 0.64 ...... Frame ( 13) shift: 0.49 0.72 ...... Frame ( 14) shift: 0.56 0.80 ...... Frame ( 15) shift: 0.62 0.86 ...... Frame ( 16) shift: 0.69 0.92 ...... Frame ( 17) shift: 0.75 0.97 ...... Frame ( 18) shift: 0.76 1.03 ...... Frame ( 19) shift: 0.73 1.08 ...... Frame ( 20) shift: 0.70 1.14 ...... Frame ( 21) shift: 0.69 1.20 ...... Frame ( 22) shift: 0.71 1.27 ...... Frame ( 23) shift: 0.72 1.34 ...... Frame ( 24) shift: 0.72 1.39 ...... Frame ( 25) shift: 0.70 1.44 ...... Frame ( 26) shift: 0.68 1.49 ...... Frame ( 27) shift: 0.70 1.53 ...... Frame ( 28) shift: 0.76 1.56 ...... Frame ( 29) shift: 0.82 1.59 ...... Frame ( 30) shift: 0.89 1.55 ...... Frame ( 31) shift: 0.98 1.45 ...... Frame ( 32) shift: 1.06 1.34 ...... Frame ( 33) shift: 1.10 1.32 ...... Frame ( 34) shift: 1.10 1.38 ...... Frame ( 35) shift: 1.10 1.45 ...... Frame ( 36) shift: 1.12 1.49 ...... Frame ( 37) shift: 1.16 1.50 ...... Frame ( 38) shift: 1.21 1.51 ...... Frame ( 39) shift: 1.25 1.53 ...... Frame ( 40) shift: 1.29 1.54 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.998290 Iteration 2 Error: 0.234554 Iteration 3 Error: 0.067266 Iteration 4 Error: 0.032577 Align patch 2 23 left Iteration 1 Error: 0.719748 Iteration 2 Error: 0.171789 Iteration 3 Error: 0.055869 Iteration 4 Error: 0.028156 Align patch 3 22 left Iteration 1 Error: 0.804790 Iteration 2 Error: 0.156614 Iteration 3 Error: 0.038701 Align patch 4 21 left Iteration 1 Error: 0.870263 Iteration 2 Error: 0.198583 Iteration 3 Error: 0.116626 Iteration 4 Error: 0.034947 Align patch 5 20 left Iteration 1 Error: 1.286231 Iteration 2 Error: 0.321485 Iteration 3 Error: 0.102530 Iteration 4 Error: 0.062125 Iteration 5 Error: 0.030019 Align patch 6 19 left Iteration 1 Error: 1.018198 Iteration 2 Error: 0.262207 Iteration 3 Error: 0.045460 Align patch 7 18 left Iteration 1 Error: 1.178456 Iteration 2 Error: 0.245726 Iteration 3 Error: 0.076918 Iteration 4 Error: 0.028789 Align patch 8 17 left Iteration 1 Error: 0.706681 Iteration 2 Error: 0.150996 Iteration 3 Error: 0.057427 Iteration 4 Error: 0.026583 Align patch 9 16 left Iteration 1 Error: 0.455997 Iteration 2 Error: 0.076389 Iteration 3 Error: 0.019411 Align patch 10 15 left Iteration 1 Error: 0.868448 Iteration 2 Error: 0.145550 Iteration 3 Error: 0.032309 Align patch 11 14 left Iteration 1 Error: 1.929366 Iteration 2 Error: 0.298514 Iteration 3 Error: 0.110387 Iteration 4 Error: 0.049014 Align patch 12 13 left Iteration 1 Error: 1.027500 Iteration 2 Error: 0.273591 Iteration 3 Error: 0.096008 Iteration 4 Error: 0.036281 Align patch 13 12 left Iteration 1 Error: 0.960581 Iteration 2 Error: 0.118155 Iteration 3 Error: 0.034890 Align patch 14 11 left Iteration 1 Error: 0.798138 Iteration 2 Error: 0.155497 Iteration 3 Error: 0.033206 Align patch 15 10 left Iteration 1 Error: 0.859582 Iteration 2 Error: 0.214671 Iteration 3 Error: 0.076743 Iteration 4 Error: 0.023464 Align patch 16 9 left Iteration 1 Error: 0.974789 Iteration 2 Error: 0.204591 Iteration 3 Error: 0.094957 Iteration 4 Error: 0.033864 Align patch 17 8 left Iteration 1 Error: 0.782507 Iteration 2 Error: 0.258149 Iteration 3 Error: 0.072443 Iteration 4 Error: 0.043582 Align patch 18 7 left Iteration 1 Error: 0.644175 Iteration 2 Error: 0.190904 Iteration 3 Error: 0.047079 Align patch 19 6 left Iteration 1 Error: 0.622395 Iteration 2 Error: 0.142516 Iteration 3 Error: 0.047225 Align patch 20 5 left Iteration 1 Error: 1.004586 Iteration 2 Error: 0.209679 Iteration 3 Error: 0.059819 Iteration 4 Error: 0.019770 Align patch 21 4 left Iteration 1 Error: 1.205587 Iteration 2 Error: 0.158461 Iteration 3 Error: 0.026198 Align patch 22 3 left Iteration 1 Error: 1.056111 Iteration 2 Error: 0.149370 Iteration 3 Error: 0.031866 Align patch 23 2 left Iteration 1 Error: 0.619686 Iteration 2 Error: 0.094418 Iteration 3 Error: 0.014594 Align patch 24 1 left Iteration 1 Error: 1.101501 Iteration 2 Error: 0.179206 Iteration 3 Error: 0.055225 Iteration 4 Error: 0.012354 Align patch 25 0 left Iteration 1 Error: 1.347959 Iteration 2 Error: 0.112117 Iteration 3 Error: 0.024138 3D Fitting completed. Patch alignment time: 13.67(sec) Local motion has been corrected. Process thread exits. Computational time: 24.327879 sec Total time: 32.060783 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00007hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00007hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.032354s Reading file: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00007hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.240956s ........................................ >>>>>>TIME<<<<<< FFT: 0.963840s Defocus_U Defocus_V Angle CCC 12689.59 12122.96 84.40 0.036768 Final Values Defocus_U Defocus_V Angle CCC 12708.34 12122.97 83.78 0.064262 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00007sq_v01_00008hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00008hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 9.999e-02 CC threshold: 0.734 Mean Std: 42.78 7.10 Num Hot pixels: 194 Hot pixel threshold: 85.37 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.352579 Iteration 2 Error: 0.216517 Iteration 3 Error: 0.053627 Iteration 4 Error: 0.026998 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.26 -0.26 ...... Frame ( 3) shift: -0.52 -0.52 ...... Frame ( 4) shift: -0.79 -0.78 ...... Frame ( 5) shift: -1.05 -1.04 ...... Frame ( 6) shift: -1.12 -1.15 ...... Frame ( 7) shift: -1.01 -1.10 ...... Frame ( 8) shift: -0.90 -1.04 ...... Frame ( 9) shift: -0.82 -0.94 ...... Frame ( 10) shift: -0.79 -0.79 ...... Frame ( 11) shift: -0.75 -0.63 ...... Frame ( 12) shift: -0.70 -0.51 ...... Frame ( 13) shift: -0.64 -0.43 ...... Frame ( 14) shift: -0.57 -0.34 ...... Frame ( 15) shift: -0.52 -0.23 ...... Frame ( 16) shift: -0.48 -0.08 ...... Frame ( 17) shift: -0.43 0.06 ...... Frame ( 18) shift: -0.37 0.17 ...... Frame ( 19) shift: -0.30 0.24 ...... Frame ( 20) shift: -0.23 0.32 ...... Frame ( 21) shift: -0.18 0.39 ...... Frame ( 22) shift: -0.16 0.46 ...... Frame ( 23) shift: -0.13 0.52 ...... Frame ( 24) shift: -0.13 0.56 ...... Frame ( 25) shift: -0.15 0.55 ...... Frame ( 26) shift: -0.17 0.55 ...... Frame ( 27) shift: -0.15 0.56 ...... Frame ( 28) shift: -0.08 0.59 ...... Frame ( 29) shift: -0.02 0.61 ...... Frame ( 30) shift: 0.03 0.64 ...... Frame ( 31) shift: 0.06 0.67 ...... Frame ( 32) shift: 0.09 0.70 ...... Frame ( 33) shift: 0.11 0.75 ...... Frame ( 34) shift: 0.10 0.82 ...... Frame ( 35) shift: 0.10 0.89 ...... Frame ( 36) shift: 0.11 0.95 ...... Frame ( 37) shift: 0.15 1.00 ...... Frame ( 38) shift: 0.18 1.04 ...... Frame ( 39) shift: 0.22 1.09 ...... Frame ( 40) shift: 0.25 1.14 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.876644 Iteration 2 Error: 0.202240 Iteration 3 Error: 0.079345 Iteration 4 Error: 0.024315 Align patch 2 23 left Iteration 1 Error: 0.958039 Iteration 2 Error: 0.095928 Iteration 3 Error: 0.027417 Align patch 3 22 left Iteration 1 Error: 0.975874 Iteration 2 Error: 0.103322 Iteration 3 Error: 0.037092 Align patch 4 21 left Iteration 1 Error: 0.883785 Iteration 2 Error: 0.080793 Iteration 3 Error: 0.029766 Align patch 5 20 left Iteration 1 Error: 0.633860 Iteration 2 Error: 0.115084 Iteration 3 Error: 0.027902 Align patch 6 19 left Iteration 1 Error: 0.929623 Iteration 2 Error: 0.133034 Iteration 3 Error: 0.045760 Align patch 7 18 left Iteration 1 Error: 0.812008 Iteration 2 Error: 0.111531 Iteration 3 Error: 0.029687 Align patch 8 17 left Iteration 1 Error: 0.809834 Iteration 2 Error: 0.124848 Iteration 3 Error: 0.035211 Align patch 9 16 left Iteration 1 Error: 1.085212 Iteration 2 Error: 0.219442 Iteration 3 Error: 0.087540 Iteration 4 Error: 0.051838 Iteration 5 Error: 0.016755 Align patch 10 15 left Iteration 1 Error: 2.049668 Iteration 2 Error: 1.999911 Iteration 3 Error: 0.436620 Iteration 4 Error: 0.209502 Iteration 5 Error: 0.144901 Align patch 10 15 left Iteration 1 Error: 1.581518 Iteration 2 Error: 0.313844 Iteration 3 Error: 0.098401 Iteration 4 Error: 0.034240 Align patch 11 14 left Iteration 1 Error: 0.704271 Iteration 2 Error: 0.083843 Iteration 3 Error: 0.019124 Align patch 12 13 left Iteration 1 Error: 0.863180 Iteration 2 Error: 0.114506 Iteration 3 Error: 0.026945 Align patch 13 12 left Iteration 1 Error: 0.795658 Iteration 2 Error: 0.168870 Iteration 3 Error: 0.053317 Iteration 4 Error: 0.023170 Align patch 14 11 left Iteration 1 Error: 0.842595 Iteration 2 Error: 0.175485 Iteration 3 Error: 0.043269 Align patch 15 10 left Iteration 1 Error: 0.642370 Iteration 2 Error: 0.119247 Iteration 3 Error: 0.026087 Align patch 16 9 left Iteration 1 Error: 1.291993 Iteration 2 Error: 0.149198 Iteration 3 Error: 0.035539 Align patch 17 8 left Iteration 1 Error: 0.681067 Iteration 2 Error: 0.121165 Iteration 3 Error: 0.036168 Align patch 18 7 left Iteration 1 Error: 0.642765 Iteration 2 Error: 0.115408 Iteration 3 Error: 0.021918 Align patch 19 6 left Iteration 1 Error: 0.710174 Iteration 2 Error: 0.118881 Iteration 3 Error: 0.046172 Align patch 20 5 left Iteration 1 Error: 0.762724 Iteration 2 Error: 0.079855 Iteration 3 Error: 0.013627 Align patch 21 4 left Iteration 1 Error: 1.458007 Iteration 2 Error: 0.180646 Iteration 3 Error: 0.061320 Iteration 4 Error: 0.022553 Align patch 22 3 left Iteration 1 Error: 0.695949 Iteration 2 Error: 0.101857 Iteration 3 Error: 0.024715 Align patch 23 2 left Iteration 1 Error: 0.526972 Iteration 2 Error: 0.066282 Iteration 3 Error: 0.017493 Align patch 24 1 left Iteration 1 Error: 0.676659 Iteration 2 Error: 0.196407 Iteration 3 Error: 0.045248 Align patch 25 0 left Iteration 1 Error: 0.697729 Iteration 2 Error: 0.083008 Iteration 3 Error: 0.020426 3D Fitting completed. Patch alignment time: 11.84(sec) Local motion has been corrected. Process thread exits. Computational time: 23.596842 sec Total time: 30.297512 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00008hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00008hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.539343s Reading file: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00008hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.587500s ........................................ >>>>>>TIME<<<<<< FFT: 0.946027s Defocus_U Defocus_V Angle CCC 11968.75 12832.03 10.55 0.049251 Final Values Defocus_U Defocus_V Angle CCC 11990.63 12825.79 11.81 0.084841 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00007sq_v01_00008hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00008hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 41.56 6.94 Num Hot pixels: 207 Hot pixel threshold: 83.21 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.163536 Iteration 2 Error: 0.224221 Iteration 3 Error: 0.067618 Iteration 4 Error: 0.019352 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.20 -0.27 ...... Frame ( 3) shift: -0.39 -0.54 ...... Frame ( 4) shift: -0.59 -0.81 ...... Frame ( 5) shift: -0.78 -1.08 ...... Frame ( 6) shift: -0.89 -1.21 ...... Frame ( 7) shift: -0.92 -1.18 ...... Frame ( 8) shift: -0.95 -1.16 ...... Frame ( 9) shift: -0.92 -1.11 ...... Frame ( 10) shift: -0.83 -1.02 ...... Frame ( 11) shift: -0.75 -0.93 ...... Frame ( 12) shift: -0.66 -0.84 ...... Frame ( 13) shift: -0.57 -0.74 ...... Frame ( 14) shift: -0.48 -0.64 ...... Frame ( 15) shift: -0.38 -0.54 ...... Frame ( 16) shift: -0.28 -0.43 ...... Frame ( 17) shift: -0.17 -0.32 ...... Frame ( 18) shift: -0.09 -0.23 ...... Frame ( 19) shift: -0.03 -0.18 ...... Frame ( 20) shift: 0.03 -0.12 ...... Frame ( 21) shift: 0.07 -0.09 ...... Frame ( 22) shift: 0.09 -0.10 ...... Frame ( 23) shift: 0.11 -0.10 ...... Frame ( 24) shift: 0.16 -0.06 ...... Frame ( 25) shift: 0.23 0.03 ...... Frame ( 26) shift: 0.30 0.11 ...... Frame ( 27) shift: 0.36 0.17 ...... Frame ( 28) shift: 0.42 0.20 ...... Frame ( 29) shift: 0.48 0.23 ...... Frame ( 30) shift: 0.56 0.29 ...... Frame ( 31) shift: 0.67 0.37 ...... Frame ( 32) shift: 0.78 0.45 ...... Frame ( 33) shift: 0.80 0.49 ...... Frame ( 34) shift: 0.74 0.49 ...... Frame ( 35) shift: 0.68 0.48 ...... Frame ( 36) shift: 0.69 0.52 ...... Frame ( 37) shift: 0.78 0.60 ...... Frame ( 38) shift: 0.86 0.68 ...... Frame ( 39) shift: 0.94 0.76 ...... Frame ( 40) shift: 1.03 0.84 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.666193 Iteration 2 Error: 0.128624 Iteration 3 Error: 0.038040 Align patch 2 23 left Iteration 1 Error: 1.176818 Iteration 2 Error: 0.201580 Iteration 3 Error: 0.056540 Iteration 4 Error: 0.021608 Align patch 3 22 left Iteration 1 Error: 0.902382 Iteration 2 Error: 0.162240 Iteration 3 Error: 0.034328 Align patch 4 21 left Iteration 1 Error: 0.553523 Iteration 2 Error: 0.128326 Iteration 3 Error: 0.045575 Align patch 5 20 left Iteration 1 Error: 0.830596 Iteration 2 Error: 0.133681 Iteration 3 Error: 0.047649 Align patch 6 19 left Iteration 1 Error: 1.079109 Iteration 2 Error: 0.190192 Iteration 3 Error: 0.065709 Iteration 4 Error: 0.024472 Align patch 7 18 left Iteration 1 Error: 1.054666 Iteration 2 Error: 0.212853 Iteration 3 Error: 0.065468 Iteration 4 Error: 0.017441 Align patch 8 17 left Iteration 1 Error: 1.077036 Iteration 2 Error: 0.200119 Iteration 3 Error: 0.075911 Iteration 4 Error: 0.028575 Align patch 9 16 left Iteration 1 Error: 0.825073 Iteration 2 Error: 0.205672 Iteration 3 Error: 0.065150 Iteration 4 Error: 0.032308 Align patch 10 15 left Iteration 1 Error: 0.692721 Iteration 2 Error: 0.122298 Iteration 3 Error: 0.026871 Align patch 11 14 left Iteration 1 Error: 1.299115 Iteration 2 Error: 0.193297 Iteration 3 Error: 0.050733 Iteration 4 Error: 0.015321 Align patch 12 13 left Iteration 1 Error: 0.621791 Iteration 2 Error: 0.183182 Iteration 3 Error: 0.046778 Align patch 13 12 left Iteration 1 Error: 0.838786 Iteration 2 Error: 0.130371 Iteration 3 Error: 0.059265 Iteration 4 Error: 0.026796 Align patch 14 11 left Iteration 1 Error: 1.019696 Iteration 2 Error: 0.181948 Iteration 3 Error: 0.052467 Iteration 4 Error: 0.017004 Align patch 15 10 left Iteration 1 Error: 0.807124 Iteration 2 Error: 0.126266 Iteration 3 Error: 0.029349 Align patch 16 9 left Iteration 1 Error: 1.081308 Iteration 2 Error: 0.180827 Iteration 3 Error: 0.042517 Align patch 17 8 left Iteration 1 Error: 0.658167 Iteration 2 Error: 0.148575 Iteration 3 Error: 0.041998 Align patch 18 7 left Iteration 1 Error: 0.851125 Iteration 2 Error: 0.173668 Iteration 3 Error: 0.064120 Iteration 4 Error: 0.034480 Align patch 19 6 left Iteration 1 Error: 0.698716 Iteration 2 Error: 0.122142 Iteration 3 Error: 0.028133 Align patch 20 5 left Iteration 1 Error: 0.703135 Iteration 2 Error: 0.155393 Iteration 3 Error: 0.044083 Align patch 21 4 left Iteration 1 Error: 0.901539 Iteration 2 Error: 0.163182 Iteration 3 Error: 0.032341 Align patch 22 3 left Iteration 1 Error: 0.919219 Iteration 2 Error: 0.148069 Iteration 3 Error: 0.061495 Iteration 4 Error: 0.016177 Align patch 23 2 left Iteration 1 Error: 0.850015 Iteration 2 Error: 0.113147 Iteration 3 Error: 0.020308 Align patch 24 1 left Iteration 1 Error: 0.791709 Iteration 2 Error: 0.154630 Iteration 3 Error: 0.039872 Align patch 25 0 left Iteration 1 Error: 0.847704 Iteration 2 Error: 0.137619 Iteration 3 Error: 0.037872 3D Fitting completed. Patch alignment time: 12.42(sec) Local motion has been corrected. Process thread exits. Computational time: 22.789982 sec Total time: 30.066536 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00008hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00008hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.559946s Reading file: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00008hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.143686s ........................................ >>>>>>TIME<<<<<< FFT: 0.889555s Defocus_U Defocus_V Angle CCC 10740.23 11208.98 3.18 0.042633 Final Values Defocus_U Defocus_V Angle CCC 10741.80 11229.31 3.81 0.075220 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00007sq_v01_00008hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00008hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 42.20 7.00 Num Hot pixels: 189 Hot pixel threshold: 84.21 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.858746 Iteration 2 Error: 0.160148 Iteration 3 Error: 0.038455 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.17 -0.46 ...... Frame ( 3) shift: -0.34 -0.92 ...... Frame ( 4) shift: -0.51 -1.37 ...... Frame ( 5) shift: -0.68 -1.83 ...... Frame ( 6) shift: -0.78 -2.06 ...... Frame ( 7) shift: -0.80 -2.05 ...... Frame ( 8) shift: -0.81 -2.04 ...... Frame ( 9) shift: -0.80 -2.01 ...... Frame ( 10) shift: -0.76 -1.97 ...... Frame ( 11) shift: -0.72 -1.93 ...... Frame ( 12) shift: -0.71 -1.87 ...... Frame ( 13) shift: -0.74 -1.79 ...... Frame ( 14) shift: -0.76 -1.70 ...... Frame ( 15) shift: -0.77 -1.61 ...... Frame ( 16) shift: -0.74 -1.52 ...... Frame ( 17) shift: -0.72 -1.44 ...... Frame ( 18) shift: -0.70 -1.35 ...... Frame ( 19) shift: -0.67 -1.28 ...... Frame ( 20) shift: -0.65 -1.20 ...... Frame ( 21) shift: -0.62 -1.14 ...... Frame ( 22) shift: -0.59 -1.08 ...... Frame ( 23) shift: -0.57 -1.03 ...... Frame ( 24) shift: -0.54 -0.98 ...... Frame ( 25) shift: -0.52 -0.93 ...... Frame ( 26) shift: -0.50 -0.88 ...... Frame ( 27) shift: -0.50 -0.83 ...... Frame ( 28) shift: -0.52 -0.78 ...... Frame ( 29) shift: -0.54 -0.72 ...... Frame ( 30) shift: -0.49 -0.66 ...... Frame ( 31) shift: -0.36 -0.60 ...... Frame ( 32) shift: -0.24 -0.54 ...... Frame ( 33) shift: -0.19 -0.51 ...... Frame ( 34) shift: -0.20 -0.49 ...... Frame ( 35) shift: -0.22 -0.47 ...... Frame ( 36) shift: -0.22 -0.45 ...... Frame ( 37) shift: -0.20 -0.43 ...... Frame ( 38) shift: -0.19 -0.40 ...... Frame ( 39) shift: -0.17 -0.38 ...... Frame ( 40) shift: -0.16 -0.35 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.991856 Iteration 2 Error: 0.139852 Iteration 3 Error: 0.035079 Align patch 2 23 left Iteration 1 Error: 0.848631 Iteration 2 Error: 0.153565 Iteration 3 Error: 0.036195 Align patch 3 22 left Iteration 1 Error: 1.072075 Iteration 2 Error: 0.158168 Iteration 3 Error: 0.044208 Align patch 4 21 left Iteration 1 Error: 0.583099 Iteration 2 Error: 0.154460 Iteration 3 Error: 0.034507 Align patch 5 20 left Iteration 1 Error: 1.016637 Iteration 2 Error: 0.155588 Iteration 3 Error: 0.044585 Align patch 6 19 left Iteration 1 Error: 1.270135 Iteration 2 Error: 0.220758 Iteration 3 Error: 0.043413 Align patch 7 18 left Iteration 1 Error: 1.211876 Iteration 2 Error: 0.138298 Iteration 3 Error: 0.036849 Align patch 8 17 left Iteration 1 Error: 0.866193 Iteration 2 Error: 0.163861 Iteration 3 Error: 0.042555 Align patch 9 16 left Iteration 1 Error: 0.708617 Iteration 2 Error: 0.164385 Iteration 3 Error: 0.054913 Iteration 4 Error: 0.021840 Align patch 10 15 left Iteration 1 Error: 0.894509 Iteration 2 Error: 0.350099 Iteration 3 Error: 0.080138 Iteration 4 Error: 0.056702 Iteration 5 Error: 0.019741 Align patch 11 14 left Iteration 1 Error: 1.032947 Iteration 2 Error: 0.182679 Iteration 3 Error: 0.034053 Align patch 12 13 left Iteration 1 Error: 0.685660 Iteration 2 Error: 0.100673 Iteration 3 Error: 0.027018 Align patch 13 12 left Iteration 1 Error: 0.939615 Iteration 2 Error: 0.243330 Iteration 3 Error: 0.082678 Iteration 4 Error: 0.027516 Align patch 14 11 left Iteration 1 Error: 0.659786 Iteration 2 Error: 0.151660 Iteration 3 Error: 0.047937 Align patch 15 10 left Iteration 1 Error: 0.791921 Iteration 2 Error: 0.181898 Iteration 3 Error: 0.058755 Iteration 4 Error: 0.028844 Align patch 16 9 left Iteration 1 Error: 0.804780 Iteration 2 Error: 0.131754 Iteration 3 Error: 0.035831 Align patch 17 8 left Iteration 1 Error: 1.323310 Iteration 2 Error: 0.121586 Iteration 3 Error: 0.068414 Iteration 4 Error: 0.018566 Align patch 18 7 left Iteration 1 Error: 0.672997 Iteration 2 Error: 0.079406 Iteration 3 Error: 0.018813 Align patch 19 6 left Iteration 1 Error: 0.759145 Iteration 2 Error: 0.189851 Iteration 3 Error: 0.041249 Align patch 20 5 left Iteration 1 Error: 0.720121 Iteration 2 Error: 0.252829 Iteration 3 Error: 0.090302 Iteration 4 Error: 0.052501 Iteration 5 Error: 0.013905 Align patch 21 4 left Iteration 1 Error: 1.113456 Iteration 2 Error: 0.114537 Iteration 3 Error: 0.027378 Align patch 22 3 left Iteration 1 Error: 0.503464 Iteration 2 Error: 0.108138 Iteration 3 Error: 0.021712 Align patch 23 2 left Iteration 1 Error: 0.745462 Iteration 2 Error: 0.142146 Iteration 3 Error: 0.039318 Align patch 24 1 left Iteration 1 Error: 0.663889 Iteration 2 Error: 0.120878 Iteration 3 Error: 0.048208 Align patch 25 0 left Iteration 1 Error: 1.055361 Iteration 2 Error: 0.132188 Iteration 3 Error: 0.024493 3D Fitting completed. Patch alignment time: 11.84(sec) Local motion has been corrected. Process thread exits. Computational time: 24.335934 sec Total time: 33.622330 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00008hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00008hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.759526s Reading file: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00008hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.406801s ........................................ >>>>>>TIME<<<<<< FFT: 1.053801s Defocus_U Defocus_V Angle CCC 14861.35 15677.76 4.50 0.047325 Final Values Defocus_U Defocus_V Angle CCC 14848.84 15687.14 4.82 0.079664 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00007sq_v01_00008hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00008hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 1.000e-01 CC threshold: 0.735 Mean Std: 41.75 6.90 Num Hot pixels: 214 Hot pixel threshold: 83.14 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.283443 Iteration 2 Error: 0.275624 Iteration 3 Error: 0.091999 Iteration 4 Error: 0.036490 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.09 -0.34 ...... Frame ( 3) shift: -0.18 -0.69 ...... Frame ( 4) shift: -0.26 -1.03 ...... Frame ( 5) shift: -0.35 -1.38 ...... Frame ( 6) shift: -0.37 -1.54 ...... Frame ( 7) shift: -0.33 -1.51 ...... Frame ( 8) shift: -0.28 -1.48 ...... Frame ( 9) shift: -0.26 -1.40 ...... Frame ( 10) shift: -0.25 -1.26 ...... Frame ( 11) shift: -0.25 -1.13 ...... Frame ( 12) shift: -0.16 -0.96 ...... Frame ( 13) shift: 0.02 -0.76 ...... Frame ( 14) shift: 0.19 -0.56 ...... Frame ( 15) shift: 0.27 -0.43 ...... Frame ( 16) shift: 0.25 -0.36 ...... Frame ( 17) shift: 0.24 -0.29 ...... Frame ( 18) shift: 0.26 -0.20 ...... Frame ( 19) shift: 0.33 -0.09 ...... Frame ( 20) shift: 0.40 0.03 ...... Frame ( 21) shift: 0.46 0.09 ...... Frame ( 22) shift: 0.52 0.10 ...... Frame ( 23) shift: 0.57 0.12 ...... Frame ( 24) shift: 0.60 0.18 ...... Frame ( 25) shift: 0.60 0.27 ...... Frame ( 26) shift: 0.60 0.37 ...... Frame ( 27) shift: 0.62 0.45 ...... Frame ( 28) shift: 0.66 0.49 ...... Frame ( 29) shift: 0.70 0.54 ...... Frame ( 30) shift: 0.72 0.57 ...... Frame ( 31) shift: 0.70 0.58 ...... Frame ( 32) shift: 0.69 0.58 ...... Frame ( 33) shift: 0.72 0.63 ...... Frame ( 34) shift: 0.79 0.71 ...... Frame ( 35) shift: 0.87 0.80 ...... Frame ( 36) shift: 0.95 0.85 ...... Frame ( 37) shift: 1.03 0.86 ...... Frame ( 38) shift: 1.11 0.87 ...... Frame ( 39) shift: 1.19 0.88 ...... Frame ( 40) shift: 1.28 0.89 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.792681 Iteration 2 Error: 0.360898 Iteration 3 Error: 0.160292 Iteration 4 Error: 0.053614 Iteration 5 Error: 0.026578 Align patch 2 23 left Iteration 1 Error: 0.972542 Iteration 2 Error: 0.187404 Iteration 3 Error: 0.086020 Iteration 4 Error: 0.023864 Align patch 3 22 left Iteration 1 Error: 0.552007 Iteration 2 Error: 0.113260 Iteration 3 Error: 0.043950 Align patch 4 21 left Iteration 1 Error: 0.890441 Iteration 2 Error: 0.172493 Iteration 3 Error: 0.031582 Align patch 5 20 left Iteration 1 Error: 1.587041 Iteration 2 Error: 0.351576 Iteration 3 Error: 0.084699 Iteration 4 Error: 0.022614 Align patch 6 19 left Iteration 1 Error: 2.186283 Iteration 2 Error: 0.368179 Iteration 3 Error: 0.113488 Iteration 4 Error: 0.057323 Iteration 5 Error: 0.020827 Align patch 7 18 left Iteration 1 Error: 1.378762 Iteration 2 Error: 0.276475 Iteration 3 Error: 0.063954 Iteration 4 Error: 0.020458 Align patch 8 17 left Iteration 1 Error: 0.718598 Iteration 2 Error: 0.086678 Iteration 3 Error: 0.029101 Align patch 9 16 left Iteration 1 Error: 1.172186 Iteration 2 Error: 0.263367 Iteration 3 Error: 0.066312 Iteration 4 Error: 0.029753 Align patch 10 15 left Iteration 1 Error: 1.012748 Iteration 2 Error: 0.273730 Iteration 3 Error: 0.084527 Iteration 4 Error: 0.028076 Align patch 11 14 left Iteration 1 Error: 2.025556 Iteration 2 Error: 0.395682 Iteration 3 Error: 0.167900 Iteration 4 Error: 0.086210 Iteration 5 Error: 0.047265 Align patch 12 13 left Iteration 1 Error: 0.847249 Iteration 2 Error: 0.165256 Iteration 3 Error: 0.040631 Align patch 13 12 left Iteration 1 Error: 1.078527 Iteration 2 Error: 0.270041 Iteration 3 Error: 0.073036 Iteration 4 Error: 0.045033 Align patch 14 11 left Iteration 1 Error: 0.850629 Iteration 2 Error: 0.189195 Iteration 3 Error: 0.053625 Iteration 4 Error: 0.022045 Align patch 15 10 left Iteration 1 Error: 1.624299 Iteration 2 Error: 0.378089 Iteration 3 Error: 0.100576 Iteration 4 Error: 0.028375 Align patch 16 9 left Iteration 1 Error: 0.776374 Iteration 2 Error: 0.163729 Iteration 3 Error: 0.081047 Iteration 4 Error: 0.051887 Iteration 5 Error: 0.023416 Align patch 17 8 left Iteration 1 Error: 1.153713 Iteration 2 Error: 0.213211 Iteration 3 Error: 0.107817 Iteration 4 Error: 0.037746 Align patch 18 7 left Iteration 1 Error: 0.939795 Iteration 2 Error: 0.235657 Iteration 3 Error: 0.065661 Iteration 4 Error: 0.028195 Align patch 19 6 left Iteration 1 Error: 0.553265 Iteration 2 Error: 0.118625 Iteration 3 Error: 0.033196 Align patch 20 5 left Iteration 1 Error: 1.300003 Iteration 2 Error: 0.176576 Iteration 3 Error: 0.052645 Iteration 4 Error: 0.016978 Align patch 21 4 left Iteration 1 Error: 0.590701 Iteration 2 Error: 0.198509 Iteration 3 Error: 0.057630 Iteration 4 Error: 0.029757 Align patch 22 3 left Iteration 1 Error: 0.970718 Iteration 2 Error: 0.232520 Iteration 3 Error: 0.050746 Iteration 4 Error: 0.017158 Align patch 23 2 left Iteration 1 Error: 0.848792 Iteration 2 Error: 0.132828 Iteration 3 Error: 0.040987 Align patch 24 1 left Iteration 1 Error: 0.604954 Iteration 2 Error: 0.128997 Iteration 3 Error: 0.047259 Align patch 25 0 left Iteration 1 Error: 1.561924 Iteration 2 Error: 0.341895 Iteration 3 Error: 0.065551 Iteration 4 Error: 0.028639 3D Fitting completed. Patch alignment time: 12.53(sec) Local motion has been corrected. Process thread exits. Computational time: 25.010954 sec Total time: 32.793015 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00008hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00008hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.549078s Reading file: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00008hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.788503s ........................................ >>>>>>TIME<<<<<< FFT: 0.937508s Defocus_U Defocus_V Angle CCC 11377.09 10755.76 86.01 0.035060 Final Values Defocus_U Defocus_V Angle CCC 11425.55 10769.84 86.96 0.062575 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00007sq_v01_00009hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00009hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.995e-02 CC threshold: 0.734 Mean Std: 43.43 7.18 Num Hot pixels: 209 Hot pixel threshold: 86.49 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.342763 Iteration 2 Error: 0.270269 Iteration 3 Error: 0.072649 Iteration 4 Error: 0.028233 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.20 -0.08 ...... Frame ( 3) shift: -0.40 -0.17 ...... Frame ( 4) shift: -0.60 -0.25 ...... Frame ( 5) shift: -0.79 -0.33 ...... Frame ( 6) shift: -0.84 -0.30 ...... Frame ( 7) shift: -0.74 -0.13 ...... Frame ( 8) shift: -0.63 0.03 ...... Frame ( 9) shift: -0.59 0.16 ...... Frame ( 10) shift: -0.61 0.28 ...... Frame ( 11) shift: -0.63 0.39 ...... Frame ( 12) shift: -0.63 0.50 ...... Frame ( 13) shift: -0.59 0.62 ...... Frame ( 14) shift: -0.55 0.74 ...... Frame ( 15) shift: -0.51 0.82 ...... Frame ( 16) shift: -0.46 0.87 ...... Frame ( 17) shift: -0.41 0.93 ...... Frame ( 18) shift: -0.38 1.02 ...... Frame ( 19) shift: -0.38 1.17 ...... Frame ( 20) shift: -0.38 1.31 ...... Frame ( 21) shift: -0.38 1.40 ...... Frame ( 22) shift: -0.37 1.44 ...... Frame ( 23) shift: -0.37 1.47 ...... Frame ( 24) shift: -0.34 1.51 ...... Frame ( 25) shift: -0.28 1.54 ...... Frame ( 26) shift: -0.22 1.56 ...... Frame ( 27) shift: -0.16 1.61 ...... Frame ( 28) shift: -0.08 1.66 ...... Frame ( 29) shift: -0.01 1.71 ...... Frame ( 30) shift: 0.07 1.78 ...... Frame ( 31) shift: 0.14 1.87 ...... Frame ( 32) shift: 0.22 1.96 ...... Frame ( 33) shift: 0.29 2.00 ...... Frame ( 34) shift: 0.35 1.97 ...... Frame ( 35) shift: 0.41 1.94 ...... Frame ( 36) shift: 0.40 1.94 ...... Frame ( 37) shift: 0.34 1.97 ...... Frame ( 38) shift: 0.28 1.99 ...... Frame ( 39) shift: 0.22 2.02 ...... Frame ( 40) shift: 0.16 2.04 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.752379 Iteration 2 Error: 0.337189 Iteration 3 Error: 0.208863 Iteration 4 Error: 0.096430 Iteration 5 Error: 0.069933 Align patch 1 24 left Iteration 1 Error: 2.271832 Iteration 2 Error: 0.303773 Iteration 3 Error: 0.127013 Iteration 4 Error: 0.042856 Align patch 2 23 left Iteration 1 Error: 1.786192 Iteration 2 Error: 0.294976 Iteration 3 Error: 0.117661 Iteration 4 Error: 0.032682 Align patch 3 22 left Iteration 1 Error: 1.039622 Iteration 2 Error: 0.154902 Iteration 3 Error: 0.055064 Iteration 4 Error: 0.029274 Align patch 4 21 left Iteration 1 Error: 0.966723 Iteration 2 Error: 0.223880 Iteration 3 Error: 0.048915 Align patch 5 20 left Iteration 1 Error: 1.110357 Iteration 2 Error: 0.200360 Iteration 3 Error: 0.033644 Align patch 6 19 left Iteration 1 Error: 1.392101 Iteration 2 Error: 0.208885 Iteration 3 Error: 0.049560 Align patch 7 18 left Iteration 1 Error: 1.131965 Iteration 2 Error: 0.265874 Iteration 3 Error: 0.089558 Iteration 4 Error: 0.052631 Iteration 5 Error: 0.015189 Align patch 8 17 left Iteration 1 Error: 0.659443 Iteration 2 Error: 0.209137 Iteration 3 Error: 0.059260 Iteration 4 Error: 0.025591 Align patch 9 16 left Iteration 1 Error: 0.843523 Iteration 2 Error: 0.229657 Iteration 3 Error: 0.120067 Iteration 4 Error: 0.048005 Align patch 10 15 left Iteration 1 Error: 0.594418 Iteration 2 Error: 0.150083 Iteration 3 Error: 0.047874 Align patch 11 14 left Iteration 1 Error: 1.439523 Iteration 2 Error: 0.225991 Iteration 3 Error: 0.060229 Iteration 4 Error: 0.025835 Align patch 12 13 left Iteration 1 Error: 1.191698 Iteration 2 Error: 0.241330 Iteration 3 Error: 0.060285 Iteration 4 Error: 0.020820 Align patch 13 12 left Iteration 1 Error: 0.555213 Iteration 2 Error: 0.134979 Iteration 3 Error: 0.067329 Iteration 4 Error: 0.037625 Align patch 14 11 left Iteration 1 Error: 0.961061 Iteration 2 Error: 0.221097 Iteration 3 Error: 0.065930 Iteration 4 Error: 0.027895 Align patch 15 10 left Iteration 1 Error: 1.007735 Iteration 2 Error: 0.096095 Iteration 3 Error: 0.024143 Align patch 16 9 left Iteration 1 Error: 0.592384 Iteration 2 Error: 0.126085 Iteration 3 Error: 0.029167 Align patch 17 8 left Iteration 1 Error: 0.876262 Iteration 2 Error: 0.124982 Iteration 3 Error: 0.047108 Align patch 18 7 left Iteration 1 Error: 1.113840 Iteration 2 Error: 0.130048 Iteration 3 Error: 0.053102 Iteration 4 Error: 0.024479 Align patch 19 6 left Iteration 1 Error: 1.781984 Iteration 2 Error: 0.209486 Iteration 3 Error: 0.047196 Align patch 20 5 left Iteration 1 Error: 0.749870 Iteration 2 Error: 0.167038 Iteration 3 Error: 0.047649 Align patch 21 4 left Iteration 1 Error: 1.270066 Iteration 2 Error: 0.152454 Iteration 3 Error: 0.044945 Align patch 22 3 left Iteration 1 Error: 0.985817 Iteration 2 Error: 0.222271 Iteration 3 Error: 0.090483 Iteration 4 Error: 0.021354 Align patch 23 2 left Iteration 1 Error: 0.777907 Iteration 2 Error: 0.249544 Iteration 3 Error: 0.078477 Iteration 4 Error: 0.023085 Align patch 24 1 left Iteration 1 Error: 1.042062 Iteration 2 Error: 0.272677 Iteration 3 Error: 0.069627 Iteration 4 Error: 0.021554 Align patch 25 0 left Iteration 1 Error: 0.687146 Iteration 2 Error: 0.174069 Iteration 3 Error: 0.055040 Iteration 4 Error: 0.018957 3D Fitting completed. Patch alignment time: 13.62(sec) Local motion has been corrected. Process thread exits. Computational time: 27.893538 sec Total time: 37.403156 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00009hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00009hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.863401s Reading file: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00009hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.449699s ........................................ >>>>>>TIME<<<<<< FFT: 1.235025s Defocus_U Defocus_V Angle CCC 8876.95 9716.80 13.67 0.033907 Final Values Defocus_U Defocus_V Angle CCC 8875.39 9715.23 13.67 0.070241 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00007sq_v01_00009hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00009hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 1.000e-01 CC threshold: 0.734 Mean Std: 43.25 7.09 Num Hot pixels: 192 Hot pixel threshold: 85.80 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.733289 Iteration 2 Error: 0.116877 Iteration 3 Error: 0.023811 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.13 -0.05 ...... Frame ( 3) shift: -0.27 -0.10 ...... Frame ( 4) shift: -0.40 -0.15 ...... Frame ( 5) shift: -0.53 -0.19 ...... Frame ( 6) shift: -0.61 -0.21 ...... Frame ( 7) shift: -0.63 -0.19 ...... Frame ( 8) shift: -0.64 -0.18 ...... Frame ( 9) shift: -0.65 -0.14 ...... Frame ( 10) shift: -0.65 -0.10 ...... Frame ( 11) shift: -0.65 -0.05 ...... Frame ( 12) shift: -0.67 -0.00 ...... Frame ( 13) shift: -0.70 0.05 ...... Frame ( 14) shift: -0.74 0.09 ...... Frame ( 15) shift: -0.74 0.14 ...... Frame ( 16) shift: -0.70 0.19 ...... Frame ( 17) shift: -0.66 0.24 ...... Frame ( 18) shift: -0.62 0.29 ...... Frame ( 19) shift: -0.58 0.34 ...... Frame ( 20) shift: -0.55 0.39 ...... Frame ( 21) shift: -0.56 0.42 ...... Frame ( 22) shift: -0.62 0.43 ...... Frame ( 23) shift: -0.67 0.44 ...... Frame ( 24) shift: -0.68 0.48 ...... Frame ( 25) shift: -0.64 0.54 ...... Frame ( 26) shift: -0.60 0.60 ...... Frame ( 27) shift: -0.58 0.65 ...... Frame ( 28) shift: -0.59 0.69 ...... Frame ( 29) shift: -0.59 0.73 ...... Frame ( 30) shift: -0.60 0.76 ...... Frame ( 31) shift: -0.61 0.78 ...... Frame ( 32) shift: -0.62 0.80 ...... Frame ( 33) shift: -0.62 0.84 ...... Frame ( 34) shift: -0.62 0.91 ...... Frame ( 35) shift: -0.61 0.97 ...... Frame ( 36) shift: -0.59 1.03 ...... Frame ( 37) shift: -0.56 1.08 ...... Frame ( 38) shift: -0.53 1.13 ...... Frame ( 39) shift: -0.50 1.17 ...... Frame ( 40) shift: -0.47 1.22 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.833074 Iteration 2 Error: 0.169474 Iteration 3 Error: 0.045650 Align patch 2 23 left Iteration 1 Error: 0.716044 Iteration 2 Error: 0.203889 Iteration 3 Error: 0.046131 Align patch 3 22 left Iteration 1 Error: 0.794053 Iteration 2 Error: 0.134193 Iteration 3 Error: 0.034876 Align patch 4 21 left Iteration 1 Error: 0.663290 Iteration 2 Error: 0.091458 Iteration 3 Error: 0.040857 Align patch 5 20 left Iteration 1 Error: 0.643636 Iteration 2 Error: 0.103640 Iteration 3 Error: 0.031790 Align patch 6 19 left Iteration 1 Error: 0.861191 Iteration 2 Error: 0.118909 Iteration 3 Error: 0.044940 Align patch 7 18 left Iteration 1 Error: 0.708277 Iteration 2 Error: 0.219782 Iteration 3 Error: 0.034137 Align patch 8 17 left Iteration 1 Error: 0.687677 Iteration 2 Error: 0.147211 Iteration 3 Error: 0.030784 Align patch 9 16 left Iteration 1 Error: 1.023906 Iteration 2 Error: 0.142625 Iteration 3 Error: 0.038921 Align patch 10 15 left Iteration 1 Error: 0.928254 Iteration 2 Error: 0.125426 Iteration 3 Error: 0.026267 Align patch 11 14 left Iteration 1 Error: 0.855568 Iteration 2 Error: 0.213687 Iteration 3 Error: 0.073930 Iteration 4 Error: 0.016058 Align patch 12 13 left Iteration 1 Error: 0.876547 Iteration 2 Error: 0.199215 Iteration 3 Error: 0.050918 Iteration 4 Error: 0.016777 Align patch 13 12 left Iteration 1 Error: 1.017436 Iteration 2 Error: 0.111010 Iteration 3 Error: 0.029612 Align patch 14 11 left Iteration 1 Error: 0.473487 Iteration 2 Error: 0.057831 Iteration 3 Error: 0.015081 Align patch 15 10 left Iteration 1 Error: 0.691486 Iteration 2 Error: 0.143154 Iteration 3 Error: 0.028141 Align patch 16 9 left Iteration 1 Error: 0.729380 Iteration 2 Error: 0.135061 Iteration 3 Error: 0.060527 Iteration 4 Error: 0.023839 Align patch 17 8 left Iteration 1 Error: 0.929861 Iteration 2 Error: 0.139747 Iteration 3 Error: 0.046117 Align patch 18 7 left Iteration 1 Error: 0.608502 Iteration 2 Error: 0.139614 Iteration 3 Error: 0.025161 Align patch 19 6 left Iteration 1 Error: 1.003131 Iteration 2 Error: 0.172353 Iteration 3 Error: 0.039756 Align patch 20 5 left Iteration 1 Error: 0.845037 Iteration 2 Error: 0.158426 Iteration 3 Error: 0.057041 Iteration 4 Error: 0.021112 Align patch 21 4 left Iteration 1 Error: 0.822113 Iteration 2 Error: 0.130122 Iteration 3 Error: 0.037226 Align patch 22 3 left Iteration 1 Error: 0.885033 Iteration 2 Error: 0.179385 Iteration 3 Error: 0.028743 Align patch 23 2 left Iteration 1 Error: 0.637800 Iteration 2 Error: 0.084141 Iteration 3 Error: 0.024082 Align patch 24 1 left Iteration 1 Error: 0.841524 Iteration 2 Error: 0.149741 Iteration 3 Error: 0.030517 Align patch 25 0 left Iteration 1 Error: 0.674693 Iteration 2 Error: 0.073351 Iteration 3 Error: 0.021703 3D Fitting completed. Patch alignment time: 11.05(sec) Local motion has been corrected. Process thread exits. Computational time: 25.503330 sec Total time: 33.545994 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00009hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00009hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.602806s Reading file: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00009hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.621559s ........................................ >>>>>>TIME<<<<<< FFT: 0.957496s Defocus_U Defocus_V Angle CCC 13171.89 14000.01 7.19 0.046628 Final Values Defocus_U Defocus_V Angle CCC 13178.14 14006.26 7.51 0.080819 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00007sq_v01_00010hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00010hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 40.91 6.88 Num Hot pixels: 218 Hot pixel threshold: 82.21 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.337807 Iteration 2 Error: 0.279324 Iteration 3 Error: 0.078492 Iteration 4 Error: 0.038617 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.11 0.04 ...... Frame ( 3) shift: -0.22 0.07 ...... Frame ( 4) shift: -0.32 0.11 ...... Frame ( 5) shift: -0.43 0.15 ...... Frame ( 6) shift: -0.43 0.19 ...... Frame ( 7) shift: -0.31 0.25 ...... Frame ( 8) shift: -0.19 0.31 ...... Frame ( 9) shift: -0.14 0.36 ...... Frame ( 10) shift: -0.14 0.41 ...... Frame ( 11) shift: -0.14 0.45 ...... Frame ( 12) shift: -0.15 0.53 ...... Frame ( 13) shift: -0.15 0.65 ...... Frame ( 14) shift: -0.16 0.76 ...... Frame ( 15) shift: -0.16 0.87 ...... Frame ( 16) shift: -0.16 0.97 ...... Frame ( 17) shift: -0.16 1.07 ...... Frame ( 18) shift: -0.13 1.16 ...... Frame ( 19) shift: -0.06 1.25 ...... Frame ( 20) shift: 0.00 1.35 ...... Frame ( 21) shift: 0.05 1.46 ...... Frame ( 22) shift: 0.06 1.61 ...... Frame ( 23) shift: 0.08 1.75 ...... Frame ( 24) shift: 0.15 1.85 ...... Frame ( 25) shift: 0.26 1.91 ...... Frame ( 26) shift: 0.38 1.97 ...... Frame ( 27) shift: 0.44 2.00 ...... Frame ( 28) shift: 0.46 2.01 ...... Frame ( 29) shift: 0.48 2.02 ...... Frame ( 30) shift: 0.51 2.04 ...... Frame ( 31) shift: 0.55 2.08 ...... Frame ( 32) shift: 0.59 2.12 ...... Frame ( 33) shift: 0.66 2.15 ...... Frame ( 34) shift: 0.74 2.18 ...... Frame ( 35) shift: 0.82 2.20 ...... Frame ( 36) shift: 0.90 2.26 ...... Frame ( 37) shift: 0.97 2.36 ...... Frame ( 38) shift: 1.04 2.45 ...... Frame ( 39) shift: 1.11 2.54 ...... Frame ( 40) shift: 1.18 2.64 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.006576 Iteration 2 Error: 0.254779 Iteration 3 Error: 0.062337 Iteration 4 Error: 0.019530 Align patch 2 23 left Iteration 1 Error: 0.856666 Iteration 2 Error: 0.135751 Iteration 3 Error: 0.037278 Align patch 3 22 left Iteration 1 Error: 0.788444 Iteration 2 Error: 0.136558 Iteration 3 Error: 0.044593 Align patch 4 21 left Iteration 1 Error: 0.791516 Iteration 2 Error: 0.117392 Iteration 3 Error: 0.033963 Align patch 5 20 left Iteration 1 Error: 0.647674 Iteration 2 Error: 0.134670 Iteration 3 Error: 0.028192 Align patch 6 19 left Iteration 1 Error: 1.215181 Iteration 2 Error: 0.329793 Iteration 3 Error: 0.095262 Iteration 4 Error: 0.046169 Align patch 7 18 left Iteration 1 Error: 0.886673 Iteration 2 Error: 0.227191 Iteration 3 Error: 0.061870 Iteration 4 Error: 0.033403 Align patch 8 17 left Iteration 1 Error: 0.768991 Iteration 2 Error: 0.150516 Iteration 3 Error: 0.041333 Align patch 9 16 left Iteration 1 Error: 1.052323 Iteration 2 Error: 0.145421 Iteration 3 Error: 0.043182 Align patch 10 15 left Iteration 1 Error: 0.614055 Iteration 2 Error: 0.065739 Iteration 3 Error: 0.018290 Align patch 11 14 left Iteration 1 Error: 1.181260 Iteration 2 Error: 0.194533 Iteration 3 Error: 0.041797 Align patch 12 13 left Iteration 1 Error: 1.232913 Iteration 2 Error: 0.273977 Iteration 3 Error: 0.136301 Iteration 4 Error: 0.098711 Iteration 5 Error: 0.050090 Align patch 12 13 left Iteration 1 Error: 1.070634 Iteration 2 Error: 0.201244 Iteration 3 Error: 0.040295 Align patch 13 12 left Iteration 1 Error: 0.953051 Iteration 2 Error: 0.201677 Iteration 3 Error: 0.057867 Iteration 4 Error: 0.014308 Align patch 14 11 left Iteration 1 Error: 0.783931 Iteration 2 Error: 0.205592 Iteration 3 Error: 0.080468 Iteration 4 Error: 0.032940 Align patch 15 10 left Iteration 1 Error: 0.722287 Iteration 2 Error: 0.160135 Iteration 3 Error: 0.049819 Align patch 16 9 left Iteration 1 Error: 0.714948 Iteration 2 Error: 0.132826 Iteration 3 Error: 0.043064 Align patch 17 8 left Iteration 1 Error: 1.674060 Iteration 2 Error: 0.324566 Iteration 3 Error: 0.057698 Iteration 4 Error: 0.042286 Align patch 18 7 left Iteration 1 Error: 0.638156 Iteration 2 Error: 0.148207 Iteration 3 Error: 0.039250 Align patch 19 6 left Iteration 1 Error: 0.685659 Iteration 2 Error: 0.163177 Iteration 3 Error: 0.060072 Iteration 4 Error: 0.023672 Align patch 20 5 left Iteration 1 Error: 0.673497 Iteration 2 Error: 0.100919 Iteration 3 Error: 0.028231 Align patch 21 4 left Iteration 1 Error: 0.833140 Iteration 2 Error: 0.212112 Iteration 3 Error: 0.071327 Iteration 4 Error: 0.024793 Align patch 22 3 left Iteration 1 Error: 0.574973 Iteration 2 Error: 0.121383 Iteration 3 Error: 0.026461 Align patch 23 2 left Iteration 1 Error: 0.778181 Iteration 2 Error: 0.244639 Iteration 3 Error: 0.045948 Align patch 24 1 left Iteration 1 Error: 0.831704 Iteration 2 Error: 0.200284 Iteration 3 Error: 0.044019 Align patch 25 0 left Iteration 1 Error: 0.959172 Iteration 2 Error: 0.142465 Iteration 3 Error: 0.062562 Iteration 4 Error: 0.021900 3D Fitting completed. Patch alignment time: 12.89(sec) Local motion has been corrected. Process thread exits. Computational time: 25.600443 sec Total time: 33.830845 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00010hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00010hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.622043s Reading file: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00010hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.596329s ........................................ >>>>>>TIME<<<<<< FFT: 0.941477s Defocus_U Defocus_V Angle CCC 13177.73 14048.86 13.38 0.048104 Final Values Defocus_U Defocus_V Angle CCC 13180.85 14048.87 13.38 0.078111 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00007sq_v01_00010hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00010hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 41.47 6.96 Num Hot pixels: 198 Hot pixel threshold: 83.22 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.268459 Iteration 2 Error: 0.247267 Iteration 3 Error: 0.074008 Iteration 4 Error: 0.019959 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.11 -0.07 ...... Frame ( 3) shift: -0.23 -0.14 ...... Frame ( 4) shift: -0.34 -0.21 ...... Frame ( 5) shift: -0.45 -0.27 ...... Frame ( 6) shift: -0.49 -0.28 ...... Frame ( 7) shift: -0.44 -0.23 ...... Frame ( 8) shift: -0.40 -0.17 ...... Frame ( 9) shift: -0.32 -0.11 ...... Frame ( 10) shift: -0.21 -0.04 ...... Frame ( 11) shift: -0.11 0.02 ...... Frame ( 12) shift: 0.01 0.10 ...... Frame ( 13) shift: 0.12 0.19 ...... Frame ( 14) shift: 0.24 0.28 ...... Frame ( 15) shift: 0.31 0.36 ...... Frame ( 16) shift: 0.34 0.42 ...... Frame ( 17) shift: 0.37 0.49 ...... Frame ( 18) shift: 0.44 0.49 ...... Frame ( 19) shift: 0.56 0.43 ...... Frame ( 20) shift: 0.67 0.37 ...... Frame ( 21) shift: 0.74 0.39 ...... Frame ( 22) shift: 0.77 0.48 ...... Frame ( 23) shift: 0.80 0.58 ...... Frame ( 24) shift: 0.84 0.68 ...... Frame ( 25) shift: 0.90 0.78 ...... Frame ( 26) shift: 0.96 0.87 ...... Frame ( 27) shift: 0.99 0.99 ...... Frame ( 28) shift: 1.02 1.13 ...... Frame ( 29) shift: 1.04 1.26 ...... Frame ( 30) shift: 1.01 1.41 ...... Frame ( 31) shift: 0.92 1.57 ...... Frame ( 32) shift: 0.84 1.72 ...... Frame ( 33) shift: 0.85 1.84 ...... Frame ( 34) shift: 0.95 1.91 ...... Frame ( 35) shift: 1.05 1.97 ...... Frame ( 36) shift: 1.06 2.02 ...... Frame ( 37) shift: 0.97 2.04 ...... Frame ( 38) shift: 0.88 2.07 ...... Frame ( 39) shift: 0.78 2.10 ...... Frame ( 40) shift: 0.69 2.12 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.910442 Iteration 2 Error: 0.198263 Iteration 3 Error: 0.065926 Iteration 4 Error: 0.038794 Align patch 2 23 left Iteration 1 Error: 1.055217 Iteration 2 Error: 0.215855 Iteration 3 Error: 0.095267 Iteration 4 Error: 0.051672 Iteration 5 Error: 0.030267 Align patch 3 22 left Iteration 1 Error: 0.699499 Iteration 2 Error: 0.109555 Iteration 3 Error: 0.034679 Align patch 4 21 left Iteration 1 Error: 0.785230 Iteration 2 Error: 0.113489 Iteration 3 Error: 0.041911 Align patch 5 20 left Iteration 1 Error: 0.798013 Iteration 2 Error: 0.130333 Iteration 3 Error: 0.021057 Align patch 6 19 left Iteration 1 Error: 0.909037 Iteration 2 Error: 0.124125 Iteration 3 Error: 0.031196 Align patch 7 18 left Iteration 1 Error: 0.905018 Iteration 2 Error: 0.133297 Iteration 3 Error: 0.032101 Align patch 8 17 left Iteration 1 Error: 1.036367 Iteration 2 Error: 0.191261 Iteration 3 Error: 0.048321 Align patch 9 16 left Iteration 1 Error: 0.742202 Iteration 2 Error: 0.185969 Iteration 3 Error: 0.070233 Iteration 4 Error: 0.021112 Align patch 10 15 left Iteration 1 Error: 0.643970 Iteration 2 Error: 0.148938 Iteration 3 Error: 0.028741 Align patch 11 14 left Iteration 1 Error: 0.671684 Iteration 2 Error: 0.150113 Iteration 3 Error: 0.045061 Align patch 12 13 left Iteration 1 Error: 0.851713 Iteration 2 Error: 0.190620 Iteration 3 Error: 0.049515 Align patch 13 12 left Iteration 1 Error: 0.508865 Iteration 2 Error: 0.076221 Iteration 3 Error: 0.023530 Align patch 14 11 left Iteration 1 Error: 0.543113 Iteration 2 Error: 0.143153 Iteration 3 Error: 0.029510 Align patch 15 10 left Iteration 1 Error: 0.638130 Iteration 2 Error: 0.088863 Iteration 3 Error: 0.023666 Align patch 16 9 left Iteration 1 Error: 0.715441 Iteration 2 Error: 0.124041 Iteration 3 Error: 0.021712 Align patch 17 8 left Iteration 1 Error: 0.676242 Iteration 2 Error: 0.148317 Iteration 3 Error: 0.043849 Align patch 18 7 left Iteration 1 Error: 0.574235 Iteration 2 Error: 0.082767 Iteration 3 Error: 0.026422 Align patch 19 6 left Iteration 1 Error: 0.580180 Iteration 2 Error: 0.084189 Iteration 3 Error: 0.018699 Align patch 20 5 left Iteration 1 Error: 0.652364 Iteration 2 Error: 0.104613 Iteration 3 Error: 0.024119 Align patch 21 4 left Iteration 1 Error: 0.997673 Iteration 2 Error: 0.238892 Iteration 3 Error: 0.078135 Iteration 4 Error: 0.032889 Align patch 22 3 left Iteration 1 Error: 0.925133 Iteration 2 Error: 0.145990 Iteration 3 Error: 0.041512 Align patch 23 2 left Iteration 1 Error: 0.641568 Iteration 2 Error: 0.101696 Iteration 3 Error: 0.037645 Align patch 24 1 left Iteration 1 Error: 0.584612 Iteration 2 Error: 0.069229 Iteration 3 Error: 0.014691 Align patch 25 0 left Iteration 1 Error: 1.018943 Iteration 2 Error: 0.170893 Iteration 3 Error: 0.038145 3D Fitting completed. Patch alignment time: 11.10(sec) Local motion has been corrected. Process thread exits. Computational time: 26.744350 sec Total time: 35.545521 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00010hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00010hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.854633s Reading file: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00010hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.056582s ........................................ >>>>>>TIME<<<<<< FFT: 1.162944s Defocus_U Defocus_V Angle CCC 12746.10 13246.10 2.35 0.049009 Final Values Defocus_U Defocus_V Angle CCC 12764.87 13264.87 2.04 0.082846 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00007sq_v01_00010hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00010hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 40.60 6.80 Num Hot pixels: 190 Hot pixel threshold: 81.42 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.021981 Iteration 2 Error: 0.176216 Iteration 3 Error: 0.034981 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.05 -0.04 ...... Frame ( 3) shift: 0.10 -0.08 ...... Frame ( 4) shift: 0.16 -0.12 ...... Frame ( 5) shift: 0.21 -0.16 ...... Frame ( 6) shift: 0.33 -0.14 ...... Frame ( 7) shift: 0.53 -0.07 ...... Frame ( 8) shift: 0.72 0.01 ...... Frame ( 9) shift: 0.85 0.08 ...... Frame ( 10) shift: 0.91 0.14 ...... Frame ( 11) shift: 0.97 0.21 ...... Frame ( 12) shift: 1.01 0.30 ...... Frame ( 13) shift: 1.03 0.40 ...... Frame ( 14) shift: 1.05 0.51 ...... Frame ( 15) shift: 1.08 0.62 ...... Frame ( 16) shift: 1.10 0.73 ...... Frame ( 17) shift: 1.12 0.84 ...... Frame ( 18) shift: 1.11 0.88 ...... Frame ( 19) shift: 1.07 0.84 ...... Frame ( 20) shift: 1.03 0.81 ...... Frame ( 21) shift: 1.05 0.83 ...... Frame ( 22) shift: 1.12 0.90 ...... Frame ( 23) shift: 1.20 0.97 ...... Frame ( 24) shift: 1.26 1.00 ...... Frame ( 25) shift: 1.29 0.99 ...... Frame ( 26) shift: 1.33 0.98 ...... Frame ( 27) shift: 1.36 1.00 ...... Frame ( 28) shift: 1.38 1.03 ...... Frame ( 29) shift: 1.40 1.06 ...... Frame ( 30) shift: 1.39 1.16 ...... Frame ( 31) shift: 1.37 1.30 ...... Frame ( 32) shift: 1.35 1.45 ...... Frame ( 33) shift: 1.32 1.52 ...... Frame ( 34) shift: 1.30 1.51 ...... Frame ( 35) shift: 1.28 1.51 ...... Frame ( 36) shift: 1.24 1.49 ...... Frame ( 37) shift: 1.17 1.45 ...... Frame ( 38) shift: 1.09 1.42 ...... Frame ( 39) shift: 1.02 1.38 ...... Frame ( 40) shift: 0.95 1.35 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.393801 Iteration 2 Error: 0.202283 Iteration 3 Error: 0.057053 Iteration 4 Error: 0.016697 Align patch 2 23 left Iteration 1 Error: 0.838646 Iteration 2 Error: 0.166592 Iteration 3 Error: 0.059177 Iteration 4 Error: 0.017139 Align patch 3 22 left Iteration 1 Error: 0.673480 Iteration 2 Error: 0.088896 Iteration 3 Error: 0.016177 Align patch 4 21 left Iteration 1 Error: 0.618038 Iteration 2 Error: 0.071618 Iteration 3 Error: 0.014648 Align patch 5 20 left Iteration 1 Error: 0.926167 Iteration 2 Error: 0.101441 Iteration 3 Error: 0.021774 Align patch 6 19 left Iteration 1 Error: 0.840396 Iteration 2 Error: 0.251312 Iteration 3 Error: 0.080988 Iteration 4 Error: 0.034112 Align patch 7 18 left Iteration 1 Error: 0.707429 Iteration 2 Error: 0.156281 Iteration 3 Error: 0.038375 Align patch 8 17 left Iteration 1 Error: 0.666984 Iteration 2 Error: 0.113010 Iteration 3 Error: 0.040448 Align patch 9 16 left Iteration 1 Error: 0.851651 Iteration 2 Error: 0.144089 Iteration 3 Error: 0.049138 Align patch 10 15 left Iteration 1 Error: 0.861067 Iteration 2 Error: 0.149712 Iteration 3 Error: 0.031674 Align patch 11 14 left Iteration 1 Error: 0.682355 Iteration 2 Error: 0.126542 Iteration 3 Error: 0.021935 Align patch 12 13 left Iteration 1 Error: 0.951286 Iteration 2 Error: 0.155422 Iteration 3 Error: 0.037774 Align patch 13 12 left Iteration 1 Error: 0.846442 Iteration 2 Error: 0.145573 Iteration 3 Error: 0.042762 Align patch 14 11 left Iteration 1 Error: 1.127186 Iteration 2 Error: 0.146965 Iteration 3 Error: 0.041944 Align patch 15 10 left Iteration 1 Error: 0.980949 Iteration 2 Error: 0.145342 Iteration 3 Error: 0.030921 Align patch 16 9 left Iteration 1 Error: 0.753296 Iteration 2 Error: 0.127763 Iteration 3 Error: 0.027802 Align patch 17 8 left Iteration 1 Error: 0.619337 Iteration 2 Error: 0.122667 Iteration 3 Error: 0.033661 Align patch 18 7 left Iteration 1 Error: 0.834016 Iteration 2 Error: 0.097049 Iteration 3 Error: 0.029670 Align patch 19 6 left Iteration 1 Error: 0.593580 Iteration 2 Error: 0.110481 Iteration 3 Error: 0.033406 Align patch 20 5 left Iteration 1 Error: 0.602360 Iteration 2 Error: 0.066619 Iteration 3 Error: 0.014608 Align patch 21 4 left Iteration 1 Error: 0.929909 Iteration 2 Error: 0.136673 Iteration 3 Error: 0.031748 Align patch 22 3 left Iteration 1 Error: 0.656271 Iteration 2 Error: 0.138626 Iteration 3 Error: 0.035844 Align patch 23 2 left Iteration 1 Error: 0.892607 Iteration 2 Error: 0.221073 Iteration 3 Error: 0.034425 Align patch 24 1 left Iteration 1 Error: 0.652443 Iteration 2 Error: 0.084844 Iteration 3 Error: 0.020505 Align patch 25 0 left Iteration 1 Error: 0.502020 Iteration 2 Error: 0.099145 Iteration 3 Error: 0.018920 3D Fitting completed. Patch alignment time: 11.69(sec) Local motion has been corrected. Process thread exits. Computational time: 26.909464 sec Total time: 33.954395 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00010hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00010hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.733562s Reading file: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00010hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.895044s ........................................ >>>>>>TIME<<<<<< FFT: 0.994573s Defocus_U Defocus_V Angle CCC 10587.89 11482.45 8.82 0.043798 Final Values Defocus_U Defocus_V Angle CCC 10595.71 11509.03 9.13 0.074942 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00007sq_v01_00010hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00010hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 40.89 6.87 Num Hot pixels: 196 Hot pixel threshold: 82.09 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.736204 Iteration 2 Error: 0.137237 Iteration 3 Error: 0.029962 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.05 0.01 ...... Frame ( 3) shift: -0.10 0.03 ...... Frame ( 4) shift: -0.14 0.04 ...... Frame ( 5) shift: -0.19 0.05 ...... Frame ( 6) shift: -0.21 0.06 ...... Frame ( 7) shift: -0.19 0.07 ...... Frame ( 8) shift: -0.17 0.07 ...... Frame ( 9) shift: -0.17 0.11 ...... Frame ( 10) shift: -0.17 0.19 ...... Frame ( 11) shift: -0.18 0.27 ...... Frame ( 12) shift: -0.20 0.34 ...... Frame ( 13) shift: -0.25 0.40 ...... Frame ( 14) shift: -0.30 0.46 ...... Frame ( 15) shift: -0.33 0.54 ...... Frame ( 16) shift: -0.33 0.64 ...... Frame ( 17) shift: -0.33 0.75 ...... Frame ( 18) shift: -0.32 0.84 ...... Frame ( 19) shift: -0.29 0.92 ...... Frame ( 20) shift: -0.26 1.01 ...... Frame ( 21) shift: -0.27 1.09 ...... Frame ( 22) shift: -0.31 1.17 ...... Frame ( 23) shift: -0.36 1.26 ...... Frame ( 24) shift: -0.37 1.29 ...... Frame ( 25) shift: -0.34 1.28 ...... Frame ( 26) shift: -0.30 1.26 ...... Frame ( 27) shift: -0.30 1.28 ...... Frame ( 28) shift: -0.32 1.34 ...... Frame ( 29) shift: -0.34 1.39 ...... Frame ( 30) shift: -0.36 1.43 ...... Frame ( 31) shift: -0.37 1.45 ...... Frame ( 32) shift: -0.39 1.46 ...... Frame ( 33) shift: -0.44 1.46 ...... Frame ( 34) shift: -0.51 1.45 ...... Frame ( 35) shift: -0.59 1.44 ...... Frame ( 36) shift: -0.61 1.45 ...... Frame ( 37) shift: -0.56 1.46 ...... Frame ( 38) shift: -0.52 1.48 ...... Frame ( 39) shift: -0.47 1.49 ...... Frame ( 40) shift: -0.43 1.51 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.820136 Iteration 2 Error: 0.164522 Iteration 3 Error: 0.031754 Align patch 2 23 left Iteration 1 Error: 0.814735 Iteration 2 Error: 0.144083 Iteration 3 Error: 0.038351 Align patch 3 22 left Iteration 1 Error: 0.506050 Iteration 2 Error: 0.083435 Iteration 3 Error: 0.019815 Align patch 4 21 left Iteration 1 Error: 0.720049 Iteration 2 Error: 0.156190 Iteration 3 Error: 0.037852 Align patch 5 20 left Iteration 1 Error: 0.824142 Iteration 2 Error: 0.126208 Iteration 3 Error: 0.031860 Align patch 6 19 left Iteration 1 Error: 0.845829 Iteration 2 Error: 0.112205 Iteration 3 Error: 0.025926 Align patch 7 18 left Iteration 1 Error: 0.495468 Iteration 2 Error: 0.094799 Iteration 3 Error: 0.029161 Align patch 8 17 left Iteration 1 Error: 0.667432 Iteration 2 Error: 0.138577 Iteration 3 Error: 0.022358 Align patch 9 16 left Iteration 1 Error: 0.634315 Iteration 2 Error: 0.092570 Iteration 3 Error: 0.022188 Align patch 10 15 left Iteration 1 Error: 0.775095 Iteration 2 Error: 0.163869 Iteration 3 Error: 0.049173 Align patch 11 14 left Iteration 1 Error: 0.424882 Iteration 2 Error: 0.093574 Iteration 3 Error: 0.023617 Align patch 12 13 left Iteration 1 Error: 0.567542 Iteration 2 Error: 0.109187 Iteration 3 Error: 0.019755 Align patch 13 12 left Iteration 1 Error: 0.535111 Iteration 2 Error: 0.093488 Iteration 3 Error: 0.012575 Align patch 14 11 left Iteration 1 Error: 0.528973 Iteration 2 Error: 0.069989 Iteration 3 Error: 0.009928 Align patch 15 10 left Iteration 1 Error: 0.692718 Iteration 2 Error: 0.099642 Iteration 3 Error: 0.022515 Align patch 16 9 left Iteration 1 Error: 0.544461 Iteration 2 Error: 0.055694 Iteration 3 Error: 0.011949 Align patch 17 8 left Iteration 1 Error: 0.518347 Iteration 2 Error: 0.062117 Iteration 3 Error: 0.019552 Align patch 18 7 left Iteration 1 Error: 0.715954 Iteration 2 Error: 0.146476 Iteration 3 Error: 0.033697 Align patch 19 6 left Iteration 1 Error: 0.621874 Iteration 2 Error: 0.109549 Iteration 3 Error: 0.032835 Align patch 20 5 left Iteration 1 Error: 0.637816 Iteration 2 Error: 0.076478 Iteration 3 Error: 0.019840 Align patch 21 4 left Iteration 1 Error: 0.647366 Iteration 2 Error: 0.099606 Iteration 3 Error: 0.026883 Align patch 22 3 left Iteration 1 Error: 0.625695 Iteration 2 Error: 0.136055 Iteration 3 Error: 0.040758 Align patch 23 2 left Iteration 1 Error: 0.700330 Iteration 2 Error: 0.118898 Iteration 3 Error: 0.027355 Align patch 24 1 left Iteration 1 Error: 0.592462 Iteration 2 Error: 0.083941 Iteration 3 Error: 0.024108 Align patch 25 0 left Iteration 1 Error: 0.793545 Iteration 2 Error: 0.082684 Iteration 3 Error: 0.015002 3D Fitting completed. Patch alignment time: 13.30(sec) Local motion has been corrected. Process thread exits. Computational time: 28.920561 sec Total time: 35.635452 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00010hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00010hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.503098s Reading file: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00010hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.546749s ........................................ >>>>>>TIME<<<<<< FFT: 1.182215s Defocus_U Defocus_V Angle CCC 15841.80 15205.08 86.66 0.047811 Final Values Defocus_U Defocus_V Angle CCC 15840.24 15197.27 85.41 0.076003 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00007sq_v01_00011hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00011hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.998e-02 CC threshold: 0.734 Mean Std: 39.81 6.75 Num Hot pixels: 196 Hot pixel threshold: 80.28 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.266495 Iteration 2 Error: 0.315728 Iteration 3 Error: 0.084958 Iteration 4 Error: 0.033119 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.07 -0.04 ...... Frame ( 3) shift: -0.13 -0.09 ...... Frame ( 4) shift: -0.20 -0.13 ...... Frame ( 5) shift: -0.27 -0.18 ...... Frame ( 6) shift: -0.31 -0.14 ...... Frame ( 7) shift: -0.31 -0.02 ...... Frame ( 8) shift: -0.32 0.10 ...... Frame ( 9) shift: -0.27 0.20 ...... Frame ( 10) shift: -0.16 0.27 ...... Frame ( 11) shift: -0.05 0.35 ...... Frame ( 12) shift: 0.03 0.44 ...... Frame ( 13) shift: 0.09 0.53 ...... Frame ( 14) shift: 0.15 0.62 ...... Frame ( 15) shift: 0.17 0.68 ...... Frame ( 16) shift: 0.15 0.71 ...... Frame ( 17) shift: 0.13 0.74 ...... Frame ( 18) shift: 0.11 0.78 ...... Frame ( 19) shift: 0.10 0.83 ...... Frame ( 20) shift: 0.09 0.88 ...... Frame ( 21) shift: 0.13 0.90 ...... Frame ( 22) shift: 0.22 0.90 ...... Frame ( 23) shift: 0.31 0.90 ...... Frame ( 24) shift: 0.40 0.95 ...... Frame ( 25) shift: 0.49 1.03 ...... Frame ( 26) shift: 0.57 1.12 ...... Frame ( 27) shift: 0.64 1.20 ...... Frame ( 28) shift: 0.68 1.26 ...... Frame ( 29) shift: 0.72 1.33 ...... Frame ( 30) shift: 0.77 1.44 ...... Frame ( 31) shift: 0.83 1.58 ...... Frame ( 32) shift: 0.90 1.73 ...... Frame ( 33) shift: 0.94 1.84 ...... Frame ( 34) shift: 0.98 1.90 ...... Frame ( 35) shift: 1.02 1.97 ...... Frame ( 36) shift: 1.06 2.01 ...... Frame ( 37) shift: 1.12 2.01 ...... Frame ( 38) shift: 1.18 2.01 ...... Frame ( 39) shift: 1.23 2.01 ...... Frame ( 40) shift: 1.29 2.01 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.623705 Iteration 2 Error: 0.245986 Iteration 3 Error: 0.144093 Iteration 4 Error: 0.062089 Iteration 5 Error: 0.032640 Align patch 2 23 left Iteration 1 Error: 1.048995 Iteration 2 Error: 0.237805 Iteration 3 Error: 0.056724 Iteration 4 Error: 0.021434 Align patch 3 22 left Iteration 1 Error: 0.910921 Iteration 2 Error: 0.169619 Iteration 3 Error: 0.060187 Iteration 4 Error: 0.024838 Align patch 4 21 left Iteration 1 Error: 0.795757 Iteration 2 Error: 0.109466 Iteration 3 Error: 0.019358 Align patch 5 20 left Iteration 1 Error: 0.800738 Iteration 2 Error: 0.131925 Iteration 3 Error: 0.030168 Align patch 6 19 left Iteration 1 Error: 0.896773 Iteration 2 Error: 0.256088 Iteration 3 Error: 0.078921 Iteration 4 Error: 0.046382 Align patch 7 18 left Iteration 1 Error: 0.803562 Iteration 2 Error: 0.192446 Iteration 3 Error: 0.118294 Iteration 4 Error: 0.038946 Align patch 8 17 left Iteration 1 Error: 0.820145 Iteration 2 Error: 0.191983 Iteration 3 Error: 0.060187 Iteration 4 Error: 0.030489 Align patch 9 16 left Iteration 1 Error: 0.712889 Iteration 2 Error: 0.153404 Iteration 3 Error: 0.028580 Align patch 10 15 left Iteration 1 Error: 0.612504 Iteration 2 Error: 0.152514 Iteration 3 Error: 0.031947 Align patch 11 14 left Iteration 1 Error: 0.833750 Iteration 2 Error: 0.321928 Iteration 3 Error: 0.117463 Iteration 4 Error: 0.046795 Align patch 12 13 left Iteration 1 Error: 1.217984 Iteration 2 Error: 0.295622 Iteration 3 Error: 0.112641 Iteration 4 Error: 0.042296 Align patch 13 12 left Iteration 1 Error: 0.666072 Iteration 2 Error: 0.091095 Iteration 3 Error: 0.018015 Align patch 14 11 left Iteration 1 Error: 0.503202 Iteration 2 Error: 0.113475 Iteration 3 Error: 0.024428 Align patch 15 10 left Iteration 1 Error: 1.027505 Iteration 2 Error: 0.298541 Iteration 3 Error: 0.114673 Iteration 4 Error: 0.047089 Align patch 16 9 left Iteration 1 Error: 0.863299 Iteration 2 Error: 0.173434 Iteration 3 Error: 0.080638 Iteration 4 Error: 0.027999 Align patch 17 8 left Iteration 1 Error: 0.875250 Iteration 2 Error: 0.267483 Iteration 3 Error: 0.101436 Iteration 4 Error: 0.035085 Align patch 18 7 left Iteration 1 Error: 0.803696 Iteration 2 Error: 0.157098 Iteration 3 Error: 0.043277 Align patch 19 6 left Iteration 1 Error: 0.483149 Iteration 2 Error: 0.061509 Iteration 3 Error: 0.012155 Align patch 20 5 left Iteration 1 Error: 0.759456 Iteration 2 Error: 0.174378 Iteration 3 Error: 0.041370 Align patch 21 4 left Iteration 1 Error: 0.914721 Iteration 2 Error: 0.130474 Iteration 3 Error: 0.037092 Align patch 22 3 left Iteration 1 Error: 1.052285 Iteration 2 Error: 0.172930 Iteration 3 Error: 0.070383 Iteration 4 Error: 0.043625 Align patch 23 2 left Iteration 1 Error: 1.063029 Iteration 2 Error: 0.198024 Iteration 3 Error: 0.075105 Iteration 4 Error: 0.023154 Align patch 24 1 left Iteration 1 Error: 0.779611 Iteration 2 Error: 0.111274 Iteration 3 Error: 0.018642 Align patch 25 0 left Iteration 1 Error: 0.971142 Iteration 2 Error: 0.143801 Iteration 3 Error: 0.036517 3D Fitting completed. Patch alignment time: 12.36(sec) Local motion has been corrected. Process thread exits. Computational time: 25.953283 sec Total time: 34.090656 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00011hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00011hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.593113s Reading file: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00011hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.482898s ........................................ >>>>>>TIME<<<<<< FFT: 1.209715s Defocus_U Defocus_V Angle CCC 11160.16 11992.19 12.91 0.035189 Final Values Defocus_U Defocus_V Angle CCC 11202.36 12012.51 13.55 0.057272 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00007sq_v01_00011hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00011hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 39.42 6.72 Num Hot pixels: 203 Hot pixel threshold: 79.75 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.979816 Iteration 2 Error: 0.175998 Iteration 3 Error: 0.043030 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.01 0.09 ...... Frame ( 3) shift: 0.01 0.18 ...... Frame ( 4) shift: 0.02 0.27 ...... Frame ( 5) shift: 0.03 0.36 ...... Frame ( 6) shift: 0.05 0.43 ...... Frame ( 7) shift: 0.09 0.47 ...... Frame ( 8) shift: 0.13 0.51 ...... Frame ( 9) shift: 0.17 0.58 ...... Frame ( 10) shift: 0.19 0.66 ...... Frame ( 11) shift: 0.22 0.75 ...... Frame ( 12) shift: 0.22 0.82 ...... Frame ( 13) shift: 0.21 0.87 ...... Frame ( 14) shift: 0.20 0.92 ...... Frame ( 15) shift: 0.20 0.94 ...... Frame ( 16) shift: 0.22 0.93 ...... Frame ( 17) shift: 0.24 0.92 ...... Frame ( 18) shift: 0.28 0.97 ...... Frame ( 19) shift: 0.35 1.07 ...... Frame ( 20) shift: 0.42 1.17 ...... Frame ( 21) shift: 0.46 1.21 ...... Frame ( 22) shift: 0.48 1.20 ...... Frame ( 23) shift: 0.50 1.19 ...... Frame ( 24) shift: 0.51 1.18 ...... Frame ( 25) shift: 0.50 1.19 ...... Frame ( 26) shift: 0.49 1.19 ...... Frame ( 27) shift: 0.53 1.25 ...... Frame ( 28) shift: 0.60 1.37 ...... Frame ( 29) shift: 0.67 1.49 ...... Frame ( 30) shift: 0.68 1.56 ...... Frame ( 31) shift: 0.63 1.57 ...... Frame ( 32) shift: 0.58 1.59 ...... Frame ( 33) shift: 0.55 1.65 ...... Frame ( 34) shift: 0.57 1.76 ...... Frame ( 35) shift: 0.58 1.87 ...... Frame ( 36) shift: 0.61 1.95 ...... Frame ( 37) shift: 0.68 2.02 ...... Frame ( 38) shift: 0.74 2.08 ...... Frame ( 39) shift: 0.80 2.15 ...... Frame ( 40) shift: 0.86 2.21 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.817882 Iteration 2 Error: 0.191703 Iteration 3 Error: 0.114883 Iteration 4 Error: 0.049338 Align patch 2 23 left Iteration 1 Error: 0.632909 Iteration 2 Error: 0.157603 Iteration 3 Error: 0.060684 Iteration 4 Error: 0.029152 Align patch 3 22 left Iteration 1 Error: 0.662365 Iteration 2 Error: 0.103730 Iteration 3 Error: 0.034604 Align patch 4 21 left Iteration 1 Error: 0.821592 Iteration 2 Error: 0.187808 Iteration 3 Error: 0.048335 Align patch 5 20 left Iteration 1 Error: 1.142504 Iteration 2 Error: 0.226876 Iteration 3 Error: 0.049047 Align patch 6 19 left Iteration 1 Error: 0.841531 Iteration 2 Error: 0.162068 Iteration 3 Error: 0.058578 Iteration 4 Error: 0.027368 Align patch 7 18 left Iteration 1 Error: 0.693032 Iteration 2 Error: 0.075544 Iteration 3 Error: 0.024046 Align patch 8 17 left Iteration 1 Error: 0.622714 Iteration 2 Error: 0.126933 Iteration 3 Error: 0.043485 Align patch 9 16 left Iteration 1 Error: 0.742769 Iteration 2 Error: 0.131098 Iteration 3 Error: 0.043164 Align patch 10 15 left Iteration 1 Error: 0.792536 Iteration 2 Error: 0.113952 Iteration 3 Error: 0.022477 Align patch 11 14 left Iteration 1 Error: 0.947638 Iteration 2 Error: 0.216770 Iteration 3 Error: 0.090999 Iteration 4 Error: 0.032500 Align patch 12 13 left Iteration 1 Error: 0.808783 Iteration 2 Error: 0.108166 Iteration 3 Error: 0.035452 Align patch 13 12 left Iteration 1 Error: 0.757025 Iteration 2 Error: 0.112305 Iteration 3 Error: 0.033341 Align patch 14 11 left Iteration 1 Error: 0.598708 Iteration 2 Error: 0.121836 Iteration 3 Error: 0.031560 Align patch 15 10 left Iteration 1 Error: 0.953900 Iteration 2 Error: 0.110816 Iteration 3 Error: 0.033156 Align patch 16 9 left Iteration 1 Error: 1.170552 Iteration 2 Error: 0.116105 Iteration 3 Error: 0.026326 Align patch 17 8 left Iteration 1 Error: 1.023908 Iteration 2 Error: 0.111502 Iteration 3 Error: 0.031411 Align patch 18 7 left Iteration 1 Error: 0.741184 Iteration 2 Error: 0.119958 Iteration 3 Error: 0.039375 Align patch 19 6 left Iteration 1 Error: 0.632064 Iteration 2 Error: 0.124579 Iteration 3 Error: 0.030227 Align patch 20 5 left Iteration 1 Error: 0.718029 Iteration 2 Error: 0.222346 Iteration 3 Error: 0.082028 Iteration 4 Error: 0.033146 Align patch 21 4 left Iteration 1 Error: 0.648670 Iteration 2 Error: 0.108135 Iteration 3 Error: 0.034875 Align patch 22 3 left Iteration 1 Error: 0.818115 Iteration 2 Error: 0.103712 Iteration 3 Error: 0.029972 Align patch 23 2 left Iteration 1 Error: 0.811662 Iteration 2 Error: 0.195100 Iteration 3 Error: 0.068227 Iteration 4 Error: 0.023276 Align patch 24 1 left Iteration 1 Error: 0.634877 Iteration 2 Error: 0.071577 Iteration 3 Error: 0.018632 Align patch 25 0 left Iteration 1 Error: 0.631263 Iteration 2 Error: 0.108034 Iteration 3 Error: 0.031301 3D Fitting completed. Patch alignment time: 12.57(sec) Local motion has been corrected. Process thread exits. Computational time: 28.492769 sec Total time: 37.383579 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00011hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00011hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.688806s Reading file: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00011hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.438041s ........................................ >>>>>>TIME<<<<<< FFT: 0.907794s Defocus_U Defocus_V Angle CCC 9015.47 9429.92 7.18 0.025726 Final Values Defocus_U Defocus_V Angle CCC 9012.34 9470.58 6.56 0.047425 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00007sq_v01_00011hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00011hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 39.99 6.75 Num Hot pixels: 224 Hot pixel threshold: 80.48 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.842286 Iteration 2 Error: 0.191796 Iteration 3 Error: 0.052486 Iteration 4 Error: 0.013433 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.15 -0.23 ...... Frame ( 3) shift: -0.30 -0.45 ...... Frame ( 4) shift: -0.44 -0.68 ...... Frame ( 5) shift: -0.59 -0.90 ...... Frame ( 6) shift: -0.65 -1.02 ...... Frame ( 7) shift: -0.62 -1.03 ...... Frame ( 8) shift: -0.59 -1.03 ...... Frame ( 9) shift: -0.57 -0.98 ...... Frame ( 10) shift: -0.55 -0.86 ...... Frame ( 11) shift: -0.53 -0.74 ...... Frame ( 12) shift: -0.49 -0.66 ...... Frame ( 13) shift: -0.42 -0.61 ...... Frame ( 14) shift: -0.36 -0.57 ...... Frame ( 15) shift: -0.33 -0.49 ...... Frame ( 16) shift: -0.34 -0.38 ...... Frame ( 17) shift: -0.36 -0.27 ...... Frame ( 18) shift: -0.35 -0.16 ...... Frame ( 19) shift: -0.32 -0.06 ...... Frame ( 20) shift: -0.29 0.04 ...... Frame ( 21) shift: -0.26 0.10 ...... Frame ( 22) shift: -0.24 0.13 ...... Frame ( 23) shift: -0.22 0.15 ...... Frame ( 24) shift: -0.18 0.16 ...... Frame ( 25) shift: -0.13 0.16 ...... Frame ( 26) shift: -0.08 0.15 ...... Frame ( 27) shift: -0.06 0.16 ...... Frame ( 28) shift: -0.08 0.20 ...... Frame ( 29) shift: -0.10 0.23 ...... Frame ( 30) shift: -0.12 0.29 ...... Frame ( 31) shift: -0.14 0.37 ...... Frame ( 32) shift: -0.15 0.45 ...... Frame ( 33) shift: -0.12 0.53 ...... Frame ( 34) shift: -0.03 0.59 ...... Frame ( 35) shift: 0.07 0.66 ...... Frame ( 36) shift: 0.10 0.72 ...... Frame ( 37) shift: 0.07 0.76 ...... Frame ( 38) shift: 0.04 0.81 ...... Frame ( 39) shift: 0.01 0.86 ...... Frame ( 40) shift: -0.02 0.90 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.917539 Iteration 2 Error: 0.185888 Iteration 3 Error: 0.033846 Align patch 2 23 left Iteration 1 Error: 1.366041 Iteration 2 Error: 0.249800 Iteration 3 Error: 0.088592 Iteration 4 Error: 0.028956 Align patch 3 22 left Iteration 1 Error: 0.777369 Iteration 2 Error: 0.080210 Iteration 3 Error: 0.015308 Align patch 4 21 left Iteration 1 Error: 0.647371 Iteration 2 Error: 0.090944 Iteration 3 Error: 0.028538 Align patch 5 20 left Iteration 1 Error: 0.893830 Iteration 2 Error: 0.157403 Iteration 3 Error: 0.034619 Align patch 6 19 left Iteration 1 Error: 0.835469 Iteration 2 Error: 0.140046 Iteration 3 Error: 0.049384 Align patch 7 18 left Iteration 1 Error: 1.079066 Iteration 2 Error: 0.312587 Iteration 3 Error: 0.093322 Iteration 4 Error: 0.031637 Align patch 8 17 left Iteration 1 Error: 0.693095 Iteration 2 Error: 0.148267 Iteration 3 Error: 0.041587 Align patch 9 16 left Iteration 1 Error: 0.871637 Iteration 2 Error: 0.114059 Iteration 3 Error: 0.038147 Align patch 10 15 left Iteration 1 Error: 0.906794 Iteration 2 Error: 0.279500 Iteration 3 Error: 0.053412 Iteration 4 Error: 0.025980 Align patch 11 14 left Iteration 1 Error: 0.907629 Iteration 2 Error: 0.188880 Iteration 3 Error: 0.071249 Iteration 4 Error: 0.022962 Align patch 12 13 left Iteration 1 Error: 0.767592 Iteration 2 Error: 0.132711 Iteration 3 Error: 0.036645 Align patch 13 12 left Iteration 1 Error: 1.455423 Iteration 2 Error: 0.202424 Iteration 3 Error: 0.055548 Iteration 4 Error: 0.015913 Align patch 14 11 left Iteration 1 Error: 0.706157 Iteration 2 Error: 0.118701 Iteration 3 Error: 0.027895 Align patch 15 10 left Iteration 1 Error: 0.736037 Iteration 2 Error: 0.212029 Iteration 3 Error: 0.068079 Iteration 4 Error: 0.021569 Align patch 16 9 left Iteration 1 Error: 1.161060 Iteration 2 Error: 0.168690 Iteration 3 Error: 0.048034 Align patch 17 8 left Iteration 1 Error: 0.616724 Iteration 2 Error: 0.086098 Iteration 3 Error: 0.021486 Align patch 18 7 left Iteration 1 Error: 0.780602 Iteration 2 Error: 0.093869 Iteration 3 Error: 0.020328 Align patch 19 6 left Iteration 1 Error: 0.687211 Iteration 2 Error: 0.147905 Iteration 3 Error: 0.036418 Align patch 20 5 left Iteration 1 Error: 1.006781 Iteration 2 Error: 0.169962 Iteration 3 Error: 0.026548 Align patch 21 4 left Iteration 1 Error: 0.939326 Iteration 2 Error: 0.182982 Iteration 3 Error: 0.049307 Align patch 22 3 left Iteration 1 Error: 0.754593 Iteration 2 Error: 0.165094 Iteration 3 Error: 0.055659 Iteration 4 Error: 0.012840 Align patch 23 2 left Iteration 1 Error: 0.412887 Iteration 2 Error: 0.085055 Iteration 3 Error: 0.018874 Align patch 24 1 left Iteration 1 Error: 0.824794 Iteration 2 Error: 0.095253 Iteration 3 Error: 0.025550 Align patch 25 0 left Iteration 1 Error: 0.485844 Iteration 2 Error: 0.087793 Iteration 3 Error: 0.021741 3D Fitting completed. Patch alignment time: 11.74(sec) Local motion has been corrected. Process thread exits. Computational time: 25.988398 sec Total time: 32.824390 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00011hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00011hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.609451s Reading file: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00011hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.065376s ........................................ >>>>>>TIME<<<<<< FFT: 0.947274s Defocus_U Defocus_V Angle CCC 11087.91 11978.53 6.72 0.036974 Final Values Defocus_U Defocus_V Angle CCC 11139.49 12048.90 3.03 0.060062 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00007sq_v01_00011hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00011hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 39.37 6.68 Num Hot pixels: 203 Hot pixel threshold: 79.47 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.699353 Iteration 2 Error: 0.149623 Iteration 3 Error: 0.033854 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.03 -0.07 ...... Frame ( 3) shift: -0.05 -0.13 ...... Frame ( 4) shift: -0.08 -0.20 ...... Frame ( 5) shift: -0.11 -0.26 ...... Frame ( 6) shift: -0.11 -0.30 ...... Frame ( 7) shift: -0.07 -0.31 ...... Frame ( 8) shift: -0.04 -0.32 ...... Frame ( 9) shift: 0.00 -0.29 ...... Frame ( 10) shift: 0.06 -0.22 ...... Frame ( 11) shift: 0.12 -0.14 ...... Frame ( 12) shift: 0.13 -0.11 ...... Frame ( 13) shift: 0.10 -0.12 ...... Frame ( 14) shift: 0.07 -0.14 ...... Frame ( 15) shift: 0.08 -0.10 ...... Frame ( 16) shift: 0.14 -0.01 ...... Frame ( 17) shift: 0.20 0.08 ...... Frame ( 18) shift: 0.24 0.16 ...... Frame ( 19) shift: 0.24 0.22 ...... Frame ( 20) shift: 0.25 0.29 ...... Frame ( 21) shift: 0.24 0.30 ...... Frame ( 22) shift: 0.22 0.26 ...... Frame ( 23) shift: 0.20 0.23 ...... Frame ( 24) shift: 0.22 0.25 ...... Frame ( 25) shift: 0.28 0.35 ...... Frame ( 26) shift: 0.34 0.44 ...... Frame ( 27) shift: 0.39 0.49 ...... Frame ( 28) shift: 0.45 0.49 ...... Frame ( 29) shift: 0.51 0.50 ...... Frame ( 30) shift: 0.54 0.53 ...... Frame ( 31) shift: 0.52 0.59 ...... Frame ( 32) shift: 0.50 0.65 ...... Frame ( 33) shift: 0.50 0.69 ...... Frame ( 34) shift: 0.52 0.71 ...... Frame ( 35) shift: 0.54 0.73 ...... Frame ( 36) shift: 0.59 0.76 ...... Frame ( 37) shift: 0.65 0.78 ...... Frame ( 38) shift: 0.72 0.81 ...... Frame ( 39) shift: 0.78 0.84 ...... Frame ( 40) shift: 0.85 0.87 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.034118 Iteration 2 Error: 0.238598 Iteration 3 Error: 0.110653 Iteration 4 Error: 0.047637 Align patch 2 23 left Iteration 1 Error: 1.219284 Iteration 2 Error: 0.183309 Iteration 3 Error: 0.035824 Align patch 3 22 left Iteration 1 Error: 0.656662 Iteration 2 Error: 0.078035 Iteration 3 Error: 0.016583 Align patch 4 21 left Iteration 1 Error: 0.555460 Iteration 2 Error: 0.093458 Iteration 3 Error: 0.032202 Align patch 5 20 left Iteration 1 Error: 0.702995 Iteration 2 Error: 0.169885 Iteration 3 Error: 0.047348 Align patch 6 19 left Iteration 1 Error: 0.737960 Iteration 2 Error: 0.141630 Iteration 3 Error: 0.050828 Iteration 4 Error: 0.019942 Align patch 7 18 left Iteration 1 Error: 0.913125 Iteration 2 Error: 0.181461 Iteration 3 Error: 0.046690 Align patch 8 17 left Iteration 1 Error: 0.987071 Iteration 2 Error: 0.099983 Iteration 3 Error: 0.026073 Align patch 9 16 left Iteration 1 Error: 1.082713 Iteration 2 Error: 0.167945 Iteration 3 Error: 0.037257 Align patch 10 15 left Iteration 1 Error: 1.252750 Iteration 2 Error: 0.151016 Iteration 3 Error: 0.037574 Align patch 11 14 left Iteration 1 Error: 0.787154 Iteration 2 Error: 0.245699 Iteration 3 Error: 0.071106 Iteration 4 Error: 0.020043 Align patch 12 13 left Iteration 1 Error: 0.631120 Iteration 2 Error: 0.145675 Iteration 3 Error: 0.046026 Align patch 13 12 left Iteration 1 Error: 0.558171 Iteration 2 Error: 0.079338 Iteration 3 Error: 0.038117 Align patch 14 11 left Iteration 1 Error: 0.766058 Iteration 2 Error: 0.057612 Iteration 3 Error: 0.014447 Align patch 15 10 left Iteration 1 Error: 0.367637 Iteration 2 Error: 0.044419 Align patch 16 9 left Iteration 1 Error: 0.780447 Iteration 2 Error: 0.090304 Iteration 3 Error: 0.015089 Align patch 17 8 left Iteration 1 Error: 0.506936 Iteration 2 Error: 0.075664 Iteration 3 Error: 0.016258 Align patch 18 7 left Iteration 1 Error: 0.892079 Iteration 2 Error: 0.097106 Iteration 3 Error: 0.031290 Align patch 19 6 left Iteration 1 Error: 0.532467 Iteration 2 Error: 0.056831 Iteration 3 Error: 0.010753 Align patch 20 5 left Iteration 1 Error: 0.778016 Iteration 2 Error: 0.090030 Iteration 3 Error: 0.024083 Align patch 21 4 left Iteration 1 Error: 0.712601 Iteration 2 Error: 0.078101 Iteration 3 Error: 0.018346 Align patch 22 3 left Iteration 1 Error: 0.664732 Iteration 2 Error: 0.107185 Iteration 3 Error: 0.038440 Align patch 23 2 left Iteration 1 Error: 0.615260 Iteration 2 Error: 0.193075 Iteration 3 Error: 0.075119 Iteration 4 Error: 0.021402 Align patch 24 1 left Iteration 1 Error: 1.173172 Iteration 2 Error: 0.123749 Iteration 3 Error: 0.032899 Align patch 25 0 left Iteration 1 Error: 0.785026 Iteration 2 Error: 0.172948 Iteration 3 Error: 0.045782 3D Fitting completed. Patch alignment time: 11.18(sec) Local motion has been corrected. Process thread exits. Computational time: 25.707346 sec Total time: 34.470158 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00011hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00011hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.641077s Reading file: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00011hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.677868s ........................................ >>>>>>TIME<<<<<< FFT: 0.980850s Defocus_U Defocus_V Angle CCC 13042.99 12292.99 81.24 0.033274 Final Values Defocus_U Defocus_V Angle CCC 13052.35 12324.28 80.61 0.053918 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00007sq_v01_00012hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00012hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 40.37 6.81 Num Hot pixels: 211 Hot pixel threshold: 81.25 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.877494 Iteration 2 Error: 0.209112 Iteration 3 Error: 0.070140 Iteration 4 Error: 0.027236 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.08 -0.25 ...... Frame ( 3) shift: -0.15 -0.51 ...... Frame ( 4) shift: -0.23 -0.76 ...... Frame ( 5) shift: -0.31 -1.01 ...... Frame ( 6) shift: -0.35 -1.10 ...... Frame ( 7) shift: -0.36 -1.00 ...... Frame ( 8) shift: -0.36 -0.91 ...... Frame ( 9) shift: -0.38 -0.82 ...... Frame ( 10) shift: -0.40 -0.73 ...... Frame ( 11) shift: -0.42 -0.65 ...... Frame ( 12) shift: -0.40 -0.59 ...... Frame ( 13) shift: -0.33 -0.56 ...... Frame ( 14) shift: -0.27 -0.53 ...... Frame ( 15) shift: -0.19 -0.48 ...... Frame ( 16) shift: -0.09 -0.39 ...... Frame ( 17) shift: 0.01 -0.31 ...... Frame ( 18) shift: 0.09 -0.25 ...... Frame ( 19) shift: 0.14 -0.21 ...... Frame ( 20) shift: 0.19 -0.17 ...... Frame ( 21) shift: 0.23 -0.13 ...... Frame ( 22) shift: 0.28 -0.09 ...... Frame ( 23) shift: 0.33 -0.04 ...... Frame ( 24) shift: 0.35 0.00 ...... Frame ( 25) shift: 0.36 0.05 ...... Frame ( 26) shift: 0.37 0.10 ...... Frame ( 27) shift: 0.46 0.13 ...... Frame ( 28) shift: 0.63 0.15 ...... Frame ( 29) shift: 0.81 0.16 ...... Frame ( 30) shift: 0.88 0.20 ...... Frame ( 31) shift: 0.84 0.26 ...... Frame ( 32) shift: 0.80 0.32 ...... Frame ( 33) shift: 0.79 0.35 ...... Frame ( 34) shift: 0.81 0.34 ...... Frame ( 35) shift: 0.83 0.34 ...... Frame ( 36) shift: 0.86 0.38 ...... Frame ( 37) shift: 0.90 0.46 ...... Frame ( 38) shift: 0.94 0.55 ...... Frame ( 39) shift: 0.98 0.64 ...... Frame ( 40) shift: 1.02 0.72 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.830658 Iteration 2 Error: 0.408763 Iteration 3 Error: 0.259956 Iteration 4 Error: 0.148772 Iteration 5 Error: 0.091423 Align patch 1 24 left Iteration 1 Error: 2.060397 Iteration 2 Error: 0.309006 Iteration 3 Error: 0.098922 Iteration 4 Error: 0.028164 Align patch 2 23 left Iteration 1 Error: 1.389828 Iteration 2 Error: 0.306639 Iteration 3 Error: 0.104392 Iteration 4 Error: 0.046532 Align patch 3 22 left Iteration 1 Error: 0.932044 Iteration 2 Error: 0.157778 Iteration 3 Error: 0.045102 Align patch 4 21 left Iteration 1 Error: 0.555507 Iteration 2 Error: 0.111668 Iteration 3 Error: 0.038377 Align patch 5 20 left Iteration 1 Error: 0.871230 Iteration 2 Error: 0.155751 Iteration 3 Error: 0.027207 Align patch 6 19 left Iteration 1 Error: 1.766339 Iteration 2 Error: 0.240745 Iteration 3 Error: 0.122782 Iteration 4 Error: 0.052213 Iteration 5 Error: 0.026738 Align patch 7 18 left Iteration 1 Error: 1.196381 Iteration 2 Error: 0.236656 Iteration 3 Error: 0.088501 Iteration 4 Error: 0.032784 Align patch 8 17 left Iteration 1 Error: 0.687171 Iteration 2 Error: 0.342938 Iteration 3 Error: 0.120489 Iteration 4 Error: 0.041753 Align patch 9 16 left Iteration 1 Error: 0.823868 Iteration 2 Error: 0.155824 Iteration 3 Error: 0.051711 Iteration 4 Error: 0.018264 Align patch 10 15 left Iteration 1 Error: 0.847366 Iteration 2 Error: 0.110256 Iteration 3 Error: 0.021533 Align patch 11 14 left Iteration 1 Error: 0.835584 Iteration 2 Error: 0.156247 Iteration 3 Error: 0.041826 Align patch 12 13 left Iteration 1 Error: 1.083534 Iteration 2 Error: 0.289038 Iteration 3 Error: 0.080213 Iteration 4 Error: 0.039447 Align patch 13 12 left Iteration 1 Error: 0.886235 Iteration 2 Error: 0.209852 Iteration 3 Error: 0.089668 Iteration 4 Error: 0.035818 Align patch 14 11 left Iteration 1 Error: 0.679331 Iteration 2 Error: 0.278219 Iteration 3 Error: 0.087397 Iteration 4 Error: 0.040758 Align patch 15 10 left Iteration 1 Error: 0.624892 Iteration 2 Error: 0.103928 Iteration 3 Error: 0.036211 Align patch 16 9 left Iteration 1 Error: 0.726942 Iteration 2 Error: 0.192424 Iteration 3 Error: 0.115104 Iteration 4 Error: 0.070772 Iteration 5 Error: 0.040297 Align patch 17 8 left Iteration 1 Error: 0.663414 Iteration 2 Error: 0.209344 Iteration 3 Error: 0.086978 Iteration 4 Error: 0.040780 Align patch 18 7 left Iteration 1 Error: 1.126697 Iteration 2 Error: 0.213248 Iteration 3 Error: 0.065296 Iteration 4 Error: 0.033171 Align patch 19 6 left Iteration 1 Error: 0.551183 Iteration 2 Error: 0.105331 Iteration 3 Error: 0.025744 Align patch 20 5 left Iteration 1 Error: 0.773432 Iteration 2 Error: 0.072575 Iteration 3 Error: 0.017541 Align patch 21 4 left Iteration 1 Error: 0.898522 Iteration 2 Error: 0.237626 Iteration 3 Error: 0.068253 Iteration 4 Error: 0.021443 Align patch 22 3 left Iteration 1 Error: 0.613846 Iteration 2 Error: 0.178059 Iteration 3 Error: 0.054234 Iteration 4 Error: 0.015996 Align patch 23 2 left Iteration 1 Error: 0.475389 Iteration 2 Error: 0.123558 Iteration 3 Error: 0.050497 Iteration 4 Error: 0.023149 Align patch 24 1 left Iteration 1 Error: 0.999827 Iteration 2 Error: 0.158626 Iteration 3 Error: 0.026925 Align patch 25 0 left Iteration 1 Error: 0.520492 Iteration 2 Error: 0.113262 Iteration 3 Error: 0.031534 3D Fitting completed. Patch alignment time: 12.75(sec) Local motion has been corrected. Process thread exits. Computational time: 27.774721 sec Total time: 34.351357 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00012hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00012hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.592613s Reading file: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00012hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.444930s ........................................ >>>>>>TIME<<<<<< FFT: 0.962349s Defocus_U Defocus_V Angle CCC 12574.22 13394.53 11.37 0.038015 Final Values Defocus_U Defocus_V Angle CCC 12600.74 13414.90 10.43 0.061136 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00007sq_v01_00012hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00012hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 1.000e-01 CC threshold: 0.735 Mean Std: 39.34 6.69 Num Hot pixels: 190 Hot pixel threshold: 79.49 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.923084 Iteration 2 Error: 0.190839 Iteration 3 Error: 0.054333 Iteration 4 Error: 0.017816 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.21 -0.34 ...... Frame ( 3) shift: -0.41 -0.68 ...... Frame ( 4) shift: -0.62 -1.02 ...... Frame ( 5) shift: -0.83 -1.36 ...... Frame ( 6) shift: -0.91 -1.51 ...... Frame ( 7) shift: -0.87 -1.48 ...... Frame ( 8) shift: -0.83 -1.45 ...... Frame ( 9) shift: -0.80 -1.41 ...... Frame ( 10) shift: -0.78 -1.35 ...... Frame ( 11) shift: -0.76 -1.29 ...... Frame ( 12) shift: -0.74 -1.20 ...... Frame ( 13) shift: -0.71 -1.08 ...... Frame ( 14) shift: -0.69 -0.97 ...... Frame ( 15) shift: -0.70 -0.87 ...... Frame ( 16) shift: -0.73 -0.80 ...... Frame ( 17) shift: -0.77 -0.72 ...... Frame ( 18) shift: -0.75 -0.67 ...... Frame ( 19) shift: -0.67 -0.64 ...... Frame ( 20) shift: -0.59 -0.62 ...... Frame ( 21) shift: -0.54 -0.58 ...... Frame ( 22) shift: -0.53 -0.52 ...... Frame ( 23) shift: -0.53 -0.47 ...... Frame ( 24) shift: -0.52 -0.39 ...... Frame ( 25) shift: -0.51 -0.27 ...... Frame ( 26) shift: -0.50 -0.15 ...... Frame ( 27) shift: -0.48 -0.07 ...... Frame ( 28) shift: -0.44 -0.03 ...... Frame ( 29) shift: -0.41 0.02 ...... Frame ( 30) shift: -0.36 0.07 ...... Frame ( 31) shift: -0.32 0.13 ...... Frame ( 32) shift: -0.27 0.18 ...... Frame ( 33) shift: -0.23 0.24 ...... Frame ( 34) shift: -0.21 0.29 ...... Frame ( 35) shift: -0.18 0.33 ...... Frame ( 36) shift: -0.18 0.38 ...... Frame ( 37) shift: -0.20 0.41 ...... Frame ( 38) shift: -0.22 0.45 ...... Frame ( 39) shift: -0.24 0.49 ...... Frame ( 40) shift: -0.26 0.52 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.313929 Iteration 2 Error: 0.236212 Iteration 3 Error: 0.096268 Iteration 4 Error: 0.045756 Align patch 2 23 left Iteration 1 Error: 1.134323 Iteration 2 Error: 0.411130 Iteration 3 Error: 0.164153 Iteration 4 Error: 0.108093 Iteration 5 Error: 0.054804 Align patch 2 23 left Iteration 1 Error: 1.165169 Iteration 2 Error: 0.193263 Iteration 3 Error: 0.052653 Iteration 4 Error: 0.014996 Align patch 3 22 left Iteration 1 Error: 1.229787 Iteration 2 Error: 0.297325 Iteration 3 Error: 0.135014 Iteration 4 Error: 0.047445 Align patch 4 21 left Iteration 1 Error: 0.765220 Iteration 2 Error: 0.139064 Iteration 3 Error: 0.040502 Align patch 5 20 left Iteration 1 Error: 0.710923 Iteration 2 Error: 0.060642 Iteration 3 Error: 0.017590 Align patch 6 19 left Iteration 1 Error: 1.358245 Iteration 2 Error: 0.239881 Iteration 3 Error: 0.079654 Iteration 4 Error: 0.032193 Align patch 7 18 left Iteration 1 Error: 0.741313 Iteration 2 Error: 0.169276 Iteration 3 Error: 0.051681 Iteration 4 Error: 0.016227 Align patch 8 17 left Iteration 1 Error: 0.979286 Iteration 2 Error: 0.291467 Iteration 3 Error: 0.085760 Iteration 4 Error: 0.030861 Align patch 9 16 left Iteration 1 Error: 0.822239 Iteration 2 Error: 0.103829 Iteration 3 Error: 0.026677 Align patch 10 15 left Iteration 1 Error: 0.597111 Iteration 2 Error: 0.084575 Iteration 3 Error: 0.017164 Align patch 11 14 left Iteration 1 Error: 1.036878 Iteration 2 Error: 0.381896 Iteration 3 Error: 0.169419 Iteration 4 Error: 0.089622 Iteration 5 Error: 0.054891 Align patch 11 14 left Iteration 1 Error: 1.219443 Iteration 2 Error: 0.261753 Iteration 3 Error: 0.055004 Iteration 4 Error: 0.019076 Align patch 12 13 left Iteration 1 Error: 1.098044 Iteration 2 Error: 0.173010 Iteration 3 Error: 0.105899 Iteration 4 Error: 0.024976 Align patch 13 12 left Iteration 1 Error: 1.003351 Iteration 2 Error: 0.202168 Iteration 3 Error: 0.047649 Align patch 14 11 left Iteration 1 Error: 0.482282 Iteration 2 Error: 0.162597 Iteration 3 Error: 0.029934 Align patch 15 10 left Iteration 1 Error: 0.802301 Iteration 2 Error: 0.122531 Iteration 3 Error: 0.019908 Align patch 16 9 left Iteration 1 Error: 0.918126 Iteration 2 Error: 0.155465 Iteration 3 Error: 0.067579 Iteration 4 Error: 0.027793 Align patch 17 8 left Iteration 1 Error: 0.842894 Iteration 2 Error: 0.155610 Iteration 3 Error: 0.039547 Align patch 18 7 left Iteration 1 Error: 0.946031 Iteration 2 Error: 0.266416 Iteration 3 Error: 0.068204 Iteration 4 Error: 0.023221 Align patch 19 6 left Iteration 1 Error: 0.914229 Iteration 2 Error: 0.287419 Iteration 3 Error: 0.080916 Iteration 4 Error: 0.030918 Align patch 20 5 left Iteration 1 Error: 0.974803 Iteration 2 Error: 0.188564 Iteration 3 Error: 0.039376 Align patch 21 4 left Iteration 1 Error: 0.823295 Iteration 2 Error: 0.209618 Iteration 3 Error: 0.060528 Iteration 4 Error: 0.022331 Align patch 22 3 left Iteration 1 Error: 0.660008 Iteration 2 Error: 0.133742 Iteration 3 Error: 0.031329 Align patch 23 2 left Iteration 1 Error: 1.232189 Iteration 2 Error: 0.244048 Iteration 3 Error: 0.070805 Iteration 4 Error: 0.014278 Align patch 24 1 left Iteration 1 Error: 1.030684 Iteration 2 Error: 0.250562 Iteration 3 Error: 0.052702 Iteration 4 Error: 0.019466 Align patch 25 0 left Iteration 1 Error: 1.074171 Iteration 2 Error: 0.222732 Iteration 3 Error: 0.044048 3D Fitting completed. Patch alignment time: 13.20(sec) Local motion has been corrected. Process thread exits. Computational time: 27.546637 sec Total time: 34.402882 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00012hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00012hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.702599s Reading file: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00012hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.814773s ........................................ >>>>>>TIME<<<<<< FFT: 1.089764s Defocus_U Defocus_V Angle CCC 13291.03 13908.22 7.12 0.040027 Final Values Defocus_U Defocus_V Angle CCC 13292.59 13909.79 6.50 0.063711 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00007sq_v01_00012hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00012hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 40.97 6.85 Num Hot pixels: 206 Hot pixel threshold: 82.09 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.802677 Iteration 2 Error: 0.106422 Iteration 3 Error: 0.025557 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.07 -0.22 ...... Frame ( 3) shift: -0.14 -0.44 ...... Frame ( 4) shift: -0.20 -0.66 ...... Frame ( 5) shift: -0.27 -0.88 ...... Frame ( 6) shift: -0.30 -0.99 ...... Frame ( 7) shift: -0.29 -0.99 ...... Frame ( 8) shift: -0.28 -0.98 ...... Frame ( 9) shift: -0.33 -0.92 ...... Frame ( 10) shift: -0.43 -0.81 ...... Frame ( 11) shift: -0.54 -0.70 ...... Frame ( 12) shift: -0.59 -0.59 ...... Frame ( 13) shift: -0.60 -0.49 ...... Frame ( 14) shift: -0.60 -0.38 ...... Frame ( 15) shift: -0.61 -0.29 ...... Frame ( 16) shift: -0.61 -0.21 ...... Frame ( 17) shift: -0.62 -0.13 ...... Frame ( 18) shift: -0.63 -0.09 ...... Frame ( 19) shift: -0.66 -0.08 ...... Frame ( 20) shift: -0.68 -0.07 ...... Frame ( 21) shift: -0.64 -0.07 ...... Frame ( 22) shift: -0.54 -0.07 ...... Frame ( 23) shift: -0.43 -0.07 ...... Frame ( 24) shift: -0.41 -0.05 ...... Frame ( 25) shift: -0.47 0.01 ...... Frame ( 26) shift: -0.53 0.07 ...... Frame ( 27) shift: -0.57 0.11 ...... Frame ( 28) shift: -0.58 0.14 ...... Frame ( 29) shift: -0.59 0.17 ...... Frame ( 30) shift: -0.59 0.22 ...... Frame ( 31) shift: -0.59 0.27 ...... Frame ( 32) shift: -0.60 0.33 ...... Frame ( 33) shift: -0.61 0.38 ...... Frame ( 34) shift: -0.65 0.42 ...... Frame ( 35) shift: -0.68 0.47 ...... Frame ( 36) shift: -0.67 0.50 ...... Frame ( 37) shift: -0.60 0.53 ...... Frame ( 38) shift: -0.53 0.55 ...... Frame ( 39) shift: -0.46 0.57 ...... Frame ( 40) shift: -0.39 0.59 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.716778 Iteration 2 Error: 0.278245 Iteration 3 Error: 0.058690 Iteration 4 Error: 0.026217 Align patch 2 23 left Iteration 1 Error: 0.801396 Iteration 2 Error: 0.142304 Iteration 3 Error: 0.056814 Iteration 4 Error: 0.019035 Align patch 3 22 left Iteration 1 Error: 0.907962 Iteration 2 Error: 0.189959 Iteration 3 Error: 0.075954 Iteration 4 Error: 0.032900 Align patch 4 21 left Iteration 1 Error: 0.714734 Iteration 2 Error: 0.132385 Iteration 3 Error: 0.026883 Align patch 5 20 left Iteration 1 Error: 1.101961 Iteration 2 Error: 0.140779 Iteration 3 Error: 0.027195 Align patch 6 19 left Iteration 1 Error: 0.748326 Iteration 2 Error: 0.137157 Iteration 3 Error: 0.052128 Iteration 4 Error: 0.014148 Align patch 7 18 left Iteration 1 Error: 0.731375 Iteration 2 Error: 0.105580 Iteration 3 Error: 0.034478 Align patch 8 17 left Iteration 1 Error: 0.649379 Iteration 2 Error: 0.218950 Iteration 3 Error: 0.066492 Iteration 4 Error: 0.022430 Align patch 9 16 left Iteration 1 Error: 0.577722 Iteration 2 Error: 0.044958 Align patch 10 15 left Iteration 1 Error: 0.789835 Iteration 2 Error: 0.111592 Iteration 3 Error: 0.025523 Align patch 11 14 left Iteration 1 Error: 0.841372 Iteration 2 Error: 0.091536 Iteration 3 Error: 0.032545 Align patch 12 13 left Iteration 1 Error: 0.794679 Iteration 2 Error: 0.151743 Iteration 3 Error: 0.039820 Align patch 13 12 left Iteration 1 Error: 0.715881 Iteration 2 Error: 0.138522 Iteration 3 Error: 0.040470 Align patch 14 11 left Iteration 1 Error: 0.537407 Iteration 2 Error: 0.093220 Iteration 3 Error: 0.023051 Align patch 15 10 left Iteration 1 Error: 0.626580 Iteration 2 Error: 0.145174 Iteration 3 Error: 0.035233 Align patch 16 9 left Iteration 1 Error: 0.894166 Iteration 2 Error: 0.196316 Iteration 3 Error: 0.067840 Iteration 4 Error: 0.020511 Align patch 17 8 left Iteration 1 Error: 0.871895 Iteration 2 Error: 0.133106 Iteration 3 Error: 0.033919 Align patch 18 7 left Iteration 1 Error: 0.608149 Iteration 2 Error: 0.134746 Iteration 3 Error: 0.027779 Align patch 19 6 left Iteration 1 Error: 0.736629 Iteration 2 Error: 0.107574 Iteration 3 Error: 0.025224 Align patch 20 5 left Iteration 1 Error: 0.653151 Iteration 2 Error: 0.110147 Iteration 3 Error: 0.016685 Align patch 21 4 left Iteration 1 Error: 0.690669 Iteration 2 Error: 0.160347 Iteration 3 Error: 0.033013 Align patch 22 3 left Iteration 1 Error: 0.687002 Iteration 2 Error: 0.130821 Iteration 3 Error: 0.026438 Align patch 23 2 left Iteration 1 Error: 0.965629 Iteration 2 Error: 0.196106 Iteration 3 Error: 0.068467 Iteration 4 Error: 0.027963 Align patch 24 1 left Iteration 1 Error: 0.930575 Iteration 2 Error: 0.261804 Iteration 3 Error: 0.048228 Align patch 25 0 left Iteration 1 Error: 0.930421 Iteration 2 Error: 0.149184 Iteration 3 Error: 0.029309 3D Fitting completed. Patch alignment time: 11.52(sec) Local motion has been corrected. Process thread exits. Computational time: 24.075264 sec Total time: 31.241770 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00012hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00012hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.446687s Reading file: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00012hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.360210s ........................................ >>>>>>TIME<<<<<< FFT: 1.272688s Defocus_U Defocus_V Angle CCC 11660.17 12570.33 6.71 0.040853 Final Values Defocus_U Defocus_V Angle CCC 11672.68 12579.71 6.40 0.070801 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00007sq_v01_00012hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00012hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 1.000e-01 CC threshold: 0.734 Mean Std: 39.82 6.73 Num Hot pixels: 203 Hot pixel threshold: 80.22 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.922473 Iteration 2 Error: 0.166421 Iteration 3 Error: 0.036736 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.19 -0.21 ...... Frame ( 3) shift: -0.37 -0.43 ...... Frame ( 4) shift: -0.56 -0.64 ...... Frame ( 5) shift: -0.74 -0.86 ...... Frame ( 6) shift: -0.82 -0.97 ...... Frame ( 7) shift: -0.80 -0.97 ...... Frame ( 8) shift: -0.78 -0.97 ...... Frame ( 9) shift: -0.74 -0.94 ...... Frame ( 10) shift: -0.69 -0.88 ...... Frame ( 11) shift: -0.64 -0.82 ...... Frame ( 12) shift: -0.60 -0.78 ...... Frame ( 13) shift: -0.56 -0.76 ...... Frame ( 14) shift: -0.52 -0.75 ...... Frame ( 15) shift: -0.49 -0.69 ...... Frame ( 16) shift: -0.47 -0.61 ...... Frame ( 17) shift: -0.45 -0.52 ...... Frame ( 18) shift: -0.43 -0.42 ...... Frame ( 19) shift: -0.40 -0.33 ...... Frame ( 20) shift: -0.37 -0.23 ...... Frame ( 21) shift: -0.34 -0.14 ...... Frame ( 22) shift: -0.30 -0.05 ...... Frame ( 23) shift: -0.27 0.04 ...... Frame ( 24) shift: -0.27 0.10 ...... Frame ( 25) shift: -0.32 0.15 ...... Frame ( 26) shift: -0.37 0.19 ...... Frame ( 27) shift: -0.42 0.25 ...... Frame ( 28) shift: -0.46 0.32 ...... Frame ( 29) shift: -0.51 0.39 ...... Frame ( 30) shift: -0.50 0.45 ...... Frame ( 31) shift: -0.44 0.47 ...... Frame ( 32) shift: -0.38 0.50 ...... Frame ( 33) shift: -0.34 0.55 ...... Frame ( 34) shift: -0.32 0.63 ...... Frame ( 35) shift: -0.31 0.70 ...... Frame ( 36) shift: -0.26 0.76 ...... Frame ( 37) shift: -0.20 0.78 ...... Frame ( 38) shift: -0.13 0.81 ...... Frame ( 39) shift: -0.06 0.84 ...... Frame ( 40) shift: 0.01 0.87 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.181575 Iteration 2 Error: 0.204147 Iteration 3 Error: 0.079458 Iteration 4 Error: 0.028845 Align patch 2 23 left Iteration 1 Error: 0.913719 Iteration 2 Error: 0.129195 Iteration 3 Error: 0.037864 Align patch 3 22 left Iteration 1 Error: 0.860821 Iteration 2 Error: 0.109883 Iteration 3 Error: 0.029049 Align patch 4 21 left Iteration 1 Error: 0.775773 Iteration 2 Error: 0.083157 Iteration 3 Error: 0.036209 Align patch 5 20 left Iteration 1 Error: 1.257477 Iteration 2 Error: 0.142059 Iteration 3 Error: 0.051217 Iteration 4 Error: 0.016338 Align patch 6 19 left Iteration 1 Error: 1.036541 Iteration 2 Error: 0.430397 Iteration 3 Error: 0.179231 Iteration 4 Error: 0.074652 Iteration 5 Error: 0.044684 Align patch 7 18 left Iteration 1 Error: 1.270342 Iteration 2 Error: 0.192587 Iteration 3 Error: 0.079753 Iteration 4 Error: 0.023528 Align patch 8 17 left Iteration 1 Error: 0.638280 Iteration 2 Error: 0.227534 Iteration 3 Error: 0.063305 Iteration 4 Error: 0.021121 Align patch 9 16 left Iteration 1 Error: 0.714913 Iteration 2 Error: 0.124991 Iteration 3 Error: 0.038704 Align patch 10 15 left Iteration 1 Error: 0.891281 Iteration 2 Error: 0.148980 Iteration 3 Error: 0.042608 Align patch 11 14 left Iteration 1 Error: 1.057906 Iteration 2 Error: 0.188952 Iteration 3 Error: 0.076771 Iteration 4 Error: 0.033516 Align patch 12 13 left Iteration 1 Error: 0.886171 Iteration 2 Error: 0.112938 Iteration 3 Error: 0.029056 Align patch 13 12 left Iteration 1 Error: 0.639076 Iteration 2 Error: 0.128945 Iteration 3 Error: 0.028581 Align patch 14 11 left Iteration 1 Error: 0.577815 Iteration 2 Error: 0.109170 Iteration 3 Error: 0.023062 Align patch 15 10 left Iteration 1 Error: 1.121985 Iteration 2 Error: 0.134794 Iteration 3 Error: 0.042623 Align patch 16 9 left Iteration 1 Error: 0.551545 Iteration 2 Error: 0.072444 Iteration 3 Error: 0.015387 Align patch 17 8 left Iteration 1 Error: 0.677772 Iteration 2 Error: 0.089360 Iteration 3 Error: 0.033764 Align patch 18 7 left Iteration 1 Error: 0.958688 Iteration 2 Error: 0.145380 Iteration 3 Error: 0.044445 Align patch 19 6 left Iteration 1 Error: 0.705725 Iteration 2 Error: 0.110172 Iteration 3 Error: 0.029925 Align patch 20 5 left Iteration 1 Error: 0.716037 Iteration 2 Error: 0.095968 Iteration 3 Error: 0.021774 Align patch 21 4 left Iteration 1 Error: 0.727324 Iteration 2 Error: 0.139189 Iteration 3 Error: 0.031451 Align patch 22 3 left Iteration 1 Error: 0.701576 Iteration 2 Error: 0.109497 Iteration 3 Error: 0.038563 Align patch 23 2 left Iteration 1 Error: 0.672787 Iteration 2 Error: 0.205326 Iteration 3 Error: 0.042035 Align patch 24 1 left Iteration 1 Error: 0.927537 Iteration 2 Error: 0.112499 Iteration 3 Error: 0.029310 Align patch 25 0 left Iteration 1 Error: 0.702136 Iteration 2 Error: 0.135092 Iteration 3 Error: 0.034870 3D Fitting completed. Patch alignment time: 13.13(sec) Local motion has been corrected. Process thread exits. Computational time: 24.504877 sec Total time: 31.539019 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00012hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00012hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.602519s Reading file: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00012hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.224792s ........................................ >>>>>>TIME<<<<<< FFT: 0.976133s Defocus_U Defocus_V Angle CCC 14293.29 13714.62 82.43 0.042119 Final Values Defocus_U Defocus_V Angle CCC 14283.89 13736.54 81.49 0.065085 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00007sq_v01_00013hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00013hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 42.81 7.11 Num Hot pixels: 186 Hot pixel threshold: 85.47 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.106919 Iteration 2 Error: 0.203976 Iteration 3 Error: 0.053658 Iteration 4 Error: 0.018072 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.16 -0.05 ...... Frame ( 3) shift: -0.32 -0.11 ...... Frame ( 4) shift: -0.48 -0.16 ...... Frame ( 5) shift: -0.64 -0.21 ...... Frame ( 6) shift: -0.71 -0.20 ...... Frame ( 7) shift: -0.68 -0.12 ...... Frame ( 8) shift: -0.65 -0.04 ...... Frame ( 9) shift: -0.64 0.03 ...... Frame ( 10) shift: -0.63 0.10 ...... Frame ( 11) shift: -0.63 0.17 ...... Frame ( 12) shift: -0.60 0.27 ...... Frame ( 13) shift: -0.56 0.41 ...... Frame ( 14) shift: -0.51 0.55 ...... Frame ( 15) shift: -0.50 0.65 ...... Frame ( 16) shift: -0.51 0.72 ...... Frame ( 17) shift: -0.53 0.78 ...... Frame ( 18) shift: -0.49 0.85 ...... Frame ( 19) shift: -0.39 0.90 ...... Frame ( 20) shift: -0.30 0.96 ...... Frame ( 21) shift: -0.27 0.99 ...... Frame ( 22) shift: -0.30 1.00 ...... Frame ( 23) shift: -0.33 1.02 ...... Frame ( 24) shift: -0.32 1.07 ...... Frame ( 25) shift: -0.26 1.17 ...... Frame ( 26) shift: -0.20 1.26 ...... Frame ( 27) shift: -0.14 1.34 ...... Frame ( 28) shift: -0.06 1.40 ...... Frame ( 29) shift: 0.01 1.46 ...... Frame ( 30) shift: 0.04 1.51 ...... Frame ( 31) shift: 0.05 1.56 ...... Frame ( 32) shift: 0.05 1.61 ...... Frame ( 33) shift: 0.08 1.66 ...... Frame ( 34) shift: 0.16 1.70 ...... Frame ( 35) shift: 0.23 1.75 ...... Frame ( 36) shift: 0.27 1.81 ...... Frame ( 37) shift: 0.28 1.89 ...... Frame ( 38) shift: 0.29 1.97 ...... Frame ( 39) shift: 0.30 2.04 ...... Frame ( 40) shift: 0.32 2.12 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.580637 Iteration 2 Error: 0.308039 Iteration 3 Error: 0.089568 Iteration 4 Error: 0.054195 Iteration 5 Error: 0.018589 Align patch 2 23 left Iteration 1 Error: 0.821814 Iteration 2 Error: 0.183133 Iteration 3 Error: 0.052595 Iteration 4 Error: 0.022556 Align patch 3 22 left Iteration 1 Error: 0.925078 Iteration 2 Error: 0.162506 Iteration 3 Error: 0.041671 Align patch 4 21 left Iteration 1 Error: 0.656383 Iteration 2 Error: 0.148210 Iteration 3 Error: 0.066392 Iteration 4 Error: 0.031714 Align patch 5 20 left Iteration 1 Error: 0.585009 Iteration 2 Error: 0.111172 Iteration 3 Error: 0.029239 Align patch 6 19 left Iteration 1 Error: 1.301691 Iteration 2 Error: 0.372706 Iteration 3 Error: 0.115080 Iteration 4 Error: 0.071229 Iteration 5 Error: 0.028472 Align patch 7 18 left Iteration 1 Error: 0.905698 Iteration 2 Error: 0.235004 Iteration 3 Error: 0.104014 Iteration 4 Error: 0.036461 Align patch 8 17 left Iteration 1 Error: 0.747678 Iteration 2 Error: 0.120976 Iteration 3 Error: 0.032100 Align patch 9 16 left Iteration 1 Error: 0.637770 Iteration 2 Error: 0.122205 Iteration 3 Error: 0.039115 Align patch 10 15 left Iteration 1 Error: 1.084917 Iteration 2 Error: 0.225286 Iteration 3 Error: 0.032923 Align patch 11 14 left Iteration 1 Error: 0.786983 Iteration 2 Error: 0.113573 Iteration 3 Error: 0.027054 Align patch 12 13 left Iteration 1 Error: 1.207393 Iteration 2 Error: 0.170333 Iteration 3 Error: 0.045800 Align patch 13 12 left Iteration 1 Error: 0.634437 Iteration 2 Error: 0.105966 Iteration 3 Error: 0.031662 Align patch 14 11 left Iteration 1 Error: 0.437836 Iteration 2 Error: 0.071992 Iteration 3 Error: 0.025590 Align patch 15 10 left Iteration 1 Error: 0.668116 Iteration 2 Error: 0.130027 Iteration 3 Error: 0.026119 Align patch 16 9 left Iteration 1 Error: 0.466167 Iteration 2 Error: 0.133211 Iteration 3 Error: 0.034087 Align patch 17 8 left Iteration 1 Error: 1.009214 Iteration 2 Error: 0.182316 Iteration 3 Error: 0.062275 Iteration 4 Error: 0.031395 Align patch 18 7 left Iteration 1 Error: 0.722440 Iteration 2 Error: 0.160523 Iteration 3 Error: 0.047731 Align patch 19 6 left Iteration 1 Error: 0.575979 Iteration 2 Error: 0.152033 Iteration 3 Error: 0.022361 Align patch 20 5 left Iteration 1 Error: 0.869226 Iteration 2 Error: 0.088795 Iteration 3 Error: 0.019121 Align patch 21 4 left Iteration 1 Error: 0.731732 Iteration 2 Error: 0.121135 Iteration 3 Error: 0.039581 Align patch 22 3 left Iteration 1 Error: 0.899040 Iteration 2 Error: 0.123603 Iteration 3 Error: 0.041810 Align patch 23 2 left Iteration 1 Error: 0.853024 Iteration 2 Error: 0.120184 Iteration 3 Error: 0.026672 Align patch 24 1 left Iteration 1 Error: 0.599483 Iteration 2 Error: 0.067627 Iteration 3 Error: 0.014542 Align patch 25 0 left Iteration 1 Error: 0.644200 Iteration 2 Error: 0.195519 Iteration 3 Error: 0.055137 Iteration 4 Error: 0.024386 3D Fitting completed. Patch alignment time: 12.18(sec) Local motion has been corrected. Process thread exits. Computational time: 23.452623 sec Total time: 33.287498 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00013hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00013hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.847929s Reading file: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00013hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.406137s ........................................ >>>>>>TIME<<<<<< FFT: 0.944311s Defocus_U Defocus_V Angle CCC 10468.73 11222.72 12.44 0.042787 Final Values Defocus_U Defocus_V Angle CCC 10490.60 11253.98 12.75 0.078504 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00007sq_v01_00013hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00013hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 1.000e-01 CC threshold: 0.735 Mean Std: 43.15 7.20 Num Hot pixels: 210 Hot pixel threshold: 86.36 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.029057 Iteration 2 Error: 0.118447 Iteration 3 Error: 0.031937 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.26 0.04 ...... Frame ( 3) shift: -0.52 0.08 ...... Frame ( 4) shift: -0.78 0.12 ...... Frame ( 5) shift: -1.04 0.16 ...... Frame ( 6) shift: -1.19 0.25 ...... Frame ( 7) shift: -1.22 0.37 ...... Frame ( 8) shift: -1.24 0.50 ...... Frame ( 9) shift: -1.27 0.55 ...... Frame ( 10) shift: -1.30 0.54 ...... Frame ( 11) shift: -1.33 0.52 ...... Frame ( 12) shift: -1.31 0.60 ...... Frame ( 13) shift: -1.26 0.79 ...... Frame ( 14) shift: -1.21 0.97 ...... Frame ( 15) shift: -1.16 1.07 ...... Frame ( 16) shift: -1.10 1.09 ...... Frame ( 17) shift: -1.05 1.11 ...... Frame ( 18) shift: -1.02 1.17 ...... Frame ( 19) shift: -1.03 1.26 ...... Frame ( 20) shift: -1.03 1.35 ...... Frame ( 21) shift: -0.99 1.38 ...... Frame ( 22) shift: -0.92 1.33 ...... Frame ( 23) shift: -0.85 1.28 ...... Frame ( 24) shift: -0.81 1.27 ...... Frame ( 25) shift: -0.79 1.29 ...... Frame ( 26) shift: -0.78 1.31 ...... Frame ( 27) shift: -0.76 1.30 ...... Frame ( 28) shift: -0.73 1.25 ...... Frame ( 29) shift: -0.70 1.21 ...... Frame ( 30) shift: -0.65 1.21 ...... Frame ( 31) shift: -0.59 1.26 ...... Frame ( 32) shift: -0.52 1.32 ...... Frame ( 33) shift: -0.47 1.34 ...... Frame ( 34) shift: -0.45 1.35 ...... Frame ( 35) shift: -0.43 1.36 ...... Frame ( 36) shift: -0.42 1.37 ...... Frame ( 37) shift: -0.43 1.40 ...... Frame ( 38) shift: -0.44 1.44 ...... Frame ( 39) shift: -0.46 1.47 ...... Frame ( 40) shift: -0.47 1.50 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.934684 Iteration 2 Error: 0.149539 Iteration 3 Error: 0.032075 Align patch 2 23 left Iteration 1 Error: 1.194556 Iteration 2 Error: 0.160340 Iteration 3 Error: 0.037597 Align patch 3 22 left Iteration 1 Error: 0.661454 Iteration 2 Error: 0.114055 Iteration 3 Error: 0.031202 Align patch 4 21 left Iteration 1 Error: 0.632216 Iteration 2 Error: 0.090240 Iteration 3 Error: 0.028017 Align patch 5 20 left Iteration 1 Error: 0.724975 Iteration 2 Error: 0.112654 Iteration 3 Error: 0.017242 Align patch 6 19 left Iteration 1 Error: 1.074238 Iteration 2 Error: 0.251612 Iteration 3 Error: 0.047881 Align patch 7 18 left Iteration 1 Error: 0.913632 Iteration 2 Error: 0.093032 Iteration 3 Error: 0.019384 Align patch 8 17 left Iteration 1 Error: 0.882285 Iteration 2 Error: 0.214788 Iteration 3 Error: 0.038973 Align patch 9 16 left Iteration 1 Error: 0.517818 Iteration 2 Error: 0.061402 Iteration 3 Error: 0.022152 Align patch 10 15 left Iteration 1 Error: 0.754645 Iteration 2 Error: 0.128613 Iteration 3 Error: 0.018434 Align patch 11 14 left Iteration 1 Error: 0.976305 Iteration 2 Error: 0.188799 Iteration 3 Error: 0.074058 Iteration 4 Error: 0.019736 Align patch 12 13 left Iteration 1 Error: 0.640717 Iteration 2 Error: 0.092455 Iteration 3 Error: 0.017523 Align patch 13 12 left Iteration 1 Error: 0.863212 Iteration 2 Error: 0.119723 Iteration 3 Error: 0.037050 Align patch 14 11 left Iteration 1 Error: 0.750128 Iteration 2 Error: 0.178984 Iteration 3 Error: 0.058669 Iteration 4 Error: 0.017131 Align patch 15 10 left Iteration 1 Error: 0.892398 Iteration 2 Error: 0.166700 Iteration 3 Error: 0.034299 Align patch 16 9 left Iteration 1 Error: 0.809901 Iteration 2 Error: 0.120286 Iteration 3 Error: 0.036874 Align patch 17 8 left Iteration 1 Error: 0.804238 Iteration 2 Error: 0.135816 Iteration 3 Error: 0.043994 Align patch 18 7 left Iteration 1 Error: 0.814890 Iteration 2 Error: 0.180348 Iteration 3 Error: 0.057914 Iteration 4 Error: 0.026588 Align patch 19 6 left Iteration 1 Error: 0.600477 Iteration 2 Error: 0.089149 Iteration 3 Error: 0.028747 Align patch 20 5 left Iteration 1 Error: 0.622386 Iteration 2 Error: 0.124254 Iteration 3 Error: 0.023723 Align patch 21 4 left Iteration 1 Error: 1.389235 Iteration 2 Error: 0.132847 Iteration 3 Error: 0.027046 Align patch 22 3 left Iteration 1 Error: 1.305224 Iteration 2 Error: 0.129561 Iteration 3 Error: 0.032826 Align patch 23 2 left Iteration 1 Error: 1.139230 Iteration 2 Error: 0.152701 Iteration 3 Error: 0.039927 Align patch 24 1 left Iteration 1 Error: 0.736616 Iteration 2 Error: 0.107741 Iteration 3 Error: 0.029294 Align patch 25 0 left Iteration 1 Error: 0.778781 Iteration 2 Error: 0.221242 Iteration 3 Error: 0.050111 Iteration 4 Error: 0.027896 3D Fitting completed. Patch alignment time: 12.38(sec) Local motion has been corrected. Process thread exits. Computational time: 23.737486 sec Total time: 30.934345 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00013hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00013hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.569030s Reading file: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00013hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.463666s ........................................ >>>>>>TIME<<<<<< FFT: 1.010048s Defocus_U Defocus_V Angle CCC 13250.01 12718.74 88.88 0.044055 Final Values Defocus_U Defocus_V Angle CCC 13264.12 12720.35 89.82 0.076777 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00007sq_v01_00013hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00013hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.001e-01 CC threshold: 0.735 Mean Std: 42.84 7.08 Num Hot pixels: 191 Hot pixel threshold: 85.34 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.525453 Iteration 2 Error: 0.074262 Iteration 3 Error: 0.015571 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.23 -0.13 ...... Frame ( 3) shift: -0.47 -0.25 ...... Frame ( 4) shift: -0.70 -0.38 ...... Frame ( 5) shift: -0.94 -0.50 ...... Frame ( 6) shift: -1.08 -0.57 ...... Frame ( 7) shift: -1.12 -0.57 ...... Frame ( 8) shift: -1.16 -0.58 ...... Frame ( 9) shift: -1.16 -0.56 ...... Frame ( 10) shift: -1.12 -0.52 ...... Frame ( 11) shift: -1.09 -0.47 ...... Frame ( 12) shift: -1.05 -0.43 ...... Frame ( 13) shift: -1.02 -0.38 ...... Frame ( 14) shift: -0.99 -0.33 ...... Frame ( 15) shift: -0.94 -0.28 ...... Frame ( 16) shift: -0.86 -0.23 ...... Frame ( 17) shift: -0.79 -0.18 ...... Frame ( 18) shift: -0.75 -0.14 ...... Frame ( 19) shift: -0.76 -0.11 ...... Frame ( 20) shift: -0.76 -0.08 ...... Frame ( 21) shift: -0.74 -0.10 ...... Frame ( 22) shift: -0.69 -0.14 ...... Frame ( 23) shift: -0.64 -0.19 ...... Frame ( 24) shift: -0.59 -0.20 ...... Frame ( 25) shift: -0.55 -0.16 ...... Frame ( 26) shift: -0.51 -0.11 ...... Frame ( 27) shift: -0.51 -0.11 ...... Frame ( 28) shift: -0.53 -0.14 ...... Frame ( 29) shift: -0.56 -0.17 ...... Frame ( 30) shift: -0.59 -0.16 ...... Frame ( 31) shift: -0.62 -0.12 ...... Frame ( 32) shift: -0.66 -0.09 ...... Frame ( 33) shift: -0.65 -0.04 ...... Frame ( 34) shift: -0.61 0.01 ...... Frame ( 35) shift: -0.57 0.07 ...... Frame ( 36) shift: -0.54 0.11 ...... Frame ( 37) shift: -0.53 0.15 ...... Frame ( 38) shift: -0.51 0.19 ...... Frame ( 39) shift: -0.50 0.23 ...... Frame ( 40) shift: -0.49 0.27 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.291153 Iteration 2 Error: 0.172738 Iteration 3 Error: 0.055204 Iteration 4 Error: 0.026363 Align patch 2 23 left Iteration 1 Error: 1.084165 Iteration 2 Error: 0.136476 Iteration 3 Error: 0.026010 Align patch 3 22 left Iteration 1 Error: 1.063643 Iteration 2 Error: 0.195522 Iteration 3 Error: 0.039042 Align patch 4 21 left Iteration 1 Error: 0.790644 Iteration 2 Error: 0.105912 Iteration 3 Error: 0.027604 Align patch 5 20 left Iteration 1 Error: 0.725613 Iteration 2 Error: 0.100093 Iteration 3 Error: 0.018165 Align patch 6 19 left Iteration 1 Error: 1.344419 Iteration 2 Error: 0.224888 Iteration 3 Error: 0.059554 Iteration 4 Error: 0.030586 Align patch 7 18 left Iteration 1 Error: 1.007391 Iteration 2 Error: 0.205746 Iteration 3 Error: 0.041629 Align patch 8 17 left Iteration 1 Error: 0.566354 Iteration 2 Error: 0.092667 Iteration 3 Error: 0.027667 Align patch 9 16 left Iteration 1 Error: 0.700633 Iteration 2 Error: 0.137784 Iteration 3 Error: 0.030493 Align patch 10 15 left Iteration 1 Error: 0.723413 Iteration 2 Error: 0.148999 Iteration 3 Error: 0.032355 Align patch 11 14 left Iteration 1 Error: 0.648068 Iteration 2 Error: 0.094070 Iteration 3 Error: 0.019108 Align patch 12 13 left Iteration 1 Error: 0.710753 Iteration 2 Error: 0.092948 Iteration 3 Error: 0.021674 Align patch 13 12 left Iteration 1 Error: 0.572678 Iteration 2 Error: 0.102909 Iteration 3 Error: 0.038696 Align patch 14 11 left Iteration 1 Error: 0.506841 Iteration 2 Error: 0.060923 Iteration 3 Error: 0.014597 Align patch 15 10 left Iteration 1 Error: 0.983116 Iteration 2 Error: 0.151626 Iteration 3 Error: 0.053475 Iteration 4 Error: 0.018293 Align patch 16 9 left Iteration 1 Error: 0.585809 Iteration 2 Error: 0.187743 Iteration 3 Error: 0.033606 Align patch 17 8 left Iteration 1 Error: 0.505570 Iteration 2 Error: 0.132386 Iteration 3 Error: 0.026396 Align patch 18 7 left Iteration 1 Error: 0.800220 Iteration 2 Error: 0.125809 Iteration 3 Error: 0.025436 Align patch 19 6 left Iteration 1 Error: 0.694279 Iteration 2 Error: 0.104026 Iteration 3 Error: 0.029142 Align patch 20 5 left Iteration 1 Error: 0.630297 Iteration 2 Error: 0.065291 Iteration 3 Error: 0.013567 Align patch 21 4 left Iteration 1 Error: 0.932393 Iteration 2 Error: 0.098450 Iteration 3 Error: 0.021059 Align patch 22 3 left Iteration 1 Error: 0.933268 Iteration 2 Error: 0.096883 Iteration 3 Error: 0.036381 Align patch 23 2 left Iteration 1 Error: 0.732465 Iteration 2 Error: 0.114814 Iteration 3 Error: 0.020119 Align patch 24 1 left Iteration 1 Error: 0.737254 Iteration 2 Error: 0.093123 Iteration 3 Error: 0.026984 Align patch 25 0 left Iteration 1 Error: 0.561436 Iteration 2 Error: 0.073087 Iteration 3 Error: 0.014178 3D Fitting completed. Patch alignment time: 11.81(sec) Local motion has been corrected. Process thread exits. Computational time: 22.893023 sec Total time: 30.330553 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00013hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00013hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.598076s Reading file: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00013hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.460054s ........................................ >>>>>>TIME<<<<<< FFT: 0.976038s Defocus_U Defocus_V Angle CCC 14267.61 15084.01 3.54 0.050611 Final Values Defocus_U Defocus_V Angle CCC 14273.86 15084.01 3.22 0.083298 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00007sq_v01_00013hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00013hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 42.94 7.15 Num Hot pixels: 196 Hot pixel threshold: 85.83 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.755531 Iteration 2 Error: 0.103741 Iteration 3 Error: 0.021891 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.26 -0.01 ...... Frame ( 3) shift: -0.51 -0.01 ...... Frame ( 4) shift: -0.77 -0.02 ...... Frame ( 5) shift: -1.02 -0.02 ...... Frame ( 6) shift: -1.15 0.00 ...... Frame ( 7) shift: -1.14 0.05 ...... Frame ( 8) shift: -1.14 0.10 ...... Frame ( 9) shift: -1.12 0.19 ...... Frame ( 10) shift: -1.08 0.32 ...... Frame ( 11) shift: -1.05 0.45 ...... Frame ( 12) shift: -1.00 0.53 ...... Frame ( 13) shift: -0.93 0.55 ...... Frame ( 14) shift: -0.87 0.58 ...... Frame ( 15) shift: -0.82 0.60 ...... Frame ( 16) shift: -0.79 0.61 ...... Frame ( 17) shift: -0.75 0.62 ...... Frame ( 18) shift: -0.72 0.66 ...... Frame ( 19) shift: -0.70 0.74 ...... Frame ( 20) shift: -0.67 0.82 ...... Frame ( 21) shift: -0.63 0.84 ...... Frame ( 22) shift: -0.58 0.80 ...... Frame ( 23) shift: -0.53 0.76 ...... Frame ( 24) shift: -0.51 0.78 ...... Frame ( 25) shift: -0.54 0.84 ...... Frame ( 26) shift: -0.57 0.90 ...... Frame ( 27) shift: -0.56 0.92 ...... Frame ( 28) shift: -0.51 0.90 ...... Frame ( 29) shift: -0.47 0.88 ...... Frame ( 30) shift: -0.42 0.87 ...... Frame ( 31) shift: -0.35 0.87 ...... Frame ( 32) shift: -0.29 0.87 ...... Frame ( 33) shift: -0.28 0.89 ...... Frame ( 34) shift: -0.33 0.95 ...... Frame ( 35) shift: -0.38 1.01 ...... Frame ( 36) shift: -0.38 1.06 ...... Frame ( 37) shift: -0.34 1.11 ...... Frame ( 38) shift: -0.30 1.15 ...... Frame ( 39) shift: -0.27 1.20 ...... Frame ( 40) shift: -0.23 1.25 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.890446 Iteration 2 Error: 0.175284 Iteration 3 Error: 0.046474 Align patch 2 23 left Iteration 1 Error: 0.793692 Iteration 2 Error: 0.165827 Iteration 3 Error: 0.043401 Align patch 3 22 left Iteration 1 Error: 0.649585 Iteration 2 Error: 0.125394 Iteration 3 Error: 0.030681 Align patch 4 21 left Iteration 1 Error: 0.661548 Iteration 2 Error: 0.110666 Iteration 3 Error: 0.028473 Align patch 5 20 left Iteration 1 Error: 0.637413 Iteration 2 Error: 0.098860 Iteration 3 Error: 0.013563 Align patch 6 19 left Iteration 1 Error: 1.637647 Iteration 2 Error: 0.184346 Iteration 3 Error: 0.057436 Iteration 4 Error: 0.014148 Align patch 7 18 left Iteration 1 Error: 0.925645 Iteration 2 Error: 0.167659 Iteration 3 Error: 0.055515 Iteration 4 Error: 0.015299 Align patch 8 17 left Iteration 1 Error: 0.683944 Iteration 2 Error: 0.130272 Iteration 3 Error: 0.037498 Align patch 9 16 left Iteration 1 Error: 0.781624 Iteration 2 Error: 0.065033 Iteration 3 Error: 0.009407 Align patch 10 15 left Iteration 1 Error: 0.687332 Iteration 2 Error: 0.121128 Iteration 3 Error: 0.017924 Align patch 11 14 left Iteration 1 Error: 0.826566 Iteration 2 Error: 0.092450 Iteration 3 Error: 0.023111 Align patch 12 13 left Iteration 1 Error: 0.705939 Iteration 2 Error: 0.139441 Iteration 3 Error: 0.019960 Align patch 13 12 left Iteration 1 Error: 0.732969 Iteration 2 Error: 0.093553 Iteration 3 Error: 0.023360 Align patch 14 11 left Iteration 1 Error: 1.023726 Iteration 2 Error: 0.132817 Iteration 3 Error: 0.026791 Align patch 15 10 left Iteration 1 Error: 0.598362 Iteration 2 Error: 0.100015 Iteration 3 Error: 0.021989 Align patch 16 9 left Iteration 1 Error: 0.684733 Iteration 2 Error: 0.070222 Iteration 3 Error: 0.015985 Align patch 17 8 left Iteration 1 Error: 0.715004 Iteration 2 Error: 0.129926 Iteration 3 Error: 0.029830 Align patch 18 7 left Iteration 1 Error: 1.052831 Iteration 2 Error: 0.118506 Iteration 3 Error: 0.017932 Align patch 19 6 left Iteration 1 Error: 1.341611 Iteration 2 Error: 0.157549 Iteration 3 Error: 0.041461 Align patch 20 5 left Iteration 1 Error: 0.794571 Iteration 2 Error: 0.252933 Iteration 3 Error: 0.074092 Iteration 4 Error: 0.027317 Align patch 21 4 left Iteration 1 Error: 1.137078 Iteration 2 Error: 0.143833 Iteration 3 Error: 0.043279 Align patch 22 3 left Iteration 1 Error: 0.838651 Iteration 2 Error: 0.131426 Iteration 3 Error: 0.033618 Align patch 23 2 left Iteration 1 Error: 0.742822 Iteration 2 Error: 0.117466 Iteration 3 Error: 0.023262 Align patch 24 1 left Iteration 1 Error: 0.727799 Iteration 2 Error: 0.162776 Iteration 3 Error: 0.046126 Align patch 25 0 left Iteration 1 Error: 0.655493 Iteration 2 Error: 0.116727 Iteration 3 Error: 0.027067 3D Fitting completed. Patch alignment time: 11.14(sec) Local motion has been corrected. Process thread exits. Computational time: 24.524063 sec Total time: 32.118153 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00013hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00013hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.630930s Reading file: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00013hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.822904s ........................................ >>>>>>TIME<<<<<< FFT: 0.934790s Defocus_U Defocus_V Angle CCC 15136.76 14468.75 83.04 0.053800 Final Values Defocus_U Defocus_V Angle CCC 15158.61 14459.40 83.36 0.088767 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00007sq_v01_00014hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00014hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 40.39 6.83 Num Hot pixels: 207 Hot pixel threshold: 81.35 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.280491 Iteration 2 Error: 0.313337 Iteration 3 Error: 0.081593 Iteration 4 Error: 0.032035 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.02 -0.03 ...... Frame ( 3) shift: 0.03 -0.07 ...... Frame ( 4) shift: 0.05 -0.10 ...... Frame ( 5) shift: 0.06 -0.13 ...... Frame ( 6) shift: 0.13 -0.09 ...... Frame ( 7) shift: 0.25 0.01 ...... Frame ( 8) shift: 0.38 0.12 ...... Frame ( 9) shift: 0.47 0.20 ...... Frame ( 10) shift: 0.52 0.25 ...... Frame ( 11) shift: 0.58 0.30 ...... Frame ( 12) shift: 0.65 0.36 ...... Frame ( 13) shift: 0.72 0.42 ...... Frame ( 14) shift: 0.80 0.49 ...... Frame ( 15) shift: 0.85 0.56 ...... Frame ( 16) shift: 0.86 0.65 ...... Frame ( 17) shift: 0.87 0.74 ...... Frame ( 18) shift: 0.93 0.81 ...... Frame ( 19) shift: 1.02 0.87 ...... Frame ( 20) shift: 1.12 0.93 ...... Frame ( 21) shift: 1.18 0.97 ...... Frame ( 22) shift: 1.21 1.01 ...... Frame ( 23) shift: 1.24 1.05 ...... Frame ( 24) shift: 1.31 1.11 ...... Frame ( 25) shift: 1.43 1.19 ...... Frame ( 26) shift: 1.55 1.28 ...... Frame ( 27) shift: 1.67 1.35 ...... Frame ( 28) shift: 1.79 1.41 ...... Frame ( 29) shift: 1.91 1.47 ...... Frame ( 30) shift: 1.95 1.50 ...... Frame ( 31) shift: 1.92 1.51 ...... Frame ( 32) shift: 1.88 1.51 ...... Frame ( 33) shift: 1.91 1.52 ...... Frame ( 34) shift: 2.00 1.52 ...... Frame ( 35) shift: 2.10 1.53 ...... Frame ( 36) shift: 2.19 1.53 ...... Frame ( 37) shift: 2.27 1.54 ...... Frame ( 38) shift: 2.36 1.54 ...... Frame ( 39) shift: 2.44 1.55 ...... Frame ( 40) shift: 2.53 1.55 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.640967 Iteration 2 Error: 0.163169 Iteration 3 Error: 0.066705 Iteration 4 Error: 0.041621 Align patch 2 23 left Iteration 1 Error: 1.511586 Iteration 2 Error: 0.198494 Iteration 3 Error: 0.057850 Iteration 4 Error: 0.019979 Align patch 3 22 left Iteration 1 Error: 0.733543 Iteration 2 Error: 0.193245 Iteration 3 Error: 0.034137 Align patch 4 21 left Iteration 1 Error: 0.904190 Iteration 2 Error: 0.223370 Iteration 3 Error: 0.061900 Iteration 4 Error: 0.020846 Align patch 5 20 left Iteration 1 Error: 0.582082 Iteration 2 Error: 0.069226 Iteration 3 Error: 0.018829 Align patch 6 19 left Iteration 1 Error: 0.907158 Iteration 2 Error: 0.118400 Iteration 3 Error: 0.022593 Align patch 7 18 left Iteration 1 Error: 0.502999 Iteration 2 Error: 0.072000 Iteration 3 Error: 0.021440 Align patch 8 17 left Iteration 1 Error: 0.643852 Iteration 2 Error: 0.090471 Iteration 3 Error: 0.036842 Align patch 9 16 left Iteration 1 Error: 0.800605 Iteration 2 Error: 0.149103 Iteration 3 Error: 0.057814 Iteration 4 Error: 0.020070 Align patch 10 15 left Iteration 1 Error: 0.698240 Iteration 2 Error: 0.134772 Iteration 3 Error: 0.045639 Align patch 11 14 left Iteration 1 Error: 0.816433 Iteration 2 Error: 0.267531 Iteration 3 Error: 0.126822 Iteration 4 Error: 0.080939 Iteration 5 Error: 0.040554 Align patch 12 13 left Iteration 1 Error: 0.896074 Iteration 2 Error: 0.196544 Iteration 3 Error: 0.076743 Iteration 4 Error: 0.032703 Align patch 13 12 left Iteration 1 Error: 0.722205 Iteration 2 Error: 0.107555 Iteration 3 Error: 0.045579 Align patch 14 11 left Iteration 1 Error: 0.714309 Iteration 2 Error: 0.104389 Iteration 3 Error: 0.025828 Align patch 15 10 left Iteration 1 Error: 0.927624 Iteration 2 Error: 0.066664 Iteration 3 Error: 0.016240 Align patch 16 9 left Iteration 1 Error: 0.460661 Iteration 2 Error: 0.121808 Iteration 3 Error: 0.040009 Align patch 17 8 left Iteration 1 Error: 0.524244 Iteration 2 Error: 0.090424 Iteration 3 Error: 0.018126 Align patch 18 7 left Iteration 1 Error: 0.738337 Iteration 2 Error: 0.121921 Iteration 3 Error: 0.020482 Align patch 19 6 left Iteration 1 Error: 0.573460 Iteration 2 Error: 0.071776 Iteration 3 Error: 0.015272 Align patch 20 5 left Iteration 1 Error: 1.270351 Iteration 2 Error: 0.173853 Iteration 3 Error: 0.021643 Align patch 21 4 left Iteration 1 Error: 0.714232 Iteration 2 Error: 0.097470 Iteration 3 Error: 0.022304 Align patch 22 3 left Iteration 1 Error: 0.546033 Iteration 2 Error: 0.092197 Iteration 3 Error: 0.020151 Align patch 23 2 left Iteration 1 Error: 0.758119 Iteration 2 Error: 0.141821 Iteration 3 Error: 0.023295 Align patch 24 1 left Iteration 1 Error: 0.719467 Iteration 2 Error: 0.163331 Iteration 3 Error: 0.048164 Align patch 25 0 left Iteration 1 Error: 0.596329 Iteration 2 Error: 0.080138 Iteration 3 Error: 0.023424 3D Fitting completed. Patch alignment time: 11.96(sec) Local motion has been corrected. Process thread exits. Computational time: 25.903316 sec Total time: 33.372414 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00014hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00014hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.667298s Reading file: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00014hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.066528s ........................................ >>>>>>TIME<<<<<< FFT: 1.155761s Defocus_U Defocus_V Angle CCC 9218.79 10132.85 13.36 0.034461 Final Values Defocus_U Defocus_V Angle CCC 9232.86 10143.80 13.99 0.059604 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00007sq_v01_00014hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00014hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 41.08 6.94 Num Hot pixels: 186 Hot pixel threshold: 82.70 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.713701 Iteration 2 Error: 0.116663 Iteration 3 Error: 0.029175 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.10 -0.05 ...... Frame ( 3) shift: -0.20 -0.09 ...... Frame ( 4) shift: -0.30 -0.14 ...... Frame ( 5) shift: -0.40 -0.18 ...... Frame ( 6) shift: -0.43 -0.13 ...... Frame ( 7) shift: -0.37 0.01 ...... Frame ( 8) shift: -0.31 0.16 ...... Frame ( 9) shift: -0.26 0.25 ...... Frame ( 10) shift: -0.22 0.27 ...... Frame ( 11) shift: -0.19 0.29 ...... Frame ( 12) shift: -0.19 0.32 ...... Frame ( 13) shift: -0.22 0.37 ...... Frame ( 14) shift: -0.25 0.42 ...... Frame ( 15) shift: -0.26 0.47 ...... Frame ( 16) shift: -0.26 0.50 ...... Frame ( 17) shift: -0.26 0.54 ...... Frame ( 18) shift: -0.22 0.55 ...... Frame ( 19) shift: -0.16 0.53 ...... Frame ( 20) shift: -0.10 0.52 ...... Frame ( 21) shift: -0.04 0.50 ...... Frame ( 22) shift: 0.00 0.50 ...... Frame ( 23) shift: 0.05 0.49 ...... Frame ( 24) shift: 0.06 0.49 ...... Frame ( 25) shift: 0.03 0.49 ...... Frame ( 26) shift: 0.01 0.48 ...... Frame ( 27) shift: 0.02 0.53 ...... Frame ( 28) shift: 0.07 0.63 ...... Frame ( 29) shift: 0.12 0.73 ...... Frame ( 30) shift: 0.13 0.81 ...... Frame ( 31) shift: 0.11 0.88 ...... Frame ( 32) shift: 0.09 0.95 ...... Frame ( 33) shift: 0.09 1.04 ...... Frame ( 34) shift: 0.11 1.13 ...... Frame ( 35) shift: 0.12 1.23 ...... Frame ( 36) shift: 0.15 1.24 ...... Frame ( 37) shift: 0.19 1.16 ...... Frame ( 38) shift: 0.23 1.08 ...... Frame ( 39) shift: 0.27 1.01 ...... Frame ( 40) shift: 0.31 0.93 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.796791 Iteration 2 Error: 0.129137 Iteration 3 Error: 0.032625 Align patch 2 23 left Iteration 1 Error: 0.831838 Iteration 2 Error: 0.189159 Iteration 3 Error: 0.036769 Align patch 3 22 left Iteration 1 Error: 0.514618 Iteration 2 Error: 0.110095 Iteration 3 Error: 0.023210 Align patch 4 21 left Iteration 1 Error: 0.395936 Iteration 2 Error: 0.043072 Align patch 5 20 left Iteration 1 Error: 0.746544 Iteration 2 Error: 0.122179 Iteration 3 Error: 0.016550 Align patch 6 19 left Iteration 1 Error: 1.031628 Iteration 2 Error: 0.141423 Iteration 3 Error: 0.041133 Align patch 7 18 left Iteration 1 Error: 0.707730 Iteration 2 Error: 0.128046 Iteration 3 Error: 0.024271 Align patch 8 17 left Iteration 1 Error: 0.626034 Iteration 2 Error: 0.128496 Iteration 3 Error: 0.025790 Align patch 9 16 left Iteration 1 Error: 0.856430 Iteration 2 Error: 0.078390 Iteration 3 Error: 0.014828 Align patch 10 15 left Iteration 1 Error: 0.591545 Iteration 2 Error: 0.091396 Iteration 3 Error: 0.031364 Align patch 11 14 left Iteration 1 Error: 0.773278 Iteration 2 Error: 0.110206 Iteration 3 Error: 0.023485 Align patch 12 13 left Iteration 1 Error: 0.763827 Iteration 2 Error: 0.163472 Iteration 3 Error: 0.029954 Align patch 13 12 left Iteration 1 Error: 0.600904 Iteration 2 Error: 0.070059 Iteration 3 Error: 0.026392 Align patch 14 11 left Iteration 1 Error: 0.641895 Iteration 2 Error: 0.101852 Iteration 3 Error: 0.016978 Align patch 15 10 left Iteration 1 Error: 0.553064 Iteration 2 Error: 0.094021 Iteration 3 Error: 0.016964 Align patch 16 9 left Iteration 1 Error: 0.810797 Iteration 2 Error: 0.106513 Iteration 3 Error: 0.027448 Align patch 17 8 left Iteration 1 Error: 0.722503 Iteration 2 Error: 0.093536 Iteration 3 Error: 0.027105 Align patch 18 7 left Iteration 1 Error: 1.155550 Iteration 2 Error: 0.168058 Iteration 3 Error: 0.051327 Iteration 4 Error: 0.023369 Align patch 19 6 left Iteration 1 Error: 0.625595 Iteration 2 Error: 0.096803 Iteration 3 Error: 0.012132 Align patch 20 5 left Iteration 1 Error: 0.576232 Iteration 2 Error: 0.055380 Iteration 3 Error: 0.016177 Align patch 21 4 left Iteration 1 Error: 0.718306 Iteration 2 Error: 0.151451 Iteration 3 Error: 0.047929 Align patch 22 3 left Iteration 1 Error: 0.915832 Iteration 2 Error: 0.160277 Iteration 3 Error: 0.065928 Iteration 4 Error: 0.020085 Align patch 23 2 left Iteration 1 Error: 0.913077 Iteration 2 Error: 0.104819 Iteration 3 Error: 0.022216 Align patch 24 1 left Iteration 1 Error: 0.891760 Iteration 2 Error: 0.125549 Iteration 3 Error: 0.022054 Align patch 25 0 left Iteration 1 Error: 0.878964 Iteration 2 Error: 0.132144 Iteration 3 Error: 0.031311 3D Fitting completed. Patch alignment time: 11.51(sec) Local motion has been corrected. Process thread exits. Computational time: 23.858030 sec Total time: 30.919109 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00014hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00014hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.478360s Reading file: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00014hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.795498s ........................................ >>>>>>TIME<<<<<< FFT: 0.943771s Defocus_U Defocus_V Angle CCC 13722.90 13218.56 83.45 0.051754 Final Values Defocus_U Defocus_V Angle CCC 13722.90 13218.56 84.08 0.083522 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00007sq_v01_00014hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00014hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 40.53 6.85 Num Hot pixels: 190 Hot pixel threshold: 81.63 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.563108 Iteration 2 Error: 0.082936 Iteration 3 Error: 0.014289 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.04 -0.05 ...... Frame ( 3) shift: -0.09 -0.10 ...... Frame ( 4) shift: -0.13 -0.15 ...... Frame ( 5) shift: -0.18 -0.20 ...... Frame ( 6) shift: -0.19 -0.19 ...... Frame ( 7) shift: -0.17 -0.13 ...... Frame ( 8) shift: -0.15 -0.06 ...... Frame ( 9) shift: -0.11 -0.00 ...... Frame ( 10) shift: -0.05 0.06 ...... Frame ( 11) shift: 0.00 0.12 ...... Frame ( 12) shift: 0.01 0.16 ...... Frame ( 13) shift: -0.02 0.17 ...... Frame ( 14) shift: -0.05 0.18 ...... Frame ( 15) shift: -0.07 0.21 ...... Frame ( 16) shift: -0.09 0.25 ...... Frame ( 17) shift: -0.11 0.29 ...... Frame ( 18) shift: -0.11 0.33 ...... Frame ( 19) shift: -0.08 0.37 ...... Frame ( 20) shift: -0.04 0.41 ...... Frame ( 21) shift: -0.01 0.46 ...... Frame ( 22) shift: 0.02 0.52 ...... Frame ( 23) shift: 0.06 0.58 ...... Frame ( 24) shift: 0.10 0.63 ...... Frame ( 25) shift: 0.14 0.66 ...... Frame ( 26) shift: 0.19 0.70 ...... Frame ( 27) shift: 0.22 0.70 ...... Frame ( 28) shift: 0.23 0.66 ...... Frame ( 29) shift: 0.24 0.63 ...... Frame ( 30) shift: 0.23 0.62 ...... Frame ( 31) shift: 0.20 0.64 ...... Frame ( 32) shift: 0.17 0.66 ...... Frame ( 33) shift: 0.17 0.70 ...... Frame ( 34) shift: 0.18 0.75 ...... Frame ( 35) shift: 0.19 0.80 ...... Frame ( 36) shift: 0.20 0.82 ...... Frame ( 37) shift: 0.20 0.80 ...... Frame ( 38) shift: 0.21 0.79 ...... Frame ( 39) shift: 0.21 0.77 ...... Frame ( 40) shift: 0.22 0.76 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.679725 Iteration 2 Error: 0.115775 Iteration 3 Error: 0.040604 Align patch 2 23 left Iteration 1 Error: 0.596000 Iteration 2 Error: 0.078409 Iteration 3 Error: 0.017642 Align patch 3 22 left Iteration 1 Error: 0.702954 Iteration 2 Error: 0.103809 Iteration 3 Error: 0.025576 Align patch 4 21 left Iteration 1 Error: 0.726078 Iteration 2 Error: 0.133057 Iteration 3 Error: 0.018193 Align patch 5 20 left Iteration 1 Error: 0.681498 Iteration 2 Error: 0.131721 Iteration 3 Error: 0.031358 Align patch 6 19 left Iteration 1 Error: 0.672762 Iteration 2 Error: 0.137173 Iteration 3 Error: 0.025172 Align patch 7 18 left Iteration 1 Error: 0.683930 Iteration 2 Error: 0.107389 Iteration 3 Error: 0.017064 Align patch 8 17 left Iteration 1 Error: 0.776469 Iteration 2 Error: 0.068975 Iteration 3 Error: 0.014492 Align patch 9 16 left Iteration 1 Error: 0.746372 Iteration 2 Error: 0.142372 Iteration 3 Error: 0.056637 Iteration 4 Error: 0.016579 Align patch 10 15 left Iteration 1 Error: 0.907023 Iteration 2 Error: 0.086828 Iteration 3 Error: 0.018108 Align patch 11 14 left Iteration 1 Error: 0.698031 Iteration 2 Error: 0.148402 Iteration 3 Error: 0.028795 Align patch 12 13 left Iteration 1 Error: 0.756257 Iteration 2 Error: 0.056712 Iteration 3 Error: 0.013650 Align patch 13 12 left Iteration 1 Error: 0.405505 Iteration 2 Error: 0.070017 Iteration 3 Error: 0.015883 Align patch 14 11 left Iteration 1 Error: 0.776688 Iteration 2 Error: 0.140544 Iteration 3 Error: 0.022839 Align patch 15 10 left Iteration 1 Error: 0.580826 Iteration 2 Error: 0.095267 Iteration 3 Error: 0.016783 Align patch 16 9 left Iteration 1 Error: 0.663924 Iteration 2 Error: 0.098895 Iteration 3 Error: 0.019451 Align patch 17 8 left Iteration 1 Error: 0.627717 Iteration 2 Error: 0.062577 Iteration 3 Error: 0.011536 Align patch 18 7 left Iteration 1 Error: 0.599899 Iteration 2 Error: 0.072028 Iteration 3 Error: 0.015259 Align patch 19 6 left Iteration 1 Error: 0.861561 Iteration 2 Error: 0.088105 Iteration 3 Error: 0.017669 Align patch 20 5 left Iteration 1 Error: 0.679674 Iteration 2 Error: 0.092246 Iteration 3 Error: 0.019186 Align patch 21 4 left Iteration 1 Error: 0.666596 Iteration 2 Error: 0.082402 Iteration 3 Error: 0.017350 Align patch 22 3 left Iteration 1 Error: 0.649678 Iteration 2 Error: 0.056490 Iteration 3 Error: 0.013591 Align patch 23 2 left Iteration 1 Error: 0.557138 Iteration 2 Error: 0.096077 Iteration 3 Error: 0.017109 Align patch 24 1 left Iteration 1 Error: 0.522218 Iteration 2 Error: 0.082643 Iteration 3 Error: 0.014346 Align patch 25 0 left Iteration 1 Error: 0.550608 Iteration 2 Error: 0.060463 Iteration 3 Error: 0.016717 3D Fitting completed. Patch alignment time: 11.51(sec) Local motion has been corrected. Process thread exits. Computational time: 25.852156 sec Total time: 35.233685 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00014hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00014hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.587981s Reading file: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00014hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.600908s ........................................ >>>>>>TIME<<<<<< FFT: 0.942179s Defocus_U Defocus_V Angle CCC 13660.17 14472.67 5.44 0.049097 Final Values Defocus_U Defocus_V Angle CCC 13655.48 14527.40 5.13 0.076867 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00007sq_v01_00014hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00014hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 41.23 6.92 Num Hot pixels: 207 Hot pixel threshold: 82.77 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.609359 Iteration 2 Error: 0.142152 Iteration 3 Error: 0.022876 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.06 -0.05 ...... Frame ( 3) shift: -0.12 -0.10 ...... Frame ( 4) shift: -0.18 -0.15 ...... Frame ( 5) shift: -0.24 -0.20 ...... Frame ( 6) shift: -0.25 -0.20 ...... Frame ( 7) shift: -0.23 -0.15 ...... Frame ( 8) shift: -0.21 -0.11 ...... Frame ( 9) shift: -0.22 -0.07 ...... Frame ( 10) shift: -0.25 -0.04 ...... Frame ( 11) shift: -0.28 -0.01 ...... Frame ( 12) shift: -0.32 0.02 ...... Frame ( 13) shift: -0.36 0.06 ...... Frame ( 14) shift: -0.41 0.10 ...... Frame ( 15) shift: -0.42 0.14 ...... Frame ( 16) shift: -0.40 0.19 ...... Frame ( 17) shift: -0.39 0.23 ...... Frame ( 18) shift: -0.39 0.31 ...... Frame ( 19) shift: -0.42 0.41 ...... Frame ( 20) shift: -0.44 0.50 ...... Frame ( 21) shift: -0.46 0.56 ...... Frame ( 22) shift: -0.46 0.57 ...... Frame ( 23) shift: -0.46 0.57 ...... Frame ( 24) shift: -0.46 0.61 ...... Frame ( 25) shift: -0.45 0.68 ...... Frame ( 26) shift: -0.44 0.75 ...... Frame ( 27) shift: -0.42 0.77 ...... Frame ( 28) shift: -0.39 0.74 ...... Frame ( 29) shift: -0.36 0.71 ...... Frame ( 30) shift: -0.38 0.74 ...... Frame ( 31) shift: -0.44 0.83 ...... Frame ( 32) shift: -0.50 0.93 ...... Frame ( 33) shift: -0.52 1.00 ...... Frame ( 34) shift: -0.51 1.04 ...... Frame ( 35) shift: -0.49 1.09 ...... Frame ( 36) shift: -0.45 1.11 ...... Frame ( 37) shift: -0.39 1.10 ...... Frame ( 38) shift: -0.33 1.10 ...... Frame ( 39) shift: -0.27 1.10 ...... Frame ( 40) shift: -0.21 1.10 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.142340 Iteration 2 Error: 0.177530 Iteration 3 Error: 0.030078 Align patch 2 23 left Iteration 1 Error: 0.741901 Iteration 2 Error: 0.095317 Iteration 3 Error: 0.026929 Align patch 3 22 left Iteration 1 Error: 0.539721 Iteration 2 Error: 0.079457 Iteration 3 Error: 0.017471 Align patch 4 21 left Iteration 1 Error: 1.012207 Iteration 2 Error: 0.168292 Iteration 3 Error: 0.049940 Align patch 5 20 left Iteration 1 Error: 0.682630 Iteration 2 Error: 0.145248 Iteration 3 Error: 0.022647 Align patch 6 19 left Iteration 1 Error: 0.863185 Iteration 2 Error: 0.114865 Iteration 3 Error: 0.049016 Align patch 7 18 left Iteration 1 Error: 1.032273 Iteration 2 Error: 0.236106 Iteration 3 Error: 0.049395 Align patch 8 17 left Iteration 1 Error: 0.581224 Iteration 2 Error: 0.117976 Iteration 3 Error: 0.026776 Align patch 9 16 left Iteration 1 Error: 0.921191 Iteration 2 Error: 0.082937 Iteration 3 Error: 0.020207 Align patch 10 15 left Iteration 1 Error: 0.607881 Iteration 2 Error: 0.113274 Iteration 3 Error: 0.017987 Align patch 11 14 left Iteration 1 Error: 0.715825 Iteration 2 Error: 0.149686 Iteration 3 Error: 0.037152 Align patch 12 13 left Iteration 1 Error: 0.603828 Iteration 2 Error: 0.110226 Iteration 3 Error: 0.019410 Align patch 13 12 left Iteration 1 Error: 0.760901 Iteration 2 Error: 0.099849 Iteration 3 Error: 0.032678 Align patch 14 11 left Iteration 1 Error: 0.727178 Iteration 2 Error: 0.119893 Iteration 3 Error: 0.023933 Align patch 15 10 left Iteration 1 Error: 0.542622 Iteration 2 Error: 0.129076 Iteration 3 Error: 0.043389 Align patch 16 9 left Iteration 1 Error: 0.777238 Iteration 2 Error: 0.102161 Iteration 3 Error: 0.026423 Align patch 17 8 left Iteration 1 Error: 0.714582 Iteration 2 Error: 0.150685 Iteration 3 Error: 0.037730 Align patch 18 7 left Iteration 1 Error: 0.863955 Iteration 2 Error: 0.120492 Iteration 3 Error: 0.032919 Align patch 19 6 left Iteration 1 Error: 0.588340 Iteration 2 Error: 0.084291 Iteration 3 Error: 0.017260 Align patch 20 5 left Iteration 1 Error: 0.604675 Iteration 2 Error: 0.101383 Iteration 3 Error: 0.027391 Align patch 21 4 left Iteration 1 Error: 0.533385 Iteration 2 Error: 0.100014 Iteration 3 Error: 0.021292 Align patch 22 3 left Iteration 1 Error: 0.899612 Iteration 2 Error: 0.110225 Iteration 3 Error: 0.023574 Align patch 23 2 left Iteration 1 Error: 0.604365 Iteration 2 Error: 0.088402 Iteration 3 Error: 0.024769 Align patch 24 1 left Iteration 1 Error: 0.482072 Iteration 2 Error: 0.037628 Align patch 25 0 left Iteration 1 Error: 0.755365 Iteration 2 Error: 0.079278 Iteration 3 Error: 0.017292 3D Fitting completed. Patch alignment time: 11.10(sec) Local motion has been corrected. Process thread exits. Computational time: 23.839531 sec Total time: 32.600449 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00014hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00014hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.603487s Reading file: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00014hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.651539s ........................................ >>>>>>TIME<<<<<< FFT: 1.062956s Defocus_U Defocus_V Angle CCC 12560.61 12001.98 81.48 0.045936 Final Values Defocus_U Defocus_V Angle CCC 12576.24 12020.76 82.42 0.078746 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00007sq_v01_00015hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00015hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.001e-01 CC threshold: 0.735 Mean Std: 39.43 6.70 Num Hot pixels: 204 Hot pixel threshold: 79.60 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.813670 Iteration 2 Error: 0.157067 Iteration 3 Error: 0.045941 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.06 -0.21 ...... Frame ( 3) shift: -0.11 -0.41 ...... Frame ( 4) shift: -0.17 -0.62 ...... Frame ( 5) shift: -0.23 -0.82 ...... Frame ( 6) shift: -0.24 -0.94 ...... Frame ( 7) shift: -0.20 -0.97 ...... Frame ( 8) shift: -0.16 -1.00 ...... Frame ( 9) shift: -0.11 -0.95 ...... Frame ( 10) shift: -0.06 -0.82 ...... Frame ( 11) shift: -0.01 -0.70 ...... Frame ( 12) shift: 0.04 -0.60 ...... Frame ( 13) shift: 0.08 -0.53 ...... Frame ( 14) shift: 0.13 -0.45 ...... Frame ( 15) shift: 0.21 -0.38 ...... Frame ( 16) shift: 0.31 -0.29 ...... Frame ( 17) shift: 0.42 -0.21 ...... Frame ( 18) shift: 0.45 -0.13 ...... Frame ( 19) shift: 0.40 -0.04 ...... Frame ( 20) shift: 0.35 0.04 ...... Frame ( 21) shift: 0.35 0.09 ...... Frame ( 22) shift: 0.41 0.10 ...... Frame ( 23) shift: 0.46 0.12 ...... Frame ( 24) shift: 0.48 0.11 ...... Frame ( 25) shift: 0.46 0.07 ...... Frame ( 26) shift: 0.44 0.04 ...... Frame ( 27) shift: 0.46 0.07 ...... Frame ( 28) shift: 0.50 0.17 ...... Frame ( 29) shift: 0.54 0.26 ...... Frame ( 30) shift: 0.57 0.30 ...... Frame ( 31) shift: 0.58 0.29 ...... Frame ( 32) shift: 0.58 0.28 ...... Frame ( 33) shift: 0.57 0.32 ...... Frame ( 34) shift: 0.54 0.40 ...... Frame ( 35) shift: 0.50 0.49 ...... Frame ( 36) shift: 0.51 0.53 ...... Frame ( 37) shift: 0.56 0.54 ...... Frame ( 38) shift: 0.60 0.55 ...... Frame ( 39) shift: 0.64 0.56 ...... Frame ( 40) shift: 0.69 0.57 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.784030 Iteration 2 Error: 0.147610 Iteration 3 Error: 0.054379 Iteration 4 Error: 0.016168 Align patch 2 23 left Iteration 1 Error: 0.913551 Iteration 2 Error: 0.200709 Iteration 3 Error: 0.091668 Iteration 4 Error: 0.036689 Align patch 3 22 left Iteration 1 Error: 0.694540 Iteration 2 Error: 0.160292 Iteration 3 Error: 0.044205 Align patch 4 21 left Iteration 1 Error: 0.662639 Iteration 2 Error: 0.154946 Iteration 3 Error: 0.034766 Align patch 5 20 left Iteration 1 Error: 0.887191 Iteration 2 Error: 0.135843 Iteration 3 Error: 0.027898 Align patch 6 19 left Iteration 1 Error: 0.874878 Iteration 2 Error: 0.156374 Iteration 3 Error: 0.039469 Align patch 7 18 left Iteration 1 Error: 0.626118 Iteration 2 Error: 0.124030 Iteration 3 Error: 0.058839 Iteration 4 Error: 0.019919 Align patch 8 17 left Iteration 1 Error: 0.697346 Iteration 2 Error: 0.298807 Iteration 3 Error: 0.063838 Iteration 4 Error: 0.031543 Align patch 9 16 left Iteration 1 Error: 1.074750 Iteration 2 Error: 0.151202 Iteration 3 Error: 0.031597 Align patch 10 15 left Iteration 1 Error: 1.065208 Iteration 2 Error: 0.131606 Iteration 3 Error: 0.017425 Align patch 11 14 left Iteration 1 Error: 0.938853 Iteration 2 Error: 0.140402 Iteration 3 Error: 0.042702 Align patch 12 13 left Iteration 1 Error: 0.819918 Iteration 2 Error: 0.092461 Iteration 3 Error: 0.019460 Align patch 13 12 left Iteration 1 Error: 0.701091 Iteration 2 Error: 0.131254 Iteration 3 Error: 0.040827 Align patch 14 11 left Iteration 1 Error: 0.819058 Iteration 2 Error: 0.142348 Iteration 3 Error: 0.044066 Align patch 15 10 left Iteration 1 Error: 1.023663 Iteration 2 Error: 0.207827 Iteration 3 Error: 0.058137 Iteration 4 Error: 0.030959 Align patch 16 9 left Iteration 1 Error: 0.641820 Iteration 2 Error: 0.121119 Iteration 3 Error: 0.027861 Align patch 17 8 left Iteration 1 Error: 0.669540 Iteration 2 Error: 0.105047 Iteration 3 Error: 0.029791 Align patch 18 7 left Iteration 1 Error: 0.681151 Iteration 2 Error: 0.147944 Iteration 3 Error: 0.035676 Align patch 19 6 left Iteration 1 Error: 0.562597 Iteration 2 Error: 0.141662 Iteration 3 Error: 0.025517 Align patch 20 5 left Iteration 1 Error: 0.526836 Iteration 2 Error: 0.081003 Iteration 3 Error: 0.018057 Align patch 21 4 left Iteration 1 Error: 0.913868 Iteration 2 Error: 0.112143 Iteration 3 Error: 0.025115 Align patch 22 3 left Iteration 1 Error: 0.708445 Iteration 2 Error: 0.114777 Iteration 3 Error: 0.021858 Align patch 23 2 left Iteration 1 Error: 0.935290 Iteration 2 Error: 0.207049 Iteration 3 Error: 0.042434 Align patch 24 1 left Iteration 1 Error: 0.632457 Iteration 2 Error: 0.113875 Iteration 3 Error: 0.032332 Align patch 25 0 left Iteration 1 Error: 0.742945 Iteration 2 Error: 0.139609 Iteration 3 Error: 0.036286 3D Fitting completed. Patch alignment time: 11.87(sec) Local motion has been corrected. Process thread exits. Computational time: 21.643812 sec Total time: 30.316137 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00015hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00015hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.694083s Reading file: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00015hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.662685s ........................................ >>>>>>TIME<<<<<< FFT: 0.930873s Defocus_U Defocus_V Angle CCC 9373.05 10318.36 11.83 0.030081 Final Values Defocus_U Defocus_V Angle CCC 9383.99 10348.11 12.15 0.052903 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00007sq_v01_00015hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00015hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.001e-01 CC threshold: 0.735 Mean Std: 39.90 6.74 Num Hot pixels: 198 Hot pixel threshold: 80.36 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.012033 Iteration 2 Error: 0.206848 Iteration 3 Error: 0.051648 Iteration 4 Error: 0.012001 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.06 -0.01 ...... Frame ( 3) shift: -0.13 -0.02 ...... Frame ( 4) shift: -0.19 -0.04 ...... Frame ( 5) shift: -0.25 -0.05 ...... Frame ( 6) shift: -0.30 -0.03 ...... Frame ( 7) shift: -0.33 0.02 ...... Frame ( 8) shift: -0.36 0.06 ...... Frame ( 9) shift: -0.36 0.14 ...... Frame ( 10) shift: -0.32 0.25 ...... Frame ( 11) shift: -0.28 0.37 ...... Frame ( 12) shift: -0.21 0.45 ...... Frame ( 13) shift: -0.10 0.51 ...... Frame ( 14) shift: 0.01 0.57 ...... Frame ( 15) shift: 0.08 0.66 ...... Frame ( 16) shift: 0.12 0.78 ...... Frame ( 17) shift: 0.16 0.90 ...... Frame ( 18) shift: 0.16 0.99 ...... Frame ( 19) shift: 0.14 1.06 ...... Frame ( 20) shift: 0.11 1.13 ...... Frame ( 21) shift: 0.13 1.23 ...... Frame ( 22) shift: 0.21 1.37 ...... Frame ( 23) shift: 0.28 1.51 ...... Frame ( 24) shift: 0.31 1.62 ...... Frame ( 25) shift: 0.29 1.71 ...... Frame ( 26) shift: 0.27 1.80 ...... Frame ( 27) shift: 0.28 1.87 ...... Frame ( 28) shift: 0.32 1.93 ...... Frame ( 29) shift: 0.36 1.99 ...... Frame ( 30) shift: 0.38 2.01 ...... Frame ( 31) shift: 0.38 1.99 ...... Frame ( 32) shift: 0.37 1.97 ...... Frame ( 33) shift: 0.35 1.98 ...... Frame ( 34) shift: 0.33 2.01 ...... Frame ( 35) shift: 0.31 2.04 ...... Frame ( 36) shift: 0.30 2.08 ...... Frame ( 37) shift: 0.32 2.12 ...... Frame ( 38) shift: 0.33 2.16 ...... Frame ( 39) shift: 0.34 2.20 ...... Frame ( 40) shift: 0.35 2.24 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.575586 Iteration 2 Error: 0.162245 Iteration 3 Error: 0.042322 Align patch 2 23 left Iteration 1 Error: 0.549111 Iteration 2 Error: 0.068374 Iteration 3 Error: 0.016752 Align patch 3 22 left Iteration 1 Error: 0.983761 Iteration 2 Error: 0.194942 Iteration 3 Error: 0.050811 Iteration 4 Error: 0.015732 Align patch 4 21 left Iteration 1 Error: 0.836668 Iteration 2 Error: 0.095323 Iteration 3 Error: 0.016951 Align patch 5 20 left Iteration 1 Error: 0.855503 Iteration 2 Error: 0.142068 Iteration 3 Error: 0.039334 Align patch 6 19 left Iteration 1 Error: 0.910708 Iteration 2 Error: 0.139903 Iteration 3 Error: 0.037835 Align patch 7 18 left Iteration 1 Error: 0.589373 Iteration 2 Error: 0.112083 Iteration 3 Error: 0.028016 Align patch 8 17 left Iteration 1 Error: 0.788039 Iteration 2 Error: 0.182777 Iteration 3 Error: 0.044617 Align patch 9 16 left Iteration 1 Error: 0.460295 Iteration 2 Error: 0.058462 Iteration 3 Error: 0.011888 Align patch 10 15 left Iteration 1 Error: 0.602720 Iteration 2 Error: 0.101235 Iteration 3 Error: 0.018589 Align patch 11 14 left Iteration 1 Error: 0.894825 Iteration 2 Error: 0.234626 Iteration 3 Error: 0.053251 Iteration 4 Error: 0.020684 Align patch 12 13 left Iteration 1 Error: 1.007654 Iteration 2 Error: 0.159186 Iteration 3 Error: 0.045183 Align patch 13 12 left Iteration 1 Error: 0.743231 Iteration 2 Error: 0.180395 Iteration 3 Error: 0.031099 Align patch 14 11 left Iteration 1 Error: 0.641608 Iteration 2 Error: 0.104555 Iteration 3 Error: 0.020308 Align patch 15 10 left Iteration 1 Error: 0.630078 Iteration 2 Error: 0.155512 Iteration 3 Error: 0.040548 Align patch 16 9 left Iteration 1 Error: 0.836826 Iteration 2 Error: 0.122519 Iteration 3 Error: 0.017557 Align patch 17 8 left Iteration 1 Error: 1.209410 Iteration 2 Error: 0.196535 Iteration 3 Error: 0.054964 Iteration 4 Error: 0.019484 Align patch 18 7 left Iteration 1 Error: 0.769935 Iteration 2 Error: 0.111485 Iteration 3 Error: 0.031950 Align patch 19 6 left Iteration 1 Error: 0.924286 Iteration 2 Error: 0.130768 Iteration 3 Error: 0.035269 Align patch 20 5 left Iteration 1 Error: 0.769637 Iteration 2 Error: 0.179848 Iteration 3 Error: 0.048950 Align patch 21 4 left Iteration 1 Error: 0.598753 Iteration 2 Error: 0.106144 Iteration 3 Error: 0.019938 Align patch 22 3 left Iteration 1 Error: 0.617069 Iteration 2 Error: 0.137898 Iteration 3 Error: 0.041292 Align patch 23 2 left Iteration 1 Error: 0.648246 Iteration 2 Error: 0.113165 Iteration 3 Error: 0.033962 Align patch 24 1 left Iteration 1 Error: 1.130994 Iteration 2 Error: 0.134035 Iteration 3 Error: 0.040926 Align patch 25 0 left Iteration 1 Error: 1.127836 Iteration 2 Error: 0.200863 Iteration 3 Error: 0.041953 3D Fitting completed. Patch alignment time: 11.09(sec) Local motion has been corrected. Process thread exits. Computational time: 21.313366 sec Total time: 27.790604 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00015hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00015hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.623588s Reading file: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00015hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.044887s ........................................ >>>>>>TIME<<<<<< FFT: 0.889922s Defocus_U Defocus_V Angle CCC 12909.11 13469.90 0.16 0.045011 Final Values Defocus_U Defocus_V Angle CCC 13487.10 12916.93 89.53 0.071811 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00007sq_v01_00015hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00015hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.998e-02 CC threshold: 0.734 Mean Std: 40.55 6.69 Num Hot pixels: 223 Hot pixel threshold: 80.72 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 23.434582 Iteration 2 Error: 33.385593 Iteration 3 Error: 3.395458 Iteration 4 Error: 0.234928 Iteration 5 Error: 0.040231 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.11 1.69 ...... Frame ( 3) shift: 0.21 3.39 ...... Frame ( 4) shift: 0.32 5.08 ...... Frame ( 5) shift: 0.43 6.77 ...... Frame ( 6) shift: 0.57 8.58 ...... Frame ( 7) shift: 0.76 10.51 ...... Frame ( 8) shift: 0.95 12.44 ...... Frame ( 9) shift: 1.08 14.35 ...... Frame ( 10) shift: 1.17 16.23 ...... Frame ( 11) shift: 1.25 18.11 ...... Frame ( 12) shift: 1.39 19.87 ...... Frame ( 13) shift: 1.58 21.50 ...... Frame ( 14) shift: 1.77 23.13 ...... Frame ( 15) shift: 1.93 24.70 ...... Frame ( 16) shift: 2.08 26.21 ...... Frame ( 17) shift: 2.22 27.71 ...... Frame ( 18) shift: 2.40 29.25 ...... Frame ( 19) shift: 2.62 30.82 ...... Frame ( 20) shift: 2.84 32.38 ...... Frame ( 21) shift: 3.06 33.85 ...... Frame ( 22) shift: 3.27 35.20 ...... Frame ( 23) shift: 3.47 36.55 ...... Frame ( 24) shift: 3.63 37.93 ...... Frame ( 25) shift: 3.73 39.33 ...... Frame ( 26) shift: 3.83 40.73 ...... Frame ( 27) shift: 3.94 42.06 ...... Frame ( 28) shift: 4.04 43.32 ...... Frame ( 29) shift: 4.15 44.59 ...... Frame ( 30) shift: 4.28 45.84 ...... Frame ( 31) shift: 4.43 47.08 ...... Frame ( 32) shift: 4.58 48.32 ...... Frame ( 33) shift: 4.71 49.50 ...... Frame ( 34) shift: 4.83 50.64 ...... Frame ( 35) shift: 4.94 51.78 ...... Frame ( 36) shift: 5.05 52.89 ...... Frame ( 37) shift: 5.15 53.95 ...... Frame ( 38) shift: 5.25 55.02 ...... Frame ( 39) shift: 5.35 56.09 ...... Frame ( 40) shift: 5.45 57.15 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.511920 Iteration 2 Error: 0.310879 Iteration 3 Error: 0.101485 Iteration 4 Error: 0.038947 Align patch 2 23 left Iteration 1 Error: 1.038858 Iteration 2 Error: 0.198738 Iteration 3 Error: 0.088725 Iteration 4 Error: 0.030516 Align patch 3 22 left Iteration 1 Error: 0.860542 Iteration 2 Error: 0.234137 Iteration 3 Error: 0.066802 Iteration 4 Error: 0.018195 Align patch 4 21 left Iteration 1 Error: 1.179276 Iteration 2 Error: 0.157147 Iteration 3 Error: 0.036830 Align patch 5 20 left Iteration 1 Error: 1.362324 Iteration 2 Error: 0.319235 Iteration 3 Error: 0.158822 Iteration 4 Error: 0.072110 Iteration 5 Error: 0.036714 Align patch 6 19 left Iteration 1 Error: 1.654456 Iteration 2 Error: 0.312167 Iteration 3 Error: 0.073203 Iteration 4 Error: 0.030108 Align patch 7 18 left Iteration 1 Error: 1.164723 Iteration 2 Error: 0.237382 Iteration 3 Error: 0.056063 Iteration 4 Error: 0.035337 Align patch 8 17 left Iteration 1 Error: 1.145912 Iteration 2 Error: 0.333806 Iteration 3 Error: 0.119133 Iteration 4 Error: 0.053437 Iteration 5 Error: 0.022565 Align patch 9 16 left Iteration 1 Error: 0.854499 Iteration 2 Error: 0.177675 Iteration 3 Error: 0.054624 Iteration 4 Error: 0.027697 Align patch 10 15 left Iteration 1 Error: 1.217650 Iteration 2 Error: 0.209059 Iteration 3 Error: 0.086863 Iteration 4 Error: 0.036258 Align patch 11 14 left Iteration 1 Error: 1.168460 Iteration 2 Error: 0.141481 Iteration 3 Error: 0.047621 Align patch 12 13 left Iteration 1 Error: 1.725991 Iteration 2 Error: 0.182566 Iteration 3 Error: 0.053807 Iteration 4 Error: 0.019409 Align patch 13 12 left Iteration 1 Error: 1.129626 Iteration 2 Error: 0.301133 Iteration 3 Error: 0.102646 Iteration 4 Error: 0.061183 Iteration 5 Error: 0.017995 Align patch 14 11 left Iteration 1 Error: 1.046206 Iteration 2 Error: 0.227196 Iteration 3 Error: 0.056551 Iteration 4 Error: 0.019573 Align patch 15 10 left Iteration 1 Error: 0.850195 Iteration 2 Error: 0.377536 Iteration 3 Error: 0.149090 Iteration 4 Error: 0.095671 Iteration 5 Error: 0.030547 Align patch 16 9 left Iteration 1 Error: 1.251396 Iteration 2 Error: 0.299341 Iteration 3 Error: 0.139388 Iteration 4 Error: 0.044298 Align patch 17 8 left Iteration 1 Error: 0.997112 Iteration 2 Error: 0.308485 Iteration 3 Error: 0.089644 Iteration 4 Error: 0.039999 Align patch 18 7 left Iteration 1 Error: 0.882308 Iteration 2 Error: 0.219529 Iteration 3 Error: 0.076652 Iteration 4 Error: 0.036950 Align patch 19 6 left Iteration 1 Error: 1.107108 Iteration 2 Error: 0.199470 Iteration 3 Error: 0.083838 Iteration 4 Error: 0.024901 Align patch 20 5 left Iteration 1 Error: 1.245895 Iteration 2 Error: 0.206782 Iteration 3 Error: 0.078049 Iteration 4 Error: 0.043511 Align patch 21 4 left Iteration 1 Error: 1.565157 Iteration 2 Error: 0.314376 Iteration 3 Error: 0.125527 Iteration 4 Error: 0.042557 Align patch 22 3 left Iteration 1 Error: 0.948016 Iteration 2 Error: 0.273335 Iteration 3 Error: 0.097782 Iteration 4 Error: 0.032043 Align patch 23 2 left Iteration 1 Error: 1.448287 Iteration 2 Error: 0.185300 Iteration 3 Error: 0.039586 Align patch 24 1 left Iteration 1 Error: 1.238677 Iteration 2 Error: 0.191851 Iteration 3 Error: 0.049792 Align patch 25 0 left Iteration 1 Error: 1.535555 Iteration 2 Error: 0.383580 Iteration 3 Error: 0.107605 Iteration 4 Error: 0.055711 Iteration 5 Error: 0.017735 3D Fitting completed. Patch alignment time: 12.96(sec) Local motion has been corrected. Process thread exits. Computational time: 23.525999 sec Total time: 29.189585 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00015hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00015hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.473791s Reading file: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00015hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.557361s ........................................ >>>>>>TIME<<<<<< FFT: 0.907020s Defocus_U Defocus_V Angle CCC 14443.39 15310.60 4.52 0.087219 Final Values Defocus_U Defocus_V Angle CCC 14437.13 15326.24 4.21 0.157014 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00007sq_v01_00015hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00015hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 40.61 6.78 Num Hot pixels: 207 Hot pixel threshold: 81.31 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.698552 Iteration 2 Error: 0.790148 Iteration 3 Error: 0.329418 Iteration 4 Error: 0.123597 Iteration 5 Error: 0.049456 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.15 0.05 ...... Frame ( 3) shift: -0.30 0.09 ...... Frame ( 4) shift: -0.45 0.14 ...... Frame ( 5) shift: -0.60 0.18 ...... Frame ( 6) shift: -0.69 0.30 ...... Frame ( 7) shift: -0.72 0.49 ...... Frame ( 8) shift: -0.75 0.68 ...... Frame ( 9) shift: -0.77 0.92 ...... Frame ( 10) shift: -0.77 1.22 ...... Frame ( 11) shift: -0.78 1.53 ...... Frame ( 12) shift: -0.81 1.79 ...... Frame ( 13) shift: -0.86 2.02 ...... Frame ( 14) shift: -0.92 2.25 ...... Frame ( 15) shift: -0.94 2.50 ...... Frame ( 16) shift: -0.93 2.77 ...... Frame ( 17) shift: -0.92 3.04 ...... Frame ( 18) shift: -0.95 3.26 ...... Frame ( 19) shift: -1.03 3.42 ...... Frame ( 20) shift: -1.11 3.58 ...... Frame ( 21) shift: -1.14 3.75 ...... Frame ( 22) shift: -1.12 3.94 ...... Frame ( 23) shift: -1.10 4.14 ...... Frame ( 24) shift: -1.08 4.35 ...... Frame ( 25) shift: -1.05 4.58 ...... Frame ( 26) shift: -1.03 4.82 ...... Frame ( 27) shift: -1.04 5.04 ...... Frame ( 28) shift: -1.08 5.25 ...... Frame ( 29) shift: -1.13 5.46 ...... Frame ( 30) shift: -1.14 5.67 ...... Frame ( 31) shift: -1.10 5.88 ...... Frame ( 32) shift: -1.06 6.09 ...... Frame ( 33) shift: -1.02 6.22 ...... Frame ( 34) shift: -0.97 6.26 ...... Frame ( 35) shift: -0.93 6.30 ...... Frame ( 36) shift: -0.86 6.46 ...... Frame ( 37) shift: -0.77 6.75 ...... Frame ( 38) shift: -0.68 7.03 ...... Frame ( 39) shift: -0.59 7.32 ...... Frame ( 40) shift: -0.50 7.61 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.203037 Iteration 2 Error: 0.315494 Iteration 3 Error: 0.097212 Iteration 4 Error: 0.041632 Align patch 2 23 left Iteration 1 Error: 0.934456 Iteration 2 Error: 0.356331 Iteration 3 Error: 0.123645 Iteration 4 Error: 0.060942 Iteration 5 Error: 0.025060 Align patch 3 22 left Iteration 1 Error: 1.056728 Iteration 2 Error: 0.242277 Iteration 3 Error: 0.085775 Iteration 4 Error: 0.038008 Align patch 4 21 left Iteration 1 Error: 1.115735 Iteration 2 Error: 0.279903 Iteration 3 Error: 0.106267 Iteration 4 Error: 0.045374 Align patch 5 20 left Iteration 1 Error: 1.141769 Iteration 2 Error: 0.173592 Iteration 3 Error: 0.069930 Iteration 4 Error: 0.018886 Align patch 6 19 left Iteration 1 Error: 0.794180 Iteration 2 Error: 0.216027 Iteration 3 Error: 0.057572 Iteration 4 Error: 0.030074 Align patch 7 18 left Iteration 1 Error: 0.952784 Iteration 2 Error: 0.334330 Iteration 3 Error: 0.104141 Iteration 4 Error: 0.065548 Iteration 5 Error: 0.027289 Align patch 8 17 left Iteration 1 Error: 0.877741 Iteration 2 Error: 0.308229 Iteration 3 Error: 0.092108 Iteration 4 Error: 0.035905 Align patch 9 16 left Iteration 1 Error: 0.999295 Iteration 2 Error: 0.274173 Iteration 3 Error: 0.092696 Iteration 4 Error: 0.039656 Align patch 10 15 left Iteration 1 Error: 0.901259 Iteration 2 Error: 0.152550 Iteration 3 Error: 0.053924 Iteration 4 Error: 0.012959 Align patch 11 14 left Iteration 1 Error: 0.966514 Iteration 2 Error: 0.159429 Iteration 3 Error: 0.062811 Iteration 4 Error: 0.016172 Align patch 12 13 left Iteration 1 Error: 1.251901 Iteration 2 Error: 0.351405 Iteration 3 Error: 0.155872 Iteration 4 Error: 0.061305 Iteration 5 Error: 0.052533 Align patch 12 13 left Iteration 1 Error: 1.060828 Iteration 2 Error: 0.099529 Iteration 3 Error: 0.026579 Align patch 13 12 left Iteration 1 Error: 0.750988 Iteration 2 Error: 0.157335 Iteration 3 Error: 0.058505 Iteration 4 Error: 0.019633 Align patch 14 11 left Iteration 1 Error: 0.631042 Iteration 2 Error: 0.238896 Iteration 3 Error: 0.068853 Iteration 4 Error: 0.038633 Align patch 15 10 left Iteration 1 Error: 1.231527 Iteration 2 Error: 0.186582 Iteration 3 Error: 0.087375 Iteration 4 Error: 0.019823 Align patch 16 9 left Iteration 1 Error: 1.067107 Iteration 2 Error: 0.333451 Iteration 3 Error: 0.124654 Iteration 4 Error: 0.057860 Iteration 5 Error: 0.025998 Align patch 17 8 left Iteration 1 Error: 0.829055 Iteration 2 Error: 0.141204 Iteration 3 Error: 0.051892 Iteration 4 Error: 0.016482 Align patch 18 7 left Iteration 1 Error: 1.136585 Iteration 2 Error: 0.163044 Iteration 3 Error: 0.031273 Align patch 19 6 left Iteration 1 Error: 1.490411 Iteration 2 Error: 0.206020 Iteration 3 Error: 0.050853 Iteration 4 Error: 0.017328 Align patch 20 5 left Iteration 1 Error: 1.639409 Iteration 2 Error: 0.265375 Iteration 3 Error: 0.067380 Iteration 4 Error: 0.025148 Align patch 21 4 left Iteration 1 Error: 0.635518 Iteration 2 Error: 0.152781 Iteration 3 Error: 0.088171 Iteration 4 Error: 0.033696 Align patch 22 3 left Iteration 1 Error: 0.921185 Iteration 2 Error: 0.267914 Iteration 3 Error: 0.060893 Iteration 4 Error: 0.027158 Align patch 23 2 left Iteration 1 Error: 0.787569 Iteration 2 Error: 0.159551 Iteration 3 Error: 0.056176 Iteration 4 Error: 0.015018 Align patch 24 1 left Iteration 1 Error: 0.682440 Iteration 2 Error: 0.093393 Iteration 3 Error: 0.021546 Align patch 25 0 left Iteration 1 Error: 0.685159 Iteration 2 Error: 0.190208 Iteration 3 Error: 0.058766 Iteration 4 Error: 0.022946 3D Fitting completed. Patch alignment time: 13.28(sec) Local motion has been corrected. Process thread exits. Computational time: 24.222818 sec Total time: 31.507303 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00015hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00015hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.598093s Reading file: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00015hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.376806s ........................................ >>>>>>TIME<<<<<< FFT: 1.008370s Defocus_U Defocus_V Angle CCC 10896.49 10318.36 87.20 0.047926 Final Values Defocus_U Defocus_V Angle CCC 10926.17 10313.67 87.52 0.082421 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00007sq_v01_00016hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00016hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 37.85 6.82 Num Hot pixels: 182 Hot pixel threshold: 78.75 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.439414 Iteration 2 Error: 1.051800 Iteration 3 Error: 3.882910 Iteration 4 Error: 2.671219 Iteration 5 Error: 1.560753 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.06 -0.47 ...... Frame ( 3) shift: -0.12 -0.94 ...... Frame ( 4) shift: -0.18 -1.41 ...... Frame ( 5) shift: -0.24 -1.88 ...... Frame ( 6) shift: -0.36 -2.37 ...... Frame ( 7) shift: -0.53 -2.87 ...... Frame ( 8) shift: -0.71 -3.37 ...... Frame ( 9) shift: -0.83 -3.49 ...... Frame ( 10) shift: -0.89 -3.22 ...... Frame ( 11) shift: -0.95 -2.96 ...... Frame ( 12) shift: -0.98 -2.49 ...... Frame ( 13) shift: -0.98 -1.81 ...... Frame ( 14) shift: -0.98 -1.13 ...... Frame ( 15) shift: -0.87 -0.62 ...... Frame ( 16) shift: -0.64 -0.27 ...... Frame ( 17) shift: -0.42 0.07 ...... Frame ( 18) shift: -0.32 0.39 ...... Frame ( 19) shift: -0.35 0.68 ...... Frame ( 20) shift: -0.38 0.98 ...... Frame ( 21) shift: -0.42 1.20 ...... Frame ( 22) shift: -0.48 1.34 ...... Frame ( 23) shift: -0.54 1.49 ...... Frame ( 24) shift: -0.52 1.63 ...... Frame ( 25) shift: -0.41 1.77 ...... Frame ( 26) shift: -0.30 1.90 ...... Frame ( 27) shift: -0.16 2.08 ...... Frame ( 28) shift: 0.01 2.29 ...... Frame ( 29) shift: 0.18 2.50 ...... Frame ( 30) shift: 0.32 2.96 ...... Frame ( 31) shift: 0.44 3.66 ...... Frame ( 32) shift: 0.56 4.36 ...... Frame ( 33) shift: 0.67 5.11 ...... Frame ( 34) shift: 0.77 5.90 ...... Frame ( 35) shift: 0.87 6.70 ...... Frame ( 36) shift: 0.97 7.55 ...... Frame ( 37) shift: 1.07 8.46 ...... Frame ( 38) shift: 1.17 9.37 ...... Frame ( 39) shift: 1.27 10.28 ...... Frame ( 40) shift: 1.37 11.19 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 6.645469 Iteration 2 Error: 18.328907 Iteration 3 Error: 16.551165 Iteration 4 Error: 18.245165 Iteration 5 Error: 1.986223 Align patch 1 24 left Iteration 1 Error: 17.610439 Iteration 2 Error: 7.771931 Iteration 3 Error: 5.500865 Iteration 4 Error: 2.206177 Iteration 5 Error: 1.413069 Align patch 2 23 left Iteration 1 Error: 18.564840 Iteration 2 Error: 12.633786 Iteration 3 Error: 7.956483 Iteration 4 Error: 3.555179 Iteration 5 Error: 2.615341 Align patch 2 23 left Iteration 1 Error: 82.880287 Iteration 2 Error: 75.771423 Iteration 3 Error: 53.506226 Iteration 4 Error: 47.435307 Iteration 5 Error: 40.346729 Align patch 3 22 left Iteration 1 Error: 3.989993 Iteration 2 Error: 2.404416 Iteration 3 Error: 1.024052 Iteration 4 Error: 0.685110 Iteration 5 Error: 0.424791 Align patch 3 22 left Iteration 1 Error: 81.317276 Iteration 2 Error: 56.794521 Iteration 3 Error: 30.924273 Iteration 4 Error: 27.561274 Iteration 5 Error: 17.566839 Align patch 4 21 left Iteration 1 Error: 1.935725 Iteration 2 Error: 1.153222 Iteration 3 Error: 0.722992 Iteration 4 Error: 0.684709 Iteration 5 Error: 0.488461 Align patch 4 21 left Iteration 1 Error: 2.970801 Iteration 2 Error: 2.423358 Iteration 3 Error: 0.983947 Iteration 4 Error: 0.456045 Iteration 5 Error: 0.230618 Align patch 5 20 left Iteration 1 Error: 2.182416 Iteration 2 Error: 1.209208 Iteration 3 Error: 0.301730 Iteration 4 Error: 0.214449 Iteration 5 Error: 0.073736 Align patch 5 20 left Iteration 1 Error: 2.483509 Iteration 2 Error: 2.114821 Iteration 3 Error: 0.593012 Iteration 4 Error: 0.386948 Iteration 5 Error: 0.178455 Align patch 6 19 left Iteration 1 Error: 16.122728 Iteration 2 Error: 18.198498 Iteration 3 Error: 26.548273 Iteration 4 Error: 29.628012 Iteration 5 Error: 12.882770 Align patch 6 19 left Iteration 1 Error: 22.225033 Iteration 2 Error: 12.797030 Iteration 3 Error: 4.195995 Iteration 4 Error: 1.634592 Iteration 5 Error: 1.168016 Align patch 7 18 left Iteration 1 Error: 36.966110 Iteration 2 Error: 36.682167 Iteration 3 Error: 26.774261 Iteration 4 Error: 19.345415 Iteration 5 Error: 16.641586 Align patch 7 18 left Iteration 1 Error: 82.381500 Iteration 2 Error: 28.976542 Iteration 3 Error: 22.873814 Iteration 4 Error: 20.106329 Iteration 5 Error: 20.876753 Align patch 8 17 left Iteration 1 Error: 37.664482 Iteration 2 Error: 22.425892 Iteration 3 Error: 35.170216 Iteration 4 Error: 34.193657 Iteration 5 Error: 28.247173 Align patch 8 17 left Iteration 1 Error: 83.313774 Iteration 2 Error: 56.543594 Iteration 3 Error: 31.811907 Iteration 4 Error: 27.984341 Iteration 5 Error: 18.518612 Align patch 9 16 left Iteration 1 Error: 4.210459 Iteration 2 Error: 2.016142 Iteration 3 Error: 2.246833 Iteration 4 Error: 2.556602 Iteration 5 Error: 5.064795 Align patch 9 16 left Iteration 1 Error: 3.501897 Iteration 2 Error: 2.390366 Iteration 3 Error: 1.222993 Iteration 4 Error: 0.765012 Iteration 5 Error: 0.519242 Align patch 10 15 left Iteration 1 Error: 2.891020 Iteration 2 Error: 1.644140 Iteration 3 Error: 0.599729 Iteration 4 Error: 0.362347 Iteration 5 Error: 0.163270 Align patch 10 15 left Iteration 1 Error: 2.854042 Iteration 2 Error: 1.726578 Iteration 3 Error: 0.527609 Iteration 4 Error: 0.408908 Iteration 5 Error: 0.245403 Align patch 11 14 left Iteration 1 Error: 4.933777 Iteration 2 Error: 4.715603 Iteration 3 Error: 2.746127 Iteration 4 Error: 1.963227 Iteration 5 Error: 1.889770 Align patch 11 14 left Iteration 1 Error: 4.152366 Iteration 2 Error: 1.813620 Iteration 3 Error: 1.048467 Iteration 4 Error: 0.719620 Iteration 5 Error: 0.693340 Align patch 12 13 left Iteration 1 Error: 6.380946 Iteration 2 Error: 3.252455 Iteration 3 Error: 1.885279 Iteration 4 Error: 1.033231 Iteration 5 Error: 1.146524 Align patch 12 13 left Iteration 1 Error: 7.759798 Iteration 2 Error: 3.248858 Iteration 3 Error: 1.628215 Iteration 4 Error: 1.176231 Iteration 5 Error: 0.840543 Align patch 13 12 left Iteration 1 Error: 24.996027 Iteration 2 Error: 10.129204 Iteration 3 Error: 2.333138 Iteration 4 Error: 1.254405 Iteration 5 Error: 0.744822 Align patch 13 12 left Iteration 1 Error: 8.365870 Iteration 2 Error: 6.152567 Iteration 3 Error: 2.568525 Iteration 4 Error: 1.604074 Iteration 5 Error: 0.876661 Align patch 14 11 left Iteration 1 Error: 2.929243 Iteration 2 Error: 2.556897 Iteration 3 Error: 10.718763 Iteration 4 Error: 4.778504 Iteration 5 Error: 1.613924 Align patch 14 11 left Iteration 1 Error: 3.296671 Iteration 2 Error: 3.150136 Iteration 3 Error: 2.341991 Iteration 4 Error: 1.616796 Iteration 5 Error: 1.065481 Align patch 15 10 left Iteration 1 Error: 2.482850 Iteration 2 Error: 1.228504 Iteration 3 Error: 0.592631 Iteration 4 Error: 0.464928 Iteration 5 Error: 0.330182 Align patch 15 10 left Iteration 1 Error: 3.158836 Iteration 2 Error: 1.960951 Iteration 3 Error: 1.159571 Iteration 4 Error: 1.031375 Iteration 5 Error: 0.876375 Align patch 16 9 left Iteration 1 Error: 1.525907 Iteration 2 Error: 1.059974 Iteration 3 Error: 0.695266 Iteration 4 Error: 0.594166 Iteration 5 Error: 0.758476 Align patch 16 9 left Iteration 1 Error: 2.700331 Iteration 2 Error: 1.292697 Iteration 3 Error: 0.703621 Iteration 4 Error: 0.546946 Iteration 5 Error: 0.385172 Align patch 17 8 left Iteration 1 Error: 3.795918 Iteration 2 Error: 1.963378 Iteration 3 Error: 1.453974 Iteration 4 Error: 0.897630 Iteration 5 Error: 1.142912 Align patch 17 8 left Iteration 1 Error: 2.980561 Iteration 2 Error: 1.287707 Iteration 3 Error: 0.877718 Iteration 4 Error: 0.728963 Iteration 5 Error: 0.405247 Align patch 18 7 left Iteration 1 Error: 3.093296 Iteration 2 Error: 0.896276 Iteration 3 Error: 0.562565 Iteration 4 Error: 0.570439 Iteration 5 Error: 0.480403 Align patch 18 7 left Iteration 1 Error: 3.220122 Iteration 2 Error: 1.426086 Iteration 3 Error: 0.772753 Iteration 4 Error: 0.559352 Iteration 5 Error: 0.385333 Align patch 19 6 left Iteration 1 Error: 5.373783 Iteration 2 Error: 0.863144 Iteration 3 Error: 0.518722 Iteration 4 Error: 0.328222 Iteration 5 Error: 0.275063 Align patch 19 6 left Iteration 1 Error: 2.182069 Iteration 2 Error: 0.837886 Iteration 3 Error: 0.354957 Iteration 4 Error: 0.247422 Iteration 5 Error: 0.166528 Align patch 20 5 left Iteration 1 Error: 1.623414 Iteration 2 Error: 0.901466 Iteration 3 Error: 0.242215 Iteration 4 Error: 0.376328 Iteration 5 Error: 0.169950 Align patch 20 5 left Iteration 1 Error: 1.487168 Iteration 2 Error: 0.521671 Iteration 3 Error: 0.231126 Iteration 4 Error: 0.095135 Iteration 5 Error: 0.049796 Align patch 21 4 left Iteration 1 Error: 1.974939 Iteration 2 Error: 0.690544 Iteration 3 Error: 0.442807 Iteration 4 Error: 0.555142 Iteration 5 Error: 0.412165 Align patch 21 4 left Iteration 1 Error: 1.846187 Iteration 2 Error: 0.907237 Iteration 3 Error: 0.466427 Iteration 4 Error: 0.410644 Iteration 5 Error: 0.250605 Align patch 22 3 left Iteration 1 Error: 1.670837 Iteration 2 Error: 0.714115 Iteration 3 Error: 0.665774 Iteration 4 Error: 0.522603 Iteration 5 Error: 0.419902 Align patch 22 3 left Iteration 1 Error: 2.076509 Iteration 2 Error: 1.390908 Iteration 3 Error: 1.049035 Iteration 4 Error: 0.587064 Iteration 5 Error: 0.381015 Align patch 23 2 left Iteration 1 Error: 2.872945 Iteration 2 Error: 2.681999 Iteration 3 Error: 1.025703 Iteration 4 Error: 1.007996 Iteration 5 Error: 0.673051 Align patch 23 2 left Iteration 1 Error: 1.507283 Iteration 2 Error: 0.984392 Iteration 3 Error: 0.715650 Iteration 4 Error: 0.491157 Iteration 5 Error: 0.336516 Align patch 24 1 left Iteration 1 Error: 2.594331 Iteration 2 Error: 1.058465 Iteration 3 Error: 0.754923 Iteration 4 Error: 0.497109 Iteration 5 Error: 0.704012 Align patch 24 1 left Iteration 1 Error: 1.548805 Iteration 2 Error: 0.835012 Iteration 3 Error: 0.397102 Iteration 4 Error: 0.314909 Iteration 5 Error: 0.199424 Align patch 25 0 left Iteration 1 Error: 1.372007 Iteration 2 Error: 0.368071 Iteration 3 Error: 0.221035 Iteration 4 Error: 0.135074 Iteration 5 Error: 0.096941 Align patch 25 0 left Iteration 1 Error: 1.142244 Iteration 2 Error: 0.358662 Iteration 3 Error: 0.196304 Iteration 4 Error: 0.102432 Iteration 5 Error: 0.066047 3D Fitting completed. Patch alignment time: 32.64(sec) Local motion has been corrected. Process thread exits. Computational time: 43.624451 sec Total time: 51.150600 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00016hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00016hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.561184s Reading file: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00016hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.771816s ........................................ >>>>>>TIME<<<<<< FFT: 0.906451s Defocus_U Defocus_V Angle CCC 9779.31 10392.60 7.43 0.070215 Final Values Defocus_U Defocus_V Angle CCC 9766.81 10423.86 6.49 0.135330 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00007sq_v01_00016hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00016hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.998e-02 CC threshold: 0.734 Mean Std: 39.79 6.73 Num Hot pixels: 191 Hot pixel threshold: 80.16 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.498799 Iteration 2 Error: 0.240012 Iteration 3 Error: 0.069108 Iteration 4 Error: 0.023643 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.04 -0.16 ...... Frame ( 3) shift: -0.09 -0.32 ...... Frame ( 4) shift: -0.13 -0.49 ...... Frame ( 5) shift: -0.18 -0.65 ...... Frame ( 6) shift: -0.20 -0.68 ...... Frame ( 7) shift: -0.21 -0.59 ...... Frame ( 8) shift: -0.22 -0.50 ...... Frame ( 9) shift: -0.15 -0.35 ...... Frame ( 10) shift: 0.00 -0.13 ...... Frame ( 11) shift: 0.15 0.09 ...... Frame ( 12) shift: 0.23 0.29 ...... Frame ( 13) shift: 0.23 0.47 ...... Frame ( 14) shift: 0.23 0.65 ...... Frame ( 15) shift: 0.24 0.78 ...... Frame ( 16) shift: 0.24 0.86 ...... Frame ( 17) shift: 0.24 0.94 ...... Frame ( 18) shift: 0.23 1.02 ...... Frame ( 19) shift: 0.20 1.11 ...... Frame ( 20) shift: 0.17 1.19 ...... Frame ( 21) shift: 0.15 1.29 ...... Frame ( 22) shift: 0.14 1.39 ...... Frame ( 23) shift: 0.13 1.50 ...... Frame ( 24) shift: 0.11 1.60 ...... Frame ( 25) shift: 0.08 1.70 ...... Frame ( 26) shift: 0.05 1.80 ...... Frame ( 27) shift: -0.00 1.87 ...... Frame ( 28) shift: -0.07 1.90 ...... Frame ( 29) shift: -0.14 1.93 ...... Frame ( 30) shift: -0.12 1.94 ...... Frame ( 31) shift: -0.03 1.92 ...... Frame ( 32) shift: 0.07 1.90 ...... Frame ( 33) shift: 0.06 1.92 ...... Frame ( 34) shift: -0.05 1.98 ...... Frame ( 35) shift: -0.16 2.05 ...... Frame ( 36) shift: -0.23 2.09 ...... Frame ( 37) shift: -0.24 2.10 ...... Frame ( 38) shift: -0.25 2.11 ...... Frame ( 39) shift: -0.27 2.13 ...... Frame ( 40) shift: -0.28 2.14 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.784902 Iteration 2 Error: 0.130010 Iteration 3 Error: 0.023065 Align patch 2 23 left Iteration 1 Error: 0.984831 Iteration 2 Error: 0.276763 Iteration 3 Error: 0.118758 Iteration 4 Error: 0.048319 Align patch 3 22 left Iteration 1 Error: 0.739766 Iteration 2 Error: 0.127936 Iteration 3 Error: 0.048937 Align patch 4 21 left Iteration 1 Error: 0.746342 Iteration 2 Error: 0.194226 Iteration 3 Error: 0.069036 Iteration 4 Error: 0.023477 Align patch 5 20 left Iteration 1 Error: 1.407930 Iteration 2 Error: 0.210357 Iteration 3 Error: 0.055922 Iteration 4 Error: 0.018329 Align patch 6 19 left Iteration 1 Error: 0.925307 Iteration 2 Error: 0.191744 Iteration 3 Error: 0.059298 Iteration 4 Error: 0.021725 Align patch 7 18 left Iteration 1 Error: 0.832797 Iteration 2 Error: 0.252816 Iteration 3 Error: 0.087514 Iteration 4 Error: 0.038493 Align patch 8 17 left Iteration 1 Error: 0.919807 Iteration 2 Error: 0.126393 Iteration 3 Error: 0.029317 Align patch 9 16 left Iteration 1 Error: 0.761075 Iteration 2 Error: 0.146180 Iteration 3 Error: 0.030371 Align patch 10 15 left Iteration 1 Error: 0.904183 Iteration 2 Error: 0.193198 Iteration 3 Error: 0.045898 Align patch 11 14 left Iteration 1 Error: 0.747452 Iteration 2 Error: 0.246644 Iteration 3 Error: 0.072351 Iteration 4 Error: 0.036363 Align patch 12 13 left Iteration 1 Error: 0.478076 Iteration 2 Error: 0.060221 Iteration 3 Error: 0.020067 Align patch 13 12 left Iteration 1 Error: 1.128682 Iteration 2 Error: 0.140991 Iteration 3 Error: 0.033367 Align patch 14 11 left Iteration 1 Error: 1.174787 Iteration 2 Error: 0.263634 Iteration 3 Error: 0.085286 Iteration 4 Error: 0.031269 Align patch 15 10 left Iteration 1 Error: 0.791480 Iteration 2 Error: 0.145333 Iteration 3 Error: 0.034623 Align patch 16 9 left Iteration 1 Error: 1.015844 Iteration 2 Error: 0.195114 Iteration 3 Error: 0.048686 Align patch 17 8 left Iteration 1 Error: 0.909638 Iteration 2 Error: 0.165899 Iteration 3 Error: 0.036392 Align patch 18 7 left Iteration 1 Error: 1.067266 Iteration 2 Error: 0.167576 Iteration 3 Error: 0.061461 Iteration 4 Error: 0.027694 Align patch 19 6 left Iteration 1 Error: 0.790789 Iteration 2 Error: 0.165294 Iteration 3 Error: 0.054566 Iteration 4 Error: 0.012121 Align patch 20 5 left Iteration 1 Error: 0.764411 Iteration 2 Error: 0.101728 Iteration 3 Error: 0.029801 Align patch 21 4 left Iteration 1 Error: 0.609780 Iteration 2 Error: 0.099847 Iteration 3 Error: 0.021941 Align patch 22 3 left Iteration 1 Error: 0.866261 Iteration 2 Error: 0.271738 Iteration 3 Error: 0.088849 Iteration 4 Error: 0.037055 Align patch 23 2 left Iteration 1 Error: 0.949040 Iteration 2 Error: 0.201742 Iteration 3 Error: 0.059040 Iteration 4 Error: 0.017407 Align patch 24 1 left Iteration 1 Error: 0.470211 Iteration 2 Error: 0.138168 Iteration 3 Error: 0.047228 Align patch 25 0 left Iteration 1 Error: 0.814779 Iteration 2 Error: 0.093093 Iteration 3 Error: 0.019938 3D Fitting completed. Patch alignment time: 12.09(sec) Local motion has been corrected. Process thread exits. Computational time: 22.814445 sec Total time: 30.248192 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00016hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00016hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.739061s Reading file: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00016hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.470742s ........................................ >>>>>>TIME<<<<<< FFT: 0.938987s Defocus_U Defocus_V Angle CCC 10757.81 11300.86 2.78 0.038477 Final Values Defocus_U Defocus_V Angle CCC 10760.89 11341.54 3.41 0.063179 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00007sq_v01_00016hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00016hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 41.06 6.87 Num Hot pixels: 189 Hot pixel threshold: 82.30 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.638643 Iteration 2 Error: 0.088700 Iteration 3 Error: 0.019520 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.12 -0.07 ...... Frame ( 3) shift: -0.25 -0.14 ...... Frame ( 4) shift: -0.37 -0.20 ...... Frame ( 5) shift: -0.49 -0.27 ...... Frame ( 6) shift: -0.60 -0.28 ...... Frame ( 7) shift: -0.69 -0.23 ...... Frame ( 8) shift: -0.78 -0.18 ...... Frame ( 9) shift: -0.81 -0.14 ...... Frame ( 10) shift: -0.76 -0.13 ...... Frame ( 11) shift: -0.72 -0.12 ...... Frame ( 12) shift: -0.73 -0.11 ...... Frame ( 13) shift: -0.80 -0.09 ...... Frame ( 14) shift: -0.86 -0.07 ...... Frame ( 15) shift: -0.90 -0.05 ...... Frame ( 16) shift: -0.92 -0.04 ...... Frame ( 17) shift: -0.94 -0.03 ...... Frame ( 18) shift: -0.97 0.01 ...... Frame ( 19) shift: -1.03 0.06 ...... Frame ( 20) shift: -1.09 0.11 ...... Frame ( 21) shift: -1.11 0.17 ...... Frame ( 22) shift: -1.07 0.25 ...... Frame ( 23) shift: -1.03 0.33 ...... Frame ( 24) shift: -0.99 0.38 ...... Frame ( 25) shift: -0.93 0.40 ...... Frame ( 26) shift: -0.87 0.42 ...... Frame ( 27) shift: -0.84 0.45 ...... Frame ( 28) shift: -0.83 0.50 ...... Frame ( 29) shift: -0.82 0.55 ...... Frame ( 30) shift: -0.81 0.57 ...... Frame ( 31) shift: -0.81 0.55 ...... Frame ( 32) shift: -0.81 0.54 ...... Frame ( 33) shift: -0.81 0.54 ...... Frame ( 34) shift: -0.80 0.56 ...... Frame ( 35) shift: -0.80 0.59 ...... Frame ( 36) shift: -0.79 0.62 ...... Frame ( 37) shift: -0.76 0.68 ...... Frame ( 38) shift: -0.73 0.73 ...... Frame ( 39) shift: -0.70 0.78 ...... Frame ( 40) shift: -0.67 0.83 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.211281 Iteration 2 Error: 0.157559 Iteration 3 Error: 0.049572 Align patch 2 23 left Iteration 1 Error: 0.899035 Iteration 2 Error: 0.108235 Iteration 3 Error: 0.025804 Align patch 3 22 left Iteration 1 Error: 0.540014 Iteration 2 Error: 0.068408 Iteration 3 Error: 0.013979 Align patch 4 21 left Iteration 1 Error: 0.814952 Iteration 2 Error: 0.101755 Iteration 3 Error: 0.024122 Align patch 5 20 left Iteration 1 Error: 0.834531 Iteration 2 Error: 0.128680 Iteration 3 Error: 0.041565 Align patch 6 19 left Iteration 1 Error: 0.837801 Iteration 2 Error: 0.149698 Iteration 3 Error: 0.032356 Align patch 7 18 left Iteration 1 Error: 0.464869 Iteration 2 Error: 0.119813 Iteration 3 Error: 0.045119 Align patch 8 17 left Iteration 1 Error: 0.581934 Iteration 2 Error: 0.113954 Iteration 3 Error: 0.041556 Align patch 9 16 left Iteration 1 Error: 0.455206 Iteration 2 Error: 0.112406 Iteration 3 Error: 0.024525 Align patch 10 15 left Iteration 1 Error: 0.836500 Iteration 2 Error: 0.137184 Iteration 3 Error: 0.021704 Align patch 11 14 left Iteration 1 Error: 0.807759 Iteration 2 Error: 0.187749 Iteration 3 Error: 0.070387 Iteration 4 Error: 0.015957 Align patch 12 13 left Iteration 1 Error: 0.490710 Iteration 2 Error: 0.077400 Iteration 3 Error: 0.024664 Align patch 13 12 left Iteration 1 Error: 0.546461 Iteration 2 Error: 0.066106 Iteration 3 Error: 0.016929 Align patch 14 11 left Iteration 1 Error: 0.526988 Iteration 2 Error: 0.095977 Iteration 3 Error: 0.018731 Align patch 15 10 left Iteration 1 Error: 0.715822 Iteration 2 Error: 0.106465 Iteration 3 Error: 0.016272 Align patch 16 9 left Iteration 1 Error: 0.489756 Iteration 2 Error: 0.100382 Iteration 3 Error: 0.021491 Align patch 17 8 left Iteration 1 Error: 0.669110 Iteration 2 Error: 0.093074 Iteration 3 Error: 0.024982 Align patch 18 7 left Iteration 1 Error: 1.267411 Iteration 2 Error: 0.137794 Iteration 3 Error: 0.021488 Align patch 19 6 left Iteration 1 Error: 0.796031 Iteration 2 Error: 0.102358 Iteration 3 Error: 0.028941 Align patch 20 5 left Iteration 1 Error: 0.708144 Iteration 2 Error: 0.130906 Iteration 3 Error: 0.032874 Align patch 21 4 left Iteration 1 Error: 0.761455 Iteration 2 Error: 0.101449 Iteration 3 Error: 0.029288 Align patch 22 3 left Iteration 1 Error: 0.779780 Iteration 2 Error: 0.073405 Iteration 3 Error: 0.021646 Align patch 23 2 left Iteration 1 Error: 0.706489 Iteration 2 Error: 0.146365 Iteration 3 Error: 0.026218 Align patch 24 1 left Iteration 1 Error: 0.522287 Iteration 2 Error: 0.060185 Iteration 3 Error: 0.013524 Align patch 25 0 left Iteration 1 Error: 0.639609 Iteration 2 Error: 0.114419 Iteration 3 Error: 0.020038 3D Fitting completed. Patch alignment time: 11.33(sec) Local motion has been corrected. Process thread exits. Computational time: 23.110128 sec Total time: 29.398571 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00016hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00016hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.559923s Reading file: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00016hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.325422s ........................................ >>>>>>TIME<<<<<< FFT: 1.101412s Defocus_U Defocus_V Angle CCC 12259.80 13103.55 5.31 0.045728 Final Values Defocus_U Defocus_V Angle CCC 12266.05 13100.43 5.31 0.076854 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00007sq_v01_00016hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00016hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 41.03 6.88 Num Hot pixels: 200 Hot pixel threshold: 82.32 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.754642 Iteration 2 Error: 0.102849 Iteration 3 Error: 0.018599 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.23 -0.10 ...... Frame ( 3) shift: -0.46 -0.21 ...... Frame ( 4) shift: -0.69 -0.31 ...... Frame ( 5) shift: -0.91 -0.41 ...... Frame ( 6) shift: -1.03 -0.49 ...... Frame ( 7) shift: -1.04 -0.54 ...... Frame ( 8) shift: -1.05 -0.59 ...... Frame ( 9) shift: -1.06 -0.61 ...... Frame ( 10) shift: -1.05 -0.58 ...... Frame ( 11) shift: -1.05 -0.56 ...... Frame ( 12) shift: -1.06 -0.54 ...... Frame ( 13) shift: -1.09 -0.51 ...... Frame ( 14) shift: -1.12 -0.48 ...... Frame ( 15) shift: -1.12 -0.45 ...... Frame ( 16) shift: -1.10 -0.41 ...... Frame ( 17) shift: -1.07 -0.37 ...... Frame ( 18) shift: -1.09 -0.33 ...... Frame ( 19) shift: -1.14 -0.29 ...... Frame ( 20) shift: -1.19 -0.26 ...... Frame ( 21) shift: -1.22 -0.21 ...... Frame ( 22) shift: -1.22 -0.14 ...... Frame ( 23) shift: -1.22 -0.07 ...... Frame ( 24) shift: -1.23 0.01 ...... Frame ( 25) shift: -1.23 0.11 ...... Frame ( 26) shift: -1.23 0.21 ...... Frame ( 27) shift: -1.23 0.27 ...... Frame ( 28) shift: -1.23 0.30 ...... Frame ( 29) shift: -1.22 0.32 ...... Frame ( 30) shift: -1.20 0.33 ...... Frame ( 31) shift: -1.17 0.33 ...... Frame ( 32) shift: -1.13 0.32 ...... Frame ( 33) shift: -1.13 0.33 ...... Frame ( 34) shift: -1.17 0.33 ...... Frame ( 35) shift: -1.20 0.34 ...... Frame ( 36) shift: -1.23 0.38 ...... Frame ( 37) shift: -1.23 0.45 ...... Frame ( 38) shift: -1.24 0.52 ...... Frame ( 39) shift: -1.25 0.59 ...... Frame ( 40) shift: -1.25 0.65 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.101364 Iteration 2 Error: 0.091014 Iteration 3 Error: 0.024431 Align patch 2 23 left Iteration 1 Error: 0.576676 Iteration 2 Error: 0.062157 Iteration 3 Error: 0.019317 Align patch 3 22 left Iteration 1 Error: 0.516531 Iteration 2 Error: 0.092849 Iteration 3 Error: 0.027163 Align patch 4 21 left Iteration 1 Error: 0.705367 Iteration 2 Error: 0.094600 Iteration 3 Error: 0.016851 Align patch 5 20 left Iteration 1 Error: 0.692939 Iteration 2 Error: 0.123316 Iteration 3 Error: 0.065547 Iteration 4 Error: 0.019078 Align patch 6 19 left Iteration 1 Error: 0.972150 Iteration 2 Error: 0.261482 Iteration 3 Error: 0.047220 Align patch 7 18 left Iteration 1 Error: 0.722150 Iteration 2 Error: 0.093751 Iteration 3 Error: 0.017627 Align patch 8 17 left Iteration 1 Error: 0.596294 Iteration 2 Error: 0.117936 Iteration 3 Error: 0.040759 Align patch 9 16 left Iteration 1 Error: 0.702810 Iteration 2 Error: 0.116401 Iteration 3 Error: 0.044453 Align patch 10 15 left Iteration 1 Error: 0.867384 Iteration 2 Error: 0.081688 Iteration 3 Error: 0.014912 Align patch 11 14 left Iteration 1 Error: 0.736393 Iteration 2 Error: 0.156620 Iteration 3 Error: 0.041072 Align patch 12 13 left Iteration 1 Error: 0.478675 Iteration 2 Error: 0.075316 Iteration 3 Error: 0.021172 Align patch 13 12 left Iteration 1 Error: 0.640149 Iteration 2 Error: 0.099373 Iteration 3 Error: 0.023552 Align patch 14 11 left Iteration 1 Error: 0.673037 Iteration 2 Error: 0.130064 Iteration 3 Error: 0.034920 Align patch 15 10 left Iteration 1 Error: 0.961856 Iteration 2 Error: 0.146753 Iteration 3 Error: 0.029337 Align patch 16 9 left Iteration 1 Error: 0.748408 Iteration 2 Error: 0.177702 Iteration 3 Error: 0.055935 Iteration 4 Error: 0.017464 Align patch 17 8 left Iteration 1 Error: 0.583071 Iteration 2 Error: 0.078526 Iteration 3 Error: 0.017328 Align patch 18 7 left Iteration 1 Error: 0.592261 Iteration 2 Error: 0.097170 Iteration 3 Error: 0.015785 Align patch 19 6 left Iteration 1 Error: 0.476765 Iteration 2 Error: 0.119813 Iteration 3 Error: 0.022909 Align patch 20 5 left Iteration 1 Error: 1.106843 Iteration 2 Error: 0.134818 Iteration 3 Error: 0.025816 Align patch 21 4 left Iteration 1 Error: 0.873069 Iteration 2 Error: 0.179829 Iteration 3 Error: 0.032092 Align patch 22 3 left Iteration 1 Error: 0.615320 Iteration 2 Error: 0.087486 Iteration 3 Error: 0.025092 Align patch 23 2 left Iteration 1 Error: 0.713101 Iteration 2 Error: 0.090543 Iteration 3 Error: 0.028972 Align patch 24 1 left Iteration 1 Error: 0.810022 Iteration 2 Error: 0.153777 Iteration 3 Error: 0.028734 Align patch 25 0 left Iteration 1 Error: 0.841972 Iteration 2 Error: 0.125485 Iteration 3 Error: 0.022039 3D Fitting completed. Patch alignment time: 11.14(sec) Local motion has been corrected. Process thread exits. Computational time: 23.545101 sec Total time: 31.417093 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00016hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00016hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.441880s Reading file: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00016hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.605359s ........................................ >>>>>>TIME<<<<<< FFT: 0.930776s Defocus_U Defocus_V Angle CCC 15267.58 14626.95 84.99 0.049301 Final Values Defocus_U Defocus_V Angle CCC 15250.38 14634.78 84.99 0.077681 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00007sq_v01_00017hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00017hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 42.58 7.09 Num Hot pixels: 189 Hot pixel threshold: 85.12 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.807777 Iteration 2 Error: 0.147239 Iteration 3 Error: 0.034089 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.21 -0.09 ...... Frame ( 3) shift: -0.42 -0.18 ...... Frame ( 4) shift: -0.63 -0.26 ...... Frame ( 5) shift: -0.84 -0.35 ...... Frame ( 6) shift: -0.91 -0.40 ...... Frame ( 7) shift: -0.84 -0.40 ...... Frame ( 8) shift: -0.77 -0.40 ...... Frame ( 9) shift: -0.74 -0.35 ...... Frame ( 10) shift: -0.76 -0.25 ...... Frame ( 11) shift: -0.78 -0.16 ...... Frame ( 12) shift: -0.76 -0.08 ...... Frame ( 13) shift: -0.70 -0.01 ...... Frame ( 14) shift: -0.64 0.05 ...... Frame ( 15) shift: -0.62 0.10 ...... Frame ( 16) shift: -0.63 0.13 ...... Frame ( 17) shift: -0.64 0.17 ...... Frame ( 18) shift: -0.62 0.20 ...... Frame ( 19) shift: -0.57 0.24 ...... Frame ( 20) shift: -0.52 0.28 ...... Frame ( 21) shift: -0.46 0.32 ...... Frame ( 22) shift: -0.40 0.37 ...... Frame ( 23) shift: -0.33 0.41 ...... Frame ( 24) shift: -0.30 0.45 ...... Frame ( 25) shift: -0.30 0.48 ...... Frame ( 26) shift: -0.31 0.51 ...... Frame ( 27) shift: -0.30 0.53 ...... Frame ( 28) shift: -0.28 0.55 ...... Frame ( 29) shift: -0.25 0.56 ...... Frame ( 30) shift: -0.23 0.61 ...... Frame ( 31) shift: -0.21 0.69 ...... Frame ( 32) shift: -0.18 0.78 ...... Frame ( 33) shift: -0.15 0.87 ...... Frame ( 34) shift: -0.11 0.96 ...... Frame ( 35) shift: -0.08 1.06 ...... Frame ( 36) shift: -0.05 1.12 ...... Frame ( 37) shift: -0.04 1.13 ...... Frame ( 38) shift: -0.02 1.14 ...... Frame ( 39) shift: -0.01 1.16 ...... Frame ( 40) shift: 0.01 1.17 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.737028 Iteration 2 Error: 0.132917 Iteration 3 Error: 0.039039 Align patch 2 23 left Iteration 1 Error: 1.013966 Iteration 2 Error: 0.126100 Iteration 3 Error: 0.034066 Align patch 3 22 left Iteration 1 Error: 0.788207 Iteration 2 Error: 0.081068 Iteration 3 Error: 0.027665 Align patch 4 21 left Iteration 1 Error: 0.788798 Iteration 2 Error: 0.068373 Iteration 3 Error: 0.017632 Align patch 5 20 left Iteration 1 Error: 0.802146 Iteration 2 Error: 0.095355 Iteration 3 Error: 0.016582 Align patch 6 19 left Iteration 1 Error: 0.711144 Iteration 2 Error: 0.235638 Iteration 3 Error: 0.043775 Align patch 7 18 left Iteration 1 Error: 0.757062 Iteration 2 Error: 0.209419 Iteration 3 Error: 0.069613 Iteration 4 Error: 0.048022 Align patch 8 17 left Iteration 1 Error: 0.818655 Iteration 2 Error: 0.150719 Iteration 3 Error: 0.044627 Align patch 9 16 left Iteration 1 Error: 0.777111 Iteration 2 Error: 0.175521 Iteration 3 Error: 0.040009 Align patch 10 15 left Iteration 1 Error: 0.517796 Iteration 2 Error: 0.113361 Iteration 3 Error: 0.028235 Align patch 11 14 left Iteration 1 Error: 0.599925 Iteration 2 Error: 0.165274 Iteration 3 Error: 0.044748 Align patch 12 13 left Iteration 1 Error: 0.501992 Iteration 2 Error: 0.087561 Iteration 3 Error: 0.028047 Align patch 13 12 left Iteration 1 Error: 1.037271 Iteration 2 Error: 0.173042 Iteration 3 Error: 0.028246 Align patch 14 11 left Iteration 1 Error: 0.542359 Iteration 2 Error: 0.137127 Iteration 3 Error: 0.035375 Align patch 15 10 left Iteration 1 Error: 0.559821 Iteration 2 Error: 0.087992 Iteration 3 Error: 0.025752 Align patch 16 9 left Iteration 1 Error: 0.786911 Iteration 2 Error: 0.171323 Iteration 3 Error: 0.045424 Align patch 17 8 left Iteration 1 Error: 0.618362 Iteration 2 Error: 0.077942 Iteration 3 Error: 0.028276 Align patch 18 7 left Iteration 1 Error: 0.843908 Iteration 2 Error: 0.163847 Iteration 3 Error: 0.036186 Align patch 19 6 left Iteration 1 Error: 0.599563 Iteration 2 Error: 0.096713 Iteration 3 Error: 0.019154 Align patch 20 5 left Iteration 1 Error: 0.735270 Iteration 2 Error: 0.103741 Iteration 3 Error: 0.017557 Align patch 21 4 left Iteration 1 Error: 0.606035 Iteration 2 Error: 0.118710 Iteration 3 Error: 0.030563 Align patch 22 3 left Iteration 1 Error: 0.712486 Iteration 2 Error: 0.094709 Iteration 3 Error: 0.019717 Align patch 23 2 left Iteration 1 Error: 1.033016 Iteration 2 Error: 0.119545 Iteration 3 Error: 0.032574 Align patch 24 1 left Iteration 1 Error: 0.648533 Iteration 2 Error: 0.150798 Iteration 3 Error: 0.026919 Align patch 25 0 left Iteration 1 Error: 0.905079 Iteration 2 Error: 0.163053 Iteration 3 Error: 0.027172 3D Fitting completed. Patch alignment time: 11.50(sec) Local motion has been corrected. Process thread exits. Computational time: 25.975752 sec Total time: 32.641960 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00017hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00017hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.625773s Reading file: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00017hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.416663s ........................................ >>>>>>TIME<<<<<< FFT: 1.051733s Defocus_U Defocus_V Angle CCC 10542.96 11398.44 11.85 0.044173 Final Values Defocus_U Defocus_V Angle CCC 10546.09 11420.34 12.48 0.080297 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00007sq_v01_00017hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00017hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 41.13 6.99 Num Hot pixels: 175 Hot pixel threshold: 83.05 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.591530 Iteration 2 Error: 0.121534 Iteration 3 Error: 0.031877 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.17 -0.09 ...... Frame ( 3) shift: -0.34 -0.17 ...... Frame ( 4) shift: -0.50 -0.26 ...... Frame ( 5) shift: -0.67 -0.35 ...... Frame ( 6) shift: -0.74 -0.38 ...... Frame ( 7) shift: -0.70 -0.35 ...... Frame ( 8) shift: -0.67 -0.33 ...... Frame ( 9) shift: -0.63 -0.29 ...... Frame ( 10) shift: -0.60 -0.23 ...... Frame ( 11) shift: -0.57 -0.17 ...... Frame ( 12) shift: -0.56 -0.13 ...... Frame ( 13) shift: -0.57 -0.12 ...... Frame ( 14) shift: -0.59 -0.10 ...... Frame ( 15) shift: -0.55 -0.09 ...... Frame ( 16) shift: -0.45 -0.08 ...... Frame ( 17) shift: -0.35 -0.07 ...... Frame ( 18) shift: -0.29 -0.06 ...... Frame ( 19) shift: -0.27 -0.04 ...... Frame ( 20) shift: -0.24 -0.02 ...... Frame ( 21) shift: -0.20 -0.02 ...... Frame ( 22) shift: -0.14 -0.04 ...... Frame ( 23) shift: -0.08 -0.05 ...... Frame ( 24) shift: -0.04 -0.02 ...... Frame ( 25) shift: -0.01 0.07 ...... Frame ( 26) shift: 0.02 0.16 ...... Frame ( 27) shift: 0.04 0.23 ...... Frame ( 28) shift: 0.03 0.28 ...... Frame ( 29) shift: 0.02 0.33 ...... Frame ( 30) shift: 0.04 0.37 ...... Frame ( 31) shift: 0.09 0.40 ...... Frame ( 32) shift: 0.14 0.44 ...... Frame ( 33) shift: 0.12 0.46 ...... Frame ( 34) shift: 0.04 0.48 ...... Frame ( 35) shift: -0.05 0.49 ...... Frame ( 36) shift: -0.05 0.51 ...... Frame ( 37) shift: 0.04 0.52 ...... Frame ( 38) shift: 0.14 0.54 ...... Frame ( 39) shift: 0.23 0.55 ...... Frame ( 40) shift: 0.32 0.57 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.884580 Iteration 2 Error: 0.212966 Iteration 3 Error: 0.051025 Iteration 4 Error: 0.022365 Align patch 2 23 left Iteration 1 Error: 1.035328 Iteration 2 Error: 0.130895 Iteration 3 Error: 0.045358 Align patch 3 22 left Iteration 1 Error: 0.827416 Iteration 2 Error: 0.164646 Iteration 3 Error: 0.047213 Align patch 4 21 left Iteration 1 Error: 0.834513 Iteration 2 Error: 0.139618 Iteration 3 Error: 0.024777 Align patch 5 20 left Iteration 1 Error: 0.365041 Iteration 2 Error: 0.097815 Iteration 3 Error: 0.032476 Align patch 6 19 left Iteration 1 Error: 1.430475 Iteration 2 Error: 0.254126 Iteration 3 Error: 0.058312 Iteration 4 Error: 0.029299 Align patch 7 18 left Iteration 1 Error: 1.546819 Iteration 2 Error: 0.178591 Iteration 3 Error: 0.045843 Align patch 8 17 left Iteration 1 Error: 0.875026 Iteration 2 Error: 0.176820 Iteration 3 Error: 0.059266 Iteration 4 Error: 0.025543 Align patch 9 16 left Iteration 1 Error: 0.586489 Iteration 2 Error: 0.082865 Iteration 3 Error: 0.014491 Align patch 10 15 left Iteration 1 Error: 0.853926 Iteration 2 Error: 0.134270 Iteration 3 Error: 0.034300 Align patch 11 14 left Iteration 1 Error: 0.886337 Iteration 2 Error: 0.133981 Iteration 3 Error: 0.031003 Align patch 12 13 left Iteration 1 Error: 0.794657 Iteration 2 Error: 0.192053 Iteration 3 Error: 0.063940 Iteration 4 Error: 0.028337 Align patch 13 12 left Iteration 1 Error: 1.276399 Iteration 2 Error: 0.180381 Iteration 3 Error: 0.072070 Iteration 4 Error: 0.032838 Align patch 14 11 left Iteration 1 Error: 1.176327 Iteration 2 Error: 0.231504 Iteration 3 Error: 0.075357 Iteration 4 Error: 0.027191 Align patch 15 10 left Iteration 1 Error: 0.946349 Iteration 2 Error: 0.112720 Iteration 3 Error: 0.018719 Align patch 16 9 left Iteration 1 Error: 0.896501 Iteration 2 Error: 0.115673 Iteration 3 Error: 0.026889 Align patch 17 8 left Iteration 1 Error: 1.411080 Iteration 2 Error: 0.189616 Iteration 3 Error: 0.075879 Iteration 4 Error: 0.021954 Align patch 18 7 left Iteration 1 Error: 0.862781 Iteration 2 Error: 0.109879 Iteration 3 Error: 0.025094 Align patch 19 6 left Iteration 1 Error: 1.133651 Iteration 2 Error: 0.169515 Iteration 3 Error: 0.050090 Iteration 4 Error: 0.011906 Align patch 20 5 left Iteration 1 Error: 0.701891 Iteration 2 Error: 0.200669 Iteration 3 Error: 0.034658 Align patch 21 4 left Iteration 1 Error: 0.964433 Iteration 2 Error: 0.130628 Iteration 3 Error: 0.043148 Align patch 22 3 left Iteration 1 Error: 0.963400 Iteration 2 Error: 0.199962 Iteration 3 Error: 0.052732 Iteration 4 Error: 0.029765 Align patch 23 2 left Iteration 1 Error: 0.739066 Iteration 2 Error: 0.068516 Iteration 3 Error: 0.025548 Align patch 24 1 left Iteration 1 Error: 0.672203 Iteration 2 Error: 0.108879 Iteration 3 Error: 0.047233 Align patch 25 0 left Iteration 1 Error: 0.667879 Iteration 2 Error: 0.134663 Iteration 3 Error: 0.028535 3D Fitting completed. Patch alignment time: 12.65(sec) Local motion has been corrected. Process thread exits. Computational time: 26.102079 sec Total time: 33.488640 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00017hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00017hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.678661s Reading file: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00017hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.850307s ........................................ >>>>>>TIME<<<<<< FFT: 0.958061s Defocus_U Defocus_V Angle CCC 9652.56 10140.46 1.25 0.030326 Final Values Defocus_U Defocus_V Angle CCC 9660.35 10163.94 0.94 0.057373 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00007sq_v01_00017hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00017hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 1.000e-01 CC threshold: 0.735 Mean Std: 42.53 7.05 Num Hot pixels: 178 Hot pixel threshold: 84.84 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.606652 Iteration 2 Error: 0.093125 Iteration 3 Error: 0.016675 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.20 -0.12 ...... Frame ( 3) shift: -0.39 -0.25 ...... Frame ( 4) shift: -0.59 -0.37 ...... Frame ( 5) shift: -0.79 -0.49 ...... Frame ( 6) shift: -0.89 -0.54 ...... Frame ( 7) shift: -0.89 -0.50 ...... Frame ( 8) shift: -0.90 -0.47 ...... Frame ( 9) shift: -0.90 -0.43 ...... Frame ( 10) shift: -0.90 -0.39 ...... Frame ( 11) shift: -0.89 -0.35 ...... Frame ( 12) shift: -0.90 -0.29 ...... Frame ( 13) shift: -0.92 -0.21 ...... Frame ( 14) shift: -0.94 -0.13 ...... Frame ( 15) shift: -0.94 -0.06 ...... Frame ( 16) shift: -0.92 -0.01 ...... Frame ( 17) shift: -0.90 0.04 ...... Frame ( 18) shift: -0.88 0.12 ...... Frame ( 19) shift: -0.86 0.24 ...... Frame ( 20) shift: -0.84 0.36 ...... Frame ( 21) shift: -0.83 0.43 ...... Frame ( 22) shift: -0.81 0.46 ...... Frame ( 23) shift: -0.80 0.49 ...... Frame ( 24) shift: -0.78 0.52 ...... Frame ( 25) shift: -0.75 0.55 ...... Frame ( 26) shift: -0.73 0.59 ...... Frame ( 27) shift: -0.74 0.59 ...... Frame ( 28) shift: -0.80 0.56 ...... Frame ( 29) shift: -0.86 0.54 ...... Frame ( 30) shift: -0.89 0.53 ...... Frame ( 31) shift: -0.90 0.55 ...... Frame ( 32) shift: -0.91 0.56 ...... Frame ( 33) shift: -0.88 0.54 ...... Frame ( 34) shift: -0.82 0.47 ...... Frame ( 35) shift: -0.76 0.41 ...... Frame ( 36) shift: -0.73 0.37 ...... Frame ( 37) shift: -0.73 0.37 ...... Frame ( 38) shift: -0.73 0.38 ...... Frame ( 39) shift: -0.73 0.38 ...... Frame ( 40) shift: -0.74 0.38 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.310774 Iteration 2 Error: 0.220604 Iteration 3 Error: 0.048880 Align patch 2 23 left Iteration 1 Error: 0.891526 Iteration 2 Error: 0.126861 Iteration 3 Error: 0.041067 Align patch 3 22 left Iteration 1 Error: 0.611602 Iteration 2 Error: 0.123682 Iteration 3 Error: 0.036877 Align patch 4 21 left Iteration 1 Error: 0.725875 Iteration 2 Error: 0.117087 Iteration 3 Error: 0.022455 Align patch 5 20 left Iteration 1 Error: 0.661388 Iteration 2 Error: 0.082894 Iteration 3 Error: 0.015941 Align patch 6 19 left Iteration 1 Error: 1.521368 Iteration 2 Error: 0.304891 Iteration 3 Error: 0.083711 Iteration 4 Error: 0.029882 Align patch 7 18 left Iteration 1 Error: 0.909137 Iteration 2 Error: 0.206217 Iteration 3 Error: 0.060205 Iteration 4 Error: 0.024638 Align patch 8 17 left Iteration 1 Error: 0.627083 Iteration 2 Error: 0.188674 Iteration 3 Error: 0.049899 Align patch 9 16 left Iteration 1 Error: 0.637949 Iteration 2 Error: 0.121390 Iteration 3 Error: 0.042215 Align patch 10 15 left Iteration 1 Error: 0.694587 Iteration 2 Error: 0.127132 Iteration 3 Error: 0.028247 Align patch 11 14 left Iteration 1 Error: 0.650788 Iteration 2 Error: 0.185862 Iteration 3 Error: 0.039477 Align patch 12 13 left Iteration 1 Error: 0.552140 Iteration 2 Error: 0.111058 Iteration 3 Error: 0.034328 Align patch 13 12 left Iteration 1 Error: 0.924552 Iteration 2 Error: 0.144165 Iteration 3 Error: 0.030504 Align patch 14 11 left Iteration 1 Error: 0.674599 Iteration 2 Error: 0.095833 Iteration 3 Error: 0.022281 Align patch 15 10 left Iteration 1 Error: 0.687864 Iteration 2 Error: 0.115839 Iteration 3 Error: 0.025226 Align patch 16 9 left Iteration 1 Error: 1.025563 Iteration 2 Error: 0.176914 Iteration 3 Error: 0.042878 Align patch 17 8 left Iteration 1 Error: 0.741616 Iteration 2 Error: 0.136473 Iteration 3 Error: 0.042555 Align patch 18 7 left Iteration 1 Error: 0.853736 Iteration 2 Error: 0.142834 Iteration 3 Error: 0.036628 Align patch 19 6 left Iteration 1 Error: 0.932805 Iteration 2 Error: 0.114699 Iteration 3 Error: 0.023097 Align patch 20 5 left Iteration 1 Error: 0.612420 Iteration 2 Error: 0.133019 Iteration 3 Error: 0.029787 Align patch 21 4 left Iteration 1 Error: 0.650180 Iteration 2 Error: 0.163178 Iteration 3 Error: 0.058619 Iteration 4 Error: 0.015760 Align patch 22 3 left Iteration 1 Error: 0.954761 Iteration 2 Error: 0.152183 Iteration 3 Error: 0.035585 Align patch 23 2 left Iteration 1 Error: 0.792188 Iteration 2 Error: 0.134045 Iteration 3 Error: 0.042159 Align patch 24 1 left Iteration 1 Error: 0.579816 Iteration 2 Error: 0.068141 Iteration 3 Error: 0.015417 Align patch 25 0 left Iteration 1 Error: 0.722410 Iteration 2 Error: 0.165558 Iteration 3 Error: 0.041695 3D Fitting completed. Patch alignment time: 12.11(sec) Local motion has been corrected. Process thread exits. Computational time: 24.903704 sec Total time: 31.880873 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00017hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00017hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.462287s Reading file: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00017hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.960971s ........................................ >>>>>>TIME<<<<<< FFT: 1.000341s Defocus_U Defocus_V Angle CCC 13707.06 14589.87 5.20 0.043278 Final Values Defocus_U Defocus_V Angle CCC 13705.50 14591.44 5.20 0.075561 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00007sq_v01_00017hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00017hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 1.000e-01 CC threshold: 0.734 Mean Std: 40.41 6.87 Num Hot pixels: 172 Hot pixel threshold: 81.60 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.714459 Iteration 2 Error: 0.118798 Iteration 3 Error: 0.027825 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.09 -0.11 ...... Frame ( 3) shift: -0.18 -0.21 ...... Frame ( 4) shift: -0.27 -0.32 ...... Frame ( 5) shift: -0.36 -0.42 ...... Frame ( 6) shift: -0.43 -0.51 ...... Frame ( 7) shift: -0.48 -0.58 ...... Frame ( 8) shift: -0.52 -0.65 ...... Frame ( 9) shift: -0.57 -0.65 ...... Frame ( 10) shift: -0.64 -0.59 ...... Frame ( 11) shift: -0.70 -0.53 ...... Frame ( 12) shift: -0.72 -0.50 ...... Frame ( 13) shift: -0.71 -0.50 ...... Frame ( 14) shift: -0.71 -0.49 ...... Frame ( 15) shift: -0.68 -0.45 ...... Frame ( 16) shift: -0.65 -0.38 ...... Frame ( 17) shift: -0.61 -0.31 ...... Frame ( 18) shift: -0.57 -0.25 ...... Frame ( 19) shift: -0.53 -0.18 ...... Frame ( 20) shift: -0.49 -0.12 ...... Frame ( 21) shift: -0.47 -0.07 ...... Frame ( 22) shift: -0.47 -0.03 ...... Frame ( 23) shift: -0.46 0.02 ...... Frame ( 24) shift: -0.45 0.05 ...... Frame ( 25) shift: -0.45 0.09 ...... Frame ( 26) shift: -0.44 0.13 ...... Frame ( 27) shift: -0.47 0.16 ...... Frame ( 28) shift: -0.53 0.20 ...... Frame ( 29) shift: -0.60 0.24 ...... Frame ( 30) shift: -0.59 0.30 ...... Frame ( 31) shift: -0.51 0.38 ...... Frame ( 32) shift: -0.43 0.46 ...... Frame ( 33) shift: -0.39 0.53 ...... Frame ( 34) shift: -0.37 0.60 ...... Frame ( 35) shift: -0.36 0.68 ...... Frame ( 36) shift: -0.33 0.72 ...... Frame ( 37) shift: -0.30 0.75 ...... Frame ( 38) shift: -0.27 0.77 ...... Frame ( 39) shift: -0.24 0.79 ...... Frame ( 40) shift: -0.22 0.81 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.102561 Iteration 2 Error: 0.157739 Iteration 3 Error: 0.029731 Align patch 2 23 left Iteration 1 Error: 1.031067 Iteration 2 Error: 0.152472 Iteration 3 Error: 0.060608 Iteration 4 Error: 0.017175 Align patch 3 22 left Iteration 1 Error: 0.710057 Iteration 2 Error: 0.112869 Iteration 3 Error: 0.024042 Align patch 4 21 left Iteration 1 Error: 0.937743 Iteration 2 Error: 0.187597 Iteration 3 Error: 0.028532 Align patch 5 20 left Iteration 1 Error: 0.515410 Iteration 2 Error: 0.092084 Iteration 3 Error: 0.036231 Align patch 6 19 left Iteration 1 Error: 0.867118 Iteration 2 Error: 0.135827 Iteration 3 Error: 0.036197 Align patch 7 18 left Iteration 1 Error: 0.876864 Iteration 2 Error: 0.139274 Iteration 3 Error: 0.036766 Align patch 8 17 left Iteration 1 Error: 0.575013 Iteration 2 Error: 0.131951 Iteration 3 Error: 0.029806 Align patch 9 16 left Iteration 1 Error: 0.948641 Iteration 2 Error: 0.174909 Iteration 3 Error: 0.046590 Align patch 10 15 left Iteration 1 Error: 0.888871 Iteration 2 Error: 0.168987 Iteration 3 Error: 0.044567 Align patch 11 14 left Iteration 1 Error: 0.942643 Iteration 2 Error: 0.229925 Iteration 3 Error: 0.060365 Iteration 4 Error: 0.019914 Align patch 12 13 left Iteration 1 Error: 0.580763 Iteration 2 Error: 0.093370 Iteration 3 Error: 0.028768 Align patch 13 12 left Iteration 1 Error: 0.671373 Iteration 2 Error: 0.107794 Iteration 3 Error: 0.025115 Align patch 14 11 left Iteration 1 Error: 1.124486 Iteration 2 Error: 0.309738 Iteration 3 Error: 0.145570 Iteration 4 Error: 0.061118 Iteration 5 Error: 0.038713 Align patch 15 10 left Iteration 1 Error: 0.706968 Iteration 2 Error: 0.137884 Iteration 3 Error: 0.025206 Align patch 16 9 left Iteration 1 Error: 0.672427 Iteration 2 Error: 0.120165 Iteration 3 Error: 0.022725 Align patch 17 8 left Iteration 1 Error: 0.466323 Iteration 2 Error: 0.096249 Iteration 3 Error: 0.022449 Align patch 18 7 left Iteration 1 Error: 1.948003 Iteration 2 Error: 0.550418 Iteration 3 Error: 0.197377 Iteration 4 Error: 0.087684 Iteration 5 Error: 0.042421 Align patch 19 6 left Iteration 1 Error: 2.029330 Iteration 2 Error: 0.797041 Iteration 3 Error: 0.657504 Iteration 4 Error: 0.583729 Iteration 5 Error: 0.521747 Align patch 19 6 left Iteration 1 Error: 1.714082 Iteration 2 Error: 0.450463 Iteration 3 Error: 0.150516 Iteration 4 Error: 0.079066 Iteration 5 Error: 0.030293 Align patch 20 5 left Iteration 1 Error: 0.701084 Iteration 2 Error: 0.131656 Iteration 3 Error: 0.038243 Align patch 21 4 left Iteration 1 Error: 1.735943 Iteration 2 Error: 0.189040 Iteration 3 Error: 0.037108 Align patch 22 3 left Iteration 1 Error: 0.905171 Iteration 2 Error: 0.152672 Iteration 3 Error: 0.047939 Align patch 23 2 left Iteration 1 Error: 0.875657 Iteration 2 Error: 0.206359 Iteration 3 Error: 0.063441 Iteration 4 Error: 0.027285 Align patch 24 1 left Iteration 1 Error: 1.049483 Iteration 2 Error: 0.150869 Iteration 3 Error: 0.043312 Align patch 25 0 left Iteration 1 Error: 1.280116 Iteration 2 Error: 0.152283 Iteration 3 Error: 0.042702 3D Fitting completed. Patch alignment time: 12.90(sec) Local motion has been corrected. Process thread exits. Computational time: 28.367868 sec Total time: 35.389755 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00017hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00017hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.889547s Reading file: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00017hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 5.183286s ........................................ >>>>>>TIME<<<<<< FFT: 1.222956s Defocus_U Defocus_V Angle CCC 11793.06 11089.86 86.63 0.032506 Final Values Defocus_U Defocus_V Angle CCC 11816.51 11116.44 88.20 0.054835 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00007sq_v01_00018hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00018hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 41.07 6.92 Num Hot pixels: 196 Hot pixel threshold: 82.59 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.577746 Iteration 2 Error: 0.071904 Iteration 3 Error: 0.015319 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.08 -0.05 ...... Frame ( 3) shift: -0.16 -0.11 ...... Frame ( 4) shift: -0.24 -0.16 ...... Frame ( 5) shift: -0.31 -0.22 ...... Frame ( 6) shift: -0.33 -0.23 ...... Frame ( 7) shift: -0.27 -0.21 ...... Frame ( 8) shift: -0.22 -0.19 ...... Frame ( 9) shift: -0.17 -0.15 ...... Frame ( 10) shift: -0.13 -0.11 ...... Frame ( 11) shift: -0.09 -0.07 ...... Frame ( 12) shift: -0.07 -0.03 ...... Frame ( 13) shift: -0.10 -0.00 ...... Frame ( 14) shift: -0.12 0.03 ...... Frame ( 15) shift: -0.13 0.02 ...... Frame ( 16) shift: -0.13 -0.02 ...... Frame ( 17) shift: -0.13 -0.06 ...... Frame ( 18) shift: -0.13 -0.06 ...... Frame ( 19) shift: -0.13 -0.02 ...... Frame ( 20) shift: -0.13 0.02 ...... Frame ( 21) shift: -0.12 0.07 ...... Frame ( 22) shift: -0.09 0.13 ...... Frame ( 23) shift: -0.06 0.19 ...... Frame ( 24) shift: -0.04 0.21 ...... Frame ( 25) shift: -0.03 0.19 ...... Frame ( 26) shift: -0.02 0.18 ...... Frame ( 27) shift: 0.00 0.19 ...... Frame ( 28) shift: 0.03 0.24 ...... Frame ( 29) shift: 0.06 0.28 ...... Frame ( 30) shift: 0.10 0.26 ...... Frame ( 31) shift: 0.15 0.18 ...... Frame ( 32) shift: 0.19 0.09 ...... Frame ( 33) shift: 0.27 0.04 ...... Frame ( 34) shift: 0.39 0.00 ...... Frame ( 35) shift: 0.50 -0.03 ...... Frame ( 36) shift: 0.57 -0.04 ...... Frame ( 37) shift: 0.59 -0.03 ...... Frame ( 38) shift: 0.61 -0.03 ...... Frame ( 39) shift: 0.63 -0.02 ...... Frame ( 40) shift: 0.65 -0.01 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.020807 Iteration 2 Error: 0.186479 Iteration 3 Error: 0.045363 Align patch 2 23 left Iteration 1 Error: 0.520711 Iteration 2 Error: 0.115158 Iteration 3 Error: 0.041539 Align patch 3 22 left Iteration 1 Error: 0.541687 Iteration 2 Error: 0.062130 Iteration 3 Error: 0.013490 Align patch 4 21 left Iteration 1 Error: 0.604656 Iteration 2 Error: 0.172657 Iteration 3 Error: 0.027787 Align patch 5 20 left Iteration 1 Error: 0.867975 Iteration 2 Error: 0.210134 Iteration 3 Error: 0.073695 Iteration 4 Error: 0.032919 Align patch 6 19 left Iteration 1 Error: 0.624146 Iteration 2 Error: 0.075790 Iteration 3 Error: 0.014008 Align patch 7 18 left Iteration 1 Error: 0.550243 Iteration 2 Error: 0.108791 Iteration 3 Error: 0.025599 Align patch 8 17 left Iteration 1 Error: 0.632249 Iteration 2 Error: 0.125360 Iteration 3 Error: 0.031961 Align patch 9 16 left Iteration 1 Error: 0.638144 Iteration 2 Error: 0.114517 Iteration 3 Error: 0.028951 Align patch 10 15 left Iteration 1 Error: 0.603816 Iteration 2 Error: 0.073195 Iteration 3 Error: 0.026262 Align patch 11 14 left Iteration 1 Error: 0.945758 Iteration 2 Error: 0.055408 Iteration 3 Error: 0.020332 Align patch 12 13 left Iteration 1 Error: 0.554775 Iteration 2 Error: 0.071182 Iteration 3 Error: 0.015308 Align patch 13 12 left Iteration 1 Error: 1.061775 Iteration 2 Error: 0.108869 Iteration 3 Error: 0.029909 Align patch 14 11 left Iteration 1 Error: 0.724475 Iteration 2 Error: 0.080592 Iteration 3 Error: 0.018889 Align patch 15 10 left Iteration 1 Error: 0.669907 Iteration 2 Error: 0.108973 Iteration 3 Error: 0.028822 Align patch 16 9 left Iteration 1 Error: 0.580708 Iteration 2 Error: 0.061967 Iteration 3 Error: 0.016878 Align patch 17 8 left Iteration 1 Error: 0.834310 Iteration 2 Error: 0.077881 Iteration 3 Error: 0.019156 Align patch 18 7 left Iteration 1 Error: 0.847839 Iteration 2 Error: 0.116838 Iteration 3 Error: 0.027589 Align patch 19 6 left Iteration 1 Error: 1.025275 Iteration 2 Error: 0.096823 Iteration 3 Error: 0.018044 Align patch 20 5 left Iteration 1 Error: 0.452160 Iteration 2 Error: 0.052867 Iteration 3 Error: 0.012104 Align patch 21 4 left Iteration 1 Error: 0.693129 Iteration 2 Error: 0.094120 Iteration 3 Error: 0.020202 Align patch 22 3 left Iteration 1 Error: 0.715444 Iteration 2 Error: 0.103887 Iteration 3 Error: 0.015087 Align patch 23 2 left Iteration 1 Error: 0.789823 Iteration 2 Error: 0.309338 Iteration 3 Error: 0.076115 Iteration 4 Error: 0.034100 Align patch 24 1 left Iteration 1 Error: 0.554205 Iteration 2 Error: 0.122359 Iteration 3 Error: 0.021247 Align patch 25 0 left Iteration 1 Error: 1.119467 Iteration 2 Error: 0.110082 Iteration 3 Error: 0.021612 3D Fitting completed. Patch alignment time: 11.40(sec) Local motion has been corrected. Process thread exits. Computational time: 28.496122 sec Total time: 37.186279 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00018hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00018hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.653894s Reading file: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00018hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 4.770167s ........................................ >>>>>>TIME<<<<<< FFT: 1.050514s Defocus_U Defocus_V Angle CCC 9195.33 10109.39 11.10 0.038204 Final Values Defocus_U Defocus_V Angle CCC 9207.84 10115.65 11.42 0.071043 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00007sq_v01_00018hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00018hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 41.75 6.98 Num Hot pixels: 195 Hot pixel threshold: 83.65 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.754890 Iteration 2 Error: 0.448929 Iteration 3 Error: 0.111907 Iteration 4 Error: 0.044810 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.18 -0.08 ...... Frame ( 3) shift: -0.36 -0.16 ...... Frame ( 4) shift: -0.55 -0.23 ...... Frame ( 5) shift: -0.73 -0.31 ...... Frame ( 6) shift: -0.78 -0.38 ...... Frame ( 7) shift: -0.70 -0.43 ...... Frame ( 8) shift: -0.61 -0.48 ...... Frame ( 9) shift: -0.54 -0.48 ...... Frame ( 10) shift: -0.48 -0.41 ...... Frame ( 11) shift: -0.42 -0.35 ...... Frame ( 12) shift: -0.37 -0.23 ...... Frame ( 13) shift: -0.35 -0.07 ...... Frame ( 14) shift: -0.32 0.10 ...... Frame ( 15) shift: -0.28 0.21 ...... Frame ( 16) shift: -0.23 0.26 ...... Frame ( 17) shift: -0.18 0.32 ...... Frame ( 18) shift: -0.14 0.41 ...... Frame ( 19) shift: -0.12 0.54 ...... Frame ( 20) shift: -0.10 0.67 ...... Frame ( 21) shift: -0.05 0.75 ...... Frame ( 22) shift: 0.02 0.79 ...... Frame ( 23) shift: 0.10 0.83 ...... Frame ( 24) shift: 0.15 0.87 ...... Frame ( 25) shift: 0.17 0.92 ...... Frame ( 26) shift: 0.19 0.97 ...... Frame ( 27) shift: 0.26 1.04 ...... Frame ( 28) shift: 0.38 1.12 ...... Frame ( 29) shift: 0.50 1.21 ...... Frame ( 30) shift: 0.57 1.29 ...... Frame ( 31) shift: 0.58 1.37 ...... Frame ( 32) shift: 0.60 1.44 ...... Frame ( 33) shift: 0.64 1.54 ...... Frame ( 34) shift: 0.70 1.65 ...... Frame ( 35) shift: 0.76 1.77 ...... Frame ( 36) shift: 0.84 1.86 ...... Frame ( 37) shift: 0.92 1.94 ...... Frame ( 38) shift: 1.00 2.02 ...... Frame ( 39) shift: 1.08 2.09 ...... Frame ( 40) shift: 1.16 2.17 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.082153 Iteration 2 Error: 0.788449 Iteration 3 Error: 0.449330 Iteration 4 Error: 0.484129 Iteration 5 Error: 0.373095 Align patch 1 24 left Iteration 1 Error: 3.649632 Iteration 2 Error: 0.764911 Iteration 3 Error: 0.317499 Iteration 4 Error: 0.116997 Iteration 5 Error: 0.059883 Align patch 2 23 left Iteration 1 Error: 1.258739 Iteration 2 Error: 0.515702 Iteration 3 Error: 0.407223 Iteration 4 Error: 0.309488 Iteration 5 Error: 0.259160 Align patch 2 23 left Iteration 1 Error: 2.579918 Iteration 2 Error: 0.697567 Iteration 3 Error: 0.167094 Iteration 4 Error: 0.080600 Iteration 5 Error: 0.025076 Align patch 3 22 left Iteration 1 Error: 0.878337 Iteration 2 Error: 0.262967 Iteration 3 Error: 0.103545 Iteration 4 Error: 0.038557 Align patch 4 21 left Iteration 1 Error: 0.969703 Iteration 2 Error: 0.135819 Iteration 3 Error: 0.030950 Align patch 5 20 left Iteration 1 Error: 1.084129 Iteration 2 Error: 0.302393 Iteration 3 Error: 0.066379 Iteration 4 Error: 0.020844 Align patch 6 19 left Iteration 1 Error: 5.158184 Iteration 2 Error: 1.934419 Iteration 3 Error: 0.624574 Iteration 4 Error: 0.253536 Iteration 5 Error: 0.167406 Align patch 6 19 left Iteration 1 Error: 3.922066 Iteration 2 Error: 0.942532 Iteration 3 Error: 0.246116 Iteration 4 Error: 0.090953 Iteration 5 Error: 0.033956 Align patch 7 18 left Iteration 1 Error: 2.495462 Iteration 2 Error: 0.665959 Iteration 3 Error: 0.333183 Iteration 4 Error: 0.259522 Iteration 5 Error: 0.207929 Align patch 7 18 left Iteration 1 Error: 3.009052 Iteration 2 Error: 0.870618 Iteration 3 Error: 0.189701 Iteration 4 Error: 0.081657 Iteration 5 Error: 0.027281 Align patch 8 17 left Iteration 1 Error: 2.012900 Iteration 2 Error: 0.492430 Iteration 3 Error: 0.083090 Iteration 4 Error: 0.039583 Align patch 9 16 left Iteration 1 Error: 0.631049 Iteration 2 Error: 0.235398 Iteration 3 Error: 0.068329 Iteration 4 Error: 0.026840 Align patch 10 15 left Iteration 1 Error: 1.258148 Iteration 2 Error: 0.187576 Iteration 3 Error: 0.061540 Iteration 4 Error: 0.020203 Align patch 11 14 left Iteration 1 Error: 2.462638 Iteration 2 Error: 0.664755 Iteration 3 Error: 0.380548 Iteration 4 Error: 0.167617 Iteration 5 Error: 0.165708 Align patch 11 14 left Iteration 1 Error: 2.247667 Iteration 2 Error: 0.568880 Iteration 3 Error: 0.155723 Iteration 4 Error: 0.039285 Align patch 12 13 left Iteration 1 Error: 0.944305 Iteration 2 Error: 0.528868 Iteration 3 Error: 0.217946 Iteration 4 Error: 0.129059 Iteration 5 Error: 0.073706 Align patch 12 13 left Iteration 1 Error: 2.016943 Iteration 2 Error: 0.538739 Iteration 3 Error: 0.112996 Iteration 4 Error: 0.036773 Align patch 13 12 left Iteration 1 Error: 1.072069 Iteration 2 Error: 0.355301 Iteration 3 Error: 0.091991 Iteration 4 Error: 0.066973 Iteration 5 Error: 0.025576 Align patch 14 11 left Iteration 1 Error: 0.483992 Iteration 2 Error: 0.136383 Iteration 3 Error: 0.043127 Align patch 15 10 left Iteration 1 Error: 1.208959 Iteration 2 Error: 0.291648 Iteration 3 Error: 0.068741 Iteration 4 Error: 0.026752 Align patch 16 9 left Iteration 1 Error: 1.041655 Iteration 2 Error: 0.232192 Iteration 3 Error: 0.094056 Iteration 4 Error: 0.052519 Iteration 5 Error: 0.017536 Align patch 17 8 left Iteration 1 Error: 1.417264 Iteration 2 Error: 0.283658 Iteration 3 Error: 0.187824 Iteration 4 Error: 0.091320 Iteration 5 Error: 0.068260 Align patch 17 8 left Iteration 1 Error: 1.349653 Iteration 2 Error: 0.258722 Iteration 3 Error: 0.059821 Iteration 4 Error: 0.019187 Align patch 18 7 left Iteration 1 Error: 1.024674 Iteration 2 Error: 0.216543 Iteration 3 Error: 0.067673 Iteration 4 Error: 0.039039 Align patch 19 6 left Iteration 1 Error: 1.001928 Iteration 2 Error: 0.234724 Iteration 3 Error: 0.063658 Iteration 4 Error: 0.014203 Align patch 20 5 left Iteration 1 Error: 1.065306 Iteration 2 Error: 0.237957 Iteration 3 Error: 0.040981 Align patch 21 4 left Iteration 1 Error: 0.593692 Iteration 2 Error: 0.146418 Iteration 3 Error: 0.045135 Align patch 22 3 left Iteration 1 Error: 0.738362 Iteration 2 Error: 0.131167 Iteration 3 Error: 0.041098 Align patch 23 2 left Iteration 1 Error: 0.738086 Iteration 2 Error: 0.135833 Iteration 3 Error: 0.054421 Iteration 4 Error: 0.023122 Align patch 24 1 left Iteration 1 Error: 0.925212 Iteration 2 Error: 0.273934 Iteration 3 Error: 0.047491 Align patch 25 0 left Iteration 1 Error: 1.597916 Iteration 2 Error: 0.242478 Iteration 3 Error: 0.037253 3D Fitting completed. Patch alignment time: 17.63(sec) Local motion has been corrected. Process thread exits. Computational time: 34.673016 sec Total time: 43.294964 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00018hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00018hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.984263s Reading file: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00018hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.960239s ........................................ >>>>>>TIME<<<<<< FFT: 1.002682s Defocus_U Defocus_V Angle CCC 11224.61 10759.77 88.12 0.044557 Final Values Defocus_U Defocus_V Angle CCC 11248.05 10761.33 88.12 0.079649 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00007sq_v01_00018hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00018hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.003e-01 CC threshold: 0.736 Mean Std: 41.61 6.98 Num Hot pixels: 194 Hot pixel threshold: 83.50 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.344886 Iteration 2 Error: 0.041167 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.12 -0.01 ...... Frame ( 3) shift: -0.24 -0.01 ...... Frame ( 4) shift: -0.37 -0.02 ...... Frame ( 5) shift: -0.49 -0.03 ...... Frame ( 6) shift: -0.56 -0.02 ...... Frame ( 7) shift: -0.57 0.01 ...... Frame ( 8) shift: -0.59 0.04 ...... Frame ( 9) shift: -0.58 0.06 ...... Frame ( 10) shift: -0.54 0.09 ...... Frame ( 11) shift: -0.51 0.12 ...... Frame ( 12) shift: -0.50 0.13 ...... Frame ( 13) shift: -0.51 0.12 ...... Frame ( 14) shift: -0.53 0.12 ...... Frame ( 15) shift: -0.51 0.14 ...... Frame ( 16) shift: -0.46 0.18 ...... Frame ( 17) shift: -0.41 0.23 ...... Frame ( 18) shift: -0.40 0.23 ...... Frame ( 19) shift: -0.43 0.20 ...... Frame ( 20) shift: -0.46 0.17 ...... Frame ( 21) shift: -0.47 0.14 ...... Frame ( 22) shift: -0.45 0.13 ...... Frame ( 23) shift: -0.44 0.11 ...... Frame ( 24) shift: -0.44 0.13 ...... Frame ( 25) shift: -0.45 0.18 ...... Frame ( 26) shift: -0.46 0.24 ...... Frame ( 27) shift: -0.47 0.28 ...... Frame ( 28) shift: -0.48 0.30 ...... Frame ( 29) shift: -0.48 0.33 ...... Frame ( 30) shift: -0.50 0.37 ...... Frame ( 31) shift: -0.52 0.42 ...... Frame ( 32) shift: -0.55 0.46 ...... Frame ( 33) shift: -0.54 0.49 ...... Frame ( 34) shift: -0.51 0.48 ...... Frame ( 35) shift: -0.47 0.48 ...... Frame ( 36) shift: -0.43 0.46 ...... Frame ( 37) shift: -0.39 0.44 ...... Frame ( 38) shift: -0.34 0.42 ...... Frame ( 39) shift: -0.29 0.39 ...... Frame ( 40) shift: -0.24 0.37 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.844204 Iteration 2 Error: 0.089893 Iteration 3 Error: 0.026609 Align patch 2 23 left Iteration 1 Error: 0.550279 Iteration 2 Error: 0.136451 Iteration 3 Error: 0.021805 Align patch 3 22 left Iteration 1 Error: 0.911766 Iteration 2 Error: 0.105108 Iteration 3 Error: 0.032300 Align patch 4 21 left Iteration 1 Error: 0.615350 Iteration 2 Error: 0.101278 Iteration 3 Error: 0.017474 Align patch 5 20 left Iteration 1 Error: 0.540602 Iteration 2 Error: 0.094785 Iteration 3 Error: 0.026646 Align patch 6 19 left Iteration 1 Error: 0.620478 Iteration 2 Error: 0.069386 Iteration 3 Error: 0.030949 Align patch 7 18 left Iteration 1 Error: 0.564716 Iteration 2 Error: 0.073957 Iteration 3 Error: 0.024946 Align patch 8 17 left Iteration 1 Error: 0.554584 Iteration 2 Error: 0.062260 Iteration 3 Error: 0.018340 Align patch 9 16 left Iteration 1 Error: 0.580228 Iteration 2 Error: 0.050824 Iteration 3 Error: 0.016169 Align patch 10 15 left Iteration 1 Error: 0.405097 Iteration 2 Error: 0.076839 Iteration 3 Error: 0.010882 Align patch 11 14 left Iteration 1 Error: 0.581861 Iteration 2 Error: 0.095548 Iteration 3 Error: 0.027079 Align patch 12 13 left Iteration 1 Error: 0.581264 Iteration 2 Error: 0.122738 Iteration 3 Error: 0.024425 Align patch 13 12 left Iteration 1 Error: 0.605340 Iteration 2 Error: 0.112331 Iteration 3 Error: 0.017695 Align patch 14 11 left Iteration 1 Error: 0.580287 Iteration 2 Error: 0.076810 Iteration 3 Error: 0.013475 Align patch 15 10 left Iteration 1 Error: 0.647763 Iteration 2 Error: 0.079308 Iteration 3 Error: 0.017520 Align patch 16 9 left Iteration 1 Error: 0.652152 Iteration 2 Error: 0.145618 Iteration 3 Error: 0.026905 Align patch 17 8 left Iteration 1 Error: 0.789847 Iteration 2 Error: 0.127865 Iteration 3 Error: 0.036679 Align patch 18 7 left Iteration 1 Error: 0.481596 Iteration 2 Error: 0.051554 Iteration 3 Error: 0.015425 Align patch 19 6 left Iteration 1 Error: 0.506700 Iteration 2 Error: 0.069995 Iteration 3 Error: 0.012892 Align patch 20 5 left Iteration 1 Error: 0.539312 Iteration 2 Error: 0.080702 Iteration 3 Error: 0.017945 Align patch 21 4 left Iteration 1 Error: 0.954962 Iteration 2 Error: 0.119491 Iteration 3 Error: 0.027062 Align patch 22 3 left Iteration 1 Error: 0.375004 Iteration 2 Error: 0.048401 Align patch 23 2 left Iteration 1 Error: 0.786013 Iteration 2 Error: 0.131004 Iteration 3 Error: 0.031902 Align patch 24 1 left Iteration 1 Error: 0.854239 Iteration 2 Error: 0.085436 Iteration 3 Error: 0.021920 Align patch 25 0 left Iteration 1 Error: 0.661637 Iteration 2 Error: 0.131513 Iteration 3 Error: 0.022125 3D Fitting completed. Patch alignment time: 11.37(sec) Local motion has been corrected. Process thread exits. Computational time: 25.592148 sec Total time: 33.950378 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00018hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00018hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.680006s Reading file: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00018hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.358887s ........................................ >>>>>>TIME<<<<<< FFT: 1.047022s Defocus_U Defocus_V Angle CCC 12966.78 13845.72 3.60 0.056865 Final Values Defocus_U Defocus_V Angle CCC 13007.42 13842.60 3.91 0.090486 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00007sq_v01_00018hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00018hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 32.13 8.21 Num Hot pixels: 93 Hot pixel threshold: 81.38 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 9.622933 Iteration 2 Error: 3.655904 Iteration 3 Error: 1.917505 Iteration 4 Error: 1.837879 Iteration 5 Error: 0.964330 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.94 0.55 ...... Frame ( 3) shift: -1.88 1.10 ...... Frame ( 4) shift: -2.82 1.65 ...... Frame ( 5) shift: -3.76 2.20 ...... Frame ( 6) shift: -4.41 2.65 ...... Frame ( 7) shift: -4.76 3.00 ...... Frame ( 8) shift: -5.12 3.36 ...... Frame ( 9) shift: -5.47 3.64 ...... Frame ( 10) shift: -5.83 3.85 ...... Frame ( 11) shift: -6.18 4.05 ...... Frame ( 12) shift: -6.55 4.24 ...... Frame ( 13) shift: -6.93 4.42 ...... Frame ( 14) shift: -7.31 4.60 ...... Frame ( 15) shift: -7.57 4.83 ...... Frame ( 16) shift: -7.69 5.10 ...... Frame ( 17) shift: -7.82 5.38 ...... Frame ( 18) shift: -7.97 5.64 ...... Frame ( 19) shift: -8.14 5.88 ...... Frame ( 20) shift: -8.31 6.13 ...... Frame ( 21) shift: -8.52 6.39 ...... Frame ( 22) shift: -8.77 6.69 ...... Frame ( 23) shift: -9.01 6.98 ...... Frame ( 24) shift: -9.29 7.25 ...... Frame ( 25) shift: -9.61 7.49 ...... Frame ( 26) shift: -9.92 7.72 ...... Frame ( 27) shift: -10.36 8.09 ...... Frame ( 28) shift: -10.91 8.60 ...... Frame ( 29) shift: -11.46 9.10 ...... Frame ( 30) shift: -12.02 9.60 ...... Frame ( 31) shift: -12.59 10.11 ...... Frame ( 32) shift: -13.16 10.61 ...... Frame ( 33) shift: -13.96 11.14 ...... Frame ( 34) shift: -14.98 11.70 ...... Frame ( 35) shift: -16.01 12.25 ...... Frame ( 36) shift: -17.07 12.91 ...... Frame ( 37) shift: -18.19 13.65 ...... Frame ( 38) shift: -19.30 14.40 ...... Frame ( 39) shift: -20.41 15.14 ...... Frame ( 40) shift: -21.53 15.89 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 7.174809 Iteration 2 Error: 3.249136 Iteration 3 Error: 1.797613 Iteration 4 Error: 1.421512 Iteration 5 Error: 1.069421 Align patch 1 24 left Iteration 1 Error: 3.444039 Iteration 2 Error: 1.724637 Iteration 3 Error: 1.387444 Iteration 4 Error: 1.012282 Iteration 5 Error: 0.843812 Align patch 2 23 left Iteration 1 Error: 35.938786 Iteration 2 Error: 36.310360 Iteration 3 Error: 32.040321 Iteration 4 Error: 2.036366 Iteration 5 Error: 0.637180 Align patch 2 23 left Iteration 1 Error: 57.545578 Iteration 2 Error: 37.192940 Iteration 3 Error: 15.404735 Iteration 4 Error: 1.385943 Iteration 5 Error: 0.518656 Align patch 3 22 left Iteration 1 Error: 35.949333 Iteration 2 Error: 37.137081 Iteration 3 Error: 35.983723 Iteration 4 Error: 37.151649 Iteration 5 Error: 23.972206 Align patch 3 22 left Iteration 1 Error: 37.192772 Iteration 2 Error: 30.683632 Iteration 3 Error: 20.835037 Iteration 4 Error: 12.645385 Iteration 5 Error: 12.120884 Align patch 4 21 left Iteration 1 Error: 30.450350 Iteration 2 Error: 19.023075 Iteration 3 Error: 11.685822 Iteration 4 Error: 9.086192 Iteration 5 Error: 7.104655 Align patch 4 21 left Iteration 1 Error: 30.871517 Iteration 2 Error: 17.930094 Iteration 3 Error: 6.196787 Iteration 4 Error: 2.933011 Iteration 5 Error: 4.621291 Align patch 5 20 left Iteration 1 Error: 3.352796 Iteration 2 Error: 0.546345 Iteration 3 Error: 0.230518 Iteration 4 Error: 0.137390 Iteration 5 Error: 0.076368 Align patch 5 20 left Iteration 1 Error: 2.890771 Iteration 2 Error: 1.539905 Iteration 3 Error: 0.991245 Iteration 4 Error: 0.669843 Iteration 5 Error: 0.517425 Align patch 6 19 left Iteration 1 Error: 4.870428 Iteration 2 Error: 1.664957 Iteration 3 Error: 1.042756 Iteration 4 Error: 0.578530 Iteration 5 Error: 0.229055 Align patch 6 19 left Iteration 1 Error: 2.492401 Iteration 2 Error: 0.597353 Iteration 3 Error: 0.422839 Iteration 4 Error: 0.250580 Iteration 5 Error: 0.192074 Align patch 7 18 left Iteration 1 Error: 36.463879 Iteration 2 Error: 33.498581 Iteration 3 Error: 12.768729 Iteration 4 Error: 3.525877 Iteration 5 Error: 2.166709 Align patch 7 18 left Iteration 1 Error: 58.027744 Iteration 2 Error: 49.644642 Iteration 3 Error: 19.403967 Iteration 4 Error: 2.277163 Iteration 5 Error: 0.564350 Align patch 8 17 left Iteration 1 Error: 39.050793 Iteration 2 Error: 37.331810 Iteration 3 Error: 37.115936 Iteration 4 Error: 38.432941 Iteration 5 Error: 36.785740 Align patch 8 17 left Iteration 1 Error: 46.856640 Iteration 2 Error: 31.601391 Iteration 3 Error: 12.296200 Iteration 4 Error: 5.824070 Iteration 5 Error: 5.102340 Align patch 9 16 left Iteration 1 Error: 10.241892 Iteration 2 Error: 26.170074 Iteration 3 Error: 9.800389 Iteration 4 Error: 2.688707 Iteration 5 Error: 5.318952 Align patch 9 16 left Iteration 1 Error: 33.134003 Iteration 2 Error: 18.267199 Iteration 3 Error: 10.413042 Iteration 4 Error: 3.810186 Iteration 5 Error: 7.432662 Align patch 10 15 left Iteration 1 Error: 15.888976 Iteration 2 Error: 6.754996 Iteration 3 Error: 1.441901 Iteration 4 Error: 0.757864 Iteration 5 Error: 0.552887 Align patch 10 15 left Iteration 1 Error: 3.863998 Iteration 2 Error: 2.245409 Iteration 3 Error: 1.648073 Iteration 4 Error: 1.315128 Iteration 5 Error: 1.057765 Align patch 11 14 left Iteration 1 Error: 4.565102 Iteration 2 Error: 1.670981 Iteration 3 Error: 0.612678 Iteration 4 Error: 0.449455 Iteration 5 Error: 0.214689 Align patch 11 14 left Iteration 1 Error: 58.029549 Iteration 2 Error: 12.031135 Iteration 3 Error: 2.471642 Iteration 4 Error: 1.754160 Iteration 5 Error: 1.584079 Align patch 12 13 left Iteration 1 Error: 36.023666 Iteration 2 Error: 36.683865 Iteration 3 Error: 37.264420 Iteration 4 Error: 36.547310 Iteration 5 Error: 36.982841 Align patch 12 13 left Iteration 1 Error: 58.862133 Iteration 2 Error: 48.401066 Iteration 3 Error: 20.008041 Iteration 4 Error: 2.612075 Iteration 5 Error: 2.651304 Align patch 13 12 left Iteration 1 Error: 11.768354 Iteration 2 Error: 8.150764 Iteration 3 Error: 2.740020 Iteration 4 Error: 1.500610 Iteration 5 Error: 3.650838 Align patch 13 12 left Iteration 1 Error: 47.194675 Iteration 2 Error: 25.422310 Iteration 3 Error: 19.145611 Iteration 4 Error: 14.138922 Iteration 5 Error: 8.166681 Align patch 14 11 left Iteration 1 Error: 18.594030 Iteration 2 Error: 16.782045 Iteration 3 Error: 9.757016 Iteration 4 Error: 8.545191 Iteration 5 Error: 6.003613 Align patch 14 11 left Iteration 1 Error: 43.005936 Iteration 2 Error: 22.796593 Iteration 3 Error: 13.492054 Iteration 4 Error: 6.532965 Iteration 5 Error: 3.257983 Align patch 15 10 left Iteration 1 Error: 27.047253 Iteration 2 Error: 18.567223 Iteration 3 Error: 12.571203 Iteration 4 Error: 14.641081 Iteration 5 Error: 12.821383 Align patch 15 10 left Iteration 1 Error: 35.281857 Iteration 2 Error: 61.511570 Iteration 3 Error: 59.535770 Iteration 4 Error: 35.491974 Iteration 5 Error: 39.914749 Align patch 16 9 left Iteration 1 Error: 5.016988 Iteration 2 Error: 2.638083 Iteration 3 Error: 0.757953 Iteration 4 Error: 0.418076 Iteration 5 Error: 0.330947 Align patch 16 9 left Iteration 1 Error: 6.745526 Iteration 2 Error: 1.871076 Iteration 3 Error: 0.986156 Iteration 4 Error: 0.752789 Iteration 5 Error: 0.495505 Align patch 17 8 left Iteration 1 Error: 35.971874 Iteration 2 Error: 32.218048 Iteration 3 Error: 1.505865 Iteration 4 Error: 0.717945 Iteration 5 Error: 0.582195 Align patch 17 8 left Iteration 1 Error: 7.529512 Iteration 2 Error: 2.156252 Iteration 3 Error: 1.304346 Iteration 4 Error: 1.198800 Iteration 5 Error: 1.271083 Align patch 18 7 left Iteration 1 Error: 52.025097 Iteration 2 Error: 43.115433 Iteration 3 Error: 29.728830 Iteration 4 Error: 28.688341 Iteration 5 Error: 14.469196 Align patch 18 7 left Iteration 1 Error: 57.790718 Iteration 2 Error: 46.805264 Iteration 3 Error: 25.334984 Iteration 4 Error: 37.554390 Iteration 5 Error: 35.135906 Align patch 19 6 left Iteration 1 Error: 36.937149 Iteration 2 Error: 35.839207 Iteration 3 Error: 28.633430 Iteration 4 Error: 25.212801 Iteration 5 Error: 17.169395 Align patch 19 6 left Iteration 1 Error: 65.674469 Iteration 2 Error: 69.976379 Iteration 3 Error: 60.914089 Iteration 4 Error: 11.378631 Iteration 5 Error: 9.815165 Align patch 20 5 left Iteration 1 Error: 36.155506 Iteration 2 Error: 37.353748 Iteration 3 Error: 37.407459 Iteration 4 Error: 36.278355 Iteration 5 Error: 36.242870 Align patch 20 5 left Iteration 1 Error: 58.272293 Iteration 2 Error: 58.057762 Iteration 3 Error: 58.811443 Iteration 4 Error: 45.162243 Iteration 5 Error: 41.606258 Align patch 21 4 left Iteration 1 Error: 18.434118 Iteration 2 Error: 18.910109 Iteration 3 Error: 19.513161 Iteration 4 Error: 20.441303 Iteration 5 Error: 7.270582 Align patch 21 4 left Iteration 1 Error: 4.625963 Iteration 2 Error: 1.726057 Iteration 3 Error: 0.922671 Iteration 4 Error: 0.589146 Iteration 5 Error: 0.384941 Align patch 22 3 left Iteration 1 Error: 25.002193 Iteration 2 Error: 26.199713 Iteration 3 Error: 5.120767 Iteration 4 Error: 5.318118 Iteration 5 Error: 1.978109 Align patch 22 3 left Iteration 1 Error: 5.670153 Iteration 2 Error: 1.583043 Iteration 3 Error: 1.318686 Iteration 4 Error: 0.799463 Iteration 5 Error: 0.404512 Align patch 23 2 left Iteration 1 Error: 13.808306 Iteration 2 Error: 9.934480 Iteration 3 Error: 5.074947 Iteration 4 Error: 1.343761 Iteration 5 Error: 0.577421 Align patch 23 2 left Iteration 1 Error: 27.008856 Iteration 2 Error: 57.532024 Iteration 3 Error: 53.935501 Iteration 4 Error: 50.044746 Iteration 5 Error: 44.131851 Align patch 24 1 left Iteration 1 Error: 37.306812 Iteration 2 Error: 36.186409 Iteration 3 Error: 38.577785 Iteration 4 Error: 19.521925 Iteration 5 Error: 32.329842 Align patch 24 1 left Iteration 1 Error: 53.683933 Iteration 2 Error: 58.147045 Iteration 3 Error: 32.482792 Iteration 4 Error: 32.242241 Iteration 5 Error: 20.042217 Align patch 25 0 left Iteration 1 Error: 21.311813 Iteration 2 Error: 20.609032 Iteration 3 Error: 19.386189 Iteration 4 Error: 18.784006 Iteration 5 Error: 24.785517 Align patch 25 0 left Iteration 1 Error: 57.678909 Iteration 2 Error: 57.554222 Iteration 3 Error: 32.257496 Iteration 4 Error: 22.611832 Iteration 5 Error: 43.694229 3D Fitting completed. Patch alignment time: 31.09(sec) Local motion has been corrected. Process thread exits. Computational time: 47.771507 sec Total time: 55.156277 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00018hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00018hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.798422s Reading file: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00018hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.595924s ........................................ >>>>>>TIME<<<<<< FFT: 1.059582s Defocus_U Defocus_V Angle CCC 14877.00 14318.39 87.28 0.055243 Final Values Defocus_U Defocus_V Angle CCC 14862.91 14348.14 85.16 0.112386 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00007sq_v01_00019hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00019hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 40.50 6.85 Num Hot pixels: 203 Hot pixel threshold: 81.62 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.029051 Iteration 2 Error: 0.158309 Iteration 3 Error: 0.033729 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.16 -0.10 ...... Frame ( 3) shift: -0.33 -0.20 ...... Frame ( 4) shift: -0.49 -0.29 ...... Frame ( 5) shift: -0.66 -0.39 ...... Frame ( 6) shift: -0.76 -0.40 ...... Frame ( 7) shift: -0.80 -0.33 ...... Frame ( 8) shift: -0.84 -0.25 ...... Frame ( 9) shift: -0.82 -0.15 ...... Frame ( 10) shift: -0.75 -0.02 ...... Frame ( 11) shift: -0.67 0.12 ...... Frame ( 12) shift: -0.63 0.23 ...... Frame ( 13) shift: -0.61 0.31 ...... Frame ( 14) shift: -0.59 0.39 ...... Frame ( 15) shift: -0.56 0.46 ...... Frame ( 16) shift: -0.53 0.52 ...... Frame ( 17) shift: -0.49 0.58 ...... Frame ( 18) shift: -0.48 0.64 ...... Frame ( 19) shift: -0.49 0.72 ...... Frame ( 20) shift: -0.50 0.79 ...... Frame ( 21) shift: -0.48 0.85 ...... Frame ( 22) shift: -0.42 0.91 ...... Frame ( 23) shift: -0.36 0.96 ...... Frame ( 24) shift: -0.31 0.98 ...... Frame ( 25) shift: -0.25 0.97 ...... Frame ( 26) shift: -0.20 0.95 ...... Frame ( 27) shift: -0.15 0.97 ...... Frame ( 28) shift: -0.09 1.02 ...... Frame ( 29) shift: -0.04 1.06 ...... Frame ( 30) shift: -0.01 1.11 ...... Frame ( 31) shift: 0.01 1.16 ...... Frame ( 32) shift: 0.03 1.21 ...... Frame ( 33) shift: 0.07 1.25 ...... Frame ( 34) shift: 0.15 1.29 ...... Frame ( 35) shift: 0.22 1.33 ...... Frame ( 36) shift: 0.24 1.36 ...... Frame ( 37) shift: 0.21 1.39 ...... Frame ( 38) shift: 0.18 1.43 ...... Frame ( 39) shift: 0.15 1.46 ...... Frame ( 40) shift: 0.12 1.49 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.674800 Iteration 2 Error: 0.108358 Iteration 3 Error: 0.030997 Align patch 2 23 left Iteration 1 Error: 1.339282 Iteration 2 Error: 0.157920 Iteration 3 Error: 0.039152 Align patch 3 22 left Iteration 1 Error: 0.447325 Iteration 2 Error: 0.080289 Iteration 3 Error: 0.016115 Align patch 4 21 left Iteration 1 Error: 0.658720 Iteration 2 Error: 0.053119 Iteration 3 Error: 0.014081 Align patch 5 20 left Iteration 1 Error: 0.666795 Iteration 2 Error: 0.056053 Iteration 3 Error: 0.009725 Align patch 6 19 left Iteration 1 Error: 0.785825 Iteration 2 Error: 0.156018 Iteration 3 Error: 0.041822 Align patch 7 18 left Iteration 1 Error: 0.483901 Iteration 2 Error: 0.139261 Iteration 3 Error: 0.048016 Align patch 8 17 left Iteration 1 Error: 0.757392 Iteration 2 Error: 0.135368 Iteration 3 Error: 0.039408 Align patch 9 16 left Iteration 1 Error: 0.665573 Iteration 2 Error: 0.074780 Iteration 3 Error: 0.016122 Align patch 10 15 left Iteration 1 Error: 0.864303 Iteration 2 Error: 0.135308 Iteration 3 Error: 0.039150 Align patch 11 14 left Iteration 1 Error: 0.517072 Iteration 2 Error: 0.137608 Iteration 3 Error: 0.054561 Iteration 4 Error: 0.021453 Align patch 12 13 left Iteration 1 Error: 0.721067 Iteration 2 Error: 0.165765 Iteration 3 Error: 0.047578 Align patch 13 12 left Iteration 1 Error: 0.687537 Iteration 2 Error: 0.100068 Iteration 3 Error: 0.020838 Align patch 14 11 left Iteration 1 Error: 0.880687 Iteration 2 Error: 0.157172 Iteration 3 Error: 0.031010 Align patch 15 10 left Iteration 1 Error: 0.555966 Iteration 2 Error: 0.094264 Iteration 3 Error: 0.028928 Align patch 16 9 left Iteration 1 Error: 0.509341 Iteration 2 Error: 0.125889 Iteration 3 Error: 0.042463 Align patch 17 8 left Iteration 1 Error: 0.798892 Iteration 2 Error: 0.120223 Iteration 3 Error: 0.029832 Align patch 18 7 left Iteration 1 Error: 0.647424 Iteration 2 Error: 0.123941 Iteration 3 Error: 0.041222 Align patch 19 6 left Iteration 1 Error: 0.916742 Iteration 2 Error: 0.149509 Iteration 3 Error: 0.036879 Align patch 20 5 left Iteration 1 Error: 0.920581 Iteration 2 Error: 0.181867 Iteration 3 Error: 0.037483 Align patch 21 4 left Iteration 1 Error: 0.609711 Iteration 2 Error: 0.126108 Iteration 3 Error: 0.020782 Align patch 22 3 left Iteration 1 Error: 1.046209 Iteration 2 Error: 0.147789 Iteration 3 Error: 0.023360 Align patch 23 2 left Iteration 1 Error: 0.930064 Iteration 2 Error: 0.114005 Iteration 3 Error: 0.028093 Align patch 24 1 left Iteration 1 Error: 0.694875 Iteration 2 Error: 0.102877 Iteration 3 Error: 0.022552 Align patch 25 0 left Iteration 1 Error: 0.814323 Iteration 2 Error: 0.105838 Iteration 3 Error: 0.029564 3D Fitting completed. Patch alignment time: 11.03(sec) Local motion has been corrected. Process thread exits. Computational time: 25.785645 sec Total time: 37.031723 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00019hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00019hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.815099s Reading file: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00019hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.761322s ........................................ >>>>>>TIME<<<<<< FFT: 0.957888s Defocus_U Defocus_V Angle CCC 10388.70 11154.32 11.25 0.043668 Final Values Defocus_U Defocus_V Angle CCC 10405.88 11193.41 10.93 0.074614 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00007sq_v01_00019hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00019hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 40.85 6.94 Num Hot pixels: 186 Hot pixel threshold: 82.49 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.619047 Iteration 2 Error: 0.102159 Iteration 3 Error: 0.019237 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.15 0.01 ...... Frame ( 3) shift: -0.31 0.03 ...... Frame ( 4) shift: -0.46 0.04 ...... Frame ( 5) shift: -0.61 0.06 ...... Frame ( 6) shift: -0.72 0.06 ...... Frame ( 7) shift: -0.78 0.04 ...... Frame ( 8) shift: -0.85 0.02 ...... Frame ( 9) shift: -0.88 0.04 ...... Frame ( 10) shift: -0.89 0.08 ...... Frame ( 11) shift: -0.90 0.12 ...... Frame ( 12) shift: -0.87 0.18 ...... Frame ( 13) shift: -0.81 0.24 ...... Frame ( 14) shift: -0.74 0.30 ...... Frame ( 15) shift: -0.69 0.34 ...... Frame ( 16) shift: -0.65 0.36 ...... Frame ( 17) shift: -0.60 0.38 ...... Frame ( 18) shift: -0.61 0.44 ...... Frame ( 19) shift: -0.67 0.53 ...... Frame ( 20) shift: -0.72 0.62 ...... Frame ( 21) shift: -0.74 0.66 ...... Frame ( 22) shift: -0.73 0.65 ...... Frame ( 23) shift: -0.71 0.63 ...... Frame ( 24) shift: -0.68 0.65 ...... Frame ( 25) shift: -0.63 0.69 ...... Frame ( 26) shift: -0.59 0.72 ...... Frame ( 27) shift: -0.58 0.75 ...... Frame ( 28) shift: -0.61 0.78 ...... Frame ( 29) shift: -0.63 0.80 ...... Frame ( 30) shift: -0.63 0.84 ...... Frame ( 31) shift: -0.59 0.89 ...... Frame ( 32) shift: -0.54 0.95 ...... Frame ( 33) shift: -0.53 0.98 ...... Frame ( 34) shift: -0.54 1.01 ...... Frame ( 35) shift: -0.55 1.03 ...... Frame ( 36) shift: -0.56 1.03 ...... Frame ( 37) shift: -0.55 1.02 ...... Frame ( 38) shift: -0.54 1.02 ...... Frame ( 39) shift: -0.53 1.01 ...... Frame ( 40) shift: -0.53 1.00 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.685469 Iteration 2 Error: 0.121846 Iteration 3 Error: 0.046437 Align patch 2 23 left Iteration 1 Error: 0.687424 Iteration 2 Error: 0.143048 Iteration 3 Error: 0.028812 Align patch 3 22 left Iteration 1 Error: 1.036387 Iteration 2 Error: 0.140626 Iteration 3 Error: 0.018340 Align patch 4 21 left Iteration 1 Error: 1.026536 Iteration 2 Error: 0.149531 Iteration 3 Error: 0.032437 Align patch 5 20 left Iteration 1 Error: 0.701271 Iteration 2 Error: 0.087741 Iteration 3 Error: 0.018902 Align patch 6 19 left Iteration 1 Error: 0.588033 Iteration 2 Error: 0.096080 Iteration 3 Error: 0.021717 Align patch 7 18 left Iteration 1 Error: 0.809767 Iteration 2 Error: 0.067755 Iteration 3 Error: 0.035571 Align patch 8 17 left Iteration 1 Error: 0.529759 Iteration 2 Error: 0.066829 Iteration 3 Error: 0.016292 Align patch 9 16 left Iteration 1 Error: 0.662441 Iteration 2 Error: 0.110060 Iteration 3 Error: 0.027129 Align patch 10 15 left Iteration 1 Error: 0.399441 Iteration 2 Error: 0.060907 Iteration 3 Error: 0.008977 Align patch 11 14 left Iteration 1 Error: 0.562056 Iteration 2 Error: 0.093562 Iteration 3 Error: 0.023036 Align patch 12 13 left Iteration 1 Error: 0.646194 Iteration 2 Error: 0.141112 Iteration 3 Error: 0.035542 Align patch 13 12 left Iteration 1 Error: 0.491454 Iteration 2 Error: 0.064529 Iteration 3 Error: 0.010364 Align patch 14 11 left Iteration 1 Error: 0.701612 Iteration 2 Error: 0.103584 Iteration 3 Error: 0.024862 Align patch 15 10 left Iteration 1 Error: 0.607532 Iteration 2 Error: 0.097969 Iteration 3 Error: 0.015502 Align patch 16 9 left Iteration 1 Error: 0.968994 Iteration 2 Error: 0.144770 Iteration 3 Error: 0.030639 Align patch 17 8 left Iteration 1 Error: 0.624960 Iteration 2 Error: 0.127966 Iteration 3 Error: 0.036917 Align patch 18 7 left Iteration 1 Error: 0.854608 Iteration 2 Error: 0.189399 Iteration 3 Error: 0.050107 Iteration 4 Error: 0.023190 Align patch 19 6 left Iteration 1 Error: 0.612698 Iteration 2 Error: 0.112797 Iteration 3 Error: 0.024073 Align patch 20 5 left Iteration 1 Error: 1.065893 Iteration 2 Error: 0.145051 Iteration 3 Error: 0.034167 Align patch 21 4 left Iteration 1 Error: 0.733975 Iteration 2 Error: 0.057022 Iteration 3 Error: 0.014155 Align patch 22 3 left Iteration 1 Error: 0.672116 Iteration 2 Error: 0.094687 Iteration 3 Error: 0.027016 Align patch 23 2 left Iteration 1 Error: 1.106077 Iteration 2 Error: 0.146442 Iteration 3 Error: 0.046360 Align patch 24 1 left Iteration 1 Error: 0.841397 Iteration 2 Error: 0.084862 Iteration 3 Error: 0.018230 Align patch 25 0 left Iteration 1 Error: 0.960110 Iteration 2 Error: 0.112953 Iteration 3 Error: 0.030832 3D Fitting completed. Patch alignment time: 11.27(sec) Local motion has been corrected. Process thread exits. Computational time: 29.021360 sec Total time: 36.412674 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00019hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00019hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.805419s Reading file: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00019hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.587267s ........................................ >>>>>>TIME<<<<<< FFT: 1.043535s Defocus_U Defocus_V Angle CCC 10537.03 10068.49 87.40 0.043455 Final Values Defocus_U Defocus_V Angle CCC 10549.53 10080.99 85.84 0.076901 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00007sq_v01_00019hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00019hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 41.03 6.92 Num Hot pixels: 207 Hot pixel threshold: 82.53 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.030255 Iteration 2 Error: 0.187364 Iteration 3 Error: 0.033171 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.26 -0.13 ...... Frame ( 3) shift: -0.53 -0.25 ...... Frame ( 4) shift: -0.79 -0.38 ...... Frame ( 5) shift: -1.06 -0.50 ...... Frame ( 6) shift: -1.18 -0.56 ...... Frame ( 7) shift: -1.17 -0.55 ...... Frame ( 8) shift: -1.16 -0.54 ...... Frame ( 9) shift: -1.13 -0.51 ...... Frame ( 10) shift: -1.08 -0.45 ...... Frame ( 11) shift: -1.03 -0.39 ...... Frame ( 12) shift: -1.02 -0.29 ...... Frame ( 13) shift: -1.06 -0.15 ...... Frame ( 14) shift: -1.10 -0.02 ...... Frame ( 15) shift: -1.12 0.08 ...... Frame ( 16) shift: -1.12 0.15 ...... Frame ( 17) shift: -1.13 0.21 ...... Frame ( 18) shift: -1.13 0.28 ...... Frame ( 19) shift: -1.15 0.38 ...... Frame ( 20) shift: -1.16 0.47 ...... Frame ( 21) shift: -1.18 0.55 ...... Frame ( 22) shift: -1.21 0.60 ...... Frame ( 23) shift: -1.24 0.64 ...... Frame ( 24) shift: -1.26 0.68 ...... Frame ( 25) shift: -1.26 0.71 ...... Frame ( 26) shift: -1.25 0.74 ...... Frame ( 27) shift: -1.27 0.79 ...... Frame ( 28) shift: -1.31 0.84 ...... Frame ( 29) shift: -1.34 0.89 ...... Frame ( 30) shift: -1.33 0.95 ...... Frame ( 31) shift: -1.26 1.02 ...... Frame ( 32) shift: -1.20 1.09 ...... Frame ( 33) shift: -1.12 1.16 ...... Frame ( 34) shift: -1.02 1.23 ...... Frame ( 35) shift: -0.92 1.30 ...... Frame ( 36) shift: -0.89 1.36 ...... Frame ( 37) shift: -0.93 1.42 ...... Frame ( 38) shift: -0.96 1.48 ...... Frame ( 39) shift: -1.00 1.55 ...... Frame ( 40) shift: -1.04 1.61 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.200548 Iteration 2 Error: 0.197354 Iteration 3 Error: 0.042219 Align patch 2 23 left Iteration 1 Error: 0.835132 Iteration 2 Error: 0.114737 Iteration 3 Error: 0.022905 Align patch 3 22 left Iteration 1 Error: 0.847701 Iteration 2 Error: 0.097565 Iteration 3 Error: 0.019575 Align patch 4 21 left Iteration 1 Error: 0.794676 Iteration 2 Error: 0.079654 Iteration 3 Error: 0.012808 Align patch 5 20 left Iteration 1 Error: 0.947334 Iteration 2 Error: 0.125864 Iteration 3 Error: 0.027708 Align patch 6 19 left Iteration 1 Error: 1.162561 Iteration 2 Error: 0.163811 Iteration 3 Error: 0.045866 Align patch 7 18 left Iteration 1 Error: 0.696075 Iteration 2 Error: 0.140159 Iteration 3 Error: 0.053356 Iteration 4 Error: 0.017770 Align patch 8 17 left Iteration 1 Error: 0.717235 Iteration 2 Error: 0.114764 Iteration 3 Error: 0.050226 Iteration 4 Error: 0.016011 Align patch 9 16 left Iteration 1 Error: 0.503548 Iteration 2 Error: 0.053717 Iteration 3 Error: 0.009425 Align patch 10 15 left Iteration 1 Error: 0.705860 Iteration 2 Error: 0.119995 Iteration 3 Error: 0.027249 Align patch 11 14 left Iteration 1 Error: 0.968525 Iteration 2 Error: 0.232676 Iteration 3 Error: 0.041356 Align patch 12 13 left Iteration 1 Error: 0.747904 Iteration 2 Error: 0.265061 Iteration 3 Error: 0.113583 Iteration 4 Error: 0.029441 Align patch 13 12 left Iteration 1 Error: 0.587332 Iteration 2 Error: 0.155743 Iteration 3 Error: 0.040164 Align patch 14 11 left Iteration 1 Error: 0.624446 Iteration 2 Error: 0.108618 Iteration 3 Error: 0.036702 Align patch 15 10 left Iteration 1 Error: 0.714244 Iteration 2 Error: 0.113935 Iteration 3 Error: 0.019371 Align patch 16 9 left Iteration 1 Error: 0.889237 Iteration 2 Error: 0.120069 Iteration 3 Error: 0.025517 Align patch 17 8 left Iteration 1 Error: 0.631639 Iteration 2 Error: 0.107343 Iteration 3 Error: 0.036018 Align patch 18 7 left Iteration 1 Error: 0.851870 Iteration 2 Error: 0.171601 Iteration 3 Error: 0.033004 Align patch 19 6 left Iteration 1 Error: 0.780782 Iteration 2 Error: 0.086236 Iteration 3 Error: 0.019159 Align patch 20 5 left Iteration 1 Error: 0.586673 Iteration 2 Error: 0.141753 Iteration 3 Error: 0.042302 Align patch 21 4 left Iteration 1 Error: 0.831872 Iteration 2 Error: 0.110999 Iteration 3 Error: 0.031171 Align patch 22 3 left Iteration 1 Error: 0.899245 Iteration 2 Error: 0.135177 Iteration 3 Error: 0.034083 Align patch 23 2 left Iteration 1 Error: 0.834739 Iteration 2 Error: 0.124733 Iteration 3 Error: 0.023160 Align patch 24 1 left Iteration 1 Error: 0.685562 Iteration 2 Error: 0.092876 Iteration 3 Error: 0.015006 Align patch 25 0 left Iteration 1 Error: 0.866466 Iteration 2 Error: 0.203846 Iteration 3 Error: 0.054024 Iteration 4 Error: 0.025236 3D Fitting completed. Patch alignment time: 15.15(sec) Local motion has been corrected. Process thread exits. Computational time: 23.198509 sec Total time: 29.551353 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00019hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00019hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.545303s Reading file: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00019hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.679555s ........................................ >>>>>>TIME<<<<<< FFT: 0.942525s Defocus_U Defocus_V Angle CCC 13472.66 14332.03 3.48 0.053484 Final Values Defocus_U Defocus_V Angle CCC 13472.66 14341.41 3.48 0.082995 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00007sq_v01_00019hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00019hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.350e-01 1.004e-01 CC threshold: 0.738 Mean Std: 23.39 7.72 Num Hot pixels: 58 Hot pixel threshold: 69.72 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.547410 Iteration 2 Error: 0.036143 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.04 -0.02 ...... Frame ( 3) shift: -0.07 -0.04 ...... Frame ( 4) shift: -0.11 -0.06 ...... Frame ( 5) shift: -0.15 -0.08 ...... Frame ( 6) shift: -0.23 -0.14 ...... Frame ( 7) shift: -0.37 -0.24 ...... Frame ( 8) shift: -0.50 -0.34 ...... Frame ( 9) shift: -0.60 -0.33 ...... Frame ( 10) shift: -0.67 -0.23 ...... Frame ( 11) shift: -0.73 -0.12 ...... Frame ( 12) shift: -0.73 -0.06 ...... Frame ( 13) shift: -0.66 -0.02 ...... Frame ( 14) shift: -0.58 0.01 ...... Frame ( 15) shift: -0.55 0.07 ...... Frame ( 16) shift: -0.56 0.15 ...... Frame ( 17) shift: -0.57 0.22 ...... Frame ( 18) shift: -0.61 0.24 ...... Frame ( 19) shift: -0.69 0.21 ...... Frame ( 20) shift: -0.76 0.18 ...... Frame ( 21) shift: -0.77 0.17 ...... Frame ( 22) shift: -0.70 0.16 ...... Frame ( 23) shift: -0.64 0.16 ...... Frame ( 24) shift: -0.61 0.16 ...... Frame ( 25) shift: -0.62 0.15 ...... Frame ( 26) shift: -0.63 0.14 ...... Frame ( 27) shift: -0.64 0.13 ...... Frame ( 28) shift: -0.66 0.14 ...... Frame ( 29) shift: -0.68 0.14 ...... Frame ( 30) shift: -0.69 0.18 ...... Frame ( 31) shift: -0.70 0.27 ...... Frame ( 32) shift: -0.71 0.35 ...... Frame ( 33) shift: -0.69 0.36 ...... Frame ( 34) shift: -0.64 0.30 ...... Frame ( 35) shift: -0.59 0.24 ...... Frame ( 36) shift: -0.59 0.25 ...... Frame ( 37) shift: -0.63 0.34 ...... Frame ( 38) shift: -0.67 0.44 ...... Frame ( 39) shift: -0.70 0.53 ...... Frame ( 40) shift: -0.74 0.62 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 32.624901 Iteration 2 Error: 37.321690 Iteration 3 Error: 37.205727 Iteration 4 Error: 30.824678 Iteration 5 Error: 25.199114 Align patch 1 24 left Iteration 1 Error: 15.928443 Iteration 2 Error: 10.585814 Iteration 3 Error: 4.275453 Iteration 4 Error: 3.943137 Iteration 5 Error: 2.014420 Align patch 2 23 left Iteration 1 Error: 45.438477 Iteration 2 Error: 40.019684 Iteration 3 Error: 9.235637 Iteration 4 Error: 34.369106 Iteration 5 Error: 33.892464 Align patch 2 23 left Iteration 1 Error: 14.348665 Iteration 2 Error: 10.350199 Iteration 3 Error: 9.250463 Iteration 4 Error: 2.407682 Iteration 5 Error: 1.390148 Align patch 3 22 left Iteration 1 Error: 16.724201 Iteration 2 Error: 25.911095 Iteration 3 Error: 22.246147 Iteration 4 Error: 22.379576 Iteration 5 Error: 21.646263 Align patch 3 22 left Iteration 1 Error: 4.522899 Iteration 2 Error: 9.465537 Iteration 3 Error: 2.731518 Iteration 4 Error: 7.697349 Iteration 5 Error: 32.222843 Align patch 4 21 left Iteration 1 Error: 2.216545 Iteration 2 Error: 0.767751 Iteration 3 Error: 0.278527 Iteration 4 Error: 0.362302 Iteration 5 Error: 0.089192 Align patch 4 21 left Iteration 1 Error: 1.617191 Iteration 2 Error: 0.362084 Iteration 3 Error: 0.065793 Iteration 4 Error: 0.028101 Align patch 5 20 left Iteration 1 Error: 2.168427 Iteration 2 Error: 0.730632 Iteration 3 Error: 0.626360 Iteration 4 Error: 0.347526 Iteration 5 Error: 0.247443 Align patch 5 20 left Iteration 1 Error: 1.648886 Iteration 2 Error: 0.414743 Iteration 3 Error: 0.067257 Iteration 4 Error: 0.019212 Align patch 6 19 left Iteration 1 Error: 2.306144 Iteration 2 Error: 0.995863 Iteration 3 Error: 0.601140 Iteration 4 Error: 0.234674 Iteration 5 Error: 0.201975 Align patch 6 19 left Iteration 1 Error: 1.539269 Iteration 2 Error: 0.325398 Iteration 3 Error: 0.123305 Iteration 4 Error: 0.059755 Iteration 5 Error: 0.026365 Align patch 7 18 left Iteration 1 Error: 1.882666 Iteration 2 Error: 1.158880 Iteration 3 Error: 0.925010 Iteration 4 Error: 0.497867 Iteration 5 Error: 0.394953 Align patch 7 18 left Iteration 1 Error: 1.971903 Iteration 2 Error: 0.686038 Iteration 3 Error: 0.399865 Iteration 4 Error: 0.282385 Iteration 5 Error: 0.162560 Align patch 8 17 left Iteration 1 Error: 6.951144 Iteration 2 Error: 25.923759 Iteration 3 Error: 25.755642 Iteration 4 Error: 26.293800 Iteration 5 Error: 26.352087 Align patch 8 17 left Iteration 1 Error: 2.206196 Iteration 2 Error: 0.852963 Iteration 3 Error: 0.362326 Iteration 4 Error: 0.334169 Iteration 5 Error: 0.126434 Align patch 9 16 left Iteration 1 Error: 3.220311 Iteration 2 Error: 1.586822 Iteration 3 Error: 0.596642 Iteration 4 Error: 0.352990 Iteration 5 Error: 0.195500 Align patch 9 16 left Iteration 1 Error: 1.680917 Iteration 2 Error: 0.134370 Iteration 3 Error: 0.021189 Align patch 10 15 left Iteration 1 Error: 2.282968 Iteration 2 Error: 0.307327 Iteration 3 Error: 0.120703 Iteration 4 Error: 0.041150 Align patch 11 14 left Iteration 1 Error: 12.715014 Iteration 2 Error: 14.245708 Iteration 3 Error: 14.413819 Iteration 4 Error: 14.709215 Iteration 5 Error: 14.665529 Align patch 11 14 left Iteration 1 Error: 1.797398 Iteration 2 Error: 0.269451 Iteration 3 Error: 0.067087 Iteration 4 Error: 0.034316 Align patch 12 13 left Iteration 1 Error: 1.856536 Iteration 2 Error: 0.606811 Iteration 3 Error: 0.276211 Iteration 4 Error: 0.521908 Iteration 5 Error: 0.238322 Align patch 12 13 left Iteration 1 Error: 2.669034 Iteration 2 Error: 0.682789 Iteration 3 Error: 0.280883 Iteration 4 Error: 0.168303 Iteration 5 Error: 0.069825 Align patch 13 12 left Iteration 1 Error: 34.688789 Iteration 2 Error: 33.454826 Iteration 3 Error: 33.170647 Iteration 4 Error: 33.374454 Iteration 5 Error: 33.221073 Align patch 13 12 left Iteration 1 Error: 3.768300 Iteration 2 Error: 1.162789 Iteration 3 Error: 1.797709 Iteration 4 Error: 0.452534 Iteration 5 Error: 0.650542 Align patch 14 11 left Iteration 1 Error: 2.059339 Iteration 2 Error: 0.595952 Iteration 3 Error: 0.294462 Iteration 4 Error: 0.214128 Iteration 5 Error: 0.103274 Align patch 14 11 left Iteration 1 Error: 1.639754 Iteration 2 Error: 0.243432 Iteration 3 Error: 0.071700 Iteration 4 Error: 0.031008 Align patch 15 10 left Iteration 1 Error: 1.734378 Iteration 2 Error: 0.159404 Iteration 3 Error: 0.087769 Iteration 4 Error: 0.031137 Align patch 16 9 left Iteration 1 Error: 3.449289 Iteration 2 Error: 2.526443 Iteration 3 Error: 2.964957 Iteration 4 Error: 2.137263 Iteration 5 Error: 2.650627 Align patch 16 9 left Iteration 1 Error: 1.918337 Iteration 2 Error: 0.386818 Iteration 3 Error: 0.153309 Iteration 4 Error: 0.067383 Iteration 5 Error: 0.032895 Align patch 17 8 left Iteration 1 Error: 18.684059 Iteration 2 Error: 7.318392 Iteration 3 Error: 6.773787 Iteration 4 Error: 6.389449 Iteration 5 Error: 5.769161 Align patch 17 8 left Iteration 1 Error: 2.074355 Iteration 2 Error: 0.654260 Iteration 3 Error: 0.210103 Iteration 4 Error: 0.104291 Iteration 5 Error: 0.086204 Align patch 18 7 left Iteration 1 Error: 17.918823 Iteration 2 Error: 17.226772 Iteration 3 Error: 17.088186 Iteration 4 Error: 13.832116 Iteration 5 Error: 17.911015 Align patch 18 7 left Iteration 1 Error: 2.911624 Iteration 2 Error: 0.610820 Iteration 3 Error: 0.500027 Iteration 4 Error: 0.263137 Iteration 5 Error: 0.144540 Align patch 19 6 left Iteration 1 Error: 24.243021 Iteration 2 Error: 5.663239 Iteration 3 Error: 3.522869 Iteration 4 Error: 2.862639 Iteration 5 Error: 2.459433 Align patch 19 6 left Iteration 1 Error: 2.983702 Iteration 2 Error: 0.644422 Iteration 3 Error: 0.333033 Iteration 4 Error: 0.100634 Iteration 5 Error: 0.088027 Align patch 20 5 left Iteration 1 Error: 3.763652 Iteration 2 Error: 0.645481 Iteration 3 Error: 0.296959 Iteration 4 Error: 0.198011 Iteration 5 Error: 0.106880 Align patch 20 5 left Iteration 1 Error: 2.387534 Iteration 2 Error: 0.559297 Iteration 3 Error: 0.196098 Iteration 4 Error: 0.097824 Iteration 5 Error: 0.052487 Align patch 21 4 left Iteration 1 Error: 17.110437 Iteration 2 Error: 18.300497 Iteration 3 Error: 19.416229 Iteration 4 Error: 19.789806 Iteration 5 Error: 19.437120 Align patch 21 4 left Iteration 1 Error: 3.397358 Iteration 2 Error: 0.778260 Iteration 3 Error: 0.223936 Iteration 4 Error: 0.102629 Iteration 5 Error: 0.065049 Align patch 22 3 left Iteration 1 Error: 7.915193 Iteration 2 Error: 7.863516 Iteration 3 Error: 7.731934 Iteration 4 Error: 7.901168 Iteration 5 Error: 7.873215 Align patch 22 3 left Iteration 1 Error: 1.935883 Iteration 2 Error: 0.559564 Iteration 3 Error: 0.163436 Iteration 4 Error: 0.058127 Iteration 5 Error: 0.036781 Align patch 23 2 left Iteration 1 Error: 13.995062 Iteration 2 Error: 3.228604 Iteration 3 Error: 7.220760 Iteration 4 Error: 7.304179 Iteration 5 Error: 8.567409 Align patch 23 2 left Iteration 1 Error: 3.662464 Iteration 2 Error: 1.444877 Iteration 3 Error: 0.730898 Iteration 4 Error: 0.287548 Iteration 5 Error: 0.179688 Align patch 24 1 left Iteration 1 Error: 36.263699 Iteration 2 Error: 35.292358 Iteration 3 Error: 33.949718 Iteration 4 Error: 34.414139 Iteration 5 Error: 33.977642 Align patch 24 1 left Iteration 1 Error: 3.953610 Iteration 2 Error: 0.688281 Iteration 3 Error: 0.416161 Iteration 4 Error: 0.194504 Iteration 5 Error: 0.210955 Align patch 25 0 left Iteration 1 Error: 32.689453 Iteration 2 Error: 30.515350 Iteration 3 Error: 30.941559 Iteration 4 Error: 30.996611 Iteration 5 Error: 31.129744 Align patch 25 0 left Iteration 1 Error: 3.776733 Iteration 2 Error: 1.175861 Iteration 3 Error: 0.397800 Iteration 4 Error: 0.203545 Iteration 5 Error: 0.132592 3D Fitting completed. Patch alignment time: 39.72(sec) Local motion has been corrected. Process thread exits. Computational time: 47.243942 sec Total time: 53.630798 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00019hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00019hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.254943s Reading file: gc_18feb27f_CTD_g1_00012gr_00007sq_v01_00019hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.328522s ........................................ >>>>>>TIME<<<<<< FFT: 1.012423s Defocus_U Defocus_V Angle CCC 11792.97 11687.53 8.59 0.032812 Final Values Defocus_U Defocus_V Angle CCC 11785.15 11692.21 26.98 0.064974 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00002hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00002hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.314e-01 9.799e-02 CC threshold: 0.719 Mean Std: 42.01 7.19 Num Hot pixels: 182 Hot pixel threshold: 85.13 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.153432 Iteration 2 Error: 0.180300 Iteration 3 Error: 0.045302 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.06 0.10 ...... Frame ( 3) shift: 0.13 0.20 ...... Frame ( 4) shift: 0.19 0.29 ...... Frame ( 5) shift: 0.25 0.39 ...... Frame ( 6) shift: 0.32 0.47 ...... Frame ( 7) shift: 0.41 0.54 ...... Frame ( 8) shift: 0.49 0.61 ...... Frame ( 9) shift: 0.55 0.63 ...... Frame ( 10) shift: 0.59 0.61 ...... Frame ( 11) shift: 0.62 0.59 ...... Frame ( 12) shift: 0.67 0.64 ...... Frame ( 13) shift: 0.73 0.77 ...... Frame ( 14) shift: 0.78 0.90 ...... Frame ( 15) shift: 0.83 0.98 ...... Frame ( 16) shift: 0.88 1.02 ...... Frame ( 17) shift: 0.93 1.06 ...... Frame ( 18) shift: 0.96 1.09 ...... Frame ( 19) shift: 0.96 1.12 ...... Frame ( 20) shift: 0.96 1.14 ...... Frame ( 21) shift: 0.96 1.18 ...... Frame ( 22) shift: 0.97 1.22 ...... Frame ( 23) shift: 0.99 1.27 ...... Frame ( 24) shift: 1.00 1.30 ...... Frame ( 25) shift: 1.02 1.31 ...... Frame ( 26) shift: 1.04 1.32 ...... Frame ( 27) shift: 1.11 1.35 ...... Frame ( 28) shift: 1.25 1.38 ...... Frame ( 29) shift: 1.39 1.42 ...... Frame ( 30) shift: 1.43 1.49 ...... Frame ( 31) shift: 1.38 1.59 ...... Frame ( 32) shift: 1.32 1.69 ...... Frame ( 33) shift: 1.34 1.74 ...... Frame ( 34) shift: 1.44 1.74 ...... Frame ( 35) shift: 1.53 1.73 ...... Frame ( 36) shift: 1.62 1.78 ...... Frame ( 37) shift: 1.70 1.88 ...... Frame ( 38) shift: 1.78 1.97 ...... Frame ( 39) shift: 1.87 2.07 ...... Frame ( 40) shift: 1.95 2.16 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.652965 Iteration 2 Error: 0.075577 Iteration 3 Error: 0.023376 Align patch 2 23 left Iteration 1 Error: 0.611628 Iteration 2 Error: 0.113326 Iteration 3 Error: 0.023266 Align patch 3 22 left Iteration 1 Error: 0.622454 Iteration 2 Error: 0.123724 Iteration 3 Error: 0.034343 Align patch 4 21 left Iteration 1 Error: 0.775090 Iteration 2 Error: 0.155564 Iteration 3 Error: 0.033657 Align patch 5 20 left Iteration 1 Error: 0.664528 Iteration 2 Error: 0.142129 Iteration 3 Error: 0.035995 Align patch 6 19 left Iteration 1 Error: 0.926250 Iteration 2 Error: 0.124301 Iteration 3 Error: 0.021874 Align patch 7 18 left Iteration 1 Error: 0.773304 Iteration 2 Error: 0.123218 Iteration 3 Error: 0.028016 Align patch 8 17 left Iteration 1 Error: 0.648153 Iteration 2 Error: 0.150646 Iteration 3 Error: 0.055557 Iteration 4 Error: 0.010418 Align patch 9 16 left Iteration 1 Error: 0.529682 Iteration 2 Error: 0.105218 Iteration 3 Error: 0.020783 Align patch 10 15 left Iteration 1 Error: 0.821684 Iteration 2 Error: 0.157552 Iteration 3 Error: 0.050333 Iteration 4 Error: 0.015738 Align patch 11 14 left Iteration 1 Error: 0.627322 Iteration 2 Error: 0.112095 Iteration 3 Error: 0.020028 Align patch 12 13 left Iteration 1 Error: 0.791573 Iteration 2 Error: 0.167575 Iteration 3 Error: 0.046088 Align patch 13 12 left Iteration 1 Error: 0.551660 Iteration 2 Error: 0.078569 Iteration 3 Error: 0.018213 Align patch 14 11 left Iteration 1 Error: 0.584452 Iteration 2 Error: 0.133168 Iteration 3 Error: 0.039543 Align patch 15 10 left Iteration 1 Error: 0.752176 Iteration 2 Error: 0.119760 Iteration 3 Error: 0.055891 Iteration 4 Error: 0.019504 Align patch 16 9 left Iteration 1 Error: 0.907483 Iteration 2 Error: 0.137762 Iteration 3 Error: 0.028581 Align patch 17 8 left Iteration 1 Error: 0.579954 Iteration 2 Error: 0.097948 Iteration 3 Error: 0.026410 Align patch 18 7 left Iteration 1 Error: 0.447065 Iteration 2 Error: 0.052774 Iteration 3 Error: 0.010583 Align patch 19 6 left Iteration 1 Error: 0.662288 Iteration 2 Error: 0.111218 Iteration 3 Error: 0.028164 Align patch 20 5 left Iteration 1 Error: 0.613129 Iteration 2 Error: 0.103464 Iteration 3 Error: 0.024106 Align patch 21 4 left Iteration 1 Error: 0.819658 Iteration 2 Error: 0.118636 Iteration 3 Error: 0.018337 Align patch 22 3 left Iteration 1 Error: 0.935517 Iteration 2 Error: 0.126247 Iteration 3 Error: 0.049986 Align patch 23 2 left Iteration 1 Error: 0.624864 Iteration 2 Error: 0.114699 Iteration 3 Error: 0.030189 Align patch 24 1 left Iteration 1 Error: 0.342112 Iteration 2 Error: 0.055014 Iteration 3 Error: 0.008935 Align patch 25 0 left Iteration 1 Error: 0.679707 Iteration 2 Error: 0.146840 Iteration 3 Error: 0.029282 3D Fitting completed. Patch alignment time: 15.38(sec) Local motion has been corrected. Process thread exits. Computational time: 22.982817 sec Total time: 29.170874 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00002hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00002hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.695244s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00002hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.331506s ........................................ >>>>>>TIME<<<<<< FFT: 0.936149s Defocus_U Defocus_V Angle CCC 9337.90 10248.06 14.89 -0.031125 Final Values Defocus_U Defocus_V Angle CCC 9341.03 10257.43 13.95 -0.195477 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00002hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00002hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.302e-01 9.722e-02 CC threshold: 0.713 Mean Std: 40.23 7.11 Num Hot pixels: 181 Hot pixel threshold: 82.91 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.169725 Iteration 2 Error: 0.257914 Iteration 3 Error: 0.076957 Iteration 4 Error: 0.027041 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.20 -0.23 ...... Frame ( 3) shift: -0.40 -0.46 ...... Frame ( 4) shift: -0.60 -0.68 ...... Frame ( 5) shift: -0.81 -0.91 ...... Frame ( 6) shift: -0.92 -1.14 ...... Frame ( 7) shift: -0.96 -1.38 ...... Frame ( 8) shift: -0.99 -1.61 ...... Frame ( 9) shift: -1.05 -1.80 ...... Frame ( 10) shift: -1.12 -1.93 ...... Frame ( 11) shift: -1.19 -2.07 ...... Frame ( 12) shift: -1.26 -2.21 ...... Frame ( 13) shift: -1.32 -2.37 ...... Frame ( 14) shift: -1.39 -2.52 ...... Frame ( 15) shift: -1.42 -2.66 ...... Frame ( 16) shift: -1.43 -2.76 ...... Frame ( 17) shift: -1.44 -2.86 ...... Frame ( 18) shift: -1.49 -2.94 ...... Frame ( 19) shift: -1.57 -2.98 ...... Frame ( 20) shift: -1.66 -3.02 ...... Frame ( 21) shift: -1.70 -3.06 ...... Frame ( 22) shift: -1.71 -3.09 ...... Frame ( 23) shift: -1.71 -3.13 ...... Frame ( 24) shift: -1.68 -3.13 ...... Frame ( 25) shift: -1.61 -3.10 ...... Frame ( 26) shift: -1.55 -3.08 ...... Frame ( 27) shift: -1.49 -3.11 ...... Frame ( 28) shift: -1.42 -3.19 ...... Frame ( 29) shift: -1.36 -3.28 ...... Frame ( 30) shift: -1.32 -3.33 ...... Frame ( 31) shift: -1.31 -3.34 ...... Frame ( 32) shift: -1.29 -3.34 ...... Frame ( 33) shift: -1.26 -3.36 ...... Frame ( 34) shift: -1.21 -3.39 ...... Frame ( 35) shift: -1.16 -3.42 ...... Frame ( 36) shift: -1.16 -3.46 ...... Frame ( 37) shift: -1.22 -3.50 ...... Frame ( 38) shift: -1.28 -3.53 ...... Frame ( 39) shift: -1.34 -3.57 ...... Frame ( 40) shift: -1.40 -3.61 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 5.059955 Iteration 2 Error: 1.101157 Iteration 3 Error: 0.272543 Iteration 4 Error: 0.109100 Iteration 5 Error: 0.035087 Align patch 2 23 left Iteration 1 Error: 4.025214 Iteration 2 Error: 0.457410 Iteration 3 Error: 0.143382 Iteration 4 Error: 0.039341 Align patch 3 22 left Iteration 1 Error: 2.072488 Iteration 2 Error: 0.480975 Iteration 3 Error: 0.132944 Iteration 4 Error: 0.038657 Align patch 4 21 left Iteration 1 Error: 0.934761 Iteration 2 Error: 0.137162 Iteration 3 Error: 0.029308 Align patch 5 20 left Iteration 1 Error: 1.659047 Iteration 2 Error: 0.293112 Iteration 3 Error: 0.033411 Align patch 6 19 left Iteration 1 Error: 3.650872 Iteration 2 Error: 0.689483 Iteration 3 Error: 0.219934 Iteration 4 Error: 0.092727 Iteration 5 Error: 0.038345 Align patch 7 18 left Iteration 1 Error: 2.527624 Iteration 2 Error: 0.637799 Iteration 3 Error: 0.306940 Iteration 4 Error: 0.112571 Iteration 5 Error: 0.078765 Align patch 7 18 left Iteration 1 Error: 2.770580 Iteration 2 Error: 0.318807 Iteration 3 Error: 0.067046 Iteration 4 Error: 0.014214 Align patch 8 17 left Iteration 1 Error: 1.221117 Iteration 2 Error: 0.171521 Iteration 3 Error: 0.039011 Align patch 9 16 left Iteration 1 Error: 0.917190 Iteration 2 Error: 0.144873 Iteration 3 Error: 0.023885 Align patch 10 15 left Iteration 1 Error: 1.104756 Iteration 2 Error: 0.148217 Iteration 3 Error: 0.027889 Align patch 11 14 left Iteration 1 Error: 3.373246 Iteration 2 Error: 0.477698 Iteration 3 Error: 0.139723 Iteration 4 Error: 0.048412 Align patch 12 13 left Iteration 1 Error: 1.394090 Iteration 2 Error: 0.303385 Iteration 3 Error: 0.079951 Iteration 4 Error: 0.040336 Align patch 13 12 left Iteration 1 Error: 0.833036 Iteration 2 Error: 0.279281 Iteration 3 Error: 0.084851 Iteration 4 Error: 0.037078 Align patch 14 11 left Iteration 1 Error: 1.290385 Iteration 2 Error: 0.274548 Iteration 3 Error: 0.051953 Iteration 4 Error: 0.017906 Align patch 15 10 left Iteration 1 Error: 1.824896 Iteration 2 Error: 0.304564 Iteration 3 Error: 0.063684 Iteration 4 Error: 0.015286 Align patch 16 9 left Iteration 1 Error: 2.630177 Iteration 2 Error: 0.221207 Iteration 3 Error: 0.064201 Iteration 4 Error: 0.020193 Align patch 17 8 left Iteration 1 Error: 1.742500 Iteration 2 Error: 0.260355 Iteration 3 Error: 0.089283 Iteration 4 Error: 0.017952 Align patch 18 7 left Iteration 1 Error: 0.596297 Iteration 2 Error: 0.087645 Iteration 3 Error: 0.024097 Align patch 19 6 left Iteration 1 Error: 1.538108 Iteration 2 Error: 0.228969 Iteration 3 Error: 0.068425 Iteration 4 Error: 0.012027 Align patch 20 5 left Iteration 1 Error: 2.524391 Iteration 2 Error: 0.301453 Iteration 3 Error: 0.099751 Iteration 4 Error: 0.023257 Align patch 21 4 left Iteration 1 Error: 1.775034 Iteration 2 Error: 0.318396 Iteration 3 Error: 0.075773 Iteration 4 Error: 0.024877 Align patch 22 3 left Iteration 1 Error: 1.064531 Iteration 2 Error: 0.289547 Iteration 3 Error: 0.045546 Align patch 23 2 left Iteration 1 Error: 0.524747 Iteration 2 Error: 0.060197 Iteration 3 Error: 0.019164 Align patch 24 1 left Iteration 1 Error: 1.442670 Iteration 2 Error: 0.206845 Iteration 3 Error: 0.048333 Align patch 25 0 left Iteration 1 Error: 2.080617 Iteration 2 Error: 0.411122 Iteration 3 Error: 0.070202 Iteration 4 Error: 0.019012 3D Fitting completed. Patch alignment time: 17.25(sec) Local motion has been corrected. Process thread exits. Computational time: 25.620096 sec Total time: 31.955242 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00002hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00002hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.716943s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00002hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.521640s ........................................ >>>>>>TIME<<<<<< FFT: 1.464002s Defocus_U Defocus_V Angle CCC 10785.16 11257.82 3.66 -0.032537 Final Values Defocus_U Defocus_V Angle CCC 10869.54 11239.08 2.10 -0.204371 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00002hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00002hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.002e-01 CC threshold: 0.736 Mean Std: 41.10 7.00 Num Hot pixels: 214 Hot pixel threshold: 83.12 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.669766 Iteration 2 Error: 0.091048 Iteration 3 Error: 0.015812 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.21 -0.02 ...... Frame ( 3) shift: -0.43 -0.04 ...... Frame ( 4) shift: -0.64 -0.06 ...... Frame ( 5) shift: -0.86 -0.08 ...... Frame ( 6) shift: -1.01 -0.06 ...... Frame ( 7) shift: -1.11 -0.02 ...... Frame ( 8) shift: -1.21 0.02 ...... Frame ( 9) shift: -1.22 0.06 ...... Frame ( 10) shift: -1.14 0.09 ...... Frame ( 11) shift: -1.05 0.12 ...... Frame ( 12) shift: -1.02 0.16 ...... Frame ( 13) shift: -1.04 0.20 ...... Frame ( 14) shift: -1.06 0.24 ...... Frame ( 15) shift: -1.08 0.27 ...... Frame ( 16) shift: -1.10 0.29 ...... Frame ( 17) shift: -1.11 0.31 ...... Frame ( 18) shift: -1.12 0.32 ...... Frame ( 19) shift: -1.12 0.33 ...... Frame ( 20) shift: -1.12 0.33 ...... Frame ( 21) shift: -1.09 0.35 ...... Frame ( 22) shift: -1.03 0.39 ...... Frame ( 23) shift: -0.97 0.42 ...... Frame ( 24) shift: -0.90 0.45 ...... Frame ( 25) shift: -0.81 0.48 ...... Frame ( 26) shift: -0.73 0.51 ...... Frame ( 27) shift: -0.69 0.54 ...... Frame ( 28) shift: -0.70 0.59 ...... Frame ( 29) shift: -0.70 0.64 ...... Frame ( 30) shift: -0.72 0.65 ...... Frame ( 31) shift: -0.73 0.64 ...... Frame ( 32) shift: -0.75 0.62 ...... Frame ( 33) shift: -0.73 0.64 ...... Frame ( 34) shift: -0.69 0.70 ...... Frame ( 35) shift: -0.64 0.76 ...... Frame ( 36) shift: -0.60 0.81 ...... Frame ( 37) shift: -0.55 0.85 ...... Frame ( 38) shift: -0.51 0.90 ...... Frame ( 39) shift: -0.47 0.94 ...... Frame ( 40) shift: -0.42 0.99 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.840357 Iteration 2 Error: 0.135472 Iteration 3 Error: 0.034590 Align patch 2 23 left Iteration 1 Error: 0.716664 Iteration 2 Error: 0.049811 Align patch 3 22 left Iteration 1 Error: 0.474054 Iteration 2 Error: 0.055073 Iteration 3 Error: 0.011221 Align patch 4 21 left Iteration 1 Error: 0.711781 Iteration 2 Error: 0.112676 Iteration 3 Error: 0.033938 Align patch 5 20 left Iteration 1 Error: 0.739688 Iteration 2 Error: 0.073744 Iteration 3 Error: 0.014576 Align patch 6 19 left Iteration 1 Error: 0.634211 Iteration 2 Error: 0.065035 Iteration 3 Error: 0.016409 Align patch 7 18 left Iteration 1 Error: 0.726699 Iteration 2 Error: 0.075652 Iteration 3 Error: 0.014038 Align patch 8 17 left Iteration 1 Error: 0.834975 Iteration 2 Error: 0.106820 Iteration 3 Error: 0.034167 Align patch 9 16 left Iteration 1 Error: 0.719332 Iteration 2 Error: 0.071547 Iteration 3 Error: 0.016929 Align patch 10 15 left Iteration 1 Error: 0.720125 Iteration 2 Error: 0.053847 Iteration 3 Error: 0.011267 Align patch 11 14 left Iteration 1 Error: 0.795284 Iteration 2 Error: 0.093801 Iteration 3 Error: 0.019531 Align patch 12 13 left Iteration 1 Error: 0.657821 Iteration 2 Error: 0.095530 Iteration 3 Error: 0.026241 Align patch 13 12 left Iteration 1 Error: 0.884858 Iteration 2 Error: 0.101437 Iteration 3 Error: 0.019822 Align patch 14 11 left Iteration 1 Error: 0.541998 Iteration 2 Error: 0.074488 Iteration 3 Error: 0.016772 Align patch 15 10 left Iteration 1 Error: 0.609732 Iteration 2 Error: 0.066274 Iteration 3 Error: 0.014509 Align patch 16 9 left Iteration 1 Error: 1.062645 Iteration 2 Error: 0.164795 Iteration 3 Error: 0.029896 Align patch 17 8 left Iteration 1 Error: 0.542311 Iteration 2 Error: 0.069951 Iteration 3 Error: 0.016812 Align patch 18 7 left Iteration 1 Error: 0.657462 Iteration 2 Error: 0.074974 Iteration 3 Error: 0.016356 Align patch 19 6 left Iteration 1 Error: 0.634610 Iteration 2 Error: 0.053343 Iteration 3 Error: 0.011278 Align patch 20 5 left Iteration 1 Error: 0.439050 Iteration 2 Error: 0.061454 Iteration 3 Error: 0.013010 Align patch 21 4 left Iteration 1 Error: 1.393153 Iteration 2 Error: 0.151576 Iteration 3 Error: 0.027619 Align patch 22 3 left Iteration 1 Error: 0.822740 Iteration 2 Error: 0.087256 Iteration 3 Error: 0.014164 Align patch 23 2 left Iteration 1 Error: 0.739516 Iteration 2 Error: 0.075381 Iteration 3 Error: 0.016280 Align patch 24 1 left Iteration 1 Error: 0.907885 Iteration 2 Error: 0.138411 Iteration 3 Error: 0.021822 Align patch 25 0 left Iteration 1 Error: 0.621441 Iteration 2 Error: 0.063772 Iteration 3 Error: 0.017607 3D Fitting completed. Patch alignment time: 15.36(sec) Local motion has been corrected. Process thread exits. Computational time: 23.229853 sec Total time: 28.400881 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00002hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00002hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.921536s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00002hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.988286s ........................................ >>>>>>TIME<<<<<< FFT: 0.940949s Defocus_U Defocus_V Angle CCC 13560.55 14412.11 4.91 0.054919 Final Values Defocus_U Defocus_V Angle CCC 13569.92 14408.99 4.28 0.088338 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00002hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00002hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.002e-01 CC threshold: 0.736 Mean Std: 42.44 7.04 Num Hot pixels: 187 Hot pixel threshold: 84.69 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.868412 Iteration 2 Error: 0.112496 Iteration 3 Error: 0.023599 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.12 0.07 ...... Frame ( 3) shift: -0.24 0.14 ...... Frame ( 4) shift: -0.35 0.20 ...... Frame ( 5) shift: -0.47 0.27 ...... Frame ( 6) shift: -0.49 0.34 ...... Frame ( 7) shift: -0.41 0.41 ...... Frame ( 8) shift: -0.33 0.48 ...... Frame ( 9) shift: -0.31 0.55 ...... Frame ( 10) shift: -0.35 0.61 ...... Frame ( 11) shift: -0.39 0.67 ...... Frame ( 12) shift: -0.42 0.75 ...... Frame ( 13) shift: -0.45 0.86 ...... Frame ( 14) shift: -0.48 0.96 ...... Frame ( 15) shift: -0.45 1.02 ...... Frame ( 16) shift: -0.35 1.03 ...... Frame ( 17) shift: -0.26 1.04 ...... Frame ( 18) shift: -0.18 1.08 ...... Frame ( 19) shift: -0.13 1.14 ...... Frame ( 20) shift: -0.08 1.21 ...... Frame ( 21) shift: -0.03 1.25 ...... Frame ( 22) shift: 0.01 1.27 ...... Frame ( 23) shift: 0.06 1.28 ...... Frame ( 24) shift: 0.09 1.29 ...... Frame ( 25) shift: 0.08 1.30 ...... Frame ( 26) shift: 0.08 1.30 ...... Frame ( 27) shift: 0.07 1.32 ...... Frame ( 28) shift: 0.05 1.34 ...... Frame ( 29) shift: 0.02 1.36 ...... Frame ( 30) shift: 0.00 1.39 ...... Frame ( 31) shift: -0.01 1.43 ...... Frame ( 32) shift: -0.03 1.47 ...... Frame ( 33) shift: -0.02 1.51 ...... Frame ( 34) shift: -0.00 1.55 ...... Frame ( 35) shift: 0.02 1.60 ...... Frame ( 36) shift: 0.04 1.64 ...... Frame ( 37) shift: 0.07 1.69 ...... Frame ( 38) shift: 0.10 1.73 ...... Frame ( 39) shift: 0.13 1.78 ...... Frame ( 40) shift: 0.16 1.83 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.733154 Iteration 2 Error: 0.126731 Iteration 3 Error: 0.048954 Align patch 2 23 left Iteration 1 Error: 0.684186 Iteration 2 Error: 0.111426 Iteration 3 Error: 0.026410 Align patch 3 22 left Iteration 1 Error: 0.613401 Iteration 2 Error: 0.115498 Iteration 3 Error: 0.020759 Align patch 4 21 left Iteration 1 Error: 0.645598 Iteration 2 Error: 0.078741 Iteration 3 Error: 0.022439 Align patch 5 20 left Iteration 1 Error: 0.665717 Iteration 2 Error: 0.104158 Iteration 3 Error: 0.021531 Align patch 6 19 left Iteration 1 Error: 0.992167 Iteration 2 Error: 0.120453 Iteration 3 Error: 0.031284 Align patch 7 18 left Iteration 1 Error: 0.643909 Iteration 2 Error: 0.067457 Iteration 3 Error: 0.018761 Align patch 8 17 left Iteration 1 Error: 0.491355 Iteration 2 Error: 0.094038 Iteration 3 Error: 0.018008 Align patch 9 16 left Iteration 1 Error: 0.593483 Iteration 2 Error: 0.066624 Iteration 3 Error: 0.015465 Align patch 10 15 left Iteration 1 Error: 0.762635 Iteration 2 Error: 0.126067 Iteration 3 Error: 0.025185 Align patch 11 14 left Iteration 1 Error: 0.971323 Iteration 2 Error: 0.125624 Iteration 3 Error: 0.028905 Align patch 12 13 left Iteration 1 Error: 0.830468 Iteration 2 Error: 0.132934 Iteration 3 Error: 0.027292 Align patch 13 12 left Iteration 1 Error: 0.823176 Iteration 2 Error: 0.147614 Iteration 3 Error: 0.027640 Align patch 14 11 left Iteration 1 Error: 0.647621 Iteration 2 Error: 0.201839 Iteration 3 Error: 0.039240 Align patch 15 10 left Iteration 1 Error: 0.745399 Iteration 2 Error: 0.069498 Iteration 3 Error: 0.019853 Align patch 16 9 left Iteration 1 Error: 0.683384 Iteration 2 Error: 0.095816 Iteration 3 Error: 0.021513 Align patch 17 8 left Iteration 1 Error: 0.702314 Iteration 2 Error: 0.123840 Iteration 3 Error: 0.022934 Align patch 18 7 left Iteration 1 Error: 0.508777 Iteration 2 Error: 0.042850 Align patch 19 6 left Iteration 1 Error: 0.595696 Iteration 2 Error: 0.108673 Iteration 3 Error: 0.019962 Align patch 20 5 left Iteration 1 Error: 0.362068 Iteration 2 Error: 0.107594 Iteration 3 Error: 0.020829 Align patch 21 4 left Iteration 1 Error: 1.324978 Iteration 2 Error: 0.180402 Iteration 3 Error: 0.036030 Align patch 22 3 left Iteration 1 Error: 1.046956 Iteration 2 Error: 0.185815 Iteration 3 Error: 0.040721 Align patch 23 2 left Iteration 1 Error: 0.723857 Iteration 2 Error: 0.095120 Iteration 3 Error: 0.017992 Align patch 24 1 left Iteration 1 Error: 0.718119 Iteration 2 Error: 0.067347 Iteration 3 Error: 0.022144 Align patch 25 0 left Iteration 1 Error: 0.684945 Iteration 2 Error: 0.162836 Iteration 3 Error: 0.040721 3D Fitting completed. Patch alignment time: 15.28(sec) Local motion has been corrected. Process thread exits. Computational time: 23.024418 sec Total time: 33.222195 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00002hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00002hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.723702s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00002hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.469544s ........................................ >>>>>>TIME<<<<<< FFT: 0.914103s Defocus_U Defocus_V Angle CCC 14796.88 14167.97 85.51 0.057722 Final Values Defocus_U Defocus_V Angle CCC 14793.75 14167.97 84.26 0.096405 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00003hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00003hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.320e-01 9.842e-02 CC threshold: 0.723 Mean Std: 41.64 7.21 Num Hot pixels: 183 Hot pixel threshold: 84.90 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.574580 Iteration 2 Error: 0.187380 Iteration 3 Error: 0.039972 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.12 0.08 ...... Frame ( 3) shift: 0.24 0.17 ...... Frame ( 4) shift: 0.36 0.25 ...... Frame ( 5) shift: 0.48 0.34 ...... Frame ( 6) shift: 0.62 0.38 ...... Frame ( 7) shift: 0.76 0.39 ...... Frame ( 8) shift: 0.91 0.40 ...... Frame ( 9) shift: 1.03 0.42 ...... Frame ( 10) shift: 1.12 0.47 ...... Frame ( 11) shift: 1.22 0.51 ...... Frame ( 12) shift: 1.32 0.54 ...... Frame ( 13) shift: 1.42 0.57 ...... Frame ( 14) shift: 1.52 0.60 ...... Frame ( 15) shift: 1.60 0.62 ...... Frame ( 16) shift: 1.65 0.65 ...... Frame ( 17) shift: 1.70 0.68 ...... Frame ( 18) shift: 1.75 0.72 ...... Frame ( 19) shift: 1.78 0.77 ...... Frame ( 20) shift: 1.81 0.82 ...... Frame ( 21) shift: 1.87 0.85 ...... Frame ( 22) shift: 1.95 0.86 ...... Frame ( 23) shift: 2.04 0.88 ...... Frame ( 24) shift: 2.08 0.89 ...... Frame ( 25) shift: 2.09 0.89 ...... Frame ( 26) shift: 2.09 0.90 ...... Frame ( 27) shift: 2.14 0.90 ...... Frame ( 28) shift: 2.23 0.88 ...... Frame ( 29) shift: 2.32 0.87 ...... Frame ( 30) shift: 2.43 0.88 ...... Frame ( 31) shift: 2.57 0.92 ...... Frame ( 32) shift: 2.71 0.95 ...... Frame ( 33) shift: 2.80 0.99 ...... Frame ( 34) shift: 2.85 1.03 ...... Frame ( 35) shift: 2.89 1.06 ...... Frame ( 36) shift: 2.94 1.08 ...... Frame ( 37) shift: 3.00 1.07 ...... Frame ( 38) shift: 3.06 1.07 ...... Frame ( 39) shift: 3.12 1.07 ...... Frame ( 40) shift: 3.18 1.06 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.771502 Iteration 2 Error: 0.089045 Iteration 3 Error: 0.024876 Align patch 2 23 left Iteration 1 Error: 1.068107 Iteration 2 Error: 0.145097 Iteration 3 Error: 0.027178 Align patch 3 22 left Iteration 1 Error: 0.499776 Iteration 2 Error: 0.054281 Iteration 3 Error: 0.012446 Align patch 4 21 left Iteration 1 Error: 0.483612 Iteration 2 Error: 0.063100 Iteration 3 Error: 0.013288 Align patch 5 20 left Iteration 1 Error: 0.678428 Iteration 2 Error: 0.093565 Iteration 3 Error: 0.019490 Align patch 6 19 left Iteration 1 Error: 0.648485 Iteration 2 Error: 0.119780 Iteration 3 Error: 0.023514 Align patch 7 18 left Iteration 1 Error: 1.091168 Iteration 2 Error: 0.175702 Iteration 3 Error: 0.046957 Align patch 8 17 left Iteration 1 Error: 0.681866 Iteration 2 Error: 0.105241 Iteration 3 Error: 0.024994 Align patch 9 16 left Iteration 1 Error: 0.517654 Iteration 2 Error: 0.068705 Iteration 3 Error: 0.019364 Align patch 10 15 left Iteration 1 Error: 0.689954 Iteration 2 Error: 0.100138 Iteration 3 Error: 0.019826 Align patch 11 14 left Iteration 1 Error: 0.702688 Iteration 2 Error: 0.121999 Iteration 3 Error: 0.032808 Align patch 12 13 left Iteration 1 Error: 0.709049 Iteration 2 Error: 0.093214 Iteration 3 Error: 0.031556 Align patch 13 12 left Iteration 1 Error: 0.584867 Iteration 2 Error: 0.061486 Iteration 3 Error: 0.015437 Align patch 14 11 left Iteration 1 Error: 0.482056 Iteration 2 Error: 0.056067 Iteration 3 Error: 0.016802 Align patch 15 10 left Iteration 1 Error: 0.672228 Iteration 2 Error: 0.089584 Iteration 3 Error: 0.017909 Align patch 16 9 left Iteration 1 Error: 0.713453 Iteration 2 Error: 0.156323 Iteration 3 Error: 0.048307 Align patch 17 8 left Iteration 1 Error: 0.500407 Iteration 2 Error: 0.100448 Iteration 3 Error: 0.022114 Align patch 18 7 left Iteration 1 Error: 0.588028 Iteration 2 Error: 0.076327 Iteration 3 Error: 0.026253 Align patch 19 6 left Iteration 1 Error: 0.526320 Iteration 2 Error: 0.067641 Iteration 3 Error: 0.009369 Align patch 20 5 left Iteration 1 Error: 0.401552 Iteration 2 Error: 0.073879 Iteration 3 Error: 0.015428 Align patch 21 4 left Iteration 1 Error: 0.643022 Iteration 2 Error: 0.134981 Iteration 3 Error: 0.039398 Align patch 22 3 left Iteration 1 Error: 0.799942 Iteration 2 Error: 0.106997 Iteration 3 Error: 0.027627 Align patch 23 2 left Iteration 1 Error: 0.497827 Iteration 2 Error: 0.061369 Iteration 3 Error: 0.019505 Align patch 24 1 left Iteration 1 Error: 0.566145 Iteration 2 Error: 0.091712 Iteration 3 Error: 0.023512 Align patch 25 0 left Iteration 1 Error: 0.859780 Iteration 2 Error: 0.124204 Iteration 3 Error: 0.036609 3D Fitting completed. Patch alignment time: 15.40(sec) Local motion has been corrected. Process thread exits. Computational time: 23.306505 sec Total time: 29.907066 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00003hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00003hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.110025s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00003hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.319254s ........................................ >>>>>>TIME<<<<<< FFT: 1.005960s Defocus_U Defocus_V Angle CCC 8546.86 9339.86 14.27 -0.029625 Final Values Defocus_U Defocus_V Angle CCC 8545.31 9375.83 14.58 -0.187354 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00003hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00003hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.341e-01 9.973e-02 CC threshold: 0.732 Mean Std: 42.45 7.09 Num Hot pixels: 209 Hot pixel threshold: 85.02 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 4.003092 Iteration 2 Error: 0.536058 Iteration 3 Error: 0.175039 Iteration 4 Error: 0.056276 Iteration 5 Error: 0.021547 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.04 -0.60 ...... Frame ( 3) shift: -0.08 -1.19 ...... Frame ( 4) shift: -0.13 -1.79 ...... Frame ( 5) shift: -0.17 -2.38 ...... Frame ( 6) shift: -0.16 -2.88 ...... Frame ( 7) shift: -0.09 -3.28 ...... Frame ( 8) shift: -0.03 -3.68 ...... Frame ( 9) shift: 0.01 -4.00 ...... Frame ( 10) shift: 0.02 -4.25 ...... Frame ( 11) shift: 0.02 -4.50 ...... Frame ( 12) shift: 0.01 -4.73 ...... Frame ( 13) shift: -0.03 -4.94 ...... Frame ( 14) shift: -0.07 -5.15 ...... Frame ( 15) shift: -0.07 -5.31 ...... Frame ( 16) shift: -0.04 -5.43 ...... Frame ( 17) shift: -0.02 -5.54 ...... Frame ( 18) shift: 0.01 -5.65 ...... Frame ( 19) shift: 0.03 -5.76 ...... Frame ( 20) shift: 0.05 -5.87 ...... Frame ( 21) shift: 0.03 -6.02 ...... Frame ( 22) shift: -0.04 -6.20 ...... Frame ( 23) shift: -0.10 -6.37 ...... Frame ( 24) shift: -0.14 -6.52 ...... Frame ( 25) shift: -0.14 -6.64 ...... Frame ( 26) shift: -0.14 -6.75 ...... Frame ( 27) shift: -0.12 -6.83 ...... Frame ( 28) shift: -0.06 -6.87 ...... Frame ( 29) shift: -0.00 -6.92 ...... Frame ( 30) shift: 0.05 -6.95 ...... Frame ( 31) shift: 0.09 -6.96 ...... Frame ( 32) shift: 0.12 -6.98 ...... Frame ( 33) shift: 0.15 -7.03 ...... Frame ( 34) shift: 0.15 -7.10 ...... Frame ( 35) shift: 0.16 -7.18 ...... Frame ( 36) shift: 0.19 -7.23 ...... Frame ( 37) shift: 0.26 -7.26 ...... Frame ( 38) shift: 0.32 -7.29 ...... Frame ( 39) shift: 0.38 -7.32 ...... Frame ( 40) shift: 0.44 -7.35 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.831318 Iteration 2 Error: 0.189081 Iteration 3 Error: 0.073540 Iteration 4 Error: 0.027102 Align patch 2 23 left Iteration 1 Error: 2.376369 Iteration 2 Error: 0.273701 Iteration 3 Error: 0.124889 Iteration 4 Error: 0.020838 Align patch 3 22 left Iteration 1 Error: 1.524715 Iteration 2 Error: 0.221905 Iteration 3 Error: 0.047818 Align patch 4 21 left Iteration 1 Error: 2.074575 Iteration 2 Error: 0.267992 Iteration 3 Error: 0.064362 Iteration 4 Error: 0.017713 Align patch 5 20 left Iteration 1 Error: 3.163076 Iteration 2 Error: 0.274620 Iteration 3 Error: 0.063709 Iteration 4 Error: 0.014877 Align patch 6 19 left Iteration 1 Error: 2.658015 Iteration 2 Error: 0.326181 Iteration 3 Error: 0.089319 Iteration 4 Error: 0.028909 Align patch 7 18 left Iteration 1 Error: 1.499406 Iteration 2 Error: 0.246897 Iteration 3 Error: 0.075616 Iteration 4 Error: 0.038678 Align patch 8 17 left Iteration 1 Error: 1.440196 Iteration 2 Error: 0.171269 Iteration 3 Error: 0.055990 Iteration 4 Error: 0.015393 Align patch 9 16 left Iteration 1 Error: 1.079614 Iteration 2 Error: 0.320357 Iteration 3 Error: 0.080312 Iteration 4 Error: 0.040347 Align patch 10 15 left Iteration 1 Error: 1.866341 Iteration 2 Error: 0.274611 Iteration 3 Error: 0.089581 Iteration 4 Error: 0.025476 Align patch 11 14 left Iteration 1 Error: 3.947922 Iteration 2 Error: 0.579448 Iteration 3 Error: 0.187478 Iteration 4 Error: 0.084450 Iteration 5 Error: 0.039581 Align patch 12 13 left Iteration 1 Error: 2.388214 Iteration 2 Error: 0.542454 Iteration 3 Error: 0.127025 Iteration 4 Error: 0.054316 Iteration 5 Error: 0.016781 Align patch 13 12 left Iteration 1 Error: 2.214776 Iteration 2 Error: 0.296603 Iteration 3 Error: 0.065409 Iteration 4 Error: 0.027484 Align patch 14 11 left Iteration 1 Error: 0.655531 Iteration 2 Error: 0.088378 Iteration 3 Error: 0.025923 Align patch 15 10 left Iteration 1 Error: 1.353773 Iteration 2 Error: 0.169721 Iteration 3 Error: 0.052574 Iteration 4 Error: 0.013564 Align patch 16 9 left Iteration 1 Error: 3.536562 Iteration 2 Error: 0.684330 Iteration 3 Error: 0.161819 Iteration 4 Error: 0.095305 Iteration 5 Error: 0.041846 Align patch 17 8 left Iteration 1 Error: 2.836386 Iteration 2 Error: 0.633944 Iteration 3 Error: 0.154160 Iteration 4 Error: 0.094165 Iteration 5 Error: 0.026181 Align patch 18 7 left Iteration 1 Error: 2.180136 Iteration 2 Error: 0.274105 Iteration 3 Error: 0.081048 Iteration 4 Error: 0.021718 Align patch 19 6 left Iteration 1 Error: 0.929480 Iteration 2 Error: 0.156478 Iteration 3 Error: 0.042611 Align patch 20 5 left Iteration 1 Error: 2.013840 Iteration 2 Error: 0.287009 Iteration 3 Error: 0.064641 Iteration 4 Error: 0.020440 Align patch 21 4 left Iteration 1 Error: 2.914946 Iteration 2 Error: 0.507513 Iteration 3 Error: 0.161722 Iteration 4 Error: 0.047368 Align patch 22 3 left Iteration 1 Error: 2.572798 Iteration 2 Error: 0.506313 Iteration 3 Error: 0.169064 Iteration 4 Error: 0.059979 Iteration 5 Error: 0.018381 Align patch 23 2 left Iteration 1 Error: 1.450932 Iteration 2 Error: 0.277600 Iteration 3 Error: 0.094535 Iteration 4 Error: 0.042364 Align patch 24 1 left Iteration 1 Error: 1.283552 Iteration 2 Error: 0.239972 Iteration 3 Error: 0.059200 Iteration 4 Error: 0.018046 Align patch 25 0 left Iteration 1 Error: 2.747187 Iteration 2 Error: 0.462712 Iteration 3 Error: 0.099119 Iteration 4 Error: 0.032859 3D Fitting completed. Patch alignment time: 17.55(sec) Local motion has been corrected. Process thread exits. Computational time: 26.426060 sec Total time: 31.474173 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00003hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00003hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.745517s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00003hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.329503s ........................................ >>>>>>TIME<<<<<< FFT: 1.048259s Defocus_U Defocus_V Angle CCC 9255.86 9701.18 0.29 0.028471 Final Values Defocus_U Defocus_V Angle CCC 9263.68 9696.49 1.24 0.012406 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00003hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00003hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 42.28 7.03 Num Hot pixels: 212 Hot pixel threshold: 84.46 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.983783 Iteration 2 Error: 0.255726 Iteration 3 Error: 0.084272 Iteration 4 Error: 0.030872 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.15 -0.30 ...... Frame ( 3) shift: -0.29 -0.59 ...... Frame ( 4) shift: -0.44 -0.89 ...... Frame ( 5) shift: -0.59 -1.19 ...... Frame ( 6) shift: -0.59 -1.45 ...... Frame ( 7) shift: -0.46 -1.70 ...... Frame ( 8) shift: -0.32 -1.94 ...... Frame ( 9) shift: -0.22 -2.09 ...... Frame ( 10) shift: -0.15 -2.16 ...... Frame ( 11) shift: -0.08 -2.23 ...... Frame ( 12) shift: -0.03 -2.32 ...... Frame ( 13) shift: -0.01 -2.42 ...... Frame ( 14) shift: 0.02 -2.52 ...... Frame ( 15) shift: 0.08 -2.60 ...... Frame ( 16) shift: 0.18 -2.65 ...... Frame ( 17) shift: 0.29 -2.70 ...... Frame ( 18) shift: 0.34 -2.76 ...... Frame ( 19) shift: 0.35 -2.84 ...... Frame ( 20) shift: 0.35 -2.91 ...... Frame ( 21) shift: 0.41 -2.95 ...... Frame ( 22) shift: 0.51 -2.96 ...... Frame ( 23) shift: 0.61 -2.96 ...... Frame ( 24) shift: 0.66 -3.00 ...... Frame ( 25) shift: 0.67 -3.07 ...... Frame ( 26) shift: 0.67 -3.13 ...... Frame ( 27) shift: 0.71 -3.16 ...... Frame ( 28) shift: 0.80 -3.17 ...... Frame ( 29) shift: 0.89 -3.17 ...... Frame ( 30) shift: 0.97 -3.16 ...... Frame ( 31) shift: 1.02 -3.14 ...... Frame ( 32) shift: 1.08 -3.13 ...... Frame ( 33) shift: 1.15 -3.15 ...... Frame ( 34) shift: 1.24 -3.20 ...... Frame ( 35) shift: 1.33 -3.26 ...... Frame ( 36) shift: 1.43 -3.25 ...... Frame ( 37) shift: 1.54 -3.19 ...... Frame ( 38) shift: 1.65 -3.13 ...... Frame ( 39) shift: 1.76 -3.07 ...... Frame ( 40) shift: 1.88 -3.00 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.159112 Iteration 2 Error: 0.189561 Iteration 3 Error: 0.044902 Align patch 2 23 left Iteration 1 Error: 0.676823 Iteration 2 Error: 0.097930 Iteration 3 Error: 0.025417 Align patch 3 22 left Iteration 1 Error: 0.858588 Iteration 2 Error: 0.213051 Iteration 3 Error: 0.075750 Iteration 4 Error: 0.028631 Align patch 4 21 left Iteration 1 Error: 1.313448 Iteration 2 Error: 0.253276 Iteration 3 Error: 0.046799 Align patch 5 20 left Iteration 1 Error: 1.985977 Iteration 2 Error: 0.319566 Iteration 3 Error: 0.071884 Iteration 4 Error: 0.020647 Align patch 6 19 left Iteration 1 Error: 2.157637 Iteration 2 Error: 0.448688 Iteration 3 Error: 0.132006 Iteration 4 Error: 0.048186 Align patch 7 18 left Iteration 1 Error: 2.052744 Iteration 2 Error: 0.489562 Iteration 3 Error: 0.141992 Iteration 4 Error: 0.074662 Iteration 5 Error: 0.028895 Align patch 8 17 left Iteration 1 Error: 0.769003 Iteration 2 Error: 0.137971 Iteration 3 Error: 0.035457 Align patch 9 16 left Iteration 1 Error: 0.823019 Iteration 2 Error: 0.123121 Iteration 3 Error: 0.037453 Align patch 10 15 left Iteration 1 Error: 1.241319 Iteration 2 Error: 0.216277 Iteration 3 Error: 0.046232 Align patch 11 14 left Iteration 1 Error: 1.699903 Iteration 2 Error: 0.621002 Iteration 3 Error: 0.236640 Iteration 4 Error: 0.107800 Iteration 5 Error: 0.057030 Align patch 11 14 left Iteration 1 Error: 1.863048 Iteration 2 Error: 0.364528 Iteration 3 Error: 0.091986 Iteration 4 Error: 0.027544 Align patch 12 13 left Iteration 1 Error: 1.131841 Iteration 2 Error: 0.355323 Iteration 3 Error: 0.176078 Iteration 4 Error: 0.091742 Iteration 5 Error: 0.053443 Align patch 12 13 left Iteration 1 Error: 1.931330 Iteration 2 Error: 0.345313 Iteration 3 Error: 0.101768 Iteration 4 Error: 0.032113 Align patch 13 12 left Iteration 1 Error: 0.618565 Iteration 2 Error: 0.218118 Iteration 3 Error: 0.090359 Iteration 4 Error: 0.049767 Align patch 14 11 left Iteration 1 Error: 0.939489 Iteration 2 Error: 0.089480 Iteration 3 Error: 0.016344 Align patch 15 10 left Iteration 1 Error: 1.150952 Iteration 2 Error: 0.177759 Iteration 3 Error: 0.030287 Align patch 16 9 left Iteration 1 Error: 1.902125 Iteration 2 Error: 0.342373 Iteration 3 Error: 0.121195 Iteration 4 Error: 0.029776 Align patch 17 8 left Iteration 1 Error: 2.038692 Iteration 2 Error: 0.548355 Iteration 3 Error: 0.249706 Iteration 4 Error: 0.144840 Iteration 5 Error: 0.068805 Align patch 17 8 left Iteration 1 Error: 2.317558 Iteration 2 Error: 0.529485 Iteration 3 Error: 0.132133 Iteration 4 Error: 0.045877 Align patch 18 7 left Iteration 1 Error: 1.221832 Iteration 2 Error: 0.425631 Iteration 3 Error: 0.114132 Iteration 4 Error: 0.043090 Align patch 19 6 left Iteration 1 Error: 0.622334 Iteration 2 Error: 0.120787 Iteration 3 Error: 0.035402 Align patch 20 5 left Iteration 1 Error: 1.263459 Iteration 2 Error: 0.197929 Iteration 3 Error: 0.044892 Align patch 21 4 left Iteration 1 Error: 1.848730 Iteration 2 Error: 0.310833 Iteration 3 Error: 0.115936 Iteration 4 Error: 0.062498 Iteration 5 Error: 0.033780 Align patch 22 3 left Iteration 1 Error: 3.019162 Iteration 2 Error: 0.854639 Iteration 3 Error: 0.416800 Iteration 4 Error: 0.255016 Iteration 5 Error: 0.120569 Align patch 22 3 left Iteration 1 Error: 2.697033 Iteration 2 Error: 0.558719 Iteration 3 Error: 0.135415 Iteration 4 Error: 0.057491 Iteration 5 Error: 0.017127 Align patch 23 2 left Iteration 1 Error: 1.922844 Iteration 2 Error: 0.369425 Iteration 3 Error: 0.138275 Iteration 4 Error: 0.056031 Iteration 5 Error: 0.027665 Align patch 24 1 left Iteration 1 Error: 0.799365 Iteration 2 Error: 0.075840 Iteration 3 Error: 0.022507 Align patch 25 0 left Iteration 1 Error: 1.178204 Iteration 2 Error: 0.210008 Iteration 3 Error: 0.060288 Iteration 4 Error: 0.014791 3D Fitting completed. Patch alignment time: 20.67(sec) Local motion has been corrected. Process thread exits. Computational time: 29.299917 sec Total time: 34.657471 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00003hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00003hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.885303s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00003hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.328990s ........................................ >>>>>>TIME<<<<<< FFT: 0.962223s Defocus_U Defocus_V Angle CCC 14167.99 15066.42 3.15 0.060523 Final Values Defocus_U Defocus_V Angle CCC 14174.22 15066.45 3.77 0.095858 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00003hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00003hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.002e-01 CC threshold: 0.736 Mean Std: 42.75 7.08 Num Hot pixels: 203 Hot pixel threshold: 85.25 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.148621 Iteration 2 Error: 0.170600 Iteration 3 Error: 0.033710 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.13 0.15 ...... Frame ( 3) shift: -0.26 0.29 ...... Frame ( 4) shift: -0.39 0.44 ...... Frame ( 5) shift: -0.52 0.58 ...... Frame ( 6) shift: -0.54 0.67 ...... Frame ( 7) shift: -0.46 0.69 ...... Frame ( 8) shift: -0.39 0.71 ...... Frame ( 9) shift: -0.30 0.77 ...... Frame ( 10) shift: -0.22 0.85 ...... Frame ( 11) shift: -0.13 0.94 ...... Frame ( 12) shift: -0.08 1.00 ...... Frame ( 13) shift: -0.07 1.03 ...... Frame ( 14) shift: -0.05 1.07 ...... Frame ( 15) shift: -0.03 1.13 ...... Frame ( 16) shift: -0.01 1.21 ...... Frame ( 17) shift: 0.01 1.28 ...... Frame ( 18) shift: 0.05 1.34 ...... Frame ( 19) shift: 0.11 1.39 ...... Frame ( 20) shift: 0.17 1.43 ...... Frame ( 21) shift: 0.22 1.51 ...... Frame ( 22) shift: 0.28 1.62 ...... Frame ( 23) shift: 0.33 1.74 ...... Frame ( 24) shift: 0.34 1.81 ...... Frame ( 25) shift: 0.31 1.83 ...... Frame ( 26) shift: 0.28 1.85 ...... Frame ( 27) shift: 0.27 1.90 ...... Frame ( 28) shift: 0.28 1.98 ...... Frame ( 29) shift: 0.29 2.05 ...... Frame ( 30) shift: 0.32 2.10 ...... Frame ( 31) shift: 0.36 2.13 ...... Frame ( 32) shift: 0.41 2.15 ...... Frame ( 33) shift: 0.45 2.16 ...... Frame ( 34) shift: 0.50 2.16 ...... Frame ( 35) shift: 0.55 2.15 ...... Frame ( 36) shift: 0.60 2.14 ...... Frame ( 37) shift: 0.64 2.13 ...... Frame ( 38) shift: 0.69 2.11 ...... Frame ( 39) shift: 0.73 2.10 ...... Frame ( 40) shift: 0.78 2.08 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.220265 Iteration 2 Error: 0.173087 Iteration 3 Error: 0.048338 Align patch 2 23 left Iteration 1 Error: 0.894453 Iteration 2 Error: 0.172736 Iteration 3 Error: 0.054302 Iteration 4 Error: 0.017891 Align patch 3 22 left Iteration 1 Error: 0.888774 Iteration 2 Error: 0.225350 Iteration 3 Error: 0.102628 Iteration 4 Error: 0.022085 Align patch 4 21 left Iteration 1 Error: 0.879631 Iteration 2 Error: 0.222433 Iteration 3 Error: 0.048789 Align patch 5 20 left Iteration 1 Error: 0.692864 Iteration 2 Error: 0.082526 Iteration 3 Error: 0.019531 Align patch 6 19 left Iteration 1 Error: 1.184470 Iteration 2 Error: 0.146997 Iteration 3 Error: 0.035185 Align patch 7 18 left Iteration 1 Error: 0.735231 Iteration 2 Error: 0.139917 Iteration 3 Error: 0.022277 Align patch 8 17 left Iteration 1 Error: 0.952215 Iteration 2 Error: 0.167571 Iteration 3 Error: 0.045880 Align patch 9 16 left Iteration 1 Error: 0.805467 Iteration 2 Error: 0.209822 Iteration 3 Error: 0.056068 Iteration 4 Error: 0.018901 Align patch 10 15 left Iteration 1 Error: 0.667616 Iteration 2 Error: 0.084606 Iteration 3 Error: 0.020677 Align patch 11 14 left Iteration 1 Error: 0.751041 Iteration 2 Error: 0.122565 Iteration 3 Error: 0.032929 Align patch 12 13 left Iteration 1 Error: 0.624092 Iteration 2 Error: 0.057929 Iteration 3 Error: 0.015768 Align patch 13 12 left Iteration 1 Error: 0.504172 Iteration 2 Error: 0.083647 Iteration 3 Error: 0.029108 Align patch 14 11 left Iteration 1 Error: 0.486741 Iteration 2 Error: 0.096874 Iteration 3 Error: 0.024025 Align patch 15 10 left Iteration 1 Error: 0.435582 Iteration 2 Error: 0.057799 Iteration 3 Error: 0.016950 Align patch 16 9 left Iteration 1 Error: 1.042677 Iteration 2 Error: 0.144721 Iteration 3 Error: 0.037507 Align patch 17 8 left Iteration 1 Error: 0.647415 Iteration 2 Error: 0.114360 Iteration 3 Error: 0.018750 Align patch 18 7 left Iteration 1 Error: 0.727183 Iteration 2 Error: 0.113745 Iteration 3 Error: 0.019988 Align patch 19 6 left Iteration 1 Error: 0.908271 Iteration 2 Error: 0.141731 Iteration 3 Error: 0.032554 Align patch 20 5 left Iteration 1 Error: 0.612206 Iteration 2 Error: 0.103037 Iteration 3 Error: 0.021699 Align patch 21 4 left Iteration 1 Error: 1.024330 Iteration 2 Error: 0.120894 Iteration 3 Error: 0.025378 Align patch 22 3 left Iteration 1 Error: 0.883956 Iteration 2 Error: 0.118709 Iteration 3 Error: 0.013554 Align patch 23 2 left Iteration 1 Error: 0.582000 Iteration 2 Error: 0.077680 Iteration 3 Error: 0.013496 Align patch 24 1 left Iteration 1 Error: 0.551036 Iteration 2 Error: 0.065092 Iteration 3 Error: 0.012283 Align patch 25 0 left Iteration 1 Error: 0.744862 Iteration 2 Error: 0.061083 Iteration 3 Error: 0.008785 3D Fitting completed. Patch alignment time: 15.50(sec) Local motion has been corrected. Process thread exits. Computational time: 23.735012 sec Total time: 29.306452 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00003hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00003hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.690407s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00003hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.068817s ........................................ >>>>>>TIME<<<<<< FFT: 1.030212s Defocus_U Defocus_V Angle CCC 13422.10 12745.94 82.32 0.058221 Final Values Defocus_U Defocus_V Angle CCC 13418.94 12761.61 82.00 0.097524 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00004hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00004hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.278e-01 9.552e-02 CC threshold: 0.701 Mean Std: 36.38 7.06 Num Hot pixels: 158 Hot pixel threshold: 78.74 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.795011 Iteration 2 Error: 0.088024 Iteration 3 Error: 0.017910 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.11 -0.06 ...... Frame ( 3) shift: 0.21 -0.13 ...... Frame ( 4) shift: 0.32 -0.19 ...... Frame ( 5) shift: 0.43 -0.26 ...... Frame ( 6) shift: 0.51 -0.33 ...... Frame ( 7) shift: 0.58 -0.41 ...... Frame ( 8) shift: 0.64 -0.49 ...... Frame ( 9) shift: 0.70 -0.52 ...... Frame ( 10) shift: 0.75 -0.50 ...... Frame ( 11) shift: 0.79 -0.49 ...... Frame ( 12) shift: 0.82 -0.51 ...... Frame ( 13) shift: 0.83 -0.57 ...... Frame ( 14) shift: 0.83 -0.64 ...... Frame ( 15) shift: 0.84 -0.65 ...... Frame ( 16) shift: 0.86 -0.60 ...... Frame ( 17) shift: 0.87 -0.55 ...... Frame ( 18) shift: 0.86 -0.55 ...... Frame ( 19) shift: 0.83 -0.58 ...... Frame ( 20) shift: 0.79 -0.61 ...... Frame ( 21) shift: 0.81 -0.65 ...... Frame ( 22) shift: 0.88 -0.68 ...... Frame ( 23) shift: 0.95 -0.72 ...... Frame ( 24) shift: 0.98 -0.78 ...... Frame ( 25) shift: 0.97 -0.86 ...... Frame ( 26) shift: 0.96 -0.94 ...... Frame ( 27) shift: 0.95 -0.99 ...... Frame ( 28) shift: 0.96 -1.00 ...... Frame ( 29) shift: 0.96 -1.02 ...... Frame ( 30) shift: 0.96 -1.04 ...... Frame ( 31) shift: 0.95 -1.09 ...... Frame ( 32) shift: 0.95 -1.13 ...... Frame ( 33) shift: 0.91 -1.16 ...... Frame ( 34) shift: 0.86 -1.18 ...... Frame ( 35) shift: 0.80 -1.19 ...... Frame ( 36) shift: 0.75 -1.19 ...... Frame ( 37) shift: 0.70 -1.17 ...... Frame ( 38) shift: 0.66 -1.15 ...... Frame ( 39) shift: 0.61 -1.13 ...... Frame ( 40) shift: 0.56 -1.11 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.833838 Iteration 2 Error: 0.121221 Iteration 3 Error: 0.023953 Align patch 2 23 left Iteration 1 Error: 0.830676 Iteration 2 Error: 0.143709 Iteration 3 Error: 0.048717 Align patch 3 22 left Iteration 1 Error: 0.669736 Iteration 2 Error: 0.124698 Iteration 3 Error: 0.025761 Align patch 4 21 left Iteration 1 Error: 1.003122 Iteration 2 Error: 0.161889 Iteration 3 Error: 0.037190 Align patch 5 20 left Iteration 1 Error: 0.664201 Iteration 2 Error: 0.179708 Iteration 3 Error: 0.036560 Align patch 6 19 left Iteration 1 Error: 0.822465 Iteration 2 Error: 0.177430 Iteration 3 Error: 0.046074 Align patch 7 18 left Iteration 1 Error: 0.916211 Iteration 2 Error: 0.234192 Iteration 3 Error: 0.044296 Align patch 8 17 left Iteration 1 Error: 0.891925 Iteration 2 Error: 0.104559 Iteration 3 Error: 0.026914 Align patch 9 16 left Iteration 1 Error: 0.650463 Iteration 2 Error: 0.103488 Iteration 3 Error: 0.020167 Align patch 10 15 left Iteration 1 Error: 0.765439 Iteration 2 Error: 0.080839 Iteration 3 Error: 0.015845 Align patch 11 14 left Iteration 1 Error: 0.502100 Iteration 2 Error: 0.069134 Iteration 3 Error: 0.016981 Align patch 12 13 left Iteration 1 Error: 0.545123 Iteration 2 Error: 0.159640 Iteration 3 Error: 0.036818 Align patch 13 12 left Iteration 1 Error: 1.465416 Iteration 2 Error: 0.142773 Iteration 3 Error: 0.040646 Align patch 14 11 left Iteration 1 Error: 0.657683 Iteration 2 Error: 0.135415 Iteration 3 Error: 0.026523 Align patch 15 10 left Iteration 1 Error: 0.970394 Iteration 2 Error: 0.219634 Iteration 3 Error: 0.043532 Align patch 16 9 left Iteration 1 Error: 0.729325 Iteration 2 Error: 0.171404 Iteration 3 Error: 0.044687 Align patch 17 8 left Iteration 1 Error: 0.835090 Iteration 2 Error: 0.154624 Iteration 3 Error: 0.062432 Iteration 4 Error: 0.017648 Align patch 18 7 left Iteration 1 Error: 0.463095 Iteration 2 Error: 0.053867 Iteration 3 Error: 0.016268 Align patch 19 6 left Iteration 1 Error: 0.928814 Iteration 2 Error: 0.132696 Iteration 3 Error: 0.031015 Align patch 20 5 left Iteration 1 Error: 0.816937 Iteration 2 Error: 0.180131 Iteration 3 Error: 0.036625 Align patch 21 4 left Iteration 1 Error: 1.009291 Iteration 2 Error: 0.161320 Iteration 3 Error: 0.040217 Align patch 22 3 left Iteration 1 Error: 0.769695 Iteration 2 Error: 0.142287 Iteration 3 Error: 0.039537 Align patch 23 2 left Iteration 1 Error: 0.702836 Iteration 2 Error: 0.100783 Iteration 3 Error: 0.011704 Align patch 24 1 left Iteration 1 Error: 0.845852 Iteration 2 Error: 0.129200 Iteration 3 Error: 0.029097 Align patch 25 0 left Iteration 1 Error: 0.828522 Iteration 2 Error: 0.140964 Iteration 3 Error: 0.029136 3D Fitting completed. Patch alignment time: 15.34(sec) Local motion has been corrected. Process thread exits. Computational time: 23.620981 sec Total time: 30.434109 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00004hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00004hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.556357s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00004hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.049722s ........................................ >>>>>>TIME<<<<<< FFT: 0.930559s Defocus_U Defocus_V Angle CCC 12193.51 11693.29 85.05 -0.055227 Final Values Defocus_U Defocus_V Angle CCC 12134.12 11746.44 78.90 -0.264123 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00004hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00004hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.311e-01 9.783e-02 CC threshold: 0.718 Mean Std: 36.19 6.87 Num Hot pixels: 153 Hot pixel threshold: 77.41 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 3.518320 Iteration 2 Error: 0.110086 Iteration 3 Error: 0.022932 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.11 -0.57 ...... Frame ( 3) shift: -0.22 -1.14 ...... Frame ( 4) shift: -0.34 -1.72 ...... Frame ( 5) shift: -0.45 -2.29 ...... Frame ( 6) shift: -0.48 -2.77 ...... Frame ( 7) shift: -0.43 -3.17 ...... Frame ( 8) shift: -0.39 -3.57 ...... Frame ( 9) shift: -0.36 -3.95 ...... Frame ( 10) shift: -0.37 -4.30 ...... Frame ( 11) shift: -0.38 -4.65 ...... Frame ( 12) shift: -0.35 -4.88 ...... Frame ( 13) shift: -0.29 -4.99 ...... Frame ( 14) shift: -0.23 -5.10 ...... Frame ( 15) shift: -0.17 -5.19 ...... Frame ( 16) shift: -0.12 -5.24 ...... Frame ( 17) shift: -0.06 -5.30 ...... Frame ( 18) shift: -0.03 -5.34 ...... Frame ( 19) shift: -0.02 -5.35 ...... Frame ( 20) shift: -0.00 -5.36 ...... Frame ( 21) shift: 0.03 -5.32 ...... Frame ( 22) shift: 0.09 -5.23 ...... Frame ( 23) shift: 0.14 -5.14 ...... Frame ( 24) shift: 0.21 -5.07 ...... Frame ( 25) shift: 0.30 -5.03 ...... Frame ( 26) shift: 0.38 -4.99 ...... Frame ( 27) shift: 0.42 -4.94 ...... Frame ( 28) shift: 0.40 -4.87 ...... Frame ( 29) shift: 0.38 -4.80 ...... Frame ( 30) shift: 0.36 -4.73 ...... Frame ( 31) shift: 0.36 -4.65 ...... Frame ( 32) shift: 0.35 -4.57 ...... Frame ( 33) shift: 0.33 -4.49 ...... Frame ( 34) shift: 0.30 -4.40 ...... Frame ( 35) shift: 0.28 -4.31 ...... Frame ( 36) shift: 0.30 -4.23 ...... Frame ( 37) shift: 0.37 -4.15 ...... Frame ( 38) shift: 0.43 -4.07 ...... Frame ( 39) shift: 0.50 -3.99 ...... Frame ( 40) shift: 0.57 -3.92 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.206571 Iteration 2 Error: 0.124933 Iteration 3 Error: 0.017187 Align patch 2 23 left Iteration 1 Error: 0.809946 Iteration 2 Error: 0.070643 Iteration 3 Error: 0.008687 Align patch 3 22 left Iteration 1 Error: 2.138968 Iteration 2 Error: 0.073024 Iteration 3 Error: 0.008886 Align patch 4 21 left Iteration 1 Error: 1.804243 Iteration 2 Error: 0.273299 Iteration 3 Error: 0.054535 Iteration 4 Error: 0.013221 Align patch 5 20 left Iteration 1 Error: 1.542488 Iteration 2 Error: 0.296643 Iteration 3 Error: 0.071157 Iteration 4 Error: 0.024767 Align patch 6 19 left Iteration 1 Error: 0.949136 Iteration 2 Error: 0.174945 Iteration 3 Error: 0.058761 Iteration 4 Error: 0.022805 Align patch 7 18 left Iteration 1 Error: 0.568022 Iteration 2 Error: 0.127767 Iteration 3 Error: 0.028488 Align patch 8 17 left Iteration 1 Error: 0.979789 Iteration 2 Error: 0.191869 Iteration 3 Error: 0.061321 Iteration 4 Error: 0.016744 Align patch 9 16 left Iteration 1 Error: 1.355924 Iteration 2 Error: 0.144711 Iteration 3 Error: 0.023465 Align patch 10 15 left Iteration 1 Error: 1.024099 Iteration 2 Error: 0.150179 Iteration 3 Error: 0.027562 Align patch 11 14 left Iteration 1 Error: 0.858426 Iteration 2 Error: 0.143682 Iteration 3 Error: 0.025017 Align patch 12 13 left Iteration 1 Error: 0.591601 Iteration 2 Error: 0.042807 Align patch 13 12 left Iteration 1 Error: 0.713739 Iteration 2 Error: 0.150122 Iteration 3 Error: 0.027059 Align patch 14 11 left Iteration 1 Error: 0.886696 Iteration 2 Error: 0.169905 Iteration 3 Error: 0.034583 Align patch 15 10 left Iteration 1 Error: 1.071613 Iteration 2 Error: 0.119073 Iteration 3 Error: 0.028465 Align patch 16 9 left Iteration 1 Error: 0.660917 Iteration 2 Error: 0.074640 Iteration 3 Error: 0.017788 Align patch 17 8 left Iteration 1 Error: 0.982762 Iteration 2 Error: 0.070443 Iteration 3 Error: 0.016541 Align patch 18 7 left Iteration 1 Error: 0.836358 Iteration 2 Error: 0.150987 Iteration 3 Error: 0.023900 Align patch 19 6 left Iteration 1 Error: 1.452620 Iteration 2 Error: 0.124971 Iteration 3 Error: 0.023218 Align patch 20 5 left Iteration 1 Error: 2.444715 Iteration 2 Error: 0.216236 Iteration 3 Error: 0.054637 Iteration 4 Error: 0.011425 Align patch 21 4 left Iteration 1 Error: 0.761717 Iteration 2 Error: 0.108481 Iteration 3 Error: 0.024205 Align patch 22 3 left Iteration 1 Error: 1.365522 Iteration 2 Error: 0.108840 Iteration 3 Error: 0.020980 Align patch 23 2 left Iteration 1 Error: 1.122360 Iteration 2 Error: 0.133703 Iteration 3 Error: 0.026990 Align patch 24 1 left Iteration 1 Error: 1.600401 Iteration 2 Error: 0.124915 Iteration 3 Error: 0.027943 Align patch 25 0 left Iteration 1 Error: 1.903242 Iteration 2 Error: 0.195166 Iteration 3 Error: 0.050157 Iteration 4 Error: 0.012921 3D Fitting completed. Patch alignment time: 15.76(sec) Local motion has been corrected. Process thread exits. Computational time: 24.662392 sec Total time: 34.827782 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00004hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00004hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.957574s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00004hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.316113s ........................................ >>>>>>TIME<<<<<< FFT: 1.019462s Defocus_U Defocus_V Angle CCC 13140.63 12839.85 76.49 -0.014593 Final Values Defocus_U Defocus_V Angle CCC 13135.94 12844.54 76.17 -0.186457 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00004hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00004hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.283e-01 9.585e-02 CC threshold: 0.703 Mean Std: 41.29 7.32 Num Hot pixels: 192 Hot pixel threshold: 85.24 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.625386 Iteration 2 Error: 0.059048 Iteration 3 Error: 0.014789 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.12 -0.00 ...... Frame ( 3) shift: 0.23 -0.00 ...... Frame ( 4) shift: 0.35 -0.01 ...... Frame ( 5) shift: 0.47 -0.01 ...... Frame ( 6) shift: 0.53 -0.02 ...... Frame ( 7) shift: 0.54 -0.05 ...... Frame ( 8) shift: 0.55 -0.07 ...... Frame ( 9) shift: 0.55 -0.12 ...... Frame ( 10) shift: 0.53 -0.19 ...... Frame ( 11) shift: 0.52 -0.26 ...... Frame ( 12) shift: 0.53 -0.33 ...... Frame ( 13) shift: 0.56 -0.39 ...... Frame ( 14) shift: 0.60 -0.46 ...... Frame ( 15) shift: 0.62 -0.46 ...... Frame ( 16) shift: 0.61 -0.41 ...... Frame ( 17) shift: 0.61 -0.36 ...... Frame ( 18) shift: 0.61 -0.34 ...... Frame ( 19) shift: 0.62 -0.35 ...... Frame ( 20) shift: 0.63 -0.36 ...... Frame ( 21) shift: 0.68 -0.37 ...... Frame ( 22) shift: 0.76 -0.38 ...... Frame ( 23) shift: 0.85 -0.38 ...... Frame ( 24) shift: 0.93 -0.42 ...... Frame ( 25) shift: 0.98 -0.50 ...... Frame ( 26) shift: 1.03 -0.58 ...... Frame ( 27) shift: 1.04 -0.60 ...... Frame ( 28) shift: 1.00 -0.57 ...... Frame ( 29) shift: 0.96 -0.54 ...... Frame ( 30) shift: 0.96 -0.52 ...... Frame ( 31) shift: 1.00 -0.51 ...... Frame ( 32) shift: 1.05 -0.51 ...... Frame ( 33) shift: 1.08 -0.51 ...... Frame ( 34) shift: 1.09 -0.52 ...... Frame ( 35) shift: 1.11 -0.52 ...... Frame ( 36) shift: 1.12 -0.53 ...... Frame ( 37) shift: 1.14 -0.54 ...... Frame ( 38) shift: 1.15 -0.55 ...... Frame ( 39) shift: 1.16 -0.57 ...... Frame ( 40) shift: 1.18 -0.58 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.668141 Iteration 2 Error: 0.085279 Iteration 3 Error: 0.016039 Align patch 2 23 left Iteration 1 Error: 0.612134 Iteration 2 Error: 0.068293 Iteration 3 Error: 0.017057 Align patch 3 22 left Iteration 1 Error: 0.632579 Iteration 2 Error: 0.091709 Iteration 3 Error: 0.017083 Align patch 4 21 left Iteration 1 Error: 0.587821 Iteration 2 Error: 0.073937 Iteration 3 Error: 0.013764 Align patch 5 20 left Iteration 1 Error: 0.550666 Iteration 2 Error: 0.078802 Iteration 3 Error: 0.010320 Align patch 6 19 left Iteration 1 Error: 0.638135 Iteration 2 Error: 0.095571 Iteration 3 Error: 0.014344 Align patch 7 18 left Iteration 1 Error: 0.509259 Iteration 2 Error: 0.068405 Iteration 3 Error: 0.013408 Align patch 8 17 left Iteration 1 Error: 0.610332 Iteration 2 Error: 0.082497 Iteration 3 Error: 0.015875 Align patch 9 16 left Iteration 1 Error: 0.509774 Iteration 2 Error: 0.068461 Iteration 3 Error: 0.014663 Align patch 10 15 left Iteration 1 Error: 0.661958 Iteration 2 Error: 0.102119 Iteration 3 Error: 0.019493 Align patch 11 14 left Iteration 1 Error: 0.833298 Iteration 2 Error: 0.103285 Iteration 3 Error: 0.018568 Align patch 12 13 left Iteration 1 Error: 0.950571 Iteration 2 Error: 0.093557 Iteration 3 Error: 0.020635 Align patch 13 12 left Iteration 1 Error: 1.079626 Iteration 2 Error: 0.187710 Iteration 3 Error: 0.038836 Align patch 14 11 left Iteration 1 Error: 0.567727 Iteration 2 Error: 0.057294 Iteration 3 Error: 0.009901 Align patch 15 10 left Iteration 1 Error: 0.785107 Iteration 2 Error: 0.110690 Iteration 3 Error: 0.016984 Align patch 16 9 left Iteration 1 Error: 0.533109 Iteration 2 Error: 0.087063 Iteration 3 Error: 0.012014 Align patch 17 8 left Iteration 1 Error: 0.594244 Iteration 2 Error: 0.088408 Iteration 3 Error: 0.020059 Align patch 18 7 left Iteration 1 Error: 0.857888 Iteration 2 Error: 0.064223 Iteration 3 Error: 0.014204 Align patch 19 6 left Iteration 1 Error: 0.801972 Iteration 2 Error: 0.183075 Iteration 3 Error: 0.048713 Align patch 20 5 left Iteration 1 Error: 0.755334 Iteration 2 Error: 0.105431 Iteration 3 Error: 0.026077 Align patch 21 4 left Iteration 1 Error: 0.712261 Iteration 2 Error: 0.137378 Iteration 3 Error: 0.034958 Align patch 22 3 left Iteration 1 Error: 0.733341 Iteration 2 Error: 0.091087 Iteration 3 Error: 0.015244 Align patch 23 2 left Iteration 1 Error: 0.588049 Iteration 2 Error: 0.101750 Iteration 3 Error: 0.020418 Align patch 24 1 left Iteration 1 Error: 0.461425 Iteration 2 Error: 0.048783 Align patch 25 0 left Iteration 1 Error: 0.548790 Iteration 2 Error: 0.067487 Iteration 3 Error: 0.019408 3D Fitting completed. Patch alignment time: 15.51(sec) Local motion has been corrected. Process thread exits. Computational time: 24.226997 sec Total time: 30.854666 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00004hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00004hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.744103s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00004hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.990413s ........................................ >>>>>>TIME<<<<<< FFT: 0.928432s Defocus_U Defocus_V Angle CCC 15238.31 16117.22 3.70 -0.023912 Final Values Defocus_U Defocus_V Angle CCC 15235.18 16110.98 4.96 -0.199035 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00004hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00004hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.003e-01 CC threshold: 0.736 Mean Std: 41.89 6.99 Num Hot pixels: 210 Hot pixel threshold: 83.82 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.902248 Iteration 2 Error: 0.073816 Iteration 3 Error: 0.014716 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.16 -0.24 ...... Frame ( 3) shift: -0.33 -0.48 ...... Frame ( 4) shift: -0.49 -0.72 ...... Frame ( 5) shift: -0.66 -0.96 ...... Frame ( 6) shift: -0.68 -1.12 ...... Frame ( 7) shift: -0.57 -1.20 ...... Frame ( 8) shift: -0.45 -1.28 ...... Frame ( 9) shift: -0.40 -1.33 ...... Frame ( 10) shift: -0.41 -1.37 ...... Frame ( 11) shift: -0.42 -1.41 ...... Frame ( 12) shift: -0.39 -1.44 ...... Frame ( 13) shift: -0.30 -1.46 ...... Frame ( 14) shift: -0.22 -1.48 ...... Frame ( 15) shift: -0.15 -1.47 ...... Frame ( 16) shift: -0.10 -1.44 ...... Frame ( 17) shift: -0.04 -1.41 ...... Frame ( 18) shift: -0.01 -1.38 ...... Frame ( 19) shift: 0.00 -1.35 ...... Frame ( 20) shift: 0.01 -1.31 ...... Frame ( 21) shift: 0.02 -1.28 ...... Frame ( 22) shift: 0.02 -1.24 ...... Frame ( 23) shift: 0.02 -1.20 ...... Frame ( 24) shift: 0.07 -1.20 ...... Frame ( 25) shift: 0.19 -1.24 ...... Frame ( 26) shift: 0.30 -1.28 ...... Frame ( 27) shift: 0.35 -1.31 ...... Frame ( 28) shift: 0.34 -1.34 ...... Frame ( 29) shift: 0.33 -1.36 ...... Frame ( 30) shift: 0.32 -1.36 ...... Frame ( 31) shift: 0.30 -1.34 ...... Frame ( 32) shift: 0.29 -1.32 ...... Frame ( 33) shift: 0.28 -1.30 ...... Frame ( 34) shift: 0.25 -1.26 ...... Frame ( 35) shift: 0.23 -1.22 ...... Frame ( 36) shift: 0.27 -1.19 ...... Frame ( 37) shift: 0.36 -1.17 ...... Frame ( 38) shift: 0.45 -1.15 ...... Frame ( 39) shift: 0.55 -1.13 ...... Frame ( 40) shift: 0.64 -1.11 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.828034 Iteration 2 Error: 0.068886 Iteration 3 Error: 0.022371 Align patch 2 23 left Iteration 1 Error: 0.861969 Iteration 2 Error: 0.070053 Iteration 3 Error: 0.013572 Align patch 3 22 left Iteration 1 Error: 1.101224 Iteration 2 Error: 0.119219 Iteration 3 Error: 0.023733 Align patch 4 21 left Iteration 1 Error: 0.866416 Iteration 2 Error: 0.116213 Iteration 3 Error: 0.027886 Align patch 5 20 left Iteration 1 Error: 1.247449 Iteration 2 Error: 0.188969 Iteration 3 Error: 0.032612 Align patch 6 19 left Iteration 1 Error: 0.567886 Iteration 2 Error: 0.076246 Iteration 3 Error: 0.017086 Align patch 7 18 left Iteration 1 Error: 0.651186 Iteration 2 Error: 0.156992 Iteration 3 Error: 0.031771 Align patch 8 17 left Iteration 1 Error: 0.646497 Iteration 2 Error: 0.082810 Iteration 3 Error: 0.018919 Align patch 9 16 left Iteration 1 Error: 0.728149 Iteration 2 Error: 0.176051 Iteration 3 Error: 0.023107 Align patch 10 15 left Iteration 1 Error: 0.978061 Iteration 2 Error: 0.143314 Iteration 3 Error: 0.020509 Align patch 11 14 left Iteration 1 Error: 0.942643 Iteration 2 Error: 0.152619 Iteration 3 Error: 0.048415 Align patch 12 13 left Iteration 1 Error: 0.540362 Iteration 2 Error: 0.081049 Iteration 3 Error: 0.018321 Align patch 13 12 left Iteration 1 Error: 0.865116 Iteration 2 Error: 0.111051 Iteration 3 Error: 0.021759 Align patch 14 11 left Iteration 1 Error: 0.684091 Iteration 2 Error: 0.060400 Iteration 3 Error: 0.009978 Align patch 15 10 left Iteration 1 Error: 0.599428 Iteration 2 Error: 0.060039 Iteration 3 Error: 0.011694 Align patch 16 9 left Iteration 1 Error: 1.331780 Iteration 2 Error: 0.212495 Iteration 3 Error: 0.039360 Align patch 17 8 left Iteration 1 Error: 0.773196 Iteration 2 Error: 0.135153 Iteration 3 Error: 0.026844 Align patch 18 7 left Iteration 1 Error: 0.690912 Iteration 2 Error: 0.093069 Iteration 3 Error: 0.028331 Align patch 19 6 left Iteration 1 Error: 0.543030 Iteration 2 Error: 0.084961 Iteration 3 Error: 0.014815 Align patch 20 5 left Iteration 1 Error: 0.472577 Iteration 2 Error: 0.084584 Iteration 3 Error: 0.013255 Align patch 21 4 left Iteration 1 Error: 1.342678 Iteration 2 Error: 0.219034 Iteration 3 Error: 0.049660 Align patch 22 3 left Iteration 1 Error: 1.342916 Iteration 2 Error: 0.177760 Iteration 3 Error: 0.043082 Align patch 23 2 left Iteration 1 Error: 0.914359 Iteration 2 Error: 0.099098 Iteration 3 Error: 0.024386 Align patch 24 1 left Iteration 1 Error: 1.008133 Iteration 2 Error: 0.093372 Iteration 3 Error: 0.018128 Align patch 25 0 left Iteration 1 Error: 0.565090 Iteration 2 Error: 0.082465 Iteration 3 Error: 0.016619 3D Fitting completed. Patch alignment time: 15.12(sec) Local motion has been corrected. Process thread exits. Computational time: 23.416006 sec Total time: 30.953300 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00004hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00004hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.765267s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00004hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.684192s ........................................ >>>>>>TIME<<<<<< FFT: 1.022488s Defocus_U Defocus_V Angle CCC 12945.32 12210.94 83.96 0.057335 Final Values Defocus_U Defocus_V Angle CCC 12950.00 12237.52 83.64 0.096893 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00005hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00005hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 41.06 6.94 Num Hot pixels: 172 Hot pixel threshold: 82.72 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.137295 Iteration 2 Error: 0.267827 Iteration 3 Error: 0.078218 Iteration 4 Error: 0.031327 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.10 0.03 ...... Frame ( 3) shift: -0.21 0.07 ...... Frame ( 4) shift: -0.31 0.10 ...... Frame ( 5) shift: -0.42 0.13 ...... Frame ( 6) shift: -0.45 0.17 ...... Frame ( 7) shift: -0.40 0.20 ...... Frame ( 8) shift: -0.36 0.24 ...... Frame ( 9) shift: -0.30 0.27 ...... Frame ( 10) shift: -0.25 0.31 ...... Frame ( 11) shift: -0.20 0.35 ...... Frame ( 12) shift: -0.13 0.38 ...... Frame ( 13) shift: -0.06 0.43 ...... Frame ( 14) shift: 0.02 0.47 ...... Frame ( 15) shift: 0.08 0.53 ...... Frame ( 16) shift: 0.14 0.60 ...... Frame ( 17) shift: 0.20 0.67 ...... Frame ( 18) shift: 0.28 0.77 ...... Frame ( 19) shift: 0.39 0.89 ...... Frame ( 20) shift: 0.50 1.02 ...... Frame ( 21) shift: 0.58 1.14 ...... Frame ( 22) shift: 0.62 1.26 ...... Frame ( 23) shift: 0.66 1.38 ...... Frame ( 24) shift: 0.72 1.47 ...... Frame ( 25) shift: 0.81 1.55 ...... Frame ( 26) shift: 0.89 1.63 ...... Frame ( 27) shift: 0.95 1.70 ...... Frame ( 28) shift: 0.96 1.76 ...... Frame ( 29) shift: 0.98 1.82 ...... Frame ( 30) shift: 0.98 1.88 ...... Frame ( 31) shift: 0.95 1.93 ...... Frame ( 32) shift: 0.93 1.98 ...... Frame ( 33) shift: 0.96 2.02 ...... Frame ( 34) shift: 1.06 2.05 ...... Frame ( 35) shift: 1.16 2.08 ...... Frame ( 36) shift: 1.23 2.11 ...... Frame ( 37) shift: 1.27 2.14 ...... Frame ( 38) shift: 1.31 2.16 ...... Frame ( 39) shift: 1.35 2.18 ...... Frame ( 40) shift: 1.39 2.21 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.275027 Iteration 2 Error: 0.280134 Iteration 3 Error: 0.118305 Iteration 4 Error: 0.053237 Iteration 5 Error: 0.027336 Align patch 2 23 left Iteration 1 Error: 0.899716 Iteration 2 Error: 0.115373 Iteration 3 Error: 0.037776 Align patch 3 22 left Iteration 1 Error: 1.071700 Iteration 2 Error: 0.159808 Iteration 3 Error: 0.052122 Iteration 4 Error: 0.017160 Align patch 4 21 left Iteration 1 Error: 0.710661 Iteration 2 Error: 0.131098 Iteration 3 Error: 0.045975 Align patch 5 20 left Iteration 1 Error: 0.450941 Iteration 2 Error: 0.052726 Iteration 3 Error: 0.017550 Align patch 6 19 left Iteration 1 Error: 0.782734 Iteration 2 Error: 0.235429 Iteration 3 Error: 0.083329 Iteration 4 Error: 0.044151 Align patch 7 18 left Iteration 1 Error: 1.018981 Iteration 2 Error: 0.127903 Iteration 3 Error: 0.035115 Align patch 8 17 left Iteration 1 Error: 0.629337 Iteration 2 Error: 0.087641 Iteration 3 Error: 0.030016 Align patch 9 16 left Iteration 1 Error: 0.740905 Iteration 2 Error: 0.071373 Iteration 3 Error: 0.013871 Align patch 10 15 left Iteration 1 Error: 0.436064 Iteration 2 Error: 0.046532 Align patch 11 14 left Iteration 1 Error: 0.730825 Iteration 2 Error: 0.249662 Iteration 3 Error: 0.085224 Iteration 4 Error: 0.026680 Align patch 12 13 left Iteration 1 Error: 0.664171 Iteration 2 Error: 0.080094 Iteration 3 Error: 0.029205 Align patch 13 12 left Iteration 1 Error: 0.521177 Iteration 2 Error: 0.110492 Iteration 3 Error: 0.035475 Align patch 14 11 left Iteration 1 Error: 0.619468 Iteration 2 Error: 0.166563 Iteration 3 Error: 0.053671 Iteration 4 Error: 0.017833 Align patch 15 10 left Iteration 1 Error: 0.656044 Iteration 2 Error: 0.119847 Iteration 3 Error: 0.037381 Align patch 16 9 left Iteration 1 Error: 1.065225 Iteration 2 Error: 0.256285 Iteration 3 Error: 0.082657 Iteration 4 Error: 0.028363 Align patch 17 8 left Iteration 1 Error: 0.930464 Iteration 2 Error: 0.119203 Iteration 3 Error: 0.020221 Align patch 18 7 left Iteration 1 Error: 0.628006 Iteration 2 Error: 0.091109 Iteration 3 Error: 0.033968 Align patch 19 6 left Iteration 1 Error: 0.811935 Iteration 2 Error: 0.195798 Iteration 3 Error: 0.028279 Align patch 20 5 left Iteration 1 Error: 0.575700 Iteration 2 Error: 0.098703 Iteration 3 Error: 0.035199 Align patch 21 4 left Iteration 1 Error: 0.778198 Iteration 2 Error: 0.188472 Iteration 3 Error: 0.064302 Iteration 4 Error: 0.020286 Align patch 22 3 left Iteration 1 Error: 0.765723 Iteration 2 Error: 0.103315 Iteration 3 Error: 0.022213 Align patch 23 2 left Iteration 1 Error: 0.989029 Iteration 2 Error: 0.150058 Iteration 3 Error: 0.047449 Align patch 24 1 left Iteration 1 Error: 0.692061 Iteration 2 Error: 0.092821 Iteration 3 Error: 0.032130 Align patch 25 0 left Iteration 1 Error: 0.909375 Iteration 2 Error: 0.170527 Iteration 3 Error: 0.039194 3D Fitting completed. Patch alignment time: 16.34(sec) Local motion has been corrected. Process thread exits. Computational time: 25.404921 sec Total time: 31.401091 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00005hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00005hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.668945s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00005hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.752393s ........................................ >>>>>>TIME<<<<<< FFT: 0.944490s Defocus_U Defocus_V Angle CCC 11000.00 11906.25 13.72 0.046967 Final Values Defocus_U Defocus_V Angle CCC 11020.36 11939.12 14.34 0.080308 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00005hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00005hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 40.93 6.98 Num Hot pixels: 204 Hot pixel threshold: 82.79 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.003205 Iteration 2 Error: 0.231067 Iteration 3 Error: 0.061053 Iteration 4 Error: 0.021442 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.24 -0.06 ...... Frame ( 3) shift: -0.49 -0.12 ...... Frame ( 4) shift: -0.73 -0.18 ...... Frame ( 5) shift: -0.97 -0.24 ...... Frame ( 6) shift: -1.08 -0.24 ...... Frame ( 7) shift: -1.06 -0.19 ...... Frame ( 8) shift: -1.04 -0.14 ...... Frame ( 9) shift: -1.00 -0.04 ...... Frame ( 10) shift: -0.93 0.11 ...... Frame ( 11) shift: -0.87 0.26 ...... Frame ( 12) shift: -0.85 0.37 ...... Frame ( 13) shift: -0.87 0.45 ...... Frame ( 14) shift: -0.88 0.52 ...... Frame ( 15) shift: -0.90 0.59 ...... Frame ( 16) shift: -0.90 0.67 ...... Frame ( 17) shift: -0.91 0.76 ...... Frame ( 18) shift: -0.91 0.83 ...... Frame ( 19) shift: -0.91 0.88 ...... Frame ( 20) shift: -0.91 0.94 ...... Frame ( 21) shift: -0.89 0.95 ...... Frame ( 22) shift: -0.85 0.91 ...... Frame ( 23) shift: -0.80 0.86 ...... Frame ( 24) shift: -0.76 0.90 ...... Frame ( 25) shift: -0.70 1.01 ...... Frame ( 26) shift: -0.65 1.12 ...... Frame ( 27) shift: -0.57 1.19 ...... Frame ( 28) shift: -0.46 1.22 ...... Frame ( 29) shift: -0.35 1.25 ...... Frame ( 30) shift: -0.27 1.36 ...... Frame ( 31) shift: -0.20 1.54 ...... Frame ( 32) shift: -0.13 1.73 ...... Frame ( 33) shift: -0.07 1.82 ...... Frame ( 34) shift: -0.03 1.80 ...... Frame ( 35) shift: 0.02 1.79 ...... Frame ( 36) shift: 0.04 1.80 ...... Frame ( 37) shift: 0.05 1.81 ...... Frame ( 38) shift: 0.05 1.83 ...... Frame ( 39) shift: 0.06 1.84 ...... Frame ( 40) shift: 0.06 1.86 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.147444 Iteration 2 Error: 0.239727 Iteration 3 Error: 0.083403 Iteration 4 Error: 0.034838 Align patch 2 23 left Iteration 1 Error: 0.750047 Iteration 2 Error: 0.104226 Iteration 3 Error: 0.035265 Align patch 3 22 left Iteration 1 Error: 0.561567 Iteration 2 Error: 0.117032 Iteration 3 Error: 0.031977 Align patch 4 21 left Iteration 1 Error: 0.455578 Iteration 2 Error: 0.060189 Iteration 3 Error: 0.012994 Align patch 5 20 left Iteration 1 Error: 0.607218 Iteration 2 Error: 0.089735 Iteration 3 Error: 0.012503 Align patch 6 19 left Iteration 1 Error: 0.745120 Iteration 2 Error: 0.132517 Iteration 3 Error: 0.044439 Align patch 7 18 left Iteration 1 Error: 0.869960 Iteration 2 Error: 0.173429 Iteration 3 Error: 0.049954 Align patch 8 17 left Iteration 1 Error: 0.790711 Iteration 2 Error: 0.191892 Iteration 3 Error: 0.056579 Iteration 4 Error: 0.017445 Align patch 9 16 left Iteration 1 Error: 0.448710 Iteration 2 Error: 0.064127 Iteration 3 Error: 0.030766 Align patch 10 15 left Iteration 1 Error: 0.471389 Iteration 2 Error: 0.085666 Iteration 3 Error: 0.021282 Align patch 11 14 left Iteration 1 Error: 0.789296 Iteration 2 Error: 0.079045 Iteration 3 Error: 0.021911 Align patch 12 13 left Iteration 1 Error: 0.659118 Iteration 2 Error: 0.158104 Iteration 3 Error: 0.021127 Align patch 13 12 left Iteration 1 Error: 0.894261 Iteration 2 Error: 0.175082 Iteration 3 Error: 0.054628 Iteration 4 Error: 0.022829 Align patch 14 11 left Iteration 1 Error: 0.622529 Iteration 2 Error: 0.063453 Iteration 3 Error: 0.015193 Align patch 15 10 left Iteration 1 Error: 0.703676 Iteration 2 Error: 0.076476 Iteration 3 Error: 0.018062 Align patch 16 9 left Iteration 1 Error: 0.759438 Iteration 2 Error: 0.092612 Iteration 3 Error: 0.020373 Align patch 17 8 left Iteration 1 Error: 0.954763 Iteration 2 Error: 0.124388 Iteration 3 Error: 0.030163 Align patch 18 7 left Iteration 1 Error: 0.733195 Iteration 2 Error: 0.114700 Iteration 3 Error: 0.034607 Align patch 19 6 left Iteration 1 Error: 0.531959 Iteration 2 Error: 0.078856 Iteration 3 Error: 0.013301 Align patch 20 5 left Iteration 1 Error: 0.585986 Iteration 2 Error: 0.101266 Iteration 3 Error: 0.022981 Align patch 21 4 left Iteration 1 Error: 0.922253 Iteration 2 Error: 0.094882 Iteration 3 Error: 0.024651 Align patch 22 3 left Iteration 1 Error: 0.922824 Iteration 2 Error: 0.119728 Iteration 3 Error: 0.027369 Align patch 23 2 left Iteration 1 Error: 0.884664 Iteration 2 Error: 0.168651 Iteration 3 Error: 0.053476 Iteration 4 Error: 0.018013 Align patch 24 1 left Iteration 1 Error: 0.560573 Iteration 2 Error: 0.064060 Iteration 3 Error: 0.011918 Align patch 25 0 left Iteration 1 Error: 0.602519 Iteration 2 Error: 0.096599 Iteration 3 Error: 0.013429 3D Fitting completed. Patch alignment time: 15.67(sec) Local motion has been corrected. Process thread exits. Computational time: 24.824966 sec Total time: 30.448620 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00005hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00005hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.534506s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00005hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.941912s ........................................ >>>>>>TIME<<<<<< FFT: 0.978725s Defocus_U Defocus_V Angle CCC 10732.36 11248.11 3.40 0.048684 Final Values Defocus_U Defocus_V Angle CCC 10755.83 11277.83 4.34 0.085468 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00005hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00005hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.002e-01 CC threshold: 0.736 Mean Std: 40.89 6.93 Num Hot pixels: 204 Hot pixel threshold: 82.50 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.510827 Iteration 2 Error: 0.118184 Iteration 3 Error: 0.026466 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.06 -0.02 ...... Frame ( 3) shift: -0.13 -0.03 ...... Frame ( 4) shift: -0.19 -0.05 ...... Frame ( 5) shift: -0.26 -0.07 ...... Frame ( 6) shift: -0.29 -0.06 ...... Frame ( 7) shift: -0.28 -0.02 ...... Frame ( 8) shift: -0.27 0.01 ...... Frame ( 9) shift: -0.26 0.01 ...... Frame ( 10) shift: -0.24 -0.03 ...... Frame ( 11) shift: -0.22 -0.06 ...... Frame ( 12) shift: -0.19 -0.05 ...... Frame ( 13) shift: -0.15 0.01 ...... Frame ( 14) shift: -0.10 0.07 ...... Frame ( 15) shift: -0.06 0.09 ...... Frame ( 16) shift: -0.03 0.09 ...... Frame ( 17) shift: 0.01 0.09 ...... Frame ( 18) shift: 0.06 0.10 ...... Frame ( 19) shift: 0.13 0.13 ...... Frame ( 20) shift: 0.20 0.17 ...... Frame ( 21) shift: 0.23 0.18 ...... Frame ( 22) shift: 0.23 0.17 ...... Frame ( 23) shift: 0.24 0.17 ...... Frame ( 24) shift: 0.26 0.20 ...... Frame ( 25) shift: 0.29 0.27 ...... Frame ( 26) shift: 0.33 0.34 ...... Frame ( 27) shift: 0.38 0.36 ...... Frame ( 28) shift: 0.44 0.31 ...... Frame ( 29) shift: 0.51 0.26 ...... Frame ( 30) shift: 0.57 0.25 ...... Frame ( 31) shift: 0.65 0.26 ...... Frame ( 32) shift: 0.72 0.27 ...... Frame ( 33) shift: 0.77 0.27 ...... Frame ( 34) shift: 0.80 0.27 ...... Frame ( 35) shift: 0.82 0.27 ...... Frame ( 36) shift: 0.83 0.27 ...... Frame ( 37) shift: 0.82 0.28 ...... Frame ( 38) shift: 0.80 0.28 ...... Frame ( 39) shift: 0.79 0.28 ...... Frame ( 40) shift: 0.77 0.28 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.584138 Iteration 2 Error: 0.191919 Iteration 3 Error: 0.065527 Iteration 4 Error: 0.020213 Align patch 2 23 left Iteration 1 Error: 0.934775 Iteration 2 Error: 0.199753 Iteration 3 Error: 0.066565 Iteration 4 Error: 0.017818 Align patch 3 22 left Iteration 1 Error: 0.599436 Iteration 2 Error: 0.092472 Iteration 3 Error: 0.031096 Align patch 4 21 left Iteration 1 Error: 0.381371 Iteration 2 Error: 0.036190 Align patch 5 20 left Iteration 1 Error: 0.642324 Iteration 2 Error: 0.080322 Iteration 3 Error: 0.012979 Align patch 6 19 left Iteration 1 Error: 0.860714 Iteration 2 Error: 0.181230 Iteration 3 Error: 0.047150 Align patch 7 18 left Iteration 1 Error: 1.143792 Iteration 2 Error: 0.157569 Iteration 3 Error: 0.026635 Align patch 8 17 left Iteration 1 Error: 0.607774 Iteration 2 Error: 0.117898 Iteration 3 Error: 0.019000 Align patch 9 16 left Iteration 1 Error: 0.766846 Iteration 2 Error: 0.164875 Iteration 3 Error: 0.043772 Align patch 10 15 left Iteration 1 Error: 0.588247 Iteration 2 Error: 0.064886 Iteration 3 Error: 0.015343 Align patch 11 14 left Iteration 1 Error: 0.755356 Iteration 2 Error: 0.159322 Iteration 3 Error: 0.048838 Align patch 12 13 left Iteration 1 Error: 0.492257 Iteration 2 Error: 0.059735 Iteration 3 Error: 0.021030 Align patch 13 12 left Iteration 1 Error: 0.781774 Iteration 2 Error: 0.147649 Iteration 3 Error: 0.030216 Align patch 14 11 left Iteration 1 Error: 0.583813 Iteration 2 Error: 0.100637 Iteration 3 Error: 0.021817 Align patch 15 10 left Iteration 1 Error: 0.582654 Iteration 2 Error: 0.099953 Iteration 3 Error: 0.028323 Align patch 16 9 left Iteration 1 Error: 0.355373 Iteration 2 Error: 0.098461 Iteration 3 Error: 0.019602 Align patch 17 8 left Iteration 1 Error: 0.573288 Iteration 2 Error: 0.077811 Iteration 3 Error: 0.025470 Align patch 18 7 left Iteration 1 Error: 0.674102 Iteration 2 Error: 0.083869 Iteration 3 Error: 0.014023 Align patch 19 6 left Iteration 1 Error: 0.672793 Iteration 2 Error: 0.139701 Iteration 3 Error: 0.027690 Align patch 20 5 left Iteration 1 Error: 0.856423 Iteration 2 Error: 0.134314 Iteration 3 Error: 0.039642 Align patch 21 4 left Iteration 1 Error: 0.960877 Iteration 2 Error: 0.168216 Iteration 3 Error: 0.028241 Align patch 22 3 left Iteration 1 Error: 1.044363 Iteration 2 Error: 0.142721 Iteration 3 Error: 0.026375 Align patch 23 2 left Iteration 1 Error: 0.827797 Iteration 2 Error: 0.117049 Iteration 3 Error: 0.032829 Align patch 24 1 left Iteration 1 Error: 0.758054 Iteration 2 Error: 0.108605 Iteration 3 Error: 0.040797 Align patch 25 0 left Iteration 1 Error: 0.651384 Iteration 2 Error: 0.130570 Iteration 3 Error: 0.031889 3D Fitting completed. Patch alignment time: 15.31(sec) Local motion has been corrected. Process thread exits. Computational time: 23.395395 sec Total time: 29.232904 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00005hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00005hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.765804s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00005hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.324265s ........................................ >>>>>>TIME<<<<<< FFT: 1.037884s Defocus_U Defocus_V Angle CCC 12140.63 13062.51 4.60 0.050129 Final Values Defocus_U Defocus_V Angle CCC 12142.22 13089.17 4.91 0.085047 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00005hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00005hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 40.86 6.93 Num Hot pixels: 184 Hot pixel threshold: 82.41 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.992192 Iteration 2 Error: 0.191643 Iteration 3 Error: 0.055313 Iteration 4 Error: 0.014326 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.08 0.01 ...... Frame ( 3) shift: -0.16 0.01 ...... Frame ( 4) shift: -0.24 0.02 ...... Frame ( 5) shift: -0.32 0.03 ...... Frame ( 6) shift: -0.36 0.03 ...... Frame ( 7) shift: -0.35 0.04 ...... Frame ( 8) shift: -0.34 0.04 ...... Frame ( 9) shift: -0.31 0.10 ...... Frame ( 10) shift: -0.26 0.22 ...... Frame ( 11) shift: -0.21 0.34 ...... Frame ( 12) shift: -0.18 0.43 ...... Frame ( 13) shift: -0.18 0.48 ...... Frame ( 14) shift: -0.18 0.54 ...... Frame ( 15) shift: -0.14 0.62 ...... Frame ( 16) shift: -0.06 0.71 ...... Frame ( 17) shift: 0.02 0.81 ...... Frame ( 18) shift: 0.04 0.88 ...... Frame ( 19) shift: 0.02 0.93 ...... Frame ( 20) shift: 0.00 0.97 ...... Frame ( 21) shift: 0.06 1.04 ...... Frame ( 22) shift: 0.19 1.11 ...... Frame ( 23) shift: 0.33 1.19 ...... Frame ( 24) shift: 0.40 1.25 ...... Frame ( 25) shift: 0.39 1.29 ...... Frame ( 26) shift: 0.39 1.33 ...... Frame ( 27) shift: 0.42 1.35 ...... Frame ( 28) shift: 0.49 1.34 ...... Frame ( 29) shift: 0.56 1.34 ...... Frame ( 30) shift: 0.61 1.38 ...... Frame ( 31) shift: 0.65 1.47 ...... Frame ( 32) shift: 0.69 1.55 ...... Frame ( 33) shift: 0.71 1.59 ...... Frame ( 34) shift: 0.73 1.60 ...... Frame ( 35) shift: 0.75 1.60 ...... Frame ( 36) shift: 0.80 1.62 ...... Frame ( 37) shift: 0.87 1.66 ...... Frame ( 38) shift: 0.94 1.70 ...... Frame ( 39) shift: 1.02 1.74 ...... Frame ( 40) shift: 1.09 1.78 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.737222 Iteration 2 Error: 0.273780 Iteration 3 Error: 0.076768 Iteration 4 Error: 0.021784 Align patch 2 23 left Iteration 1 Error: 1.099799 Iteration 2 Error: 0.131772 Iteration 3 Error: 0.041183 Align patch 3 22 left Iteration 1 Error: 0.929649 Iteration 2 Error: 0.105483 Iteration 3 Error: 0.045249 Align patch 4 21 left Iteration 1 Error: 0.621990 Iteration 2 Error: 0.156824 Iteration 3 Error: 0.033956 Align patch 5 20 left Iteration 1 Error: 0.609868 Iteration 2 Error: 0.097130 Iteration 3 Error: 0.023862 Align patch 6 19 left Iteration 1 Error: 1.496645 Iteration 2 Error: 0.248817 Iteration 3 Error: 0.068843 Iteration 4 Error: 0.025338 Align patch 7 18 left Iteration 1 Error: 1.305316 Iteration 2 Error: 0.162399 Iteration 3 Error: 0.063812 Iteration 4 Error: 0.028576 Align patch 8 17 left Iteration 1 Error: 1.041709 Iteration 2 Error: 0.161374 Iteration 3 Error: 0.042467 Align patch 9 16 left Iteration 1 Error: 0.677928 Iteration 2 Error: 0.099585 Iteration 3 Error: 0.027813 Align patch 10 15 left Iteration 1 Error: 0.618479 Iteration 2 Error: 0.070736 Iteration 3 Error: 0.015566 Align patch 11 14 left Iteration 1 Error: 0.865419 Iteration 2 Error: 0.184736 Iteration 3 Error: 0.058723 Iteration 4 Error: 0.024766 Align patch 12 13 left Iteration 1 Error: 0.780155 Iteration 2 Error: 0.180158 Iteration 3 Error: 0.042976 Align patch 13 12 left Iteration 1 Error: 0.620452 Iteration 2 Error: 0.109524 Iteration 3 Error: 0.033539 Align patch 14 11 left Iteration 1 Error: 0.546538 Iteration 2 Error: 0.110008 Iteration 3 Error: 0.029880 Align patch 15 10 left Iteration 1 Error: 0.828298 Iteration 2 Error: 0.215659 Iteration 3 Error: 0.055665 Iteration 4 Error: 0.016796 Align patch 16 9 left Iteration 1 Error: 0.555057 Iteration 2 Error: 0.095468 Iteration 3 Error: 0.015735 Align patch 17 8 left Iteration 1 Error: 0.586702 Iteration 2 Error: 0.107522 Iteration 3 Error: 0.023997 Align patch 18 7 left Iteration 1 Error: 0.502733 Iteration 2 Error: 0.136014 Iteration 3 Error: 0.030649 Align patch 19 6 left Iteration 1 Error: 0.817228 Iteration 2 Error: 0.149221 Iteration 3 Error: 0.038536 Align patch 20 5 left Iteration 1 Error: 1.007971 Iteration 2 Error: 0.129877 Iteration 3 Error: 0.028135 Align patch 21 4 left Iteration 1 Error: 1.227313 Iteration 2 Error: 0.134338 Iteration 3 Error: 0.032354 Align patch 22 3 left Iteration 1 Error: 1.150548 Iteration 2 Error: 0.154996 Iteration 3 Error: 0.027148 Align patch 23 2 left Iteration 1 Error: 0.711716 Iteration 2 Error: 0.136227 Iteration 3 Error: 0.035350 Align patch 24 1 left Iteration 1 Error: 0.666707 Iteration 2 Error: 0.154843 Iteration 3 Error: 0.044827 Align patch 25 0 left Iteration 1 Error: 0.522775 Iteration 2 Error: 0.107708 Iteration 3 Error: 0.020377 3D Fitting completed. Patch alignment time: 15.86(sec) Local motion has been corrected. Process thread exits. Computational time: 24.775909 sec Total time: 33.263863 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00005hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00005hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.708084s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00005hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.565601s ........................................ >>>>>>TIME<<<<<< FFT: 1.136574s Defocus_U Defocus_V Angle CCC 13105.51 12398.48 86.59 0.050201 Final Values Defocus_U Defocus_V Angle CCC 13103.95 12412.55 85.96 0.084302 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00006hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00006hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.001e-01 CC threshold: 0.735 Mean Std: 40.88 6.86 Num Hot pixels: 212 Hot pixel threshold: 82.02 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.088653 Iteration 2 Error: 0.598282 Iteration 3 Error: 0.211474 Iteration 4 Error: 0.112316 Iteration 5 Error: 0.046648 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.16 -0.08 ...... Frame ( 3) shift: -0.33 -0.17 ...... Frame ( 4) shift: -0.49 -0.25 ...... Frame ( 5) shift: -0.65 -0.33 ...... Frame ( 6) shift: -0.69 -0.29 ...... Frame ( 7) shift: -0.61 -0.14 ...... Frame ( 8) shift: -0.52 0.02 ...... Frame ( 9) shift: -0.37 0.18 ...... Frame ( 10) shift: -0.16 0.34 ...... Frame ( 11) shift: 0.06 0.49 ...... Frame ( 12) shift: 0.23 0.65 ...... Frame ( 13) shift: 0.35 0.79 ...... Frame ( 14) shift: 0.48 0.94 ...... Frame ( 15) shift: 0.60 1.07 ...... Frame ( 16) shift: 0.72 1.19 ...... Frame ( 17) shift: 0.85 1.31 ...... Frame ( 18) shift: 0.96 1.40 ...... Frame ( 19) shift: 1.07 1.45 ...... Frame ( 20) shift: 1.18 1.51 ...... Frame ( 21) shift: 1.31 1.62 ...... Frame ( 22) shift: 1.45 1.77 ...... Frame ( 23) shift: 1.59 1.93 ...... Frame ( 24) shift: 1.70 2.05 ...... Frame ( 25) shift: 1.78 2.13 ...... Frame ( 26) shift: 1.86 2.21 ...... Frame ( 27) shift: 1.98 2.33 ...... Frame ( 28) shift: 2.12 2.49 ...... Frame ( 29) shift: 2.27 2.65 ...... Frame ( 30) shift: 2.39 2.78 ...... Frame ( 31) shift: 2.48 2.87 ...... Frame ( 32) shift: 2.56 2.97 ...... Frame ( 33) shift: 2.66 3.03 ...... Frame ( 34) shift: 2.77 3.07 ...... Frame ( 35) shift: 2.88 3.11 ...... Frame ( 36) shift: 2.97 3.16 ...... Frame ( 37) shift: 3.05 3.23 ...... Frame ( 38) shift: 3.13 3.31 ...... Frame ( 39) shift: 3.20 3.38 ...... Frame ( 40) shift: 3.28 3.45 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.093779 Iteration 2 Error: 0.572670 Iteration 3 Error: 0.241644 Iteration 4 Error: 0.121488 Iteration 5 Error: 0.064248 Align patch 1 24 left Iteration 1 Error: 2.060806 Iteration 2 Error: 0.320667 Iteration 3 Error: 0.069464 Iteration 4 Error: 0.020237 Align patch 2 23 left Iteration 1 Error: 2.191820 Iteration 2 Error: 0.301918 Iteration 3 Error: 0.144183 Iteration 4 Error: 0.057249 Iteration 5 Error: 0.026832 Align patch 3 22 left Iteration 1 Error: 0.976466 Iteration 2 Error: 0.148702 Iteration 3 Error: 0.081540 Iteration 4 Error: 0.020699 Align patch 4 21 left Iteration 1 Error: 0.775164 Iteration 2 Error: 0.158773 Iteration 3 Error: 0.043529 Align patch 5 20 left Iteration 1 Error: 0.768983 Iteration 2 Error: 0.157369 Iteration 3 Error: 0.051648 Iteration 4 Error: 0.022338 Align patch 6 19 left Iteration 1 Error: 1.889407 Iteration 2 Error: 0.482646 Iteration 3 Error: 0.148332 Iteration 4 Error: 0.057496 Iteration 5 Error: 0.021501 Align patch 7 18 left Iteration 1 Error: 1.370800 Iteration 2 Error: 0.332433 Iteration 3 Error: 0.188846 Iteration 4 Error: 0.078442 Iteration 5 Error: 0.038647 Align patch 8 17 left Iteration 1 Error: 0.935228 Iteration 2 Error: 0.257361 Iteration 3 Error: 0.117236 Iteration 4 Error: 0.051213 Iteration 5 Error: 0.038371 Align patch 9 16 left Iteration 1 Error: 0.682425 Iteration 2 Error: 0.110318 Iteration 3 Error: 0.047324 Align patch 10 15 left Iteration 1 Error: 0.876460 Iteration 2 Error: 0.202720 Iteration 3 Error: 0.065676 Iteration 4 Error: 0.020748 Align patch 11 14 left Iteration 1 Error: 1.757015 Iteration 2 Error: 0.364512 Iteration 3 Error: 0.128205 Iteration 4 Error: 0.060196 Iteration 5 Error: 0.025778 Align patch 12 13 left Iteration 1 Error: 1.515034 Iteration 2 Error: 0.489594 Iteration 3 Error: 0.173282 Iteration 4 Error: 0.084101 Iteration 5 Error: 0.029841 Align patch 13 12 left Iteration 1 Error: 0.605730 Iteration 2 Error: 0.171796 Iteration 3 Error: 0.060552 Iteration 4 Error: 0.027506 Align patch 14 11 left Iteration 1 Error: 0.505778 Iteration 2 Error: 0.103395 Iteration 3 Error: 0.041195 Align patch 15 10 left Iteration 1 Error: 0.687661 Iteration 2 Error: 0.177497 Iteration 3 Error: 0.082296 Iteration 4 Error: 0.032494 Align patch 16 9 left Iteration 1 Error: 1.174356 Iteration 2 Error: 0.259180 Iteration 3 Error: 0.114233 Iteration 4 Error: 0.042673 Align patch 17 8 left Iteration 1 Error: 0.687586 Iteration 2 Error: 0.168125 Iteration 3 Error: 0.090335 Iteration 4 Error: 0.046977 Align patch 18 7 left Iteration 1 Error: 0.821243 Iteration 2 Error: 0.223474 Iteration 3 Error: 0.074117 Iteration 4 Error: 0.021853 Align patch 19 6 left Iteration 1 Error: 0.658858 Iteration 2 Error: 0.282602 Iteration 3 Error: 0.175760 Iteration 4 Error: 0.099458 Iteration 5 Error: 0.054780 Align patch 19 6 left Iteration 1 Error: 0.362220 Iteration 2 Error: 0.048597 Align patch 20 5 left Iteration 1 Error: 1.114352 Iteration 2 Error: 0.346092 Iteration 3 Error: 0.104423 Iteration 4 Error: 0.041058 Align patch 21 4 left Iteration 1 Error: 1.102477 Iteration 2 Error: 0.466368 Iteration 3 Error: 0.167480 Iteration 4 Error: 0.071271 Iteration 5 Error: 0.037520 Align patch 22 3 left Iteration 1 Error: 1.142261 Iteration 2 Error: 0.373559 Iteration 3 Error: 0.158522 Iteration 4 Error: 0.092639 Iteration 5 Error: 0.028210 Align patch 23 2 left Iteration 1 Error: 1.019434 Iteration 2 Error: 0.294489 Iteration 3 Error: 0.155624 Iteration 4 Error: 0.065707 Iteration 5 Error: 0.032465 Align patch 24 1 left Iteration 1 Error: 0.859711 Iteration 2 Error: 0.285901 Iteration 3 Error: 0.129888 Iteration 4 Error: 0.052982 Iteration 5 Error: 0.026904 Align patch 25 0 left Iteration 1 Error: 1.753398 Iteration 2 Error: 0.414703 Iteration 3 Error: 0.095401 Iteration 4 Error: 0.034174 3D Fitting completed. Patch alignment time: 19.66(sec) Local motion has been corrected. Process thread exits. Computational time: 28.612587 sec Total time: 34.246765 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00006hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00006hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.584656s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00006hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.669004s ........................................ >>>>>>TIME<<<<<< FFT: 0.960336s Defocus_U Defocus_V Angle CCC 9763.68 10580.09 15.21 0.047825 Final Values Defocus_U Defocus_V Angle CCC 9774.62 10600.41 14.28 0.083858 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00006hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00006hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.002e-01 CC threshold: 0.736 Mean Std: 40.13 6.88 Num Hot pixels: 215 Hot pixel threshold: 81.44 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.982585 Iteration 2 Error: 0.211675 Iteration 3 Error: 0.067143 Iteration 4 Error: 0.020519 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.05 0.03 ...... Frame ( 3) shift: 0.10 0.07 ...... Frame ( 4) shift: 0.16 0.10 ...... Frame ( 5) shift: 0.21 0.13 ...... Frame ( 6) shift: 0.27 0.20 ...... Frame ( 7) shift: 0.34 0.29 ...... Frame ( 8) shift: 0.40 0.37 ...... Frame ( 9) shift: 0.42 0.40 ...... Frame ( 10) shift: 0.38 0.37 ...... Frame ( 11) shift: 0.33 0.34 ...... Frame ( 12) shift: 0.35 0.36 ...... Frame ( 13) shift: 0.42 0.44 ...... Frame ( 14) shift: 0.50 0.51 ...... Frame ( 15) shift: 0.58 0.57 ...... Frame ( 16) shift: 0.67 0.62 ...... Frame ( 17) shift: 0.76 0.66 ...... Frame ( 18) shift: 0.81 0.70 ...... Frame ( 19) shift: 0.83 0.73 ...... Frame ( 20) shift: 0.85 0.76 ...... Frame ( 21) shift: 0.87 0.81 ...... Frame ( 22) shift: 0.89 0.87 ...... Frame ( 23) shift: 0.91 0.93 ...... Frame ( 24) shift: 0.91 1.02 ...... Frame ( 25) shift: 0.90 1.13 ...... Frame ( 26) shift: 0.88 1.24 ...... Frame ( 27) shift: 0.92 1.32 ...... Frame ( 28) shift: 1.00 1.36 ...... Frame ( 29) shift: 1.08 1.40 ...... Frame ( 30) shift: 1.14 1.42 ...... Frame ( 31) shift: 1.18 1.41 ...... Frame ( 32) shift: 1.22 1.40 ...... Frame ( 33) shift: 1.24 1.42 ...... Frame ( 34) shift: 1.26 1.47 ...... Frame ( 35) shift: 1.27 1.52 ...... Frame ( 36) shift: 1.27 1.60 ...... Frame ( 37) shift: 1.24 1.71 ...... Frame ( 38) shift: 1.22 1.82 ...... Frame ( 39) shift: 1.19 1.94 ...... Frame ( 40) shift: 1.17 2.05 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.050031 Iteration 2 Error: 0.394609 Iteration 3 Error: 0.159762 Iteration 4 Error: 0.071871 Iteration 5 Error: 0.040733 Align patch 2 23 left Iteration 1 Error: 0.870317 Iteration 2 Error: 0.286336 Iteration 3 Error: 0.087671 Iteration 4 Error: 0.042592 Align patch 3 22 left Iteration 1 Error: 0.626308 Iteration 2 Error: 0.123172 Iteration 3 Error: 0.039603 Align patch 4 21 left Iteration 1 Error: 0.497870 Iteration 2 Error: 0.107026 Iteration 3 Error: 0.022776 Align patch 5 20 left Iteration 1 Error: 0.984547 Iteration 2 Error: 0.181550 Iteration 3 Error: 0.039740 Align patch 6 19 left Iteration 1 Error: 1.007338 Iteration 2 Error: 0.309716 Iteration 3 Error: 0.128333 Iteration 4 Error: 0.059384 Iteration 5 Error: 0.032935 Align patch 7 18 left Iteration 1 Error: 0.528910 Iteration 2 Error: 0.108513 Iteration 3 Error: 0.034785 Align patch 8 17 left Iteration 1 Error: 0.545338 Iteration 2 Error: 0.083486 Iteration 3 Error: 0.015190 Align patch 9 16 left Iteration 1 Error: 0.856279 Iteration 2 Error: 0.160327 Iteration 3 Error: 0.044781 Align patch 10 15 left Iteration 1 Error: 0.662301 Iteration 2 Error: 0.108771 Iteration 3 Error: 0.015000 Align patch 11 14 left Iteration 1 Error: 1.017674 Iteration 2 Error: 0.157819 Iteration 3 Error: 0.059537 Iteration 4 Error: 0.030459 Align patch 12 13 left Iteration 1 Error: 0.759954 Iteration 2 Error: 0.137478 Iteration 3 Error: 0.047723 Align patch 13 12 left Iteration 1 Error: 0.500492 Iteration 2 Error: 0.104121 Iteration 3 Error: 0.039772 Align patch 14 11 left Iteration 1 Error: 0.859345 Iteration 2 Error: 0.199804 Iteration 3 Error: 0.048615 Align patch 15 10 left Iteration 1 Error: 0.733563 Iteration 2 Error: 0.155202 Iteration 3 Error: 0.033757 Align patch 16 9 left Iteration 1 Error: 0.958230 Iteration 2 Error: 0.198081 Iteration 3 Error: 0.064423 Iteration 4 Error: 0.027378 Align patch 17 8 left Iteration 1 Error: 0.614027 Iteration 2 Error: 0.135735 Iteration 3 Error: 0.046755 Align patch 18 7 left Iteration 1 Error: 0.851136 Iteration 2 Error: 0.159167 Iteration 3 Error: 0.041990 Align patch 19 6 left Iteration 1 Error: 0.479344 Iteration 2 Error: 0.084262 Iteration 3 Error: 0.014887 Align patch 20 5 left Iteration 1 Error: 0.655517 Iteration 2 Error: 0.123740 Iteration 3 Error: 0.044714 Align patch 21 4 left Iteration 1 Error: 0.855543 Iteration 2 Error: 0.150164 Iteration 3 Error: 0.065539 Iteration 4 Error: 0.031784 Align patch 22 3 left Iteration 1 Error: 0.942511 Iteration 2 Error: 0.134929 Iteration 3 Error: 0.034887 Align patch 23 2 left Iteration 1 Error: 0.667160 Iteration 2 Error: 0.094155 Iteration 3 Error: 0.021713 Align patch 24 1 left Iteration 1 Error: 0.632624 Iteration 2 Error: 0.100637 Iteration 3 Error: 0.020140 Align patch 25 0 left Iteration 1 Error: 0.590368 Iteration 2 Error: 0.099710 Iteration 3 Error: 0.018765 3D Fitting completed. Patch alignment time: 15.02(sec) Local motion has been corrected. Process thread exits. Computational time: 24.081390 sec Total time: 29.766401 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00006hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00006hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.616724s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00006hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.603138s ........................................ >>>>>>TIME<<<<<< FFT: 1.057730s Defocus_U Defocus_V Angle CCC 8105.47 8652.34 2.13 0.027852 Final Values Defocus_U Defocus_V Angle CCC 8105.47 8652.34 2.44 0.060633 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00006hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00006hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.001e-01 CC threshold: 0.735 Mean Std: 41.44 6.90 Num Hot pixels: 204 Hot pixel threshold: 82.84 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.681696 Iteration 2 Error: 0.495660 Iteration 3 Error: 0.137587 Iteration 4 Error: 0.068037 Iteration 5 Error: 0.027992 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.16 -0.11 ...... Frame ( 3) shift: -0.32 -0.21 ...... Frame ( 4) shift: -0.47 -0.32 ...... Frame ( 5) shift: -0.63 -0.42 ...... Frame ( 6) shift: -0.68 -0.47 ...... Frame ( 7) shift: -0.61 -0.46 ...... Frame ( 8) shift: -0.54 -0.45 ...... Frame ( 9) shift: -0.45 -0.37 ...... Frame ( 10) shift: -0.34 -0.22 ...... Frame ( 11) shift: -0.23 -0.07 ...... Frame ( 12) shift: -0.10 0.09 ...... Frame ( 13) shift: 0.05 0.27 ...... Frame ( 14) shift: 0.21 0.45 ...... Frame ( 15) shift: 0.34 0.61 ...... Frame ( 16) shift: 0.44 0.76 ...... Frame ( 17) shift: 0.54 0.91 ...... Frame ( 18) shift: 0.63 1.02 ...... Frame ( 19) shift: 0.72 1.10 ...... Frame ( 20) shift: 0.81 1.18 ...... Frame ( 21) shift: 0.88 1.27 ...... Frame ( 22) shift: 0.95 1.38 ...... Frame ( 23) shift: 1.02 1.50 ...... Frame ( 24) shift: 1.09 1.56 ...... Frame ( 25) shift: 1.17 1.58 ...... Frame ( 26) shift: 1.26 1.60 ...... Frame ( 27) shift: 1.32 1.63 ...... Frame ( 28) shift: 1.36 1.69 ...... Frame ( 29) shift: 1.41 1.75 ...... Frame ( 30) shift: 1.46 1.82 ...... Frame ( 31) shift: 1.51 1.90 ...... Frame ( 32) shift: 1.57 1.98 ...... Frame ( 33) shift: 1.60 2.05 ...... Frame ( 34) shift: 1.60 2.10 ...... Frame ( 35) shift: 1.60 2.14 ...... Frame ( 36) shift: 1.63 2.21 ...... Frame ( 37) shift: 1.69 2.28 ...... Frame ( 38) shift: 1.76 2.36 ...... Frame ( 39) shift: 1.82 2.44 ...... Frame ( 40) shift: 1.88 2.51 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 3.467408 Iteration 2 Error: 0.778692 Iteration 3 Error: 0.317687 Iteration 4 Error: 0.121562 Iteration 5 Error: 0.066670 Align patch 1 24 left Iteration 1 Error: 4.006503 Iteration 2 Error: 0.611273 Iteration 3 Error: 0.106691 Iteration 4 Error: 0.019272 Align patch 2 23 left Iteration 1 Error: 2.305317 Iteration 2 Error: 0.544718 Iteration 3 Error: 0.207648 Iteration 4 Error: 0.098031 Iteration 5 Error: 0.055105 Align patch 2 23 left Iteration 1 Error: 3.249895 Iteration 2 Error: 0.463243 Iteration 3 Error: 0.086958 Iteration 4 Error: 0.020089 Align patch 3 22 left Iteration 1 Error: 1.240668 Iteration 2 Error: 0.315714 Iteration 3 Error: 0.137267 Iteration 4 Error: 0.089983 Iteration 5 Error: 0.040248 Align patch 4 21 left Iteration 1 Error: 0.563981 Iteration 2 Error: 0.144323 Iteration 3 Error: 0.060522 Iteration 4 Error: 0.025358 Align patch 5 20 left Iteration 1 Error: 1.253827 Iteration 2 Error: 0.238587 Iteration 3 Error: 0.057345 Iteration 4 Error: 0.018579 Align patch 6 19 left Iteration 1 Error: 3.138469 Iteration 2 Error: 0.816657 Iteration 3 Error: 0.234396 Iteration 4 Error: 0.072026 Iteration 5 Error: 0.029888 Align patch 7 18 left Iteration 1 Error: 3.426190 Iteration 2 Error: 0.886741 Iteration 3 Error: 0.373809 Iteration 4 Error: 0.194668 Iteration 5 Error: 0.096438 Align patch 7 18 left Iteration 1 Error: 3.112589 Iteration 2 Error: 0.425182 Iteration 3 Error: 0.069775 Iteration 4 Error: 0.024216 Align patch 8 17 left Iteration 1 Error: 1.179384 Iteration 2 Error: 0.400627 Iteration 3 Error: 0.285104 Iteration 4 Error: 0.121111 Iteration 5 Error: 0.048244 Align patch 9 16 left Iteration 1 Error: 1.054759 Iteration 2 Error: 0.157885 Iteration 3 Error: 0.044886 Align patch 10 15 left Iteration 1 Error: 1.057988 Iteration 2 Error: 0.263313 Iteration 3 Error: 0.085068 Iteration 4 Error: 0.022133 Align patch 11 14 left Iteration 1 Error: 2.231622 Iteration 2 Error: 0.543322 Iteration 3 Error: 0.227343 Iteration 4 Error: 0.098998 Iteration 5 Error: 0.029088 Align patch 12 13 left Iteration 1 Error: 2.117668 Iteration 2 Error: 0.492615 Iteration 3 Error: 0.223084 Iteration 4 Error: 0.114552 Iteration 5 Error: 0.076407 Align patch 12 13 left Iteration 1 Error: 2.116736 Iteration 2 Error: 0.298870 Iteration 3 Error: 0.066823 Iteration 4 Error: 0.027467 Align patch 13 12 left Iteration 1 Error: 1.176749 Iteration 2 Error: 0.150608 Iteration 3 Error: 0.030824 Align patch 14 11 left Iteration 1 Error: 0.677990 Iteration 2 Error: 0.291249 Iteration 3 Error: 0.058242 Iteration 4 Error: 0.026231 Align patch 15 10 left Iteration 1 Error: 1.495300 Iteration 2 Error: 0.197472 Iteration 3 Error: 0.044720 Align patch 16 9 left Iteration 1 Error: 1.669119 Iteration 2 Error: 0.385286 Iteration 3 Error: 0.161425 Iteration 4 Error: 0.096663 Iteration 5 Error: 0.045437 Align patch 17 8 left Iteration 1 Error: 0.912563 Iteration 2 Error: 0.164897 Iteration 3 Error: 0.079368 Iteration 4 Error: 0.041391 Align patch 18 7 left Iteration 1 Error: 0.545014 Iteration 2 Error: 0.113851 Iteration 3 Error: 0.039008 Align patch 19 6 left Iteration 1 Error: 0.913075 Iteration 2 Error: 0.299347 Iteration 3 Error: 0.114354 Iteration 4 Error: 0.040589 Align patch 20 5 left Iteration 1 Error: 1.444117 Iteration 2 Error: 0.238306 Iteration 3 Error: 0.062504 Iteration 4 Error: 0.013790 Align patch 21 4 left Iteration 1 Error: 1.015011 Iteration 2 Error: 0.125683 Iteration 3 Error: 0.038759 Align patch 22 3 left Iteration 1 Error: 0.872004 Iteration 2 Error: 0.162643 Iteration 3 Error: 0.051052 Iteration 4 Error: 0.019260 Align patch 23 2 left Iteration 1 Error: 0.740926 Iteration 2 Error: 0.158197 Iteration 3 Error: 0.065250 Iteration 4 Error: 0.024857 Align patch 24 1 left Iteration 1 Error: 1.817127 Iteration 2 Error: 0.361580 Iteration 3 Error: 0.066267 Iteration 4 Error: 0.021748 Align patch 25 0 left Iteration 1 Error: 1.997693 Iteration 2 Error: 0.368550 Iteration 3 Error: 0.095454 Iteration 4 Error: 0.022949 3D Fitting completed. Patch alignment time: 21.11(sec) Local motion has been corrected. Process thread exits. Computational time: 30.437454 sec Total time: 36.755749 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00006hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00006hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.899114s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00006hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.632441s ........................................ >>>>>>TIME<<<<<< FFT: 1.052341s Defocus_U Defocus_V Angle CCC 13154.30 14060.55 8.96 0.053204 Final Values Defocus_U Defocus_V Angle CCC 13179.30 14029.31 8.65 0.085773 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00006hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00006hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 39.77 6.83 Num Hot pixels: 199 Hot pixel threshold: 80.74 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.602385 Iteration 2 Error: 0.126642 Iteration 3 Error: 0.034312 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.06 0.05 ...... Frame ( 3) shift: -0.11 0.10 ...... Frame ( 4) shift: -0.17 0.15 ...... Frame ( 5) shift: -0.22 0.20 ...... Frame ( 6) shift: -0.27 0.24 ...... Frame ( 7) shift: -0.31 0.26 ...... Frame ( 8) shift: -0.36 0.27 ...... Frame ( 9) shift: -0.36 0.28 ...... Frame ( 10) shift: -0.34 0.27 ...... Frame ( 11) shift: -0.31 0.27 ...... Frame ( 12) shift: -0.25 0.27 ...... Frame ( 13) shift: -0.17 0.28 ...... Frame ( 14) shift: -0.09 0.28 ...... Frame ( 15) shift: -0.05 0.31 ...... Frame ( 16) shift: -0.06 0.36 ...... Frame ( 17) shift: -0.06 0.42 ...... Frame ( 18) shift: -0.02 0.46 ...... Frame ( 19) shift: 0.06 0.48 ...... Frame ( 20) shift: 0.14 0.51 ...... Frame ( 21) shift: 0.18 0.57 ...... Frame ( 22) shift: 0.18 0.67 ...... Frame ( 23) shift: 0.18 0.76 ...... Frame ( 24) shift: 0.23 0.78 ...... Frame ( 25) shift: 0.32 0.73 ...... Frame ( 26) shift: 0.41 0.68 ...... Frame ( 27) shift: 0.48 0.64 ...... Frame ( 28) shift: 0.54 0.62 ...... Frame ( 29) shift: 0.59 0.60 ...... Frame ( 30) shift: 0.63 0.62 ...... Frame ( 31) shift: 0.65 0.67 ...... Frame ( 32) shift: 0.66 0.72 ...... Frame ( 33) shift: 0.71 0.75 ...... Frame ( 34) shift: 0.78 0.76 ...... Frame ( 35) shift: 0.85 0.77 ...... Frame ( 36) shift: 0.86 0.76 ...... Frame ( 37) shift: 0.82 0.73 ...... Frame ( 38) shift: 0.78 0.70 ...... Frame ( 39) shift: 0.75 0.67 ...... Frame ( 40) shift: 0.71 0.64 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.560859 Iteration 2 Error: 0.540286 Iteration 3 Error: 0.186895 Iteration 4 Error: 0.097845 Iteration 5 Error: 0.034460 Align patch 2 23 left Iteration 1 Error: 1.213114 Iteration 2 Error: 0.305126 Iteration 3 Error: 0.098466 Iteration 4 Error: 0.041415 Align patch 3 22 left Iteration 1 Error: 0.818022 Iteration 2 Error: 0.209745 Iteration 3 Error: 0.044742 Align patch 4 21 left Iteration 1 Error: 0.647476 Iteration 2 Error: 0.111677 Iteration 3 Error: 0.025575 Align patch 5 20 left Iteration 1 Error: 0.833414 Iteration 2 Error: 0.190774 Iteration 3 Error: 0.042089 Align patch 6 19 left Iteration 1 Error: 2.287466 Iteration 2 Error: 0.334834 Iteration 3 Error: 0.136160 Iteration 4 Error: 0.039131 Align patch 7 18 left Iteration 1 Error: 1.065685 Iteration 2 Error: 0.236837 Iteration 3 Error: 0.060028 Iteration 4 Error: 0.021094 Align patch 8 17 left Iteration 1 Error: 0.692186 Iteration 2 Error: 0.163864 Iteration 3 Error: 0.029329 Align patch 9 16 left Iteration 1 Error: 0.526317 Iteration 2 Error: 0.044089 Align patch 10 15 left Iteration 1 Error: 0.746125 Iteration 2 Error: 0.244480 Iteration 3 Error: 0.046382 Align patch 11 14 left Iteration 1 Error: 0.876421 Iteration 2 Error: 0.228855 Iteration 3 Error: 0.093129 Iteration 4 Error: 0.044909 Align patch 12 13 left Iteration 1 Error: 0.694864 Iteration 2 Error: 0.190170 Iteration 3 Error: 0.069603 Iteration 4 Error: 0.030533 Align patch 13 12 left Iteration 1 Error: 0.754840 Iteration 2 Error: 0.087831 Iteration 3 Error: 0.016956 Align patch 14 11 left Iteration 1 Error: 0.497042 Iteration 2 Error: 0.100890 Iteration 3 Error: 0.021844 Align patch 15 10 left Iteration 1 Error: 0.586424 Iteration 2 Error: 0.143162 Iteration 3 Error: 0.038539 Align patch 16 9 left Iteration 1 Error: 0.785846 Iteration 2 Error: 0.144019 Iteration 3 Error: 0.081631 Iteration 4 Error: 0.024540 Align patch 17 8 left Iteration 1 Error: 0.785541 Iteration 2 Error: 0.120657 Iteration 3 Error: 0.041734 Align patch 18 7 left Iteration 1 Error: 0.509053 Iteration 2 Error: 0.082669 Iteration 3 Error: 0.018312 Align patch 19 6 left Iteration 1 Error: 0.710319 Iteration 2 Error: 0.074515 Iteration 3 Error: 0.015621 Align patch 20 5 left Iteration 1 Error: 0.824688 Iteration 2 Error: 0.152975 Iteration 3 Error: 0.029593 Align patch 21 4 left Iteration 1 Error: 0.826201 Iteration 2 Error: 0.206711 Iteration 3 Error: 0.040896 Align patch 22 3 left Iteration 1 Error: 0.848032 Iteration 2 Error: 0.114724 Iteration 3 Error: 0.037986 Align patch 23 2 left Iteration 1 Error: 1.040830 Iteration 2 Error: 0.150550 Iteration 3 Error: 0.022197 Align patch 24 1 left Iteration 1 Error: 0.910257 Iteration 2 Error: 0.153370 Iteration 3 Error: 0.030357 Align patch 25 0 left Iteration 1 Error: 0.643313 Iteration 2 Error: 0.080666 Iteration 3 Error: 0.019194 3D Fitting completed. Patch alignment time: 15.95(sec) Local motion has been corrected. Process thread exits. Computational time: 24.599064 sec Total time: 30.560665 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00006hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00006hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.778342s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00006hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.681623s ........................................ >>>>>>TIME<<<<<< FFT: 1.026030s Defocus_U Defocus_V Angle CCC 13724.91 13013.37 88.76 0.043705 Final Values Defocus_U Defocus_V Angle CCC 13723.35 13021.19 89.07 0.071092 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00007hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00007hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 39.47 6.82 Num Hot pixels: 214 Hot pixel threshold: 80.38 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.644634 Iteration 2 Error: 0.374631 Iteration 3 Error: 0.090085 Iteration 4 Error: 0.032498 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.38 -0.31 ...... Frame ( 3) shift: -0.76 -0.63 ...... Frame ( 4) shift: -1.14 -0.94 ...... Frame ( 5) shift: -1.52 -1.25 ...... Frame ( 6) shift: -1.68 -1.40 ...... Frame ( 7) shift: -1.61 -1.38 ...... Frame ( 8) shift: -1.55 -1.36 ...... Frame ( 9) shift: -1.49 -1.31 ...... Frame ( 10) shift: -1.45 -1.24 ...... Frame ( 11) shift: -1.40 -1.17 ...... Frame ( 12) shift: -1.33 -1.03 ...... Frame ( 13) shift: -1.23 -0.83 ...... Frame ( 14) shift: -1.13 -0.63 ...... Frame ( 15) shift: -1.05 -0.49 ...... Frame ( 16) shift: -0.98 -0.41 ...... Frame ( 17) shift: -0.91 -0.34 ...... Frame ( 18) shift: -0.82 -0.23 ...... Frame ( 19) shift: -0.71 -0.08 ...... Frame ( 20) shift: -0.60 0.06 ...... Frame ( 21) shift: -0.54 0.17 ...... Frame ( 22) shift: -0.53 0.24 ...... Frame ( 23) shift: -0.52 0.32 ...... Frame ( 24) shift: -0.50 0.41 ...... Frame ( 25) shift: -0.45 0.51 ...... Frame ( 26) shift: -0.41 0.61 ...... Frame ( 27) shift: -0.36 0.71 ...... Frame ( 28) shift: -0.30 0.81 ...... Frame ( 29) shift: -0.24 0.92 ...... Frame ( 30) shift: -0.18 1.01 ...... Frame ( 31) shift: -0.12 1.09 ...... Frame ( 32) shift: -0.05 1.18 ...... Frame ( 33) shift: 0.02 1.26 ...... Frame ( 34) shift: 0.10 1.34 ...... Frame ( 35) shift: 0.19 1.41 ...... Frame ( 36) shift: 0.24 1.49 ...... Frame ( 37) shift: 0.28 1.57 ...... Frame ( 38) shift: 0.31 1.65 ...... Frame ( 39) shift: 0.34 1.72 ...... Frame ( 40) shift: 0.37 1.80 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.452006 Iteration 2 Error: 0.189504 Iteration 3 Error: 0.062329 Iteration 4 Error: 0.026600 Align patch 2 23 left Iteration 1 Error: 1.490931 Iteration 2 Error: 0.288256 Iteration 3 Error: 0.097430 Iteration 4 Error: 0.039949 Align patch 3 22 left Iteration 1 Error: 0.776232 Iteration 2 Error: 0.189261 Iteration 3 Error: 0.059246 Iteration 4 Error: 0.020648 Align patch 4 21 left Iteration 1 Error: 0.690376 Iteration 2 Error: 0.117777 Iteration 3 Error: 0.026730 Align patch 5 20 left Iteration 1 Error: 0.926702 Iteration 2 Error: 0.161140 Iteration 3 Error: 0.050079 Iteration 4 Error: 0.010416 Align patch 6 19 left Iteration 1 Error: 0.808697 Iteration 2 Error: 0.275126 Iteration 3 Error: 0.113602 Iteration 4 Error: 0.047226 Align patch 7 18 left Iteration 1 Error: 1.388335 Iteration 2 Error: 0.343459 Iteration 3 Error: 0.130392 Iteration 4 Error: 0.065859 Iteration 5 Error: 0.027036 Align patch 8 17 left Iteration 1 Error: 0.609176 Iteration 2 Error: 0.118760 Iteration 3 Error: 0.046538 Align patch 9 16 left Iteration 1 Error: 0.513352 Iteration 2 Error: 0.064328 Iteration 3 Error: 0.019476 Align patch 10 15 left Iteration 1 Error: 0.871685 Iteration 2 Error: 0.205107 Iteration 3 Error: 0.052027 Iteration 4 Error: 0.013807 Align patch 11 14 left Iteration 1 Error: 1.090334 Iteration 2 Error: 0.270415 Iteration 3 Error: 0.103081 Iteration 4 Error: 0.033613 Align patch 12 13 left Iteration 1 Error: 1.094671 Iteration 2 Error: 0.216063 Iteration 3 Error: 0.071919 Iteration 4 Error: 0.032009 Align patch 13 12 left Iteration 1 Error: 0.581990 Iteration 2 Error: 0.089522 Iteration 3 Error: 0.013966 Align patch 14 11 left Iteration 1 Error: 0.846693 Iteration 2 Error: 0.160038 Iteration 3 Error: 0.056604 Iteration 4 Error: 0.018156 Align patch 15 10 left Iteration 1 Error: 0.543579 Iteration 2 Error: 0.117133 Iteration 3 Error: 0.031319 Align patch 16 9 left Iteration 1 Error: 0.816619 Iteration 2 Error: 0.118281 Iteration 3 Error: 0.032170 Align patch 17 8 left Iteration 1 Error: 0.561720 Iteration 2 Error: 0.076837 Iteration 3 Error: 0.022021 Align patch 18 7 left Iteration 1 Error: 0.656685 Iteration 2 Error: 0.080410 Iteration 3 Error: 0.026417 Align patch 19 6 left Iteration 1 Error: 0.769840 Iteration 2 Error: 0.130413 Iteration 3 Error: 0.030477 Align patch 20 5 left Iteration 1 Error: 0.714060 Iteration 2 Error: 0.211586 Iteration 3 Error: 0.052353 Iteration 4 Error: 0.018693 Align patch 21 4 left Iteration 1 Error: 0.668844 Iteration 2 Error: 0.108406 Iteration 3 Error: 0.035138 Align patch 22 3 left Iteration 1 Error: 0.590313 Iteration 2 Error: 0.102172 Iteration 3 Error: 0.023635 Align patch 23 2 left Iteration 1 Error: 0.943365 Iteration 2 Error: 0.140536 Iteration 3 Error: 0.026159 Align patch 24 1 left Iteration 1 Error: 0.799478 Iteration 2 Error: 0.148953 Iteration 3 Error: 0.055690 Iteration 4 Error: 0.021201 Align patch 25 0 left Iteration 1 Error: 0.888877 Iteration 2 Error: 0.163449 Iteration 3 Error: 0.033451 3D Fitting completed. Patch alignment time: 16.47(sec) Local motion has been corrected. Process thread exits. Computational time: 25.366741 sec Total time: 30.796396 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00007hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00007hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.721299s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00007hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.676654s ........................................ >>>>>>TIME<<<<<< FFT: 1.047066s Defocus_U Defocus_V Angle CCC 12138.69 13041.03 12.78 0.057266 Final Values Defocus_U Defocus_V Angle CCC 12143.38 13045.72 12.78 0.093071 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00007hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00007hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 39.43 6.79 Num Hot pixels: 203 Hot pixel threshold: 80.18 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.836197 Iteration 2 Error: 0.455972 Iteration 3 Error: 0.179823 Iteration 4 Error: 0.083942 Iteration 5 Error: 0.035304 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.47 -0.37 ...... Frame ( 3) shift: -0.95 -0.74 ...... Frame ( 4) shift: -1.42 -1.10 ...... Frame ( 5) shift: -1.90 -1.47 ...... Frame ( 6) shift: -2.13 -1.67 ...... Frame ( 7) shift: -2.11 -1.71 ...... Frame ( 8) shift: -2.09 -1.74 ...... Frame ( 9) shift: -1.99 -1.68 ...... Frame ( 10) shift: -1.81 -1.52 ...... Frame ( 11) shift: -1.63 -1.36 ...... Frame ( 12) shift: -1.48 -1.23 ...... Frame ( 13) shift: -1.37 -1.13 ...... Frame ( 14) shift: -1.26 -1.03 ...... Frame ( 15) shift: -1.16 -0.90 ...... Frame ( 16) shift: -1.07 -0.76 ...... Frame ( 17) shift: -0.98 -0.61 ...... Frame ( 18) shift: -0.88 -0.46 ...... Frame ( 19) shift: -0.78 -0.32 ...... Frame ( 20) shift: -0.67 -0.18 ...... Frame ( 21) shift: -0.53 -0.03 ...... Frame ( 22) shift: -0.37 0.12 ...... Frame ( 23) shift: -0.20 0.28 ...... Frame ( 24) shift: -0.06 0.37 ...... Frame ( 25) shift: 0.05 0.42 ...... Frame ( 26) shift: 0.16 0.46 ...... Frame ( 27) shift: 0.27 0.54 ...... Frame ( 28) shift: 0.38 0.66 ...... Frame ( 29) shift: 0.48 0.77 ...... Frame ( 30) shift: 0.58 0.86 ...... Frame ( 31) shift: 0.65 0.92 ...... Frame ( 32) shift: 0.73 0.98 ...... Frame ( 33) shift: 0.75 1.04 ...... Frame ( 34) shift: 0.71 1.11 ...... Frame ( 35) shift: 0.67 1.18 ...... Frame ( 36) shift: 0.66 1.26 ...... Frame ( 37) shift: 0.68 1.34 ...... Frame ( 38) shift: 0.70 1.42 ...... Frame ( 39) shift: 0.72 1.50 ...... Frame ( 40) shift: 0.74 1.58 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.907053 Iteration 2 Error: 0.924442 Iteration 3 Error: 0.228031 Iteration 4 Error: 0.108339 Iteration 5 Error: 0.044624 Align patch 2 23 left Iteration 1 Error: 2.021603 Iteration 2 Error: 0.520075 Iteration 3 Error: 0.229977 Iteration 4 Error: 0.123304 Iteration 5 Error: 0.069356 Align patch 2 23 left Iteration 1 Error: 1.830601 Iteration 2 Error: 0.341392 Iteration 3 Error: 0.088247 Iteration 4 Error: 0.033802 Align patch 3 22 left Iteration 1 Error: 0.542667 Iteration 2 Error: 0.132197 Iteration 3 Error: 0.052186 Iteration 4 Error: 0.024803 Align patch 4 21 left Iteration 1 Error: 0.993729 Iteration 2 Error: 0.174702 Iteration 3 Error: 0.060694 Iteration 4 Error: 0.024779 Align patch 5 20 left Iteration 1 Error: 1.616922 Iteration 2 Error: 0.376747 Iteration 3 Error: 0.078629 Iteration 4 Error: 0.030011 Align patch 6 19 left Iteration 1 Error: 1.753951 Iteration 2 Error: 0.504465 Iteration 3 Error: 0.285507 Iteration 4 Error: 0.161114 Iteration 5 Error: 0.081731 Align patch 6 19 left Iteration 1 Error: 2.285489 Iteration 2 Error: 0.540942 Iteration 3 Error: 0.151836 Iteration 4 Error: 0.053892 Iteration 5 Error: 0.021521 Align patch 7 18 left Iteration 1 Error: 1.196957 Iteration 2 Error: 0.262043 Iteration 3 Error: 0.135412 Iteration 4 Error: 0.055286 Iteration 5 Error: 0.026450 Align patch 8 17 left Iteration 1 Error: 0.830501 Iteration 2 Error: 0.141009 Iteration 3 Error: 0.040222 Align patch 9 16 left Iteration 1 Error: 0.700696 Iteration 2 Error: 0.084456 Iteration 3 Error: 0.024176 Align patch 10 15 left Iteration 1 Error: 1.626084 Iteration 2 Error: 0.243748 Iteration 3 Error: 0.054927 Iteration 4 Error: 0.019000 Align patch 11 14 left Iteration 1 Error: 2.071244 Iteration 2 Error: 0.682101 Iteration 3 Error: 0.284568 Iteration 4 Error: 0.145074 Iteration 5 Error: 0.080773 Align patch 11 14 left Iteration 1 Error: 1.952387 Iteration 2 Error: 0.419592 Iteration 3 Error: 0.129361 Iteration 4 Error: 0.043098 Align patch 12 13 left Iteration 1 Error: 1.371215 Iteration 2 Error: 0.503660 Iteration 3 Error: 0.330334 Iteration 4 Error: 0.213694 Iteration 5 Error: 0.132126 Align patch 12 13 left Iteration 1 Error: 1.650804 Iteration 2 Error: 0.393887 Iteration 3 Error: 0.126344 Iteration 4 Error: 0.054134 Iteration 5 Error: 0.021406 Align patch 13 12 left Iteration 1 Error: 0.805206 Iteration 2 Error: 0.252113 Iteration 3 Error: 0.114909 Iteration 4 Error: 0.059642 Iteration 5 Error: 0.029031 Align patch 14 11 left Iteration 1 Error: 0.842886 Iteration 2 Error: 0.247834 Iteration 3 Error: 0.112977 Iteration 4 Error: 0.055958 Iteration 5 Error: 0.024944 Align patch 15 10 left Iteration 1 Error: 0.769452 Iteration 2 Error: 0.288571 Iteration 3 Error: 0.090369 Iteration 4 Error: 0.046549 Align patch 16 9 left Iteration 1 Error: 1.983771 Iteration 2 Error: 0.488033 Iteration 3 Error: 0.228801 Iteration 4 Error: 0.119019 Iteration 5 Error: 0.055648 Align patch 16 9 left Iteration 1 Error: 1.755592 Iteration 2 Error: 0.302959 Iteration 3 Error: 0.100843 Iteration 4 Error: 0.030560 Align patch 17 8 left Iteration 1 Error: 1.581820 Iteration 2 Error: 0.313978 Iteration 3 Error: 0.127793 Iteration 4 Error: 0.058257 Iteration 5 Error: 0.023558 Align patch 18 7 left Iteration 1 Error: 0.679520 Iteration 2 Error: 0.191598 Iteration 3 Error: 0.069839 Iteration 4 Error: 0.029520 Align patch 19 6 left Iteration 1 Error: 0.725858 Iteration 2 Error: 0.130150 Iteration 3 Error: 0.040671 Align patch 20 5 left Iteration 1 Error: 1.153549 Iteration 2 Error: 0.235275 Iteration 3 Error: 0.090025 Iteration 4 Error: 0.039695 Align patch 21 4 left Iteration 1 Error: 1.664126 Iteration 2 Error: 0.299715 Iteration 3 Error: 0.109953 Iteration 4 Error: 0.046908 Align patch 22 3 left Iteration 1 Error: 1.143660 Iteration 2 Error: 0.242622 Iteration 3 Error: 0.091819 Iteration 4 Error: 0.059023 Iteration 5 Error: 0.040806 Align patch 23 2 left Iteration 1 Error: 0.816976 Iteration 2 Error: 0.337376 Iteration 3 Error: 0.135473 Iteration 4 Error: 0.065030 Iteration 5 Error: 0.027839 Align patch 24 1 left Iteration 1 Error: 0.820540 Iteration 2 Error: 0.272248 Iteration 3 Error: 0.106738 Iteration 4 Error: 0.049829 Align patch 25 0 left Iteration 1 Error: 1.285343 Iteration 2 Error: 0.285893 Iteration 3 Error: 0.064362 Iteration 4 Error: 0.020076 3D Fitting completed. Patch alignment time: 22.39(sec) Local motion has been corrected. Process thread exits. Computational time: 31.249722 sec Total time: 36.764526 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00007hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00007hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.547899s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00007hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.497459s ........................................ >>>>>>TIME<<<<<< FFT: 0.948850s Defocus_U Defocus_V Angle CCC 9585.94 10082.03 0.91 0.037053 Final Values Defocus_U Defocus_V Angle CCC 9592.19 10091.41 2.16 0.066943 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00007hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00007hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 39.82 6.81 Num Hot pixels: 204 Hot pixel threshold: 80.67 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.576149 Iteration 2 Error: 0.325055 Iteration 3 Error: 0.098789 Iteration 4 Error: 0.038301 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.32 -0.41 ...... Frame ( 3) shift: -0.64 -0.81 ...... Frame ( 4) shift: -0.96 -1.22 ...... Frame ( 5) shift: -1.27 -1.63 ...... Frame ( 6) shift: -1.45 -1.85 ...... Frame ( 7) shift: -1.50 -1.90 ...... Frame ( 8) shift: -1.54 -1.94 ...... Frame ( 9) shift: -1.58 -1.86 ...... Frame ( 10) shift: -1.61 -1.67 ...... Frame ( 11) shift: -1.63 -1.48 ...... Frame ( 12) shift: -1.61 -1.31 ...... Frame ( 13) shift: -1.53 -1.18 ...... Frame ( 14) shift: -1.46 -1.04 ...... Frame ( 15) shift: -1.34 -0.90 ...... Frame ( 16) shift: -1.20 -0.74 ...... Frame ( 17) shift: -1.05 -0.59 ...... Frame ( 18) shift: -0.94 -0.45 ...... Frame ( 19) shift: -0.86 -0.32 ...... Frame ( 20) shift: -0.78 -0.19 ...... Frame ( 21) shift: -0.72 -0.06 ...... Frame ( 22) shift: -0.67 0.06 ...... Frame ( 23) shift: -0.62 0.18 ...... Frame ( 24) shift: -0.58 0.29 ...... Frame ( 25) shift: -0.53 0.38 ...... Frame ( 26) shift: -0.49 0.48 ...... Frame ( 27) shift: -0.43 0.54 ...... Frame ( 28) shift: -0.37 0.58 ...... Frame ( 29) shift: -0.30 0.62 ...... Frame ( 30) shift: -0.26 0.66 ...... Frame ( 31) shift: -0.25 0.70 ...... Frame ( 32) shift: -0.23 0.74 ...... Frame ( 33) shift: -0.22 0.80 ...... Frame ( 34) shift: -0.19 0.86 ...... Frame ( 35) shift: -0.16 0.92 ...... Frame ( 36) shift: -0.13 0.98 ...... Frame ( 37) shift: -0.11 1.04 ...... Frame ( 38) shift: -0.08 1.10 ...... Frame ( 39) shift: -0.05 1.15 ...... Frame ( 40) shift: -0.03 1.21 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.277349 Iteration 2 Error: 0.349422 Iteration 3 Error: 0.069861 Iteration 4 Error: 0.035438 Align patch 2 23 left Iteration 1 Error: 1.174140 Iteration 2 Error: 0.331870 Iteration 3 Error: 0.103746 Iteration 4 Error: 0.041426 Align patch 3 22 left Iteration 1 Error: 0.528988 Iteration 2 Error: 0.128631 Iteration 3 Error: 0.033070 Align patch 4 21 left Iteration 1 Error: 1.274217 Iteration 2 Error: 0.179667 Iteration 3 Error: 0.043886 Align patch 5 20 left Iteration 1 Error: 1.061505 Iteration 2 Error: 0.149014 Iteration 3 Error: 0.042781 Align patch 6 19 left Iteration 1 Error: 2.162778 Iteration 2 Error: 0.421347 Iteration 3 Error: 0.106918 Iteration 4 Error: 0.027712 Align patch 7 18 left Iteration 1 Error: 1.768343 Iteration 2 Error: 0.537330 Iteration 3 Error: 0.116716 Iteration 4 Error: 0.042139 Align patch 8 17 left Iteration 1 Error: 0.807040 Iteration 2 Error: 0.296054 Iteration 3 Error: 0.080275 Iteration 4 Error: 0.042753 Align patch 9 16 left Iteration 1 Error: 0.722192 Iteration 2 Error: 0.172428 Iteration 3 Error: 0.032685 Align patch 10 15 left Iteration 1 Error: 1.034982 Iteration 2 Error: 0.174264 Iteration 3 Error: 0.058934 Iteration 4 Error: 0.011848 Align patch 11 14 left Iteration 1 Error: 1.086941 Iteration 2 Error: 0.155625 Iteration 3 Error: 0.049174 Align patch 12 13 left Iteration 1 Error: 0.920001 Iteration 2 Error: 0.139294 Iteration 3 Error: 0.035642 Align patch 13 12 left Iteration 1 Error: 0.729928 Iteration 2 Error: 0.145816 Iteration 3 Error: 0.039445 Align patch 14 11 left Iteration 1 Error: 0.698476 Iteration 2 Error: 0.140888 Iteration 3 Error: 0.030154 Align patch 15 10 left Iteration 1 Error: 0.861922 Iteration 2 Error: 0.207407 Iteration 3 Error: 0.056302 Iteration 4 Error: 0.014268 Align patch 16 9 left Iteration 1 Error: 1.167997 Iteration 2 Error: 0.331289 Iteration 3 Error: 0.130975 Iteration 4 Error: 0.056027 Iteration 5 Error: 0.029683 Align patch 17 8 left Iteration 1 Error: 0.793385 Iteration 2 Error: 0.150602 Iteration 3 Error: 0.039786 Align patch 18 7 left Iteration 1 Error: 0.724037 Iteration 2 Error: 0.119216 Iteration 3 Error: 0.033147 Align patch 19 6 left Iteration 1 Error: 0.908382 Iteration 2 Error: 0.224503 Iteration 3 Error: 0.040819 Align patch 20 5 left Iteration 1 Error: 1.134978 Iteration 2 Error: 0.273323 Iteration 3 Error: 0.106770 Iteration 4 Error: 0.033635 Align patch 21 4 left Iteration 1 Error: 1.047791 Iteration 2 Error: 0.182445 Iteration 3 Error: 0.055322 Iteration 4 Error: 0.013985 Align patch 22 3 left Iteration 1 Error: 0.783887 Iteration 2 Error: 0.254156 Iteration 3 Error: 0.086259 Iteration 4 Error: 0.024428 Align patch 23 2 left Iteration 1 Error: 0.677435 Iteration 2 Error: 0.176305 Iteration 3 Error: 0.074973 Iteration 4 Error: 0.037935 Align patch 24 1 left Iteration 1 Error: 0.937274 Iteration 2 Error: 0.180608 Iteration 3 Error: 0.074609 Iteration 4 Error: 0.034005 Align patch 25 0 left Iteration 1 Error: 1.419026 Iteration 2 Error: 0.321227 Iteration 3 Error: 0.083996 Iteration 4 Error: 0.031361 3D Fitting completed. Patch alignment time: 16.91(sec) Local motion has been corrected. Process thread exits. Computational time: 25.308378 sec Total time: 31.800425 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00007hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00007hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.567944s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00007hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.851668s ........................................ >>>>>>TIME<<<<<< FFT: 0.944033s Defocus_U Defocus_V Angle CCC 14812.50 15718.75 7.14 0.056038 Final Values Defocus_U Defocus_V Angle CCC 14821.88 15721.88 6.52 0.088674 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00007hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00007hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 37.12 7.25 Num Hot pixels: 149 Hot pixel threshold: 80.61 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 3.357556 Iteration 2 Error: 0.300268 Iteration 3 Error: 0.095999 Iteration 4 Error: 0.032726 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.58 -0.55 ...... Frame ( 3) shift: -1.15 -1.10 ...... Frame ( 4) shift: -1.73 -1.65 ...... Frame ( 5) shift: -2.31 -2.19 ...... Frame ( 6) shift: -2.66 -2.56 ...... Frame ( 7) shift: -2.79 -2.74 ...... Frame ( 8) shift: -2.91 -2.93 ...... Frame ( 9) shift: -3.06 -3.00 ...... Frame ( 10) shift: -3.22 -2.96 ...... Frame ( 11) shift: -3.38 -2.91 ...... Frame ( 12) shift: -3.51 -2.89 ...... Frame ( 13) shift: -3.61 -2.90 ...... Frame ( 14) shift: -3.70 -2.91 ...... Frame ( 15) shift: -3.76 -2.93 ...... Frame ( 16) shift: -3.79 -2.96 ...... Frame ( 17) shift: -3.81 -2.99 ...... Frame ( 18) shift: -3.86 -3.01 ...... Frame ( 19) shift: -3.95 -3.02 ...... Frame ( 20) shift: -4.03 -3.02 ...... Frame ( 21) shift: -4.11 -3.02 ...... Frame ( 22) shift: -4.18 -2.99 ...... Frame ( 23) shift: -4.25 -2.97 ...... Frame ( 24) shift: -4.31 -2.96 ...... Frame ( 25) shift: -4.37 -2.96 ...... Frame ( 26) shift: -4.43 -2.96 ...... Frame ( 27) shift: -4.47 -2.96 ...... Frame ( 28) shift: -4.49 -2.97 ...... Frame ( 29) shift: -4.52 -2.98 ...... Frame ( 30) shift: -4.55 -3.00 ...... Frame ( 31) shift: -4.59 -3.05 ...... Frame ( 32) shift: -4.63 -3.09 ...... Frame ( 33) shift: -4.70 -3.15 ...... Frame ( 34) shift: -4.81 -3.22 ...... Frame ( 35) shift: -4.91 -3.29 ...... Frame ( 36) shift: -5.02 -3.31 ...... Frame ( 37) shift: -5.13 -3.29 ...... Frame ( 38) shift: -5.24 -3.26 ...... Frame ( 39) shift: -5.35 -3.23 ...... Frame ( 40) shift: -5.46 -3.20 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.643553 Iteration 2 Error: 0.652858 Iteration 3 Error: 0.170522 Iteration 4 Error: 0.044930 Align patch 2 23 left Iteration 1 Error: 2.522855 Iteration 2 Error: 0.544380 Iteration 3 Error: 0.140177 Iteration 4 Error: 0.046876 Align patch 3 22 left Iteration 1 Error: 1.956848 Iteration 2 Error: 0.460113 Iteration 3 Error: 0.119660 Iteration 4 Error: 0.036379 Align patch 4 21 left Iteration 1 Error: 0.880000 Iteration 2 Error: 0.192756 Iteration 3 Error: 0.058075 Iteration 4 Error: 0.022440 Align patch 5 20 left Iteration 1 Error: 39.690578 Iteration 2 Error: 36.887089 Iteration 3 Error: 29.620710 Iteration 4 Error: 19.186460 Iteration 5 Error: 17.587700 Align patch 5 20 left Iteration 1 Error: 2.783005 Iteration 2 Error: 0.540741 Iteration 3 Error: 0.236686 Iteration 4 Error: 0.080619 Iteration 5 Error: 0.038386 Align patch 6 19 left Iteration 1 Error: 2.265474 Iteration 2 Error: 0.400789 Iteration 3 Error: 0.116265 Iteration 4 Error: 0.041917 Align patch 7 18 left Iteration 1 Error: 1.858027 Iteration 2 Error: 0.425717 Iteration 3 Error: 0.113778 Iteration 4 Error: 0.042403 Align patch 8 17 left Iteration 1 Error: 1.876517 Iteration 2 Error: 0.369815 Iteration 3 Error: 0.069939 Iteration 4 Error: 0.022211 Align patch 9 16 left Iteration 1 Error: 0.624248 Iteration 2 Error: 0.078785 Iteration 3 Error: 0.018755 Align patch 10 15 left Iteration 1 Error: 2.380094 Iteration 2 Error: 0.592670 Iteration 3 Error: 0.455229 Iteration 4 Error: 0.257786 Iteration 5 Error: 0.159367 Align patch 10 15 left Iteration 1 Error: 2.675931 Iteration 2 Error: 0.587371 Iteration 3 Error: 0.234723 Iteration 4 Error: 0.091229 Iteration 5 Error: 0.033734 Align patch 11 14 left Iteration 1 Error: 1.484217 Iteration 2 Error: 0.340109 Iteration 3 Error: 0.114280 Iteration 4 Error: 0.043786 Align patch 12 13 left Iteration 1 Error: 1.053992 Iteration 2 Error: 0.172216 Iteration 3 Error: 0.041941 Align patch 13 12 left Iteration 1 Error: 1.850990 Iteration 2 Error: 0.536190 Iteration 3 Error: 0.143356 Iteration 4 Error: 0.057667 Iteration 5 Error: 0.017341 Align patch 14 11 left Iteration 1 Error: 1.573215 Iteration 2 Error: 0.280315 Iteration 3 Error: 0.083422 Iteration 4 Error: 0.027850 Align patch 15 10 left Iteration 1 Error: 1.281570 Iteration 2 Error: 0.361379 Iteration 3 Error: 0.113290 Iteration 4 Error: 0.046327 Align patch 16 9 left Iteration 1 Error: 1.532763 Iteration 2 Error: 0.354256 Iteration 3 Error: 0.084621 Iteration 4 Error: 0.025744 Align patch 17 8 left Iteration 1 Error: 3.754379 Iteration 2 Error: 0.717678 Iteration 3 Error: 0.218396 Iteration 4 Error: 0.092679 Iteration 5 Error: 0.042511 Align patch 18 7 left Iteration 1 Error: 1.732368 Iteration 2 Error: 0.465351 Iteration 3 Error: 0.153140 Iteration 4 Error: 0.045930 Align patch 19 6 left Iteration 1 Error: 1.555945 Iteration 2 Error: 0.226509 Iteration 3 Error: 0.054322 Iteration 4 Error: 0.016054 Align patch 20 5 left Iteration 1 Error: 4.273326 Iteration 2 Error: 1.419501 Iteration 3 Error: 0.867122 Iteration 4 Error: 0.963123 Iteration 5 Error: 0.666215 Align patch 20 5 left Iteration 1 Error: 3.464086 Iteration 2 Error: 0.922753 Iteration 3 Error: 0.460873 Iteration 4 Error: 0.258425 Iteration 5 Error: 0.167812 Align patch 21 4 left Iteration 1 Error: 3.078082 Iteration 2 Error: 0.639606 Iteration 3 Error: 0.186663 Iteration 4 Error: 0.092246 Iteration 5 Error: 0.035356 Align patch 22 3 left Iteration 1 Error: 37.362064 Iteration 2 Error: 23.068314 Iteration 3 Error: 1.797042 Iteration 4 Error: 0.827849 Iteration 5 Error: 11.534909 Align patch 22 3 left Iteration 1 Error: 38.788479 Iteration 2 Error: 23.024755 Iteration 3 Error: 2.754151 Iteration 4 Error: 0.923073 Iteration 5 Error: 0.828324 Align patch 23 2 left Iteration 1 Error: 2.339099 Iteration 2 Error: 0.752885 Iteration 3 Error: 0.356079 Iteration 4 Error: 0.187099 Iteration 5 Error: 0.092735 Align patch 23 2 left Iteration 1 Error: 2.812055 Iteration 2 Error: 0.627899 Iteration 3 Error: 0.239297 Iteration 4 Error: 0.091768 Iteration 5 Error: 0.040509 Align patch 24 1 left Iteration 1 Error: 2.887340 Iteration 2 Error: 0.933071 Iteration 3 Error: 0.472863 Iteration 4 Error: 0.378670 Iteration 5 Error: 0.260680 Align patch 24 1 left Iteration 1 Error: 2.829974 Iteration 2 Error: 0.809426 Iteration 3 Error: 0.397571 Iteration 4 Error: 0.245081 Iteration 5 Error: 0.116155 Align patch 25 0 left Iteration 1 Error: 6.911575 Iteration 2 Error: 1.728597 Iteration 3 Error: 0.810245 Iteration 4 Error: 0.621885 Iteration 5 Error: 0.430731 Align patch 25 0 left Iteration 1 Error: 4.534450 Iteration 2 Error: 1.376399 Iteration 3 Error: 1.017580 Iteration 4 Error: 0.773114 Iteration 5 Error: 0.661225 3D Fitting completed. Patch alignment time: 24.63(sec) Local motion has been corrected. Process thread exits. Computational time: 33.195328 sec Total time: 38.694027 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00007hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00007hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.577819s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00007hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.962500s ........................................ >>>>>>TIME<<<<<< FFT: 0.914713s Defocus_U Defocus_V Angle CCC 13291.50 12540.56 83.18 0.042568 Final Values Defocus_U Defocus_V Angle CCC 13304.01 12574.95 82.87 0.068661 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00008hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00008hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 41.09 6.93 Num Hot pixels: 218 Hot pixel threshold: 82.70 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.030577 Iteration 2 Error: 0.248187 Iteration 3 Error: 0.071351 Iteration 4 Error: 0.028309 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.04 0.06 ...... Frame ( 3) shift: -0.07 0.11 ...... Frame ( 4) shift: -0.11 0.17 ...... Frame ( 5) shift: -0.14 0.22 ...... Frame ( 6) shift: -0.13 0.27 ...... Frame ( 7) shift: -0.08 0.30 ...... Frame ( 8) shift: -0.02 0.33 ...... Frame ( 9) shift: -0.02 0.38 ...... Frame ( 10) shift: -0.08 0.44 ...... Frame ( 11) shift: -0.13 0.51 ...... Frame ( 12) shift: -0.13 0.54 ...... Frame ( 13) shift: -0.07 0.54 ...... Frame ( 14) shift: -0.02 0.54 ...... Frame ( 15) shift: 0.04 0.56 ...... Frame ( 16) shift: 0.11 0.61 ...... Frame ( 17) shift: 0.17 0.65 ...... Frame ( 18) shift: 0.26 0.68 ...... Frame ( 19) shift: 0.38 0.70 ...... Frame ( 20) shift: 0.50 0.73 ...... Frame ( 21) shift: 0.60 0.77 ...... Frame ( 22) shift: 0.68 0.85 ...... Frame ( 23) shift: 0.77 0.93 ...... Frame ( 24) shift: 0.83 1.00 ...... Frame ( 25) shift: 0.85 1.08 ...... Frame ( 26) shift: 0.87 1.15 ...... Frame ( 27) shift: 0.95 1.22 ...... Frame ( 28) shift: 1.07 1.28 ...... Frame ( 29) shift: 1.20 1.34 ...... Frame ( 30) shift: 1.25 1.40 ...... Frame ( 31) shift: 1.23 1.47 ...... Frame ( 32) shift: 1.22 1.53 ...... Frame ( 33) shift: 1.25 1.59 ...... Frame ( 34) shift: 1.33 1.65 ...... Frame ( 35) shift: 1.42 1.70 ...... Frame ( 36) shift: 1.48 1.73 ...... Frame ( 37) shift: 1.50 1.74 ...... Frame ( 38) shift: 1.52 1.74 ...... Frame ( 39) shift: 1.54 1.74 ...... Frame ( 40) shift: 1.57 1.75 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.982776 Iteration 2 Error: 0.253791 Iteration 3 Error: 0.073950 Iteration 4 Error: 0.027943 Align patch 2 23 left Iteration 1 Error: 0.965293 Iteration 2 Error: 0.306366 Iteration 3 Error: 0.131147 Iteration 4 Error: 0.055464 Iteration 5 Error: 0.027614 Align patch 3 22 left Iteration 1 Error: 0.562457 Iteration 2 Error: 0.113691 Iteration 3 Error: 0.035102 Align patch 4 21 left Iteration 1 Error: 0.668840 Iteration 2 Error: 0.114655 Iteration 3 Error: 0.025748 Align patch 5 20 left Iteration 1 Error: 0.477837 Iteration 2 Error: 0.073333 Iteration 3 Error: 0.013599 Align patch 6 19 left Iteration 1 Error: 0.870832 Iteration 2 Error: 0.353771 Iteration 3 Error: 0.154409 Iteration 4 Error: 0.067219 Iteration 5 Error: 0.030914 Align patch 7 18 left Iteration 1 Error: 0.688766 Iteration 2 Error: 0.142055 Iteration 3 Error: 0.043105 Align patch 8 17 left Iteration 1 Error: 0.869832 Iteration 2 Error: 0.165722 Iteration 3 Error: 0.050620 Iteration 4 Error: 0.014579 Align patch 9 16 left Iteration 1 Error: 0.670036 Iteration 2 Error: 0.063543 Iteration 3 Error: 0.012520 Align patch 10 15 left Iteration 1 Error: 0.615157 Iteration 2 Error: 0.082813 Iteration 3 Error: 0.014392 Align patch 11 14 left Iteration 1 Error: 1.050358 Iteration 2 Error: 0.245356 Iteration 3 Error: 0.142674 Iteration 4 Error: 0.054239 Iteration 5 Error: 0.033865 Align patch 12 13 left Iteration 1 Error: 0.607403 Iteration 2 Error: 0.132444 Iteration 3 Error: 0.025005 Align patch 13 12 left Iteration 1 Error: 0.581159 Iteration 2 Error: 0.057916 Iteration 3 Error: 0.013526 Align patch 14 11 left Iteration 1 Error: 0.567802 Iteration 2 Error: 0.062132 Iteration 3 Error: 0.015197 Align patch 15 10 left Iteration 1 Error: 0.470315 Iteration 2 Error: 0.100510 Iteration 3 Error: 0.020331 Align patch 16 9 left Iteration 1 Error: 0.816030 Iteration 2 Error: 0.169621 Iteration 3 Error: 0.028818 Align patch 17 8 left Iteration 1 Error: 0.767322 Iteration 2 Error: 0.076454 Iteration 3 Error: 0.022872 Align patch 18 7 left Iteration 1 Error: 0.625795 Iteration 2 Error: 0.165892 Iteration 3 Error: 0.039104 Align patch 19 6 left Iteration 1 Error: 0.580930 Iteration 2 Error: 0.107826 Iteration 3 Error: 0.020876 Align patch 20 5 left Iteration 1 Error: 0.703185 Iteration 2 Error: 0.117437 Iteration 3 Error: 0.023594 Align patch 21 4 left Iteration 1 Error: 1.248107 Iteration 2 Error: 0.139524 Iteration 3 Error: 0.028986 Align patch 22 3 left Iteration 1 Error: 0.980661 Iteration 2 Error: 0.116128 Iteration 3 Error: 0.025174 Align patch 23 2 left Iteration 1 Error: 0.445994 Iteration 2 Error: 0.066030 Iteration 3 Error: 0.019518 Align patch 24 1 left Iteration 1 Error: 0.689864 Iteration 2 Error: 0.130783 Iteration 3 Error: 0.020465 Align patch 25 0 left Iteration 1 Error: 0.425815 Iteration 2 Error: 0.102964 Iteration 3 Error: 0.013864 3D Fitting completed. Patch alignment time: 15.45(sec) Local motion has been corrected. Process thread exits. Computational time: 23.510469 sec Total time: 30.857813 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00008hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00008hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.538624s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00008hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.710016s ........................................ >>>>>>TIME<<<<<< FFT: 0.969836s Defocus_U Defocus_V Angle CCC 11212.91 12087.91 12.94 0.049901 Final Values Defocus_U Defocus_V Angle CCC 11230.10 12108.24 12.31 0.085222 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00008hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00008hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.002e-01 CC threshold: 0.736 Mean Std: 41.68 7.01 Num Hot pixels: 225 Hot pixel threshold: 83.77 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.090426 Iteration 2 Error: 0.287600 Iteration 3 Error: 0.078531 Iteration 4 Error: 0.030078 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.05 0.07 ...... Frame ( 3) shift: -0.10 0.13 ...... Frame ( 4) shift: -0.15 0.20 ...... Frame ( 5) shift: -0.19 0.26 ...... Frame ( 6) shift: -0.20 0.31 ...... Frame ( 7) shift: -0.17 0.34 ...... Frame ( 8) shift: -0.13 0.37 ...... Frame ( 9) shift: -0.10 0.46 ...... Frame ( 10) shift: -0.06 0.60 ...... Frame ( 11) shift: -0.03 0.75 ...... Frame ( 12) shift: 0.02 0.83 ...... Frame ( 13) shift: 0.09 0.87 ...... Frame ( 14) shift: 0.15 0.91 ...... Frame ( 15) shift: 0.21 0.96 ...... Frame ( 16) shift: 0.27 1.02 ...... Frame ( 17) shift: 0.32 1.09 ...... Frame ( 18) shift: 0.37 1.15 ...... Frame ( 19) shift: 0.42 1.22 ...... Frame ( 20) shift: 0.46 1.28 ...... Frame ( 21) shift: 0.49 1.34 ...... Frame ( 22) shift: 0.52 1.39 ...... Frame ( 23) shift: 0.54 1.45 ...... Frame ( 24) shift: 0.58 1.48 ...... Frame ( 25) shift: 0.63 1.51 ...... Frame ( 26) shift: 0.69 1.53 ...... Frame ( 27) shift: 0.75 1.60 ...... Frame ( 28) shift: 0.81 1.72 ...... Frame ( 29) shift: 0.88 1.84 ...... Frame ( 30) shift: 0.95 1.95 ...... Frame ( 31) shift: 1.01 2.05 ...... Frame ( 32) shift: 1.08 2.15 ...... Frame ( 33) shift: 1.15 2.20 ...... Frame ( 34) shift: 1.21 2.22 ...... Frame ( 35) shift: 1.28 2.24 ...... Frame ( 36) shift: 1.33 2.26 ...... Frame ( 37) shift: 1.36 2.29 ...... Frame ( 38) shift: 1.40 2.32 ...... Frame ( 39) shift: 1.43 2.35 ...... Frame ( 40) shift: 1.46 2.38 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.050448 Iteration 2 Error: 0.318037 Iteration 3 Error: 0.144263 Iteration 4 Error: 0.064013 Iteration 5 Error: 0.031961 Align patch 2 23 left Iteration 1 Error: 0.918441 Iteration 2 Error: 0.206754 Iteration 3 Error: 0.081706 Iteration 4 Error: 0.031110 Align patch 3 22 left Iteration 1 Error: 0.592703 Iteration 2 Error: 0.126472 Iteration 3 Error: 0.019829 Align patch 4 21 left Iteration 1 Error: 0.729443 Iteration 2 Error: 0.088040 Iteration 3 Error: 0.022126 Align patch 5 20 left Iteration 1 Error: 0.509599 Iteration 2 Error: 0.091185 Iteration 3 Error: 0.016269 Align patch 6 19 left Iteration 1 Error: 1.617390 Iteration 2 Error: 0.339798 Iteration 3 Error: 0.105435 Iteration 4 Error: 0.045196 Align patch 7 18 left Iteration 1 Error: 1.489214 Iteration 2 Error: 0.402379 Iteration 3 Error: 0.111608 Iteration 4 Error: 0.038299 Align patch 8 17 left Iteration 1 Error: 0.861330 Iteration 2 Error: 0.236258 Iteration 3 Error: 0.089749 Iteration 4 Error: 0.029083 Align patch 9 16 left Iteration 1 Error: 0.672791 Iteration 2 Error: 0.122512 Iteration 3 Error: 0.029341 Align patch 10 15 left Iteration 1 Error: 0.860195 Iteration 2 Error: 0.125234 Iteration 3 Error: 0.035695 Align patch 11 14 left Iteration 1 Error: 2.429810 Iteration 2 Error: 0.536149 Iteration 3 Error: 0.188002 Iteration 4 Error: 0.093920 Iteration 5 Error: 0.034437 Align patch 12 13 left Iteration 1 Error: 0.855598 Iteration 2 Error: 0.264365 Iteration 3 Error: 0.103103 Iteration 4 Error: 0.037066 Align patch 13 12 left Iteration 1 Error: 0.618663 Iteration 2 Error: 0.148249 Iteration 3 Error: 0.029153 Align patch 14 11 left Iteration 1 Error: 0.661169 Iteration 2 Error: 0.101583 Iteration 3 Error: 0.019784 Align patch 15 10 left Iteration 1 Error: 1.225993 Iteration 2 Error: 0.138313 Iteration 3 Error: 0.048164 Align patch 16 9 left Iteration 1 Error: 0.805440 Iteration 2 Error: 0.250950 Iteration 3 Error: 0.109577 Iteration 4 Error: 0.048504 Align patch 17 8 left Iteration 1 Error: 0.437744 Iteration 2 Error: 0.138689 Iteration 3 Error: 0.040812 Align patch 18 7 left Iteration 1 Error: 0.590284 Iteration 2 Error: 0.113669 Iteration 3 Error: 0.036631 Align patch 19 6 left Iteration 1 Error: 0.656366 Iteration 2 Error: 0.134054 Iteration 3 Error: 0.023962 Align patch 20 5 left Iteration 1 Error: 0.914152 Iteration 2 Error: 0.194522 Iteration 3 Error: 0.069194 Iteration 4 Error: 0.019517 Align patch 21 4 left Iteration 1 Error: 0.925553 Iteration 2 Error: 0.181443 Iteration 3 Error: 0.065678 Iteration 4 Error: 0.027261 Align patch 22 3 left Iteration 1 Error: 0.668615 Iteration 2 Error: 0.113406 Iteration 3 Error: 0.039222 Align patch 23 2 left Iteration 1 Error: 0.692521 Iteration 2 Error: 0.073620 Iteration 3 Error: 0.017466 Align patch 24 1 left Iteration 1 Error: 0.656616 Iteration 2 Error: 0.127663 Iteration 3 Error: 0.033886 Align patch 25 0 left Iteration 1 Error: 0.868991 Iteration 2 Error: 0.196871 Iteration 3 Error: 0.044942 3D Fitting completed. Patch alignment time: 15.61(sec) Local motion has been corrected. Process thread exits. Computational time: 24.392323 sec Total time: 30.057037 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00008hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00008hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.558549s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00008hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.591492s ........................................ >>>>>>TIME<<<<<< FFT: 0.930035s Defocus_U Defocus_V Angle CCC 9927.76 10443.38 3.81 0.047152 Final Values Defocus_U Defocus_V Angle CCC 9932.45 10451.20 2.88 0.089113 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00008hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00008hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.001e-01 CC threshold: 0.736 Mean Std: 40.89 6.88 Num Hot pixels: 216 Hot pixel threshold: 82.20 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.864022 Iteration 2 Error: 0.155358 Iteration 3 Error: 0.041479 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.03 0.07 ...... Frame ( 3) shift: -0.07 0.15 ...... Frame ( 4) shift: -0.10 0.22 ...... Frame ( 5) shift: -0.13 0.30 ...... Frame ( 6) shift: -0.13 0.36 ...... Frame ( 7) shift: -0.08 0.42 ...... Frame ( 8) shift: -0.04 0.48 ...... Frame ( 9) shift: 0.03 0.55 ...... Frame ( 10) shift: 0.12 0.65 ...... Frame ( 11) shift: 0.22 0.75 ...... Frame ( 12) shift: 0.29 0.82 ...... Frame ( 13) shift: 0.34 0.85 ...... Frame ( 14) shift: 0.39 0.88 ...... Frame ( 15) shift: 0.45 0.94 ...... Frame ( 16) shift: 0.53 1.03 ...... Frame ( 17) shift: 0.61 1.13 ...... Frame ( 18) shift: 0.64 1.16 ...... Frame ( 19) shift: 0.63 1.13 ...... Frame ( 20) shift: 0.62 1.10 ...... Frame ( 21) shift: 0.63 1.09 ...... Frame ( 22) shift: 0.66 1.11 ...... Frame ( 23) shift: 0.68 1.12 ...... Frame ( 24) shift: 0.70 1.15 ...... Frame ( 25) shift: 0.71 1.19 ...... Frame ( 26) shift: 0.71 1.23 ...... Frame ( 27) shift: 0.71 1.28 ...... Frame ( 28) shift: 0.68 1.34 ...... Frame ( 29) shift: 0.65 1.40 ...... Frame ( 30) shift: 0.63 1.45 ...... Frame ( 31) shift: 0.62 1.48 ...... Frame ( 32) shift: 0.60 1.51 ...... Frame ( 33) shift: 0.63 1.52 ...... Frame ( 34) shift: 0.70 1.50 ...... Frame ( 35) shift: 0.77 1.48 ...... Frame ( 36) shift: 0.80 1.51 ...... Frame ( 37) shift: 0.79 1.59 ...... Frame ( 38) shift: 0.78 1.66 ...... Frame ( 39) shift: 0.77 1.73 ...... Frame ( 40) shift: 0.76 1.81 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.870752 Iteration 2 Error: 0.261914 Iteration 3 Error: 0.118707 Iteration 4 Error: 0.036137 Align patch 2 23 left Iteration 1 Error: 1.312478 Iteration 2 Error: 0.225871 Iteration 3 Error: 0.090490 Iteration 4 Error: 0.038421 Align patch 3 22 left Iteration 1 Error: 1.095513 Iteration 2 Error: 0.349461 Iteration 3 Error: 0.141178 Iteration 4 Error: 0.061585 Iteration 5 Error: 0.030259 Align patch 4 21 left Iteration 1 Error: 0.844777 Iteration 2 Error: 0.139408 Iteration 3 Error: 0.041683 Align patch 5 20 left Iteration 1 Error: 0.623432 Iteration 2 Error: 0.102052 Iteration 3 Error: 0.027187 Align patch 6 19 left Iteration 1 Error: 1.077932 Iteration 2 Error: 0.321174 Iteration 3 Error: 0.134783 Iteration 4 Error: 0.068873 Iteration 5 Error: 0.022060 Align patch 7 18 left Iteration 1 Error: 1.067704 Iteration 2 Error: 0.240156 Iteration 3 Error: 0.074818 Iteration 4 Error: 0.028941 Align patch 8 17 left Iteration 1 Error: 0.708239 Iteration 2 Error: 0.146027 Iteration 3 Error: 0.045254 Align patch 9 16 left Iteration 1 Error: 0.665699 Iteration 2 Error: 0.155450 Iteration 3 Error: 0.044055 Align patch 10 15 left Iteration 1 Error: 0.700291 Iteration 2 Error: 0.087281 Iteration 3 Error: 0.019226 Align patch 11 14 left Iteration 1 Error: 0.611123 Iteration 2 Error: 0.112395 Iteration 3 Error: 0.021873 Align patch 12 13 left Iteration 1 Error: 0.662912 Iteration 2 Error: 0.122747 Iteration 3 Error: 0.036246 Align patch 13 12 left Iteration 1 Error: 0.850218 Iteration 2 Error: 0.340401 Iteration 3 Error: 0.099007 Iteration 4 Error: 0.038222 Align patch 14 11 left Iteration 1 Error: 0.820084 Iteration 2 Error: 0.163910 Iteration 3 Error: 0.040824 Align patch 15 10 left Iteration 1 Error: 0.710912 Iteration 2 Error: 0.112063 Iteration 3 Error: 0.031203 Align patch 16 9 left Iteration 1 Error: 0.673737 Iteration 2 Error: 0.076936 Iteration 3 Error: 0.027996 Align patch 17 8 left Iteration 1 Error: 0.606981 Iteration 2 Error: 0.125169 Iteration 3 Error: 0.019604 Align patch 18 7 left Iteration 1 Error: 0.801851 Iteration 2 Error: 0.134574 Iteration 3 Error: 0.044690 Align patch 19 6 left Iteration 1 Error: 0.990938 Iteration 2 Error: 0.150230 Iteration 3 Error: 0.030374 Align patch 20 5 left Iteration 1 Error: 0.572498 Iteration 2 Error: 0.163165 Iteration 3 Error: 0.038491 Align patch 21 4 left Iteration 1 Error: 0.934463 Iteration 2 Error: 0.078600 Iteration 3 Error: 0.021564 Align patch 22 3 left Iteration 1 Error: 0.755753 Iteration 2 Error: 0.194465 Iteration 3 Error: 0.061081 Iteration 4 Error: 0.020335 Align patch 23 2 left Iteration 1 Error: 0.903687 Iteration 2 Error: 0.140253 Iteration 3 Error: 0.046999 Align patch 24 1 left Iteration 1 Error: 0.516930 Iteration 2 Error: 0.060818 Iteration 3 Error: 0.012614 Align patch 25 0 left Iteration 1 Error: 0.747427 Iteration 2 Error: 0.163002 Iteration 3 Error: 0.037510 3D Fitting completed. Patch alignment time: 16.59(sec) Local motion has been corrected. Process thread exits. Computational time: 25.278067 sec Total time: 30.932381 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00008hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00008hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.730728s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00008hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.558888s ........................................ >>>>>>TIME<<<<<< FFT: 1.032972s Defocus_U Defocus_V Angle CCC 10740.26 11611.36 7.90 0.045184 Final Values Defocus_U Defocus_V Angle CCC 10751.21 11625.43 7.60 0.075713 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00008hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00008hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 41.99 7.02 Num Hot pixels: 234 Hot pixel threshold: 84.13 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.927185 Iteration 2 Error: 0.085885 Iteration 3 Error: 0.019302 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.11 0.15 ...... Frame ( 3) shift: -0.21 0.30 ...... Frame ( 4) shift: -0.32 0.44 ...... Frame ( 5) shift: -0.42 0.59 ...... Frame ( 6) shift: -0.49 0.68 ...... Frame ( 7) shift: -0.53 0.72 ...... Frame ( 8) shift: -0.56 0.76 ...... Frame ( 9) shift: -0.56 0.81 ...... Frame ( 10) shift: -0.52 0.85 ...... Frame ( 11) shift: -0.49 0.90 ...... Frame ( 12) shift: -0.47 0.95 ...... Frame ( 13) shift: -0.45 0.99 ...... Frame ( 14) shift: -0.44 1.04 ...... Frame ( 15) shift: -0.43 1.10 ...... Frame ( 16) shift: -0.42 1.16 ...... Frame ( 17) shift: -0.41 1.22 ...... Frame ( 18) shift: -0.39 1.27 ...... Frame ( 19) shift: -0.36 1.30 ...... Frame ( 20) shift: -0.33 1.33 ...... Frame ( 21) shift: -0.30 1.34 ...... Frame ( 22) shift: -0.26 1.31 ...... Frame ( 23) shift: -0.23 1.28 ...... Frame ( 24) shift: -0.22 1.31 ...... Frame ( 25) shift: -0.25 1.38 ...... Frame ( 26) shift: -0.28 1.45 ...... Frame ( 27) shift: -0.25 1.51 ...... Frame ( 28) shift: -0.16 1.55 ...... Frame ( 29) shift: -0.08 1.60 ...... Frame ( 30) shift: -0.02 1.60 ...... Frame ( 31) shift: -0.01 1.56 ...... Frame ( 32) shift: 0.01 1.52 ...... Frame ( 33) shift: 0.03 1.49 ...... Frame ( 34) shift: 0.07 1.46 ...... Frame ( 35) shift: 0.11 1.42 ...... Frame ( 36) shift: 0.14 1.42 ...... Frame ( 37) shift: 0.15 1.44 ...... Frame ( 38) shift: 0.16 1.46 ...... Frame ( 39) shift: 0.17 1.48 ...... Frame ( 40) shift: 0.19 1.49 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.143761 Iteration 2 Error: 0.141304 Iteration 3 Error: 0.026084 Align patch 2 23 left Iteration 1 Error: 0.584310 Iteration 2 Error: 0.128582 Iteration 3 Error: 0.032503 Align patch 3 22 left Iteration 1 Error: 0.454899 Iteration 2 Error: 0.103959 Iteration 3 Error: 0.025612 Align patch 4 21 left Iteration 1 Error: 0.539354 Iteration 2 Error: 0.058846 Iteration 3 Error: 0.007076 Align patch 5 20 left Iteration 1 Error: 0.587441 Iteration 2 Error: 0.090995 Iteration 3 Error: 0.018518 Align patch 6 19 left Iteration 1 Error: 1.372369 Iteration 2 Error: 0.218860 Iteration 3 Error: 0.046510 Align patch 7 18 left Iteration 1 Error: 0.828443 Iteration 2 Error: 0.132368 Iteration 3 Error: 0.030485 Align patch 8 17 left Iteration 1 Error: 0.462981 Iteration 2 Error: 0.071549 Iteration 3 Error: 0.015755 Align patch 9 16 left Iteration 1 Error: 0.589906 Iteration 2 Error: 0.101788 Iteration 3 Error: 0.015491 Align patch 10 15 left Iteration 1 Error: 0.847506 Iteration 2 Error: 0.097266 Iteration 3 Error: 0.018495 Align patch 11 14 left Iteration 1 Error: 1.171724 Iteration 2 Error: 0.139688 Iteration 3 Error: 0.034757 Align patch 12 13 left Iteration 1 Error: 0.537482 Iteration 2 Error: 0.074120 Iteration 3 Error: 0.010775 Align patch 13 12 left Iteration 1 Error: 0.485501 Iteration 2 Error: 0.076611 Iteration 3 Error: 0.020180 Align patch 14 11 left Iteration 1 Error: 0.551924 Iteration 2 Error: 0.085733 Iteration 3 Error: 0.013588 Align patch 15 10 left Iteration 1 Error: 0.516531 Iteration 2 Error: 0.060142 Iteration 3 Error: 0.012390 Align patch 16 9 left Iteration 1 Error: 0.675083 Iteration 2 Error: 0.084548 Iteration 3 Error: 0.021424 Align patch 17 8 left Iteration 1 Error: 0.678765 Iteration 2 Error: 0.101079 Iteration 3 Error: 0.025825 Align patch 18 7 left Iteration 1 Error: 0.503449 Iteration 2 Error: 0.062727 Iteration 3 Error: 0.016252 Align patch 19 6 left Iteration 1 Error: 0.485166 Iteration 2 Error: 0.062021 Iteration 3 Error: 0.012846 Align patch 20 5 left Iteration 1 Error: 0.591415 Iteration 2 Error: 0.073394 Iteration 3 Error: 0.020231 Align patch 21 4 left Iteration 1 Error: 0.699193 Iteration 2 Error: 0.115416 Iteration 3 Error: 0.022730 Align patch 22 3 left Iteration 1 Error: 0.458756 Iteration 2 Error: 0.078148 Iteration 3 Error: 0.022663 Align patch 23 2 left Iteration 1 Error: 0.658398 Iteration 2 Error: 0.108410 Iteration 3 Error: 0.020774 Align patch 24 1 left Iteration 1 Error: 0.729353 Iteration 2 Error: 0.075390 Iteration 3 Error: 0.013814 Align patch 25 0 left Iteration 1 Error: 0.792630 Iteration 2 Error: 0.120135 Iteration 3 Error: 0.024980 3D Fitting completed. Patch alignment time: 15.54(sec) Local motion has been corrected. Process thread exits. Computational time: 23.960342 sec Total time: 30.322592 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00008hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00008hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.549106s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00008hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.485452s ........................................ >>>>>>TIME<<<<<< FFT: 0.954022s Defocus_U Defocus_V Angle CCC 14746.15 14054.63 82.65 0.059444 Final Values Defocus_U Defocus_V Angle CCC 14752.40 14057.76 82.34 0.096697 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00009hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00009hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.736 Mean Std: 39.43 6.73 Num Hot pixels: 217 Hot pixel threshold: 79.79 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.944400 Iteration 2 Error: 0.491552 Iteration 3 Error: 0.168440 Iteration 4 Error: 0.096359 Iteration 5 Error: 0.044196 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.08 -0.02 ...... Frame ( 3) shift: -0.17 -0.04 ...... Frame ( 4) shift: -0.25 -0.06 ...... Frame ( 5) shift: -0.34 -0.08 ...... Frame ( 6) shift: -0.35 -0.08 ...... Frame ( 7) shift: -0.29 -0.08 ...... Frame ( 8) shift: -0.23 -0.08 ...... Frame ( 9) shift: -0.15 -0.01 ...... Frame ( 10) shift: -0.04 0.12 ...... Frame ( 11) shift: 0.07 0.25 ...... Frame ( 12) shift: 0.22 0.39 ...... Frame ( 13) shift: 0.41 0.52 ...... Frame ( 14) shift: 0.60 0.65 ...... Frame ( 15) shift: 0.75 0.77 ...... Frame ( 16) shift: 0.84 0.87 ...... Frame ( 17) shift: 0.93 0.97 ...... Frame ( 18) shift: 1.02 1.07 ...... Frame ( 19) shift: 1.09 1.16 ...... Frame ( 20) shift: 1.16 1.25 ...... Frame ( 21) shift: 1.25 1.36 ...... Frame ( 22) shift: 1.35 1.51 ...... Frame ( 23) shift: 1.46 1.65 ...... Frame ( 24) shift: 1.54 1.75 ...... Frame ( 25) shift: 1.60 1.80 ...... Frame ( 26) shift: 1.67 1.84 ...... Frame ( 27) shift: 1.72 1.94 ...... Frame ( 28) shift: 1.77 2.08 ...... Frame ( 29) shift: 1.82 2.22 ...... Frame ( 30) shift: 1.86 2.33 ...... Frame ( 31) shift: 1.88 2.40 ...... Frame ( 32) shift: 1.90 2.47 ...... Frame ( 33) shift: 1.98 2.52 ...... Frame ( 34) shift: 2.12 2.56 ...... Frame ( 35) shift: 2.26 2.60 ...... Frame ( 36) shift: 2.38 2.68 ...... Frame ( 37) shift: 2.48 2.79 ...... Frame ( 38) shift: 2.58 2.91 ...... Frame ( 39) shift: 2.68 3.02 ...... Frame ( 40) shift: 2.78 3.14 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.581020 Iteration 2 Error: 0.582639 Iteration 3 Error: 0.226649 Iteration 4 Error: 0.112531 Iteration 5 Error: 0.051550 Align patch 1 24 left Iteration 1 Error: 3.017369 Iteration 2 Error: 0.675926 Iteration 3 Error: 0.178040 Iteration 4 Error: 0.061644 Iteration 5 Error: 0.024952 Align patch 2 23 left Iteration 1 Error: 1.916450 Iteration 2 Error: 0.684775 Iteration 3 Error: 0.504249 Iteration 4 Error: 0.354482 Iteration 5 Error: 0.233906 Align patch 2 23 left Iteration 1 Error: 2.287809 Iteration 2 Error: 0.582280 Iteration 3 Error: 0.180168 Iteration 4 Error: 0.064283 Iteration 5 Error: 0.027551 Align patch 3 22 left Iteration 1 Error: 1.094878 Iteration 2 Error: 0.247129 Iteration 3 Error: 0.062383 Iteration 4 Error: 0.025896 Align patch 4 21 left Iteration 1 Error: 0.730965 Iteration 2 Error: 0.153866 Iteration 3 Error: 0.060676 Iteration 4 Error: 0.021684 Align patch 5 20 left Iteration 1 Error: 0.804346 Iteration 2 Error: 0.202911 Iteration 3 Error: 0.070242 Iteration 4 Error: 0.034602 Align patch 6 19 left Iteration 1 Error: 2.537107 Iteration 2 Error: 0.822606 Iteration 3 Error: 0.261451 Iteration 4 Error: 0.141251 Iteration 5 Error: 0.075052 Align patch 6 19 left Iteration 1 Error: 3.001430 Iteration 2 Error: 0.660702 Iteration 3 Error: 0.147457 Iteration 4 Error: 0.051875 Iteration 5 Error: 0.016579 Align patch 7 18 left Iteration 1 Error: 2.150711 Iteration 2 Error: 0.618962 Iteration 3 Error: 0.234173 Iteration 4 Error: 0.119509 Iteration 5 Error: 0.049176 Align patch 8 17 left Iteration 1 Error: 0.926007 Iteration 2 Error: 0.161316 Iteration 3 Error: 0.080599 Iteration 4 Error: 0.035779 Align patch 9 16 left Iteration 1 Error: 0.774952 Iteration 2 Error: 0.082708 Iteration 3 Error: 0.022634 Align patch 10 15 left Iteration 1 Error: 0.787918 Iteration 2 Error: 0.231762 Iteration 3 Error: 0.064477 Iteration 4 Error: 0.024362 Align patch 11 14 left Iteration 1 Error: 2.280547 Iteration 2 Error: 0.684017 Iteration 3 Error: 0.279671 Iteration 4 Error: 0.155938 Iteration 5 Error: 0.077326 Align patch 11 14 left Iteration 1 Error: 2.102912 Iteration 2 Error: 0.481296 Iteration 3 Error: 0.153402 Iteration 4 Error: 0.054858 Iteration 5 Error: 0.028818 Align patch 12 13 left Iteration 1 Error: 0.995796 Iteration 2 Error: 0.426929 Iteration 3 Error: 0.263642 Iteration 4 Error: 0.143502 Iteration 5 Error: 0.084966 Align patch 12 13 left Iteration 1 Error: 1.207012 Iteration 2 Error: 0.440012 Iteration 3 Error: 0.157807 Iteration 4 Error: 0.062457 Iteration 5 Error: 0.027498 Align patch 13 12 left Iteration 1 Error: 0.587965 Iteration 2 Error: 0.092190 Iteration 3 Error: 0.028914 Align patch 14 11 left Iteration 1 Error: 0.651090 Iteration 2 Error: 0.178057 Iteration 3 Error: 0.074371 Iteration 4 Error: 0.030004 Align patch 15 10 left Iteration 1 Error: 0.747778 Iteration 2 Error: 0.215063 Iteration 3 Error: 0.090567 Iteration 4 Error: 0.037310 Align patch 16 9 left Iteration 1 Error: 0.926488 Iteration 2 Error: 0.275519 Iteration 3 Error: 0.165378 Iteration 4 Error: 0.085298 Iteration 5 Error: 0.052516 Align patch 16 9 left Iteration 1 Error: 1.305742 Iteration 2 Error: 0.254268 Iteration 3 Error: 0.087481 Iteration 4 Error: 0.034641 Align patch 17 8 left Iteration 1 Error: 1.024979 Iteration 2 Error: 0.204398 Iteration 3 Error: 0.097402 Iteration 4 Error: 0.024251 Align patch 18 7 left Iteration 1 Error: 0.724642 Iteration 2 Error: 0.194715 Iteration 3 Error: 0.049344 Align patch 19 6 left Iteration 1 Error: 0.914797 Iteration 2 Error: 0.341961 Iteration 3 Error: 0.073830 Iteration 4 Error: 0.033339 Align patch 20 5 left Iteration 1 Error: 1.310350 Iteration 2 Error: 0.286501 Iteration 3 Error: 0.073197 Iteration 4 Error: 0.027764 Align patch 21 4 left Iteration 1 Error: 1.294694 Iteration 2 Error: 0.210474 Iteration 3 Error: 0.067109 Iteration 4 Error: 0.022241 Align patch 22 3 left Iteration 1 Error: 1.241726 Iteration 2 Error: 0.159119 Iteration 3 Error: 0.045481 Align patch 23 2 left Iteration 1 Error: 1.176162 Iteration 2 Error: 0.323441 Iteration 3 Error: 0.092668 Iteration 4 Error: 0.037720 Align patch 24 1 left Iteration 1 Error: 1.301391 Iteration 2 Error: 0.321128 Iteration 3 Error: 0.081179 Iteration 4 Error: 0.030684 Align patch 25 0 left Iteration 1 Error: 1.222558 Iteration 2 Error: 0.333858 Iteration 3 Error: 0.104936 Iteration 4 Error: 0.029857 3D Fitting completed. Patch alignment time: 21.89(sec) Local motion has been corrected. Process thread exits. Computational time: 30.924995 sec Total time: 36.702950 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00009hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00009hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.721857s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00009hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.862342s ........................................ >>>>>>TIME<<<<<< FFT: 0.938719s Defocus_U Defocus_V Angle CCC 8849.61 9794.92 13.07 0.030544 Final Values Defocus_U Defocus_V Angle CCC 8869.94 9840.25 13.39 0.059432 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00009hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00009hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.001e-01 CC threshold: 0.736 Mean Std: 39.47 6.77 Num Hot pixels: 191 Hot pixel threshold: 80.10 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.020302 Iteration 2 Error: 0.201322 Iteration 3 Error: 0.067135 Iteration 4 Error: 0.032301 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.05 0.14 ...... Frame ( 3) shift: -0.10 0.28 ...... Frame ( 4) shift: -0.15 0.43 ...... Frame ( 5) shift: -0.20 0.57 ...... Frame ( 6) shift: -0.22 0.66 ...... Frame ( 7) shift: -0.20 0.71 ...... Frame ( 8) shift: -0.19 0.75 ...... Frame ( 9) shift: -0.16 0.81 ...... Frame ( 10) shift: -0.11 0.88 ...... Frame ( 11) shift: -0.07 0.95 ...... Frame ( 12) shift: -0.03 1.04 ...... Frame ( 13) shift: 0.01 1.15 ...... Frame ( 14) shift: 0.05 1.26 ...... Frame ( 15) shift: 0.10 1.31 ...... Frame ( 16) shift: 0.17 1.30 ...... Frame ( 17) shift: 0.24 1.30 ...... Frame ( 18) shift: 0.31 1.33 ...... Frame ( 19) shift: 0.39 1.41 ...... Frame ( 20) shift: 0.48 1.49 ...... Frame ( 21) shift: 0.51 1.52 ...... Frame ( 22) shift: 0.49 1.51 ...... Frame ( 23) shift: 0.47 1.49 ...... Frame ( 24) shift: 0.49 1.50 ...... Frame ( 25) shift: 0.55 1.54 ...... Frame ( 26) shift: 0.61 1.57 ...... Frame ( 27) shift: 0.69 1.59 ...... Frame ( 28) shift: 0.78 1.61 ...... Frame ( 29) shift: 0.88 1.63 ...... Frame ( 30) shift: 0.94 1.64 ...... Frame ( 31) shift: 0.97 1.65 ...... Frame ( 32) shift: 1.01 1.66 ...... Frame ( 33) shift: 1.05 1.69 ...... Frame ( 34) shift: 1.10 1.73 ...... Frame ( 35) shift: 1.15 1.78 ...... Frame ( 36) shift: 1.17 1.85 ...... Frame ( 37) shift: 1.16 1.93 ...... Frame ( 38) shift: 1.14 2.01 ...... Frame ( 39) shift: 1.13 2.08 ...... Frame ( 40) shift: 1.11 2.16 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.281844 Iteration 2 Error: 0.646161 Iteration 3 Error: 0.192642 Iteration 4 Error: 0.107460 Iteration 5 Error: 0.047256 Align patch 2 23 left Iteration 1 Error: 0.799594 Iteration 2 Error: 0.189839 Iteration 3 Error: 0.061979 Iteration 4 Error: 0.026806 Align patch 3 22 left Iteration 1 Error: 0.494801 Iteration 2 Error: 0.065466 Iteration 3 Error: 0.010489 Align patch 4 21 left Iteration 1 Error: 0.778856 Iteration 2 Error: 0.156673 Iteration 3 Error: 0.040696 Align patch 5 20 left Iteration 1 Error: 0.496117 Iteration 2 Error: 0.118601 Iteration 3 Error: 0.028916 Align patch 6 19 left Iteration 1 Error: 2.536396 Iteration 2 Error: 0.670503 Iteration 3 Error: 0.299991 Iteration 4 Error: 0.127238 Iteration 5 Error: 0.068776 Align patch 6 19 left Iteration 1 Error: 1.750246 Iteration 2 Error: 0.333500 Iteration 3 Error: 0.076398 Iteration 4 Error: 0.033736 Align patch 7 18 left Iteration 1 Error: 0.892722 Iteration 2 Error: 0.250292 Iteration 3 Error: 0.116518 Iteration 4 Error: 0.053399 Iteration 5 Error: 0.029637 Align patch 8 17 left Iteration 1 Error: 0.567342 Iteration 2 Error: 0.084753 Iteration 3 Error: 0.025351 Align patch 9 16 left Iteration 1 Error: 0.855170 Iteration 2 Error: 0.212329 Iteration 3 Error: 0.059506 Iteration 4 Error: 0.019150 Align patch 10 15 left Iteration 1 Error: 0.855720 Iteration 2 Error: 0.167852 Iteration 3 Error: 0.052665 Iteration 4 Error: 0.014723 Align patch 11 14 left Iteration 1 Error: 1.673127 Iteration 2 Error: 0.415000 Iteration 3 Error: 0.182938 Iteration 4 Error: 0.128710 Iteration 5 Error: 0.066056 Align patch 11 14 left Iteration 1 Error: 1.564844 Iteration 2 Error: 0.407502 Iteration 3 Error: 0.122939 Iteration 4 Error: 0.046761 Align patch 12 13 left Iteration 1 Error: 0.837911 Iteration 2 Error: 0.149255 Iteration 3 Error: 0.053341 Iteration 4 Error: 0.020802 Align patch 13 12 left Iteration 1 Error: 0.619227 Iteration 2 Error: 0.074618 Iteration 3 Error: 0.016482 Align patch 14 11 left Iteration 1 Error: 0.567650 Iteration 2 Error: 0.093732 Iteration 3 Error: 0.027034 Align patch 15 10 left Iteration 1 Error: 0.579037 Iteration 2 Error: 0.151069 Iteration 3 Error: 0.029123 Align patch 16 9 left Iteration 1 Error: 0.928562 Iteration 2 Error: 0.291535 Iteration 3 Error: 0.138815 Iteration 4 Error: 0.083839 Iteration 5 Error: 0.050371 Align patch 16 9 left Iteration 1 Error: 1.014473 Iteration 2 Error: 0.254107 Iteration 3 Error: 0.089712 Iteration 4 Error: 0.036061 Align patch 17 8 left Iteration 1 Error: 0.745905 Iteration 2 Error: 0.174973 Iteration 3 Error: 0.090416 Iteration 4 Error: 0.044047 Align patch 18 7 left Iteration 1 Error: 0.745138 Iteration 2 Error: 0.110137 Iteration 3 Error: 0.042694 Align patch 19 6 left Iteration 1 Error: 0.705439 Iteration 2 Error: 0.117048 Iteration 3 Error: 0.022016 Align patch 20 5 left Iteration 1 Error: 0.772058 Iteration 2 Error: 0.123048 Iteration 3 Error: 0.033980 Align patch 21 4 left Iteration 1 Error: 1.011479 Iteration 2 Error: 0.205964 Iteration 3 Error: 0.084952 Iteration 4 Error: 0.018931 Align patch 22 3 left Iteration 1 Error: 0.693629 Iteration 2 Error: 0.086578 Iteration 3 Error: 0.017958 Align patch 23 2 left Iteration 1 Error: 0.652749 Iteration 2 Error: 0.178541 Iteration 3 Error: 0.033116 Align patch 24 1 left Iteration 1 Error: 0.703564 Iteration 2 Error: 0.138966 Iteration 3 Error: 0.036313 Align patch 25 0 left Iteration 1 Error: 0.920715 Iteration 2 Error: 0.180071 Iteration 3 Error: 0.039368 3D Fitting completed. Patch alignment time: 19.24(sec) Local motion has been corrected. Process thread exits. Computational time: 28.134850 sec Total time: 34.205070 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00009hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00009hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.699777s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00009hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.994476s ........................................ >>>>>>TIME<<<<<< FFT: 0.982456s Defocus_U Defocus_V Angle CCC 8632.82 9156.26 5.10 0.024473 Final Values Defocus_U Defocus_V Angle CCC 8651.56 9159.40 4.78 0.051279 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00009hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00009hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 39.99 6.78 Num Hot pixels: 193 Hot pixel threshold: 80.67 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.071070 Iteration 2 Error: 0.263436 Iteration 3 Error: 0.089140 Iteration 4 Error: 0.032434 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.22 -0.23 ...... Frame ( 3) shift: -0.45 -0.47 ...... Frame ( 4) shift: -0.67 -0.70 ...... Frame ( 5) shift: -0.90 -0.93 ...... Frame ( 6) shift: -0.99 -1.05 ...... Frame ( 7) shift: -0.96 -1.05 ...... Frame ( 8) shift: -0.93 -1.05 ...... Frame ( 9) shift: -0.89 -1.00 ...... Frame ( 10) shift: -0.83 -0.90 ...... Frame ( 11) shift: -0.78 -0.80 ...... Frame ( 12) shift: -0.69 -0.70 ...... Frame ( 13) shift: -0.56 -0.61 ...... Frame ( 14) shift: -0.43 -0.51 ...... Frame ( 15) shift: -0.33 -0.42 ...... Frame ( 16) shift: -0.25 -0.33 ...... Frame ( 17) shift: -0.18 -0.23 ...... Frame ( 18) shift: -0.09 -0.13 ...... Frame ( 19) shift: -0.00 -0.01 ...... Frame ( 20) shift: 0.09 0.10 ...... Frame ( 21) shift: 0.16 0.18 ...... Frame ( 22) shift: 0.19 0.22 ...... Frame ( 23) shift: 0.22 0.26 ...... Frame ( 24) shift: 0.24 0.29 ...... Frame ( 25) shift: 0.24 0.31 ...... Frame ( 26) shift: 0.24 0.33 ...... Frame ( 27) shift: 0.27 0.39 ...... Frame ( 28) shift: 0.33 0.50 ...... Frame ( 29) shift: 0.39 0.60 ...... Frame ( 30) shift: 0.45 0.68 ...... Frame ( 31) shift: 0.50 0.71 ...... Frame ( 32) shift: 0.55 0.75 ...... Frame ( 33) shift: 0.59 0.81 ...... Frame ( 34) shift: 0.63 0.89 ...... Frame ( 35) shift: 0.67 0.98 ...... Frame ( 36) shift: 0.69 1.04 ...... Frame ( 37) shift: 0.67 1.07 ...... Frame ( 38) shift: 0.66 1.11 ...... Frame ( 39) shift: 0.65 1.14 ...... Frame ( 40) shift: 0.63 1.18 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 3.248969 Iteration 2 Error: 1.120567 Iteration 3 Error: 0.391988 Iteration 4 Error: 0.233277 Iteration 5 Error: 0.125087 Align patch 1 24 left Iteration 1 Error: 3.079541 Iteration 2 Error: 0.639598 Iteration 3 Error: 0.120456 Iteration 4 Error: 0.038320 Align patch 2 23 left Iteration 1 Error: 2.319761 Iteration 2 Error: 0.493764 Iteration 3 Error: 0.178849 Iteration 4 Error: 0.092676 Iteration 5 Error: 0.046437 Align patch 3 22 left Iteration 1 Error: 1.120631 Iteration 2 Error: 0.312138 Iteration 3 Error: 0.110877 Iteration 4 Error: 0.051074 Iteration 5 Error: 0.021334 Align patch 4 21 left Iteration 1 Error: 0.579527 Iteration 2 Error: 0.130593 Iteration 3 Error: 0.036245 Align patch 5 20 left Iteration 1 Error: 0.871111 Iteration 2 Error: 0.163872 Iteration 3 Error: 0.042222 Align patch 6 19 left Iteration 1 Error: 2.174127 Iteration 2 Error: 0.747343 Iteration 3 Error: 0.286450 Iteration 4 Error: 0.159912 Iteration 5 Error: 0.072582 Align patch 6 19 left Iteration 1 Error: 2.692080 Iteration 2 Error: 0.579638 Iteration 3 Error: 0.093021 Iteration 4 Error: 0.034904 Align patch 7 18 left Iteration 1 Error: 1.243450 Iteration 2 Error: 0.365384 Iteration 3 Error: 0.143715 Iteration 4 Error: 0.059925 Iteration 5 Error: 0.025611 Align patch 8 17 left Iteration 1 Error: 0.904124 Iteration 2 Error: 0.246654 Iteration 3 Error: 0.096735 Iteration 4 Error: 0.050337 Iteration 5 Error: 0.019674 Align patch 9 16 left Iteration 1 Error: 0.758330 Iteration 2 Error: 0.110877 Iteration 3 Error: 0.032381 Align patch 10 15 left Iteration 1 Error: 0.827083 Iteration 2 Error: 0.180488 Iteration 3 Error: 0.035033 Align patch 11 14 left Iteration 1 Error: 2.214259 Iteration 2 Error: 0.539077 Iteration 3 Error: 0.195252 Iteration 4 Error: 0.091245 Iteration 5 Error: 0.048876 Align patch 12 13 left Iteration 1 Error: 1.737507 Iteration 2 Error: 0.574275 Iteration 3 Error: 0.248958 Iteration 4 Error: 0.134700 Iteration 5 Error: 0.063002 Align patch 12 13 left Iteration 1 Error: 1.305742 Iteration 2 Error: 0.279545 Iteration 3 Error: 0.059222 Iteration 4 Error: 0.022038 Align patch 13 12 left Iteration 1 Error: 0.720915 Iteration 2 Error: 0.121250 Iteration 3 Error: 0.021875 Align patch 14 11 left Iteration 1 Error: 0.840549 Iteration 2 Error: 0.138747 Iteration 3 Error: 0.052486 Iteration 4 Error: 0.013043 Align patch 15 10 left Iteration 1 Error: 0.991091 Iteration 2 Error: 0.100369 Iteration 3 Error: 0.023642 Align patch 16 9 left Iteration 1 Error: 1.766284 Iteration 2 Error: 0.328435 Iteration 3 Error: 0.123451 Iteration 4 Error: 0.051125 Iteration 5 Error: 0.031382 Align patch 17 8 left Iteration 1 Error: 0.899534 Iteration 2 Error: 0.172038 Iteration 3 Error: 0.063579 Iteration 4 Error: 0.021023 Align patch 18 7 left Iteration 1 Error: 0.692489 Iteration 2 Error: 0.129060 Iteration 3 Error: 0.035314 Align patch 19 6 left Iteration 1 Error: 0.794777 Iteration 2 Error: 0.179818 Iteration 3 Error: 0.059699 Iteration 4 Error: 0.014972 Align patch 20 5 left Iteration 1 Error: 0.898286 Iteration 2 Error: 0.162240 Iteration 3 Error: 0.041644 Align patch 21 4 left Iteration 1 Error: 0.671206 Iteration 2 Error: 0.125302 Iteration 3 Error: 0.029641 Align patch 22 3 left Iteration 1 Error: 0.564577 Iteration 2 Error: 0.135241 Iteration 3 Error: 0.036294 Align patch 23 2 left Iteration 1 Error: 0.674847 Iteration 2 Error: 0.167773 Iteration 3 Error: 0.065431 Iteration 4 Error: 0.023172 Align patch 24 1 left Iteration 1 Error: 0.891603 Iteration 2 Error: 0.216549 Iteration 3 Error: 0.054771 Iteration 4 Error: 0.015846 Align patch 25 0 left Iteration 1 Error: 0.922660 Iteration 2 Error: 0.245917 Iteration 3 Error: 0.043371 3D Fitting completed. Patch alignment time: 19.89(sec) Local motion has been corrected. Process thread exits. Computational time: 28.670227 sec Total time: 34.925602 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00009hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00009hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.673729s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00009hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.024134s ........................................ >>>>>>TIME<<<<<< FFT: 0.908336s Defocus_U Defocus_V Angle CCC 14292.96 15117.23 5.03 0.050043 Final Values Defocus_U Defocus_V Angle CCC 14292.95 15126.60 5.03 0.078007 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00009hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00009hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 40.30 6.83 Num Hot pixels: 217 Hot pixel threshold: 81.26 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.008677 Iteration 2 Error: 0.197149 Iteration 3 Error: 0.051458 Iteration 4 Error: 0.014890 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.12 -0.00 ...... Frame ( 3) shift: -0.24 -0.01 ...... Frame ( 4) shift: -0.36 -0.01 ...... Frame ( 5) shift: -0.48 -0.02 ...... Frame ( 6) shift: -0.51 0.02 ...... Frame ( 7) shift: -0.46 0.11 ...... Frame ( 8) shift: -0.41 0.20 ...... Frame ( 9) shift: -0.35 0.28 ...... Frame ( 10) shift: -0.28 0.36 ...... Frame ( 11) shift: -0.22 0.43 ...... Frame ( 12) shift: -0.15 0.51 ...... Frame ( 13) shift: -0.08 0.60 ...... Frame ( 14) shift: -0.00 0.68 ...... Frame ( 15) shift: 0.05 0.79 ...... Frame ( 16) shift: 0.09 0.93 ...... Frame ( 17) shift: 0.13 1.07 ...... Frame ( 18) shift: 0.18 1.14 ...... Frame ( 19) shift: 0.24 1.15 ...... Frame ( 20) shift: 0.31 1.15 ...... Frame ( 21) shift: 0.34 1.21 ...... Frame ( 22) shift: 0.34 1.31 ...... Frame ( 23) shift: 0.35 1.41 ...... Frame ( 24) shift: 0.33 1.47 ...... Frame ( 25) shift: 0.30 1.49 ...... Frame ( 26) shift: 0.27 1.51 ...... Frame ( 27) shift: 0.24 1.55 ...... Frame ( 28) shift: 0.22 1.62 ...... Frame ( 29) shift: 0.19 1.69 ...... Frame ( 30) shift: 0.18 1.74 ...... Frame ( 31) shift: 0.17 1.77 ...... Frame ( 32) shift: 0.17 1.81 ...... Frame ( 33) shift: 0.19 1.81 ...... Frame ( 34) shift: 0.22 1.78 ...... Frame ( 35) shift: 0.26 1.76 ...... Frame ( 36) shift: 0.31 1.74 ...... Frame ( 37) shift: 0.36 1.74 ...... Frame ( 38) shift: 0.42 1.74 ...... Frame ( 39) shift: 0.47 1.74 ...... Frame ( 40) shift: 0.53 1.74 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.123044 Iteration 2 Error: 2.055846 Iteration 3 Error: 0.501330 Iteration 4 Error: 0.232952 Iteration 5 Error: 0.145784 Align patch 1 24 left Iteration 1 Error: 3.024809 Iteration 2 Error: 0.390943 Iteration 3 Error: 0.073897 Iteration 4 Error: 0.024955 Align patch 2 23 left Iteration 1 Error: 1.675478 Iteration 2 Error: 0.452047 Iteration 3 Error: 0.129518 Iteration 4 Error: 0.078510 Iteration 5 Error: 0.033287 Align patch 3 22 left Iteration 1 Error: 0.660487 Iteration 2 Error: 0.117229 Iteration 3 Error: 0.049938 Align patch 4 21 left Iteration 1 Error: 1.549857 Iteration 2 Error: 0.218612 Iteration 3 Error: 0.047075 Align patch 5 20 left Iteration 1 Error: 1.027641 Iteration 2 Error: 0.210757 Iteration 3 Error: 0.053982 Iteration 4 Error: 0.015727 Align patch 6 19 left Iteration 1 Error: 2.321209 Iteration 2 Error: 0.668368 Iteration 3 Error: 0.381736 Iteration 4 Error: 0.224890 Iteration 5 Error: 0.131737 Align patch 6 19 left Iteration 1 Error: 2.639941 Iteration 2 Error: 0.318592 Iteration 3 Error: 0.099985 Iteration 4 Error: 0.028791 Align patch 7 18 left Iteration 1 Error: 1.800318 Iteration 2 Error: 0.402558 Iteration 3 Error: 0.194158 Iteration 4 Error: 0.084293 Iteration 5 Error: 0.036282 Align patch 8 17 left Iteration 1 Error: 0.632045 Iteration 2 Error: 0.158967 Iteration 3 Error: 0.047347 Align patch 9 16 left Iteration 1 Error: 0.567844 Iteration 2 Error: 0.080076 Iteration 3 Error: 0.024180 Align patch 10 15 left Iteration 1 Error: 1.167615 Iteration 2 Error: 0.235489 Iteration 3 Error: 0.043043 Align patch 11 14 left Iteration 1 Error: 1.736010 Iteration 2 Error: 0.466734 Iteration 3 Error: 0.252481 Iteration 4 Error: 0.188069 Iteration 5 Error: 0.123718 Align patch 11 14 left Iteration 1 Error: 2.162102 Iteration 2 Error: 0.341037 Iteration 3 Error: 0.091142 Iteration 4 Error: 0.025014 Align patch 12 13 left Iteration 1 Error: 1.031623 Iteration 2 Error: 0.307339 Iteration 3 Error: 0.132073 Iteration 4 Error: 0.061529 Iteration 5 Error: 0.022460 Align patch 13 12 left Iteration 1 Error: 0.782112 Iteration 2 Error: 0.154155 Iteration 3 Error: 0.049925 Align patch 14 11 left Iteration 1 Error: 0.770425 Iteration 2 Error: 0.114028 Iteration 3 Error: 0.022601 Align patch 15 10 left Iteration 1 Error: 0.919984 Iteration 2 Error: 0.207177 Iteration 3 Error: 0.036704 Align patch 16 9 left Iteration 1 Error: 1.712164 Iteration 2 Error: 0.273350 Iteration 3 Error: 0.087234 Iteration 4 Error: 0.040058 Align patch 17 8 left Iteration 1 Error: 0.782949 Iteration 2 Error: 0.115852 Iteration 3 Error: 0.047304 Align patch 18 7 left Iteration 1 Error: 0.737483 Iteration 2 Error: 0.071298 Iteration 3 Error: 0.019003 Align patch 19 6 left Iteration 1 Error: 1.053073 Iteration 2 Error: 0.151190 Iteration 3 Error: 0.039382 Align patch 20 5 left Iteration 1 Error: 1.008556 Iteration 2 Error: 0.222287 Iteration 3 Error: 0.053059 Iteration 4 Error: 0.014975 Align patch 21 4 left Iteration 1 Error: 1.103169 Iteration 2 Error: 0.250903 Iteration 3 Error: 0.058236 Iteration 4 Error: 0.020671 Align patch 22 3 left Iteration 1 Error: 0.661965 Iteration 2 Error: 0.181535 Iteration 3 Error: 0.046055 Align patch 23 2 left Iteration 1 Error: 1.041850 Iteration 2 Error: 0.100294 Iteration 3 Error: 0.020467 Align patch 24 1 left Iteration 1 Error: 0.884311 Iteration 2 Error: 0.141238 Iteration 3 Error: 0.031612 Align patch 25 0 left Iteration 1 Error: 0.998411 Iteration 2 Error: 0.138309 Iteration 3 Error: 0.024801 3D Fitting completed. Patch alignment time: 18.96(sec) Local motion has been corrected. Process thread exits. Computational time: 27.322166 sec Total time: 34.114933 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00009hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00009hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.704418s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00009hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.386641s ........................................ >>>>>>TIME<<<<<< FFT: 0.943215s Defocus_U Defocus_V Angle CCC 15353.58 14693.30 86.91 0.048823 Final Values Defocus_U Defocus_V Angle CCC 15367.65 14691.74 86.60 0.076147 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00010hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00010hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 38.77 6.67 Num Hot pixels: 202 Hot pixel threshold: 78.81 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.492222 Iteration 2 Error: 0.319638 Iteration 3 Error: 0.099763 Iteration 4 Error: 0.047891 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.21 -0.25 ...... Frame ( 3) shift: -0.42 -0.51 ...... Frame ( 4) shift: -0.63 -0.76 ...... Frame ( 5) shift: -0.84 -1.02 ...... Frame ( 6) shift: -0.94 -1.12 ...... Frame ( 7) shift: -0.93 -1.07 ...... Frame ( 8) shift: -0.92 -1.02 ...... Frame ( 9) shift: -0.87 -0.95 ...... Frame ( 10) shift: -0.79 -0.84 ...... Frame ( 11) shift: -0.71 -0.74 ...... Frame ( 12) shift: -0.62 -0.60 ...... Frame ( 13) shift: -0.50 -0.44 ...... Frame ( 14) shift: -0.39 -0.27 ...... Frame ( 15) shift: -0.30 -0.15 ...... Frame ( 16) shift: -0.24 -0.09 ...... Frame ( 17) shift: -0.18 -0.02 ...... Frame ( 18) shift: -0.16 0.05 ...... Frame ( 19) shift: -0.19 0.13 ...... Frame ( 20) shift: -0.22 0.22 ...... Frame ( 21) shift: -0.19 0.32 ...... Frame ( 22) shift: -0.10 0.43 ...... Frame ( 23) shift: -0.01 0.54 ...... Frame ( 24) shift: 0.04 0.61 ...... Frame ( 25) shift: 0.06 0.62 ...... Frame ( 26) shift: 0.08 0.64 ...... Frame ( 27) shift: 0.11 0.70 ...... Frame ( 28) shift: 0.15 0.80 ...... Frame ( 29) shift: 0.19 0.90 ...... Frame ( 30) shift: 0.21 0.98 ...... Frame ( 31) shift: 0.22 1.03 ...... Frame ( 32) shift: 0.24 1.08 ...... Frame ( 33) shift: 0.32 1.16 ...... Frame ( 34) shift: 0.48 1.29 ...... Frame ( 35) shift: 0.64 1.42 ...... Frame ( 36) shift: 0.71 1.53 ...... Frame ( 37) shift: 0.69 1.64 ...... Frame ( 38) shift: 0.68 1.75 ...... Frame ( 39) shift: 0.67 1.85 ...... Frame ( 40) shift: 0.66 1.96 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.292599 Iteration 2 Error: 0.924735 Iteration 3 Error: 0.310428 Iteration 4 Error: 0.174319 Iteration 5 Error: 0.077934 Align patch 1 24 left Iteration 1 Error: 2.851935 Iteration 2 Error: 0.486032 Iteration 3 Error: 0.099266 Iteration 4 Error: 0.027609 Align patch 2 23 left Iteration 1 Error: 1.906998 Iteration 2 Error: 0.425398 Iteration 3 Error: 0.209116 Iteration 4 Error: 0.078737 Iteration 5 Error: 0.038721 Align patch 3 22 left Iteration 1 Error: 0.791846 Iteration 2 Error: 0.156740 Iteration 3 Error: 0.061325 Iteration 4 Error: 0.020708 Align patch 4 21 left Iteration 1 Error: 1.062415 Iteration 2 Error: 0.194444 Iteration 3 Error: 0.041336 Align patch 5 20 left Iteration 1 Error: 0.669053 Iteration 2 Error: 0.135111 Iteration 3 Error: 0.037839 Align patch 6 19 left Iteration 1 Error: 2.341033 Iteration 2 Error: 0.526223 Iteration 3 Error: 0.182576 Iteration 4 Error: 0.097886 Iteration 5 Error: 0.058535 Align patch 6 19 left Iteration 1 Error: 2.469298 Iteration 2 Error: 0.441193 Iteration 3 Error: 0.100174 Iteration 4 Error: 0.024865 Align patch 7 18 left Iteration 1 Error: 1.937575 Iteration 2 Error: 0.333350 Iteration 3 Error: 0.090579 Iteration 4 Error: 0.036420 Align patch 8 17 left Iteration 1 Error: 0.676334 Iteration 2 Error: 0.157457 Iteration 3 Error: 0.030868 Align patch 9 16 left Iteration 1 Error: 1.057547 Iteration 2 Error: 0.170862 Iteration 3 Error: 0.032340 Align patch 10 15 left Iteration 1 Error: 0.757129 Iteration 2 Error: 0.179307 Iteration 3 Error: 0.042566 Align patch 11 14 left Iteration 1 Error: 0.883366 Iteration 2 Error: 0.233717 Iteration 3 Error: 0.145964 Iteration 4 Error: 0.081073 Iteration 5 Error: 0.038654 Align patch 12 13 left Iteration 1 Error: 1.488732 Iteration 2 Error: 0.270142 Iteration 3 Error: 0.092313 Iteration 4 Error: 0.049883 Align patch 13 12 left Iteration 1 Error: 0.931609 Iteration 2 Error: 0.221020 Iteration 3 Error: 0.066595 Iteration 4 Error: 0.025636 Align patch 14 11 left Iteration 1 Error: 1.031848 Iteration 2 Error: 0.224026 Iteration 3 Error: 0.066406 Iteration 4 Error: 0.025895 Align patch 15 10 left Iteration 1 Error: 0.688439 Iteration 2 Error: 0.146017 Iteration 3 Error: 0.044821 Align patch 16 9 left Iteration 1 Error: 0.870835 Iteration 2 Error: 0.219731 Iteration 3 Error: 0.087650 Iteration 4 Error: 0.043186 Align patch 17 8 left Iteration 1 Error: 0.974539 Iteration 2 Error: 0.348276 Iteration 3 Error: 0.063493 Iteration 4 Error: 0.025653 Align patch 18 7 left Iteration 1 Error: 1.211646 Iteration 2 Error: 0.199008 Iteration 3 Error: 0.087534 Iteration 4 Error: 0.044532 Align patch 19 6 left Iteration 1 Error: 0.859152 Iteration 2 Error: 0.132983 Iteration 3 Error: 0.037092 Align patch 20 5 left Iteration 1 Error: 1.339120 Iteration 2 Error: 0.318901 Iteration 3 Error: 0.043675 Align patch 21 4 left Iteration 1 Error: 1.654512 Iteration 2 Error: 0.224018 Iteration 3 Error: 0.054799 Iteration 4 Error: 0.016511 Align patch 22 3 left Iteration 1 Error: 0.720041 Iteration 2 Error: 0.138932 Iteration 3 Error: 0.042463 Align patch 23 2 left Iteration 1 Error: 0.513992 Iteration 2 Error: 0.117261 Iteration 3 Error: 0.053168 Iteration 4 Error: 0.020572 Align patch 24 1 left Iteration 1 Error: 0.857134 Iteration 2 Error: 0.211007 Iteration 3 Error: 0.055589 Iteration 4 Error: 0.022930 Align patch 25 0 left Iteration 1 Error: 0.664892 Iteration 2 Error: 0.111693 Iteration 3 Error: 0.032923 3D Fitting completed. Patch alignment time: 17.97(sec) Local motion has been corrected. Process thread exits. Computational time: 27.229916 sec Total time: 33.884064 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00010hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00010hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.789968s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00010hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.762951s ........................................ >>>>>>TIME<<<<<< FFT: 0.816728s Defocus_U Defocus_V Angle CCC 12339.85 13207.03 12.80 0.044056 Final Values Defocus_U Defocus_V Angle CCC 12344.52 13221.11 12.80 0.072662 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00010hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00010hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.001e-01 CC threshold: 0.735 Mean Std: 39.38 6.71 Num Hot pixels: 190 Hot pixel threshold: 79.63 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.036156 Iteration 2 Error: 0.274748 Iteration 3 Error: 0.094951 Iteration 4 Error: 0.040764 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.26 -0.24 ...... Frame ( 3) shift: -0.52 -0.48 ...... Frame ( 4) shift: -0.78 -0.72 ...... Frame ( 5) shift: -1.04 -0.96 ...... Frame ( 6) shift: -1.17 -1.07 ...... Frame ( 7) shift: -1.15 -1.03 ...... Frame ( 8) shift: -1.13 -1.00 ...... Frame ( 9) shift: -1.08 -0.91 ...... Frame ( 10) shift: -0.98 -0.77 ...... Frame ( 11) shift: -0.88 -0.62 ...... Frame ( 12) shift: -0.80 -0.53 ...... Frame ( 13) shift: -0.74 -0.50 ...... Frame ( 14) shift: -0.67 -0.47 ...... Frame ( 15) shift: -0.59 -0.41 ...... Frame ( 16) shift: -0.49 -0.34 ...... Frame ( 17) shift: -0.39 -0.26 ...... Frame ( 18) shift: -0.30 -0.19 ...... Frame ( 19) shift: -0.24 -0.13 ...... Frame ( 20) shift: -0.18 -0.06 ...... Frame ( 21) shift: -0.15 -0.00 ...... Frame ( 22) shift: -0.16 0.05 ...... Frame ( 23) shift: -0.17 0.11 ...... Frame ( 24) shift: -0.14 0.19 ...... Frame ( 25) shift: -0.05 0.29 ...... Frame ( 26) shift: 0.03 0.39 ...... Frame ( 27) shift: 0.08 0.50 ...... Frame ( 28) shift: 0.08 0.63 ...... Frame ( 29) shift: 0.08 0.75 ...... Frame ( 30) shift: 0.11 0.83 ...... Frame ( 31) shift: 0.15 0.88 ...... Frame ( 32) shift: 0.20 0.92 ...... Frame ( 33) shift: 0.24 0.92 ...... Frame ( 34) shift: 0.29 0.88 ...... Frame ( 35) shift: 0.34 0.84 ...... Frame ( 36) shift: 0.41 0.82 ...... Frame ( 37) shift: 0.49 0.84 ...... Frame ( 38) shift: 0.57 0.86 ...... Frame ( 39) shift: 0.65 0.88 ...... Frame ( 40) shift: 0.73 0.90 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.137427 Iteration 2 Error: 0.741989 Iteration 3 Error: 0.338913 Iteration 4 Error: 0.175547 Iteration 5 Error: 0.095865 Align patch 1 24 left Iteration 1 Error: 2.814809 Iteration 2 Error: 0.507155 Iteration 3 Error: 0.137783 Iteration 4 Error: 0.050282 Iteration 5 Error: 0.021584 Align patch 2 23 left Iteration 1 Error: 1.900126 Iteration 2 Error: 0.529121 Iteration 3 Error: 0.293028 Iteration 4 Error: 0.153220 Iteration 5 Error: 0.086843 Align patch 2 23 left Iteration 1 Error: 2.484018 Iteration 2 Error: 0.473839 Iteration 3 Error: 0.131433 Iteration 4 Error: 0.048302 Align patch 3 22 left Iteration 1 Error: 0.998658 Iteration 2 Error: 0.249034 Iteration 3 Error: 0.094809 Iteration 4 Error: 0.031321 Align patch 4 21 left Iteration 1 Error: 0.885707 Iteration 2 Error: 0.141208 Iteration 3 Error: 0.042471 Align patch 5 20 left Iteration 1 Error: 0.777467 Iteration 2 Error: 0.153544 Iteration 3 Error: 0.041690 Align patch 6 19 left Iteration 1 Error: 2.400356 Iteration 2 Error: 0.771548 Iteration 3 Error: 0.321646 Iteration 4 Error: 0.200758 Iteration 5 Error: 0.118510 Align patch 6 19 left Iteration 1 Error: 2.874575 Iteration 2 Error: 0.456737 Iteration 3 Error: 0.114940 Iteration 4 Error: 0.042492 Align patch 7 18 left Iteration 1 Error: 1.521729 Iteration 2 Error: 0.587522 Iteration 3 Error: 0.237846 Iteration 4 Error: 0.142928 Iteration 5 Error: 0.079377 Align patch 7 18 left Iteration 1 Error: 2.421252 Iteration 2 Error: 0.424553 Iteration 3 Error: 0.125000 Iteration 4 Error: 0.046677 Align patch 8 17 left Iteration 1 Error: 0.890654 Iteration 2 Error: 0.322918 Iteration 3 Error: 0.144284 Iteration 4 Error: 0.072055 Iteration 5 Error: 0.032226 Align patch 9 16 left Iteration 1 Error: 0.506188 Iteration 2 Error: 0.088166 Iteration 3 Error: 0.035556 Align patch 10 15 left Iteration 1 Error: 0.807644 Iteration 2 Error: 0.139775 Iteration 3 Error: 0.047370 Align patch 11 14 left Iteration 1 Error: 2.002460 Iteration 2 Error: 0.456704 Iteration 3 Error: 0.189552 Iteration 4 Error: 0.105237 Iteration 5 Error: 0.071331 Align patch 11 14 left Iteration 1 Error: 2.023203 Iteration 2 Error: 0.375939 Iteration 3 Error: 0.127012 Iteration 4 Error: 0.043149 Align patch 12 13 left Iteration 1 Error: 0.813385 Iteration 2 Error: 0.320360 Iteration 3 Error: 0.146970 Iteration 4 Error: 0.065519 Iteration 5 Error: 0.029000 Align patch 13 12 left Iteration 1 Error: 0.603582 Iteration 2 Error: 0.142168 Iteration 3 Error: 0.040459 Align patch 14 11 left Iteration 1 Error: 0.578451 Iteration 2 Error: 0.074565 Iteration 3 Error: 0.023612 Align patch 15 10 left Iteration 1 Error: 1.072486 Iteration 2 Error: 0.220927 Iteration 3 Error: 0.033411 Align patch 16 9 left Iteration 1 Error: 1.181058 Iteration 2 Error: 0.411567 Iteration 3 Error: 0.230859 Iteration 4 Error: 0.144678 Iteration 5 Error: 0.099864 Align patch 16 9 left Iteration 1 Error: 1.162819 Iteration 2 Error: 0.386084 Iteration 3 Error: 0.133359 Iteration 4 Error: 0.060785 Iteration 5 Error: 0.025770 Align patch 17 8 left Iteration 1 Error: 1.225328 Iteration 2 Error: 0.345306 Iteration 3 Error: 0.183511 Iteration 4 Error: 0.098779 Iteration 5 Error: 0.062477 Align patch 17 8 left Iteration 1 Error: 0.952016 Iteration 2 Error: 0.311030 Iteration 3 Error: 0.115178 Iteration 4 Error: 0.047821 Align patch 18 7 left Iteration 1 Error: 0.728692 Iteration 2 Error: 0.154060 Iteration 3 Error: 0.048689 Align patch 19 6 left Iteration 1 Error: 0.845379 Iteration 2 Error: 0.165319 Iteration 3 Error: 0.047497 Align patch 20 5 left Iteration 1 Error: 1.523070 Iteration 2 Error: 0.281718 Iteration 3 Error: 0.054385 Iteration 4 Error: 0.018480 Align patch 21 4 left Iteration 1 Error: 1.182159 Iteration 2 Error: 0.278707 Iteration 3 Error: 0.079840 Iteration 4 Error: 0.040955 Align patch 22 3 left Iteration 1 Error: 0.921503 Iteration 2 Error: 0.116938 Iteration 3 Error: 0.056096 Iteration 4 Error: 0.015006 Align patch 23 2 left Iteration 1 Error: 0.765172 Iteration 2 Error: 0.137364 Iteration 3 Error: 0.047869 Align patch 24 1 left Iteration 1 Error: 1.647740 Iteration 2 Error: 0.327842 Iteration 3 Error: 0.070263 Iteration 4 Error: 0.023499 Align patch 25 0 left Iteration 1 Error: 1.477875 Iteration 2 Error: 0.238483 Iteration 3 Error: 0.060113 Iteration 4 Error: 0.013113 3D Fitting completed. Patch alignment time: 21.43(sec) Local motion has been corrected. Process thread exits. Computational time: 29.772314 sec Total time: 35.652912 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00010hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00010hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.718798s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00010hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.689475s ........................................ >>>>>>TIME<<<<<< FFT: 1.136816s Defocus_U Defocus_V Angle CCC 9009.42 9525.81 3.99 0.027767 Final Values Defocus_U Defocus_V Angle CCC 9012.55 9522.69 3.99 0.053914 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00010hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00010hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.001e-01 CC threshold: 0.735 Mean Std: 39.34 6.73 Num Hot pixels: 196 Hot pixel threshold: 79.69 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.194093 Iteration 2 Error: 0.305976 Iteration 3 Error: 0.078583 Iteration 4 Error: 0.030201 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.10 -0.19 ...... Frame ( 3) shift: -0.19 -0.37 ...... Frame ( 4) shift: -0.29 -0.56 ...... Frame ( 5) shift: -0.39 -0.75 ...... Frame ( 6) shift: -0.41 -0.82 ...... Frame ( 7) shift: -0.37 -0.79 ...... Frame ( 8) shift: -0.33 -0.75 ...... Frame ( 9) shift: -0.31 -0.69 ...... Frame ( 10) shift: -0.31 -0.60 ...... Frame ( 11) shift: -0.30 -0.52 ...... Frame ( 12) shift: -0.30 -0.38 ...... Frame ( 13) shift: -0.31 -0.20 ...... Frame ( 14) shift: -0.31 -0.02 ...... Frame ( 15) shift: -0.29 0.16 ...... Frame ( 16) shift: -0.25 0.34 ...... Frame ( 17) shift: -0.21 0.53 ...... Frame ( 18) shift: -0.17 0.65 ...... Frame ( 19) shift: -0.13 0.72 ...... Frame ( 20) shift: -0.10 0.79 ...... Frame ( 21) shift: -0.09 0.86 ...... Frame ( 22) shift: -0.12 0.93 ...... Frame ( 23) shift: -0.15 1.00 ...... Frame ( 24) shift: -0.18 1.12 ...... Frame ( 25) shift: -0.21 1.28 ...... Frame ( 26) shift: -0.25 1.44 ...... Frame ( 27) shift: -0.27 1.56 ...... Frame ( 28) shift: -0.28 1.64 ...... Frame ( 29) shift: -0.29 1.72 ...... Frame ( 30) shift: -0.32 1.78 ...... Frame ( 31) shift: -0.36 1.83 ...... Frame ( 32) shift: -0.40 1.88 ...... Frame ( 33) shift: -0.38 1.91 ...... Frame ( 34) shift: -0.31 1.92 ...... Frame ( 35) shift: -0.24 1.93 ...... Frame ( 36) shift: -0.21 1.94 ...... Frame ( 37) shift: -0.24 1.95 ...... Frame ( 38) shift: -0.26 1.96 ...... Frame ( 39) shift: -0.28 1.96 ...... Frame ( 40) shift: -0.30 1.97 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.605302 Iteration 2 Error: 0.474715 Iteration 3 Error: 0.285561 Iteration 4 Error: 0.118520 Iteration 5 Error: 0.064760 Align patch 1 24 left Iteration 1 Error: 1.828944 Iteration 2 Error: 0.377193 Iteration 3 Error: 0.082745 Iteration 4 Error: 0.028342 Align patch 2 23 left Iteration 1 Error: 1.077114 Iteration 2 Error: 0.264055 Iteration 3 Error: 0.105622 Iteration 4 Error: 0.043043 Align patch 3 22 left Iteration 1 Error: 1.368253 Iteration 2 Error: 0.266595 Iteration 3 Error: 0.095788 Iteration 4 Error: 0.039411 Align patch 4 21 left Iteration 1 Error: 0.936426 Iteration 2 Error: 0.193963 Iteration 3 Error: 0.055456 Iteration 4 Error: 0.017767 Align patch 5 20 left Iteration 1 Error: 0.829151 Iteration 2 Error: 0.200912 Iteration 3 Error: 0.035246 Align patch 6 19 left Iteration 1 Error: 1.348172 Iteration 2 Error: 0.545241 Iteration 3 Error: 0.193285 Iteration 4 Error: 0.105019 Iteration 5 Error: 0.044518 Align patch 7 18 left Iteration 1 Error: 0.837992 Iteration 2 Error: 0.262375 Iteration 3 Error: 0.109829 Iteration 4 Error: 0.042308 Align patch 8 17 left Iteration 1 Error: 0.753064 Iteration 2 Error: 0.207142 Iteration 3 Error: 0.084851 Iteration 4 Error: 0.027375 Align patch 9 16 left Iteration 1 Error: 0.841388 Iteration 2 Error: 0.222510 Iteration 3 Error: 0.076957 Iteration 4 Error: 0.036049 Align patch 10 15 left Iteration 1 Error: 0.964533 Iteration 2 Error: 0.329760 Iteration 3 Error: 0.083564 Iteration 4 Error: 0.030167 Align patch 11 14 left Iteration 1 Error: 1.239748 Iteration 2 Error: 0.404755 Iteration 3 Error: 0.112003 Iteration 4 Error: 0.054693 Iteration 5 Error: 0.029235 Align patch 12 13 left Iteration 1 Error: 0.570807 Iteration 2 Error: 0.184908 Iteration 3 Error: 0.101141 Iteration 4 Error: 0.052442 Iteration 5 Error: 0.035175 Align patch 13 12 left Iteration 1 Error: 1.049554 Iteration 2 Error: 0.180478 Iteration 3 Error: 0.065058 Iteration 4 Error: 0.019313 Align patch 14 11 left Iteration 1 Error: 0.589001 Iteration 2 Error: 0.138053 Iteration 3 Error: 0.044422 Align patch 15 10 left Iteration 1 Error: 0.740823 Iteration 2 Error: 0.151839 Iteration 3 Error: 0.045024 Align patch 16 9 left Iteration 1 Error: 0.710841 Iteration 2 Error: 0.167255 Iteration 3 Error: 0.054173 Iteration 4 Error: 0.028760 Align patch 17 8 left Iteration 1 Error: 0.797646 Iteration 2 Error: 0.201058 Iteration 3 Error: 0.070395 Iteration 4 Error: 0.021645 Align patch 18 7 left Iteration 1 Error: 0.718402 Iteration 2 Error: 0.275377 Iteration 3 Error: 0.078690 Iteration 4 Error: 0.038841 Align patch 19 6 left Iteration 1 Error: 0.618708 Iteration 2 Error: 0.170447 Iteration 3 Error: 0.052687 Iteration 4 Error: 0.018175 Align patch 20 5 left Iteration 1 Error: 0.944728 Iteration 2 Error: 0.293769 Iteration 3 Error: 0.089201 Iteration 4 Error: 0.031716 Align patch 21 4 left Iteration 1 Error: 0.739851 Iteration 2 Error: 0.153978 Iteration 3 Error: 0.054876 Iteration 4 Error: 0.014250 Align patch 22 3 left Iteration 1 Error: 0.573502 Iteration 2 Error: 0.181402 Iteration 3 Error: 0.049498 Align patch 23 2 left Iteration 1 Error: 0.552940 Iteration 2 Error: 0.105051 Iteration 3 Error: 0.024546 Align patch 24 1 left Iteration 1 Error: 1.754197 Iteration 2 Error: 0.271894 Iteration 3 Error: 0.065241 Iteration 4 Error: 0.014845 Align patch 25 0 left Iteration 1 Error: 1.302211 Iteration 2 Error: 0.255688 Iteration 3 Error: 0.057238 Iteration 4 Error: 0.020355 3D Fitting completed. Patch alignment time: 17.97(sec) Local motion has been corrected. Process thread exits. Computational time: 27.046392 sec Total time: 33.491150 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00010hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00010hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.774284s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00010hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.651486s ........................................ >>>>>>TIME<<<<<< FFT: 1.183299s Defocus_U Defocus_V Angle CCC 12558.60 13468.76 4.81 0.041919 Final Values Defocus_U Defocus_V Angle CCC 12596.11 13453.14 3.87 0.065952 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00010hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00010hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 39.81 6.74 Num Hot pixels: 218 Hot pixel threshold: 80.27 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.904673 Iteration 2 Error: 0.213971 Iteration 3 Error: 0.095808 Iteration 4 Error: 0.032675 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.23 -0.22 ...... Frame ( 3) shift: -0.46 -0.44 ...... Frame ( 4) shift: -0.69 -0.66 ...... Frame ( 5) shift: -0.91 -0.88 ...... Frame ( 6) shift: -1.03 -0.99 ...... Frame ( 7) shift: -1.02 -1.00 ...... Frame ( 8) shift: -1.02 -1.01 ...... Frame ( 9) shift: -0.98 -0.97 ...... Frame ( 10) shift: -0.91 -0.88 ...... Frame ( 11) shift: -0.84 -0.80 ...... Frame ( 12) shift: -0.76 -0.71 ...... Frame ( 13) shift: -0.68 -0.61 ...... Frame ( 14) shift: -0.59 -0.52 ...... Frame ( 15) shift: -0.54 -0.46 ...... Frame ( 16) shift: -0.52 -0.42 ...... Frame ( 17) shift: -0.50 -0.38 ...... Frame ( 18) shift: -0.46 -0.31 ...... Frame ( 19) shift: -0.40 -0.22 ...... Frame ( 20) shift: -0.34 -0.13 ...... Frame ( 21) shift: -0.27 -0.04 ...... Frame ( 22) shift: -0.19 0.05 ...... Frame ( 23) shift: -0.11 0.14 ...... Frame ( 24) shift: -0.04 0.21 ...... Frame ( 25) shift: 0.03 0.25 ...... Frame ( 26) shift: 0.10 0.30 ...... Frame ( 27) shift: 0.14 0.35 ...... Frame ( 28) shift: 0.13 0.40 ...... Frame ( 29) shift: 0.13 0.44 ...... Frame ( 30) shift: 0.13 0.49 ...... Frame ( 31) shift: 0.14 0.52 ...... Frame ( 32) shift: 0.15 0.56 ...... Frame ( 33) shift: 0.18 0.60 ...... Frame ( 34) shift: 0.24 0.64 ...... Frame ( 35) shift: 0.30 0.68 ...... Frame ( 36) shift: 0.36 0.72 ...... Frame ( 37) shift: 0.41 0.75 ...... Frame ( 38) shift: 0.46 0.78 ...... Frame ( 39) shift: 0.51 0.82 ...... Frame ( 40) shift: 0.56 0.85 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.474600 Iteration 2 Error: 0.383716 Iteration 3 Error: 0.125896 Iteration 4 Error: 0.042945 Align patch 2 23 left Iteration 1 Error: 2.119243 Iteration 2 Error: 0.557576 Iteration 3 Error: 0.300931 Iteration 4 Error: 0.136261 Iteration 5 Error: 0.077198 Align patch 2 23 left Iteration 1 Error: 1.835057 Iteration 2 Error: 0.398891 Iteration 3 Error: 0.116066 Iteration 4 Error: 0.059813 Iteration 5 Error: 0.025406 Align patch 3 22 left Iteration 1 Error: 0.604109 Iteration 2 Error: 0.100610 Iteration 3 Error: 0.025216 Align patch 4 21 left Iteration 1 Error: 0.737661 Iteration 2 Error: 0.188360 Iteration 3 Error: 0.050369 Iteration 4 Error: 0.016029 Align patch 5 20 left Iteration 1 Error: 0.755144 Iteration 2 Error: 0.147075 Iteration 3 Error: 0.045119 Align patch 6 19 left Iteration 1 Error: 1.762867 Iteration 2 Error: 0.341816 Iteration 3 Error: 0.172466 Iteration 4 Error: 0.102112 Iteration 5 Error: 0.058459 Align patch 6 19 left Iteration 1 Error: 2.306429 Iteration 2 Error: 0.400041 Iteration 3 Error: 0.104096 Iteration 4 Error: 0.045262 Align patch 7 18 left Iteration 1 Error: 0.955528 Iteration 2 Error: 0.463887 Iteration 3 Error: 0.267033 Iteration 4 Error: 0.185129 Iteration 5 Error: 0.120659 Align patch 7 18 left Iteration 1 Error: 1.552148 Iteration 2 Error: 0.368626 Iteration 3 Error: 0.119989 Iteration 4 Error: 0.046572 Align patch 8 17 left Iteration 1 Error: 0.844963 Iteration 2 Error: 0.149363 Iteration 3 Error: 0.093455 Iteration 4 Error: 0.033487 Align patch 9 16 left Iteration 1 Error: 0.939427 Iteration 2 Error: 0.157431 Iteration 3 Error: 0.064201 Iteration 4 Error: 0.021832 Align patch 10 15 left Iteration 1 Error: 1.147125 Iteration 2 Error: 0.194672 Iteration 3 Error: 0.058598 Iteration 4 Error: 0.030145 Align patch 11 14 left Iteration 1 Error: 1.092416 Iteration 2 Error: 0.388126 Iteration 3 Error: 0.209914 Iteration 4 Error: 0.113345 Iteration 5 Error: 0.067205 Align patch 11 14 left Iteration 1 Error: 1.525373 Iteration 2 Error: 0.372482 Iteration 3 Error: 0.124862 Iteration 4 Error: 0.037353 Align patch 12 13 left Iteration 1 Error: 0.992415 Iteration 2 Error: 0.183335 Iteration 3 Error: 0.088947 Iteration 4 Error: 0.046242 Align patch 13 12 left Iteration 1 Error: 0.574399 Iteration 2 Error: 0.149803 Iteration 3 Error: 0.051787 Iteration 4 Error: 0.022631 Align patch 14 11 left Iteration 1 Error: 0.808442 Iteration 2 Error: 0.110393 Iteration 3 Error: 0.035847 Align patch 15 10 left Iteration 1 Error: 0.933769 Iteration 2 Error: 0.214926 Iteration 3 Error: 0.049772 Align patch 16 9 left Iteration 1 Error: 1.089028 Iteration 2 Error: 0.268108 Iteration 3 Error: 0.106858 Iteration 4 Error: 0.055261 Iteration 5 Error: 0.027469 Align patch 17 8 left Iteration 1 Error: 0.508633 Iteration 2 Error: 0.103375 Iteration 3 Error: 0.051860 Iteration 4 Error: 0.020281 Align patch 18 7 left Iteration 1 Error: 0.566344 Iteration 2 Error: 0.123979 Iteration 3 Error: 0.049567 Align patch 19 6 left Iteration 1 Error: 0.576984 Iteration 2 Error: 0.091433 Iteration 3 Error: 0.027624 Align patch 20 5 left Iteration 1 Error: 1.166621 Iteration 2 Error: 0.251362 Iteration 3 Error: 0.063736 Iteration 4 Error: 0.022084 Align patch 21 4 left Iteration 1 Error: 0.896818 Iteration 2 Error: 0.226536 Iteration 3 Error: 0.078120 Iteration 4 Error: 0.033028 Align patch 22 3 left Iteration 1 Error: 0.762773 Iteration 2 Error: 0.129671 Iteration 3 Error: 0.034748 Align patch 23 2 left Iteration 1 Error: 1.138998 Iteration 2 Error: 0.153746 Iteration 3 Error: 0.058823 Iteration 4 Error: 0.022541 Align patch 24 1 left Iteration 1 Error: 0.809225 Iteration 2 Error: 0.231831 Iteration 3 Error: 0.064817 Iteration 4 Error: 0.018423 Align patch 25 0 left Iteration 1 Error: 1.841482 Iteration 2 Error: 0.381034 Iteration 3 Error: 0.094943 Iteration 4 Error: 0.036520 3D Fitting completed. Patch alignment time: 20.63(sec) Local motion has been corrected. Process thread exits. Computational time: 29.407837 sec Total time: 35.306427 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00010hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00010hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.643565s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00010hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.070121s ........................................ >>>>>>TIME<<<<<< FFT: 0.952295s Defocus_U Defocus_V Angle CCC 10912.12 10224.62 87.26 0.039940 Final Values Defocus_U Defocus_V Angle CCC 10934.02 10246.52 87.57 0.068419 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00011hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00011hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.003e-01 CC threshold: 0.736 Mean Std: 41.02 6.96 Num Hot pixels: 214 Hot pixel threshold: 82.77 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.032936 Iteration 2 Error: 0.164292 Iteration 3 Error: 0.031904 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.12 0.06 ...... Frame ( 3) shift: -0.23 0.12 ...... Frame ( 4) shift: -0.35 0.18 ...... Frame ( 5) shift: -0.47 0.23 ...... Frame ( 6) shift: -0.50 0.30 ...... Frame ( 7) shift: -0.46 0.36 ...... Frame ( 8) shift: -0.41 0.42 ...... Frame ( 9) shift: -0.38 0.48 ...... Frame ( 10) shift: -0.37 0.53 ...... Frame ( 11) shift: -0.35 0.58 ...... Frame ( 12) shift: -0.35 0.65 ...... Frame ( 13) shift: -0.36 0.74 ...... Frame ( 14) shift: -0.37 0.83 ...... Frame ( 15) shift: -0.38 0.88 ...... Frame ( 16) shift: -0.37 0.89 ...... Frame ( 17) shift: -0.36 0.90 ...... Frame ( 18) shift: -0.35 0.94 ...... Frame ( 19) shift: -0.35 1.00 ...... Frame ( 20) shift: -0.36 1.06 ...... Frame ( 21) shift: -0.37 1.08 ...... Frame ( 22) shift: -0.39 1.06 ...... Frame ( 23) shift: -0.41 1.03 ...... Frame ( 24) shift: -0.40 1.06 ...... Frame ( 25) shift: -0.37 1.15 ...... Frame ( 26) shift: -0.33 1.23 ...... Frame ( 27) shift: -0.30 1.30 ...... Frame ( 28) shift: -0.26 1.34 ...... Frame ( 29) shift: -0.22 1.39 ...... Frame ( 30) shift: -0.20 1.46 ...... Frame ( 31) shift: -0.19 1.55 ...... Frame ( 32) shift: -0.18 1.65 ...... Frame ( 33) shift: -0.14 1.74 ...... Frame ( 34) shift: -0.07 1.82 ...... Frame ( 35) shift: 0.00 1.90 ...... Frame ( 36) shift: 0.05 1.96 ...... Frame ( 37) shift: 0.07 2.01 ...... Frame ( 38) shift: 0.09 2.05 ...... Frame ( 39) shift: 0.11 2.10 ...... Frame ( 40) shift: 0.13 2.15 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.260455 Iteration 2 Error: 0.319995 Iteration 3 Error: 0.099171 Iteration 4 Error: 0.045926 Align patch 2 23 left Iteration 1 Error: 1.181147 Iteration 2 Error: 0.245341 Iteration 3 Error: 0.051669 Iteration 4 Error: 0.025188 Align patch 3 22 left Iteration 1 Error: 0.679076 Iteration 2 Error: 0.107580 Iteration 3 Error: 0.025804 Align patch 4 21 left Iteration 1 Error: 0.601460 Iteration 2 Error: 0.064575 Iteration 3 Error: 0.013449 Align patch 5 20 left Iteration 1 Error: 0.701959 Iteration 2 Error: 0.088974 Iteration 3 Error: 0.017725 Align patch 6 19 left Iteration 1 Error: 1.364742 Iteration 2 Error: 0.249600 Iteration 3 Error: 0.052085 Iteration 4 Error: 0.023692 Align patch 7 18 left Iteration 1 Error: 0.999196 Iteration 2 Error: 0.171784 Iteration 3 Error: 0.054942 Iteration 4 Error: 0.024922 Align patch 8 17 left Iteration 1 Error: 0.585946 Iteration 2 Error: 0.112513 Iteration 3 Error: 0.024843 Align patch 9 16 left Iteration 1 Error: 0.460512 Iteration 2 Error: 0.063186 Iteration 3 Error: 0.014192 Align patch 10 15 left Iteration 1 Error: 0.522197 Iteration 2 Error: 0.050421 Iteration 3 Error: 0.013619 Align patch 11 14 left Iteration 1 Error: 0.930352 Iteration 2 Error: 0.114699 Iteration 3 Error: 0.022067 Align patch 12 13 left Iteration 1 Error: 0.508705 Iteration 2 Error: 0.140107 Iteration 3 Error: 0.032158 Align patch 13 12 left Iteration 1 Error: 0.445250 Iteration 2 Error: 0.073899 Iteration 3 Error: 0.012338 Align patch 14 11 left Iteration 1 Error: 0.572278 Iteration 2 Error: 0.067653 Iteration 3 Error: 0.010214 Align patch 15 10 left Iteration 1 Error: 0.744111 Iteration 2 Error: 0.063910 Iteration 3 Error: 0.010500 Align patch 16 9 left Iteration 1 Error: 0.663587 Iteration 2 Error: 0.067595 Iteration 3 Error: 0.018753 Align patch 17 8 left Iteration 1 Error: 0.688365 Iteration 2 Error: 0.099818 Iteration 3 Error: 0.021464 Align patch 18 7 left Iteration 1 Error: 0.675549 Iteration 2 Error: 0.082960 Iteration 3 Error: 0.022566 Align patch 19 6 left Iteration 1 Error: 0.806913 Iteration 2 Error: 0.102023 Iteration 3 Error: 0.022439 Align patch 20 5 left Iteration 1 Error: 0.982258 Iteration 2 Error: 0.207768 Iteration 3 Error: 0.036332 Align patch 21 4 left Iteration 1 Error: 0.636616 Iteration 2 Error: 0.070911 Iteration 3 Error: 0.014120 Align patch 22 3 left Iteration 1 Error: 0.990187 Iteration 2 Error: 0.142517 Iteration 3 Error: 0.034325 Align patch 23 2 left Iteration 1 Error: 0.404131 Iteration 2 Error: 0.054458 Iteration 3 Error: 0.018315 Align patch 24 1 left Iteration 1 Error: 0.825969 Iteration 2 Error: 0.069619 Iteration 3 Error: 0.007532 Align patch 25 0 left Iteration 1 Error: 0.711385 Iteration 2 Error: 0.120375 Iteration 3 Error: 0.021922 3D Fitting completed. Patch alignment time: 14.69(sec) Local motion has been corrected. Process thread exits. Computational time: 22.827126 sec Total time: 29.675220 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00011hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00011hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.755216s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00011hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.593882s ........................................ >>>>>>TIME<<<<<< FFT: 1.103118s Defocus_U Defocus_V Angle CCC 11892.61 12693.39 16.11 0.050362 Final Values Defocus_U Defocus_V Angle CCC 11906.67 12698.08 16.11 0.083033 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00011hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00011hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.003e-01 CC threshold: 0.736 Mean Std: 41.57 7.05 Num Hot pixels: 204 Hot pixel threshold: 83.87 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.407152 Iteration 2 Error: 0.129820 Iteration 3 Error: 0.033066 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.06 0.11 ...... Frame ( 3) shift: -0.12 0.22 ...... Frame ( 4) shift: -0.18 0.33 ...... Frame ( 5) shift: -0.25 0.43 ...... Frame ( 6) shift: -0.27 0.56 ...... Frame ( 7) shift: -0.25 0.70 ...... Frame ( 8) shift: -0.23 0.83 ...... Frame ( 9) shift: -0.21 0.95 ...... Frame ( 10) shift: -0.18 1.05 ...... Frame ( 11) shift: -0.15 1.15 ...... Frame ( 12) shift: -0.14 1.27 ...... Frame ( 13) shift: -0.15 1.42 ...... Frame ( 14) shift: -0.16 1.56 ...... Frame ( 15) shift: -0.19 1.66 ...... Frame ( 16) shift: -0.23 1.70 ...... Frame ( 17) shift: -0.27 1.75 ...... Frame ( 18) shift: -0.27 1.78 ...... Frame ( 19) shift: -0.24 1.80 ...... Frame ( 20) shift: -0.22 1.82 ...... Frame ( 21) shift: -0.18 1.86 ...... Frame ( 22) shift: -0.14 1.92 ...... Frame ( 23) shift: -0.11 1.99 ...... Frame ( 24) shift: -0.08 2.04 ...... Frame ( 25) shift: -0.08 2.08 ...... Frame ( 26) shift: -0.08 2.12 ...... Frame ( 27) shift: -0.06 2.17 ...... Frame ( 28) shift: -0.03 2.24 ...... Frame ( 29) shift: 0.00 2.30 ...... Frame ( 30) shift: 0.02 2.32 ...... Frame ( 31) shift: 0.04 2.28 ...... Frame ( 32) shift: 0.05 2.24 ...... Frame ( 33) shift: 0.08 2.26 ...... Frame ( 34) shift: 0.13 2.33 ...... Frame ( 35) shift: 0.18 2.41 ...... Frame ( 36) shift: 0.20 2.44 ...... Frame ( 37) shift: 0.21 2.43 ...... Frame ( 38) shift: 0.22 2.42 ...... Frame ( 39) shift: 0.23 2.41 ...... Frame ( 40) shift: 0.24 2.40 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.278310 Iteration 2 Error: 0.161911 Iteration 3 Error: 0.043916 Align patch 2 23 left Iteration 1 Error: 0.781489 Iteration 2 Error: 0.107043 Iteration 3 Error: 0.029324 Align patch 3 22 left Iteration 1 Error: 0.615869 Iteration 2 Error: 0.100670 Iteration 3 Error: 0.022759 Align patch 4 21 left Iteration 1 Error: 0.473657 Iteration 2 Error: 0.094258 Iteration 3 Error: 0.032967 Align patch 5 20 left Iteration 1 Error: 0.640491 Iteration 2 Error: 0.091378 Iteration 3 Error: 0.014218 Align patch 6 19 left Iteration 1 Error: 1.097469 Iteration 2 Error: 0.264791 Iteration 3 Error: 0.078470 Iteration 4 Error: 0.030471 Align patch 7 18 left Iteration 1 Error: 0.798056 Iteration 2 Error: 0.132615 Iteration 3 Error: 0.040602 Align patch 8 17 left Iteration 1 Error: 0.658366 Iteration 2 Error: 0.076309 Iteration 3 Error: 0.017558 Align patch 9 16 left Iteration 1 Error: 0.535706 Iteration 2 Error: 0.084241 Iteration 3 Error: 0.008065 Align patch 10 15 left Iteration 1 Error: 0.778095 Iteration 2 Error: 0.133866 Iteration 3 Error: 0.030655 Align patch 11 14 left Iteration 1 Error: 0.740744 Iteration 2 Error: 0.125045 Iteration 3 Error: 0.029492 Align patch 12 13 left Iteration 1 Error: 0.688974 Iteration 2 Error: 0.125417 Iteration 3 Error: 0.041314 Align patch 13 12 left Iteration 1 Error: 0.469976 Iteration 2 Error: 0.048788 Align patch 14 11 left Iteration 1 Error: 0.484479 Iteration 2 Error: 0.061961 Iteration 3 Error: 0.013164 Align patch 15 10 left Iteration 1 Error: 0.391367 Iteration 2 Error: 0.049906 Align patch 16 9 left Iteration 1 Error: 0.736549 Iteration 2 Error: 0.105784 Iteration 3 Error: 0.022593 Align patch 17 8 left Iteration 1 Error: 0.785742 Iteration 2 Error: 0.135892 Iteration 3 Error: 0.045449 Align patch 18 7 left Iteration 1 Error: 0.503440 Iteration 2 Error: 0.056629 Iteration 3 Error: 0.012874 Align patch 19 6 left Iteration 1 Error: 0.463739 Iteration 2 Error: 0.068167 Iteration 3 Error: 0.012588 Align patch 20 5 left Iteration 1 Error: 0.826940 Iteration 2 Error: 0.081233 Iteration 3 Error: 0.026688 Align patch 21 4 left Iteration 1 Error: 0.549313 Iteration 2 Error: 0.096553 Iteration 3 Error: 0.020577 Align patch 22 3 left Iteration 1 Error: 0.582498 Iteration 2 Error: 0.053036 Iteration 3 Error: 0.011335 Align patch 23 2 left Iteration 1 Error: 0.473664 Iteration 2 Error: 0.068213 Iteration 3 Error: 0.023279 Align patch 24 1 left Iteration 1 Error: 0.980711 Iteration 2 Error: 0.134567 Iteration 3 Error: 0.024536 Align patch 25 0 left Iteration 1 Error: 0.769133 Iteration 2 Error: 0.091874 Iteration 3 Error: 0.015660 3D Fitting completed. Patch alignment time: 15.20(sec) Local motion has been corrected. Process thread exits. Computational time: 23.597633 sec Total time: 29.291248 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00011hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00011hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.568967s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00011hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.839071s ........................................ >>>>>>TIME<<<<<< FFT: 0.932765s Defocus_U Defocus_V Angle CCC 12126.96 12634.77 0.76 0.057836 Final Values Defocus_U Defocus_V Angle CCC 12147.28 12636.34 2.03 0.096204 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00011hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00011hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 41.59 6.97 Num Hot pixels: 185 Hot pixel threshold: 83.42 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.720377 Iteration 2 Error: 0.103158 Iteration 3 Error: 0.022492 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.05 0.06 ...... Frame ( 3) shift: 0.10 0.13 ...... Frame ( 4) shift: 0.15 0.19 ...... Frame ( 5) shift: 0.20 0.26 ...... Frame ( 6) shift: 0.25 0.33 ...... Frame ( 7) shift: 0.30 0.39 ...... Frame ( 8) shift: 0.35 0.46 ...... Frame ( 9) shift: 0.37 0.48 ...... Frame ( 10) shift: 0.34 0.46 ...... Frame ( 11) shift: 0.32 0.44 ...... Frame ( 12) shift: 0.33 0.48 ...... Frame ( 13) shift: 0.38 0.57 ...... Frame ( 14) shift: 0.43 0.67 ...... Frame ( 15) shift: 0.46 0.74 ...... Frame ( 16) shift: 0.48 0.76 ...... Frame ( 17) shift: 0.49 0.79 ...... Frame ( 18) shift: 0.52 0.83 ...... Frame ( 19) shift: 0.56 0.86 ...... Frame ( 20) shift: 0.61 0.90 ...... Frame ( 21) shift: 0.62 0.91 ...... Frame ( 22) shift: 0.60 0.91 ...... Frame ( 23) shift: 0.59 0.91 ...... Frame ( 24) shift: 0.58 0.91 ...... Frame ( 25) shift: 0.58 0.94 ...... Frame ( 26) shift: 0.59 0.96 ...... Frame ( 27) shift: 0.60 0.99 ...... Frame ( 28) shift: 0.63 1.03 ...... Frame ( 29) shift: 0.66 1.08 ...... Frame ( 30) shift: 0.67 1.10 ...... Frame ( 31) shift: 0.66 1.11 ...... Frame ( 32) shift: 0.64 1.12 ...... Frame ( 33) shift: 0.66 1.15 ...... Frame ( 34) shift: 0.70 1.19 ...... Frame ( 35) shift: 0.73 1.23 ...... Frame ( 36) shift: 0.76 1.27 ...... Frame ( 37) shift: 0.78 1.31 ...... Frame ( 38) shift: 0.80 1.35 ...... Frame ( 39) shift: 0.82 1.40 ...... Frame ( 40) shift: 0.84 1.44 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.499421 Iteration 2 Error: 0.253694 Iteration 3 Error: 0.065764 Iteration 4 Error: 0.029266 Align patch 2 23 left Iteration 1 Error: 1.327529 Iteration 2 Error: 0.147411 Iteration 3 Error: 0.045738 Align patch 3 22 left Iteration 1 Error: 1.117865 Iteration 2 Error: 0.126518 Iteration 3 Error: 0.022336 Align patch 4 21 left Iteration 1 Error: 0.488289 Iteration 2 Error: 0.055882 Iteration 3 Error: 0.009155 Align patch 5 20 left Iteration 1 Error: 0.778743 Iteration 2 Error: 0.098241 Iteration 3 Error: 0.019270 Align patch 6 19 left Iteration 1 Error: 1.594878 Iteration 2 Error: 0.260590 Iteration 3 Error: 0.083985 Iteration 4 Error: 0.027634 Align patch 7 18 left Iteration 1 Error: 0.957748 Iteration 2 Error: 0.144460 Iteration 3 Error: 0.060245 Iteration 4 Error: 0.013739 Align patch 8 17 left Iteration 1 Error: 0.697346 Iteration 2 Error: 0.174428 Iteration 3 Error: 0.064709 Iteration 4 Error: 0.029020 Align patch 9 16 left Iteration 1 Error: 0.591819 Iteration 2 Error: 0.058060 Iteration 3 Error: 0.015775 Align patch 10 15 left Iteration 1 Error: 0.545778 Iteration 2 Error: 0.074532 Iteration 3 Error: 0.011137 Align patch 11 14 left Iteration 1 Error: 0.891227 Iteration 2 Error: 0.205387 Iteration 3 Error: 0.070473 Iteration 4 Error: 0.025583 Align patch 12 13 left Iteration 1 Error: 0.654855 Iteration 2 Error: 0.071811 Iteration 3 Error: 0.029037 Align patch 13 12 left Iteration 1 Error: 0.646912 Iteration 2 Error: 0.079623 Iteration 3 Error: 0.030895 Align patch 14 11 left Iteration 1 Error: 0.513031 Iteration 2 Error: 0.063830 Iteration 3 Error: 0.009212 Align patch 15 10 left Iteration 1 Error: 0.678096 Iteration 2 Error: 0.089594 Iteration 3 Error: 0.024836 Align patch 16 9 left Iteration 1 Error: 0.503905 Iteration 2 Error: 0.118221 Iteration 3 Error: 0.022960 Align patch 17 8 left Iteration 1 Error: 0.825333 Iteration 2 Error: 0.142693 Iteration 3 Error: 0.027063 Align patch 18 7 left Iteration 1 Error: 0.537041 Iteration 2 Error: 0.077233 Iteration 3 Error: 0.027281 Align patch 19 6 left Iteration 1 Error: 0.720315 Iteration 2 Error: 0.099212 Iteration 3 Error: 0.025015 Align patch 20 5 left Iteration 1 Error: 0.903725 Iteration 2 Error: 0.137178 Iteration 3 Error: 0.027520 Align patch 21 4 left Iteration 1 Error: 1.308138 Iteration 2 Error: 0.105931 Iteration 3 Error: 0.014940 Align patch 22 3 left Iteration 1 Error: 1.159162 Iteration 2 Error: 0.153412 Iteration 3 Error: 0.046019 Align patch 23 2 left Iteration 1 Error: 0.746864 Iteration 2 Error: 0.121771 Iteration 3 Error: 0.030687 Align patch 24 1 left Iteration 1 Error: 0.760345 Iteration 2 Error: 0.161167 Iteration 3 Error: 0.019679 Align patch 25 0 left Iteration 1 Error: 0.984340 Iteration 2 Error: 0.162095 Iteration 3 Error: 0.035753 3D Fitting completed. Patch alignment time: 14.72(sec) Local motion has been corrected. Process thread exits. Computational time: 23.332369 sec Total time: 29.093763 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00011hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00011hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.674583s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00011hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.066218s ........................................ >>>>>>TIME<<<<<< FFT: 1.057848s Defocus_U Defocus_V Angle CCC 10482.45 11349.74 7.80 0.051085 Final Values Defocus_U Defocus_V Angle CCC 10504.36 11384.17 8.12 0.090807 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00011hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00011hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 42.29 7.08 Num Hot pixels: 209 Hot pixel threshold: 84.77 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.548792 Iteration 2 Error: 0.055838 Iteration 3 Error: 0.011300 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.09 0.06 ...... Frame ( 3) shift: -0.18 0.13 ...... Frame ( 4) shift: -0.27 0.19 ...... Frame ( 5) shift: -0.36 0.25 ...... Frame ( 6) shift: -0.42 0.29 ...... Frame ( 7) shift: -0.45 0.32 ...... Frame ( 8) shift: -0.49 0.34 ...... Frame ( 9) shift: -0.52 0.34 ...... Frame ( 10) shift: -0.53 0.33 ...... Frame ( 11) shift: -0.55 0.32 ...... Frame ( 12) shift: -0.57 0.34 ...... Frame ( 13) shift: -0.58 0.41 ...... Frame ( 14) shift: -0.60 0.48 ...... Frame ( 15) shift: -0.60 0.51 ...... Frame ( 16) shift: -0.61 0.49 ...... Frame ( 17) shift: -0.61 0.48 ...... Frame ( 18) shift: -0.61 0.50 ...... Frame ( 19) shift: -0.61 0.57 ...... Frame ( 20) shift: -0.62 0.63 ...... Frame ( 21) shift: -0.60 0.68 ...... Frame ( 22) shift: -0.57 0.71 ...... Frame ( 23) shift: -0.53 0.75 ...... Frame ( 24) shift: -0.50 0.77 ...... Frame ( 25) shift: -0.47 0.78 ...... Frame ( 26) shift: -0.44 0.79 ...... Frame ( 27) shift: -0.43 0.78 ...... Frame ( 28) shift: -0.43 0.77 ...... Frame ( 29) shift: -0.43 0.75 ...... Frame ( 30) shift: -0.41 0.77 ...... Frame ( 31) shift: -0.37 0.81 ...... Frame ( 32) shift: -0.33 0.86 ...... Frame ( 33) shift: -0.28 0.87 ...... Frame ( 34) shift: -0.22 0.85 ...... Frame ( 35) shift: -0.16 0.82 ...... Frame ( 36) shift: -0.15 0.84 ...... Frame ( 37) shift: -0.19 0.89 ...... Frame ( 38) shift: -0.23 0.94 ...... Frame ( 39) shift: -0.27 1.00 ...... Frame ( 40) shift: -0.30 1.05 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.173518 Iteration 2 Error: 0.112300 Iteration 3 Error: 0.031084 Align patch 2 23 left Iteration 1 Error: 1.055478 Iteration 2 Error: 0.122039 Iteration 3 Error: 0.025639 Align patch 3 22 left Iteration 1 Error: 0.493525 Iteration 2 Error: 0.074678 Iteration 3 Error: 0.020032 Align patch 4 21 left Iteration 1 Error: 0.938894 Iteration 2 Error: 0.127014 Iteration 3 Error: 0.043278 Align patch 5 20 left Iteration 1 Error: 0.611439 Iteration 2 Error: 0.038097 Align patch 6 19 left Iteration 1 Error: 1.771258 Iteration 2 Error: 0.177824 Iteration 3 Error: 0.047523 Align patch 7 18 left Iteration 1 Error: 0.826317 Iteration 2 Error: 0.159771 Iteration 3 Error: 0.020017 Align patch 8 17 left Iteration 1 Error: 0.542915 Iteration 2 Error: 0.083528 Iteration 3 Error: 0.012141 Align patch 9 16 left Iteration 1 Error: 0.581345 Iteration 2 Error: 0.068712 Iteration 3 Error: 0.013947 Align patch 10 15 left Iteration 1 Error: 0.622354 Iteration 2 Error: 0.073346 Iteration 3 Error: 0.014425 Align patch 11 14 left Iteration 1 Error: 0.934887 Iteration 2 Error: 0.111062 Iteration 3 Error: 0.021159 Align patch 12 13 left Iteration 1 Error: 0.598260 Iteration 2 Error: 0.087947 Iteration 3 Error: 0.018734 Align patch 13 12 left Iteration 1 Error: 0.745137 Iteration 2 Error: 0.112036 Iteration 3 Error: 0.014532 Align patch 14 11 left Iteration 1 Error: 0.665091 Iteration 2 Error: 0.074986 Iteration 3 Error: 0.018829 Align patch 15 10 left Iteration 1 Error: 0.738588 Iteration 2 Error: 0.081211 Iteration 3 Error: 0.021682 Align patch 16 9 left Iteration 1 Error: 0.721633 Iteration 2 Error: 0.106597 Iteration 3 Error: 0.023207 Align patch 17 8 left Iteration 1 Error: 0.846011 Iteration 2 Error: 0.091439 Iteration 3 Error: 0.022335 Align patch 18 7 left Iteration 1 Error: 0.524962 Iteration 2 Error: 0.057869 Iteration 3 Error: 0.010115 Align patch 19 6 left Iteration 1 Error: 0.900430 Iteration 2 Error: 0.097033 Iteration 3 Error: 0.021767 Align patch 20 5 left Iteration 1 Error: 0.602650 Iteration 2 Error: 0.087083 Iteration 3 Error: 0.011415 Align patch 21 4 left Iteration 1 Error: 0.699375 Iteration 2 Error: 0.099046 Iteration 3 Error: 0.025138 Align patch 22 3 left Iteration 1 Error: 1.023601 Iteration 2 Error: 0.068474 Iteration 3 Error: 0.014600 Align patch 23 2 left Iteration 1 Error: 1.103501 Iteration 2 Error: 0.112902 Iteration 3 Error: 0.020673 Align patch 24 1 left Iteration 1 Error: 0.851852 Iteration 2 Error: 0.110389 Iteration 3 Error: 0.021770 Align patch 25 0 left Iteration 1 Error: 0.712635 Iteration 2 Error: 0.096610 Iteration 3 Error: 0.009817 3D Fitting completed. Patch alignment time: 15.57(sec) Local motion has been corrected. Process thread exits. Computational time: 23.829523 sec Total time: 29.789154 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00011hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00011hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.777502s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00011hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.769059s ........................................ >>>>>>TIME<<<<<< FFT: 1.012436s Defocus_U Defocus_V Angle CCC 15912.12 15232.43 84.83 0.061559 Final Values Defocus_U Defocus_V Angle CCC 15924.62 15219.93 84.52 0.098428 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00012hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00012hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.002e-01 CC threshold: 0.736 Mean Std: 39.88 7.10 Num Hot pixels: 174 Hot pixel threshold: 82.49 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.847806 Iteration 2 Error: 0.107945 Iteration 3 Error: 0.024496 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.13 -0.10 ...... Frame ( 3) shift: -0.26 -0.19 ...... Frame ( 4) shift: -0.39 -0.29 ...... Frame ( 5) shift: -0.52 -0.38 ...... Frame ( 6) shift: -0.59 -0.44 ...... Frame ( 7) shift: -0.62 -0.46 ...... Frame ( 8) shift: -0.65 -0.48 ...... Frame ( 9) shift: -0.65 -0.49 ...... Frame ( 10) shift: -0.63 -0.48 ...... Frame ( 11) shift: -0.61 -0.47 ...... Frame ( 12) shift: -0.57 -0.42 ...... Frame ( 13) shift: -0.53 -0.34 ...... Frame ( 14) shift: -0.49 -0.26 ...... Frame ( 15) shift: -0.46 -0.20 ...... Frame ( 16) shift: -0.44 -0.15 ...... Frame ( 17) shift: -0.43 -0.10 ...... Frame ( 18) shift: -0.39 -0.04 ...... Frame ( 19) shift: -0.34 0.04 ...... Frame ( 20) shift: -0.30 0.12 ...... Frame ( 21) shift: -0.26 0.20 ...... Frame ( 22) shift: -0.23 0.27 ...... Frame ( 23) shift: -0.20 0.35 ...... Frame ( 24) shift: -0.21 0.41 ...... Frame ( 25) shift: -0.25 0.47 ...... Frame ( 26) shift: -0.29 0.52 ...... Frame ( 27) shift: -0.30 0.56 ...... Frame ( 28) shift: -0.26 0.57 ...... Frame ( 29) shift: -0.22 0.58 ...... Frame ( 30) shift: -0.19 0.60 ...... Frame ( 31) shift: -0.18 0.63 ...... Frame ( 32) shift: -0.16 0.66 ...... Frame ( 33) shift: -0.14 0.68 ...... Frame ( 34) shift: -0.13 0.70 ...... Frame ( 35) shift: -0.12 0.72 ...... Frame ( 36) shift: -0.10 0.76 ...... Frame ( 37) shift: -0.08 0.84 ...... Frame ( 38) shift: -0.06 0.91 ...... Frame ( 39) shift: -0.04 0.98 ...... Frame ( 40) shift: -0.02 1.05 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.671411 Iteration 2 Error: 0.460996 Iteration 3 Error: 0.160233 Iteration 4 Error: 0.065361 Iteration 5 Error: 0.031133 Align patch 2 23 left Iteration 1 Error: 1.107137 Iteration 2 Error: 0.263681 Iteration 3 Error: 0.082720 Iteration 4 Error: 0.037831 Align patch 3 22 left Iteration 1 Error: 0.779467 Iteration 2 Error: 0.173349 Iteration 3 Error: 0.048105 Align patch 4 21 left Iteration 1 Error: 0.909087 Iteration 2 Error: 0.177166 Iteration 3 Error: 0.057389 Iteration 4 Error: 0.017922 Align patch 5 20 left Iteration 1 Error: 0.715669 Iteration 2 Error: 0.144417 Iteration 3 Error: 0.040983 Align patch 6 19 left Iteration 1 Error: 1.601740 Iteration 2 Error: 0.366077 Iteration 3 Error: 0.146845 Iteration 4 Error: 0.056963 Iteration 5 Error: 0.021963 Align patch 7 18 left Iteration 1 Error: 0.889906 Iteration 2 Error: 0.156383 Iteration 3 Error: 0.035403 Align patch 8 17 left Iteration 1 Error: 0.928166 Iteration 2 Error: 0.230030 Iteration 3 Error: 0.069781 Iteration 4 Error: 0.018571 Align patch 9 16 left Iteration 1 Error: 0.671407 Iteration 2 Error: 0.074988 Iteration 3 Error: 0.020456 Align patch 10 15 left Iteration 1 Error: 0.389237 Iteration 2 Error: 0.068657 Iteration 3 Error: 0.013348 Align patch 11 14 left Iteration 1 Error: 0.665663 Iteration 2 Error: 0.228273 Iteration 3 Error: 0.107748 Iteration 4 Error: 0.044853 Align patch 12 13 left Iteration 1 Error: 0.780534 Iteration 2 Error: 0.178885 Iteration 3 Error: 0.074407 Iteration 4 Error: 0.031378 Align patch 13 12 left Iteration 1 Error: 0.621029 Iteration 2 Error: 0.155099 Iteration 3 Error: 0.030197 Align patch 14 11 left Iteration 1 Error: 0.614930 Iteration 2 Error: 0.071646 Iteration 3 Error: 0.013543 Align patch 15 10 left Iteration 1 Error: 0.543459 Iteration 2 Error: 0.067357 Iteration 3 Error: 0.016403 Align patch 16 9 left Iteration 1 Error: 1.079211 Iteration 2 Error: 0.136856 Iteration 3 Error: 0.046241 Align patch 17 8 left Iteration 1 Error: 0.561250 Iteration 2 Error: 0.116714 Iteration 3 Error: 0.038825 Align patch 18 7 left Iteration 1 Error: 0.564775 Iteration 2 Error: 0.126507 Iteration 3 Error: 0.023861 Align patch 19 6 left Iteration 1 Error: 0.507569 Iteration 2 Error: 0.104069 Iteration 3 Error: 0.017382 Align patch 20 5 left Iteration 1 Error: 0.557299 Iteration 2 Error: 0.091153 Iteration 3 Error: 0.021537 Align patch 21 4 left Iteration 1 Error: 1.142788 Iteration 2 Error: 0.087329 Iteration 3 Error: 0.022052 Align patch 22 3 left Iteration 1 Error: 0.442231 Iteration 2 Error: 0.113188 Iteration 3 Error: 0.029537 Align patch 23 2 left Iteration 1 Error: 0.635629 Iteration 2 Error: 0.096457 Iteration 3 Error: 0.019489 Align patch 24 1 left Iteration 1 Error: 0.512207 Iteration 2 Error: 0.104706 Iteration 3 Error: 0.023536 Align patch 25 0 left Iteration 1 Error: 0.293154 Iteration 2 Error: 0.078557 Iteration 3 Error: 0.022815 3D Fitting completed. Patch alignment time: 15.98(sec) Local motion has been corrected. Process thread exits. Computational time: 24.357426 sec Total time: 30.027630 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00012hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00012hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.720545s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00012hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.453247s ........................................ >>>>>>TIME<<<<<< FFT: 0.976371s Defocus_U Defocus_V Angle CCC 9556.64 10380.86 13.23 0.033026 Final Values Defocus_U Defocus_V Angle CCC 9570.71 10391.81 13.54 0.060129 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00012hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00012hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.003e-01 CC threshold: 0.737 Mean Std: 40.32 7.01 Num Hot pixels: 182 Hot pixel threshold: 82.39 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.967534 Iteration 2 Error: 0.123421 Iteration 3 Error: 0.028762 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.01 0.09 ...... Frame ( 3) shift: 0.01 0.18 ...... Frame ( 4) shift: 0.02 0.27 ...... Frame ( 5) shift: 0.03 0.37 ...... Frame ( 6) shift: 0.03 0.43 ...... Frame ( 7) shift: 0.03 0.47 ...... Frame ( 8) shift: 0.03 0.51 ...... Frame ( 9) shift: 0.03 0.60 ...... Frame ( 10) shift: 0.02 0.74 ...... Frame ( 11) shift: 0.01 0.88 ...... Frame ( 12) shift: 0.02 0.95 ...... Frame ( 13) shift: 0.05 0.97 ...... Frame ( 14) shift: 0.08 0.99 ...... Frame ( 15) shift: 0.10 1.02 ...... Frame ( 16) shift: 0.11 1.05 ...... Frame ( 17) shift: 0.12 1.09 ...... Frame ( 18) shift: 0.11 1.10 ...... Frame ( 19) shift: 0.07 1.08 ...... Frame ( 20) shift: 0.03 1.06 ...... Frame ( 21) shift: 0.04 1.10 ...... Frame ( 22) shift: 0.09 1.19 ...... Frame ( 23) shift: 0.14 1.28 ...... Frame ( 24) shift: 0.18 1.38 ...... Frame ( 25) shift: 0.22 1.50 ...... Frame ( 26) shift: 0.25 1.62 ...... Frame ( 27) shift: 0.25 1.67 ...... Frame ( 28) shift: 0.20 1.65 ...... Frame ( 29) shift: 0.14 1.63 ...... Frame ( 30) shift: 0.11 1.64 ...... Frame ( 31) shift: 0.08 1.68 ...... Frame ( 32) shift: 0.05 1.71 ...... Frame ( 33) shift: 0.06 1.74 ...... Frame ( 34) shift: 0.09 1.76 ...... Frame ( 35) shift: 0.12 1.78 ...... Frame ( 36) shift: 0.12 1.83 ...... Frame ( 37) shift: 0.08 1.91 ...... Frame ( 38) shift: 0.05 1.99 ...... Frame ( 39) shift: 0.01 2.06 ...... Frame ( 40) shift: -0.03 2.14 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.783492 Iteration 2 Error: 0.267316 Iteration 3 Error: 0.085762 Iteration 4 Error: 0.045661 Align patch 2 23 left Iteration 1 Error: 0.929169 Iteration 2 Error: 0.240530 Iteration 3 Error: 0.089667 Iteration 4 Error: 0.032289 Align patch 3 22 left Iteration 1 Error: 0.789416 Iteration 2 Error: 0.199352 Iteration 3 Error: 0.042607 Align patch 4 21 left Iteration 1 Error: 0.557504 Iteration 2 Error: 0.060186 Iteration 3 Error: 0.011034 Align patch 5 20 left Iteration 1 Error: 0.612842 Iteration 2 Error: 0.083189 Iteration 3 Error: 0.014205 Align patch 6 19 left Iteration 1 Error: 1.121750 Iteration 2 Error: 0.273765 Iteration 3 Error: 0.079188 Iteration 4 Error: 0.033710 Align patch 7 18 left Iteration 1 Error: 0.490104 Iteration 2 Error: 0.054813 Iteration 3 Error: 0.009824 Align patch 8 17 left Iteration 1 Error: 0.491282 Iteration 2 Error: 0.069631 Iteration 3 Error: 0.013815 Align patch 9 16 left Iteration 1 Error: 0.969255 Iteration 2 Error: 0.126892 Iteration 3 Error: 0.021815 Align patch 10 15 left Iteration 1 Error: 0.467136 Iteration 2 Error: 0.088822 Iteration 3 Error: 0.022479 Align patch 11 14 left Iteration 1 Error: 0.897294 Iteration 2 Error: 0.261077 Iteration 3 Error: 0.056478 Iteration 4 Error: 0.030884 Align patch 12 13 left Iteration 1 Error: 0.622741 Iteration 2 Error: 0.102924 Iteration 3 Error: 0.015458 Align patch 13 12 left Iteration 1 Error: 0.603391 Iteration 2 Error: 0.131802 Iteration 3 Error: 0.022475 Align patch 14 11 left Iteration 1 Error: 0.630423 Iteration 2 Error: 0.129420 Iteration 3 Error: 0.025843 Align patch 15 10 left Iteration 1 Error: 0.710248 Iteration 2 Error: 0.085744 Iteration 3 Error: 0.025857 Align patch 16 9 left Iteration 1 Error: 0.864667 Iteration 2 Error: 0.138888 Iteration 3 Error: 0.037788 Align patch 17 8 left Iteration 1 Error: 0.611383 Iteration 2 Error: 0.110166 Iteration 3 Error: 0.036132 Align patch 18 7 left Iteration 1 Error: 0.604535 Iteration 2 Error: 0.121476 Iteration 3 Error: 0.028789 Align patch 19 6 left Iteration 1 Error: 0.569500 Iteration 2 Error: 0.102201 Iteration 3 Error: 0.017981 Align patch 20 5 left Iteration 1 Error: 0.800764 Iteration 2 Error: 0.130056 Iteration 3 Error: 0.023154 Align patch 21 4 left Iteration 1 Error: 0.639803 Iteration 2 Error: 0.099588 Iteration 3 Error: 0.022047 Align patch 22 3 left Iteration 1 Error: 0.647915 Iteration 2 Error: 0.090697 Iteration 3 Error: 0.024198 Align patch 23 2 left Iteration 1 Error: 0.603036 Iteration 2 Error: 0.114458 Iteration 3 Error: 0.029274 Align patch 24 1 left Iteration 1 Error: 0.819730 Iteration 2 Error: 0.171259 Iteration 3 Error: 0.029394 Align patch 25 0 left Iteration 1 Error: 0.285373 Iteration 2 Error: 0.098645 Iteration 3 Error: 0.047681 3D Fitting completed. Patch alignment time: 15.58(sec) Local motion has been corrected. Process thread exits. Computational time: 23.880774 sec Total time: 29.421576 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00012hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00012hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.738981s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00012hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.452053s ........................................ >>>>>>TIME<<<<<< FFT: 1.034850s Defocus_U Defocus_V Angle CCC 12429.70 12898.45 5.45 0.047000 Final Values Defocus_U Defocus_V Angle CCC 12453.14 12915.64 4.84 0.076776 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00012hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00012hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.736 Mean Std: 40.51 6.86 Num Hot pixels: 193 Hot pixel threshold: 81.65 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.145976 Iteration 2 Error: 0.173797 Iteration 3 Error: 0.040216 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.25 -0.26 ...... Frame ( 3) shift: -0.50 -0.52 ...... Frame ( 4) shift: -0.74 -0.78 ...... Frame ( 5) shift: -0.99 -1.04 ...... Frame ( 6) shift: -1.13 -1.17 ...... Frame ( 7) shift: -1.17 -1.17 ...... Frame ( 8) shift: -1.20 -1.17 ...... Frame ( 9) shift: -1.15 -1.10 ...... Frame ( 10) shift: -1.02 -0.96 ...... Frame ( 11) shift: -0.88 -0.82 ...... Frame ( 12) shift: -0.80 -0.69 ...... Frame ( 13) shift: -0.77 -0.57 ...... Frame ( 14) shift: -0.73 -0.45 ...... Frame ( 15) shift: -0.69 -0.34 ...... Frame ( 16) shift: -0.63 -0.22 ...... Frame ( 17) shift: -0.57 -0.10 ...... Frame ( 18) shift: -0.55 -0.01 ...... Frame ( 19) shift: -0.57 0.07 ...... Frame ( 20) shift: -0.59 0.14 ...... Frame ( 21) shift: -0.55 0.22 ...... Frame ( 22) shift: -0.45 0.29 ...... Frame ( 23) shift: -0.36 0.36 ...... Frame ( 24) shift: -0.35 0.39 ...... Frame ( 25) shift: -0.44 0.39 ...... Frame ( 26) shift: -0.52 0.38 ...... Frame ( 27) shift: -0.54 0.39 ...... Frame ( 28) shift: -0.49 0.40 ...... Frame ( 29) shift: -0.44 0.42 ...... Frame ( 30) shift: -0.40 0.44 ...... Frame ( 31) shift: -0.38 0.47 ...... Frame ( 32) shift: -0.37 0.50 ...... Frame ( 33) shift: -0.37 0.54 ...... Frame ( 34) shift: -0.40 0.58 ...... Frame ( 35) shift: -0.42 0.62 ...... Frame ( 36) shift: -0.41 0.66 ...... Frame ( 37) shift: -0.37 0.69 ...... Frame ( 38) shift: -0.33 0.72 ...... Frame ( 39) shift: -0.28 0.75 ...... Frame ( 40) shift: -0.24 0.79 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.782259 Iteration 2 Error: 0.900093 Iteration 3 Error: 0.655729 Iteration 4 Error: 0.468393 Iteration 5 Error: 0.276942 Align patch 1 24 left Iteration 1 Error: 3.306591 Iteration 2 Error: 0.531701 Iteration 3 Error: 0.127116 Iteration 4 Error: 0.036015 Align patch 2 23 left Iteration 1 Error: 1.843643 Iteration 2 Error: 0.368375 Iteration 3 Error: 0.156691 Iteration 4 Error: 0.068899 Iteration 5 Error: 0.057998 Align patch 2 23 left Iteration 1 Error: 2.382461 Iteration 2 Error: 0.378714 Iteration 3 Error: 0.083978 Iteration 4 Error: 0.020423 Align patch 3 22 left Iteration 1 Error: 1.787979 Iteration 2 Error: 0.282360 Iteration 3 Error: 0.095602 Iteration 4 Error: 0.039363 Align patch 4 21 left Iteration 1 Error: 0.724239 Iteration 2 Error: 0.167614 Iteration 3 Error: 0.032871 Align patch 5 20 left Iteration 1 Error: 0.659088 Iteration 2 Error: 0.101360 Iteration 3 Error: 0.025247 Align patch 6 19 left Iteration 1 Error: 2.798580 Iteration 2 Error: 0.885571 Iteration 3 Error: 0.364988 Iteration 4 Error: 0.226152 Iteration 5 Error: 0.130107 Align patch 6 19 left Iteration 1 Error: 2.688259 Iteration 2 Error: 0.367550 Iteration 3 Error: 0.091039 Iteration 4 Error: 0.036914 Align patch 7 18 left Iteration 1 Error: 1.369076 Iteration 2 Error: 0.358371 Iteration 3 Error: 0.113418 Iteration 4 Error: 0.045293 Align patch 8 17 left Iteration 1 Error: 0.781195 Iteration 2 Error: 0.133508 Iteration 3 Error: 0.040173 Align patch 9 16 left Iteration 1 Error: 0.598459 Iteration 2 Error: 0.105056 Iteration 3 Error: 0.018414 Align patch 10 15 left Iteration 1 Error: 0.624264 Iteration 2 Error: 0.082996 Iteration 3 Error: 0.024310 Align patch 11 14 left Iteration 1 Error: 0.876607 Iteration 2 Error: 0.268147 Iteration 3 Error: 0.092199 Iteration 4 Error: 0.035187 Align patch 12 13 left Iteration 1 Error: 0.897949 Iteration 2 Error: 0.215286 Iteration 3 Error: 0.088211 Iteration 4 Error: 0.034607 Align patch 13 12 left Iteration 1 Error: 0.475710 Iteration 2 Error: 0.088630 Iteration 3 Error: 0.022772 Align patch 14 11 left Iteration 1 Error: 0.722202 Iteration 2 Error: 0.154416 Iteration 3 Error: 0.069196 Iteration 4 Error: 0.019864 Align patch 15 10 left Iteration 1 Error: 0.650747 Iteration 2 Error: 0.132448 Iteration 3 Error: 0.040930 Align patch 16 9 left Iteration 1 Error: 0.912248 Iteration 2 Error: 0.164411 Iteration 3 Error: 0.040627 Align patch 17 8 left Iteration 1 Error: 0.837871 Iteration 2 Error: 0.075335 Iteration 3 Error: 0.018940 Align patch 18 7 left Iteration 1 Error: 0.884949 Iteration 2 Error: 0.070629 Iteration 3 Error: 0.016987 Align patch 19 6 left Iteration 1 Error: 0.931312 Iteration 2 Error: 0.152946 Iteration 3 Error: 0.033936 Align patch 20 5 left Iteration 1 Error: 1.388763 Iteration 2 Error: 0.178460 Iteration 3 Error: 0.048217 Align patch 21 4 left Iteration 1 Error: 0.665982 Iteration 2 Error: 0.114542 Iteration 3 Error: 0.018389 Align patch 22 3 left Iteration 1 Error: 0.740707 Iteration 2 Error: 0.100315 Iteration 3 Error: 0.018858 Align patch 23 2 left Iteration 1 Error: 0.923373 Iteration 2 Error: 0.112148 Iteration 3 Error: 0.027867 Align patch 24 1 left Iteration 1 Error: 0.659400 Iteration 2 Error: 0.089588 Iteration 3 Error: 0.016616 Align patch 25 0 left Iteration 1 Error: 1.007476 Iteration 2 Error: 0.115092 Iteration 3 Error: 0.023787 3D Fitting completed. Patch alignment time: 19.19(sec) Local motion has been corrected. Process thread exits. Computational time: 28.815403 sec Total time: 34.617237 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00012hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00012hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.644944s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00012hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.781179s ........................................ >>>>>>TIME<<<<<< FFT: 1.039962s Defocus_U Defocus_V Angle CCC 13537.08 14447.30 5.87 0.052674 Final Values Defocus_U Defocus_V Angle CCC 13551.14 14470.74 6.19 0.081096 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00012hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00012hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.003e-01 CC threshold: 0.737 Mean Std: 40.98 6.94 Num Hot pixels: 206 Hot pixel threshold: 82.63 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.589268 Iteration 2 Error: 0.118669 Iteration 3 Error: 0.028564 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.07 0.06 ...... Frame ( 3) shift: -0.15 0.11 ...... Frame ( 4) shift: -0.22 0.17 ...... Frame ( 5) shift: -0.30 0.22 ...... Frame ( 6) shift: -0.30 0.27 ...... Frame ( 7) shift: -0.24 0.29 ...... Frame ( 8) shift: -0.18 0.32 ...... Frame ( 9) shift: -0.12 0.34 ...... Frame ( 10) shift: -0.05 0.35 ...... Frame ( 11) shift: 0.01 0.37 ...... Frame ( 12) shift: 0.02 0.39 ...... Frame ( 13) shift: -0.03 0.41 ...... Frame ( 14) shift: -0.08 0.44 ...... Frame ( 15) shift: -0.07 0.47 ...... Frame ( 16) shift: 0.00 0.49 ...... Frame ( 17) shift: 0.08 0.51 ...... Frame ( 18) shift: 0.12 0.54 ...... Frame ( 19) shift: 0.14 0.57 ...... Frame ( 20) shift: 0.16 0.60 ...... Frame ( 21) shift: 0.17 0.65 ...... Frame ( 22) shift: 0.16 0.72 ...... Frame ( 23) shift: 0.15 0.79 ...... Frame ( 24) shift: 0.17 0.86 ...... Frame ( 25) shift: 0.21 0.95 ...... Frame ( 26) shift: 0.25 1.04 ...... Frame ( 27) shift: 0.31 1.10 ...... Frame ( 28) shift: 0.38 1.13 ...... Frame ( 29) shift: 0.45 1.17 ...... Frame ( 30) shift: 0.51 1.18 ...... Frame ( 31) shift: 0.56 1.18 ...... Frame ( 32) shift: 0.61 1.18 ...... Frame ( 33) shift: 0.64 1.19 ...... Frame ( 34) shift: 0.65 1.22 ...... Frame ( 35) shift: 0.66 1.24 ...... Frame ( 36) shift: 0.65 1.25 ...... Frame ( 37) shift: 0.61 1.25 ...... Frame ( 38) shift: 0.58 1.24 ...... Frame ( 39) shift: 0.54 1.24 ...... Frame ( 40) shift: 0.51 1.23 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.765137 Iteration 2 Error: 0.324551 Iteration 3 Error: 0.085207 Iteration 4 Error: 0.031234 Align patch 2 23 left Iteration 1 Error: 0.892010 Iteration 2 Error: 0.257731 Iteration 3 Error: 0.083756 Iteration 4 Error: 0.031732 Align patch 3 22 left Iteration 1 Error: 0.639529 Iteration 2 Error: 0.115876 Iteration 3 Error: 0.028778 Align patch 4 21 left Iteration 1 Error: 0.539375 Iteration 2 Error: 0.089937 Iteration 3 Error: 0.021646 Align patch 5 20 left Iteration 1 Error: 0.609654 Iteration 2 Error: 0.086440 Iteration 3 Error: 0.018800 Align patch 6 19 left Iteration 1 Error: 1.468094 Iteration 2 Error: 0.330620 Iteration 3 Error: 0.124217 Iteration 4 Error: 0.041349 Align patch 7 18 left Iteration 1 Error: 0.600935 Iteration 2 Error: 0.130734 Iteration 3 Error: 0.049213 Align patch 8 17 left Iteration 1 Error: 0.433911 Iteration 2 Error: 0.064005 Iteration 3 Error: 0.014120 Align patch 9 16 left Iteration 1 Error: 0.758403 Iteration 2 Error: 0.096682 Iteration 3 Error: 0.021051 Align patch 10 15 left Iteration 1 Error: 0.666164 Iteration 2 Error: 0.113971 Iteration 3 Error: 0.028548 Align patch 11 14 left Iteration 1 Error: 1.016280 Iteration 2 Error: 0.314753 Iteration 3 Error: 0.093164 Iteration 4 Error: 0.037741 Align patch 12 13 left Iteration 1 Error: 0.764860 Iteration 2 Error: 0.118353 Iteration 3 Error: 0.036248 Align patch 13 12 left Iteration 1 Error: 0.648389 Iteration 2 Error: 0.122008 Iteration 3 Error: 0.023997 Align patch 14 11 left Iteration 1 Error: 0.749591 Iteration 2 Error: 0.098458 Iteration 3 Error: 0.024929 Align patch 15 10 left Iteration 1 Error: 1.060565 Iteration 2 Error: 0.207147 Iteration 3 Error: 0.064458 Iteration 4 Error: 0.022185 Align patch 16 9 left Iteration 1 Error: 0.598071 Iteration 2 Error: 0.250661 Iteration 3 Error: 0.043043 Align patch 17 8 left Iteration 1 Error: 0.620116 Iteration 2 Error: 0.080187 Iteration 3 Error: 0.016561 Align patch 18 7 left Iteration 1 Error: 0.572145 Iteration 2 Error: 0.067082 Iteration 3 Error: 0.013502 Align patch 19 6 left Iteration 1 Error: 0.532946 Iteration 2 Error: 0.070238 Iteration 3 Error: 0.014453 Align patch 20 5 left Iteration 1 Error: 0.516182 Iteration 2 Error: 0.094432 Iteration 3 Error: 0.019129 Align patch 21 4 left Iteration 1 Error: 0.636615 Iteration 2 Error: 0.105263 Iteration 3 Error: 0.019245 Align patch 22 3 left Iteration 1 Error: 0.605697 Iteration 2 Error: 0.054765 Iteration 3 Error: 0.020596 Align patch 23 2 left Iteration 1 Error: 0.745902 Iteration 2 Error: 0.060481 Iteration 3 Error: 0.012359 Align patch 24 1 left Iteration 1 Error: 0.876291 Iteration 2 Error: 0.077208 Iteration 3 Error: 0.017508 Align patch 25 0 left Iteration 1 Error: 0.528218 Iteration 2 Error: 0.078749 Iteration 3 Error: 0.017940 3D Fitting completed. Patch alignment time: 15.86(sec) Local motion has been corrected. Process thread exits. Computational time: 24.049294 sec Total time: 29.827553 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00012hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00012hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.623743s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00012hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.973503s ........................................ >>>>>>TIME<<<<<< FFT: 0.918878s Defocus_U Defocus_V Angle CCC 15605.49 14859.40 84.75 0.050875 Final Values Defocus_U Defocus_V Angle CCC 15596.09 14878.19 84.44 0.078613 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00013hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00013hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.001e-01 CC threshold: 0.735 Mean Std: 40.03 6.79 Num Hot pixels: 197 Hot pixel threshold: 80.74 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.356668 Iteration 2 Error: 0.324667 Iteration 3 Error: 0.098735 Iteration 4 Error: 0.039522 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.12 -0.10 ...... Frame ( 3) shift: -0.23 -0.20 ...... Frame ( 4) shift: -0.35 -0.30 ...... Frame ( 5) shift: -0.46 -0.40 ...... Frame ( 6) shift: -0.53 -0.43 ...... Frame ( 7) shift: -0.54 -0.39 ...... Frame ( 8) shift: -0.56 -0.35 ...... Frame ( 9) shift: -0.55 -0.26 ...... Frame ( 10) shift: -0.52 -0.13 ...... Frame ( 11) shift: -0.48 -0.01 ...... Frame ( 12) shift: -0.43 0.15 ...... Frame ( 13) shift: -0.37 0.33 ...... Frame ( 14) shift: -0.31 0.51 ...... Frame ( 15) shift: -0.23 0.66 ...... Frame ( 16) shift: -0.15 0.79 ...... Frame ( 17) shift: -0.07 0.92 ...... Frame ( 18) shift: 0.00 1.03 ...... Frame ( 19) shift: 0.08 1.13 ...... Frame ( 20) shift: 0.15 1.24 ...... Frame ( 21) shift: 0.18 1.34 ...... Frame ( 22) shift: 0.14 1.46 ...... Frame ( 23) shift: 0.11 1.57 ...... Frame ( 24) shift: 0.11 1.69 ...... Frame ( 25) shift: 0.14 1.83 ...... Frame ( 26) shift: 0.18 1.97 ...... Frame ( 27) shift: 0.20 2.06 ...... Frame ( 28) shift: 0.21 2.13 ...... Frame ( 29) shift: 0.23 2.19 ...... Frame ( 30) shift: 0.22 2.26 ...... Frame ( 31) shift: 0.19 2.33 ...... Frame ( 32) shift: 0.16 2.39 ...... Frame ( 33) shift: 0.12 2.46 ...... Frame ( 34) shift: 0.07 2.52 ...... Frame ( 35) shift: 0.01 2.58 ...... Frame ( 36) shift: -0.01 2.64 ...... Frame ( 37) shift: 0.01 2.69 ...... Frame ( 38) shift: 0.02 2.75 ...... Frame ( 39) shift: 0.04 2.80 ...... Frame ( 40) shift: 0.06 2.86 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.214784 Iteration 2 Error: 0.707131 Iteration 3 Error: 0.341081 Iteration 4 Error: 0.160983 Iteration 5 Error: 0.102799 Align patch 1 24 left Iteration 1 Error: 1.552385 Iteration 2 Error: 0.291895 Iteration 3 Error: 0.102405 Iteration 4 Error: 0.029450 Align patch 2 23 left Iteration 1 Error: 1.634516 Iteration 2 Error: 0.453523 Iteration 3 Error: 0.146043 Iteration 4 Error: 0.064534 Iteration 5 Error: 0.038054 Align patch 3 22 left Iteration 1 Error: 0.813954 Iteration 2 Error: 0.143096 Iteration 3 Error: 0.053910 Iteration 4 Error: 0.027057 Align patch 4 21 left Iteration 1 Error: 0.704711 Iteration 2 Error: 0.077740 Iteration 3 Error: 0.014956 Align patch 5 20 left Iteration 1 Error: 0.644751 Iteration 2 Error: 0.158760 Iteration 3 Error: 0.039219 Align patch 6 19 left Iteration 1 Error: 1.108366 Iteration 2 Error: 0.270608 Iteration 3 Error: 0.082568 Iteration 4 Error: 0.042630 Align patch 7 18 left Iteration 1 Error: 0.862943 Iteration 2 Error: 0.280900 Iteration 3 Error: 0.167674 Iteration 4 Error: 0.086904 Iteration 5 Error: 0.041858 Align patch 8 17 left Iteration 1 Error: 0.714883 Iteration 2 Error: 0.198214 Iteration 3 Error: 0.069211 Iteration 4 Error: 0.034317 Align patch 9 16 left Iteration 1 Error: 0.533616 Iteration 2 Error: 0.067110 Iteration 3 Error: 0.022795 Align patch 10 15 left Iteration 1 Error: 0.760543 Iteration 2 Error: 0.123163 Iteration 3 Error: 0.035609 Align patch 11 14 left Iteration 1 Error: 0.629298 Iteration 2 Error: 0.148386 Iteration 3 Error: 0.051478 Iteration 4 Error: 0.023634 Align patch 12 13 left Iteration 1 Error: 1.203049 Iteration 2 Error: 0.226939 Iteration 3 Error: 0.063629 Iteration 4 Error: 0.030425 Align patch 13 12 left Iteration 1 Error: 0.668692 Iteration 2 Error: 0.129476 Iteration 3 Error: 0.036859 Align patch 14 11 left Iteration 1 Error: 0.630289 Iteration 2 Error: 0.084381 Iteration 3 Error: 0.032051 Align patch 15 10 left Iteration 1 Error: 0.697768 Iteration 2 Error: 0.136969 Iteration 3 Error: 0.041968 Align patch 16 9 left Iteration 1 Error: 0.800777 Iteration 2 Error: 0.139260 Iteration 3 Error: 0.029195 Align patch 17 8 left Iteration 1 Error: 0.875862 Iteration 2 Error: 0.208403 Iteration 3 Error: 0.045604 Align patch 18 7 left Iteration 1 Error: 1.110635 Iteration 2 Error: 0.229165 Iteration 3 Error: 0.065387 Iteration 4 Error: 0.047196 Align patch 19 6 left Iteration 1 Error: 0.563021 Iteration 2 Error: 0.146367 Iteration 3 Error: 0.049298 Align patch 20 5 left Iteration 1 Error: 0.659957 Iteration 2 Error: 0.186153 Iteration 3 Error: 0.062175 Iteration 4 Error: 0.016589 Align patch 21 4 left Iteration 1 Error: 0.861333 Iteration 2 Error: 0.135927 Iteration 3 Error: 0.053938 Iteration 4 Error: 0.014883 Align patch 22 3 left Iteration 1 Error: 0.859373 Iteration 2 Error: 0.128010 Iteration 3 Error: 0.024786 Align patch 23 2 left Iteration 1 Error: 0.819558 Iteration 2 Error: 0.147034 Iteration 3 Error: 0.034782 Align patch 24 1 left Iteration 1 Error: 0.813786 Iteration 2 Error: 0.241293 Iteration 3 Error: 0.049971 Align patch 25 0 left Iteration 1 Error: 1.024308 Iteration 2 Error: 0.236805 Iteration 3 Error: 0.056141 Iteration 4 Error: 0.024866 3D Fitting completed. Patch alignment time: 16.52(sec) Local motion has been corrected. Process thread exits. Computational time: 25.103971 sec Total time: 30.520321 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00013hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00013hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.592722s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00013hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.622811s ........................................ >>>>>>TIME<<<<<< FFT: 1.014691s Defocus_U Defocus_V Angle CCC 9603.52 10427.74 13.77 0.039303 Final Values Defocus_U Defocus_V Angle CCC 9606.65 10437.12 13.77 0.069306 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00013hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00013hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 39.93 6.79 Num Hot pixels: 217 Hot pixel threshold: 80.68 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.064092 Iteration 2 Error: 0.206358 Iteration 3 Error: 0.050062 Iteration 4 Error: 0.021792 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.23 -0.13 ...... Frame ( 3) shift: -0.45 -0.27 ...... Frame ( 4) shift: -0.68 -0.40 ...... Frame ( 5) shift: -0.91 -0.54 ...... Frame ( 6) shift: -1.06 -0.60 ...... Frame ( 7) shift: -1.13 -0.60 ...... Frame ( 8) shift: -1.20 -0.60 ...... Frame ( 9) shift: -1.20 -0.54 ...... Frame ( 10) shift: -1.14 -0.41 ...... Frame ( 11) shift: -1.07 -0.29 ...... Frame ( 12) shift: -1.03 -0.17 ...... Frame ( 13) shift: -1.04 -0.06 ...... Frame ( 14) shift: -1.04 0.05 ...... Frame ( 15) shift: -1.01 0.16 ...... Frame ( 16) shift: -0.96 0.28 ...... Frame ( 17) shift: -0.91 0.40 ...... Frame ( 18) shift: -0.85 0.51 ...... Frame ( 19) shift: -0.80 0.60 ...... Frame ( 20) shift: -0.74 0.69 ...... Frame ( 21) shift: -0.70 0.77 ...... Frame ( 22) shift: -0.66 0.85 ...... Frame ( 23) shift: -0.62 0.93 ...... Frame ( 24) shift: -0.59 0.99 ...... Frame ( 25) shift: -0.58 1.03 ...... Frame ( 26) shift: -0.57 1.06 ...... Frame ( 27) shift: -0.56 1.10 ...... Frame ( 28) shift: -0.55 1.15 ...... Frame ( 29) shift: -0.54 1.20 ...... Frame ( 30) shift: -0.53 1.25 ...... Frame ( 31) shift: -0.50 1.30 ...... Frame ( 32) shift: -0.48 1.35 ...... Frame ( 33) shift: -0.48 1.40 ...... Frame ( 34) shift: -0.52 1.45 ...... Frame ( 35) shift: -0.55 1.50 ...... Frame ( 36) shift: -0.56 1.53 ...... Frame ( 37) shift: -0.54 1.52 ...... Frame ( 38) shift: -0.52 1.52 ...... Frame ( 39) shift: -0.51 1.51 ...... Frame ( 40) shift: -0.49 1.51 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.341764 Iteration 2 Error: 0.440601 Iteration 3 Error: 0.209941 Iteration 4 Error: 0.090056 Iteration 5 Error: 0.042975 Align patch 2 23 left Iteration 1 Error: 1.246502 Iteration 2 Error: 0.331382 Iteration 3 Error: 0.096031 Iteration 4 Error: 0.035487 Align patch 3 22 left Iteration 1 Error: 0.618013 Iteration 2 Error: 0.138391 Iteration 3 Error: 0.029696 Align patch 4 21 left Iteration 1 Error: 0.655673 Iteration 2 Error: 0.071208 Iteration 3 Error: 0.015843 Align patch 5 20 left Iteration 1 Error: 0.881864 Iteration 2 Error: 0.128135 Iteration 3 Error: 0.028906 Align patch 6 19 left Iteration 1 Error: 1.259055 Iteration 2 Error: 0.712374 Iteration 3 Error: 0.288001 Iteration 4 Error: 0.138034 Iteration 5 Error: 0.059651 Align patch 6 19 left Iteration 1 Error: 1.866803 Iteration 2 Error: 0.263968 Iteration 3 Error: 0.074362 Iteration 4 Error: 0.023644 Align patch 7 18 left Iteration 1 Error: 1.245542 Iteration 2 Error: 0.230083 Iteration 3 Error: 0.069809 Iteration 4 Error: 0.029596 Align patch 8 17 left Iteration 1 Error: 0.703832 Iteration 2 Error: 0.173417 Iteration 3 Error: 0.056021 Iteration 4 Error: 0.027381 Align patch 9 16 left Iteration 1 Error: 0.532990 Iteration 2 Error: 0.095534 Iteration 3 Error: 0.021908 Align patch 10 15 left Iteration 1 Error: 1.025579 Iteration 2 Error: 0.197394 Iteration 3 Error: 0.058729 Iteration 4 Error: 0.017125 Align patch 11 14 left Iteration 1 Error: 1.432001 Iteration 2 Error: 0.417612 Iteration 3 Error: 0.170585 Iteration 4 Error: 0.087677 Iteration 5 Error: 0.049011 Align patch 12 13 left Iteration 1 Error: 0.591804 Iteration 2 Error: 0.184851 Iteration 3 Error: 0.047543 Align patch 13 12 left Iteration 1 Error: 0.898986 Iteration 2 Error: 0.210595 Iteration 3 Error: 0.085139 Iteration 4 Error: 0.027329 Align patch 14 11 left Iteration 1 Error: 0.566268 Iteration 2 Error: 0.121367 Iteration 3 Error: 0.040187 Align patch 15 10 left Iteration 1 Error: 0.789167 Iteration 2 Error: 0.130756 Iteration 3 Error: 0.036841 Align patch 16 9 left Iteration 1 Error: 1.382662 Iteration 2 Error: 0.401118 Iteration 3 Error: 0.186621 Iteration 4 Error: 0.107990 Iteration 5 Error: 0.054795 Align patch 16 9 left Iteration 1 Error: 1.472954 Iteration 2 Error: 0.233677 Iteration 3 Error: 0.063093 Iteration 4 Error: 0.016237 Align patch 17 8 left Iteration 1 Error: 0.854867 Iteration 2 Error: 0.235227 Iteration 3 Error: 0.085323 Iteration 4 Error: 0.036766 Align patch 18 7 left Iteration 1 Error: 0.649029 Iteration 2 Error: 0.112292 Iteration 3 Error: 0.025385 Align patch 19 6 left Iteration 1 Error: 0.668482 Iteration 2 Error: 0.126213 Iteration 3 Error: 0.024913 Align patch 20 5 left Iteration 1 Error: 0.619857 Iteration 2 Error: 0.163824 Iteration 3 Error: 0.027422 Align patch 21 4 left Iteration 1 Error: 0.914659 Iteration 2 Error: 0.161684 Iteration 3 Error: 0.025881 Align patch 22 3 left Iteration 1 Error: 1.037290 Iteration 2 Error: 0.113620 Iteration 3 Error: 0.015244 Align patch 23 2 left Iteration 1 Error: 1.259949 Iteration 2 Error: 0.123222 Iteration 3 Error: 0.026139 Align patch 24 1 left Iteration 1 Error: 1.042649 Iteration 2 Error: 0.169802 Iteration 3 Error: 0.037165 Align patch 25 0 left Iteration 1 Error: 1.015762 Iteration 2 Error: 0.156762 Iteration 3 Error: 0.042647 3D Fitting completed. Patch alignment time: 18.64(sec) Local motion has been corrected. Process thread exits. Computational time: 27.077696 sec Total time: 33.201775 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00013hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00013hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.742061s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00013hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.560687s ........................................ >>>>>>TIME<<<<<< FFT: 1.047720s Defocus_U Defocus_V Angle CCC 10796.88 10359.38 87.78 0.042137 Final Values Defocus_U Defocus_V Angle CCC 10812.50 10365.65 88.10 0.071155 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00013hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00013hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 40.73 6.87 Num Hot pixels: 211 Hot pixel threshold: 81.97 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.046423 Iteration 2 Error: 0.242980 Iteration 3 Error: 0.055384 Iteration 4 Error: 0.016471 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.18 -0.16 ...... Frame ( 3) shift: -0.35 -0.32 ...... Frame ( 4) shift: -0.53 -0.47 ...... Frame ( 5) shift: -0.71 -0.63 ...... Frame ( 6) shift: -0.81 -0.71 ...... Frame ( 7) shift: -0.84 -0.70 ...... Frame ( 8) shift: -0.88 -0.69 ...... Frame ( 9) shift: -0.90 -0.64 ...... Frame ( 10) shift: -0.91 -0.55 ...... Frame ( 11) shift: -0.92 -0.46 ...... Frame ( 12) shift: -0.95 -0.32 ...... Frame ( 13) shift: -0.99 -0.14 ...... Frame ( 14) shift: -1.03 0.04 ...... Frame ( 15) shift: -1.08 0.15 ...... Frame ( 16) shift: -1.15 0.19 ...... Frame ( 17) shift: -1.21 0.22 ...... Frame ( 18) shift: -1.21 0.29 ...... Frame ( 19) shift: -1.14 0.39 ...... Frame ( 20) shift: -1.07 0.49 ...... Frame ( 21) shift: -1.00 0.58 ...... Frame ( 22) shift: -0.93 0.67 ...... Frame ( 23) shift: -0.86 0.77 ...... Frame ( 24) shift: -0.88 0.85 ...... Frame ( 25) shift: -0.99 0.92 ...... Frame ( 26) shift: -1.10 0.99 ...... Frame ( 27) shift: -1.14 1.07 ...... Frame ( 28) shift: -1.12 1.16 ...... Frame ( 29) shift: -1.10 1.25 ...... Frame ( 30) shift: -1.08 1.37 ...... Frame ( 31) shift: -1.07 1.50 ...... Frame ( 32) shift: -1.05 1.64 ...... Frame ( 33) shift: -1.04 1.74 ...... Frame ( 34) shift: -1.04 1.80 ...... Frame ( 35) shift: -1.03 1.86 ...... Frame ( 36) shift: -1.03 1.88 ...... Frame ( 37) shift: -1.04 1.86 ...... Frame ( 38) shift: -1.05 1.84 ...... Frame ( 39) shift: -1.06 1.82 ...... Frame ( 40) shift: -1.07 1.80 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.379047 Iteration 2 Error: 0.418383 Iteration 3 Error: 0.180072 Iteration 4 Error: 0.075461 Iteration 5 Error: 0.030768 Align patch 2 23 left Iteration 1 Error: 1.276173 Iteration 2 Error: 0.220115 Iteration 3 Error: 0.065079 Iteration 4 Error: 0.036178 Align patch 3 22 left Iteration 1 Error: 1.015447 Iteration 2 Error: 0.179421 Iteration 3 Error: 0.040474 Align patch 4 21 left Iteration 1 Error: 0.518481 Iteration 2 Error: 0.059926 Iteration 3 Error: 0.016239 Align patch 5 20 left Iteration 1 Error: 0.835984 Iteration 2 Error: 0.106608 Iteration 3 Error: 0.021066 Align patch 6 19 left Iteration 1 Error: 1.113390 Iteration 2 Error: 0.335340 Iteration 3 Error: 0.103441 Iteration 4 Error: 0.041272 Align patch 7 18 left Iteration 1 Error: 1.155943 Iteration 2 Error: 0.308551 Iteration 3 Error: 0.092935 Iteration 4 Error: 0.040501 Align patch 8 17 left Iteration 1 Error: 0.702431 Iteration 2 Error: 0.102528 Iteration 3 Error: 0.019639 Align patch 9 16 left Iteration 1 Error: 0.473551 Iteration 2 Error: 0.093220 Iteration 3 Error: 0.018147 Align patch 10 15 left Iteration 1 Error: 0.822161 Iteration 2 Error: 0.140661 Iteration 3 Error: 0.029359 Align patch 11 14 left Iteration 1 Error: 1.227835 Iteration 2 Error: 0.215250 Iteration 3 Error: 0.075590 Iteration 4 Error: 0.029475 Align patch 12 13 left Iteration 1 Error: 0.614845 Iteration 2 Error: 0.263569 Iteration 3 Error: 0.073471 Iteration 4 Error: 0.037948 Align patch 13 12 left Iteration 1 Error: 1.097081 Iteration 2 Error: 0.144063 Iteration 3 Error: 0.029245 Align patch 14 11 left Iteration 1 Error: 0.673492 Iteration 2 Error: 0.122386 Iteration 3 Error: 0.022510 Align patch 15 10 left Iteration 1 Error: 0.519992 Iteration 2 Error: 0.090355 Iteration 3 Error: 0.015833 Align patch 16 9 left Iteration 1 Error: 1.019196 Iteration 2 Error: 0.198299 Iteration 3 Error: 0.065353 Iteration 4 Error: 0.028752 Align patch 17 8 left Iteration 1 Error: 0.873827 Iteration 2 Error: 0.118873 Iteration 3 Error: 0.041566 Align patch 18 7 left Iteration 1 Error: 0.583674 Iteration 2 Error: 0.056136 Iteration 3 Error: 0.016181 Align patch 19 6 left Iteration 1 Error: 0.574492 Iteration 2 Error: 0.174922 Iteration 3 Error: 0.036527 Align patch 20 5 left Iteration 1 Error: 1.001026 Iteration 2 Error: 0.193712 Iteration 3 Error: 0.039372 Align patch 21 4 left Iteration 1 Error: 0.558792 Iteration 2 Error: 0.181415 Iteration 3 Error: 0.061852 Iteration 4 Error: 0.024491 Align patch 22 3 left Iteration 1 Error: 0.664255 Iteration 2 Error: 0.135377 Iteration 3 Error: 0.053058 Iteration 4 Error: 0.012909 Align patch 23 2 left Iteration 1 Error: 0.648220 Iteration 2 Error: 0.125207 Iteration 3 Error: 0.026385 Align patch 24 1 left Iteration 1 Error: 1.046582 Iteration 2 Error: 0.194049 Iteration 3 Error: 0.055092 Iteration 4 Error: 0.013305 Align patch 25 0 left Iteration 1 Error: 0.869893 Iteration 2 Error: 0.159575 Iteration 3 Error: 0.020874 3D Fitting completed. Patch alignment time: 16.18(sec) Local motion has been corrected. Process thread exits. Computational time: 24.886314 sec Total time: 30.557013 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00013hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00013hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.775222s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00013hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.563111s ........................................ >>>>>>TIME<<<<<< FFT: 1.373208s Defocus_U Defocus_V Angle CCC 10673.84 11525.40 5.64 0.046494 Final Values Defocus_U Defocus_V Angle CCC 10689.47 11550.41 5.33 0.081472 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00013hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00013hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 40.90 6.90 Num Hot pixels: 208 Hot pixel threshold: 82.28 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.022413 Iteration 2 Error: 0.164710 Iteration 3 Error: 0.037742 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.23 -0.24 ...... Frame ( 3) shift: -0.46 -0.48 ...... Frame ( 4) shift: -0.70 -0.72 ...... Frame ( 5) shift: -0.93 -0.96 ...... Frame ( 6) shift: -1.04 -1.02 ...... Frame ( 7) shift: -1.02 -0.92 ...... Frame ( 8) shift: -1.01 -0.82 ...... Frame ( 9) shift: -1.01 -0.73 ...... Frame ( 10) shift: -1.01 -0.65 ...... Frame ( 11) shift: -1.01 -0.57 ...... Frame ( 12) shift: -0.98 -0.50 ...... Frame ( 13) shift: -0.92 -0.44 ...... Frame ( 14) shift: -0.86 -0.37 ...... Frame ( 15) shift: -0.84 -0.30 ...... Frame ( 16) shift: -0.84 -0.22 ...... Frame ( 17) shift: -0.85 -0.13 ...... Frame ( 18) shift: -0.86 -0.06 ...... Frame ( 19) shift: -0.88 0.01 ...... Frame ( 20) shift: -0.90 0.08 ...... Frame ( 21) shift: -0.86 0.16 ...... Frame ( 22) shift: -0.77 0.24 ...... Frame ( 23) shift: -0.68 0.33 ...... Frame ( 24) shift: -0.68 0.39 ...... Frame ( 25) shift: -0.75 0.43 ...... Frame ( 26) shift: -0.83 0.46 ...... Frame ( 27) shift: -0.85 0.51 ...... Frame ( 28) shift: -0.81 0.56 ...... Frame ( 29) shift: -0.77 0.62 ...... Frame ( 30) shift: -0.73 0.67 ...... Frame ( 31) shift: -0.70 0.73 ...... Frame ( 32) shift: -0.66 0.78 ...... Frame ( 33) shift: -0.65 0.82 ...... Frame ( 34) shift: -0.66 0.86 ...... Frame ( 35) shift: -0.68 0.89 ...... Frame ( 36) shift: -0.71 0.90 ...... Frame ( 37) shift: -0.77 0.90 ...... Frame ( 38) shift: -0.82 0.90 ...... Frame ( 39) shift: -0.87 0.90 ...... Frame ( 40) shift: -0.92 0.90 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.884073 Iteration 2 Error: 0.256395 Iteration 3 Error: 0.067031 Iteration 4 Error: 0.021731 Align patch 2 23 left Iteration 1 Error: 1.294919 Iteration 2 Error: 0.183920 Iteration 3 Error: 0.063709 Iteration 4 Error: 0.024797 Align patch 3 22 left Iteration 1 Error: 0.526584 Iteration 2 Error: 0.074009 Iteration 3 Error: 0.018540 Align patch 4 21 left Iteration 1 Error: 0.445387 Iteration 2 Error: 0.086286 Iteration 3 Error: 0.014726 Align patch 5 20 left Iteration 1 Error: 0.531650 Iteration 2 Error: 0.086105 Iteration 3 Error: 0.025799 Align patch 6 19 left Iteration 1 Error: 1.998121 Iteration 2 Error: 0.238620 Iteration 3 Error: 0.071812 Iteration 4 Error: 0.025913 Align patch 7 18 left Iteration 1 Error: 1.282371 Iteration 2 Error: 0.188424 Iteration 3 Error: 0.047592 Align patch 8 17 left Iteration 1 Error: 0.711828 Iteration 2 Error: 0.157983 Iteration 3 Error: 0.035905 Align patch 9 16 left Iteration 1 Error: 0.831717 Iteration 2 Error: 0.191578 Iteration 3 Error: 0.047741 Align patch 10 15 left Iteration 1 Error: 0.489605 Iteration 2 Error: 0.069086 Iteration 3 Error: 0.012471 Align patch 11 14 left Iteration 1 Error: 0.910020 Iteration 2 Error: 0.241381 Iteration 3 Error: 0.093197 Iteration 4 Error: 0.041457 Align patch 12 13 left Iteration 1 Error: 0.488321 Iteration 2 Error: 0.085194 Iteration 3 Error: 0.029709 Align patch 13 12 left Iteration 1 Error: 0.703608 Iteration 2 Error: 0.119816 Iteration 3 Error: 0.031394 Align patch 14 11 left Iteration 1 Error: 0.569548 Iteration 2 Error: 0.100553 Iteration 3 Error: 0.021222 Align patch 15 10 left Iteration 1 Error: 0.738647 Iteration 2 Error: 0.071913 Iteration 3 Error: 0.021827 Align patch 16 9 left Iteration 1 Error: 1.182245 Iteration 2 Error: 0.139771 Iteration 3 Error: 0.048445 Align patch 17 8 left Iteration 1 Error: 0.694013 Iteration 2 Error: 0.136231 Iteration 3 Error: 0.041047 Align patch 18 7 left Iteration 1 Error: 0.850967 Iteration 2 Error: 0.124623 Iteration 3 Error: 0.021210 Align patch 19 6 left Iteration 1 Error: 0.696331 Iteration 2 Error: 0.123494 Iteration 3 Error: 0.018933 Align patch 20 5 left Iteration 1 Error: 0.948152 Iteration 2 Error: 0.092057 Iteration 3 Error: 0.017463 Align patch 21 4 left Iteration 1 Error: 0.703611 Iteration 2 Error: 0.116027 Iteration 3 Error: 0.026745 Align patch 22 3 left Iteration 1 Error: 0.774234 Iteration 2 Error: 0.146842 Iteration 3 Error: 0.030346 Align patch 23 2 left Iteration 1 Error: 0.866879 Iteration 2 Error: 0.280043 Iteration 3 Error: 0.106629 Iteration 4 Error: 0.047434 Align patch 24 1 left Iteration 1 Error: 1.503810 Iteration 2 Error: 0.256244 Iteration 3 Error: 0.058256 Iteration 4 Error: 0.017116 Align patch 25 0 left Iteration 1 Error: 0.799942 Iteration 2 Error: 0.133681 Iteration 3 Error: 0.028382 3D Fitting completed. Patch alignment time: 16.27(sec) Local motion has been corrected. Process thread exits. Computational time: 25.238169 sec Total time: 31.051090 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00013hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00013hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.528073s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00013hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.790020s ........................................ >>>>>>TIME<<<<<< FFT: 0.966139s Defocus_U Defocus_V Angle CCC 13730.48 13007.80 84.22 0.050249 Final Values Defocus_U Defocus_V Angle CCC 13730.48 13032.81 83.59 0.082328 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00014hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00014hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.002e-01 CC threshold: 0.736 Mean Std: 40.01 6.88 Num Hot pixels: 200 Hot pixel threshold: 81.27 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.162189 Iteration 2 Error: 0.227546 Iteration 3 Error: 0.056412 Iteration 4 Error: 0.019614 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.05 -0.17 ...... Frame ( 3) shift: -0.09 -0.33 ...... Frame ( 4) shift: -0.14 -0.50 ...... Frame ( 5) shift: -0.18 -0.67 ...... Frame ( 6) shift: -0.20 -0.74 ...... Frame ( 7) shift: -0.19 -0.70 ...... Frame ( 8) shift: -0.17 -0.67 ...... Frame ( 9) shift: -0.15 -0.60 ...... Frame ( 10) shift: -0.13 -0.48 ...... Frame ( 11) shift: -0.10 -0.36 ...... Frame ( 12) shift: -0.08 -0.25 ...... Frame ( 13) shift: -0.06 -0.16 ...... Frame ( 14) shift: -0.05 -0.07 ...... Frame ( 15) shift: -0.01 0.04 ...... Frame ( 16) shift: 0.08 0.16 ...... Frame ( 17) shift: 0.16 0.29 ...... Frame ( 18) shift: 0.26 0.41 ...... Frame ( 19) shift: 0.35 0.54 ...... Frame ( 20) shift: 0.45 0.67 ...... Frame ( 21) shift: 0.49 0.76 ...... Frame ( 22) shift: 0.47 0.80 ...... Frame ( 23) shift: 0.45 0.84 ...... Frame ( 24) shift: 0.44 0.88 ...... Frame ( 25) shift: 0.45 0.92 ...... Frame ( 26) shift: 0.45 0.96 ...... Frame ( 27) shift: 0.49 0.98 ...... Frame ( 28) shift: 0.55 0.99 ...... Frame ( 29) shift: 0.62 1.00 ...... Frame ( 30) shift: 0.64 1.05 ...... Frame ( 31) shift: 0.63 1.14 ...... Frame ( 32) shift: 0.61 1.23 ...... Frame ( 33) shift: 0.60 1.30 ...... Frame ( 34) shift: 0.59 1.35 ...... Frame ( 35) shift: 0.59 1.41 ...... Frame ( 36) shift: 0.64 1.46 ...... Frame ( 37) shift: 0.75 1.51 ...... Frame ( 38) shift: 0.86 1.56 ...... Frame ( 39) shift: 0.96 1.61 ...... Frame ( 40) shift: 1.07 1.66 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.754067 Iteration 2 Error: 0.440009 Iteration 3 Error: 0.116754 Iteration 4 Error: 0.048454 Align patch 2 23 left Iteration 1 Error: 1.437558 Iteration 2 Error: 0.303761 Iteration 3 Error: 0.076237 Iteration 4 Error: 0.040915 Align patch 3 22 left Iteration 1 Error: 1.123400 Iteration 2 Error: 0.099127 Iteration 3 Error: 0.027429 Align patch 4 21 left Iteration 1 Error: 0.569010 Iteration 2 Error: 0.079292 Iteration 3 Error: 0.014474 Align patch 5 20 left Iteration 1 Error: 0.410700 Iteration 2 Error: 0.056157 Iteration 3 Error: 0.012895 Align patch 6 19 left Iteration 1 Error: 1.455705 Iteration 2 Error: 0.460492 Iteration 3 Error: 0.217003 Iteration 4 Error: 0.091306 Iteration 5 Error: 0.037833 Align patch 7 18 left Iteration 1 Error: 0.947858 Iteration 2 Error: 0.160615 Iteration 3 Error: 0.051794 Iteration 4 Error: 0.030348 Align patch 8 17 left Iteration 1 Error: 0.481912 Iteration 2 Error: 0.066960 Iteration 3 Error: 0.012172 Align patch 9 16 left Iteration 1 Error: 0.611636 Iteration 2 Error: 0.057892 Iteration 3 Error: 0.010423 Align patch 10 15 left Iteration 1 Error: 0.529755 Iteration 2 Error: 0.059937 Iteration 3 Error: 0.010227 Align patch 11 14 left Iteration 1 Error: 0.769747 Iteration 2 Error: 0.248900 Iteration 3 Error: 0.082787 Iteration 4 Error: 0.027649 Align patch 12 13 left Iteration 1 Error: 0.835843 Iteration 2 Error: 0.202018 Iteration 3 Error: 0.068993 Iteration 4 Error: 0.025352 Align patch 13 12 left Iteration 1 Error: 0.804462 Iteration 2 Error: 0.114481 Iteration 3 Error: 0.051904 Iteration 4 Error: 0.019623 Align patch 14 11 left Iteration 1 Error: 0.633758 Iteration 2 Error: 0.134923 Iteration 3 Error: 0.032057 Align patch 15 10 left Iteration 1 Error: 0.631371 Iteration 2 Error: 0.053933 Iteration 3 Error: 0.015656 Align patch 16 9 left Iteration 1 Error: 1.308177 Iteration 2 Error: 0.109545 Iteration 3 Error: 0.043917 Align patch 17 8 left Iteration 1 Error: 0.643156 Iteration 2 Error: 0.117395 Iteration 3 Error: 0.033186 Align patch 18 7 left Iteration 1 Error: 0.775108 Iteration 2 Error: 0.130479 Iteration 3 Error: 0.024578 Align patch 19 6 left Iteration 1 Error: 0.435965 Iteration 2 Error: 0.050214 Iteration 3 Error: 0.009422 Align patch 20 5 left Iteration 1 Error: 0.482566 Iteration 2 Error: 0.070175 Iteration 3 Error: 0.012146 Align patch 21 4 left Iteration 1 Error: 1.030815 Iteration 2 Error: 0.123742 Iteration 3 Error: 0.019896 Align patch 22 3 left Iteration 1 Error: 0.844308 Iteration 2 Error: 0.096912 Iteration 3 Error: 0.019666 Align patch 23 2 left Iteration 1 Error: 0.941102 Iteration 2 Error: 0.133779 Iteration 3 Error: 0.032359 Align patch 24 1 left Iteration 1 Error: 0.647402 Iteration 2 Error: 0.132759 Iteration 3 Error: 0.035260 Align patch 25 0 left Iteration 1 Error: 0.431636 Iteration 2 Error: 0.092949 Iteration 3 Error: 0.022387 3D Fitting completed. Patch alignment time: 15.27(sec) Local motion has been corrected. Process thread exits. Computational time: 24.105936 sec Total time: 31.588875 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00014hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00014hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.586717s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00014hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.545898s ........................................ >>>>>>TIME<<<<<< FFT: 1.006310s Defocus_U Defocus_V Angle CCC 11652.35 12507.82 13.41 0.054955 Final Values Defocus_U Defocus_V Angle CCC 11678.92 12512.51 13.73 0.090892 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00014hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00014hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.002e-01 CC threshold: 0.736 Mean Std: 39.97 6.86 Num Hot pixels: 222 Hot pixel threshold: 81.13 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.936016 Iteration 2 Error: 0.153300 Iteration 3 Error: 0.035687 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.15 -0.12 ...... Frame ( 3) shift: -0.29 -0.25 ...... Frame ( 4) shift: -0.44 -0.37 ...... Frame ( 5) shift: -0.58 -0.49 ...... Frame ( 6) shift: -0.66 -0.55 ...... Frame ( 7) shift: -0.67 -0.54 ...... Frame ( 8) shift: -0.68 -0.52 ...... Frame ( 9) shift: -0.66 -0.46 ...... Frame ( 10) shift: -0.62 -0.35 ...... Frame ( 11) shift: -0.57 -0.24 ...... Frame ( 12) shift: -0.59 -0.12 ...... Frame ( 13) shift: -0.67 0.01 ...... Frame ( 14) shift: -0.75 0.14 ...... Frame ( 15) shift: -0.77 0.27 ...... Frame ( 16) shift: -0.73 0.41 ...... Frame ( 17) shift: -0.68 0.55 ...... Frame ( 18) shift: -0.64 0.62 ...... Frame ( 19) shift: -0.61 0.63 ...... Frame ( 20) shift: -0.58 0.64 ...... Frame ( 21) shift: -0.59 0.69 ...... Frame ( 22) shift: -0.66 0.80 ...... Frame ( 23) shift: -0.72 0.91 ...... Frame ( 24) shift: -0.77 0.98 ...... Frame ( 25) shift: -0.80 1.03 ...... Frame ( 26) shift: -0.83 1.08 ...... Frame ( 27) shift: -0.86 1.10 ...... Frame ( 28) shift: -0.89 1.10 ...... Frame ( 29) shift: -0.92 1.10 ...... Frame ( 30) shift: -0.93 1.13 ...... Frame ( 31) shift: -0.92 1.21 ...... Frame ( 32) shift: -0.90 1.28 ...... Frame ( 33) shift: -0.89 1.35 ...... Frame ( 34) shift: -0.87 1.41 ...... Frame ( 35) shift: -0.86 1.48 ...... Frame ( 36) shift: -0.82 1.52 ...... Frame ( 37) shift: -0.77 1.52 ...... Frame ( 38) shift: -0.72 1.53 ...... Frame ( 39) shift: -0.67 1.54 ...... Frame ( 40) shift: -0.62 1.55 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.380020 Iteration 2 Error: 0.221784 Iteration 3 Error: 0.060923 Iteration 4 Error: 0.015090 Align patch 2 23 left Iteration 1 Error: 0.749049 Iteration 2 Error: 0.143672 Iteration 3 Error: 0.031749 Align patch 3 22 left Iteration 1 Error: 0.573134 Iteration 2 Error: 0.065551 Iteration 3 Error: 0.014641 Align patch 4 21 left Iteration 1 Error: 0.778736 Iteration 2 Error: 0.099901 Iteration 3 Error: 0.025834 Align patch 5 20 left Iteration 1 Error: 0.559896 Iteration 2 Error: 0.113391 Iteration 3 Error: 0.031329 Align patch 6 19 left Iteration 1 Error: 1.028982 Iteration 2 Error: 0.136593 Iteration 3 Error: 0.037263 Align patch 7 18 left Iteration 1 Error: 0.715827 Iteration 2 Error: 0.157303 Iteration 3 Error: 0.047636 Align patch 8 17 left Iteration 1 Error: 0.681998 Iteration 2 Error: 0.106889 Iteration 3 Error: 0.030938 Align patch 9 16 left Iteration 1 Error: 0.513510 Iteration 2 Error: 0.061834 Iteration 3 Error: 0.020602 Align patch 10 15 left Iteration 1 Error: 0.489372 Iteration 2 Error: 0.051530 Iteration 3 Error: 0.011973 Align patch 11 14 left Iteration 1 Error: 0.855548 Iteration 2 Error: 0.267308 Iteration 3 Error: 0.082050 Iteration 4 Error: 0.037701 Align patch 12 13 left Iteration 1 Error: 0.791581 Iteration 2 Error: 0.147360 Iteration 3 Error: 0.044958 Align patch 13 12 left Iteration 1 Error: 0.465018 Iteration 2 Error: 0.075091 Iteration 3 Error: 0.013101 Align patch 14 11 left Iteration 1 Error: 0.551820 Iteration 2 Error: 0.071773 Iteration 3 Error: 0.020262 Align patch 15 10 left Iteration 1 Error: 0.680809 Iteration 2 Error: 0.134334 Iteration 3 Error: 0.015899 Align patch 16 9 left Iteration 1 Error: 0.479280 Iteration 2 Error: 0.082421 Iteration 3 Error: 0.029272 Align patch 17 8 left Iteration 1 Error: 0.488188 Iteration 2 Error: 0.094861 Iteration 3 Error: 0.023769 Align patch 18 7 left Iteration 1 Error: 0.994886 Iteration 2 Error: 0.120773 Iteration 3 Error: 0.025528 Align patch 19 6 left Iteration 1 Error: 0.412247 Iteration 2 Error: 0.055842 Iteration 3 Error: 0.015262 Align patch 20 5 left Iteration 1 Error: 0.774945 Iteration 2 Error: 0.109268 Iteration 3 Error: 0.026766 Align patch 21 4 left Iteration 1 Error: 0.718524 Iteration 2 Error: 0.241380 Iteration 3 Error: 0.102269 Iteration 4 Error: 0.047082 Align patch 22 3 left Iteration 1 Error: 0.785154 Iteration 2 Error: 0.230301 Iteration 3 Error: 0.078058 Iteration 4 Error: 0.027268 Align patch 23 2 left Iteration 1 Error: 0.704209 Iteration 2 Error: 0.100966 Iteration 3 Error: 0.023350 Align patch 24 1 left Iteration 1 Error: 0.820206 Iteration 2 Error: 0.067973 Iteration 3 Error: 0.016757 Align patch 25 0 left Iteration 1 Error: 0.653856 Iteration 2 Error: 0.081297 Iteration 3 Error: 0.015401 3D Fitting completed. Patch alignment time: 14.61(sec) Local motion has been corrected. Process thread exits. Computational time: 23.094687 sec Total time: 30.461861 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00014hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00014hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.604219s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00014hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.501780s ........................................ >>>>>>TIME<<<<<< FFT: 0.987040s Defocus_U Defocus_V Angle CCC 13048.83 13666.02 4.20 0.054512 Final Values Defocus_U Defocus_V Angle CCC 13051.96 13675.40 3.88 0.088221 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00014hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00014hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.003e-01 CC threshold: 0.737 Mean Std: 41.16 6.92 Num Hot pixels: 230 Hot pixel threshold: 82.69 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.525609 Iteration 2 Error: 0.083194 Iteration 3 Error: 0.019059 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.15 -0.09 ...... Frame ( 3) shift: -0.30 -0.17 ...... Frame ( 4) shift: -0.45 -0.26 ...... Frame ( 5) shift: -0.59 -0.35 ...... Frame ( 6) shift: -0.69 -0.38 ...... Frame ( 7) shift: -0.72 -0.35 ...... Frame ( 8) shift: -0.75 -0.33 ...... Frame ( 9) shift: -0.79 -0.27 ...... Frame ( 10) shift: -0.82 -0.18 ...... Frame ( 11) shift: -0.86 -0.09 ...... Frame ( 12) shift: -0.85 -0.01 ...... Frame ( 13) shift: -0.81 0.05 ...... Frame ( 14) shift: -0.76 0.11 ...... Frame ( 15) shift: -0.76 0.17 ...... Frame ( 16) shift: -0.81 0.20 ...... Frame ( 17) shift: -0.86 0.24 ...... Frame ( 18) shift: -0.85 0.28 ...... Frame ( 19) shift: -0.78 0.31 ...... Frame ( 20) shift: -0.70 0.34 ...... Frame ( 21) shift: -0.65 0.38 ...... Frame ( 22) shift: -0.62 0.43 ...... Frame ( 23) shift: -0.59 0.47 ...... Frame ( 24) shift: -0.55 0.48 ...... Frame ( 25) shift: -0.51 0.47 ...... Frame ( 26) shift: -0.47 0.45 ...... Frame ( 27) shift: -0.46 0.44 ...... Frame ( 28) shift: -0.46 0.45 ...... Frame ( 29) shift: -0.47 0.46 ...... Frame ( 30) shift: -0.46 0.46 ...... Frame ( 31) shift: -0.44 0.46 ...... Frame ( 32) shift: -0.42 0.46 ...... Frame ( 33) shift: -0.39 0.47 ...... Frame ( 34) shift: -0.36 0.48 ...... Frame ( 35) shift: -0.33 0.50 ...... Frame ( 36) shift: -0.32 0.48 ...... Frame ( 37) shift: -0.34 0.44 ...... Frame ( 38) shift: -0.36 0.40 ...... Frame ( 39) shift: -0.37 0.36 ...... Frame ( 40) shift: -0.39 0.31 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.439195 Iteration 2 Error: 0.179278 Iteration 3 Error: 0.040300 Align patch 2 23 left Iteration 1 Error: 1.082745 Iteration 2 Error: 0.218130 Iteration 3 Error: 0.045012 Align patch 3 22 left Iteration 1 Error: 0.908280 Iteration 2 Error: 0.100629 Iteration 3 Error: 0.021924 Align patch 4 21 left Iteration 1 Error: 0.763595 Iteration 2 Error: 0.088178 Iteration 3 Error: 0.020747 Align patch 5 20 left Iteration 1 Error: 0.502388 Iteration 2 Error: 0.055942 Iteration 3 Error: 0.008360 Align patch 6 19 left Iteration 1 Error: 1.010650 Iteration 2 Error: 0.158262 Iteration 3 Error: 0.074729 Iteration 4 Error: 0.025059 Align patch 7 18 left Iteration 1 Error: 0.641114 Iteration 2 Error: 0.109779 Iteration 3 Error: 0.028527 Align patch 8 17 left Iteration 1 Error: 0.630720 Iteration 2 Error: 0.131262 Iteration 3 Error: 0.035078 Align patch 9 16 left Iteration 1 Error: 0.649229 Iteration 2 Error: 0.115713 Iteration 3 Error: 0.021174 Align patch 10 15 left Iteration 1 Error: 0.502910 Iteration 2 Error: 0.085298 Iteration 3 Error: 0.016903 Align patch 11 14 left Iteration 1 Error: 1.315683 Iteration 2 Error: 0.169817 Iteration 3 Error: 0.027818 Align patch 12 13 left Iteration 1 Error: 0.835638 Iteration 2 Error: 0.153056 Iteration 3 Error: 0.035584 Align patch 13 12 left Iteration 1 Error: 0.426593 Iteration 2 Error: 0.065337 Iteration 3 Error: 0.015311 Align patch 14 11 left Iteration 1 Error: 0.439281 Iteration 2 Error: 0.049111 Align patch 15 10 left Iteration 1 Error: 0.719404 Iteration 2 Error: 0.069210 Iteration 3 Error: 0.019851 Align patch 16 9 left Iteration 1 Error: 0.876547 Iteration 2 Error: 0.107889 Iteration 3 Error: 0.037791 Align patch 17 8 left Iteration 1 Error: 0.718804 Iteration 2 Error: 0.095835 Iteration 3 Error: 0.020501 Align patch 18 7 left Iteration 1 Error: 0.675791 Iteration 2 Error: 0.097765 Iteration 3 Error: 0.022291 Align patch 19 6 left Iteration 1 Error: 0.978926 Iteration 2 Error: 0.134280 Iteration 3 Error: 0.023121 Align patch 20 5 left Iteration 1 Error: 0.680115 Iteration 2 Error: 0.112960 Iteration 3 Error: 0.026747 Align patch 21 4 left Iteration 1 Error: 0.801007 Iteration 2 Error: 0.166391 Iteration 3 Error: 0.027847 Align patch 22 3 left Iteration 1 Error: 0.671091 Iteration 2 Error: 0.069311 Iteration 3 Error: 0.019390 Align patch 23 2 left Iteration 1 Error: 0.723133 Iteration 2 Error: 0.066988 Iteration 3 Error: 0.015414 Align patch 24 1 left Iteration 1 Error: 0.735717 Iteration 2 Error: 0.085263 Iteration 3 Error: 0.020258 Align patch 25 0 left Iteration 1 Error: 0.927075 Iteration 2 Error: 0.202813 Iteration 3 Error: 0.035466 3D Fitting completed. Patch alignment time: 14.52(sec) Local motion has been corrected. Process thread exits. Computational time: 23.221676 sec Total time: 29.322910 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00014hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00014hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.783708s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00014hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.561632s ........................................ >>>>>>TIME<<<<<< FFT: 0.958539s Defocus_U Defocus_V Angle CCC 11558.60 12496.10 5.73 0.050342 Final Values Defocus_U Defocus_V Angle CCC 11567.97 12508.60 5.42 0.085678 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00014hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00014hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.350e-01 1.004e-01 CC threshold: 0.737 Mean Std: 40.96 6.96 Num Hot pixels: 218 Hot pixel threshold: 82.71 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.633329 Iteration 2 Error: 0.081642 Iteration 3 Error: 0.013323 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.21 -0.09 ...... Frame ( 3) shift: -0.41 -0.19 ...... Frame ( 4) shift: -0.62 -0.28 ...... Frame ( 5) shift: -0.83 -0.38 ...... Frame ( 6) shift: -0.90 -0.41 ...... Frame ( 7) shift: -0.84 -0.38 ...... Frame ( 8) shift: -0.78 -0.35 ...... Frame ( 9) shift: -0.74 -0.33 ...... Frame ( 10) shift: -0.72 -0.31 ...... Frame ( 11) shift: -0.70 -0.28 ...... Frame ( 12) shift: -0.71 -0.24 ...... Frame ( 13) shift: -0.76 -0.18 ...... Frame ( 14) shift: -0.80 -0.11 ...... Frame ( 15) shift: -0.81 -0.07 ...... Frame ( 16) shift: -0.79 -0.04 ...... Frame ( 17) shift: -0.77 -0.02 ...... Frame ( 18) shift: -0.75 0.00 ...... Frame ( 19) shift: -0.74 0.01 ...... Frame ( 20) shift: -0.72 0.01 ...... Frame ( 21) shift: -0.69 0.06 ...... Frame ( 22) shift: -0.65 0.16 ...... Frame ( 23) shift: -0.60 0.25 ...... Frame ( 24) shift: -0.60 0.27 ...... Frame ( 25) shift: -0.65 0.22 ...... Frame ( 26) shift: -0.69 0.17 ...... Frame ( 27) shift: -0.71 0.20 ...... Frame ( 28) shift: -0.71 0.31 ...... Frame ( 29) shift: -0.71 0.41 ...... Frame ( 30) shift: -0.72 0.47 ...... Frame ( 31) shift: -0.73 0.48 ...... Frame ( 32) shift: -0.74 0.49 ...... Frame ( 33) shift: -0.70 0.53 ...... Frame ( 34) shift: -0.62 0.61 ...... Frame ( 35) shift: -0.53 0.68 ...... Frame ( 36) shift: -0.48 0.72 ...... Frame ( 37) shift: -0.47 0.74 ...... Frame ( 38) shift: -0.46 0.75 ...... Frame ( 39) shift: -0.45 0.76 ...... Frame ( 40) shift: -0.44 0.78 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.370476 Iteration 2 Error: 0.099050 Iteration 3 Error: 0.025125 Align patch 2 23 left Iteration 1 Error: 0.726992 Iteration 2 Error: 0.091155 Iteration 3 Error: 0.016934 Align patch 3 22 left Iteration 1 Error: 0.405660 Iteration 2 Error: 0.052181 Iteration 3 Error: 0.012076 Align patch 4 21 left Iteration 1 Error: 0.606077 Iteration 2 Error: 0.077035 Iteration 3 Error: 0.015073 Align patch 5 20 left Iteration 1 Error: 0.526046 Iteration 2 Error: 0.045622 Align patch 6 19 left Iteration 1 Error: 0.856606 Iteration 2 Error: 0.129874 Iteration 3 Error: 0.038087 Align patch 7 18 left Iteration 1 Error: 0.681908 Iteration 2 Error: 0.133366 Iteration 3 Error: 0.022328 Align patch 8 17 left Iteration 1 Error: 0.710486 Iteration 2 Error: 0.117099 Iteration 3 Error: 0.027586 Align patch 9 16 left Iteration 1 Error: 0.430022 Iteration 2 Error: 0.039217 Align patch 10 15 left Iteration 1 Error: 0.599017 Iteration 2 Error: 0.026541 Align patch 11 14 left Iteration 1 Error: 0.499532 Iteration 2 Error: 0.057182 Iteration 3 Error: 0.013864 Align patch 12 13 left Iteration 1 Error: 0.692347 Iteration 2 Error: 0.094849 Iteration 3 Error: 0.023946 Align patch 13 12 left Iteration 1 Error: 0.497207 Iteration 2 Error: 0.078435 Iteration 3 Error: 0.023964 Align patch 14 11 left Iteration 1 Error: 0.422371 Iteration 2 Error: 0.048080 Align patch 15 10 left Iteration 1 Error: 0.406061 Iteration 2 Error: 0.059019 Iteration 3 Error: 0.016908 Align patch 16 9 left Iteration 1 Error: 0.535440 Iteration 2 Error: 0.049011 Align patch 17 8 left Iteration 1 Error: 0.395133 Iteration 2 Error: 0.070480 Iteration 3 Error: 0.013082 Align patch 18 7 left Iteration 1 Error: 0.635715 Iteration 2 Error: 0.053652 Iteration 3 Error: 0.008857 Align patch 19 6 left Iteration 1 Error: 0.716020 Iteration 2 Error: 0.078455 Iteration 3 Error: 0.010650 Align patch 20 5 left Iteration 1 Error: 0.585625 Iteration 2 Error: 0.060121 Iteration 3 Error: 0.008940 Align patch 21 4 left Iteration 1 Error: 0.861132 Iteration 2 Error: 0.162172 Iteration 3 Error: 0.028931 Align patch 22 3 left Iteration 1 Error: 0.587936 Iteration 2 Error: 0.057784 Iteration 3 Error: 0.022565 Align patch 23 2 left Iteration 1 Error: 0.613965 Iteration 2 Error: 0.102819 Iteration 3 Error: 0.025766 Align patch 24 1 left Iteration 1 Error: 0.574073 Iteration 2 Error: 0.064628 Iteration 3 Error: 0.013780 Align patch 25 0 left Iteration 1 Error: 0.604447 Iteration 2 Error: 0.077877 Iteration 3 Error: 0.014749 3D Fitting completed. Patch alignment time: 14.26(sec) Local motion has been corrected. Process thread exits. Computational time: 22.380007 sec Total time: 28.033709 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00014hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00014hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.696624s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00014hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.515277s ........................................ >>>>>>TIME<<<<<< FFT: 1.060135s Defocus_U Defocus_V Angle CCC 14621.49 13949.22 84.64 0.061842 Final Values Defocus_U Defocus_V Angle CCC 14634.00 13961.73 85.58 0.097645 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00015hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00015hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.003e-01 CC threshold: 0.736 Mean Std: 41.33 7.03 Num Hot pixels: 190 Hot pixel threshold: 83.52 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.351561 Iteration 2 Error: 0.262943 Iteration 3 Error: 0.056167 Iteration 4 Error: 0.019974 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.12 0.04 ...... Frame ( 3) shift: -0.24 0.08 ...... Frame ( 4) shift: -0.36 0.13 ...... Frame ( 5) shift: -0.47 0.17 ...... Frame ( 6) shift: -0.50 0.26 ...... Frame ( 7) shift: -0.45 0.41 ...... Frame ( 8) shift: -0.39 0.55 ...... Frame ( 9) shift: -0.31 0.70 ...... Frame ( 10) shift: -0.21 0.85 ...... Frame ( 11) shift: -0.12 1.01 ...... Frame ( 12) shift: -0.07 1.12 ...... Frame ( 13) shift: -0.07 1.19 ...... Frame ( 14) shift: -0.08 1.25 ...... Frame ( 15) shift: -0.07 1.32 ...... Frame ( 16) shift: -0.05 1.38 ...... Frame ( 17) shift: -0.03 1.44 ...... Frame ( 18) shift: 0.02 1.49 ...... Frame ( 19) shift: 0.10 1.53 ...... Frame ( 20) shift: 0.19 1.56 ...... Frame ( 21) shift: 0.24 1.63 ...... Frame ( 22) shift: 0.28 1.72 ...... Frame ( 23) shift: 0.31 1.81 ...... Frame ( 24) shift: 0.33 1.89 ...... Frame ( 25) shift: 0.35 1.94 ...... Frame ( 26) shift: 0.36 1.99 ...... Frame ( 27) shift: 0.40 2.04 ...... Frame ( 28) shift: 0.45 2.09 ...... Frame ( 29) shift: 0.51 2.15 ...... Frame ( 30) shift: 0.55 2.24 ...... Frame ( 31) shift: 0.59 2.37 ...... Frame ( 32) shift: 0.64 2.51 ...... Frame ( 33) shift: 0.69 2.57 ...... Frame ( 34) shift: 0.76 2.55 ...... Frame ( 35) shift: 0.83 2.53 ...... Frame ( 36) shift: 0.85 2.56 ...... Frame ( 37) shift: 0.83 2.62 ...... Frame ( 38) shift: 0.81 2.68 ...... Frame ( 39) shift: 0.79 2.74 ...... Frame ( 40) shift: 0.77 2.80 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.371020 Iteration 2 Error: 0.194971 Iteration 3 Error: 0.056469 Iteration 4 Error: 0.023126 Align patch 2 23 left Iteration 1 Error: 0.914173 Iteration 2 Error: 0.200848 Iteration 3 Error: 0.056754 Iteration 4 Error: 0.018466 Align patch 3 22 left Iteration 1 Error: 0.495972 Iteration 2 Error: 0.090748 Iteration 3 Error: 0.027587 Align patch 4 21 left Iteration 1 Error: 1.544799 Iteration 2 Error: 0.309566 Iteration 3 Error: 0.099860 Iteration 4 Error: 0.040597 Align patch 5 20 left Iteration 1 Error: 0.434008 Iteration 2 Error: 0.064611 Iteration 3 Error: 0.009426 Align patch 6 19 left Iteration 1 Error: 1.106012 Iteration 2 Error: 0.187789 Iteration 3 Error: 0.070063 Iteration 4 Error: 0.024457 Align patch 7 18 left Iteration 1 Error: 0.835647 Iteration 2 Error: 0.205370 Iteration 3 Error: 0.098473 Iteration 4 Error: 0.041781 Align patch 8 17 left Iteration 1 Error: 0.692227 Iteration 2 Error: 0.093385 Iteration 3 Error: 0.021358 Align patch 9 16 left Iteration 1 Error: 0.345752 Iteration 2 Error: 0.042441 Align patch 10 15 left Iteration 1 Error: 0.678937 Iteration 2 Error: 0.083580 Iteration 3 Error: 0.014538 Align patch 11 14 left Iteration 1 Error: 0.887785 Iteration 2 Error: 0.108612 Iteration 3 Error: 0.023991 Align patch 12 13 left Iteration 1 Error: 1.063490 Iteration 2 Error: 0.219672 Iteration 3 Error: 0.039279 Align patch 13 12 left Iteration 1 Error: 0.656832 Iteration 2 Error: 0.125298 Iteration 3 Error: 0.037387 Align patch 14 11 left Iteration 1 Error: 0.654843 Iteration 2 Error: 0.115439 Iteration 3 Error: 0.023402 Align patch 15 10 left Iteration 1 Error: 0.807162 Iteration 2 Error: 0.139232 Iteration 3 Error: 0.031695 Align patch 16 9 left Iteration 1 Error: 0.429426 Iteration 2 Error: 0.082025 Iteration 3 Error: 0.022455 Align patch 17 8 left Iteration 1 Error: 0.638746 Iteration 2 Error: 0.099805 Iteration 3 Error: 0.040030 Align patch 18 7 left Iteration 1 Error: 0.692069 Iteration 2 Error: 0.114085 Iteration 3 Error: 0.035251 Align patch 19 6 left Iteration 1 Error: 0.713752 Iteration 2 Error: 0.098561 Iteration 3 Error: 0.013771 Align patch 20 5 left Iteration 1 Error: 0.875434 Iteration 2 Error: 0.154300 Iteration 3 Error: 0.029705 Align patch 21 4 left Iteration 1 Error: 0.664828 Iteration 2 Error: 0.100448 Iteration 3 Error: 0.025540 Align patch 22 3 left Iteration 1 Error: 0.522893 Iteration 2 Error: 0.082605 Iteration 3 Error: 0.025769 Align patch 23 2 left Iteration 1 Error: 0.808431 Iteration 2 Error: 0.129414 Iteration 3 Error: 0.033686 Align patch 24 1 left Iteration 1 Error: 0.854245 Iteration 2 Error: 0.121890 Iteration 3 Error: 0.029453 Align patch 25 0 left Iteration 1 Error: 0.853219 Iteration 2 Error: 0.131963 Iteration 3 Error: 0.025340 3D Fitting completed. Patch alignment time: 14.45(sec) Local motion has been corrected. Process thread exits. Computational time: 22.884298 sec Total time: 29.230684 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00015hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00015hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.566578s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00015hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.552088s ........................................ >>>>>>TIME<<<<<< FFT: 0.983913s Defocus_U Defocus_V Angle CCC 10822.28 11654.31 12.58 0.052245 Final Values Defocus_U Defocus_V Angle CCC 10844.16 11657.44 13.21 0.091125 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00015hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00015hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 1.000e-01 CC threshold: 0.734 Mean Std: 41.33 6.98 Num Hot pixels: 214 Hot pixel threshold: 83.22 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.343761 Iteration 2 Error: 0.317829 Iteration 3 Error: 0.089299 Iteration 4 Error: 0.032404 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.16 -0.08 ...... Frame ( 3) shift: -0.32 -0.16 ...... Frame ( 4) shift: -0.48 -0.24 ...... Frame ( 5) shift: -0.64 -0.33 ...... Frame ( 6) shift: -0.66 -0.35 ...... Frame ( 7) shift: -0.53 -0.32 ...... Frame ( 8) shift: -0.40 -0.29 ...... Frame ( 9) shift: -0.33 -0.22 ...... Frame ( 10) shift: -0.31 -0.11 ...... Frame ( 11) shift: -0.29 -0.01 ...... Frame ( 12) shift: -0.27 0.09 ...... Frame ( 13) shift: -0.24 0.18 ...... Frame ( 14) shift: -0.21 0.27 ...... Frame ( 15) shift: -0.17 0.35 ...... Frame ( 16) shift: -0.12 0.43 ...... Frame ( 17) shift: -0.07 0.52 ...... Frame ( 18) shift: -0.01 0.62 ...... Frame ( 19) shift: 0.07 0.75 ...... Frame ( 20) shift: 0.15 0.88 ...... Frame ( 21) shift: 0.23 0.97 ...... Frame ( 22) shift: 0.32 1.04 ...... Frame ( 23) shift: 0.40 1.10 ...... Frame ( 24) shift: 0.44 1.20 ...... Frame ( 25) shift: 0.43 1.34 ...... Frame ( 26) shift: 0.42 1.47 ...... Frame ( 27) shift: 0.44 1.58 ...... Frame ( 28) shift: 0.48 1.66 ...... Frame ( 29) shift: 0.51 1.73 ...... Frame ( 30) shift: 0.54 1.79 ...... Frame ( 31) shift: 0.56 1.83 ...... Frame ( 32) shift: 0.59 1.88 ...... Frame ( 33) shift: 0.63 1.91 ...... Frame ( 34) shift: 0.69 1.94 ...... Frame ( 35) shift: 0.75 1.97 ...... Frame ( 36) shift: 0.80 2.02 ...... Frame ( 37) shift: 0.82 2.10 ...... Frame ( 38) shift: 0.85 2.18 ...... Frame ( 39) shift: 0.88 2.26 ...... Frame ( 40) shift: 0.91 2.33 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.792566 Iteration 2 Error: 0.331470 Iteration 3 Error: 0.176329 Iteration 4 Error: 0.054553 Iteration 5 Error: 0.038257 Align patch 2 23 left Iteration 1 Error: 1.447394 Iteration 2 Error: 0.242774 Iteration 3 Error: 0.062836 Iteration 4 Error: 0.022026 Align patch 3 22 left Iteration 1 Error: 0.754518 Iteration 2 Error: 0.148453 Iteration 3 Error: 0.032202 Align patch 4 21 left Iteration 1 Error: 0.548130 Iteration 2 Error: 0.075186 Iteration 3 Error: 0.019278 Align patch 5 20 left Iteration 1 Error: 0.794334 Iteration 2 Error: 0.118466 Iteration 3 Error: 0.023730 Align patch 6 19 left Iteration 1 Error: 1.245294 Iteration 2 Error: 0.353788 Iteration 3 Error: 0.090212 Iteration 4 Error: 0.046937 Align patch 7 18 left Iteration 1 Error: 1.047780 Iteration 2 Error: 0.270613 Iteration 3 Error: 0.076087 Iteration 4 Error: 0.031759 Align patch 8 17 left Iteration 1 Error: 0.847946 Iteration 2 Error: 0.190348 Iteration 3 Error: 0.048178 Align patch 9 16 left Iteration 1 Error: 0.709868 Iteration 2 Error: 0.159061 Iteration 3 Error: 0.047414 Align patch 10 15 left Iteration 1 Error: 0.802308 Iteration 2 Error: 0.167170 Iteration 3 Error: 0.080629 Iteration 4 Error: 0.024139 Align patch 11 14 left Iteration 1 Error: 1.990141 Iteration 2 Error: 0.278631 Iteration 3 Error: 0.124802 Iteration 4 Error: 0.047792 Align patch 12 13 left Iteration 1 Error: 0.885464 Iteration 2 Error: 0.251866 Iteration 3 Error: 0.097562 Iteration 4 Error: 0.038321 Align patch 13 12 left Iteration 1 Error: 0.588331 Iteration 2 Error: 0.111413 Iteration 3 Error: 0.033250 Align patch 14 11 left Iteration 1 Error: 0.473705 Iteration 2 Error: 0.066353 Iteration 3 Error: 0.016479 Align patch 15 10 left Iteration 1 Error: 0.716684 Iteration 2 Error: 0.125016 Iteration 3 Error: 0.038239 Align patch 16 9 left Iteration 1 Error: 0.823226 Iteration 2 Error: 0.115020 Iteration 3 Error: 0.042866 Align patch 17 8 left Iteration 1 Error: 0.866528 Iteration 2 Error: 0.154805 Iteration 3 Error: 0.036006 Align patch 18 7 left Iteration 1 Error: 0.727313 Iteration 2 Error: 0.089455 Iteration 3 Error: 0.024971 Align patch 19 6 left Iteration 1 Error: 0.659831 Iteration 2 Error: 0.146964 Iteration 3 Error: 0.056498 Iteration 4 Error: 0.029157 Align patch 20 5 left Iteration 1 Error: 0.864858 Iteration 2 Error: 0.142998 Iteration 3 Error: 0.036366 Align patch 21 4 left Iteration 1 Error: 0.807954 Iteration 2 Error: 0.159489 Iteration 3 Error: 0.045119 Align patch 22 3 left Iteration 1 Error: 1.192784 Iteration 2 Error: 0.264166 Iteration 3 Error: 0.111666 Iteration 4 Error: 0.044417 Align patch 23 2 left Iteration 1 Error: 0.764147 Iteration 2 Error: 0.070024 Iteration 3 Error: 0.018623 Align patch 24 1 left Iteration 1 Error: 0.600651 Iteration 2 Error: 0.090178 Iteration 3 Error: 0.020360 Align patch 25 0 left Iteration 1 Error: 0.730735 Iteration 2 Error: 0.105490 Iteration 3 Error: 0.038632 3D Fitting completed. Patch alignment time: 15.75(sec) Local motion has been corrected. Process thread exits. Computational time: 24.142878 sec Total time: 29.598831 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00015hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00015hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.586376s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00015hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.521570s ........................................ >>>>>>TIME<<<<<< FFT: 0.939482s Defocus_U Defocus_V Angle CCC 12853.52 13396.49 1.53 0.053221 Final Values Defocus_U Defocus_V Angle CCC 12866.03 13402.75 1.84 0.085698 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00015hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00015hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 41.76 7.01 Num Hot pixels: 198 Hot pixel threshold: 83.80 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.936711 Iteration 2 Error: 0.165562 Iteration 3 Error: 0.043634 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.04 0.12 ...... Frame ( 3) shift: -0.07 0.25 ...... Frame ( 4) shift: -0.11 0.37 ...... Frame ( 5) shift: -0.14 0.50 ...... Frame ( 6) shift: -0.14 0.58 ...... Frame ( 7) shift: -0.10 0.62 ...... Frame ( 8) shift: -0.05 0.65 ...... Frame ( 9) shift: -0.00 0.68 ...... Frame ( 10) shift: 0.05 0.71 ...... Frame ( 11) shift: 0.10 0.73 ...... Frame ( 12) shift: 0.16 0.78 ...... Frame ( 13) shift: 0.22 0.85 ...... Frame ( 14) shift: 0.29 0.91 ...... Frame ( 15) shift: 0.37 1.01 ...... Frame ( 16) shift: 0.46 1.12 ...... Frame ( 17) shift: 0.55 1.24 ...... Frame ( 18) shift: 0.63 1.31 ...... Frame ( 19) shift: 0.70 1.33 ...... Frame ( 20) shift: 0.78 1.35 ...... Frame ( 21) shift: 0.84 1.37 ...... Frame ( 22) shift: 0.91 1.38 ...... Frame ( 23) shift: 0.97 1.39 ...... Frame ( 24) shift: 1.00 1.37 ...... Frame ( 25) shift: 0.98 1.30 ...... Frame ( 26) shift: 0.97 1.24 ...... Frame ( 27) shift: 0.98 1.23 ...... Frame ( 28) shift: 1.04 1.28 ...... Frame ( 29) shift: 1.09 1.33 ...... Frame ( 30) shift: 1.10 1.37 ...... Frame ( 31) shift: 1.07 1.39 ...... Frame ( 32) shift: 1.05 1.41 ...... Frame ( 33) shift: 1.04 1.43 ...... Frame ( 34) shift: 1.05 1.46 ...... Frame ( 35) shift: 1.06 1.48 ...... Frame ( 36) shift: 1.09 1.51 ...... Frame ( 37) shift: 1.13 1.56 ...... Frame ( 38) shift: 1.18 1.60 ...... Frame ( 39) shift: 1.22 1.65 ...... Frame ( 40) shift: 1.26 1.69 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.174514 Iteration 2 Error: 0.279066 Iteration 3 Error: 0.092267 Iteration 4 Error: 0.036635 Align patch 2 23 left Iteration 1 Error: 1.100650 Iteration 2 Error: 0.223962 Iteration 3 Error: 0.064553 Iteration 4 Error: 0.019999 Align patch 3 22 left Iteration 1 Error: 0.656328 Iteration 2 Error: 0.071973 Iteration 3 Error: 0.020883 Align patch 4 21 left Iteration 1 Error: 0.707952 Iteration 2 Error: 0.083384 Iteration 3 Error: 0.027404 Align patch 5 20 left Iteration 1 Error: 0.428825 Iteration 2 Error: 0.077478 Iteration 3 Error: 0.012920 Align patch 6 19 left Iteration 1 Error: 0.767951 Iteration 2 Error: 0.183095 Iteration 3 Error: 0.046385 Align patch 7 18 left Iteration 1 Error: 0.653421 Iteration 2 Error: 0.137137 Iteration 3 Error: 0.040206 Align patch 8 17 left Iteration 1 Error: 0.663113 Iteration 2 Error: 0.102847 Iteration 3 Error: 0.023619 Align patch 9 16 left Iteration 1 Error: 0.826175 Iteration 2 Error: 0.096712 Iteration 3 Error: 0.028318 Align patch 10 15 left Iteration 1 Error: 0.555846 Iteration 2 Error: 0.084406 Iteration 3 Error: 0.013926 Align patch 11 14 left Iteration 1 Error: 0.658851 Iteration 2 Error: 0.138059 Iteration 3 Error: 0.033986 Align patch 12 13 left Iteration 1 Error: 0.776265 Iteration 2 Error: 0.073253 Iteration 3 Error: 0.022207 Align patch 13 12 left Iteration 1 Error: 0.730869 Iteration 2 Error: 0.064030 Iteration 3 Error: 0.014008 Align patch 14 11 left Iteration 1 Error: 0.433339 Iteration 2 Error: 0.084225 Iteration 3 Error: 0.016276 Align patch 15 10 left Iteration 1 Error: 0.723180 Iteration 2 Error: 0.097621 Iteration 3 Error: 0.021100 Align patch 16 9 left Iteration 1 Error: 0.742676 Iteration 2 Error: 0.085568 Iteration 3 Error: 0.023619 Align patch 17 8 left Iteration 1 Error: 0.780932 Iteration 2 Error: 0.165882 Iteration 3 Error: 0.029911 Align patch 18 7 left Iteration 1 Error: 0.759714 Iteration 2 Error: 0.092818 Iteration 3 Error: 0.018547 Align patch 19 6 left Iteration 1 Error: 0.847581 Iteration 2 Error: 0.119203 Iteration 3 Error: 0.026614 Align patch 20 5 left Iteration 1 Error: 0.592750 Iteration 2 Error: 0.088031 Iteration 3 Error: 0.020873 Align patch 21 4 left Iteration 1 Error: 0.825851 Iteration 2 Error: 0.159450 Iteration 3 Error: 0.048628 Align patch 22 3 left Iteration 1 Error: 0.619378 Iteration 2 Error: 0.064773 Iteration 3 Error: 0.012782 Align patch 23 2 left Iteration 1 Error: 0.715687 Iteration 2 Error: 0.125548 Iteration 3 Error: 0.034875 Align patch 24 1 left Iteration 1 Error: 0.785991 Iteration 2 Error: 0.121347 Iteration 3 Error: 0.026950 Align patch 25 0 left Iteration 1 Error: 0.566090 Iteration 2 Error: 0.136654 Iteration 3 Error: 0.024778 3D Fitting completed. Patch alignment time: 15.28(sec) Local motion has been corrected. Process thread exits. Computational time: 23.842388 sec Total time: 29.457779 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00015hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00015hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.648455s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00015hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.512186s ........................................ >>>>>>TIME<<<<<< FFT: 1.053894s Defocus_U Defocus_V Angle CCC 10314.48 11166.04 8.12 0.046484 Final Values Defocus_U Defocus_V Angle CCC 10328.54 11183.24 7.81 0.082842 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00015hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00015hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 40.96 6.89 Num Hot pixels: 219 Hot pixel threshold: 82.29 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.906241 Iteration 2 Error: 0.233885 Iteration 3 Error: 0.073478 Iteration 4 Error: 0.027292 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.17 -0.15 ...... Frame ( 3) shift: -0.33 -0.29 ...... Frame ( 4) shift: -0.50 -0.44 ...... Frame ( 5) shift: -0.67 -0.58 ...... Frame ( 6) shift: -0.72 -0.66 ...... Frame ( 7) shift: -0.66 -0.67 ...... Frame ( 8) shift: -0.61 -0.68 ...... Frame ( 9) shift: -0.57 -0.62 ...... Frame ( 10) shift: -0.56 -0.50 ...... Frame ( 11) shift: -0.56 -0.37 ...... Frame ( 12) shift: -0.51 -0.25 ...... Frame ( 13) shift: -0.44 -0.12 ...... Frame ( 14) shift: -0.36 0.01 ...... Frame ( 15) shift: -0.30 0.12 ...... Frame ( 16) shift: -0.27 0.21 ...... Frame ( 17) shift: -0.23 0.31 ...... Frame ( 18) shift: -0.19 0.39 ...... Frame ( 19) shift: -0.14 0.45 ...... Frame ( 20) shift: -0.10 0.52 ...... Frame ( 21) shift: -0.05 0.58 ...... Frame ( 22) shift: 0.00 0.62 ...... Frame ( 23) shift: 0.06 0.67 ...... Frame ( 24) shift: 0.10 0.73 ...... Frame ( 25) shift: 0.13 0.81 ...... Frame ( 26) shift: 0.16 0.88 ...... Frame ( 27) shift: 0.17 0.91 ...... Frame ( 28) shift: 0.16 0.90 ...... Frame ( 29) shift: 0.14 0.89 ...... Frame ( 30) shift: 0.16 0.90 ...... Frame ( 31) shift: 0.22 0.94 ...... Frame ( 32) shift: 0.27 0.98 ...... Frame ( 33) shift: 0.31 1.01 ...... Frame ( 34) shift: 0.35 1.03 ...... Frame ( 35) shift: 0.38 1.05 ...... Frame ( 36) shift: 0.39 1.09 ...... Frame ( 37) shift: 0.39 1.13 ...... Frame ( 38) shift: 0.39 1.18 ...... Frame ( 39) shift: 0.39 1.22 ...... Frame ( 40) shift: 0.39 1.27 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.688914 Iteration 2 Error: 0.255123 Iteration 3 Error: 0.097967 Iteration 4 Error: 0.033333 Align patch 2 23 left Iteration 1 Error: 1.243830 Iteration 2 Error: 0.324473 Iteration 3 Error: 0.161852 Iteration 4 Error: 0.066008 Iteration 5 Error: 0.044204 Align patch 3 22 left Iteration 1 Error: 0.821793 Iteration 2 Error: 0.216024 Iteration 3 Error: 0.061891 Iteration 4 Error: 0.017182 Align patch 4 21 left Iteration 1 Error: 0.851109 Iteration 2 Error: 0.169910 Iteration 3 Error: 0.052715 Iteration 4 Error: 0.013415 Align patch 5 20 left Iteration 1 Error: 1.042360 Iteration 2 Error: 0.175756 Iteration 3 Error: 0.031142 Align patch 6 19 left Iteration 1 Error: 1.437615 Iteration 2 Error: 0.311773 Iteration 3 Error: 0.097205 Iteration 4 Error: 0.053588 Iteration 5 Error: 0.024899 Align patch 7 18 left Iteration 1 Error: 1.001179 Iteration 2 Error: 0.304934 Iteration 3 Error: 0.108905 Iteration 4 Error: 0.057443 Iteration 5 Error: 0.029575 Align patch 8 17 left Iteration 1 Error: 0.593038 Iteration 2 Error: 0.125900 Iteration 3 Error: 0.047677 Align patch 9 16 left Iteration 1 Error: 0.817074 Iteration 2 Error: 0.137974 Iteration 3 Error: 0.044809 Align patch 10 15 left Iteration 1 Error: 1.064318 Iteration 2 Error: 0.208709 Iteration 3 Error: 0.041174 Align patch 11 14 left Iteration 1 Error: 1.538997 Iteration 2 Error: 0.409026 Iteration 3 Error: 0.119665 Iteration 4 Error: 0.058278 Iteration 5 Error: 0.020844 Align patch 12 13 left Iteration 1 Error: 0.571878 Iteration 2 Error: 0.143304 Iteration 3 Error: 0.061052 Iteration 4 Error: 0.019588 Align patch 13 12 left Iteration 1 Error: 0.776069 Iteration 2 Error: 0.194943 Iteration 3 Error: 0.069279 Iteration 4 Error: 0.033751 Align patch 14 11 left Iteration 1 Error: 0.640895 Iteration 2 Error: 0.149231 Iteration 3 Error: 0.033117 Align patch 15 10 left Iteration 1 Error: 0.723487 Iteration 2 Error: 0.138458 Iteration 3 Error: 0.035956 Align patch 16 9 left Iteration 1 Error: 0.603114 Iteration 2 Error: 0.117006 Iteration 3 Error: 0.038080 Align patch 17 8 left Iteration 1 Error: 0.742835 Iteration 2 Error: 0.168775 Iteration 3 Error: 0.044413 Align patch 18 7 left Iteration 1 Error: 0.806244 Iteration 2 Error: 0.151349 Iteration 3 Error: 0.046885 Align patch 19 6 left Iteration 1 Error: 0.582452 Iteration 2 Error: 0.092624 Iteration 3 Error: 0.025345 Align patch 20 5 left Iteration 1 Error: 0.887025 Iteration 2 Error: 0.201015 Iteration 3 Error: 0.049506 Align patch 21 4 left Iteration 1 Error: 1.124755 Iteration 2 Error: 0.389608 Iteration 3 Error: 0.113200 Iteration 4 Error: 0.036410 Align patch 22 3 left Iteration 1 Error: 0.973758 Iteration 2 Error: 0.219144 Iteration 3 Error: 0.052149 Iteration 4 Error: 0.020827 Align patch 23 2 left Iteration 1 Error: 1.075045 Iteration 2 Error: 0.166674 Iteration 3 Error: 0.056393 Iteration 4 Error: 0.016471 Align patch 24 1 left Iteration 1 Error: 0.852945 Iteration 2 Error: 0.218403 Iteration 3 Error: 0.041554 Align patch 25 0 left Iteration 1 Error: 1.147034 Iteration 2 Error: 0.255791 Iteration 3 Error: 0.033863 3D Fitting completed. Patch alignment time: 15.92(sec) Local motion has been corrected. Process thread exits. Computational time: 24.474741 sec Total time: 30.178917 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00015hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00015hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.566219s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00015hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.915036s ........................................ >>>>>>TIME<<<<<< FFT: 0.808291s Defocus_U Defocus_V Angle CCC 11833.99 11138.67 88.81 0.033478 Final Values Defocus_U Defocus_V Angle CCC 11857.46 11187.14 86.64 0.057733 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00016hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00016hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 40.96 6.94 Num Hot pixels: 194 Hot pixel threshold: 82.58 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.169633 Iteration 2 Error: 0.564331 Iteration 3 Error: 0.182734 Iteration 4 Error: 0.088098 Iteration 5 Error: 0.038386 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.08 -0.04 ...... Frame ( 3) shift: -0.15 -0.09 ...... Frame ( 4) shift: -0.23 -0.13 ...... Frame ( 5) shift: -0.31 -0.17 ...... Frame ( 6) shift: -0.29 -0.15 ...... Frame ( 7) shift: -0.18 -0.07 ...... Frame ( 8) shift: -0.07 0.02 ...... Frame ( 9) shift: 0.08 0.13 ...... Frame ( 10) shift: 0.26 0.27 ...... Frame ( 11) shift: 0.44 0.41 ...... Frame ( 12) shift: 0.62 0.55 ...... Frame ( 13) shift: 0.79 0.70 ...... Frame ( 14) shift: 0.97 0.86 ...... Frame ( 15) shift: 1.12 1.01 ...... Frame ( 16) shift: 1.24 1.16 ...... Frame ( 17) shift: 1.36 1.32 ...... Frame ( 18) shift: 1.52 1.45 ...... Frame ( 19) shift: 1.72 1.57 ...... Frame ( 20) shift: 1.91 1.68 ...... Frame ( 21) shift: 2.04 1.77 ...... Frame ( 22) shift: 2.09 1.85 ...... Frame ( 23) shift: 2.15 1.92 ...... Frame ( 24) shift: 2.22 2.00 ...... Frame ( 25) shift: 2.31 2.10 ...... Frame ( 26) shift: 2.41 2.20 ...... Frame ( 27) shift: 2.50 2.28 ...... Frame ( 28) shift: 2.60 2.35 ...... Frame ( 29) shift: 2.69 2.42 ...... Frame ( 30) shift: 2.77 2.53 ...... Frame ( 31) shift: 2.83 2.67 ...... Frame ( 32) shift: 2.89 2.82 ...... Frame ( 33) shift: 2.99 2.95 ...... Frame ( 34) shift: 3.13 3.09 ...... Frame ( 35) shift: 3.27 3.22 ...... Frame ( 36) shift: 3.35 3.34 ...... Frame ( 37) shift: 3.38 3.44 ...... Frame ( 38) shift: 3.40 3.55 ...... Frame ( 39) shift: 3.43 3.66 ...... Frame ( 40) shift: 3.46 3.77 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 3.328216 Iteration 2 Error: 0.805139 Iteration 3 Error: 0.309450 Iteration 4 Error: 0.146032 Iteration 5 Error: 0.054279 Align patch 1 24 left Iteration 1 Error: 2.767701 Iteration 2 Error: 0.398747 Iteration 3 Error: 0.103611 Iteration 4 Error: 0.037108 Align patch 2 23 left Iteration 1 Error: 1.789713 Iteration 2 Error: 0.387164 Iteration 3 Error: 0.142908 Iteration 4 Error: 0.066948 Iteration 5 Error: 0.034870 Align patch 3 22 left Iteration 1 Error: 1.080123 Iteration 2 Error: 0.246933 Iteration 3 Error: 0.122426 Iteration 4 Error: 0.053764 Iteration 5 Error: 0.031135 Align patch 4 21 left Iteration 1 Error: 1.115215 Iteration 2 Error: 0.186327 Iteration 3 Error: 0.037114 Align patch 5 20 left Iteration 1 Error: 0.974919 Iteration 2 Error: 0.236928 Iteration 3 Error: 0.076994 Iteration 4 Error: 0.016977 Align patch 6 19 left Iteration 1 Error: 2.090091 Iteration 2 Error: 0.630661 Iteration 3 Error: 0.332571 Iteration 4 Error: 0.212387 Iteration 5 Error: 0.139603 Align patch 6 19 left Iteration 1 Error: 2.680971 Iteration 2 Error: 0.378214 Iteration 3 Error: 0.088705 Iteration 4 Error: 0.027500 Align patch 7 18 left Iteration 1 Error: 1.600418 Iteration 2 Error: 0.430943 Iteration 3 Error: 0.113120 Iteration 4 Error: 0.060417 Iteration 5 Error: 0.022856 Align patch 8 17 left Iteration 1 Error: 0.778057 Iteration 2 Error: 0.182168 Iteration 3 Error: 0.070917 Iteration 4 Error: 0.022989 Align patch 9 16 left Iteration 1 Error: 0.650730 Iteration 2 Error: 0.158207 Iteration 3 Error: 0.069992 Iteration 4 Error: 0.024293 Align patch 10 15 left Iteration 1 Error: 1.143432 Iteration 2 Error: 0.303101 Iteration 3 Error: 0.086465 Iteration 4 Error: 0.035254 Align patch 11 14 left Iteration 1 Error: 2.020252 Iteration 2 Error: 0.486066 Iteration 3 Error: 0.211635 Iteration 4 Error: 0.125157 Iteration 5 Error: 0.051886 Align patch 11 14 left Iteration 1 Error: 1.940215 Iteration 2 Error: 0.373372 Iteration 3 Error: 0.086557 Iteration 4 Error: 0.028297 Align patch 12 13 left Iteration 1 Error: 1.487998 Iteration 2 Error: 0.482807 Iteration 3 Error: 0.162301 Iteration 4 Error: 0.080149 Iteration 5 Error: 0.038346 Align patch 13 12 left Iteration 1 Error: 0.717912 Iteration 2 Error: 0.211662 Iteration 3 Error: 0.090706 Iteration 4 Error: 0.041643 Align patch 14 11 left Iteration 1 Error: 0.679073 Iteration 2 Error: 0.220647 Iteration 3 Error: 0.049393 Align patch 15 10 left Iteration 1 Error: 0.661909 Iteration 2 Error: 0.175822 Iteration 3 Error: 0.067482 Iteration 4 Error: 0.036666 Align patch 16 9 left Iteration 1 Error: 1.367957 Iteration 2 Error: 0.347464 Iteration 3 Error: 0.186601 Iteration 4 Error: 0.102888 Iteration 5 Error: 0.049005 Align patch 17 8 left Iteration 1 Error: 0.532613 Iteration 2 Error: 0.193773 Iteration 3 Error: 0.099004 Iteration 4 Error: 0.045780 Align patch 18 7 left Iteration 1 Error: 0.502690 Iteration 2 Error: 0.082015 Iteration 3 Error: 0.017644 Align patch 19 6 left Iteration 1 Error: 0.691752 Iteration 2 Error: 0.160534 Iteration 3 Error: 0.053219 Iteration 4 Error: 0.014117 Align patch 20 5 left Iteration 1 Error: 0.579942 Iteration 2 Error: 0.149454 Iteration 3 Error: 0.038898 Align patch 21 4 left Iteration 1 Error: 1.033076 Iteration 2 Error: 0.264038 Iteration 3 Error: 0.105137 Iteration 4 Error: 0.044184 Align patch 22 3 left Iteration 1 Error: 0.778906 Iteration 2 Error: 0.089399 Iteration 3 Error: 0.018446 Align patch 23 2 left Iteration 1 Error: 0.679826 Iteration 2 Error: 0.162896 Iteration 3 Error: 0.033478 Align patch 24 1 left Iteration 1 Error: 0.681900 Iteration 2 Error: 0.174806 Iteration 3 Error: 0.057141 Iteration 4 Error: 0.019814 Align patch 25 0 left Iteration 1 Error: 0.916541 Iteration 2 Error: 0.260128 Iteration 3 Error: 0.065029 Iteration 4 Error: 0.017884 3D Fitting completed. Patch alignment time: 19.50(sec) Local motion has been corrected. Process thread exits. Computational time: 29.002934 sec Total time: 35.430798 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00016hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00016hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.771122s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00016hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.420032s ........................................ >>>>>>TIME<<<<<< FFT: 1.163510s Defocus_U Defocus_V Angle CCC 9441.45 10332.08 13.39 0.046316 Final Values Defocus_U Defocus_V Angle CCC 9494.62 10338.37 14.33 0.082415 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00016hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00016hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 40.81 6.97 Num Hot pixels: 189 Hot pixel threshold: 82.63 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.536039 Iteration 2 Error: 0.176981 Iteration 3 Error: 0.036991 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.04 0.23 ...... Frame ( 3) shift: 0.09 0.45 ...... Frame ( 4) shift: 0.13 0.68 ...... Frame ( 5) shift: 0.18 0.91 ...... Frame ( 6) shift: 0.23 1.05 ...... Frame ( 7) shift: 0.31 1.12 ...... Frame ( 8) shift: 0.38 1.19 ...... Frame ( 9) shift: 0.44 1.26 ...... Frame ( 10) shift: 0.48 1.35 ...... Frame ( 11) shift: 0.53 1.43 ...... Frame ( 12) shift: 0.55 1.53 ...... Frame ( 13) shift: 0.55 1.64 ...... Frame ( 14) shift: 0.56 1.76 ...... Frame ( 15) shift: 0.56 1.81 ...... Frame ( 16) shift: 0.58 1.82 ...... Frame ( 17) shift: 0.59 1.83 ...... Frame ( 18) shift: 0.63 1.86 ...... Frame ( 19) shift: 0.70 1.93 ...... Frame ( 20) shift: 0.77 1.99 ...... Frame ( 21) shift: 0.79 2.04 ...... Frame ( 22) shift: 0.78 2.08 ...... Frame ( 23) shift: 0.77 2.11 ...... Frame ( 24) shift: 0.79 2.12 ...... Frame ( 25) shift: 0.83 2.09 ...... Frame ( 26) shift: 0.87 2.06 ...... Frame ( 27) shift: 0.88 2.11 ...... Frame ( 28) shift: 0.87 2.23 ...... Frame ( 29) shift: 0.85 2.36 ...... Frame ( 30) shift: 0.86 2.45 ...... Frame ( 31) shift: 0.90 2.48 ...... Frame ( 32) shift: 0.94 2.52 ...... Frame ( 33) shift: 0.97 2.54 ...... Frame ( 34) shift: 0.99 2.53 ...... Frame ( 35) shift: 1.01 2.53 ...... Frame ( 36) shift: 1.02 2.58 ...... Frame ( 37) shift: 1.02 2.69 ...... Frame ( 38) shift: 1.02 2.79 ...... Frame ( 39) shift: 1.02 2.90 ...... Frame ( 40) shift: 1.03 3.00 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.078412 Iteration 2 Error: 0.255295 Iteration 3 Error: 0.084145 Iteration 4 Error: 0.025226 Align patch 2 23 left Iteration 1 Error: 0.895292 Iteration 2 Error: 0.179165 Iteration 3 Error: 0.052627 Iteration 4 Error: 0.016860 Align patch 3 22 left Iteration 1 Error: 0.577748 Iteration 2 Error: 0.093307 Iteration 3 Error: 0.038515 Align patch 4 21 left Iteration 1 Error: 0.465195 Iteration 2 Error: 0.038783 Align patch 5 20 left Iteration 1 Error: 0.339679 Iteration 2 Error: 0.111250 Iteration 3 Error: 0.025436 Align patch 6 19 left Iteration 1 Error: 1.162141 Iteration 2 Error: 0.194956 Iteration 3 Error: 0.055138 Iteration 4 Error: 0.015254 Align patch 7 18 left Iteration 1 Error: 0.906422 Iteration 2 Error: 0.173297 Iteration 3 Error: 0.052403 Iteration 4 Error: 0.022596 Align patch 8 17 left Iteration 1 Error: 0.506033 Iteration 2 Error: 0.081778 Iteration 3 Error: 0.011574 Align patch 9 16 left Iteration 1 Error: 0.430438 Iteration 2 Error: 0.063630 Iteration 3 Error: 0.027277 Align patch 10 15 left Iteration 1 Error: 0.447713 Iteration 2 Error: 0.063370 Iteration 3 Error: 0.014460 Align patch 11 14 left Iteration 1 Error: 0.479958 Iteration 2 Error: 0.076235 Iteration 3 Error: 0.018155 Align patch 12 13 left Iteration 1 Error: 0.700942 Iteration 2 Error: 0.062169 Iteration 3 Error: 0.015905 Align patch 13 12 left Iteration 1 Error: 0.602867 Iteration 2 Error: 0.061113 Iteration 3 Error: 0.015288 Align patch 14 11 left Iteration 1 Error: 0.406173 Iteration 2 Error: 0.073798 Iteration 3 Error: 0.018652 Align patch 15 10 left Iteration 1 Error: 0.382940 Iteration 2 Error: 0.094003 Iteration 3 Error: 0.024149 Align patch 16 9 left Iteration 1 Error: 0.585367 Iteration 2 Error: 0.095300 Iteration 3 Error: 0.032983 Align patch 17 8 left Iteration 1 Error: 0.613799 Iteration 2 Error: 0.106433 Iteration 3 Error: 0.023255 Align patch 18 7 left Iteration 1 Error: 0.555715 Iteration 2 Error: 0.083524 Iteration 3 Error: 0.017156 Align patch 19 6 left Iteration 1 Error: 0.493003 Iteration 2 Error: 0.061761 Iteration 3 Error: 0.012475 Align patch 20 5 left Iteration 1 Error: 0.607995 Iteration 2 Error: 0.114141 Iteration 3 Error: 0.019606 Align patch 21 4 left Iteration 1 Error: 0.954699 Iteration 2 Error: 0.157683 Iteration 3 Error: 0.038824 Align patch 22 3 left Iteration 1 Error: 0.771084 Iteration 2 Error: 0.118299 Iteration 3 Error: 0.034986 Align patch 23 2 left Iteration 1 Error: 0.824634 Iteration 2 Error: 0.091519 Iteration 3 Error: 0.018407 Align patch 24 1 left Iteration 1 Error: 0.488005 Iteration 2 Error: 0.090149 Iteration 3 Error: 0.017567 Align patch 25 0 left Iteration 1 Error: 0.472695 Iteration 2 Error: 0.100767 Iteration 3 Error: 0.019941 3D Fitting completed. Patch alignment time: 15.59(sec) Local motion has been corrected. Process thread exits. Computational time: 23.419270 sec Total time: 29.090879 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00016hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00016hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.977366s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00016hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.357845s ........................................ >>>>>>TIME<<<<<< FFT: 1.073741s Defocus_U Defocus_V Angle CCC 10128.91 10523.44 2.72 0.053977 Final Values Defocus_U Defocus_V Angle CCC 10125.79 10554.69 2.41 0.093542 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00016hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00016hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.002e-01 CC threshold: 0.736 Mean Std: 41.20 7.01 Num Hot pixels: 192 Hot pixel threshold: 83.25 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.041097 Iteration 2 Error: 0.206384 Iteration 3 Error: 0.049660 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.28 -0.17 ...... Frame ( 3) shift: -0.57 -0.34 ...... Frame ( 4) shift: -0.85 -0.51 ...... Frame ( 5) shift: -1.13 -0.68 ...... Frame ( 6) shift: -1.28 -0.75 ...... Frame ( 7) shift: -1.30 -0.73 ...... Frame ( 8) shift: -1.32 -0.70 ...... Frame ( 9) shift: -1.27 -0.65 ...... Frame ( 10) shift: -1.16 -0.57 ...... Frame ( 11) shift: -1.05 -0.50 ...... Frame ( 12) shift: -0.98 -0.39 ...... Frame ( 13) shift: -0.93 -0.24 ...... Frame ( 14) shift: -0.88 -0.09 ...... Frame ( 15) shift: -0.83 0.02 ...... Frame ( 16) shift: -0.78 0.10 ...... Frame ( 17) shift: -0.72 0.17 ...... Frame ( 18) shift: -0.68 0.24 ...... Frame ( 19) shift: -0.65 0.29 ...... Frame ( 20) shift: -0.62 0.34 ...... Frame ( 21) shift: -0.57 0.41 ...... Frame ( 22) shift: -0.51 0.49 ...... Frame ( 23) shift: -0.45 0.58 ...... Frame ( 24) shift: -0.42 0.63 ...... Frame ( 25) shift: -0.43 0.62 ...... Frame ( 26) shift: -0.44 0.62 ...... Frame ( 27) shift: -0.37 0.65 ...... Frame ( 28) shift: -0.23 0.70 ...... Frame ( 29) shift: -0.09 0.76 ...... Frame ( 30) shift: -0.06 0.79 ...... Frame ( 31) shift: -0.13 0.81 ...... Frame ( 32) shift: -0.19 0.83 ...... Frame ( 33) shift: -0.21 0.86 ...... Frame ( 34) shift: -0.16 0.90 ...... Frame ( 35) shift: -0.12 0.95 ...... Frame ( 36) shift: -0.07 0.97 ...... Frame ( 37) shift: -0.01 0.98 ...... Frame ( 38) shift: 0.05 0.98 ...... Frame ( 39) shift: 0.11 0.98 ...... Frame ( 40) shift: 0.16 0.98 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.912615 Iteration 2 Error: 0.509700 Iteration 3 Error: 0.190569 Iteration 4 Error: 0.103772 Iteration 5 Error: 0.054775 Align patch 1 24 left Iteration 1 Error: 2.618858 Iteration 2 Error: 0.271296 Iteration 3 Error: 0.047474 Align patch 2 23 left Iteration 1 Error: 1.412851 Iteration 2 Error: 0.329662 Iteration 3 Error: 0.094451 Iteration 4 Error: 0.038719 Align patch 3 22 left Iteration 1 Error: 0.773123 Iteration 2 Error: 0.139704 Iteration 3 Error: 0.059279 Iteration 4 Error: 0.020788 Align patch 4 21 left Iteration 1 Error: 0.430354 Iteration 2 Error: 0.114356 Iteration 3 Error: 0.014872 Align patch 5 20 left Iteration 1 Error: 0.596061 Iteration 2 Error: 0.121795 Iteration 3 Error: 0.016795 Align patch 6 19 left Iteration 1 Error: 2.240016 Iteration 2 Error: 0.473555 Iteration 3 Error: 0.188975 Iteration 4 Error: 0.089326 Iteration 5 Error: 0.049392 Align patch 7 18 left Iteration 1 Error: 0.779888 Iteration 2 Error: 0.182731 Iteration 3 Error: 0.048412 Align patch 8 17 left Iteration 1 Error: 0.866132 Iteration 2 Error: 0.200783 Iteration 3 Error: 0.058698 Iteration 4 Error: 0.027536 Align patch 9 16 left Iteration 1 Error: 0.556144 Iteration 2 Error: 0.095970 Iteration 3 Error: 0.024025 Align patch 10 15 left Iteration 1 Error: 0.653418 Iteration 2 Error: 0.067823 Iteration 3 Error: 0.020068 Align patch 11 14 left Iteration 1 Error: 2.284742 Iteration 2 Error: 0.355440 Iteration 3 Error: 0.129739 Iteration 4 Error: 0.051961 Iteration 5 Error: 0.024934 Align patch 12 13 left Iteration 1 Error: 0.964515 Iteration 2 Error: 0.213273 Iteration 3 Error: 0.059621 Iteration 4 Error: 0.019511 Align patch 13 12 left Iteration 1 Error: 0.720852 Iteration 2 Error: 0.138651 Iteration 3 Error: 0.027308 Align patch 14 11 left Iteration 1 Error: 0.705973 Iteration 2 Error: 0.167231 Iteration 3 Error: 0.032658 Align patch 15 10 left Iteration 1 Error: 0.983006 Iteration 2 Error: 0.108699 Iteration 3 Error: 0.026030 Align patch 16 9 left Iteration 1 Error: 0.918023 Iteration 2 Error: 0.234557 Iteration 3 Error: 0.069115 Iteration 4 Error: 0.020546 Align patch 17 8 left Iteration 1 Error: 0.893033 Iteration 2 Error: 0.151888 Iteration 3 Error: 0.050430 Iteration 4 Error: 0.021453 Align patch 18 7 left Iteration 1 Error: 0.617809 Iteration 2 Error: 0.095377 Iteration 3 Error: 0.022254 Align patch 19 6 left Iteration 1 Error: 0.412823 Iteration 2 Error: 0.098127 Iteration 3 Error: 0.024448 Align patch 20 5 left Iteration 1 Error: 0.886615 Iteration 2 Error: 0.124756 Iteration 3 Error: 0.025836 Align patch 21 4 left Iteration 1 Error: 0.737260 Iteration 2 Error: 0.118079 Iteration 3 Error: 0.020089 Align patch 22 3 left Iteration 1 Error: 0.626749 Iteration 2 Error: 0.093423 Iteration 3 Error: 0.015677 Align patch 23 2 left Iteration 1 Error: 0.601405 Iteration 2 Error: 0.166501 Iteration 3 Error: 0.055980 Iteration 4 Error: 0.018931 Align patch 24 1 left Iteration 1 Error: 0.644364 Iteration 2 Error: 0.074149 Iteration 3 Error: 0.013753 Align patch 25 0 left Iteration 1 Error: 0.772326 Iteration 2 Error: 0.164127 Iteration 3 Error: 0.031576 3D Fitting completed. Patch alignment time: 17.09(sec) Local motion has been corrected. Process thread exits. Computational time: 25.910494 sec Total time: 32.661064 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00016hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00016hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.672282s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00016hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.560676s ........................................ >>>>>>TIME<<<<<< FFT: 1.057998s Defocus_U Defocus_V Angle CCC 13746.11 14621.11 5.43 0.059404 Final Values Defocus_U Defocus_V Angle CCC 13747.70 14622.70 5.12 0.095645 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00016hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00016hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.003e-01 CC threshold: 0.736 Mean Std: 41.21 7.02 Num Hot pixels: 194 Hot pixel threshold: 83.35 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.987773 Iteration 2 Error: 0.196816 Iteration 3 Error: 0.033968 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.07 0.31 ...... Frame ( 3) shift: 0.13 0.61 ...... Frame ( 4) shift: 0.20 0.92 ...... Frame ( 5) shift: 0.26 1.23 ...... Frame ( 6) shift: 0.33 1.37 ...... Frame ( 7) shift: 0.39 1.34 ...... Frame ( 8) shift: 0.45 1.31 ...... Frame ( 9) shift: 0.54 1.38 ...... Frame ( 10) shift: 0.65 1.54 ...... Frame ( 11) shift: 0.76 1.70 ...... Frame ( 12) shift: 0.88 1.82 ...... Frame ( 13) shift: 1.00 1.91 ...... Frame ( 14) shift: 1.12 2.00 ...... Frame ( 15) shift: 1.19 2.08 ...... Frame ( 16) shift: 1.21 2.15 ...... Frame ( 17) shift: 1.24 2.22 ...... Frame ( 18) shift: 1.29 2.26 ...... Frame ( 19) shift: 1.35 2.26 ...... Frame ( 20) shift: 1.42 2.26 ...... Frame ( 21) shift: 1.50 2.26 ...... Frame ( 22) shift: 1.59 2.26 ...... Frame ( 23) shift: 1.68 2.26 ...... Frame ( 24) shift: 1.76 2.27 ...... Frame ( 25) shift: 1.83 2.29 ...... Frame ( 26) shift: 1.91 2.32 ...... Frame ( 27) shift: 1.96 2.32 ...... Frame ( 28) shift: 1.99 2.31 ...... Frame ( 29) shift: 2.01 2.30 ...... Frame ( 30) shift: 2.02 2.30 ...... Frame ( 31) shift: 2.00 2.30 ...... Frame ( 32) shift: 1.99 2.31 ...... Frame ( 33) shift: 2.01 2.33 ...... Frame ( 34) shift: 2.06 2.37 ...... Frame ( 35) shift: 2.12 2.41 ...... Frame ( 36) shift: 2.18 2.42 ...... Frame ( 37) shift: 2.24 2.42 ...... Frame ( 38) shift: 2.30 2.41 ...... Frame ( 39) shift: 2.36 2.41 ...... Frame ( 40) shift: 2.42 2.41 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.022953 Iteration 2 Error: 0.341827 Iteration 3 Error: 0.089657 Iteration 4 Error: 0.029602 Align patch 2 23 left Iteration 1 Error: 0.877516 Iteration 2 Error: 0.182364 Iteration 3 Error: 0.044958 Align patch 3 22 left Iteration 1 Error: 0.619733 Iteration 2 Error: 0.130630 Iteration 3 Error: 0.046713 Align patch 4 21 left Iteration 1 Error: 0.803404 Iteration 2 Error: 0.067990 Iteration 3 Error: 0.012652 Align patch 5 20 left Iteration 1 Error: 0.554959 Iteration 2 Error: 0.047497 Align patch 6 19 left Iteration 1 Error: 1.120599 Iteration 2 Error: 0.133020 Iteration 3 Error: 0.034867 Align patch 7 18 left Iteration 1 Error: 0.975778 Iteration 2 Error: 0.112532 Iteration 3 Error: 0.021939 Align patch 8 17 left Iteration 1 Error: 0.817529 Iteration 2 Error: 0.112418 Iteration 3 Error: 0.023699 Align patch 9 16 left Iteration 1 Error: 0.365059 Iteration 2 Error: 0.052039 Iteration 3 Error: 0.008070 Align patch 10 15 left Iteration 1 Error: 0.507702 Iteration 2 Error: 0.082727 Iteration 3 Error: 0.015366 Align patch 11 14 left Iteration 1 Error: 0.830460 Iteration 2 Error: 0.159526 Iteration 3 Error: 0.037385 Align patch 12 13 left Iteration 1 Error: 0.568686 Iteration 2 Error: 0.108190 Iteration 3 Error: 0.031016 Align patch 13 12 left Iteration 1 Error: 0.464560 Iteration 2 Error: 0.067490 Iteration 3 Error: 0.017377 Align patch 14 11 left Iteration 1 Error: 0.472805 Iteration 2 Error: 0.038239 Align patch 15 10 left Iteration 1 Error: 0.552698 Iteration 2 Error: 0.064991 Iteration 3 Error: 0.019341 Align patch 16 9 left Iteration 1 Error: 1.006328 Iteration 2 Error: 0.092880 Iteration 3 Error: 0.032348 Align patch 17 8 left Iteration 1 Error: 0.461792 Iteration 2 Error: 0.050029 Iteration 3 Error: 0.015377 Align patch 18 7 left Iteration 1 Error: 0.549510 Iteration 2 Error: 0.107485 Iteration 3 Error: 0.019784 Align patch 19 6 left Iteration 1 Error: 0.791401 Iteration 2 Error: 0.107094 Iteration 3 Error: 0.022346 Align patch 20 5 left Iteration 1 Error: 0.460213 Iteration 2 Error: 0.075607 Iteration 3 Error: 0.017099 Align patch 21 4 left Iteration 1 Error: 0.786076 Iteration 2 Error: 0.145289 Iteration 3 Error: 0.030500 Align patch 22 3 left Iteration 1 Error: 0.622459 Iteration 2 Error: 0.104320 Iteration 3 Error: 0.023010 Align patch 23 2 left Iteration 1 Error: 0.564287 Iteration 2 Error: 0.127643 Iteration 3 Error: 0.037618 Align patch 24 1 left Iteration 1 Error: 0.925446 Iteration 2 Error: 0.206664 Iteration 3 Error: 0.049350 Align patch 25 0 left Iteration 1 Error: 0.801719 Iteration 2 Error: 0.108860 Iteration 3 Error: 0.012974 3D Fitting completed. Patch alignment time: 15.27(sec) Local motion has been corrected. Process thread exits. Computational time: 23.529947 sec Total time: 28.729834 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00016hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00016hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.737070s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00016hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.778218s ........................................ >>>>>>TIME<<<<<< FFT: 1.013052s Defocus_U Defocus_V Angle CCC 13660.17 12980.45 85.29 0.060237 Final Values Defocus_U Defocus_V Angle CCC 13641.42 13002.33 85.61 0.094573 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00017hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00017hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 41.11 6.94 Num Hot pixels: 210 Hot pixel threshold: 82.78 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.295903 Iteration 2 Error: 0.235146 Iteration 3 Error: 0.051930 Iteration 4 Error: 0.019093 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.23 -0.15 ...... Frame ( 3) shift: -0.47 -0.30 ...... Frame ( 4) shift: -0.70 -0.45 ...... Frame ( 5) shift: -0.93 -0.60 ...... Frame ( 6) shift: -1.02 -0.65 ...... Frame ( 7) shift: -0.97 -0.61 ...... Frame ( 8) shift: -0.91 -0.57 ...... Frame ( 9) shift: -0.84 -0.48 ...... Frame ( 10) shift: -0.76 -0.34 ...... Frame ( 11) shift: -0.69 -0.19 ...... Frame ( 12) shift: -0.64 -0.09 ...... Frame ( 13) shift: -0.63 -0.03 ...... Frame ( 14) shift: -0.62 0.02 ...... Frame ( 15) shift: -0.57 0.10 ...... Frame ( 16) shift: -0.49 0.18 ...... Frame ( 17) shift: -0.41 0.27 ...... Frame ( 18) shift: -0.35 0.35 ...... Frame ( 19) shift: -0.32 0.42 ...... Frame ( 20) shift: -0.28 0.50 ...... Frame ( 21) shift: -0.27 0.57 ...... Frame ( 22) shift: -0.27 0.63 ...... Frame ( 23) shift: -0.26 0.69 ...... Frame ( 24) shift: -0.22 0.74 ...... Frame ( 25) shift: -0.12 0.80 ...... Frame ( 26) shift: -0.03 0.86 ...... Frame ( 27) shift: 0.03 0.91 ...... Frame ( 28) shift: 0.06 0.96 ...... Frame ( 29) shift: 0.08 1.01 ...... Frame ( 30) shift: 0.13 1.05 ...... Frame ( 31) shift: 0.19 1.09 ...... Frame ( 32) shift: 0.25 1.13 ...... Frame ( 33) shift: 0.29 1.19 ...... Frame ( 34) shift: 0.29 1.26 ...... Frame ( 35) shift: 0.29 1.34 ...... Frame ( 36) shift: 0.31 1.42 ...... Frame ( 37) shift: 0.36 1.50 ...... Frame ( 38) shift: 0.40 1.57 ...... Frame ( 39) shift: 0.45 1.65 ...... Frame ( 40) shift: 0.50 1.73 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.512352 Iteration 2 Error: 0.354836 Iteration 3 Error: 0.131798 Iteration 4 Error: 0.040150 Align patch 2 23 left Iteration 1 Error: 0.714006 Iteration 2 Error: 0.189466 Iteration 3 Error: 0.069226 Iteration 4 Error: 0.025060 Align patch 3 22 left Iteration 1 Error: 0.619313 Iteration 2 Error: 0.087298 Iteration 3 Error: 0.022455 Align patch 4 21 left Iteration 1 Error: 0.600652 Iteration 2 Error: 0.072988 Iteration 3 Error: 0.012851 Align patch 5 20 left Iteration 1 Error: 0.589445 Iteration 2 Error: 0.060662 Iteration 3 Error: 0.016232 Align patch 6 19 left Iteration 1 Error: 0.995769 Iteration 2 Error: 0.230539 Iteration 3 Error: 0.047808 Align patch 7 18 left Iteration 1 Error: 0.632635 Iteration 2 Error: 0.119517 Iteration 3 Error: 0.045359 Align patch 8 17 left Iteration 1 Error: 0.635627 Iteration 2 Error: 0.139907 Iteration 3 Error: 0.016424 Align patch 9 16 left Iteration 1 Error: 0.567328 Iteration 2 Error: 0.094626 Iteration 3 Error: 0.012505 Align patch 10 15 left Iteration 1 Error: 0.486450 Iteration 2 Error: 0.049774 Align patch 11 14 left Iteration 1 Error: 0.634841 Iteration 2 Error: 0.214445 Iteration 3 Error: 0.057998 Iteration 4 Error: 0.028999 Align patch 12 13 left Iteration 1 Error: 0.453764 Iteration 2 Error: 0.074880 Iteration 3 Error: 0.014829 Align patch 13 12 left Iteration 1 Error: 0.462090 Iteration 2 Error: 0.066686 Iteration 3 Error: 0.018728 Align patch 14 11 left Iteration 1 Error: 0.348259 Iteration 2 Error: 0.064811 Iteration 3 Error: 0.010767 Align patch 15 10 left Iteration 1 Error: 0.440974 Iteration 2 Error: 0.063057 Iteration 3 Error: 0.013829 Align patch 16 9 left Iteration 1 Error: 1.368884 Iteration 2 Error: 0.276408 Iteration 3 Error: 0.081622 Iteration 4 Error: 0.036798 Align patch 17 8 left Iteration 1 Error: 0.495711 Iteration 2 Error: 0.115088 Iteration 3 Error: 0.033032 Align patch 18 7 left Iteration 1 Error: 0.611069 Iteration 2 Error: 0.062437 Iteration 3 Error: 0.015204 Align patch 19 6 left Iteration 1 Error: 0.842499 Iteration 2 Error: 0.077655 Iteration 3 Error: 0.018589 Align patch 20 5 left Iteration 1 Error: 0.691679 Iteration 2 Error: 0.073572 Iteration 3 Error: 0.019594 Align patch 21 4 left Iteration 1 Error: 0.971303 Iteration 2 Error: 0.096439 Iteration 3 Error: 0.036326 Align patch 22 3 left Iteration 1 Error: 0.840711 Iteration 2 Error: 0.128473 Iteration 3 Error: 0.029052 Align patch 23 2 left Iteration 1 Error: 0.594928 Iteration 2 Error: 0.153449 Iteration 3 Error: 0.045650 Align patch 24 1 left Iteration 1 Error: 0.643794 Iteration 2 Error: 0.070770 Iteration 3 Error: 0.018515 Align patch 25 0 left Iteration 1 Error: 0.802815 Iteration 2 Error: 0.064690 Iteration 3 Error: 0.015530 3D Fitting completed. Patch alignment time: 14.54(sec) Local motion has been corrected. Process thread exits. Computational time: 23.033689 sec Total time: 29.523472 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00017hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00017hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.608577s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00017hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.822331s ........................................ >>>>>>TIME<<<<<< FFT: 0.944533s Defocus_U Defocus_V Angle CCC 11669.92 12498.05 13.65 0.056204 Final Values Defocus_U Defocus_V Angle CCC 11679.30 12510.55 13.65 0.094564 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00017hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00017hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 41.33 6.97 Num Hot pixels: 195 Hot pixel threshold: 83.14 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.365204 Iteration 2 Error: 0.242236 Iteration 3 Error: 0.059826 Iteration 4 Error: 0.019151 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.26 -0.15 ...... Frame ( 3) shift: -0.52 -0.30 ...... Frame ( 4) shift: -0.79 -0.46 ...... Frame ( 5) shift: -1.05 -0.61 ...... Frame ( 6) shift: -1.13 -0.65 ...... Frame ( 7) shift: -1.04 -0.59 ...... Frame ( 8) shift: -0.95 -0.53 ...... Frame ( 9) shift: -0.90 -0.43 ...... Frame ( 10) shift: -0.88 -0.28 ...... Frame ( 11) shift: -0.87 -0.13 ...... Frame ( 12) shift: -0.81 -0.01 ...... Frame ( 13) shift: -0.69 0.09 ...... Frame ( 14) shift: -0.58 0.18 ...... Frame ( 15) shift: -0.53 0.29 ...... Frame ( 16) shift: -0.53 0.42 ...... Frame ( 17) shift: -0.54 0.54 ...... Frame ( 18) shift: -0.52 0.65 ...... Frame ( 19) shift: -0.49 0.74 ...... Frame ( 20) shift: -0.45 0.84 ...... Frame ( 21) shift: -0.41 0.91 ...... Frame ( 22) shift: -0.35 0.96 ...... Frame ( 23) shift: -0.29 1.01 ...... Frame ( 24) shift: -0.21 1.05 ...... Frame ( 25) shift: -0.11 1.09 ...... Frame ( 26) shift: -0.01 1.12 ...... Frame ( 27) shift: 0.05 1.16 ...... Frame ( 28) shift: 0.08 1.20 ...... Frame ( 29) shift: 0.10 1.24 ...... Frame ( 30) shift: 0.12 1.29 ...... Frame ( 31) shift: 0.13 1.35 ...... Frame ( 32) shift: 0.15 1.40 ...... Frame ( 33) shift: 0.19 1.44 ...... Frame ( 34) shift: 0.26 1.46 ...... Frame ( 35) shift: 0.33 1.48 ...... Frame ( 36) shift: 0.38 1.50 ...... Frame ( 37) shift: 0.41 1.54 ...... Frame ( 38) shift: 0.44 1.58 ...... Frame ( 39) shift: 0.47 1.62 ...... Frame ( 40) shift: 0.50 1.66 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.633200 Iteration 2 Error: 0.321152 Iteration 3 Error: 0.180861 Iteration 4 Error: 0.076737 Iteration 5 Error: 0.038145 Align patch 2 23 left Iteration 1 Error: 1.084094 Iteration 2 Error: 0.251817 Iteration 3 Error: 0.065523 Iteration 4 Error: 0.033702 Align patch 3 22 left Iteration 1 Error: 0.961430 Iteration 2 Error: 0.123626 Iteration 3 Error: 0.048252 Align patch 4 21 left Iteration 1 Error: 0.711351 Iteration 2 Error: 0.107415 Iteration 3 Error: 0.027469 Align patch 5 20 left Iteration 1 Error: 0.621897 Iteration 2 Error: 0.157613 Iteration 3 Error: 0.040903 Align patch 6 19 left Iteration 1 Error: 1.541556 Iteration 2 Error: 0.333858 Iteration 3 Error: 0.097314 Iteration 4 Error: 0.042935 Align patch 7 18 left Iteration 1 Error: 0.575739 Iteration 2 Error: 0.150258 Iteration 3 Error: 0.042394 Align patch 8 17 left Iteration 1 Error: 0.723942 Iteration 2 Error: 0.136408 Iteration 3 Error: 0.049469 Align patch 9 16 left Iteration 1 Error: 0.425814 Iteration 2 Error: 0.086635 Iteration 3 Error: 0.016999 Align patch 10 15 left Iteration 1 Error: 0.739527 Iteration 2 Error: 0.127520 Iteration 3 Error: 0.025545 Align patch 11 14 left Iteration 1 Error: 1.748633 Iteration 2 Error: 0.268885 Iteration 3 Error: 0.123352 Iteration 4 Error: 0.044372 Align patch 12 13 left Iteration 1 Error: 0.768630 Iteration 2 Error: 0.207455 Iteration 3 Error: 0.070164 Iteration 4 Error: 0.027585 Align patch 13 12 left Iteration 1 Error: 0.544109 Iteration 2 Error: 0.092564 Iteration 3 Error: 0.027583 Align patch 14 11 left Iteration 1 Error: 0.987167 Iteration 2 Error: 0.194047 Iteration 3 Error: 0.072576 Iteration 4 Error: 0.015742 Align patch 15 10 left Iteration 1 Error: 0.643210 Iteration 2 Error: 0.127044 Iteration 3 Error: 0.028734 Align patch 16 9 left Iteration 1 Error: 0.670218 Iteration 2 Error: 0.095959 Iteration 3 Error: 0.027480 Align patch 17 8 left Iteration 1 Error: 0.803692 Iteration 2 Error: 0.076458 Iteration 3 Error: 0.026245 Align patch 18 7 left Iteration 1 Error: 0.652487 Iteration 2 Error: 0.121648 Iteration 3 Error: 0.040317 Align patch 19 6 left Iteration 1 Error: 0.452520 Iteration 2 Error: 0.070957 Iteration 3 Error: 0.024375 Align patch 20 5 left Iteration 1 Error: 0.904230 Iteration 2 Error: 0.219532 Iteration 3 Error: 0.066169 Iteration 4 Error: 0.018026 Align patch 21 4 left Iteration 1 Error: 1.269199 Iteration 2 Error: 0.141922 Iteration 3 Error: 0.034716 Align patch 22 3 left Iteration 1 Error: 0.586357 Iteration 2 Error: 0.084130 Iteration 3 Error: 0.017672 Align patch 23 2 left Iteration 1 Error: 0.625867 Iteration 2 Error: 0.121727 Iteration 3 Error: 0.025514 Align patch 24 1 left Iteration 1 Error: 0.729298 Iteration 2 Error: 0.124317 Iteration 3 Error: 0.049197 Align patch 25 0 left Iteration 1 Error: 0.822930 Iteration 2 Error: 0.222598 Iteration 3 Error: 0.058587 Iteration 4 Error: 0.023280 3D Fitting completed. Patch alignment time: 15.47(sec) Local motion has been corrected. Process thread exits. Computational time: 24.277458 sec Total time: 31.347479 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00017hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00017hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.598271s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00017hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.710975s ........................................ >>>>>>TIME<<<<<< FFT: 0.945741s Defocus_U Defocus_V Angle CCC 10857.43 10341.79 89.70 0.049024 Final Values Defocus_U Defocus_V Angle CCC 10888.68 10351.18 87.52 0.085741 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00017hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00017hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 40.54 6.92 Num Hot pixels: 207 Hot pixel threshold: 82.08 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.792874 Iteration 2 Error: 0.112238 Iteration 3 Error: 0.022876 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.21 -0.27 ...... Frame ( 3) shift: -0.41 -0.54 ...... Frame ( 4) shift: -0.62 -0.81 ...... Frame ( 5) shift: -0.82 -1.08 ...... Frame ( 6) shift: -0.97 -1.22 ...... Frame ( 7) shift: -1.05 -1.24 ...... Frame ( 8) shift: -1.14 -1.26 ...... Frame ( 9) shift: -1.18 -1.23 ...... Frame ( 10) shift: -1.17 -1.16 ...... Frame ( 11) shift: -1.17 -1.09 ...... Frame ( 12) shift: -1.15 -1.00 ...... Frame ( 13) shift: -1.14 -0.90 ...... Frame ( 14) shift: -1.12 -0.79 ...... Frame ( 15) shift: -1.09 -0.69 ...... Frame ( 16) shift: -1.05 -0.60 ...... Frame ( 17) shift: -1.00 -0.51 ...... Frame ( 18) shift: -0.97 -0.44 ...... Frame ( 19) shift: -0.96 -0.41 ...... Frame ( 20) shift: -0.96 -0.37 ...... Frame ( 21) shift: -0.96 -0.35 ...... Frame ( 22) shift: -0.97 -0.33 ...... Frame ( 23) shift: -0.98 -0.31 ...... Frame ( 24) shift: -0.96 -0.25 ...... Frame ( 25) shift: -0.92 -0.15 ...... Frame ( 26) shift: -0.88 -0.05 ...... Frame ( 27) shift: -0.87 -0.01 ...... Frame ( 28) shift: -0.89 -0.03 ...... Frame ( 29) shift: -0.92 -0.05 ...... Frame ( 30) shift: -0.88 -0.04 ...... Frame ( 31) shift: -0.79 -0.01 ...... Frame ( 32) shift: -0.70 0.02 ...... Frame ( 33) shift: -0.63 0.04 ...... Frame ( 34) shift: -0.59 0.03 ...... Frame ( 35) shift: -0.55 0.03 ...... Frame ( 36) shift: -0.55 0.03 ...... Frame ( 37) shift: -0.57 0.05 ...... Frame ( 38) shift: -0.60 0.06 ...... Frame ( 39) shift: -0.63 0.08 ...... Frame ( 40) shift: -0.66 0.09 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.323312 Iteration 2 Error: 0.180445 Iteration 3 Error: 0.042569 Align patch 2 23 left Iteration 1 Error: 0.908171 Iteration 2 Error: 0.193118 Iteration 3 Error: 0.041665 Align patch 3 22 left Iteration 1 Error: 1.066899 Iteration 2 Error: 0.164435 Iteration 3 Error: 0.028367 Align patch 4 21 left Iteration 1 Error: 0.688446 Iteration 2 Error: 0.072058 Iteration 3 Error: 0.015034 Align patch 5 20 left Iteration 1 Error: 0.487617 Iteration 2 Error: 0.087783 Iteration 3 Error: 0.016451 Align patch 6 19 left Iteration 1 Error: 1.334557 Iteration 2 Error: 0.214454 Iteration 3 Error: 0.046030 Align patch 7 18 left Iteration 1 Error: 0.779732 Iteration 2 Error: 0.087186 Iteration 3 Error: 0.024518 Align patch 8 17 left Iteration 1 Error: 0.607902 Iteration 2 Error: 0.080216 Iteration 3 Error: 0.022349 Align patch 9 16 left Iteration 1 Error: 0.433925 Iteration 2 Error: 0.053971 Iteration 3 Error: 0.010093 Align patch 10 15 left Iteration 1 Error: 0.629416 Iteration 2 Error: 0.096866 Iteration 3 Error: 0.015633 Align patch 11 14 left Iteration 1 Error: 0.773098 Iteration 2 Error: 0.117111 Iteration 3 Error: 0.032311 Align patch 12 13 left Iteration 1 Error: 0.800090 Iteration 2 Error: 0.090832 Iteration 3 Error: 0.019741 Align patch 13 12 left Iteration 1 Error: 0.604497 Iteration 2 Error: 0.072477 Iteration 3 Error: 0.015686 Align patch 14 11 left Iteration 1 Error: 0.631261 Iteration 2 Error: 0.075260 Iteration 3 Error: 0.017064 Align patch 15 10 left Iteration 1 Error: 0.609578 Iteration 2 Error: 0.064331 Iteration 3 Error: 0.013019 Align patch 16 9 left Iteration 1 Error: 0.518451 Iteration 2 Error: 0.045430 Align patch 17 8 left Iteration 1 Error: 0.612251 Iteration 2 Error: 0.135645 Iteration 3 Error: 0.024618 Align patch 18 7 left Iteration 1 Error: 0.559924 Iteration 2 Error: 0.100604 Iteration 3 Error: 0.029808 Align patch 19 6 left Iteration 1 Error: 0.424685 Iteration 2 Error: 0.082807 Iteration 3 Error: 0.014879 Align patch 20 5 left Iteration 1 Error: 0.447059 Iteration 2 Error: 0.048793 Align patch 21 4 left Iteration 1 Error: 0.892889 Iteration 2 Error: 0.069333 Iteration 3 Error: 0.018772 Align patch 22 3 left Iteration 1 Error: 1.196934 Iteration 2 Error: 0.090906 Iteration 3 Error: 0.013917 Align patch 23 2 left Iteration 1 Error: 0.759087 Iteration 2 Error: 0.154509 Iteration 3 Error: 0.048743 Align patch 24 1 left Iteration 1 Error: 0.653247 Iteration 2 Error: 0.099482 Iteration 3 Error: 0.022962 Align patch 25 0 left Iteration 1 Error: 0.545313 Iteration 2 Error: 0.074707 Iteration 3 Error: 0.011251 3D Fitting completed. Patch alignment time: 15.34(sec) Local motion has been corrected. Process thread exits. Computational time: 23.629086 sec Total time: 30.286215 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00017hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00017hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.751052s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00017hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.510378s ........................................ >>>>>>TIME<<<<<< FFT: 0.903433s Defocus_U Defocus_V Angle CCC 12460.94 13429.69 5.66 0.059247 Final Values Defocus_U Defocus_V Angle CCC 12475.00 13443.75 6.29 0.094875 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00017hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00017hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.003e-01 CC threshold: 0.736 Mean Std: 40.99 6.98 Num Hot pixels: 190 Hot pixel threshold: 82.84 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.775553 Iteration 2 Error: 0.126879 Iteration 3 Error: 0.029031 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.33 -0.18 ...... Frame ( 3) shift: -0.65 -0.37 ...... Frame ( 4) shift: -0.98 -0.55 ...... Frame ( 5) shift: -1.30 -0.73 ...... Frame ( 6) shift: -1.48 -0.84 ...... Frame ( 7) shift: -1.50 -0.86 ...... Frame ( 8) shift: -1.53 -0.88 ...... Frame ( 9) shift: -1.53 -0.86 ...... Frame ( 10) shift: -1.51 -0.80 ...... Frame ( 11) shift: -1.49 -0.73 ...... Frame ( 12) shift: -1.46 -0.67 ...... Frame ( 13) shift: -1.42 -0.62 ...... Frame ( 14) shift: -1.38 -0.56 ...... Frame ( 15) shift: -1.33 -0.51 ...... Frame ( 16) shift: -1.28 -0.46 ...... Frame ( 17) shift: -1.22 -0.40 ...... Frame ( 18) shift: -1.18 -0.34 ...... Frame ( 19) shift: -1.14 -0.25 ...... Frame ( 20) shift: -1.10 -0.17 ...... Frame ( 21) shift: -1.09 -0.12 ...... Frame ( 22) shift: -1.12 -0.09 ...... Frame ( 23) shift: -1.16 -0.06 ...... Frame ( 24) shift: -1.17 0.01 ...... Frame ( 25) shift: -1.16 0.10 ...... Frame ( 26) shift: -1.15 0.19 ...... Frame ( 27) shift: -1.15 0.25 ...... Frame ( 28) shift: -1.14 0.28 ...... Frame ( 29) shift: -1.14 0.31 ...... Frame ( 30) shift: -1.15 0.37 ...... Frame ( 31) shift: -1.19 0.44 ...... Frame ( 32) shift: -1.23 0.52 ...... Frame ( 33) shift: -1.22 0.56 ...... Frame ( 34) shift: -1.16 0.57 ...... Frame ( 35) shift: -1.11 0.59 ...... Frame ( 36) shift: -1.06 0.58 ...... Frame ( 37) shift: -1.01 0.57 ...... Frame ( 38) shift: -0.97 0.55 ...... Frame ( 39) shift: -0.92 0.54 ...... Frame ( 40) shift: -0.88 0.52 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.455249 Iteration 2 Error: 0.249674 Iteration 3 Error: 0.043474 Align patch 2 23 left Iteration 1 Error: 0.635126 Iteration 2 Error: 0.078140 Iteration 3 Error: 0.020039 Align patch 3 22 left Iteration 1 Error: 0.700299 Iteration 2 Error: 0.167616 Iteration 3 Error: 0.045193 Align patch 4 21 left Iteration 1 Error: 0.759369 Iteration 2 Error: 0.076983 Iteration 3 Error: 0.015900 Align patch 5 20 left Iteration 1 Error: 0.326148 Iteration 2 Error: 0.072781 Iteration 3 Error: 0.017608 Align patch 6 19 left Iteration 1 Error: 1.343310 Iteration 2 Error: 0.224785 Iteration 3 Error: 0.053822 Iteration 4 Error: 0.023375 Align patch 7 18 left Iteration 1 Error: 0.771332 Iteration 2 Error: 0.125136 Iteration 3 Error: 0.032389 Align patch 8 17 left Iteration 1 Error: 0.684758 Iteration 2 Error: 0.161096 Iteration 3 Error: 0.032186 Align patch 9 16 left Iteration 1 Error: 0.825758 Iteration 2 Error: 0.100796 Iteration 3 Error: 0.026233 Align patch 10 15 left Iteration 1 Error: 0.486592 Iteration 2 Error: 0.067858 Iteration 3 Error: 0.018998 Align patch 11 14 left Iteration 1 Error: 1.728252 Iteration 2 Error: 0.252320 Iteration 3 Error: 0.073717 Iteration 4 Error: 0.019595 Align patch 12 13 left Iteration 1 Error: 0.989312 Iteration 2 Error: 0.162732 Iteration 3 Error: 0.046375 Align patch 13 12 left Iteration 1 Error: 0.822819 Iteration 2 Error: 0.112934 Iteration 3 Error: 0.023859 Align patch 14 11 left Iteration 1 Error: 0.794949 Iteration 2 Error: 0.125278 Iteration 3 Error: 0.019494 Align patch 15 10 left Iteration 1 Error: 0.683786 Iteration 2 Error: 0.116855 Iteration 3 Error: 0.018905 Align patch 16 9 left Iteration 1 Error: 0.834762 Iteration 2 Error: 0.086833 Iteration 3 Error: 0.023963 Align patch 17 8 left Iteration 1 Error: 0.980071 Iteration 2 Error: 0.159424 Iteration 3 Error: 0.030668 Align patch 18 7 left Iteration 1 Error: 0.535003 Iteration 2 Error: 0.075481 Iteration 3 Error: 0.016917 Align patch 19 6 left Iteration 1 Error: 0.645524 Iteration 2 Error: 0.075952 Iteration 3 Error: 0.010056 Align patch 20 5 left Iteration 1 Error: 0.524160 Iteration 2 Error: 0.077616 Iteration 3 Error: 0.012628 Align patch 21 4 left Iteration 1 Error: 1.105968 Iteration 2 Error: 0.127853 Iteration 3 Error: 0.024631 Align patch 22 3 left Iteration 1 Error: 0.618032 Iteration 2 Error: 0.107100 Iteration 3 Error: 0.025481 Align patch 23 2 left Iteration 1 Error: 0.876046 Iteration 2 Error: 0.121266 Iteration 3 Error: 0.028759 Align patch 24 1 left Iteration 1 Error: 0.998971 Iteration 2 Error: 0.113671 Iteration 3 Error: 0.025757 Align patch 25 0 left Iteration 1 Error: 0.888188 Iteration 2 Error: 0.119104 Iteration 3 Error: 0.029765 3D Fitting completed. Patch alignment time: 15.60(sec) Local motion has been corrected. Process thread exits. Computational time: 23.946173 sec Total time: 29.730307 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00017hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00017hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.732045s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00017hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.896817s ........................................ >>>>>>TIME<<<<<< FFT: 0.935639s Defocus_U Defocus_V Angle CCC 14808.63 14148.44 85.07 0.063880 Final Values Defocus_U Defocus_V Angle CCC 14813.31 14156.26 85.70 0.103243 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00018hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00018hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 39.98 6.84 Num Hot pixels: 225 Hot pixel threshold: 81.02 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.796006 Iteration 2 Error: 0.140889 Iteration 3 Error: 0.035911 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.09 -0.01 ...... Frame ( 3) shift: -0.18 -0.02 ...... Frame ( 4) shift: -0.28 -0.02 ...... Frame ( 5) shift: -0.37 -0.03 ...... Frame ( 6) shift: -0.39 -0.01 ...... Frame ( 7) shift: -0.33 0.04 ...... Frame ( 8) shift: -0.28 0.09 ...... Frame ( 9) shift: -0.26 0.10 ...... Frame ( 10) shift: -0.26 0.08 ...... Frame ( 11) shift: -0.27 0.06 ...... Frame ( 12) shift: -0.23 0.09 ...... Frame ( 13) shift: -0.15 0.15 ...... Frame ( 14) shift: -0.07 0.22 ...... Frame ( 15) shift: -0.06 0.28 ...... Frame ( 16) shift: -0.11 0.34 ...... Frame ( 17) shift: -0.15 0.40 ...... Frame ( 18) shift: -0.15 0.46 ...... Frame ( 19) shift: -0.11 0.54 ...... Frame ( 20) shift: -0.06 0.62 ...... Frame ( 21) shift: -0.04 0.69 ...... Frame ( 22) shift: -0.03 0.76 ...... Frame ( 23) shift: -0.02 0.83 ...... Frame ( 24) shift: -0.02 0.90 ...... Frame ( 25) shift: -0.03 0.98 ...... Frame ( 26) shift: -0.04 1.05 ...... Frame ( 27) shift: -0.01 1.11 ...... Frame ( 28) shift: 0.06 1.15 ...... Frame ( 29) shift: 0.12 1.19 ...... Frame ( 30) shift: 0.17 1.20 ...... Frame ( 31) shift: 0.19 1.17 ...... Frame ( 32) shift: 0.21 1.14 ...... Frame ( 33) shift: 0.24 1.16 ...... Frame ( 34) shift: 0.29 1.23 ...... Frame ( 35) shift: 0.34 1.31 ...... Frame ( 36) shift: 0.38 1.35 ...... Frame ( 37) shift: 0.42 1.37 ...... Frame ( 38) shift: 0.46 1.39 ...... Frame ( 39) shift: 0.49 1.40 ...... Frame ( 40) shift: 0.53 1.42 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.588945 Iteration 2 Error: 0.057658 Iteration 3 Error: 0.018138 Align patch 2 23 left Iteration 1 Error: 1.039276 Iteration 2 Error: 0.136791 Iteration 3 Error: 0.038332 Align patch 3 22 left Iteration 1 Error: 0.662738 Iteration 2 Error: 0.109393 Iteration 3 Error: 0.024972 Align patch 4 21 left Iteration 1 Error: 1.025640 Iteration 2 Error: 0.151833 Iteration 3 Error: 0.036606 Align patch 5 20 left Iteration 1 Error: 0.978706 Iteration 2 Error: 0.104781 Iteration 3 Error: 0.028002 Align patch 6 19 left Iteration 1 Error: 0.942289 Iteration 2 Error: 0.155407 Iteration 3 Error: 0.049027 Align patch 7 18 left Iteration 1 Error: 0.739277 Iteration 2 Error: 0.156148 Iteration 3 Error: 0.034438 Align patch 8 17 left Iteration 1 Error: 0.701206 Iteration 2 Error: 0.107585 Iteration 3 Error: 0.023942 Align patch 9 16 left Iteration 1 Error: 0.781802 Iteration 2 Error: 0.116523 Iteration 3 Error: 0.032368 Align patch 10 15 left Iteration 1 Error: 0.538467 Iteration 2 Error: 0.070130 Iteration 3 Error: 0.011654 Align patch 11 14 left Iteration 1 Error: 1.111148 Iteration 2 Error: 0.154353 Iteration 3 Error: 0.045874 Align patch 12 13 left Iteration 1 Error: 0.678315 Iteration 2 Error: 0.123447 Iteration 3 Error: 0.051175 Iteration 4 Error: 0.019806 Align patch 13 12 left Iteration 1 Error: 0.687295 Iteration 2 Error: 0.059713 Iteration 3 Error: 0.015298 Align patch 14 11 left Iteration 1 Error: 0.713937 Iteration 2 Error: 0.100648 Iteration 3 Error: 0.015191 Align patch 15 10 left Iteration 1 Error: 0.501890 Iteration 2 Error: 0.071409 Iteration 3 Error: 0.015304 Align patch 16 9 left Iteration 1 Error: 0.672606 Iteration 2 Error: 0.117331 Iteration 3 Error: 0.020168 Align patch 17 8 left Iteration 1 Error: 0.659484 Iteration 2 Error: 0.119064 Iteration 3 Error: 0.035034 Align patch 18 7 left Iteration 1 Error: 0.504221 Iteration 2 Error: 0.110989 Iteration 3 Error: 0.021626 Align patch 19 6 left Iteration 1 Error: 0.480404 Iteration 2 Error: 0.112773 Iteration 3 Error: 0.022368 Align patch 20 5 left Iteration 1 Error: 0.591467 Iteration 2 Error: 0.087890 Iteration 3 Error: 0.025225 Align patch 21 4 left Iteration 1 Error: 0.733337 Iteration 2 Error: 0.075879 Iteration 3 Error: 0.015809 Align patch 22 3 left Iteration 1 Error: 0.906197 Iteration 2 Error: 0.122796 Iteration 3 Error: 0.024820 Align patch 23 2 left Iteration 1 Error: 0.997397 Iteration 2 Error: 0.103108 Iteration 3 Error: 0.018990 Align patch 24 1 left Iteration 1 Error: 0.789054 Iteration 2 Error: 0.140130 Iteration 3 Error: 0.050461 Iteration 4 Error: 0.014305 Align patch 25 0 left Iteration 1 Error: 0.652666 Iteration 2 Error: 0.161987 Iteration 3 Error: 0.040829 3D Fitting completed. Patch alignment time: 15.57(sec) Local motion has been corrected. Process thread exits. Computational time: 24.833590 sec Total time: 30.660707 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00018hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00018hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.612408s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00018hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.671245s ........................................ >>>>>>TIME<<<<<< FFT: 1.141830s Defocus_U Defocus_V Angle CCC 10279.35 11138.72 9.72 0.037736 Final Values Defocus_U Defocus_V Angle CCC 10301.24 11185.63 9.74 0.064520 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00018hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00018hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.351e-01 1.005e-01 CC threshold: 0.738 Mean Std: 40.86 6.97 Num Hot pixels: 191 Hot pixel threshold: 82.66 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.509492 Iteration 2 Error: 0.069137 Iteration 3 Error: 0.008175 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.15 -0.02 ...... Frame ( 3) shift: -0.30 -0.03 ...... Frame ( 4) shift: -0.46 -0.05 ...... Frame ( 5) shift: -0.61 -0.07 ...... Frame ( 6) shift: -0.69 -0.09 ...... Frame ( 7) shift: -0.70 -0.11 ...... Frame ( 8) shift: -0.71 -0.13 ...... Frame ( 9) shift: -0.68 -0.12 ...... Frame ( 10) shift: -0.62 -0.09 ...... Frame ( 11) shift: -0.55 -0.06 ...... Frame ( 12) shift: -0.53 -0.03 ...... Frame ( 13) shift: -0.56 0.00 ...... Frame ( 14) shift: -0.59 0.03 ...... Frame ( 15) shift: -0.61 0.06 ...... Frame ( 16) shift: -0.62 0.09 ...... Frame ( 17) shift: -0.62 0.13 ...... Frame ( 18) shift: -0.65 0.17 ...... Frame ( 19) shift: -0.68 0.22 ...... Frame ( 20) shift: -0.72 0.27 ...... Frame ( 21) shift: -0.75 0.31 ...... Frame ( 22) shift: -0.77 0.32 ...... Frame ( 23) shift: -0.79 0.33 ...... Frame ( 24) shift: -0.79 0.33 ...... Frame ( 25) shift: -0.77 0.32 ...... Frame ( 26) shift: -0.75 0.31 ...... Frame ( 27) shift: -0.77 0.33 ...... Frame ( 28) shift: -0.81 0.37 ...... Frame ( 29) shift: -0.86 0.40 ...... Frame ( 30) shift: -0.84 0.43 ...... Frame ( 31) shift: -0.76 0.43 ...... Frame ( 32) shift: -0.67 0.43 ...... Frame ( 33) shift: -0.60 0.47 ...... Frame ( 34) shift: -0.53 0.53 ...... Frame ( 35) shift: -0.47 0.59 ...... Frame ( 36) shift: -0.44 0.64 ...... Frame ( 37) shift: -0.46 0.68 ...... Frame ( 38) shift: -0.47 0.71 ...... Frame ( 39) shift: -0.48 0.74 ...... Frame ( 40) shift: -0.50 0.78 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.849191 Iteration 2 Error: 0.165065 Iteration 3 Error: 0.038389 Align patch 2 23 left Iteration 1 Error: 0.731778 Iteration 2 Error: 0.079701 Iteration 3 Error: 0.021402 Align patch 3 22 left Iteration 1 Error: 0.776255 Iteration 2 Error: 0.109806 Iteration 3 Error: 0.024297 Align patch 4 21 left Iteration 1 Error: 0.633936 Iteration 2 Error: 0.051329 Iteration 3 Error: 0.009130 Align patch 5 20 left Iteration 1 Error: 0.748052 Iteration 2 Error: 0.168913 Iteration 3 Error: 0.039026 Align patch 6 19 left Iteration 1 Error: 0.870254 Iteration 2 Error: 0.109014 Iteration 3 Error: 0.022840 Align patch 7 18 left Iteration 1 Error: 0.709855 Iteration 2 Error: 0.092750 Iteration 3 Error: 0.022260 Align patch 8 17 left Iteration 1 Error: 0.433786 Iteration 2 Error: 0.064187 Iteration 3 Error: 0.016290 Align patch 9 16 left Iteration 1 Error: 0.559482 Iteration 2 Error: 0.068089 Iteration 3 Error: 0.018408 Align patch 10 15 left Iteration 1 Error: 0.438599 Iteration 2 Error: 0.082452 Iteration 3 Error: 0.010911 Align patch 11 14 left Iteration 1 Error: 0.690380 Iteration 2 Error: 0.045822 Align patch 12 13 left Iteration 1 Error: 0.592231 Iteration 2 Error: 0.064249 Iteration 3 Error: 0.022448 Align patch 13 12 left Iteration 1 Error: 0.401416 Iteration 2 Error: 0.083050 Iteration 3 Error: 0.011635 Align patch 14 11 left Iteration 1 Error: 0.599646 Iteration 2 Error: 0.138661 Iteration 3 Error: 0.021711 Align patch 15 10 left Iteration 1 Error: 0.556321 Iteration 2 Error: 0.049011 Align patch 16 9 left Iteration 1 Error: 0.823196 Iteration 2 Error: 0.087467 Iteration 3 Error: 0.023700 Align patch 17 8 left Iteration 1 Error: 0.395472 Iteration 2 Error: 0.069100 Iteration 3 Error: 0.021980 Align patch 18 7 left Iteration 1 Error: 0.572033 Iteration 2 Error: 0.091765 Iteration 3 Error: 0.017819 Align patch 19 6 left Iteration 1 Error: 0.507201 Iteration 2 Error: 0.081030 Iteration 3 Error: 0.012024 Align patch 20 5 left Iteration 1 Error: 0.605566 Iteration 2 Error: 0.069935 Iteration 3 Error: 0.009652 Align patch 21 4 left Iteration 1 Error: 0.868337 Iteration 2 Error: 0.107701 Iteration 3 Error: 0.025530 Align patch 22 3 left Iteration 1 Error: 0.910743 Iteration 2 Error: 0.128648 Iteration 3 Error: 0.036923 Align patch 23 2 left Iteration 1 Error: 0.700695 Iteration 2 Error: 0.078804 Iteration 3 Error: 0.021129 Align patch 24 1 left Iteration 1 Error: 0.475703 Iteration 2 Error: 0.071371 Iteration 3 Error: 0.012605 Align patch 25 0 left Iteration 1 Error: 0.538517 Iteration 2 Error: 0.060441 Iteration 3 Error: 0.009319 3D Fitting completed. Patch alignment time: 14.30(sec) Local motion has been corrected. Process thread exits. Computational time: 22.610825 sec Total time: 29.165361 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00018hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00018hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.547280s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00018hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.676887s ........................................ >>>>>>TIME<<<<<< FFT: 1.011117s Defocus_U Defocus_V Angle CCC 11324.23 11855.49 0.91 0.066195 Final Values Defocus_U Defocus_V Angle CCC 11339.82 11861.79 1.85 0.108359 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00018hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00018hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 1.000e-01 CC threshold: 0.734 Mean Std: 28.55 5.81 Num Hot pixels: 168 Hot pixel threshold: 63.39 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.821964 Iteration 2 Error: 0.340918 Iteration 3 Error: 0.095024 Iteration 4 Error: 0.034000 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.43 0.44 ...... Frame ( 3) shift: 0.86 0.89 ...... Frame ( 4) shift: 1.30 1.33 ...... Frame ( 5) shift: 1.73 1.78 ...... Frame ( 6) shift: 1.97 2.07 ...... Frame ( 7) shift: 2.03 2.20 ...... Frame ( 8) shift: 2.09 2.34 ...... Frame ( 9) shift: 2.16 2.46 ...... Frame ( 10) shift: 2.25 2.57 ...... Frame ( 11) shift: 2.33 2.68 ...... Frame ( 12) shift: 2.36 2.78 ...... Frame ( 13) shift: 2.33 2.87 ...... Frame ( 14) shift: 2.31 2.97 ...... Frame ( 15) shift: 2.31 3.03 ...... Frame ( 16) shift: 2.34 3.08 ...... Frame ( 17) shift: 2.37 3.13 ...... Frame ( 18) shift: 2.38 3.17 ...... Frame ( 19) shift: 2.36 3.20 ...... Frame ( 20) shift: 2.34 3.24 ...... Frame ( 21) shift: 2.35 3.30 ...... Frame ( 22) shift: 2.40 3.38 ...... Frame ( 23) shift: 2.44 3.47 ...... Frame ( 24) shift: 2.48 3.59 ...... Frame ( 25) shift: 2.50 3.74 ...... Frame ( 26) shift: 2.52 3.89 ...... Frame ( 27) shift: 2.52 3.95 ...... Frame ( 28) shift: 2.49 3.93 ...... Frame ( 29) shift: 2.47 3.91 ...... Frame ( 30) shift: 2.49 3.95 ...... Frame ( 31) shift: 2.55 4.07 ...... Frame ( 32) shift: 2.62 4.19 ...... Frame ( 33) shift: 2.65 4.27 ...... Frame ( 34) shift: 2.63 4.32 ...... Frame ( 35) shift: 2.62 4.37 ...... Frame ( 36) shift: 2.61 4.37 ...... Frame ( 37) shift: 2.62 4.33 ...... Frame ( 38) shift: 2.62 4.29 ...... Frame ( 39) shift: 2.62 4.25 ...... Frame ( 40) shift: 2.62 4.21 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.892998 Iteration 2 Error: 0.385502 Iteration 3 Error: 0.123274 Iteration 4 Error: 0.031894 Align patch 2 23 left Iteration 1 Error: 3.855719 Iteration 2 Error: 0.622172 Iteration 3 Error: 0.196128 Iteration 4 Error: 0.064032 Iteration 5 Error: 0.038002 Align patch 3 22 left Iteration 1 Error: 2.304796 Iteration 2 Error: 0.277189 Iteration 3 Error: 0.187235 Iteration 4 Error: 0.043901 Align patch 4 21 left Iteration 1 Error: 1.160031 Iteration 2 Error: 0.190805 Iteration 3 Error: 0.050528 Iteration 4 Error: 0.015201 Align patch 5 20 left Iteration 1 Error: 1.328498 Iteration 2 Error: 0.236696 Iteration 3 Error: 0.066637 Iteration 4 Error: 0.020481 Align patch 6 19 left Iteration 1 Error: 2.949631 Iteration 2 Error: 0.432800 Iteration 3 Error: 0.092032 Iteration 4 Error: 0.036249 Align patch 7 18 left Iteration 1 Error: 2.277834 Iteration 2 Error: 0.438785 Iteration 3 Error: 0.154339 Iteration 4 Error: 0.097123 Iteration 5 Error: 0.048403 Align patch 8 17 left Iteration 1 Error: 1.468516 Iteration 2 Error: 0.506861 Iteration 3 Error: 0.093674 Iteration 4 Error: 0.066765 Iteration 5 Error: 0.017667 Align patch 9 16 left Iteration 1 Error: 1.152432 Iteration 2 Error: 0.230222 Iteration 3 Error: 0.092886 Iteration 4 Error: 0.028871 Align patch 10 15 left Iteration 1 Error: 1.016128 Iteration 2 Error: 0.406689 Iteration 3 Error: 0.092407 Iteration 4 Error: 0.045415 Align patch 11 14 left Iteration 1 Error: 2.954295 Iteration 2 Error: 0.545255 Iteration 3 Error: 0.245373 Iteration 4 Error: 0.094049 Iteration 5 Error: 0.035425 Align patch 12 13 left Iteration 1 Error: 1.238510 Iteration 2 Error: 0.207020 Iteration 3 Error: 0.068484 Iteration 4 Error: 0.018339 Align patch 13 12 left Iteration 1 Error: 1.098897 Iteration 2 Error: 0.242103 Iteration 3 Error: 0.105983 Iteration 4 Error: 0.029918 Align patch 14 11 left Iteration 1 Error: 0.954711 Iteration 2 Error: 0.262201 Iteration 3 Error: 0.140069 Iteration 4 Error: 0.093141 Iteration 5 Error: 0.044476 Align patch 15 10 left Iteration 1 Error: 1.126293 Iteration 2 Error: 0.181705 Iteration 3 Error: 0.048107 Align patch 16 9 left Iteration 1 Error: 0.875344 Iteration 2 Error: 0.218345 Iteration 3 Error: 0.078608 Iteration 4 Error: 0.035791 Align patch 17 8 left Iteration 1 Error: 1.018412 Iteration 2 Error: 0.208886 Iteration 3 Error: 0.064972 Iteration 4 Error: 0.019066 Align patch 18 7 left Iteration 1 Error: 1.110089 Iteration 2 Error: 0.352219 Iteration 3 Error: 0.077352 Iteration 4 Error: 0.040467 Align patch 19 6 left Iteration 1 Error: 1.408998 Iteration 2 Error: 0.490414 Iteration 3 Error: 0.211422 Iteration 4 Error: 0.128858 Iteration 5 Error: 0.059882 Align patch 19 6 left Iteration 1 Error: 0.920255 Iteration 2 Error: 0.131489 Iteration 3 Error: 0.025681 Align patch 20 5 left Iteration 1 Error: 1.932111 Iteration 2 Error: 0.322392 Iteration 3 Error: 0.055008 Iteration 4 Error: 0.019872 Align patch 21 4 left Iteration 1 Error: 1.658620 Iteration 2 Error: 0.216054 Iteration 3 Error: 0.069329 Iteration 4 Error: 0.024672 Align patch 22 3 left Iteration 1 Error: 0.969810 Iteration 2 Error: 0.252811 Iteration 3 Error: 0.084829 Iteration 4 Error: 0.027361 Align patch 23 2 left Iteration 1 Error: 1.152497 Iteration 2 Error: 0.251022 Iteration 3 Error: 0.057177 Iteration 4 Error: 0.041840 Align patch 24 1 left Iteration 1 Error: 1.283824 Iteration 2 Error: 0.347442 Iteration 3 Error: 0.113663 Iteration 4 Error: 0.049669 Align patch 25 0 left Iteration 1 Error: 1.854316 Iteration 2 Error: 0.337754 Iteration 3 Error: 0.084770 Iteration 4 Error: 0.016918 3D Fitting completed. Patch alignment time: 18.40(sec) Local motion has been corrected. Process thread exits. Computational time: 27.248295 sec Total time: 33.456768 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00018hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00018hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.744420s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00018hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.081335s ........................................ >>>>>>TIME<<<<<< FFT: 0.837196s Defocus_U Defocus_V Angle CCC 13304.68 12945.34 17.88 0.014934 Final Values Defocus_U Defocus_V Angle CCC 13320.31 12901.60 16.94 0.018775 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00008sq_v01_00018hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00018hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.996e-02 CC threshold: 0.734 Mean Std: 37.76 6.54 Num Hot pixels: 228 Hot pixel threshold: 77.03 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.714013 Iteration 2 Error: 0.098439 Iteration 3 Error: 0.024109 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.16 0.07 ...... Frame ( 3) shift: 0.32 0.14 ...... Frame ( 4) shift: 0.48 0.21 ...... Frame ( 5) shift: 0.64 0.27 ...... Frame ( 6) shift: 0.71 0.30 ...... Frame ( 7) shift: 0.71 0.27 ...... Frame ( 8) shift: 0.70 0.25 ...... Frame ( 9) shift: 0.72 0.23 ...... Frame ( 10) shift: 0.75 0.23 ...... Frame ( 11) shift: 0.78 0.22 ...... Frame ( 12) shift: 0.81 0.23 ...... Frame ( 13) shift: 0.83 0.25 ...... Frame ( 14) shift: 0.85 0.28 ...... Frame ( 15) shift: 0.89 0.31 ...... Frame ( 16) shift: 0.95 0.36 ...... Frame ( 17) shift: 1.01 0.41 ...... Frame ( 18) shift: 1.06 0.46 ...... Frame ( 19) shift: 1.11 0.51 ...... Frame ( 20) shift: 1.15 0.57 ...... Frame ( 21) shift: 1.18 0.58 ...... Frame ( 22) shift: 1.18 0.55 ...... Frame ( 23) shift: 1.19 0.52 ...... Frame ( 24) shift: 1.15 0.53 ...... Frame ( 25) shift: 1.08 0.56 ...... Frame ( 26) shift: 1.00 0.60 ...... Frame ( 27) shift: 0.98 0.66 ...... Frame ( 28) shift: 1.01 0.74 ...... Frame ( 29) shift: 1.03 0.82 ...... Frame ( 30) shift: 1.08 0.85 ...... Frame ( 31) shift: 1.14 0.84 ...... Frame ( 32) shift: 1.20 0.83 ...... Frame ( 33) shift: 1.23 0.84 ...... Frame ( 34) shift: 1.22 0.85 ...... Frame ( 35) shift: 1.22 0.86 ...... Frame ( 36) shift: 1.21 0.90 ...... Frame ( 37) shift: 1.19 0.95 ...... Frame ( 38) shift: 1.18 1.01 ...... Frame ( 39) shift: 1.17 1.06 ...... Frame ( 40) shift: 1.15 1.12 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.176379 Iteration 2 Error: 0.307918 Iteration 3 Error: 0.111734 Iteration 4 Error: 0.044585 Align patch 2 23 left Iteration 1 Error: 1.484575 Iteration 2 Error: 0.186589 Iteration 3 Error: 0.062334 Iteration 4 Error: 0.016683 Align patch 3 22 left Iteration 1 Error: 1.028524 Iteration 2 Error: 0.123723 Iteration 3 Error: 0.033254 Align patch 4 21 left Iteration 1 Error: 0.999968 Iteration 2 Error: 0.178096 Iteration 3 Error: 0.040859 Align patch 5 20 left Iteration 1 Error: 0.887999 Iteration 2 Error: 0.137707 Iteration 3 Error: 0.037204 Align patch 6 19 left Iteration 1 Error: 0.688316 Iteration 2 Error: 0.243948 Iteration 3 Error: 0.077307 Iteration 4 Error: 0.030681 Align patch 7 18 left Iteration 1 Error: 0.748694 Iteration 2 Error: 0.150714 Iteration 3 Error: 0.073827 Iteration 4 Error: 0.021218 Align patch 8 17 left Iteration 1 Error: 0.663096 Iteration 2 Error: 0.163955 Iteration 3 Error: 0.028104 Align patch 9 16 left Iteration 1 Error: 0.981987 Iteration 2 Error: 0.217486 Iteration 3 Error: 0.061017 Iteration 4 Error: 0.026120 Align patch 10 15 left Iteration 1 Error: 1.168534 Iteration 2 Error: 0.160807 Iteration 3 Error: 0.049563 Align patch 11 14 left Iteration 1 Error: 0.695359 Iteration 2 Error: 0.098462 Iteration 3 Error: 0.028948 Align patch 12 13 left Iteration 1 Error: 0.782886 Iteration 2 Error: 0.151292 Iteration 3 Error: 0.026384 Align patch 13 12 left Iteration 1 Error: 0.530236 Iteration 2 Error: 0.125367 Iteration 3 Error: 0.029941 Align patch 14 11 left Iteration 1 Error: 0.890884 Iteration 2 Error: 0.163431 Iteration 3 Error: 0.098723 Iteration 4 Error: 0.021156 Align patch 15 10 left Iteration 1 Error: 0.895353 Iteration 2 Error: 0.148118 Iteration 3 Error: 0.036658 Align patch 16 9 left Iteration 1 Error: 0.988348 Iteration 2 Error: 0.397812 Iteration 3 Error: 0.091780 Iteration 4 Error: 0.050505 Iteration 5 Error: 0.020824 Align patch 17 8 left Iteration 1 Error: 0.724142 Iteration 2 Error: 0.149497 Iteration 3 Error: 0.056020 Iteration 4 Error: 0.029618 Align patch 18 7 left Iteration 1 Error: 0.781862 Iteration 2 Error: 0.357582 Iteration 3 Error: 0.060957 Iteration 4 Error: 0.019321 Align patch 19 6 left Iteration 1 Error: 0.990782 Iteration 2 Error: 0.187125 Iteration 3 Error: 0.045270 Align patch 20 5 left Iteration 1 Error: 0.993293 Iteration 2 Error: 0.104658 Iteration 3 Error: 0.024035 Align patch 21 4 left Iteration 1 Error: 0.958766 Iteration 2 Error: 0.165419 Iteration 3 Error: 0.064441 Iteration 4 Error: 0.022319 Align patch 22 3 left Iteration 1 Error: 0.874220 Iteration 2 Error: 0.179957 Iteration 3 Error: 0.040408 Align patch 23 2 left Iteration 1 Error: 1.127734 Iteration 2 Error: 0.197693 Iteration 3 Error: 0.048209 Align patch 24 1 left Iteration 1 Error: 0.861980 Iteration 2 Error: 0.144188 Iteration 3 Error: 0.038512 Align patch 25 0 left Iteration 1 Error: 0.698457 Iteration 2 Error: 0.145545 Iteration 3 Error: 0.037289 3D Fitting completed. Patch alignment time: 15.65(sec) Local motion has been corrected. Process thread exits. Computational time: 23.795401 sec Total time: 29.564962 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00018hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00018hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.779753s Reading file: gc_18feb27f_CTD_g1_00012gr_00008sq_v01_00018hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.033573s ........................................ >>>>>>TIME<<<<<< FFT: 1.048624s Defocus_U Defocus_V Angle CCC 13998.06 13255.86 86.30 0.035798 Final Values Defocus_U Defocus_V Angle CCC 13281.03 13995.08 1.67 0.048852 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00002hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00002hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.998e-02 CC threshold: 0.734 Mean Std: 43.18 7.18 Num Hot pixels: 234 Hot pixel threshold: 86.26 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.470362 Iteration 2 Error: 0.251254 Iteration 3 Error: 0.062667 Iteration 4 Error: 0.016496 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.13 0.08 ...... Frame ( 3) shift: -0.25 0.16 ...... Frame ( 4) shift: -0.38 0.25 ...... Frame ( 5) shift: -0.50 0.33 ...... Frame ( 6) shift: -0.59 0.44 ...... Frame ( 7) shift: -0.63 0.59 ...... Frame ( 8) shift: -0.67 0.74 ...... Frame ( 9) shift: -0.66 0.87 ...... Frame ( 10) shift: -0.59 0.97 ...... Frame ( 11) shift: -0.52 1.07 ...... Frame ( 12) shift: -0.47 1.18 ...... Frame ( 13) shift: -0.45 1.29 ...... Frame ( 14) shift: -0.42 1.40 ...... Frame ( 15) shift: -0.41 1.53 ...... Frame ( 16) shift: -0.44 1.68 ...... Frame ( 17) shift: -0.46 1.83 ...... Frame ( 18) shift: -0.47 1.91 ...... Frame ( 19) shift: -0.47 1.90 ...... Frame ( 20) shift: -0.47 1.90 ...... Frame ( 21) shift: -0.46 1.93 ...... Frame ( 22) shift: -0.43 2.01 ...... Frame ( 23) shift: -0.41 2.09 ...... Frame ( 24) shift: -0.37 2.17 ...... Frame ( 25) shift: -0.33 2.26 ...... Frame ( 26) shift: -0.28 2.35 ...... Frame ( 27) shift: -0.24 2.41 ...... Frame ( 28) shift: -0.22 2.45 ...... Frame ( 29) shift: -0.20 2.50 ...... Frame ( 30) shift: -0.21 2.55 ...... Frame ( 31) shift: -0.25 2.61 ...... Frame ( 32) shift: -0.29 2.67 ...... Frame ( 33) shift: -0.29 2.72 ...... Frame ( 34) shift: -0.25 2.77 ...... Frame ( 35) shift: -0.21 2.81 ...... Frame ( 36) shift: -0.18 2.88 ...... Frame ( 37) shift: -0.18 2.98 ...... Frame ( 38) shift: -0.18 3.08 ...... Frame ( 39) shift: -0.18 3.18 ...... Frame ( 40) shift: -0.18 3.28 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.912351 Iteration 2 Error: 0.157324 Iteration 3 Error: 0.028090 Align patch 2 23 left Iteration 1 Error: 0.898929 Iteration 2 Error: 0.126321 Iteration 3 Error: 0.042608 Align patch 3 22 left Iteration 1 Error: 0.834133 Iteration 2 Error: 0.244381 Iteration 3 Error: 0.093168 Iteration 4 Error: 0.025063 Align patch 4 21 left Iteration 1 Error: 0.833044 Iteration 2 Error: 0.150245 Iteration 3 Error: 0.063176 Iteration 4 Error: 0.020413 Align patch 5 20 left Iteration 1 Error: 0.610136 Iteration 2 Error: 0.134996 Iteration 3 Error: 0.049891 Align patch 6 19 left Iteration 1 Error: 0.637225 Iteration 2 Error: 0.211874 Iteration 3 Error: 0.093267 Iteration 4 Error: 0.024688 Align patch 7 18 left Iteration 1 Error: 0.662087 Iteration 2 Error: 0.127516 Iteration 3 Error: 0.043673 Align patch 8 17 left Iteration 1 Error: 1.071334 Iteration 2 Error: 0.685001 Iteration 3 Error: 0.208004 Iteration 4 Error: 0.119329 Iteration 5 Error: 0.030930 Align patch 9 16 left Iteration 1 Error: 0.509785 Iteration 2 Error: 0.159090 Iteration 3 Error: 0.049868 Align patch 10 15 left Iteration 1 Error: 1.088052 Iteration 2 Error: 0.183443 Iteration 3 Error: 0.077867 Iteration 4 Error: 0.021508 Align patch 11 14 left Iteration 1 Error: 0.809163 Iteration 2 Error: 0.136419 Iteration 3 Error: 0.047598 Align patch 12 13 left Iteration 1 Error: 0.747836 Iteration 2 Error: 0.142199 Iteration 3 Error: 0.078665 Iteration 4 Error: 0.029676 Align patch 13 12 left Iteration 1 Error: 0.718137 Iteration 2 Error: 0.189871 Iteration 3 Error: 0.043727 Align patch 14 11 left Iteration 1 Error: 0.892266 Iteration 2 Error: 0.145639 Iteration 3 Error: 0.075138 Iteration 4 Error: 0.020456 Align patch 15 10 left Iteration 1 Error: 0.876526 Iteration 2 Error: 0.298636 Iteration 3 Error: 0.052298 Iteration 4 Error: 0.030506 Align patch 16 9 left Iteration 1 Error: 0.927538 Iteration 2 Error: 0.155732 Iteration 3 Error: 0.068510 Iteration 4 Error: 0.032018 Align patch 17 8 left Iteration 1 Error: 0.952216 Iteration 2 Error: 0.228094 Iteration 3 Error: 0.046949 Align patch 18 7 left Iteration 1 Error: 0.926309 Iteration 2 Error: 0.117287 Iteration 3 Error: 0.038046 Align patch 19 6 left Iteration 1 Error: 0.652036 Iteration 2 Error: 0.109653 Iteration 3 Error: 0.049718 Align patch 20 5 left Iteration 1 Error: 0.614220 Iteration 2 Error: 0.133755 Iteration 3 Error: 0.027912 Align patch 21 4 left Iteration 1 Error: 0.725164 Iteration 2 Error: 0.127935 Iteration 3 Error: 0.030140 Align patch 22 3 left Iteration 1 Error: 0.596237 Iteration 2 Error: 0.093988 Iteration 3 Error: 0.019768 Align patch 23 2 left Iteration 1 Error: 0.669004 Iteration 2 Error: 0.257909 Iteration 3 Error: 0.061046 Iteration 4 Error: 0.021466 Align patch 24 1 left Iteration 1 Error: 1.047743 Iteration 2 Error: 0.179099 Iteration 3 Error: 0.043975 Align patch 25 0 left Iteration 1 Error: 0.707196 Iteration 2 Error: 0.123011 Iteration 3 Error: 0.026705 3D Fitting completed. Patch alignment time: 16.27(sec) Local motion has been corrected. Process thread exits. Computational time: 25.179171 sec Total time: 30.617538 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00002hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00002hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.595628s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00002hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.602393s ........................................ >>>>>>TIME<<<<<< FFT: 0.954869s Defocus_U Defocus_V Angle CCC 10070.31 10925.78 12.39 0.040654 Final Values Defocus_U Defocus_V Angle CCC 10076.57 10947.67 12.08 0.075588 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00002hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00002hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 44.53 7.40 Num Hot pixels: 210 Hot pixel threshold: 88.92 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.324464 Iteration 2 Error: 0.160563 Iteration 3 Error: 0.034942 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.29 0.08 ...... Frame ( 3) shift: -0.57 0.15 ...... Frame ( 4) shift: -0.86 0.23 ...... Frame ( 5) shift: -1.14 0.31 ...... Frame ( 6) shift: -1.30 0.42 ...... Frame ( 7) shift: -1.33 0.55 ...... Frame ( 8) shift: -1.36 0.69 ...... Frame ( 9) shift: -1.36 0.78 ...... Frame ( 10) shift: -1.33 0.83 ...... Frame ( 11) shift: -1.29 0.88 ...... Frame ( 12) shift: -1.26 0.93 ...... Frame ( 13) shift: -1.22 0.97 ...... Frame ( 14) shift: -1.18 1.01 ...... Frame ( 15) shift: -1.18 1.07 ...... Frame ( 16) shift: -1.22 1.14 ...... Frame ( 17) shift: -1.27 1.20 ...... Frame ( 18) shift: -1.29 1.27 ...... Frame ( 19) shift: -1.29 1.33 ...... Frame ( 20) shift: -1.28 1.39 ...... Frame ( 21) shift: -1.25 1.45 ...... Frame ( 22) shift: -1.19 1.52 ...... Frame ( 23) shift: -1.13 1.59 ...... Frame ( 24) shift: -1.10 1.63 ...... Frame ( 25) shift: -1.09 1.64 ...... Frame ( 26) shift: -1.09 1.66 ...... Frame ( 27) shift: -1.07 1.70 ...... Frame ( 28) shift: -1.04 1.76 ...... Frame ( 29) shift: -1.01 1.82 ...... Frame ( 30) shift: -0.98 1.86 ...... Frame ( 31) shift: -0.93 1.88 ...... Frame ( 32) shift: -0.88 1.89 ...... Frame ( 33) shift: -0.88 1.93 ...... Frame ( 34) shift: -0.92 1.99 ...... Frame ( 35) shift: -0.97 2.05 ...... Frame ( 36) shift: -0.96 2.10 ...... Frame ( 37) shift: -0.91 2.15 ...... Frame ( 38) shift: -0.87 2.21 ...... Frame ( 39) shift: -0.82 2.26 ...... Frame ( 40) shift: -0.77 2.31 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.962716 Iteration 2 Error: 0.309052 Iteration 3 Error: 0.144606 Iteration 4 Error: 0.054144 Iteration 5 Error: 0.022403 Align patch 2 23 left Iteration 1 Error: 0.666658 Iteration 2 Error: 0.131876 Iteration 3 Error: 0.044180 Align patch 3 22 left Iteration 1 Error: 0.827558 Iteration 2 Error: 0.131141 Iteration 3 Error: 0.026455 Align patch 4 21 left Iteration 1 Error: 0.687072 Iteration 2 Error: 0.189412 Iteration 3 Error: 0.071491 Iteration 4 Error: 0.021934 Align patch 5 20 left Iteration 1 Error: 1.474768 Iteration 2 Error: 0.149993 Iteration 3 Error: 0.035822 Align patch 6 19 left Iteration 1 Error: 0.493736 Iteration 2 Error: 0.126270 Iteration 3 Error: 0.040103 Align patch 7 18 left Iteration 1 Error: 0.711761 Iteration 2 Error: 0.154424 Iteration 3 Error: 0.055075 Iteration 4 Error: 0.019686 Align patch 8 17 left Iteration 1 Error: 0.773321 Iteration 2 Error: 0.181975 Iteration 3 Error: 0.046023 Align patch 9 16 left Iteration 1 Error: 0.847507 Iteration 2 Error: 0.198323 Iteration 3 Error: 0.049116 Align patch 10 15 left Iteration 1 Error: 1.161894 Iteration 2 Error: 0.167788 Iteration 3 Error: 0.045307 Align patch 11 14 left Iteration 1 Error: 0.621915 Iteration 2 Error: 0.149950 Iteration 3 Error: 0.032598 Align patch 12 13 left Iteration 1 Error: 1.079676 Iteration 2 Error: 0.125623 Iteration 3 Error: 0.022839 Align patch 13 12 left Iteration 1 Error: 0.832770 Iteration 2 Error: 0.135207 Iteration 3 Error: 0.033274 Align patch 14 11 left Iteration 1 Error: 0.664081 Iteration 2 Error: 0.128294 Iteration 3 Error: 0.025211 Align patch 15 10 left Iteration 1 Error: 0.978406 Iteration 2 Error: 0.184390 Iteration 3 Error: 0.046449 Align patch 16 9 left Iteration 1 Error: 0.850405 Iteration 2 Error: 0.210755 Iteration 3 Error: 0.071800 Iteration 4 Error: 0.027220 Align patch 17 8 left Iteration 1 Error: 0.957020 Iteration 2 Error: 0.316053 Iteration 3 Error: 0.086041 Iteration 4 Error: 0.025730 Align patch 18 7 left Iteration 1 Error: 1.077750 Iteration 2 Error: 0.125284 Iteration 3 Error: 0.030725 Align patch 19 6 left Iteration 1 Error: 0.568878 Iteration 2 Error: 0.077698 Iteration 3 Error: 0.021105 Align patch 20 5 left Iteration 1 Error: 0.688358 Iteration 2 Error: 0.092553 Iteration 3 Error: 0.028311 Align patch 21 4 left Iteration 1 Error: 1.718346 Iteration 2 Error: 0.186911 Iteration 3 Error: 0.042081 Align patch 22 3 left Iteration 1 Error: 1.237648 Iteration 2 Error: 0.217959 Iteration 3 Error: 0.038021 Align patch 23 2 left Iteration 1 Error: 1.054705 Iteration 2 Error: 0.189300 Iteration 3 Error: 0.044565 Align patch 24 1 left Iteration 1 Error: 1.027738 Iteration 2 Error: 0.148099 Iteration 3 Error: 0.037110 Align patch 25 0 left Iteration 1 Error: 0.811634 Iteration 2 Error: 0.171665 Iteration 3 Error: 0.032253 3D Fitting completed. Patch alignment time: 15.24(sec) Local motion has been corrected. Process thread exits. Computational time: 23.588873 sec Total time: 29.369244 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00002hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00002hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.770618s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00002hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.656437s ........................................ >>>>>>TIME<<<<<< FFT: 1.043125s Defocus_U Defocus_V Angle CCC 10835.95 10375.00 89.78 0.045689 Final Values Defocus_U Defocus_V Angle CCC 10378.16 10864.12 0.09 0.084161 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00002hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00002hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 9.999e-02 CC threshold: 0.734 Mean Std: 45.21 7.47 Num Hot pixels: 202 Hot pixel threshold: 90.06 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.720462 Iteration 2 Error: 0.152134 Iteration 3 Error: 0.031958 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.37 0.02 ...... Frame ( 3) shift: -0.75 0.05 ...... Frame ( 4) shift: -1.12 0.07 ...... Frame ( 5) shift: -1.49 0.10 ...... Frame ( 6) shift: -1.69 0.08 ...... Frame ( 7) shift: -1.72 0.04 ...... Frame ( 8) shift: -1.75 -0.01 ...... Frame ( 9) shift: -1.74 -0.02 ...... Frame ( 10) shift: -1.69 0.01 ...... Frame ( 11) shift: -1.63 0.04 ...... Frame ( 12) shift: -1.57 0.05 ...... Frame ( 13) shift: -1.51 0.03 ...... Frame ( 14) shift: -1.44 0.01 ...... Frame ( 15) shift: -1.41 0.01 ...... Frame ( 16) shift: -1.39 0.03 ...... Frame ( 17) shift: -1.38 0.04 ...... Frame ( 18) shift: -1.34 0.05 ...... Frame ( 19) shift: -1.27 0.03 ...... Frame ( 20) shift: -1.20 0.02 ...... Frame ( 21) shift: -1.14 0.06 ...... Frame ( 22) shift: -1.10 0.15 ...... Frame ( 23) shift: -1.05 0.25 ...... Frame ( 24) shift: -1.01 0.34 ...... Frame ( 25) shift: -0.96 0.42 ...... Frame ( 26) shift: -0.92 0.51 ...... Frame ( 27) shift: -0.86 0.59 ...... Frame ( 28) shift: -0.78 0.65 ...... Frame ( 29) shift: -0.70 0.71 ...... Frame ( 30) shift: -0.69 0.75 ...... Frame ( 31) shift: -0.73 0.78 ...... Frame ( 32) shift: -0.78 0.80 ...... Frame ( 33) shift: -0.80 0.86 ...... Frame ( 34) shift: -0.80 0.94 ...... Frame ( 35) shift: -0.80 1.03 ...... Frame ( 36) shift: -0.77 1.07 ...... Frame ( 37) shift: -0.72 1.07 ...... Frame ( 38) shift: -0.68 1.06 ...... Frame ( 39) shift: -0.63 1.06 ...... Frame ( 40) shift: -0.58 1.05 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.705838 Iteration 2 Error: 0.167008 Iteration 3 Error: 0.042029 Align patch 2 23 left Iteration 1 Error: 0.798765 Iteration 2 Error: 0.133198 Iteration 3 Error: 0.022902 Align patch 3 22 left Iteration 1 Error: 0.768565 Iteration 2 Error: 0.128589 Iteration 3 Error: 0.027201 Align patch 4 21 left Iteration 1 Error: 0.757689 Iteration 2 Error: 0.109772 Iteration 3 Error: 0.024778 Align patch 5 20 left Iteration 1 Error: 1.160192 Iteration 2 Error: 0.101396 Iteration 3 Error: 0.019204 Align patch 6 19 left Iteration 1 Error: 0.794341 Iteration 2 Error: 0.207111 Iteration 3 Error: 0.034372 Align patch 7 18 left Iteration 1 Error: 0.857255 Iteration 2 Error: 0.156624 Iteration 3 Error: 0.053743 Iteration 4 Error: 0.026068 Align patch 8 17 left Iteration 1 Error: 0.576249 Iteration 2 Error: 0.095569 Iteration 3 Error: 0.029001 Align patch 9 16 left Iteration 1 Error: 0.667631 Iteration 2 Error: 0.105558 Iteration 3 Error: 0.019394 Align patch 10 15 left Iteration 1 Error: 0.854550 Iteration 2 Error: 0.200804 Iteration 3 Error: 0.082042 Iteration 4 Error: 0.020092 Align patch 11 14 left Iteration 1 Error: 0.765036 Iteration 2 Error: 0.128468 Iteration 3 Error: 0.040170 Align patch 12 13 left Iteration 1 Error: 0.955849 Iteration 2 Error: 0.150869 Iteration 3 Error: 0.041848 Align patch 13 12 left Iteration 1 Error: 0.572708 Iteration 2 Error: 0.114004 Iteration 3 Error: 0.042480 Align patch 14 11 left Iteration 1 Error: 0.870850 Iteration 2 Error: 0.151526 Iteration 3 Error: 0.071404 Iteration 4 Error: 0.015190 Align patch 15 10 left Iteration 1 Error: 0.598860 Iteration 2 Error: 0.142958 Iteration 3 Error: 0.029776 Align patch 16 9 left Iteration 1 Error: 1.376549 Iteration 2 Error: 0.195027 Iteration 3 Error: 0.055745 Iteration 4 Error: 0.029958 Align patch 17 8 left Iteration 1 Error: 0.742511 Iteration 2 Error: 0.198959 Iteration 3 Error: 0.062255 Iteration 4 Error: 0.019779 Align patch 18 7 left Iteration 1 Error: 0.915836 Iteration 2 Error: 0.102758 Iteration 3 Error: 0.024079 Align patch 19 6 left Iteration 1 Error: 0.720772 Iteration 2 Error: 0.132128 Iteration 3 Error: 0.028731 Align patch 20 5 left Iteration 1 Error: 1.023468 Iteration 2 Error: 0.248285 Iteration 3 Error: 0.053487 Iteration 4 Error: 0.018749 Align patch 21 4 left Iteration 1 Error: 2.498155 Iteration 2 Error: 0.361269 Iteration 3 Error: 0.138006 Iteration 4 Error: 0.053973 Iteration 5 Error: 0.022044 Align patch 22 3 left Iteration 1 Error: 1.853394 Iteration 2 Error: 0.221055 Iteration 3 Error: 0.060001 Iteration 4 Error: 0.018382 Align patch 23 2 left Iteration 1 Error: 0.761191 Iteration 2 Error: 0.163818 Iteration 3 Error: 0.051849 Iteration 4 Error: 0.023721 Align patch 24 1 left Iteration 1 Error: 0.826480 Iteration 2 Error: 0.226112 Iteration 3 Error: 0.091826 Iteration 4 Error: 0.036015 Align patch 25 0 left Iteration 1 Error: 0.571939 Iteration 2 Error: 0.070185 Iteration 3 Error: 0.019961 3D Fitting completed. Patch alignment time: 16.44(sec) Local motion has been corrected. Process thread exits. Computational time: 24.968817 sec Total time: 31.262814 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00002hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00002hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.547923s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00002hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.853900s ........................................ >>>>>>TIME<<<<<< FFT: 1.039953s Defocus_U Defocus_V Angle CCC 9915.82 10756.10 6.46 0.043475 Final Values Defocus_U Defocus_V Angle CCC 9914.24 10773.32 6.15 0.082387 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00002hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00002hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 44.72 7.72 Num Hot pixels: 187 Hot pixel threshold: 91.04 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.027498 Iteration 2 Error: 0.143301 Iteration 3 Error: 0.023923 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.40 -0.01 ...... Frame ( 3) shift: -0.80 -0.02 ...... Frame ( 4) shift: -1.20 -0.03 ...... Frame ( 5) shift: -1.61 -0.04 ...... Frame ( 6) shift: -1.82 -0.01 ...... Frame ( 7) shift: -1.84 0.08 ...... Frame ( 8) shift: -1.87 0.17 ...... Frame ( 9) shift: -1.84 0.24 ...... Frame ( 10) shift: -1.77 0.29 ...... Frame ( 11) shift: -1.70 0.34 ...... Frame ( 12) shift: -1.62 0.39 ...... Frame ( 13) shift: -1.54 0.44 ...... Frame ( 14) shift: -1.45 0.50 ...... Frame ( 15) shift: -1.39 0.53 ...... Frame ( 16) shift: -1.38 0.55 ...... Frame ( 17) shift: -1.36 0.56 ...... Frame ( 18) shift: -1.35 0.63 ...... Frame ( 19) shift: -1.34 0.75 ...... Frame ( 20) shift: -1.33 0.87 ...... Frame ( 21) shift: -1.34 0.94 ...... Frame ( 22) shift: -1.37 0.97 ...... Frame ( 23) shift: -1.39 0.99 ...... Frame ( 24) shift: -1.37 1.02 ...... Frame ( 25) shift: -1.29 1.04 ...... Frame ( 26) shift: -1.21 1.07 ...... Frame ( 27) shift: -1.14 1.12 ...... Frame ( 28) shift: -1.10 1.21 ...... Frame ( 29) shift: -1.05 1.29 ...... Frame ( 30) shift: -1.01 1.35 ...... Frame ( 31) shift: -0.97 1.38 ...... Frame ( 32) shift: -0.94 1.41 ...... Frame ( 33) shift: -0.95 1.47 ...... Frame ( 34) shift: -1.00 1.58 ...... Frame ( 35) shift: -1.05 1.69 ...... Frame ( 36) shift: -1.05 1.76 ...... Frame ( 37) shift: -1.00 1.80 ...... Frame ( 38) shift: -0.95 1.83 ...... Frame ( 39) shift: -0.89 1.87 ...... Frame ( 40) shift: -0.84 1.91 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.109338 Iteration 2 Error: 0.302251 Iteration 3 Error: 0.061543 Iteration 4 Error: 0.036547 Align patch 2 23 left Iteration 1 Error: 1.092500 Iteration 2 Error: 0.173128 Iteration 3 Error: 0.055226 Iteration 4 Error: 0.017712 Align patch 3 22 left Iteration 1 Error: 0.686132 Iteration 2 Error: 0.195283 Iteration 3 Error: 0.073152 Iteration 4 Error: 0.032455 Align patch 4 21 left Iteration 1 Error: 0.917699 Iteration 2 Error: 0.147202 Iteration 3 Error: 0.033149 Align patch 5 20 left Iteration 1 Error: 0.751904 Iteration 2 Error: 0.126396 Iteration 3 Error: 0.020487 Align patch 6 19 left Iteration 1 Error: 0.936449 Iteration 2 Error: 0.272062 Iteration 3 Error: 0.090752 Iteration 4 Error: 0.041151 Align patch 7 18 left Iteration 1 Error: 1.860330 Iteration 2 Error: 0.193967 Iteration 3 Error: 0.095841 Iteration 4 Error: 0.025407 Align patch 8 17 left Iteration 1 Error: 0.892077 Iteration 2 Error: 0.142726 Iteration 3 Error: 0.040279 Align patch 9 16 left Iteration 1 Error: 0.607574 Iteration 2 Error: 0.089183 Iteration 3 Error: 0.015752 Align patch 10 15 left Iteration 1 Error: 0.674986 Iteration 2 Error: 0.136623 Iteration 3 Error: 0.025433 Align patch 11 14 left Iteration 1 Error: 0.681022 Iteration 2 Error: 0.079052 Iteration 3 Error: 0.034134 Align patch 12 13 left Iteration 1 Error: 0.774478 Iteration 2 Error: 0.109238 Iteration 3 Error: 0.048258 Align patch 13 12 left Iteration 1 Error: 0.884999 Iteration 2 Error: 0.149212 Iteration 3 Error: 0.022493 Align patch 14 11 left Iteration 1 Error: 0.529162 Iteration 2 Error: 0.152337 Iteration 3 Error: 0.050273 Iteration 4 Error: 0.014696 Align patch 15 10 left Iteration 1 Error: 0.595620 Iteration 2 Error: 0.127843 Iteration 3 Error: 0.027004 Align patch 16 9 left Iteration 1 Error: 0.732288 Iteration 2 Error: 0.145858 Iteration 3 Error: 0.047272 Align patch 17 8 left Iteration 1 Error: 0.797606 Iteration 2 Error: 0.119309 Iteration 3 Error: 0.025448 Align patch 18 7 left Iteration 1 Error: 0.550469 Iteration 2 Error: 0.122286 Iteration 3 Error: 0.030836 Align patch 19 6 left Iteration 1 Error: 0.842858 Iteration 2 Error: 0.137173 Iteration 3 Error: 0.027563 Align patch 20 5 left Iteration 1 Error: 0.951624 Iteration 2 Error: 0.156077 Iteration 3 Error: 0.043819 Align patch 21 4 left Iteration 1 Error: 1.151204 Iteration 2 Error: 0.302363 Iteration 3 Error: 0.052766 Iteration 4 Error: 0.021412 Align patch 22 3 left Iteration 1 Error: 0.743354 Iteration 2 Error: 0.167085 Iteration 3 Error: 0.050724 Iteration 4 Error: 0.018616 Align patch 23 2 left Iteration 1 Error: 0.654635 Iteration 2 Error: 0.134732 Iteration 3 Error: 0.035140 Align patch 24 1 left Iteration 1 Error: 0.879750 Iteration 2 Error: 0.159587 Iteration 3 Error: 0.040124 Align patch 25 0 left Iteration 1 Error: 1.462743 Iteration 2 Error: 0.129051 Iteration 3 Error: 0.014013 3D Fitting completed. Patch alignment time: 15.04(sec) Local motion has been corrected. Process thread exits. Computational time: 23.798754 sec Total time: 29.434698 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00002hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00002hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.727926s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00002hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.706286s ........................................ >>>>>>TIME<<<<<< FFT: 0.939318s Defocus_U Defocus_V Angle CCC 13252.65 12591.82 84.09 0.046752 Final Values Defocus_U Defocus_V Angle CCC 13257.34 12596.51 84.40 0.082514 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00003hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00003hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.342e-01 9.982e-02 CC threshold: 0.733 Mean Std: 34.94 6.31 Num Hot pixels: 202 Hot pixel threshold: 72.79 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 3.924659 Iteration 2 Error: 0.381455 Iteration 3 Error: 0.109776 Iteration 4 Error: 0.051360 Iteration 5 Error: 0.013488 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.41 -0.58 ...... Frame ( 3) shift: 0.82 -1.15 ...... Frame ( 4) shift: 1.23 -1.73 ...... Frame ( 5) shift: 1.64 -2.30 ...... Frame ( 6) shift: 1.93 -2.78 ...... Frame ( 7) shift: 2.11 -3.16 ...... Frame ( 8) shift: 2.29 -3.53 ...... Frame ( 9) shift: 2.43 -3.80 ...... Frame ( 10) shift: 2.53 -3.95 ...... Frame ( 11) shift: 2.63 -4.10 ...... Frame ( 12) shift: 2.72 -4.21 ...... Frame ( 13) shift: 2.78 -4.27 ...... Frame ( 14) shift: 2.84 -4.34 ...... Frame ( 15) shift: 2.90 -4.41 ...... Frame ( 16) shift: 2.95 -4.50 ...... Frame ( 17) shift: 3.00 -4.58 ...... Frame ( 18) shift: 3.07 -4.66 ...... Frame ( 19) shift: 3.17 -4.71 ...... Frame ( 20) shift: 3.26 -4.77 ...... Frame ( 21) shift: 3.32 -4.84 ...... Frame ( 22) shift: 3.36 -4.92 ...... Frame ( 23) shift: 3.39 -5.00 ...... Frame ( 24) shift: 3.41 -5.05 ...... Frame ( 25) shift: 3.40 -5.07 ...... Frame ( 26) shift: 3.39 -5.08 ...... Frame ( 27) shift: 3.38 -5.08 ...... Frame ( 28) shift: 3.37 -5.04 ...... Frame ( 29) shift: 3.35 -5.01 ...... Frame ( 30) shift: 3.38 -4.99 ...... Frame ( 31) shift: 3.45 -4.99 ...... Frame ( 32) shift: 3.52 -5.00 ...... Frame ( 33) shift: 3.58 -5.00 ...... Frame ( 34) shift: 3.63 -5.02 ...... Frame ( 35) shift: 3.68 -5.03 ...... Frame ( 36) shift: 3.73 -5.02 ...... Frame ( 37) shift: 3.77 -5.00 ...... Frame ( 38) shift: 3.81 -4.98 ...... Frame ( 39) shift: 3.85 -4.96 ...... Frame ( 40) shift: 3.89 -4.94 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.420973 Iteration 2 Error: 0.285399 Iteration 3 Error: 0.069824 Iteration 4 Error: 0.018334 Align patch 2 23 left Iteration 1 Error: 0.932825 Iteration 2 Error: 0.231999 Iteration 3 Error: 0.084109 Iteration 4 Error: 0.043223 Align patch 3 22 left Iteration 1 Error: 0.729705 Iteration 2 Error: 0.229317 Iteration 3 Error: 0.070170 Iteration 4 Error: 0.026597 Align patch 4 21 left Iteration 1 Error: 2.704437 Iteration 2 Error: 0.460716 Iteration 3 Error: 0.101973 Iteration 4 Error: 0.033353 Align patch 5 20 left Iteration 1 Error: 4.115905 Iteration 2 Error: 0.445256 Iteration 3 Error: 0.101614 Iteration 4 Error: 0.041808 Align patch 6 19 left Iteration 1 Error: 1.979604 Iteration 2 Error: 0.262053 Iteration 3 Error: 0.095458 Iteration 4 Error: 0.041408 Align patch 7 18 left Iteration 1 Error: 1.095997 Iteration 2 Error: 0.131922 Iteration 3 Error: 0.057265 Iteration 4 Error: 0.013686 Align patch 8 17 left Iteration 1 Error: 0.757287 Iteration 2 Error: 0.122257 Iteration 3 Error: 0.032694 Align patch 9 16 left Iteration 1 Error: 1.980971 Iteration 2 Error: 0.407545 Iteration 3 Error: 0.075687 Iteration 4 Error: 0.028065 Align patch 10 15 left Iteration 1 Error: 3.673445 Iteration 2 Error: 0.340555 Iteration 3 Error: 0.085423 Iteration 4 Error: 0.026423 Align patch 11 14 left Iteration 1 Error: 3.213548 Iteration 2 Error: 0.370853 Iteration 3 Error: 0.104546 Iteration 4 Error: 0.039784 Align patch 12 13 left Iteration 1 Error: 2.560627 Iteration 2 Error: 0.217542 Iteration 3 Error: 0.072346 Iteration 4 Error: 0.022438 Align patch 13 12 left Iteration 1 Error: 1.060938 Iteration 2 Error: 0.207316 Iteration 3 Error: 0.042118 Align patch 14 11 left Iteration 1 Error: 1.251082 Iteration 2 Error: 0.226333 Iteration 3 Error: 0.048807 Align patch 15 10 left Iteration 1 Error: 2.089816 Iteration 2 Error: 0.323307 Iteration 3 Error: 0.062451 Iteration 4 Error: 0.015336 Align patch 16 9 left Iteration 1 Error: 3.710825 Iteration 2 Error: 0.505409 Iteration 3 Error: 0.230750 Iteration 4 Error: 0.092133 Iteration 5 Error: 0.050495 Align patch 16 9 left Iteration 1 Error: 3.004980 Iteration 2 Error: 0.343036 Iteration 3 Error: 0.087267 Iteration 4 Error: 0.020794 Align patch 17 8 left Iteration 1 Error: 3.159108 Iteration 2 Error: 0.352081 Iteration 3 Error: 0.096663 Iteration 4 Error: 0.032847 Align patch 18 7 left Iteration 1 Error: 1.458257 Iteration 2 Error: 0.190485 Iteration 3 Error: 0.082582 Iteration 4 Error: 0.038324 Align patch 19 6 left Iteration 1 Error: 0.993938 Iteration 2 Error: 0.184148 Iteration 3 Error: 0.062603 Iteration 4 Error: 0.018380 Align patch 20 5 left Iteration 1 Error: 1.680417 Iteration 2 Error: 0.206679 Iteration 3 Error: 0.045837 Align patch 21 4 left Iteration 1 Error: 4.507097 Iteration 2 Error: 0.857755 Iteration 3 Error: 0.229232 Iteration 4 Error: 0.121949 Iteration 5 Error: 0.042917 Align patch 22 3 left Iteration 1 Error: 3.694440 Iteration 2 Error: 0.606900 Iteration 3 Error: 0.313737 Iteration 4 Error: 0.150293 Iteration 5 Error: 0.077821 Align patch 22 3 left Iteration 1 Error: 2.947900 Iteration 2 Error: 0.273735 Iteration 3 Error: 0.063994 Iteration 4 Error: 0.017050 Align patch 23 2 left Iteration 1 Error: 2.485602 Iteration 2 Error: 0.743239 Iteration 3 Error: 0.131287 Iteration 4 Error: 0.053885 Iteration 5 Error: 0.022025 Align patch 24 1 left Iteration 1 Error: 1.319494 Iteration 2 Error: 0.239815 Iteration 3 Error: 0.077511 Iteration 4 Error: 0.030054 Align patch 25 0 left Iteration 1 Error: 2.442390 Iteration 2 Error: 0.596080 Iteration 3 Error: 0.274009 Iteration 4 Error: 0.094824 Iteration 5 Error: 0.033603 3D Fitting completed. Patch alignment time: 19.14(sec) Local motion has been corrected. Process thread exits. Computational time: 28.142984 sec Total time: 33.981335 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00003hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00003hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.999456s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00003hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.805059s ........................................ >>>>>>TIME<<<<<< FFT: 0.950022s Defocus_U Defocus_V Angle CCC 13793.04 13128.91 72.07 0.027659 Final Values Defocus_U Defocus_V Angle CCC 13818.04 13047.67 68.36 0.031452 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00003hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00003hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.999e-02 CC threshold: 0.734 Mean Std: 41.85 6.99 Num Hot pixels: 212 Hot pixel threshold: 83.81 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.556090 Iteration 2 Error: 0.079061 Iteration 3 Error: 0.018443 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.10 -0.02 ...... Frame ( 3) shift: -0.20 -0.03 ...... Frame ( 4) shift: -0.31 -0.05 ...... Frame ( 5) shift: -0.41 -0.06 ...... Frame ( 6) shift: -0.46 -0.04 ...... Frame ( 7) shift: -0.47 0.02 ...... Frame ( 8) shift: -0.47 0.07 ...... Frame ( 9) shift: -0.46 0.07 ...... Frame ( 10) shift: -0.42 0.02 ...... Frame ( 11) shift: -0.38 -0.04 ...... Frame ( 12) shift: -0.33 -0.06 ...... Frame ( 13) shift: -0.29 -0.04 ...... Frame ( 14) shift: -0.25 -0.02 ...... Frame ( 15) shift: -0.25 0.01 ...... Frame ( 16) shift: -0.30 0.04 ...... Frame ( 17) shift: -0.35 0.07 ...... Frame ( 18) shift: -0.34 0.09 ...... Frame ( 19) shift: -0.29 0.10 ...... Frame ( 20) shift: -0.23 0.11 ...... Frame ( 21) shift: -0.20 0.15 ...... Frame ( 22) shift: -0.20 0.21 ...... Frame ( 23) shift: -0.19 0.28 ...... Frame ( 24) shift: -0.18 0.31 ...... Frame ( 25) shift: -0.15 0.30 ...... Frame ( 26) shift: -0.13 0.29 ...... Frame ( 27) shift: -0.13 0.31 ...... Frame ( 28) shift: -0.14 0.37 ...... Frame ( 29) shift: -0.15 0.42 ...... Frame ( 30) shift: -0.14 0.44 ...... Frame ( 31) shift: -0.13 0.41 ...... Frame ( 32) shift: -0.11 0.39 ...... Frame ( 33) shift: -0.05 0.36 ...... Frame ( 34) shift: 0.05 0.34 ...... Frame ( 35) shift: 0.15 0.32 ...... Frame ( 36) shift: 0.22 0.33 ...... Frame ( 37) shift: 0.27 0.39 ...... Frame ( 38) shift: 0.31 0.45 ...... Frame ( 39) shift: 0.36 0.51 ...... Frame ( 40) shift: 0.41 0.56 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.825333 Iteration 2 Error: 0.185687 Iteration 3 Error: 0.034113 Align patch 2 23 left Iteration 1 Error: 0.785405 Iteration 2 Error: 0.206728 Iteration 3 Error: 0.050982 Iteration 4 Error: 0.024761 Align patch 3 22 left Iteration 1 Error: 0.848873 Iteration 2 Error: 0.149957 Iteration 3 Error: 0.048854 Align patch 4 21 left Iteration 1 Error: 0.884100 Iteration 2 Error: 0.157031 Iteration 3 Error: 0.039659 Align patch 5 20 left Iteration 1 Error: 0.573381 Iteration 2 Error: 0.104438 Iteration 3 Error: 0.029340 Align patch 6 19 left Iteration 1 Error: 0.845037 Iteration 2 Error: 0.123630 Iteration 3 Error: 0.036152 Align patch 7 18 left Iteration 1 Error: 0.771159 Iteration 2 Error: 0.157149 Iteration 3 Error: 0.053368 Iteration 4 Error: 0.018035 Align patch 8 17 left Iteration 1 Error: 0.561426 Iteration 2 Error: 0.098505 Iteration 3 Error: 0.014599 Align patch 9 16 left Iteration 1 Error: 0.586607 Iteration 2 Error: 0.103131 Iteration 3 Error: 0.020478 Align patch 10 15 left Iteration 1 Error: 0.744700 Iteration 2 Error: 0.077552 Iteration 3 Error: 0.026952 Align patch 11 14 left Iteration 1 Error: 1.530262 Iteration 2 Error: 0.322483 Iteration 3 Error: 0.068146 Iteration 4 Error: 0.017461 Align patch 12 13 left Iteration 1 Error: 0.944291 Iteration 2 Error: 0.278952 Iteration 3 Error: 0.070538 Iteration 4 Error: 0.049555 Align patch 13 12 left Iteration 1 Error: 0.719203 Iteration 2 Error: 0.119240 Iteration 3 Error: 0.032422 Align patch 14 11 left Iteration 1 Error: 0.900432 Iteration 2 Error: 0.112712 Iteration 3 Error: 0.027853 Align patch 15 10 left Iteration 1 Error: 0.497696 Iteration 2 Error: 0.126201 Iteration 3 Error: 0.024282 Align patch 16 9 left Iteration 1 Error: 0.542105 Iteration 2 Error: 0.082733 Iteration 3 Error: 0.014836 Align patch 17 8 left Iteration 1 Error: 0.698630 Iteration 2 Error: 0.077767 Iteration 3 Error: 0.023606 Align patch 18 7 left Iteration 1 Error: 0.797988 Iteration 2 Error: 0.098262 Iteration 3 Error: 0.028815 Align patch 19 6 left Iteration 1 Error: 0.818331 Iteration 2 Error: 0.147182 Iteration 3 Error: 0.035522 Align patch 20 5 left Iteration 1 Error: 0.760161 Iteration 2 Error: 0.082068 Iteration 3 Error: 0.017087 Align patch 21 4 left Iteration 1 Error: 0.721525 Iteration 2 Error: 0.103693 Iteration 3 Error: 0.029499 Align patch 22 3 left Iteration 1 Error: 0.656016 Iteration 2 Error: 0.170428 Iteration 3 Error: 0.047539 Align patch 23 2 left Iteration 1 Error: 0.795224 Iteration 2 Error: 0.142097 Iteration 3 Error: 0.037610 Align patch 24 1 left Iteration 1 Error: 0.687849 Iteration 2 Error: 0.120536 Iteration 3 Error: 0.042798 Align patch 25 0 left Iteration 1 Error: 0.515902 Iteration 2 Error: 0.131440 Iteration 3 Error: 0.026934 3D Fitting completed. Patch alignment time: 14.81(sec) Local motion has been corrected. Process thread exits. Computational time: 23.063354 sec Total time: 28.783440 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00003hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00003hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.738038s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00003hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.767836s ........................................ >>>>>>TIME<<<<<< FFT: 1.045589s Defocus_U Defocus_V Angle CCC 12765.63 12285.16 86.47 0.040123 Final Values Defocus_U Defocus_V Angle CCC 12770.33 12308.62 87.42 0.067958 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00003hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00003hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 39.77 6.74 Num Hot pixels: 191 Hot pixel threshold: 80.20 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.908081 Iteration 2 Error: 0.109723 Iteration 3 Error: 0.022610 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.02 0.15 ...... Frame ( 3) shift: 0.03 0.31 ...... Frame ( 4) shift: 0.05 0.46 ...... Frame ( 5) shift: 0.07 0.61 ...... Frame ( 6) shift: 0.12 0.70 ...... Frame ( 7) shift: 0.20 0.71 ...... Frame ( 8) shift: 0.29 0.73 ...... Frame ( 9) shift: 0.36 0.72 ...... Frame ( 10) shift: 0.40 0.69 ...... Frame ( 11) shift: 0.44 0.65 ...... Frame ( 12) shift: 0.50 0.67 ...... Frame ( 13) shift: 0.58 0.73 ...... Frame ( 14) shift: 0.66 0.79 ...... Frame ( 15) shift: 0.70 0.85 ...... Frame ( 16) shift: 0.71 0.91 ...... Frame ( 17) shift: 0.72 0.97 ...... Frame ( 18) shift: 0.71 1.01 ...... Frame ( 19) shift: 0.68 1.05 ...... Frame ( 20) shift: 0.65 1.08 ...... Frame ( 21) shift: 0.62 1.14 ...... Frame ( 22) shift: 0.57 1.22 ...... Frame ( 23) shift: 0.52 1.31 ...... Frame ( 24) shift: 0.52 1.36 ...... Frame ( 25) shift: 0.56 1.37 ...... Frame ( 26) shift: 0.61 1.38 ...... Frame ( 27) shift: 0.61 1.42 ...... Frame ( 28) shift: 0.57 1.48 ...... Frame ( 29) shift: 0.54 1.54 ...... Frame ( 30) shift: 0.50 1.58 ...... Frame ( 31) shift: 0.45 1.60 ...... Frame ( 32) shift: 0.40 1.63 ...... Frame ( 33) shift: 0.37 1.65 ...... Frame ( 34) shift: 0.34 1.66 ...... Frame ( 35) shift: 0.31 1.67 ...... Frame ( 36) shift: 0.32 1.69 ...... Frame ( 37) shift: 0.38 1.72 ...... Frame ( 38) shift: 0.43 1.75 ...... Frame ( 39) shift: 0.48 1.78 ...... Frame ( 40) shift: 0.54 1.81 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.105741 Iteration 2 Error: 0.135233 Iteration 3 Error: 0.027313 Align patch 2 23 left Iteration 1 Error: 0.855052 Iteration 2 Error: 0.186287 Iteration 3 Error: 0.042880 Align patch 3 22 left Iteration 1 Error: 0.749177 Iteration 2 Error: 0.114146 Iteration 3 Error: 0.032334 Align patch 4 21 left Iteration 1 Error: 0.522536 Iteration 2 Error: 0.082621 Iteration 3 Error: 0.023309 Align patch 5 20 left Iteration 1 Error: 0.677324 Iteration 2 Error: 0.109882 Iteration 3 Error: 0.014397 Align patch 6 19 left Iteration 1 Error: 0.586330 Iteration 2 Error: 0.089840 Iteration 3 Error: 0.016460 Align patch 7 18 left Iteration 1 Error: 0.787880 Iteration 2 Error: 0.177396 Iteration 3 Error: 0.048880 Align patch 8 17 left Iteration 1 Error: 1.047587 Iteration 2 Error: 0.133702 Iteration 3 Error: 0.030245 Align patch 9 16 left Iteration 1 Error: 0.486845 Iteration 2 Error: 0.100593 Iteration 3 Error: 0.015585 Align patch 10 15 left Iteration 1 Error: 0.592834 Iteration 2 Error: 0.082929 Iteration 3 Error: 0.015875 Align patch 11 14 left Iteration 1 Error: 0.612643 Iteration 2 Error: 0.121660 Iteration 3 Error: 0.023037 Align patch 12 13 left Iteration 1 Error: 0.771923 Iteration 2 Error: 0.087303 Iteration 3 Error: 0.021330 Align patch 13 12 left Iteration 1 Error: 0.666303 Iteration 2 Error: 0.159122 Iteration 3 Error: 0.048973 Align patch 14 11 left Iteration 1 Error: 0.768255 Iteration 2 Error: 0.144677 Iteration 3 Error: 0.039936 Align patch 15 10 left Iteration 1 Error: 0.890797 Iteration 2 Error: 0.113258 Iteration 3 Error: 0.028009 Align patch 16 9 left Iteration 1 Error: 0.542412 Iteration 2 Error: 0.104418 Iteration 3 Error: 0.018156 Align patch 17 8 left Iteration 1 Error: 0.577613 Iteration 2 Error: 0.118681 Iteration 3 Error: 0.017289 Align patch 18 7 left Iteration 1 Error: 0.687868 Iteration 2 Error: 0.056807 Iteration 3 Error: 0.016366 Align patch 19 6 left Iteration 1 Error: 0.647158 Iteration 2 Error: 0.133946 Iteration 3 Error: 0.019958 Align patch 20 5 left Iteration 1 Error: 0.474573 Iteration 2 Error: 0.091020 Iteration 3 Error: 0.020478 Align patch 21 4 left Iteration 1 Error: 0.979349 Iteration 2 Error: 0.178738 Iteration 3 Error: 0.026498 Align patch 22 3 left Iteration 1 Error: 0.701900 Iteration 2 Error: 0.179669 Iteration 3 Error: 0.057129 Iteration 4 Error: 0.017370 Align patch 23 2 left Iteration 1 Error: 0.705243 Iteration 2 Error: 0.130413 Iteration 3 Error: 0.019984 Align patch 24 1 left Iteration 1 Error: 0.836049 Iteration 2 Error: 0.190856 Iteration 3 Error: 0.078309 Iteration 4 Error: 0.020269 Align patch 25 0 left Iteration 1 Error: 1.131944 Iteration 2 Error: 0.128210 Iteration 3 Error: 0.027974 3D Fitting completed. Patch alignment time: 15.79(sec) Local motion has been corrected. Process thread exits. Computational time: 24.269453 sec Total time: 30.559229 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00003hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00003hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.723772s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00003hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.646225s ........................................ >>>>>>TIME<<<<<< FFT: 1.038856s Defocus_U Defocus_V Angle CCC 13134.77 13962.89 0.25 0.039711 Final Values Defocus_U Defocus_V Angle CCC 13134.76 13975.40 1.20 0.059941 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00003hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00003hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 43.64 7.17 Num Hot pixels: 231 Hot pixel threshold: 86.66 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.569962 Iteration 2 Error: 0.080894 Iteration 3 Error: 0.015859 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.18 -0.01 ...... Frame ( 3) shift: -0.36 -0.02 ...... Frame ( 4) shift: -0.54 -0.03 ...... Frame ( 5) shift: -0.72 -0.04 ...... Frame ( 6) shift: -0.80 -0.05 ...... Frame ( 7) shift: -0.77 -0.05 ...... Frame ( 8) shift: -0.74 -0.05 ...... Frame ( 9) shift: -0.68 -0.05 ...... Frame ( 10) shift: -0.57 -0.04 ...... Frame ( 11) shift: -0.47 -0.04 ...... Frame ( 12) shift: -0.43 -0.01 ...... Frame ( 13) shift: -0.46 0.05 ...... Frame ( 14) shift: -0.48 0.10 ...... Frame ( 15) shift: -0.47 0.14 ...... Frame ( 16) shift: -0.42 0.18 ...... Frame ( 17) shift: -0.37 0.22 ...... Frame ( 18) shift: -0.36 0.25 ...... Frame ( 19) shift: -0.40 0.27 ...... Frame ( 20) shift: -0.44 0.30 ...... Frame ( 21) shift: -0.42 0.32 ...... Frame ( 22) shift: -0.36 0.35 ...... Frame ( 23) shift: -0.30 0.37 ...... Frame ( 24) shift: -0.28 0.39 ...... Frame ( 25) shift: -0.29 0.42 ...... Frame ( 26) shift: -0.30 0.45 ...... Frame ( 27) shift: -0.31 0.46 ...... Frame ( 28) shift: -0.33 0.45 ...... Frame ( 29) shift: -0.35 0.43 ...... Frame ( 30) shift: -0.37 0.45 ...... Frame ( 31) shift: -0.39 0.49 ...... Frame ( 32) shift: -0.41 0.52 ...... Frame ( 33) shift: -0.36 0.54 ...... Frame ( 34) shift: -0.26 0.54 ...... Frame ( 35) shift: -0.15 0.55 ...... Frame ( 36) shift: -0.08 0.58 ...... Frame ( 37) shift: -0.06 0.63 ...... Frame ( 38) shift: -0.04 0.69 ...... Frame ( 39) shift: -0.02 0.75 ...... Frame ( 40) shift: 0.00 0.81 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.718171 Iteration 2 Error: 0.113875 Iteration 3 Error: 0.040640 Align patch 2 23 left Iteration 1 Error: 0.589308 Iteration 2 Error: 0.077242 Iteration 3 Error: 0.023331 Align patch 3 22 left Iteration 1 Error: 1.009334 Iteration 2 Error: 0.303976 Iteration 3 Error: 0.094874 Iteration 4 Error: 0.036528 Align patch 4 21 left Iteration 1 Error: 0.678742 Iteration 2 Error: 0.095817 Iteration 3 Error: 0.035922 Align patch 5 20 left Iteration 1 Error: 0.936373 Iteration 2 Error: 0.115230 Iteration 3 Error: 0.037883 Align patch 6 19 left Iteration 1 Error: 0.897697 Iteration 2 Error: 0.165779 Iteration 3 Error: 0.046077 Align patch 7 18 left Iteration 1 Error: 0.740981 Iteration 2 Error: 0.114942 Iteration 3 Error: 0.024865 Align patch 8 17 left Iteration 1 Error: 0.818023 Iteration 2 Error: 0.185949 Iteration 3 Error: 0.041636 Align patch 9 16 left Iteration 1 Error: 0.828438 Iteration 2 Error: 0.151309 Iteration 3 Error: 0.032820 Align patch 10 15 left Iteration 1 Error: 0.673270 Iteration 2 Error: 0.125961 Iteration 3 Error: 0.034547 Align patch 11 14 left Iteration 1 Error: 0.818029 Iteration 2 Error: 0.103170 Iteration 3 Error: 0.021586 Align patch 12 13 left Iteration 1 Error: 0.716496 Iteration 2 Error: 0.080999 Iteration 3 Error: 0.021165 Align patch 13 12 left Iteration 1 Error: 0.734775 Iteration 2 Error: 0.091768 Iteration 3 Error: 0.021852 Align patch 14 11 left Iteration 1 Error: 0.691102 Iteration 2 Error: 0.110329 Iteration 3 Error: 0.021347 Align patch 15 10 left Iteration 1 Error: 0.704231 Iteration 2 Error: 0.090011 Iteration 3 Error: 0.033780 Align patch 16 9 left Iteration 1 Error: 0.716579 Iteration 2 Error: 0.096515 Iteration 3 Error: 0.019305 Align patch 17 8 left Iteration 1 Error: 0.595324 Iteration 2 Error: 0.123468 Iteration 3 Error: 0.032724 Align patch 18 7 left Iteration 1 Error: 0.876226 Iteration 2 Error: 0.108923 Iteration 3 Error: 0.018823 Align patch 19 6 left Iteration 1 Error: 0.796043 Iteration 2 Error: 0.114144 Iteration 3 Error: 0.029552 Align patch 20 5 left Iteration 1 Error: 0.626396 Iteration 2 Error: 0.188411 Iteration 3 Error: 0.046373 Align patch 21 4 left Iteration 1 Error: 1.116267 Iteration 2 Error: 0.277222 Iteration 3 Error: 0.082170 Iteration 4 Error: 0.030695 Align patch 22 3 left Iteration 1 Error: 1.254060 Iteration 2 Error: 0.159204 Iteration 3 Error: 0.053617 Iteration 4 Error: 0.023207 Align patch 23 2 left Iteration 1 Error: 0.638793 Iteration 2 Error: 0.083205 Iteration 3 Error: 0.024194 Align patch 24 1 left Iteration 1 Error: 0.656795 Iteration 2 Error: 0.119815 Iteration 3 Error: 0.022749 Align patch 25 0 left Iteration 1 Error: 0.656038 Iteration 2 Error: 0.135940 Iteration 3 Error: 0.041610 3D Fitting completed. Patch alignment time: 15.43(sec) Local motion has been corrected. Process thread exits. Computational time: 23.760897 sec Total time: 29.728283 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00003hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00003hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.759230s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00003hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.797551s ........................................ >>>>>>TIME<<<<<< FFT: 1.037711s Defocus_U Defocus_V Angle CCC 12009.78 11334.00 84.27 0.038069 Final Values Defocus_U Defocus_V Angle CCC 12019.16 11359.01 83.95 0.070224 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00004hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00004hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.316e-01 9.818e-02 CC threshold: 0.721 Mean Std: 44.96 7.64 Num Hot pixels: 205 Hot pixel threshold: 90.78 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.577979 Iteration 2 Error: 0.161262 Iteration 3 Error: 0.036430 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.17 -0.08 ...... Frame ( 3) shift: -0.35 -0.16 ...... Frame ( 4) shift: -0.52 -0.24 ...... Frame ( 5) shift: -0.70 -0.32 ...... Frame ( 6) shift: -0.86 -0.39 ...... Frame ( 7) shift: -1.02 -0.45 ...... Frame ( 8) shift: -1.18 -0.52 ...... Frame ( 9) shift: -1.33 -0.56 ...... Frame ( 10) shift: -1.47 -0.59 ...... Frame ( 11) shift: -1.61 -0.62 ...... Frame ( 12) shift: -1.73 -0.60 ...... Frame ( 13) shift: -1.82 -0.53 ...... Frame ( 14) shift: -1.92 -0.46 ...... Frame ( 15) shift: -1.97 -0.44 ...... Frame ( 16) shift: -1.98 -0.49 ...... Frame ( 17) shift: -1.99 -0.53 ...... Frame ( 18) shift: -2.01 -0.58 ...... Frame ( 19) shift: -2.03 -0.64 ...... Frame ( 20) shift: -2.06 -0.71 ...... Frame ( 21) shift: -2.10 -0.74 ...... Frame ( 22) shift: -2.14 -0.76 ...... Frame ( 23) shift: -2.18 -0.77 ...... Frame ( 24) shift: -2.22 -0.77 ...... Frame ( 25) shift: -2.25 -0.73 ...... Frame ( 26) shift: -2.28 -0.70 ...... Frame ( 27) shift: -2.30 -0.72 ...... Frame ( 28) shift: -2.32 -0.78 ...... Frame ( 29) shift: -2.33 -0.84 ...... Frame ( 30) shift: -2.35 -0.87 ...... Frame ( 31) shift: -2.38 -0.88 ...... Frame ( 32) shift: -2.41 -0.89 ...... Frame ( 33) shift: -2.40 -0.87 ...... Frame ( 34) shift: -2.35 -0.84 ...... Frame ( 35) shift: -2.30 -0.80 ...... Frame ( 36) shift: -2.29 -0.77 ...... Frame ( 37) shift: -2.32 -0.74 ...... Frame ( 38) shift: -2.35 -0.71 ...... Frame ( 39) shift: -2.39 -0.68 ...... Frame ( 40) shift: -2.42 -0.65 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 3.624871 Iteration 2 Error: 0.389405 Iteration 3 Error: 0.162325 Iteration 4 Error: 0.053230 Iteration 5 Error: 0.023791 Align patch 2 23 left Iteration 1 Error: 3.373911 Iteration 2 Error: 0.597925 Iteration 3 Error: 0.180453 Iteration 4 Error: 0.056962 Iteration 5 Error: 0.016847 Align patch 3 22 left Iteration 1 Error: 2.464826 Iteration 2 Error: 0.356758 Iteration 3 Error: 0.109331 Iteration 4 Error: 0.021746 Align patch 4 21 left Iteration 1 Error: 0.781198 Iteration 2 Error: 0.137223 Iteration 3 Error: 0.026866 Align patch 5 20 left Iteration 1 Error: 1.100651 Iteration 2 Error: 0.203183 Iteration 3 Error: 0.046017 Align patch 6 19 left Iteration 1 Error: 2.693210 Iteration 2 Error: 0.522377 Iteration 3 Error: 0.322164 Iteration 4 Error: 0.116948 Iteration 5 Error: 0.098239 Align patch 6 19 left Iteration 1 Error: 2.701651 Iteration 2 Error: 0.292236 Iteration 3 Error: 0.083378 Iteration 4 Error: 0.039675 Align patch 7 18 left Iteration 1 Error: 2.354254 Iteration 2 Error: 0.644434 Iteration 3 Error: 0.212875 Iteration 4 Error: 0.099595 Iteration 5 Error: 0.034821 Align patch 8 17 left Iteration 1 Error: 3.094320 Iteration 2 Error: 0.408544 Iteration 3 Error: 0.136859 Iteration 4 Error: 0.033136 Align patch 9 16 left Iteration 1 Error: 0.522697 Iteration 2 Error: 0.057669 Iteration 3 Error: 0.010241 Align patch 10 15 left Iteration 1 Error: 1.203604 Iteration 2 Error: 0.213670 Iteration 3 Error: 0.046590 Align patch 11 14 left Iteration 1 Error: 1.464236 Iteration 2 Error: 0.583607 Iteration 3 Error: 0.242706 Iteration 4 Error: 0.157582 Iteration 5 Error: 0.105724 Align patch 11 14 left Iteration 1 Error: 2.331838 Iteration 2 Error: 0.380334 Iteration 3 Error: 0.076619 Iteration 4 Error: 0.052214 Iteration 5 Error: 0.019404 Align patch 12 13 left Iteration 1 Error: 2.181827 Iteration 2 Error: 0.322358 Iteration 3 Error: 0.199414 Iteration 4 Error: 0.069605 Iteration 5 Error: 0.041390 Align patch 13 12 left Iteration 1 Error: 0.943219 Iteration 2 Error: 0.347478 Iteration 3 Error: 0.152878 Iteration 4 Error: 0.069639 Iteration 5 Error: 0.041490 Align patch 14 11 left Iteration 1 Error: 1.302762 Iteration 2 Error: 0.117674 Iteration 3 Error: 0.029291 Align patch 15 10 left Iteration 1 Error: 1.157238 Iteration 2 Error: 0.117377 Iteration 3 Error: 0.024432 Align patch 16 9 left Iteration 1 Error: 0.951804 Iteration 2 Error: 0.300282 Iteration 3 Error: 0.136151 Iteration 4 Error: 0.102234 Iteration 5 Error: 0.049350 Align patch 17 8 left Iteration 1 Error: 0.884138 Iteration 2 Error: 0.263307 Iteration 3 Error: 0.158897 Iteration 4 Error: 0.069066 Iteration 5 Error: 0.039256 Align patch 18 7 left Iteration 1 Error: 0.673379 Iteration 2 Error: 0.125322 Iteration 3 Error: 0.033287 Align patch 19 6 left Iteration 1 Error: 0.898756 Iteration 2 Error: 0.165545 Iteration 3 Error: 0.029299 Align patch 20 5 left Iteration 1 Error: 1.093630 Iteration 2 Error: 0.261113 Iteration 3 Error: 0.045917 Align patch 21 4 left Iteration 1 Error: 1.309192 Iteration 2 Error: 0.283438 Iteration 3 Error: 0.140968 Iteration 4 Error: 0.098194 Iteration 5 Error: 0.053796 Align patch 21 4 left Iteration 1 Error: 1.187933 Iteration 2 Error: 0.347893 Iteration 3 Error: 0.085725 Iteration 4 Error: 0.027552 Align patch 22 3 left Iteration 1 Error: 1.147556 Iteration 2 Error: 0.232893 Iteration 3 Error: 0.043819 Align patch 23 2 left Iteration 1 Error: 0.626425 Iteration 2 Error: 0.091374 Iteration 3 Error: 0.023656 Align patch 24 1 left Iteration 1 Error: 1.254359 Iteration 2 Error: 0.163819 Iteration 3 Error: 0.026682 Align patch 25 0 left Iteration 1 Error: 1.563612 Iteration 2 Error: 0.190264 Iteration 3 Error: 0.041562 3D Fitting completed. Patch alignment time: 19.81(sec) Local motion has been corrected. Process thread exits. Computational time: 28.315889 sec Total time: 35.033684 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00004hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00004hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.692053s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00004hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.971949s ........................................ >>>>>>TIME<<<<<< FFT: 0.939190s Defocus_U Defocus_V Angle CCC 9443.36 10283.20 12.99 -0.001256 Final Values Defocus_U Defocus_V Angle CCC 9432.41 10294.15 13.30 -0.077402 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00004hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00004hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.282e-01 9.585e-02 CC threshold: 0.703 Mean Std: 41.73 7.75 Num Hot pixels: 166 Hot pixel threshold: 88.22 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.595217 Iteration 2 Error: 0.054995 Iteration 3 Error: 0.009898 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.04 0.05 ...... Frame ( 3) shift: -0.08 0.10 ...... Frame ( 4) shift: -0.12 0.16 ...... Frame ( 5) shift: -0.16 0.21 ...... Frame ( 6) shift: -0.22 0.26 ...... Frame ( 7) shift: -0.29 0.30 ...... Frame ( 8) shift: -0.36 0.34 ...... Frame ( 9) shift: -0.43 0.38 ...... Frame ( 10) shift: -0.51 0.41 ...... Frame ( 11) shift: -0.58 0.44 ...... Frame ( 12) shift: -0.61 0.44 ...... Frame ( 13) shift: -0.61 0.42 ...... Frame ( 14) shift: -0.60 0.39 ...... Frame ( 15) shift: -0.62 0.38 ...... Frame ( 16) shift: -0.67 0.38 ...... Frame ( 17) shift: -0.72 0.38 ...... Frame ( 18) shift: -0.75 0.38 ...... Frame ( 19) shift: -0.76 0.37 ...... Frame ( 20) shift: -0.78 0.36 ...... Frame ( 21) shift: -0.76 0.32 ...... Frame ( 22) shift: -0.71 0.25 ...... Frame ( 23) shift: -0.66 0.19 ...... Frame ( 24) shift: -0.68 0.17 ...... Frame ( 25) shift: -0.77 0.22 ...... Frame ( 26) shift: -0.86 0.27 ...... Frame ( 27) shift: -0.89 0.30 ...... Frame ( 28) shift: -0.86 0.31 ...... Frame ( 29) shift: -0.83 0.33 ...... Frame ( 30) shift: -0.82 0.35 ...... Frame ( 31) shift: -0.84 0.38 ...... Frame ( 32) shift: -0.86 0.41 ...... Frame ( 33) shift: -0.87 0.42 ...... Frame ( 34) shift: -0.87 0.42 ...... Frame ( 35) shift: -0.88 0.41 ...... Frame ( 36) shift: -0.85 0.43 ...... Frame ( 37) shift: -0.80 0.49 ...... Frame ( 38) shift: -0.75 0.54 ...... Frame ( 39) shift: -0.70 0.59 ...... Frame ( 40) shift: -0.66 0.64 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.176212 Iteration 2 Error: 0.138782 Iteration 3 Error: 0.037783 Align patch 2 23 left Iteration 1 Error: 1.039033 Iteration 2 Error: 0.118657 Iteration 3 Error: 0.033176 Align patch 3 22 left Iteration 1 Error: 1.091866 Iteration 2 Error: 0.108487 Iteration 3 Error: 0.029173 Align patch 4 21 left Iteration 1 Error: 0.697246 Iteration 2 Error: 0.143140 Iteration 3 Error: 0.035945 Align patch 5 20 left Iteration 1 Error: 0.888685 Iteration 2 Error: 0.143971 Iteration 3 Error: 0.029109 Align patch 6 19 left Iteration 1 Error: 0.922805 Iteration 2 Error: 0.188055 Iteration 3 Error: 0.086468 Iteration 4 Error: 0.027797 Align patch 7 18 left Iteration 1 Error: 1.033148 Iteration 2 Error: 0.101638 Iteration 3 Error: 0.031246 Align patch 8 17 left Iteration 1 Error: 0.575686 Iteration 2 Error: 0.062513 Iteration 3 Error: 0.017617 Align patch 9 16 left Iteration 1 Error: 0.683048 Iteration 2 Error: 0.094585 Iteration 3 Error: 0.016972 Align patch 10 15 left Iteration 1 Error: 0.525738 Iteration 2 Error: 0.105984 Iteration 3 Error: 0.020079 Align patch 11 14 left Iteration 1 Error: 1.387444 Iteration 2 Error: 0.217293 Iteration 3 Error: 0.063272 Iteration 4 Error: 0.024041 Align patch 12 13 left Iteration 1 Error: 0.936068 Iteration 2 Error: 0.155836 Iteration 3 Error: 0.050794 Iteration 4 Error: 0.024617 Align patch 13 12 left Iteration 1 Error: 0.547599 Iteration 2 Error: 0.078373 Iteration 3 Error: 0.025632 Align patch 14 11 left Iteration 1 Error: 1.054911 Iteration 2 Error: 0.108687 Iteration 3 Error: 0.025393 Align patch 15 10 left Iteration 1 Error: 0.883894 Iteration 2 Error: 0.125025 Iteration 3 Error: 0.021329 Align patch 16 9 left Iteration 1 Error: 0.994241 Iteration 2 Error: 0.219150 Iteration 3 Error: 0.049644 Align patch 17 8 left Iteration 1 Error: 0.717827 Iteration 2 Error: 0.138518 Iteration 3 Error: 0.038749 Align patch 18 7 left Iteration 1 Error: 0.844759 Iteration 2 Error: 0.118342 Iteration 3 Error: 0.017041 Align patch 19 6 left Iteration 1 Error: 0.582347 Iteration 2 Error: 0.113467 Iteration 3 Error: 0.020455 Align patch 20 5 left Iteration 1 Error: 1.040387 Iteration 2 Error: 0.123171 Iteration 3 Error: 0.035367 Align patch 21 4 left Iteration 1 Error: 0.761702 Iteration 2 Error: 0.211156 Iteration 3 Error: 0.070022 Iteration 4 Error: 0.019449 Align patch 22 3 left Iteration 1 Error: 0.926951 Iteration 2 Error: 0.108045 Iteration 3 Error: 0.034143 Align patch 23 2 left Iteration 1 Error: 0.784353 Iteration 2 Error: 0.113965 Iteration 3 Error: 0.033584 Align patch 24 1 left Iteration 1 Error: 0.884523 Iteration 2 Error: 0.138500 Iteration 3 Error: 0.038344 Align patch 25 0 left Iteration 1 Error: 0.771188 Iteration 2 Error: 0.064649 Iteration 3 Error: 0.017301 3D Fitting completed. Patch alignment time: 15.75(sec) Local motion has been corrected. Process thread exits. Computational time: 23.926670 sec Total time: 29.462130 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00004hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00004hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.764899s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00004hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.066330s ........................................ >>>>>>TIME<<<<<< FFT: 1.020042s Defocus_U Defocus_V Angle CCC 8645.10 9108.84 0.94 -0.043145 Final Values Defocus_U Defocus_V Angle CCC 8657.60 9068.22 1.26 -0.212264 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00004hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00004hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.001e-01 CC threshold: 0.735 Mean Std: 45.24 7.67 Num Hot pixels: 208 Hot pixel threshold: 91.27 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.832304 Iteration 2 Error: 0.041563 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.33 -0.14 ...... Frame ( 3) shift: -0.67 -0.28 ...... Frame ( 4) shift: -1.00 -0.42 ...... Frame ( 5) shift: -1.34 -0.56 ...... Frame ( 6) shift: -1.50 -0.65 ...... Frame ( 7) shift: -1.48 -0.70 ...... Frame ( 8) shift: -1.47 -0.74 ...... Frame ( 9) shift: -1.44 -0.78 ...... Frame ( 10) shift: -1.40 -0.82 ...... Frame ( 11) shift: -1.35 -0.86 ...... Frame ( 12) shift: -1.35 -0.88 ...... Frame ( 13) shift: -1.38 -0.88 ...... Frame ( 14) shift: -1.40 -0.88 ...... Frame ( 15) shift: -1.37 -0.85 ...... Frame ( 16) shift: -1.26 -0.78 ...... Frame ( 17) shift: -1.15 -0.72 ...... Frame ( 18) shift: -1.11 -0.72 ...... Frame ( 19) shift: -1.13 -0.80 ...... Frame ( 20) shift: -1.15 -0.87 ...... Frame ( 21) shift: -1.16 -0.89 ...... Frame ( 22) shift: -1.17 -0.85 ...... Frame ( 23) shift: -1.18 -0.81 ...... Frame ( 24) shift: -1.16 -0.79 ...... Frame ( 25) shift: -1.13 -0.80 ...... Frame ( 26) shift: -1.09 -0.80 ...... Frame ( 27) shift: -1.07 -0.79 ...... Frame ( 28) shift: -1.08 -0.76 ...... Frame ( 29) shift: -1.08 -0.74 ...... Frame ( 30) shift: -1.08 -0.70 ...... Frame ( 31) shift: -1.07 -0.66 ...... Frame ( 32) shift: -1.06 -0.61 ...... Frame ( 33) shift: -1.06 -0.57 ...... Frame ( 34) shift: -1.08 -0.54 ...... Frame ( 35) shift: -1.09 -0.52 ...... Frame ( 36) shift: -1.06 -0.51 ...... Frame ( 37) shift: -0.99 -0.53 ...... Frame ( 38) shift: -0.92 -0.55 ...... Frame ( 39) shift: -0.86 -0.57 ...... Frame ( 40) shift: -0.79 -0.59 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.076087 Iteration 2 Error: 0.239481 Iteration 3 Error: 0.039958 Align patch 2 23 left Iteration 1 Error: 1.179178 Iteration 2 Error: 0.157381 Iteration 3 Error: 0.061532 Iteration 4 Error: 0.016303 Align patch 3 22 left Iteration 1 Error: 1.445919 Iteration 2 Error: 0.092591 Iteration 3 Error: 0.030785 Align patch 4 21 left Iteration 1 Error: 0.685615 Iteration 2 Error: 0.128312 Iteration 3 Error: 0.028527 Align patch 5 20 left Iteration 1 Error: 0.720349 Iteration 2 Error: 0.094232 Iteration 3 Error: 0.017915 Align patch 6 19 left Iteration 1 Error: 1.094903 Iteration 2 Error: 0.248997 Iteration 3 Error: 0.066630 Iteration 4 Error: 0.031723 Align patch 7 18 left Iteration 1 Error: 1.074940 Iteration 2 Error: 0.204952 Iteration 3 Error: 0.052265 Iteration 4 Error: 0.024567 Align patch 8 17 left Iteration 1 Error: 1.128170 Iteration 2 Error: 0.122916 Iteration 3 Error: 0.040089 Align patch 9 16 left Iteration 1 Error: 0.433561 Iteration 2 Error: 0.079636 Iteration 3 Error: 0.016752 Align patch 10 15 left Iteration 1 Error: 0.771181 Iteration 2 Error: 0.082172 Iteration 3 Error: 0.016321 Align patch 11 14 left Iteration 1 Error: 1.134703 Iteration 2 Error: 0.381018 Iteration 3 Error: 0.087766 Iteration 4 Error: 0.039876 Align patch 12 13 left Iteration 1 Error: 0.736716 Iteration 2 Error: 0.170289 Iteration 3 Error: 0.064465 Iteration 4 Error: 0.013736 Align patch 13 12 left Iteration 1 Error: 1.090180 Iteration 2 Error: 0.097039 Iteration 3 Error: 0.034321 Align patch 14 11 left Iteration 1 Error: 0.648645 Iteration 2 Error: 0.080846 Iteration 3 Error: 0.019199 Align patch 15 10 left Iteration 1 Error: 0.874712 Iteration 2 Error: 0.078060 Iteration 3 Error: 0.011296 Align patch 16 9 left Iteration 1 Error: 1.527973 Iteration 2 Error: 0.151355 Iteration 3 Error: 0.060630 Iteration 4 Error: 0.020990 Align patch 17 8 left Iteration 1 Error: 0.789546 Iteration 2 Error: 0.134519 Iteration 3 Error: 0.033799 Align patch 18 7 left Iteration 1 Error: 0.609117 Iteration 2 Error: 0.118091 Iteration 3 Error: 0.029058 Align patch 19 6 left Iteration 1 Error: 0.665099 Iteration 2 Error: 0.145109 Iteration 3 Error: 0.034250 Align patch 20 5 left Iteration 1 Error: 0.695216 Iteration 2 Error: 0.079590 Iteration 3 Error: 0.012692 Align patch 21 4 left Iteration 1 Error: 1.817033 Iteration 2 Error: 0.187519 Iteration 3 Error: 0.077789 Iteration 4 Error: 0.023154 Align patch 22 3 left Iteration 1 Error: 1.281545 Iteration 2 Error: 0.123837 Iteration 3 Error: 0.024581 Align patch 23 2 left Iteration 1 Error: 0.910869 Iteration 2 Error: 0.130602 Iteration 3 Error: 0.029555 Align patch 24 1 left Iteration 1 Error: 0.465730 Iteration 2 Error: 0.055111 Iteration 3 Error: 0.016082 Align patch 25 0 left Iteration 1 Error: 0.616856 Iteration 2 Error: 0.117088 Iteration 3 Error: 0.016703 3D Fitting completed. Patch alignment time: 15.76(sec) Local motion has been corrected. Process thread exits. Computational time: 23.840780 sec Total time: 29.933981 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00004hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00004hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.644954s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00004hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.055964s ........................................ >>>>>>TIME<<<<<< FFT: 0.975107s Defocus_U Defocus_V Angle CCC 10314.44 11244.19 5.54 0.043310 Final Values Defocus_U Defocus_V Angle CCC 10298.80 11259.83 5.85 0.080696 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00004hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00004hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.337e-01 9.947e-02 CC threshold: 0.731 Mean Std: 44.95 7.62 Num Hot pixels: 201 Hot pixel threshold: 90.69 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.696060 Iteration 2 Error: 0.132055 Iteration 3 Error: 0.022794 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.25 -0.10 ...... Frame ( 3) shift: -0.50 -0.19 ...... Frame ( 4) shift: -0.75 -0.29 ...... Frame ( 5) shift: -0.99 -0.38 ...... Frame ( 6) shift: -1.18 -0.47 ...... Frame ( 7) shift: -1.30 -0.55 ...... Frame ( 8) shift: -1.42 -0.63 ...... Frame ( 9) shift: -1.55 -0.70 ...... Frame ( 10) shift: -1.70 -0.74 ...... Frame ( 11) shift: -1.85 -0.78 ...... Frame ( 12) shift: -1.98 -0.78 ...... Frame ( 13) shift: -2.08 -0.73 ...... Frame ( 14) shift: -2.17 -0.68 ...... Frame ( 15) shift: -2.23 -0.67 ...... Frame ( 16) shift: -2.26 -0.69 ...... Frame ( 17) shift: -2.28 -0.72 ...... Frame ( 18) shift: -2.31 -0.70 ...... Frame ( 19) shift: -2.35 -0.64 ...... Frame ( 20) shift: -2.38 -0.59 ...... Frame ( 21) shift: -2.44 -0.55 ...... Frame ( 22) shift: -2.51 -0.52 ...... Frame ( 23) shift: -2.58 -0.50 ...... Frame ( 24) shift: -2.58 -0.52 ...... Frame ( 25) shift: -2.49 -0.60 ...... Frame ( 26) shift: -2.41 -0.68 ...... Frame ( 27) shift: -2.40 -0.71 ...... Frame ( 28) shift: -2.46 -0.70 ...... Frame ( 29) shift: -2.52 -0.68 ...... Frame ( 30) shift: -2.54 -0.70 ...... Frame ( 31) shift: -2.54 -0.73 ...... Frame ( 32) shift: -2.54 -0.77 ...... Frame ( 33) shift: -2.54 -0.80 ...... Frame ( 34) shift: -2.54 -0.82 ...... Frame ( 35) shift: -2.54 -0.84 ...... Frame ( 36) shift: -2.51 -0.84 ...... Frame ( 37) shift: -2.44 -0.82 ...... Frame ( 38) shift: -2.38 -0.79 ...... Frame ( 39) shift: -2.32 -0.77 ...... Frame ( 40) shift: -2.26 -0.75 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.877762 Iteration 2 Error: 0.258286 Iteration 3 Error: 0.048988 Align patch 2 23 left Iteration 1 Error: 0.922176 Iteration 2 Error: 0.173621 Iteration 3 Error: 0.034786 Align patch 3 22 left Iteration 1 Error: 0.945093 Iteration 2 Error: 0.202626 Iteration 3 Error: 0.044453 Align patch 4 21 left Iteration 1 Error: 1.018525 Iteration 2 Error: 0.093382 Iteration 3 Error: 0.029043 Align patch 5 20 left Iteration 1 Error: 0.893666 Iteration 2 Error: 0.177078 Iteration 3 Error: 0.036245 Align patch 6 19 left Iteration 1 Error: 0.549997 Iteration 2 Error: 0.151359 Iteration 3 Error: 0.035612 Align patch 7 18 left Iteration 1 Error: 0.893596 Iteration 2 Error: 0.130666 Iteration 3 Error: 0.029222 Align patch 8 17 left Iteration 1 Error: 2.045580 Iteration 2 Error: 0.337016 Iteration 3 Error: 0.156568 Iteration 4 Error: 0.034883 Align patch 9 16 left Iteration 1 Error: 0.928584 Iteration 2 Error: 0.152773 Iteration 3 Error: 0.056239 Iteration 4 Error: 0.019354 Align patch 10 15 left Iteration 1 Error: 0.827660 Iteration 2 Error: 0.164835 Iteration 3 Error: 0.047259 Align patch 11 14 left Iteration 1 Error: 0.897694 Iteration 2 Error: 0.403074 Iteration 3 Error: 0.252548 Iteration 4 Error: 0.128322 Iteration 5 Error: 0.090985 Align patch 11 14 left Iteration 1 Error: 1.078211 Iteration 2 Error: 0.266160 Iteration 3 Error: 0.048463 Align patch 12 13 left Iteration 1 Error: 0.582498 Iteration 2 Error: 0.245164 Iteration 3 Error: 0.079036 Iteration 4 Error: 0.026522 Align patch 13 12 left Iteration 1 Error: 0.865434 Iteration 2 Error: 0.113991 Iteration 3 Error: 0.028256 Align patch 14 11 left Iteration 1 Error: 0.734585 Iteration 2 Error: 0.108391 Iteration 3 Error: 0.032429 Align patch 15 10 left Iteration 1 Error: 0.719430 Iteration 2 Error: 0.185463 Iteration 3 Error: 0.038150 Align patch 16 9 left Iteration 1 Error: 2.208560 Iteration 2 Error: 0.627291 Iteration 3 Error: 0.252341 Iteration 4 Error: 0.314748 Iteration 5 Error: 0.127916 Align patch 16 9 left Iteration 1 Error: 2.141872 Iteration 2 Error: 0.149285 Iteration 3 Error: 0.080806 Iteration 4 Error: 0.023366 Align patch 17 8 left Iteration 1 Error: 1.295840 Iteration 2 Error: 0.547854 Iteration 3 Error: 0.232725 Iteration 4 Error: 0.179248 Iteration 5 Error: 0.062187 Align patch 17 8 left Iteration 1 Error: 1.488947 Iteration 2 Error: 0.270194 Iteration 3 Error: 0.049217 Align patch 18 7 left Iteration 1 Error: 0.706330 Iteration 2 Error: 0.256027 Iteration 3 Error: 0.088084 Iteration 4 Error: 0.054234 Iteration 5 Error: 0.019922 Align patch 19 6 left Iteration 1 Error: 0.557612 Iteration 2 Error: 0.106075 Iteration 3 Error: 0.035006 Align patch 20 5 left Iteration 1 Error: 0.807500 Iteration 2 Error: 0.219833 Iteration 3 Error: 0.061141 Iteration 4 Error: 0.023525 Align patch 21 4 left Iteration 1 Error: 3.824720 Iteration 2 Error: 0.237239 Iteration 3 Error: 0.209144 Iteration 4 Error: 0.067482 Iteration 5 Error: 0.032702 Align patch 22 3 left Iteration 1 Error: 3.236672 Iteration 2 Error: 0.246967 Iteration 3 Error: 0.042227 Align patch 23 2 left Iteration 1 Error: 1.064503 Iteration 2 Error: 0.169184 Iteration 3 Error: 0.087285 Iteration 4 Error: 0.031505 Align patch 24 1 left Iteration 1 Error: 0.606733 Iteration 2 Error: 0.101318 Iteration 3 Error: 0.032966 Align patch 25 0 left Iteration 1 Error: 1.051363 Iteration 2 Error: 0.125312 Iteration 3 Error: 0.028645 3D Fitting completed. Patch alignment time: 18.78(sec) Local motion has been corrected. Process thread exits. Computational time: 27.336048 sec Total time: 32.903969 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00004hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00004hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.680731s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00004hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.859607s ........................................ >>>>>>TIME<<<<<< FFT: 0.970297s Defocus_U Defocus_V Angle CCC 12486.35 11841.80 86.13 0.031703 Final Values Defocus_U Defocus_V Angle CCC 12486.35 11857.43 86.45 0.029340 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00005hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00005hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.350e-01 1.004e-01 CC threshold: 0.737 Mean Std: 44.19 7.82 Num Hot pixels: 177 Hot pixel threshold: 91.11 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.629231 Iteration 2 Error: 0.187448 Iteration 3 Error: 0.023590 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.19 0.11 ...... Frame ( 3) shift: -0.38 0.21 ...... Frame ( 4) shift: -0.57 0.32 ...... Frame ( 5) shift: -0.76 0.43 ...... Frame ( 6) shift: -0.80 0.53 ...... Frame ( 7) shift: -0.71 0.63 ...... Frame ( 8) shift: -0.61 0.72 ...... Frame ( 9) shift: -0.52 0.81 ...... Frame ( 10) shift: -0.42 0.89 ...... Frame ( 11) shift: -0.33 0.97 ...... Frame ( 12) shift: -0.21 1.06 ...... Frame ( 13) shift: -0.06 1.15 ...... Frame ( 14) shift: 0.08 1.25 ...... Frame ( 15) shift: 0.14 1.32 ...... Frame ( 16) shift: 0.12 1.37 ...... Frame ( 17) shift: 0.10 1.41 ...... Frame ( 18) shift: 0.12 1.48 ...... Frame ( 19) shift: 0.19 1.57 ...... Frame ( 20) shift: 0.27 1.66 ...... Frame ( 21) shift: 0.32 1.75 ...... Frame ( 22) shift: 0.35 1.83 ...... Frame ( 23) shift: 0.38 1.92 ...... Frame ( 24) shift: 0.42 1.98 ...... Frame ( 25) shift: 0.49 2.02 ...... Frame ( 26) shift: 0.55 2.05 ...... Frame ( 27) shift: 0.60 2.07 ...... Frame ( 28) shift: 0.65 2.08 ...... Frame ( 29) shift: 0.70 2.10 ...... Frame ( 30) shift: 0.76 2.12 ...... Frame ( 31) shift: 0.83 2.15 ...... Frame ( 32) shift: 0.91 2.19 ...... Frame ( 33) shift: 0.99 2.22 ...... Frame ( 34) shift: 1.07 2.23 ...... Frame ( 35) shift: 1.15 2.24 ...... Frame ( 36) shift: 1.21 2.31 ...... Frame ( 37) shift: 1.27 2.43 ...... Frame ( 38) shift: 1.32 2.55 ...... Frame ( 39) shift: 1.37 2.67 ...... Frame ( 40) shift: 1.43 2.79 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.951738 Iteration 2 Error: 0.435678 Iteration 3 Error: 0.123376 Iteration 4 Error: 0.038964 Align patch 2 23 left Iteration 1 Error: 1.760295 Iteration 2 Error: 0.529015 Iteration 3 Error: 0.129811 Iteration 4 Error: 0.052415 Iteration 5 Error: 0.020908 Align patch 3 22 left Iteration 1 Error: 1.047372 Iteration 2 Error: 0.308429 Iteration 3 Error: 0.127142 Iteration 4 Error: 0.047231 Align patch 4 21 left Iteration 1 Error: 1.054162 Iteration 2 Error: 0.147221 Iteration 3 Error: 0.038950 Align patch 5 20 left Iteration 1 Error: 1.152370 Iteration 2 Error: 0.064549 Iteration 3 Error: 0.005497 Align patch 6 19 left Iteration 1 Error: 1.686969 Iteration 2 Error: 0.366769 Iteration 3 Error: 0.068985 Iteration 4 Error: 0.018477 Align patch 7 18 left Iteration 1 Error: 1.902354 Iteration 2 Error: 0.281680 Iteration 3 Error: 0.108243 Iteration 4 Error: 0.032931 Align patch 8 17 left Iteration 1 Error: 1.371429 Iteration 2 Error: 0.171438 Iteration 3 Error: 0.056719 Iteration 4 Error: 0.026968 Align patch 9 16 left Iteration 1 Error: 0.868491 Iteration 2 Error: 0.154005 Iteration 3 Error: 0.045127 Align patch 10 15 left Iteration 1 Error: 0.825363 Iteration 2 Error: 0.039534 Align patch 11 14 left Iteration 1 Error: 2.152161 Iteration 2 Error: 0.386143 Iteration 3 Error: 0.052912 Iteration 4 Error: 0.018260 Align patch 12 13 left Iteration 1 Error: 1.857845 Iteration 2 Error: 0.189265 Iteration 3 Error: 0.027438 Align patch 13 12 left Iteration 1 Error: 1.230028 Iteration 2 Error: 0.144946 Iteration 3 Error: 0.047804 Align patch 14 11 left Iteration 1 Error: 0.820734 Iteration 2 Error: 0.073999 Iteration 3 Error: 0.015631 Align patch 15 10 left Iteration 1 Error: 0.786416 Iteration 2 Error: 0.031660 Align patch 16 9 left Iteration 1 Error: 2.101948 Iteration 2 Error: 0.234305 Iteration 3 Error: 0.057273 Iteration 4 Error: 0.021989 Align patch 17 8 left Iteration 1 Error: 1.917074 Iteration 2 Error: 0.215884 Iteration 3 Error: 0.034926 Align patch 18 7 left Iteration 1 Error: 1.327005 Iteration 2 Error: 0.163616 Iteration 3 Error: 0.038184 Align patch 19 6 left Iteration 1 Error: 0.462335 Iteration 2 Error: 0.049779 Align patch 20 5 left Iteration 1 Error: 0.834208 Iteration 2 Error: 0.035836 Align patch 21 4 left Iteration 1 Error: 2.148507 Iteration 2 Error: 0.236051 Iteration 3 Error: 0.086260 Iteration 4 Error: 0.032266 Align patch 22 3 left Iteration 1 Error: 2.132306 Iteration 2 Error: 0.192070 Iteration 3 Error: 0.048520 Align patch 23 2 left Iteration 1 Error: 1.673607 Iteration 2 Error: 0.241670 Iteration 3 Error: 0.047831 Align patch 24 1 left Iteration 1 Error: 1.014140 Iteration 2 Error: 0.142205 Iteration 3 Error: 0.030349 Align patch 25 0 left Iteration 1 Error: 0.558627 Iteration 2 Error: 0.122383 Iteration 3 Error: 0.029915 3D Fitting completed. Patch alignment time: 16.15(sec) Local motion has been corrected. Process thread exits. Computational time: 24.973354 sec Total time: 30.676228 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00005hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00005hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.544958s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00005hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.978801s ........................................ >>>>>>TIME<<<<<< FFT: 0.799527s Defocus_U Defocus_V Angle CCC 9525.39 10361.33 13.00 0.067253 Final Values Defocus_U Defocus_V Angle CCC 9520.70 10375.40 13.00 0.126786 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00005hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00005hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 44.37 7.70 Num Hot pixels: 178 Hot pixel threshold: 90.59 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.887605 Iteration 2 Error: 0.098296 Iteration 3 Error: 0.020054 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.29 0.10 ...... Frame ( 3) shift: -0.57 0.20 ...... Frame ( 4) shift: -0.86 0.31 ...... Frame ( 5) shift: -1.14 0.41 ...... Frame ( 6) shift: -1.29 0.46 ...... Frame ( 7) shift: -1.30 0.45 ...... Frame ( 8) shift: -1.30 0.44 ...... Frame ( 9) shift: -1.27 0.43 ...... Frame ( 10) shift: -1.20 0.40 ...... Frame ( 11) shift: -1.13 0.37 ...... Frame ( 12) shift: -1.12 0.39 ...... Frame ( 13) shift: -1.15 0.46 ...... Frame ( 14) shift: -1.18 0.53 ...... Frame ( 15) shift: -1.17 0.59 ...... Frame ( 16) shift: -1.09 0.63 ...... Frame ( 17) shift: -1.02 0.67 ...... Frame ( 18) shift: -1.00 0.72 ...... Frame ( 19) shift: -1.03 0.79 ...... Frame ( 20) shift: -1.06 0.85 ...... Frame ( 21) shift: -1.07 0.91 ...... Frame ( 22) shift: -1.07 0.96 ...... Frame ( 23) shift: -1.06 1.01 ...... Frame ( 24) shift: -1.06 1.06 ...... Frame ( 25) shift: -1.08 1.11 ...... Frame ( 26) shift: -1.09 1.16 ...... Frame ( 27) shift: -1.06 1.20 ...... Frame ( 28) shift: -0.97 1.23 ...... Frame ( 29) shift: -0.88 1.26 ...... Frame ( 30) shift: -0.84 1.28 ...... Frame ( 31) shift: -0.84 1.27 ...... Frame ( 32) shift: -0.85 1.26 ...... Frame ( 33) shift: -0.85 1.28 ...... Frame ( 34) shift: -0.85 1.32 ...... Frame ( 35) shift: -0.85 1.37 ...... Frame ( 36) shift: -0.83 1.38 ...... Frame ( 37) shift: -0.80 1.38 ...... Frame ( 38) shift: -0.77 1.37 ...... Frame ( 39) shift: -0.74 1.36 ...... Frame ( 40) shift: -0.70 1.35 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.162929 Iteration 2 Error: 0.519505 Iteration 3 Error: 0.162759 Iteration 4 Error: 0.078907 Iteration 5 Error: 0.029156 Align patch 2 23 left Iteration 1 Error: 0.808535 Iteration 2 Error: 0.118215 Iteration 3 Error: 0.057319 Iteration 4 Error: 0.020004 Align patch 3 22 left Iteration 1 Error: 0.648737 Iteration 2 Error: 0.097717 Iteration 3 Error: 0.021882 Align patch 4 21 left Iteration 1 Error: 0.820320 Iteration 2 Error: 0.142489 Iteration 3 Error: 0.021790 Align patch 5 20 left Iteration 1 Error: 0.872655 Iteration 2 Error: 0.153290 Iteration 3 Error: 0.040917 Align patch 6 19 left Iteration 1 Error: 0.796942 Iteration 2 Error: 0.103722 Iteration 3 Error: 0.044831 Align patch 7 18 left Iteration 1 Error: 0.571787 Iteration 2 Error: 0.075642 Iteration 3 Error: 0.020437 Align patch 8 17 left Iteration 1 Error: 0.929249 Iteration 2 Error: 0.210286 Iteration 3 Error: 0.050953 Iteration 4 Error: 0.021394 Align patch 9 16 left Iteration 1 Error: 1.126467 Iteration 2 Error: 0.306487 Iteration 3 Error: 0.069074 Iteration 4 Error: 0.029112 Align patch 10 15 left Iteration 1 Error: 0.703901 Iteration 2 Error: 0.092269 Iteration 3 Error: 0.029968 Align patch 11 14 left Iteration 1 Error: 0.831419 Iteration 2 Error: 0.145442 Iteration 3 Error: 0.022601 Align patch 12 13 left Iteration 1 Error: 0.906592 Iteration 2 Error: 0.153244 Iteration 3 Error: 0.047455 Align patch 13 12 left Iteration 1 Error: 0.600219 Iteration 2 Error: 0.125054 Iteration 3 Error: 0.029776 Align patch 14 11 left Iteration 1 Error: 0.479165 Iteration 2 Error: 0.046525 Align patch 15 10 left Iteration 1 Error: 0.939918 Iteration 2 Error: 0.109742 Iteration 3 Error: 0.030856 Align patch 16 9 left Iteration 1 Error: 1.997293 Iteration 2 Error: 0.288073 Iteration 3 Error: 0.060862 Iteration 4 Error: 0.026884 Align patch 17 8 left Iteration 1 Error: 1.253361 Iteration 2 Error: 0.314220 Iteration 3 Error: 0.117749 Iteration 4 Error: 0.048071 Align patch 18 7 left Iteration 1 Error: 0.847643 Iteration 2 Error: 0.120284 Iteration 3 Error: 0.024320 Align patch 19 6 left Iteration 1 Error: 0.736151 Iteration 2 Error: 0.100437 Iteration 3 Error: 0.031776 Align patch 20 5 left Iteration 1 Error: 0.470287 Iteration 2 Error: 0.104876 Iteration 3 Error: 0.045718 Align patch 21 4 left Iteration 1 Error: 1.906223 Iteration 2 Error: 0.288626 Iteration 3 Error: 0.122430 Iteration 4 Error: 0.090253 Iteration 5 Error: 0.056079 Align patch 21 4 left Iteration 1 Error: 2.367836 Iteration 2 Error: 0.215372 Iteration 3 Error: 0.075788 Iteration 4 Error: 0.046370 Align patch 22 3 left Iteration 1 Error: 1.813438 Iteration 2 Error: 0.264482 Iteration 3 Error: 0.082826 Iteration 4 Error: 0.038760 Align patch 23 2 left Iteration 1 Error: 0.756176 Iteration 2 Error: 0.205974 Iteration 3 Error: 0.080061 Iteration 4 Error: 0.032269 Align patch 24 1 left Iteration 1 Error: 0.672786 Iteration 2 Error: 0.084831 Iteration 3 Error: 0.018541 Align patch 25 0 left Iteration 1 Error: 0.707347 Iteration 2 Error: 0.094478 Iteration 3 Error: 0.017968 3D Fitting completed. Patch alignment time: 16.72(sec) Local motion has been corrected. Process thread exits. Computational time: 25.262901 sec Total time: 31.203573 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00005hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00005hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.559531s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00005hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.512174s ........................................ >>>>>>TIME<<<<<< FFT: 1.021878s Defocus_U Defocus_V Angle CCC 8673.83 9126.95 2.39 0.035135 Final Values Defocus_U Defocus_V Angle CCC 8695.71 9126.96 3.65 0.075175 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00005hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00005hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 1.000e-01 CC threshold: 0.734 Mean Std: 44.98 7.89 Num Hot pixels: 183 Hot pixel threshold: 92.33 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.512752 Iteration 2 Error: 0.148598 Iteration 3 Error: 0.045291 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.41 0.03 ...... Frame ( 3) shift: -0.82 0.06 ...... Frame ( 4) shift: -1.23 0.09 ...... Frame ( 5) shift: -1.64 0.12 ...... Frame ( 6) shift: -1.85 0.17 ...... Frame ( 7) shift: -1.86 0.23 ...... Frame ( 8) shift: -1.86 0.29 ...... Frame ( 9) shift: -1.87 0.41 ...... Frame ( 10) shift: -1.89 0.57 ...... Frame ( 11) shift: -1.91 0.74 ...... Frame ( 12) shift: -1.92 0.85 ...... Frame ( 13) shift: -1.93 0.90 ...... Frame ( 14) shift: -1.93 0.96 ...... Frame ( 15) shift: -1.92 0.98 ...... Frame ( 16) shift: -1.89 0.97 ...... Frame ( 17) shift: -1.85 0.97 ...... Frame ( 18) shift: -1.83 1.00 ...... Frame ( 19) shift: -1.82 1.07 ...... Frame ( 20) shift: -1.81 1.13 ...... Frame ( 21) shift: -1.79 1.19 ...... Frame ( 22) shift: -1.78 1.24 ...... Frame ( 23) shift: -1.76 1.30 ...... Frame ( 24) shift: -1.75 1.34 ...... Frame ( 25) shift: -1.75 1.36 ...... Frame ( 26) shift: -1.74 1.39 ...... Frame ( 27) shift: -1.78 1.44 ...... Frame ( 28) shift: -1.87 1.52 ...... Frame ( 29) shift: -1.95 1.61 ...... Frame ( 30) shift: -1.99 1.65 ...... Frame ( 31) shift: -1.97 1.66 ...... Frame ( 32) shift: -1.96 1.67 ...... Frame ( 33) shift: -1.99 1.72 ...... Frame ( 34) shift: -2.06 1.81 ...... Frame ( 35) shift: -2.13 1.90 ...... Frame ( 36) shift: -2.14 1.90 ...... Frame ( 37) shift: -2.08 1.81 ...... Frame ( 38) shift: -2.02 1.72 ...... Frame ( 39) shift: -1.96 1.63 ...... Frame ( 40) shift: -1.90 1.54 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.117283 Iteration 2 Error: 0.243249 Iteration 3 Error: 0.070113 Iteration 4 Error: 0.027803 Align patch 2 23 left Iteration 1 Error: 1.472125 Iteration 2 Error: 0.406400 Iteration 3 Error: 0.121111 Iteration 4 Error: 0.046843 Align patch 3 22 left Iteration 1 Error: 2.906327 Iteration 2 Error: 0.323104 Iteration 3 Error: 0.082345 Iteration 4 Error: 0.034946 Align patch 4 21 left Iteration 1 Error: 0.645100 Iteration 2 Error: 0.133261 Iteration 3 Error: 0.037197 Align patch 5 20 left Iteration 1 Error: 2.006489 Iteration 2 Error: 0.292289 Iteration 3 Error: 0.102412 Iteration 4 Error: 0.041643 Align patch 6 19 left Iteration 1 Error: 1.100294 Iteration 2 Error: 0.118456 Iteration 3 Error: 0.023543 Align patch 7 18 left Iteration 1 Error: 1.288013 Iteration 2 Error: 0.301540 Iteration 3 Error: 0.079074 Iteration 4 Error: 0.034328 Align patch 8 17 left Iteration 1 Error: 1.226633 Iteration 2 Error: 0.164790 Iteration 3 Error: 0.067883 Iteration 4 Error: 0.022303 Align patch 9 16 left Iteration 1 Error: 1.191782 Iteration 2 Error: 0.187571 Iteration 3 Error: 0.049313 Align patch 10 15 left Iteration 1 Error: 1.271262 Iteration 2 Error: 0.187319 Iteration 3 Error: 0.054274 Iteration 4 Error: 0.025186 Align patch 11 14 left Iteration 1 Error: 1.593159 Iteration 2 Error: 0.243032 Iteration 3 Error: 0.126328 Iteration 4 Error: 0.082907 Iteration 5 Error: 0.040333 Align patch 12 13 left Iteration 1 Error: 1.910964 Iteration 2 Error: 0.206296 Iteration 3 Error: 0.044801 Align patch 13 12 left Iteration 1 Error: 0.769687 Iteration 2 Error: 0.155568 Iteration 3 Error: 0.034710 Align patch 14 11 left Iteration 1 Error: 0.834515 Iteration 2 Error: 0.107131 Iteration 3 Error: 0.033328 Align patch 15 10 left Iteration 1 Error: 1.777518 Iteration 2 Error: 0.270022 Iteration 3 Error: 0.068173 Iteration 4 Error: 0.022501 Align patch 16 9 left Iteration 1 Error: 1.912715 Iteration 2 Error: 0.604467 Iteration 3 Error: 0.319374 Iteration 4 Error: 0.179332 Iteration 5 Error: 0.106497 Align patch 16 9 left Iteration 1 Error: 2.977833 Iteration 2 Error: 0.462443 Iteration 3 Error: 0.112676 Iteration 4 Error: 0.038692 Align patch 17 8 left Iteration 1 Error: 1.218299 Iteration 2 Error: 0.192409 Iteration 3 Error: 0.047863 Align patch 18 7 left Iteration 1 Error: 1.583903 Iteration 2 Error: 0.233088 Iteration 3 Error: 0.063252 Iteration 4 Error: 0.022466 Align patch 19 6 left Iteration 1 Error: 0.996509 Iteration 2 Error: 0.146032 Iteration 3 Error: 0.027876 Align patch 20 5 left Iteration 1 Error: 0.618828 Iteration 2 Error: 0.094126 Iteration 3 Error: 0.014332 Align patch 21 4 left Iteration 1 Error: 2.024830 Iteration 2 Error: 0.206231 Iteration 3 Error: 0.073285 Iteration 4 Error: 0.014462 Align patch 22 3 left Iteration 1 Error: 2.356701 Iteration 2 Error: 0.369097 Iteration 3 Error: 0.124196 Iteration 4 Error: 0.062976 Iteration 5 Error: 0.044741 Align patch 23 2 left Iteration 1 Error: 0.805767 Iteration 2 Error: 0.131054 Iteration 3 Error: 0.030215 Align patch 24 1 left Iteration 1 Error: 1.185267 Iteration 2 Error: 0.114304 Iteration 3 Error: 0.021523 Align patch 25 0 left Iteration 1 Error: 0.612649 Iteration 2 Error: 0.081567 Iteration 3 Error: 0.015825 3D Fitting completed. Patch alignment time: 17.43(sec) Local motion has been corrected. Process thread exits. Computational time: 26.235525 sec Total time: 32.423279 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00005hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00005hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.649736s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00005hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.693228s ........................................ >>>>>>TIME<<<<<< FFT: 0.929603s Defocus_U Defocus_V Angle CCC 10708.97 11498.12 7.30 0.043393 Final Values Defocus_U Defocus_V Angle CCC 10716.79 11512.19 7.30 0.081986 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00005hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00005hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.997e-02 CC threshold: 0.734 Mean Std: 46.33 7.70 Num Hot pixels: 196 Hot pixel threshold: 92.56 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.871349 Iteration 2 Error: 0.101439 Iteration 3 Error: 0.027953 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.40 -0.07 ...... Frame ( 3) shift: -0.79 -0.15 ...... Frame ( 4) shift: -1.19 -0.22 ...... Frame ( 5) shift: -1.59 -0.30 ...... Frame ( 6) shift: -1.77 -0.31 ...... Frame ( 7) shift: -1.73 -0.27 ...... Frame ( 8) shift: -1.70 -0.22 ...... Frame ( 9) shift: -1.65 -0.16 ...... Frame ( 10) shift: -1.61 -0.08 ...... Frame ( 11) shift: -1.56 0.00 ...... Frame ( 12) shift: -1.49 0.04 ...... Frame ( 13) shift: -1.39 0.03 ...... Frame ( 14) shift: -1.30 0.02 ...... Frame ( 15) shift: -1.26 0.07 ...... Frame ( 16) shift: -1.27 0.17 ...... Frame ( 17) shift: -1.28 0.27 ...... Frame ( 18) shift: -1.29 0.37 ...... Frame ( 19) shift: -1.29 0.46 ...... Frame ( 20) shift: -1.29 0.55 ...... Frame ( 21) shift: -1.29 0.62 ...... Frame ( 22) shift: -1.29 0.66 ...... Frame ( 23) shift: -1.29 0.70 ...... Frame ( 24) shift: -1.29 0.72 ...... Frame ( 25) shift: -1.28 0.73 ...... Frame ( 26) shift: -1.27 0.73 ...... Frame ( 27) shift: -1.25 0.76 ...... Frame ( 28) shift: -1.23 0.82 ...... Frame ( 29) shift: -1.20 0.89 ...... Frame ( 30) shift: -1.22 0.90 ...... Frame ( 31) shift: -1.26 0.84 ...... Frame ( 32) shift: -1.31 0.79 ...... Frame ( 33) shift: -1.33 0.78 ...... Frame ( 34) shift: -1.34 0.81 ...... Frame ( 35) shift: -1.34 0.84 ...... Frame ( 36) shift: -1.32 0.87 ...... Frame ( 37) shift: -1.30 0.88 ...... Frame ( 38) shift: -1.27 0.89 ...... Frame ( 39) shift: -1.24 0.91 ...... Frame ( 40) shift: -1.21 0.92 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.995822 Iteration 2 Error: 0.224930 Iteration 3 Error: 0.083323 Iteration 4 Error: 0.025181 Align patch 2 23 left Iteration 1 Error: 1.059393 Iteration 2 Error: 0.172299 Iteration 3 Error: 0.070321 Iteration 4 Error: 0.025549 Align patch 3 22 left Iteration 1 Error: 0.666452 Iteration 2 Error: 0.137041 Iteration 3 Error: 0.029972 Align patch 4 21 left Iteration 1 Error: 1.380592 Iteration 2 Error: 0.130493 Iteration 3 Error: 0.027188 Align patch 5 20 left Iteration 1 Error: 1.162419 Iteration 2 Error: 0.099496 Iteration 3 Error: 0.036148 Align patch 6 19 left Iteration 1 Error: 1.095669 Iteration 2 Error: 0.180937 Iteration 3 Error: 0.047070 Align patch 7 18 left Iteration 1 Error: 0.836469 Iteration 2 Error: 0.160524 Iteration 3 Error: 0.054753 Iteration 4 Error: 0.020595 Align patch 8 17 left Iteration 1 Error: 0.649560 Iteration 2 Error: 0.136026 Iteration 3 Error: 0.025528 Align patch 9 16 left Iteration 1 Error: 0.674758 Iteration 2 Error: 0.146328 Iteration 3 Error: 0.028767 Align patch 10 15 left Iteration 1 Error: 0.776905 Iteration 2 Error: 0.122490 Iteration 3 Error: 0.050116 Iteration 4 Error: 0.012667 Align patch 11 14 left Iteration 1 Error: 1.142516 Iteration 2 Error: 0.132319 Iteration 3 Error: 0.052706 Iteration 4 Error: 0.022044 Align patch 12 13 left Iteration 1 Error: 1.102588 Iteration 2 Error: 0.186932 Iteration 3 Error: 0.033899 Align patch 13 12 left Iteration 1 Error: 0.556063 Iteration 2 Error: 0.125052 Iteration 3 Error: 0.039407 Align patch 14 11 left Iteration 1 Error: 0.957131 Iteration 2 Error: 0.192737 Iteration 3 Error: 0.066876 Iteration 4 Error: 0.022154 Align patch 15 10 left Iteration 1 Error: 0.636841 Iteration 2 Error: 0.072873 Iteration 3 Error: 0.014907 Align patch 16 9 left Iteration 1 Error: 1.265806 Iteration 2 Error: 0.213161 Iteration 3 Error: 0.032600 Align patch 17 8 left Iteration 1 Error: 1.356352 Iteration 2 Error: 0.100144 Iteration 3 Error: 0.023057 Align patch 18 7 left Iteration 1 Error: 1.202030 Iteration 2 Error: 0.195610 Iteration 3 Error: 0.051264 Iteration 4 Error: 0.016674 Align patch 19 6 left Iteration 1 Error: 0.897955 Iteration 2 Error: 0.241260 Iteration 3 Error: 0.051828 Iteration 4 Error: 0.010254 Align patch 20 5 left Iteration 1 Error: 0.591219 Iteration 2 Error: 0.147055 Iteration 3 Error: 0.041400 Align patch 21 4 left Iteration 1 Error: 1.243614 Iteration 2 Error: 0.203343 Iteration 3 Error: 0.034926 Align patch 22 3 left Iteration 1 Error: 0.801468 Iteration 2 Error: 0.111099 Iteration 3 Error: 0.037871 Align patch 23 2 left Iteration 1 Error: 1.142876 Iteration 2 Error: 0.231716 Iteration 3 Error: 0.048415 Align patch 24 1 left Iteration 1 Error: 1.132310 Iteration 2 Error: 0.213006 Iteration 3 Error: 0.035326 Align patch 25 0 left Iteration 1 Error: 0.746381 Iteration 2 Error: 0.100360 Iteration 3 Error: 0.026802 3D Fitting completed. Patch alignment time: 15.23(sec) Local motion has been corrected. Process thread exits. Computational time: 23.207500 sec Total time: 29.127449 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00005hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00005hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.541652s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00005hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.450175s ........................................ >>>>>>TIME<<<<<< FFT: 0.970667s Defocus_U Defocus_V Angle CCC 12368.90 11728.91 82.66 0.045836 Final Values Defocus_U Defocus_V Angle CCC 12400.16 11775.80 83.61 0.081866 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00006hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00006hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.998e-02 CC threshold: 0.734 Mean Std: 45.43 7.70 Num Hot pixels: 182 Hot pixel threshold: 91.64 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.052917 Iteration 2 Error: 0.156718 Iteration 3 Error: 0.040712 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.33 -0.06 ...... Frame ( 3) shift: -0.66 -0.13 ...... Frame ( 4) shift: -1.00 -0.19 ...... Frame ( 5) shift: -1.33 -0.26 ...... Frame ( 6) shift: -1.47 -0.24 ...... Frame ( 7) shift: -1.43 -0.14 ...... Frame ( 8) shift: -1.39 -0.04 ...... Frame ( 9) shift: -1.37 0.02 ...... Frame ( 10) shift: -1.38 0.04 ...... Frame ( 11) shift: -1.39 0.05 ...... Frame ( 12) shift: -1.34 0.14 ...... Frame ( 13) shift: -1.25 0.31 ...... Frame ( 14) shift: -1.16 0.49 ...... Frame ( 15) shift: -1.11 0.62 ...... Frame ( 16) shift: -1.12 0.71 ...... Frame ( 17) shift: -1.12 0.80 ...... Frame ( 18) shift: -1.12 0.89 ...... Frame ( 19) shift: -1.12 0.95 ...... Frame ( 20) shift: -1.11 1.02 ...... Frame ( 21) shift: -1.08 1.08 ...... Frame ( 22) shift: -1.04 1.11 ...... Frame ( 23) shift: -0.99 1.15 ...... Frame ( 24) shift: -0.97 1.20 ...... Frame ( 25) shift: -0.99 1.25 ...... Frame ( 26) shift: -1.00 1.31 ...... Frame ( 27) shift: -1.00 1.36 ...... Frame ( 28) shift: -0.98 1.40 ...... Frame ( 29) shift: -0.97 1.45 ...... Frame ( 30) shift: -0.95 1.45 ...... Frame ( 31) shift: -0.92 1.40 ...... Frame ( 32) shift: -0.90 1.36 ...... Frame ( 33) shift: -0.90 1.37 ...... Frame ( 34) shift: -0.92 1.43 ...... Frame ( 35) shift: -0.94 1.50 ...... Frame ( 36) shift: -0.93 1.53 ...... Frame ( 37) shift: -0.88 1.53 ...... Frame ( 38) shift: -0.84 1.53 ...... Frame ( 39) shift: -0.79 1.53 ...... Frame ( 40) shift: -0.75 1.53 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.708789 Iteration 2 Error: 0.181876 Iteration 3 Error: 0.064771 Iteration 4 Error: 0.032897 Align patch 2 23 left Iteration 1 Error: 1.761754 Iteration 2 Error: 0.333158 Iteration 3 Error: 0.048817 Align patch 3 22 left Iteration 1 Error: 0.874525 Iteration 2 Error: 0.132464 Iteration 3 Error: 0.048119 Align patch 4 21 left Iteration 1 Error: 0.737860 Iteration 2 Error: 0.147517 Iteration 3 Error: 0.040784 Align patch 5 20 left Iteration 1 Error: 0.909314 Iteration 2 Error: 0.140339 Iteration 3 Error: 0.048816 Align patch 6 19 left Iteration 1 Error: 0.687895 Iteration 2 Error: 0.168115 Iteration 3 Error: 0.044288 Align patch 7 18 left Iteration 1 Error: 0.634898 Iteration 2 Error: 0.194745 Iteration 3 Error: 0.032928 Align patch 8 17 left Iteration 1 Error: 0.662275 Iteration 2 Error: 0.092152 Iteration 3 Error: 0.027086 Align patch 9 16 left Iteration 1 Error: 0.870484 Iteration 2 Error: 0.116209 Iteration 3 Error: 0.037695 Align patch 10 15 left Iteration 1 Error: 0.905379 Iteration 2 Error: 0.173473 Iteration 3 Error: 0.062509 Iteration 4 Error: 0.020081 Align patch 11 14 left Iteration 1 Error: 0.805437 Iteration 2 Error: 0.152745 Iteration 3 Error: 0.037193 Align patch 12 13 left Iteration 1 Error: 1.169723 Iteration 2 Error: 0.158816 Iteration 3 Error: 0.035703 Align patch 13 12 left Iteration 1 Error: 0.549673 Iteration 2 Error: 0.113152 Iteration 3 Error: 0.039615 Align patch 14 11 left Iteration 1 Error: 1.128163 Iteration 2 Error: 0.100891 Iteration 3 Error: 0.029831 Align patch 15 10 left Iteration 1 Error: 0.966549 Iteration 2 Error: 0.120210 Iteration 3 Error: 0.036350 Align patch 16 9 left Iteration 1 Error: 0.798958 Iteration 2 Error: 0.140579 Iteration 3 Error: 0.030127 Align patch 17 8 left Iteration 1 Error: 0.677577 Iteration 2 Error: 0.180536 Iteration 3 Error: 0.051897 Iteration 4 Error: 0.021365 Align patch 18 7 left Iteration 1 Error: 0.820290 Iteration 2 Error: 0.110166 Iteration 3 Error: 0.032563 Align patch 19 6 left Iteration 1 Error: 0.852875 Iteration 2 Error: 0.145054 Iteration 3 Error: 0.045773 Align patch 20 5 left Iteration 1 Error: 0.921475 Iteration 2 Error: 0.111511 Iteration 3 Error: 0.023787 Align patch 21 4 left Iteration 1 Error: 1.360918 Iteration 2 Error: 0.147076 Iteration 3 Error: 0.027331 Align patch 22 3 left Iteration 1 Error: 0.896168 Iteration 2 Error: 0.197588 Iteration 3 Error: 0.059479 Iteration 4 Error: 0.020427 Align patch 23 2 left Iteration 1 Error: 0.618958 Iteration 2 Error: 0.107341 Iteration 3 Error: 0.051048 Iteration 4 Error: 0.012327 Align patch 24 1 left Iteration 1 Error: 0.718217 Iteration 2 Error: 0.097503 Iteration 3 Error: 0.022153 Align patch 25 0 left Iteration 1 Error: 0.809562 Iteration 2 Error: 0.094270 Iteration 3 Error: 0.022282 3D Fitting completed. Patch alignment time: 14.79(sec) Local motion has been corrected. Process thread exits. Computational time: 23.206438 sec Total time: 28.795359 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00006hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00006hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.708685s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00006hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.567166s ........................................ >>>>>>TIME<<<<<< FFT: 0.878816s Defocus_U Defocus_V Angle CCC 9855.47 10660.16 12.27 0.042742 Final Values Defocus_U Defocus_V Angle CCC 9850.78 10667.98 11.95 0.080909 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00006hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00006hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 45.56 7.73 Num Hot pixels: 180 Hot pixel threshold: 91.94 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.885397 Iteration 2 Error: 0.138797 Iteration 3 Error: 0.043552 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.36 -0.03 ...... Frame ( 3) shift: -0.72 -0.05 ...... Frame ( 4) shift: -1.07 -0.08 ...... Frame ( 5) shift: -1.43 -0.10 ...... Frame ( 6) shift: -1.61 -0.08 ...... Frame ( 7) shift: -1.60 -0.02 ...... Frame ( 8) shift: -1.60 0.04 ...... Frame ( 9) shift: -1.56 0.10 ...... Frame ( 10) shift: -1.51 0.15 ...... Frame ( 11) shift: -1.45 0.20 ...... Frame ( 12) shift: -1.40 0.27 ...... Frame ( 13) shift: -1.35 0.37 ...... Frame ( 14) shift: -1.31 0.46 ...... Frame ( 15) shift: -1.28 0.53 ...... Frame ( 16) shift: -1.28 0.56 ...... Frame ( 17) shift: -1.27 0.60 ...... Frame ( 18) shift: -1.27 0.65 ...... Frame ( 19) shift: -1.26 0.73 ...... Frame ( 20) shift: -1.26 0.81 ...... Frame ( 21) shift: -1.24 0.90 ...... Frame ( 22) shift: -1.20 1.01 ...... Frame ( 23) shift: -1.15 1.12 ...... Frame ( 24) shift: -1.11 1.16 ...... Frame ( 25) shift: -1.07 1.11 ...... Frame ( 26) shift: -1.04 1.06 ...... Frame ( 27) shift: -1.00 1.07 ...... Frame ( 28) shift: -0.98 1.14 ...... Frame ( 29) shift: -0.96 1.20 ...... Frame ( 30) shift: -0.93 1.23 ...... Frame ( 31) shift: -0.91 1.23 ...... Frame ( 32) shift: -0.89 1.22 ...... Frame ( 33) shift: -0.88 1.26 ...... Frame ( 34) shift: -0.89 1.33 ...... Frame ( 35) shift: -0.90 1.40 ...... Frame ( 36) shift: -0.91 1.46 ...... Frame ( 37) shift: -0.91 1.50 ...... Frame ( 38) shift: -0.91 1.54 ...... Frame ( 39) shift: -0.91 1.58 ...... Frame ( 40) shift: -0.92 1.62 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.898564 Iteration 2 Error: 0.123108 Iteration 3 Error: 0.046479 Align patch 2 23 left Iteration 1 Error: 2.114412 Iteration 2 Error: 0.311265 Iteration 3 Error: 0.114461 Iteration 4 Error: 0.060765 Iteration 5 Error: 0.032463 Align patch 3 22 left Iteration 1 Error: 1.517063 Iteration 2 Error: 0.214481 Iteration 3 Error: 0.069420 Iteration 4 Error: 0.019967 Align patch 4 21 left Iteration 1 Error: 0.592865 Iteration 2 Error: 0.134088 Iteration 3 Error: 0.043074 Align patch 5 20 left Iteration 1 Error: 0.794640 Iteration 2 Error: 0.129253 Iteration 3 Error: 0.034108 Align patch 6 19 left Iteration 1 Error: 1.144475 Iteration 2 Error: 0.192856 Iteration 3 Error: 0.044385 Align patch 7 18 left Iteration 1 Error: 1.545653 Iteration 2 Error: 0.222840 Iteration 3 Error: 0.026047 Align patch 8 17 left Iteration 1 Error: 0.933709 Iteration 2 Error: 0.155502 Iteration 3 Error: 0.075756 Iteration 4 Error: 0.023431 Align patch 9 16 left Iteration 1 Error: 1.310026 Iteration 2 Error: 0.388238 Iteration 3 Error: 0.147758 Iteration 4 Error: 0.102010 Iteration 5 Error: 0.058789 Align patch 9 16 left Iteration 1 Error: 1.162118 Iteration 2 Error: 0.112418 Iteration 3 Error: 0.019540 Align patch 10 15 left Iteration 1 Error: 0.986271 Iteration 2 Error: 0.128657 Iteration 3 Error: 0.036567 Align patch 11 14 left Iteration 1 Error: 1.413957 Iteration 2 Error: 0.130932 Iteration 3 Error: 0.030065 Align patch 12 13 left Iteration 1 Error: 1.000107 Iteration 2 Error: 0.172653 Iteration 3 Error: 0.043644 Align patch 13 12 left Iteration 1 Error: 0.556747 Iteration 2 Error: 0.113374 Iteration 3 Error: 0.037903 Align patch 14 11 left Iteration 1 Error: 0.919060 Iteration 2 Error: 0.141790 Iteration 3 Error: 0.026221 Align patch 15 10 left Iteration 1 Error: 0.745354 Iteration 2 Error: 0.072077 Iteration 3 Error: 0.013979 Align patch 16 9 left Iteration 1 Error: 0.881882 Iteration 2 Error: 0.205758 Iteration 3 Error: 0.046738 Align patch 17 8 left Iteration 1 Error: 0.743969 Iteration 2 Error: 0.127458 Iteration 3 Error: 0.029973 Align patch 18 7 left Iteration 1 Error: 1.183211 Iteration 2 Error: 0.115630 Iteration 3 Error: 0.025195 Align patch 19 6 left Iteration 1 Error: 0.825495 Iteration 2 Error: 0.161680 Iteration 3 Error: 0.050446 Iteration 4 Error: 0.011491 Align patch 20 5 left Iteration 1 Error: 0.796413 Iteration 2 Error: 0.183403 Iteration 3 Error: 0.055497 Iteration 4 Error: 0.031342 Align patch 21 4 left Iteration 1 Error: 1.374541 Iteration 2 Error: 0.164390 Iteration 3 Error: 0.029776 Align patch 22 3 left Iteration 1 Error: 1.492102 Iteration 2 Error: 0.172972 Iteration 3 Error: 0.032551 Align patch 23 2 left Iteration 1 Error: 1.750345 Iteration 2 Error: 0.118432 Iteration 3 Error: 0.036728 Align patch 24 1 left Iteration 1 Error: 1.147767 Iteration 2 Error: 0.096353 Iteration 3 Error: 0.024935 Align patch 25 0 left Iteration 1 Error: 0.601270 Iteration 2 Error: 0.117297 Iteration 3 Error: 0.030024 3D Fitting completed. Patch alignment time: 17.01(sec) Local motion has been corrected. Process thread exits. Computational time: 25.887730 sec Total time: 32.176483 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00006hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00006hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.668070s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00006hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.442413s ........................................ >>>>>>TIME<<<<<< FFT: 1.058364s Defocus_U Defocus_V Angle CCC 9880.87 9408.20 88.29 0.038709 Final Values Defocus_U Defocus_V Angle CCC 9887.12 9414.46 89.24 0.077031 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00006hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00006hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 1.000e-01 CC threshold: 0.735 Mean Std: 46.45 7.69 Num Hot pixels: 186 Hot pixel threshold: 92.60 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.945075 Iteration 2 Error: 0.139585 Iteration 3 Error: 0.027211 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.39 -0.06 ...... Frame ( 3) shift: -0.79 -0.12 ...... Frame ( 4) shift: -1.18 -0.19 ...... Frame ( 5) shift: -1.57 -0.25 ...... Frame ( 6) shift: -1.79 -0.25 ...... Frame ( 7) shift: -1.82 -0.20 ...... Frame ( 8) shift: -1.85 -0.14 ...... Frame ( 9) shift: -1.85 -0.10 ...... Frame ( 10) shift: -1.81 -0.07 ...... Frame ( 11) shift: -1.78 -0.04 ...... Frame ( 12) shift: -1.77 -0.04 ...... Frame ( 13) shift: -1.77 -0.05 ...... Frame ( 14) shift: -1.78 -0.07 ...... Frame ( 15) shift: -1.78 -0.06 ...... Frame ( 16) shift: -1.79 -0.01 ...... Frame ( 17) shift: -1.80 0.04 ...... Frame ( 18) shift: -1.80 0.04 ...... Frame ( 19) shift: -1.78 -0.01 ...... Frame ( 20) shift: -1.77 -0.06 ...... Frame ( 21) shift: -1.76 -0.06 ...... Frame ( 22) shift: -1.78 -0.02 ...... Frame ( 23) shift: -1.79 0.02 ...... Frame ( 24) shift: -1.76 0.03 ...... Frame ( 25) shift: -1.69 0.01 ...... Frame ( 26) shift: -1.61 -0.00 ...... Frame ( 27) shift: -1.54 0.07 ...... Frame ( 28) shift: -1.48 0.22 ...... Frame ( 29) shift: -1.42 0.38 ...... Frame ( 30) shift: -1.33 0.46 ...... Frame ( 31) shift: -1.22 0.46 ...... Frame ( 32) shift: -1.11 0.46 ...... Frame ( 33) shift: -1.04 0.50 ...... Frame ( 34) shift: -1.02 0.57 ...... Frame ( 35) shift: -1.00 0.65 ...... Frame ( 36) shift: -0.97 0.68 ...... Frame ( 37) shift: -0.93 0.67 ...... Frame ( 38) shift: -0.89 0.65 ...... Frame ( 39) shift: -0.86 0.64 ...... Frame ( 40) shift: -0.82 0.63 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.272432 Iteration 2 Error: 0.207340 Iteration 3 Error: 0.056275 Iteration 4 Error: 0.023498 Align patch 2 23 left Iteration 1 Error: 1.524376 Iteration 2 Error: 0.194329 Iteration 3 Error: 0.086262 Iteration 4 Error: 0.026708 Align patch 3 22 left Iteration 1 Error: 0.889872 Iteration 2 Error: 0.178820 Iteration 3 Error: 0.048963 Align patch 4 21 left Iteration 1 Error: 0.771964 Iteration 2 Error: 0.153721 Iteration 3 Error: 0.030760 Align patch 5 20 left Iteration 1 Error: 1.320734 Iteration 2 Error: 0.138957 Iteration 3 Error: 0.026395 Align patch 6 19 left Iteration 1 Error: 1.000599 Iteration 2 Error: 0.168220 Iteration 3 Error: 0.030223 Align patch 7 18 left Iteration 1 Error: 1.210128 Iteration 2 Error: 0.147328 Iteration 3 Error: 0.041214 Align patch 8 17 left Iteration 1 Error: 0.876479 Iteration 2 Error: 0.105533 Iteration 3 Error: 0.029153 Align patch 9 16 left Iteration 1 Error: 0.804463 Iteration 2 Error: 0.115230 Iteration 3 Error: 0.030719 Align patch 10 15 left Iteration 1 Error: 0.535280 Iteration 2 Error: 0.112975 Iteration 3 Error: 0.022232 Align patch 11 14 left Iteration 1 Error: 0.782240 Iteration 2 Error: 0.143009 Iteration 3 Error: 0.055859 Iteration 4 Error: 0.018457 Align patch 12 13 left Iteration 1 Error: 0.823530 Iteration 2 Error: 0.198293 Iteration 3 Error: 0.079494 Iteration 4 Error: 0.042072 Align patch 13 12 left Iteration 1 Error: 0.703892 Iteration 2 Error: 0.115753 Iteration 3 Error: 0.033807 Align patch 14 11 left Iteration 1 Error: 0.877498 Iteration 2 Error: 0.086220 Iteration 3 Error: 0.020380 Align patch 15 10 left Iteration 1 Error: 0.738004 Iteration 2 Error: 0.094838 Iteration 3 Error: 0.016672 Align patch 16 9 left Iteration 1 Error: 0.939763 Iteration 2 Error: 0.174680 Iteration 3 Error: 0.050151 Iteration 4 Error: 0.020602 Align patch 17 8 left Iteration 1 Error: 0.721829 Iteration 2 Error: 0.207465 Iteration 3 Error: 0.054393 Iteration 4 Error: 0.032146 Align patch 18 7 left Iteration 1 Error: 1.089979 Iteration 2 Error: 0.233848 Iteration 3 Error: 0.056759 Iteration 4 Error: 0.013554 Align patch 19 6 left Iteration 1 Error: 0.788391 Iteration 2 Error: 0.114600 Iteration 3 Error: 0.022717 Align patch 20 5 left Iteration 1 Error: 0.538453 Iteration 2 Error: 0.040837 Align patch 21 4 left Iteration 1 Error: 1.260477 Iteration 2 Error: 0.173018 Iteration 3 Error: 0.042349 Align patch 22 3 left Iteration 1 Error: 1.599827 Iteration 2 Error: 0.127935 Iteration 3 Error: 0.042360 Align patch 23 2 left Iteration 1 Error: 1.051946 Iteration 2 Error: 0.123651 Iteration 3 Error: 0.042525 Align patch 24 1 left Iteration 1 Error: 0.885038 Iteration 2 Error: 0.172289 Iteration 3 Error: 0.036056 Align patch 25 0 left Iteration 1 Error: 0.705292 Iteration 2 Error: 0.128865 Iteration 3 Error: 0.030189 3D Fitting completed. Patch alignment time: 16.03(sec) Local motion has been corrected. Process thread exits. Computational time: 24.751129 sec Total time: 30.686794 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00006hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00006hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.669883s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00006hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.420986s ........................................ >>>>>>TIME<<<<<< FFT: 0.943503s Defocus_U Defocus_V Angle CCC 9835.92 10609.48 3.11 0.041943 Final Values Defocus_U Defocus_V Angle CCC 9829.67 10650.12 2.80 0.083183 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00006hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00006hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 46.22 7.72 Num Hot pixels: 190 Hot pixel threshold: 92.53 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.403730 Iteration 2 Error: 0.118760 Iteration 3 Error: 0.027247 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.41 0.05 ...... Frame ( 3) shift: -0.81 0.10 ...... Frame ( 4) shift: -1.22 0.16 ...... Frame ( 5) shift: -1.62 0.21 ...... Frame ( 6) shift: -1.81 0.30 ...... Frame ( 7) shift: -1.79 0.44 ...... Frame ( 8) shift: -1.76 0.58 ...... Frame ( 9) shift: -1.75 0.65 ...... Frame ( 10) shift: -1.76 0.67 ...... Frame ( 11) shift: -1.76 0.68 ...... Frame ( 12) shift: -1.79 0.70 ...... Frame ( 13) shift: -1.84 0.73 ...... Frame ( 14) shift: -1.89 0.76 ...... Frame ( 15) shift: -1.90 0.80 ...... Frame ( 16) shift: -1.87 0.83 ...... Frame ( 17) shift: -1.83 0.87 ...... Frame ( 18) shift: -1.81 0.92 ...... Frame ( 19) shift: -1.80 1.00 ...... Frame ( 20) shift: -1.79 1.07 ...... Frame ( 21) shift: -1.76 1.14 ...... Frame ( 22) shift: -1.71 1.19 ...... Frame ( 23) shift: -1.67 1.25 ...... Frame ( 24) shift: -1.65 1.28 ...... Frame ( 25) shift: -1.67 1.28 ...... Frame ( 26) shift: -1.69 1.28 ...... Frame ( 27) shift: -1.69 1.30 ...... Frame ( 28) shift: -1.67 1.34 ...... Frame ( 29) shift: -1.66 1.37 ...... Frame ( 30) shift: -1.66 1.42 ...... Frame ( 31) shift: -1.69 1.47 ...... Frame ( 32) shift: -1.72 1.52 ...... Frame ( 33) shift: -1.71 1.51 ...... Frame ( 34) shift: -1.67 1.42 ...... Frame ( 35) shift: -1.63 1.33 ...... Frame ( 36) shift: -1.60 1.31 ...... Frame ( 37) shift: -1.58 1.35 ...... Frame ( 38) shift: -1.56 1.39 ...... Frame ( 39) shift: -1.55 1.43 ...... Frame ( 40) shift: -1.53 1.46 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.635293 Iteration 2 Error: 0.173180 Iteration 3 Error: 0.092363 Iteration 4 Error: 0.024919 Align patch 2 23 left Iteration 1 Error: 0.951050 Iteration 2 Error: 0.172906 Iteration 3 Error: 0.032926 Align patch 3 22 left Iteration 1 Error: 0.724312 Iteration 2 Error: 0.288497 Iteration 3 Error: 0.071412 Iteration 4 Error: 0.050506 Iteration 5 Error: 0.012850 Align patch 4 21 left Iteration 1 Error: 0.664424 Iteration 2 Error: 0.140310 Iteration 3 Error: 0.024951 Align patch 5 20 left Iteration 1 Error: 0.561429 Iteration 2 Error: 0.093706 Iteration 3 Error: 0.022793 Align patch 6 19 left Iteration 1 Error: 1.348449 Iteration 2 Error: 0.203483 Iteration 3 Error: 0.054495 Iteration 4 Error: 0.015718 Align patch 7 18 left Iteration 1 Error: 1.389606 Iteration 2 Error: 0.226849 Iteration 3 Error: 0.085215 Iteration 4 Error: 0.038205 Align patch 8 17 left Iteration 1 Error: 0.911887 Iteration 2 Error: 0.188936 Iteration 3 Error: 0.032706 Align patch 9 16 left Iteration 1 Error: 0.590509 Iteration 2 Error: 0.117587 Iteration 3 Error: 0.037504 Align patch 10 15 left Iteration 1 Error: 0.821647 Iteration 2 Error: 0.136232 Iteration 3 Error: 0.036085 Align patch 11 14 left Iteration 1 Error: 1.009712 Iteration 2 Error: 0.286216 Iteration 3 Error: 0.071181 Iteration 4 Error: 0.016684 Align patch 12 13 left Iteration 1 Error: 0.639323 Iteration 2 Error: 0.088754 Iteration 3 Error: 0.043391 Align patch 13 12 left Iteration 1 Error: 1.181533 Iteration 2 Error: 0.228836 Iteration 3 Error: 0.057714 Iteration 4 Error: 0.029954 Align patch 14 11 left Iteration 1 Error: 0.937117 Iteration 2 Error: 0.167937 Iteration 3 Error: 0.035580 Align patch 15 10 left Iteration 1 Error: 0.706640 Iteration 2 Error: 0.118855 Iteration 3 Error: 0.022882 Align patch 16 9 left Iteration 1 Error: 0.589981 Iteration 2 Error: 0.101465 Iteration 3 Error: 0.024860 Align patch 17 8 left Iteration 1 Error: 0.850820 Iteration 2 Error: 0.113091 Iteration 3 Error: 0.040334 Align patch 18 7 left Iteration 1 Error: 0.728401 Iteration 2 Error: 0.136001 Iteration 3 Error: 0.034602 Align patch 19 6 left Iteration 1 Error: 0.591659 Iteration 2 Error: 0.094037 Iteration 3 Error: 0.028987 Align patch 20 5 left Iteration 1 Error: 0.644943 Iteration 2 Error: 0.098985 Iteration 3 Error: 0.026323 Align patch 21 4 left Iteration 1 Error: 2.809694 Iteration 2 Error: 0.340541 Iteration 3 Error: 0.199236 Iteration 4 Error: 0.074639 Iteration 5 Error: 0.016722 Align patch 22 3 left Iteration 1 Error: 1.274206 Iteration 2 Error: 0.169133 Iteration 3 Error: 0.040030 Align patch 23 2 left Iteration 1 Error: 1.804119 Iteration 2 Error: 0.207208 Iteration 3 Error: 0.047087 Align patch 24 1 left Iteration 1 Error: 0.607433 Iteration 2 Error: 0.075320 Iteration 3 Error: 0.032406 Align patch 25 0 left Iteration 1 Error: 0.746962 Iteration 2 Error: 0.107157 Iteration 3 Error: 0.035462 3D Fitting completed. Patch alignment time: 16.24(sec) Local motion has been corrected. Process thread exits. Computational time: 24.992466 sec Total time: 30.892101 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00006hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00006hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.559153s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00006hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.451931s ........................................ >>>>>>TIME<<<<<< FFT: 0.938897s Defocus_U Defocus_V Angle CCC 10820.32 10226.56 83.84 0.043756 Final Values Defocus_U Defocus_V Angle CCC 10843.75 10228.14 83.84 0.083711 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00007hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00007hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.999e-02 CC threshold: 0.734 Mean Std: 42.83 7.34 Num Hot pixels: 190 Hot pixel threshold: 86.88 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.867960 Iteration 2 Error: 0.139340 Iteration 3 Error: 0.028641 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.35 0.03 ...... Frame ( 3) shift: -0.70 0.05 ...... Frame ( 4) shift: -1.06 0.08 ...... Frame ( 5) shift: -1.41 0.11 ...... Frame ( 6) shift: -1.60 0.15 ...... Frame ( 7) shift: -1.64 0.22 ...... Frame ( 8) shift: -1.68 0.28 ...... Frame ( 9) shift: -1.67 0.31 ...... Frame ( 10) shift: -1.62 0.32 ...... Frame ( 11) shift: -1.57 0.32 ...... Frame ( 12) shift: -1.53 0.34 ...... Frame ( 13) shift: -1.50 0.36 ...... Frame ( 14) shift: -1.47 0.38 ...... Frame ( 15) shift: -1.42 0.44 ...... Frame ( 16) shift: -1.34 0.54 ...... Frame ( 17) shift: -1.26 0.65 ...... Frame ( 18) shift: -1.22 0.71 ...... Frame ( 19) shift: -1.23 0.75 ...... Frame ( 20) shift: -1.24 0.78 ...... Frame ( 21) shift: -1.21 0.83 ...... Frame ( 22) shift: -1.12 0.90 ...... Frame ( 23) shift: -1.03 0.96 ...... Frame ( 24) shift: -0.95 1.00 ...... Frame ( 25) shift: -0.88 1.03 ...... Frame ( 26) shift: -0.81 1.06 ...... Frame ( 27) shift: -0.78 1.09 ...... Frame ( 28) shift: -0.80 1.12 ...... Frame ( 29) shift: -0.83 1.16 ...... Frame ( 30) shift: -0.85 1.17 ...... Frame ( 31) shift: -0.86 1.15 ...... Frame ( 32) shift: -0.87 1.14 ...... Frame ( 33) shift: -0.85 1.13 ...... Frame ( 34) shift: -0.80 1.12 ...... Frame ( 35) shift: -0.74 1.11 ...... Frame ( 36) shift: -0.71 1.14 ...... Frame ( 37) shift: -0.69 1.21 ...... Frame ( 38) shift: -0.68 1.28 ...... Frame ( 39) shift: -0.66 1.35 ...... Frame ( 40) shift: -0.65 1.41 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.428132 Iteration 2 Error: 0.142203 Iteration 3 Error: 0.026438 Align patch 2 23 left Iteration 1 Error: 1.018858 Iteration 2 Error: 0.191112 Iteration 3 Error: 0.034487 Align patch 3 22 left Iteration 1 Error: 1.303885 Iteration 2 Error: 0.211657 Iteration 3 Error: 0.087715 Iteration 4 Error: 0.026567 Align patch 4 21 left Iteration 1 Error: 0.506413 Iteration 2 Error: 0.069574 Iteration 3 Error: 0.015327 Align patch 5 20 left Iteration 1 Error: 0.724230 Iteration 2 Error: 0.110147 Iteration 3 Error: 0.026471 Align patch 6 19 left Iteration 1 Error: 1.087722 Iteration 2 Error: 0.121582 Iteration 3 Error: 0.024285 Align patch 7 18 left Iteration 1 Error: 0.793400 Iteration 2 Error: 0.169728 Iteration 3 Error: 0.051058 Iteration 4 Error: 0.014312 Align patch 8 17 left Iteration 1 Error: 1.148162 Iteration 2 Error: 0.240849 Iteration 3 Error: 0.070666 Iteration 4 Error: 0.030198 Align patch 9 16 left Iteration 1 Error: 0.739941 Iteration 2 Error: 0.061486 Iteration 3 Error: 0.020313 Align patch 10 15 left Iteration 1 Error: 0.582614 Iteration 2 Error: 0.054499 Iteration 3 Error: 0.009618 Align patch 11 14 left Iteration 1 Error: 0.898568 Iteration 2 Error: 0.277064 Iteration 3 Error: 0.069003 Iteration 4 Error: 0.027701 Align patch 12 13 left Iteration 1 Error: 0.716231 Iteration 2 Error: 0.186689 Iteration 3 Error: 0.052216 Iteration 4 Error: 0.024333 Align patch 13 12 left Iteration 1 Error: 0.895899 Iteration 2 Error: 0.205930 Iteration 3 Error: 0.060063 Iteration 4 Error: 0.021222 Align patch 14 11 left Iteration 1 Error: 0.468508 Iteration 2 Error: 0.067409 Iteration 3 Error: 0.010632 Align patch 15 10 left Iteration 1 Error: 0.875926 Iteration 2 Error: 0.189438 Iteration 3 Error: 0.069670 Iteration 4 Error: 0.025492 Align patch 16 9 left Iteration 1 Error: 0.890359 Iteration 2 Error: 0.252511 Iteration 3 Error: 0.097669 Iteration 4 Error: 0.041384 Align patch 17 8 left Iteration 1 Error: 0.808176 Iteration 2 Error: 0.148153 Iteration 3 Error: 0.051553 Iteration 4 Error: 0.020783 Align patch 18 7 left Iteration 1 Error: 1.146928 Iteration 2 Error: 0.248760 Iteration 3 Error: 0.045257 Align patch 19 6 left Iteration 1 Error: 0.801340 Iteration 2 Error: 0.142238 Iteration 3 Error: 0.035555 Align patch 20 5 left Iteration 1 Error: 0.947794 Iteration 2 Error: 0.227448 Iteration 3 Error: 0.059563 Iteration 4 Error: 0.019450 Align patch 21 4 left Iteration 1 Error: 1.257996 Iteration 2 Error: 0.198817 Iteration 3 Error: 0.046775 Align patch 22 3 left Iteration 1 Error: 1.123047 Iteration 2 Error: 0.208537 Iteration 3 Error: 0.047366 Align patch 23 2 left Iteration 1 Error: 0.806937 Iteration 2 Error: 0.281091 Iteration 3 Error: 0.040154 Align patch 24 1 left Iteration 1 Error: 0.985626 Iteration 2 Error: 0.099295 Iteration 3 Error: 0.031179 Align patch 25 0 left Iteration 1 Error: 0.996644 Iteration 2 Error: 0.117982 Iteration 3 Error: 0.023557 3D Fitting completed. Patch alignment time: 15.58(sec) Local motion has been corrected. Process thread exits. Computational time: 24.308197 sec Total time: 29.909733 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00007hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00007hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.555831s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00007hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.676127s ........................................ >>>>>>TIME<<<<<< FFT: 0.931054s Defocus_U Defocus_V Angle CCC 12378.95 13168.01 12.97 0.045703 Final Values Defocus_U Defocus_V Angle CCC 12374.30 13191.52 12.66 0.077848 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00007hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00007hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 44.33 7.70 Num Hot pixels: 188 Hot pixel threshold: 90.51 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.953551 Iteration 2 Error: 0.066892 Iteration 3 Error: 0.014180 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.30 0.12 ...... Frame ( 3) shift: -0.59 0.24 ...... Frame ( 4) shift: -0.89 0.35 ...... Frame ( 5) shift: -1.18 0.47 ...... Frame ( 6) shift: -1.34 0.56 ...... Frame ( 7) shift: -1.36 0.61 ...... Frame ( 8) shift: -1.38 0.66 ...... Frame ( 9) shift: -1.37 0.70 ...... Frame ( 10) shift: -1.32 0.71 ...... Frame ( 11) shift: -1.27 0.72 ...... Frame ( 12) shift: -1.23 0.73 ...... Frame ( 13) shift: -1.18 0.74 ...... Frame ( 14) shift: -1.13 0.75 ...... Frame ( 15) shift: -1.11 0.77 ...... Frame ( 16) shift: -1.10 0.80 ...... Frame ( 17) shift: -1.10 0.83 ...... Frame ( 18) shift: -1.11 0.84 ...... Frame ( 19) shift: -1.14 0.84 ...... Frame ( 20) shift: -1.17 0.84 ...... Frame ( 21) shift: -1.19 0.87 ...... Frame ( 22) shift: -1.19 0.92 ...... Frame ( 23) shift: -1.19 0.97 ...... Frame ( 24) shift: -1.18 1.00 ...... Frame ( 25) shift: -1.17 1.02 ...... Frame ( 26) shift: -1.16 1.03 ...... Frame ( 27) shift: -1.13 1.05 ...... Frame ( 28) shift: -1.10 1.08 ...... Frame ( 29) shift: -1.07 1.11 ...... Frame ( 30) shift: -1.06 1.14 ...... Frame ( 31) shift: -1.09 1.19 ...... Frame ( 32) shift: -1.12 1.23 ...... Frame ( 33) shift: -1.13 1.24 ...... Frame ( 34) shift: -1.10 1.23 ...... Frame ( 35) shift: -1.07 1.22 ...... Frame ( 36) shift: -1.05 1.25 ...... Frame ( 37) shift: -1.05 1.32 ...... Frame ( 38) shift: -1.04 1.39 ...... Frame ( 39) shift: -1.04 1.46 ...... Frame ( 40) shift: -1.03 1.52 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.396574 Iteration 2 Error: 0.091381 Iteration 3 Error: 0.022034 Align patch 2 23 left Iteration 1 Error: 0.855029 Iteration 2 Error: 0.137185 Iteration 3 Error: 0.053818 Iteration 4 Error: 0.018703 Align patch 3 22 left Iteration 1 Error: 0.778392 Iteration 2 Error: 0.181201 Iteration 3 Error: 0.057599 Iteration 4 Error: 0.021208 Align patch 4 21 left Iteration 1 Error: 0.680442 Iteration 2 Error: 0.109915 Iteration 3 Error: 0.021407 Align patch 5 20 left Iteration 1 Error: 0.730829 Iteration 2 Error: 0.116352 Iteration 3 Error: 0.028415 Align patch 6 19 left Iteration 1 Error: 0.781369 Iteration 2 Error: 0.104002 Iteration 3 Error: 0.027585 Align patch 7 18 left Iteration 1 Error: 1.179599 Iteration 2 Error: 0.124811 Iteration 3 Error: 0.025403 Align patch 8 17 left Iteration 1 Error: 0.632318 Iteration 2 Error: 0.130961 Iteration 3 Error: 0.022985 Align patch 9 16 left Iteration 1 Error: 1.119255 Iteration 2 Error: 0.134095 Iteration 3 Error: 0.026807 Align patch 10 15 left Iteration 1 Error: 0.778558 Iteration 2 Error: 0.147358 Iteration 3 Error: 0.036893 Align patch 11 14 left Iteration 1 Error: 0.764509 Iteration 2 Error: 0.127281 Iteration 3 Error: 0.023799 Align patch 12 13 left Iteration 1 Error: 1.097513 Iteration 2 Error: 0.134136 Iteration 3 Error: 0.035488 Align patch 13 12 left Iteration 1 Error: 0.562044 Iteration 2 Error: 0.114502 Iteration 3 Error: 0.020914 Align patch 14 11 left Iteration 1 Error: 1.115947 Iteration 2 Error: 0.166620 Iteration 3 Error: 0.047336 Align patch 15 10 left Iteration 1 Error: 0.643660 Iteration 2 Error: 0.165180 Iteration 3 Error: 0.027812 Align patch 16 9 left Iteration 1 Error: 0.634149 Iteration 2 Error: 0.125982 Iteration 3 Error: 0.055639 Iteration 4 Error: 0.015269 Align patch 17 8 left Iteration 1 Error: 1.651378 Iteration 2 Error: 0.117489 Iteration 3 Error: 0.025636 Align patch 18 7 left Iteration 1 Error: 0.687747 Iteration 2 Error: 0.126500 Iteration 3 Error: 0.030181 Align patch 19 6 left Iteration 1 Error: 0.794095 Iteration 2 Error: 0.101811 Iteration 3 Error: 0.016518 Align patch 20 5 left Iteration 1 Error: 1.088695 Iteration 2 Error: 0.150917 Iteration 3 Error: 0.021738 Align patch 21 4 left Iteration 1 Error: 1.101822 Iteration 2 Error: 0.159255 Iteration 3 Error: 0.040342 Align patch 22 3 left Iteration 1 Error: 0.957388 Iteration 2 Error: 0.128024 Iteration 3 Error: 0.025267 Align patch 23 2 left Iteration 1 Error: 1.228986 Iteration 2 Error: 0.213560 Iteration 3 Error: 0.027930 Align patch 24 1 left Iteration 1 Error: 0.751545 Iteration 2 Error: 0.143121 Iteration 3 Error: 0.033030 Align patch 25 0 left Iteration 1 Error: 0.968543 Iteration 2 Error: 0.084475 Iteration 3 Error: 0.009220 3D Fitting completed. Patch alignment time: 14.51(sec) Local motion has been corrected. Process thread exits. Computational time: 23.021318 sec Total time: 28.802370 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00007hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00007hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.542075s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00007hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.589306s ........................................ >>>>>>TIME<<<<<< FFT: 1.055424s Defocus_U Defocus_V Angle CCC 11031.30 11496.15 2.28 0.043331 Final Values Defocus_U Defocus_V Angle CCC 11075.07 11508.68 1.99 0.079259 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00007hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00007hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 1.000e-01 CC threshold: 0.734 Mean Std: 43.96 7.34 Num Hot pixels: 212 Hot pixel threshold: 87.99 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.985623 Iteration 2 Error: 0.100831 Iteration 3 Error: 0.021992 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.36 0.07 ...... Frame ( 3) shift: -0.73 0.15 ...... Frame ( 4) shift: -1.09 0.22 ...... Frame ( 5) shift: -1.46 0.30 ...... Frame ( 6) shift: -1.63 0.34 ...... Frame ( 7) shift: -1.62 0.35 ...... Frame ( 8) shift: -1.61 0.36 ...... Frame ( 9) shift: -1.58 0.42 ...... Frame ( 10) shift: -1.53 0.52 ...... Frame ( 11) shift: -1.48 0.62 ...... Frame ( 12) shift: -1.43 0.66 ...... Frame ( 13) shift: -1.38 0.63 ...... Frame ( 14) shift: -1.32 0.60 ...... Frame ( 15) shift: -1.29 0.60 ...... Frame ( 16) shift: -1.28 0.63 ...... Frame ( 17) shift: -1.28 0.66 ...... Frame ( 18) shift: -1.27 0.67 ...... Frame ( 19) shift: -1.26 0.68 ...... Frame ( 20) shift: -1.26 0.69 ...... Frame ( 21) shift: -1.27 0.74 ...... Frame ( 22) shift: -1.30 0.83 ...... Frame ( 23) shift: -1.33 0.92 ...... Frame ( 24) shift: -1.33 0.99 ...... Frame ( 25) shift: -1.30 1.03 ...... Frame ( 26) shift: -1.27 1.07 ...... Frame ( 27) shift: -1.26 1.11 ...... Frame ( 28) shift: -1.28 1.14 ...... Frame ( 29) shift: -1.31 1.16 ...... Frame ( 30) shift: -1.29 1.15 ...... Frame ( 31) shift: -1.25 1.11 ...... Frame ( 32) shift: -1.21 1.06 ...... Frame ( 33) shift: -1.18 1.10 ...... Frame ( 34) shift: -1.17 1.23 ...... Frame ( 35) shift: -1.16 1.35 ...... Frame ( 36) shift: -1.15 1.43 ...... Frame ( 37) shift: -1.14 1.46 ...... Frame ( 38) shift: -1.14 1.50 ...... Frame ( 39) shift: -1.13 1.53 ...... Frame ( 40) shift: -1.13 1.57 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.301354 Iteration 2 Error: 0.176689 Iteration 3 Error: 0.053979 Iteration 4 Error: 0.028754 Align patch 2 23 left Iteration 1 Error: 1.764001 Iteration 2 Error: 0.266800 Iteration 3 Error: 0.076551 Iteration 4 Error: 0.016456 Align patch 3 22 left Iteration 1 Error: 0.999612 Iteration 2 Error: 0.119100 Iteration 3 Error: 0.035977 Align patch 4 21 left Iteration 1 Error: 0.827326 Iteration 2 Error: 0.212233 Iteration 3 Error: 0.073367 Iteration 4 Error: 0.021027 Align patch 5 20 left Iteration 1 Error: 0.886553 Iteration 2 Error: 0.113684 Iteration 3 Error: 0.033933 Align patch 6 19 left Iteration 1 Error: 0.585671 Iteration 2 Error: 0.179208 Iteration 3 Error: 0.053974 Iteration 4 Error: 0.021725 Align patch 7 18 left Iteration 1 Error: 1.069695 Iteration 2 Error: 0.175695 Iteration 3 Error: 0.042928 Align patch 8 17 left Iteration 1 Error: 1.150327 Iteration 2 Error: 0.158367 Iteration 3 Error: 0.043978 Align patch 9 16 left Iteration 1 Error: 1.264943 Iteration 2 Error: 0.211045 Iteration 3 Error: 0.053107 Iteration 4 Error: 0.025943 Align patch 10 15 left Iteration 1 Error: 0.724193 Iteration 2 Error: 0.154858 Iteration 3 Error: 0.031859 Align patch 11 14 left Iteration 1 Error: 2.396884 Iteration 2 Error: 0.488118 Iteration 3 Error: 0.222371 Iteration 4 Error: 0.117044 Iteration 5 Error: 0.068345 Align patch 11 14 left Iteration 1 Error: 0.958629 Iteration 2 Error: 0.201701 Iteration 3 Error: 0.072334 Iteration 4 Error: 0.025890 Align patch 12 13 left Iteration 1 Error: 0.859313 Iteration 2 Error: 0.203897 Iteration 3 Error: 0.060956 Iteration 4 Error: 0.020440 Align patch 13 12 left Iteration 1 Error: 1.116757 Iteration 2 Error: 0.249597 Iteration 3 Error: 0.056232 Iteration 4 Error: 0.022298 Align patch 14 11 left Iteration 1 Error: 0.665704 Iteration 2 Error: 0.120438 Iteration 3 Error: 0.032794 Align patch 15 10 left Iteration 1 Error: 1.233029 Iteration 2 Error: 0.166528 Iteration 3 Error: 0.039600 Align patch 16 9 left Iteration 1 Error: 0.824407 Iteration 2 Error: 0.194574 Iteration 3 Error: 0.037976 Align patch 17 8 left Iteration 1 Error: 0.740160 Iteration 2 Error: 0.149814 Iteration 3 Error: 0.035941 Align patch 18 7 left Iteration 1 Error: 0.817477 Iteration 2 Error: 0.112873 Iteration 3 Error: 0.031756 Align patch 19 6 left Iteration 1 Error: 0.774025 Iteration 2 Error: 0.139344 Iteration 3 Error: 0.037812 Align patch 20 5 left Iteration 1 Error: 0.776408 Iteration 2 Error: 0.171746 Iteration 3 Error: 0.039793 Align patch 21 4 left Iteration 1 Error: 1.496596 Iteration 2 Error: 0.156172 Iteration 3 Error: 0.041065 Align patch 22 3 left Iteration 1 Error: 1.262693 Iteration 2 Error: 0.199498 Iteration 3 Error: 0.063612 Iteration 4 Error: 0.015467 Align patch 23 2 left Iteration 1 Error: 0.862132 Iteration 2 Error: 0.167125 Iteration 3 Error: 0.031284 Align patch 24 1 left Iteration 1 Error: 1.230737 Iteration 2 Error: 0.222988 Iteration 3 Error: 0.051120 Iteration 4 Error: 0.021453 Align patch 25 0 left Iteration 1 Error: 0.666339 Iteration 2 Error: 0.159458 Iteration 3 Error: 0.026561 3D Fitting completed. Patch alignment time: 16.91(sec) Local motion has been corrected. Process thread exits. Computational time: 25.624310 sec Total time: 31.303280 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00007hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00007hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.652346s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00007hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.837925s ........................................ >>>>>>TIME<<<<<< FFT: 1.054845s Defocus_U Defocus_V Angle CCC 10324.23 11152.36 4.22 0.037538 Final Values Defocus_U Defocus_V Angle CCC 10330.48 11174.25 4.53 0.071599 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00007hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00007hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 45.14 7.58 Num Hot pixels: 201 Hot pixel threshold: 90.60 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.079655 Iteration 2 Error: 0.089993 Iteration 3 Error: 0.013909 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.43 -0.05 ...... Frame ( 3) shift: -0.86 -0.11 ...... Frame ( 4) shift: -1.29 -0.16 ...... Frame ( 5) shift: -1.72 -0.21 ...... Frame ( 6) shift: -1.91 -0.21 ...... Frame ( 7) shift: -1.88 -0.15 ...... Frame ( 8) shift: -1.84 -0.09 ...... Frame ( 9) shift: -1.81 -0.06 ...... Frame ( 10) shift: -1.80 -0.06 ...... Frame ( 11) shift: -1.78 -0.06 ...... Frame ( 12) shift: -1.76 -0.01 ...... Frame ( 13) shift: -1.74 0.09 ...... Frame ( 14) shift: -1.73 0.18 ...... Frame ( 15) shift: -1.73 0.27 ...... Frame ( 16) shift: -1.76 0.35 ...... Frame ( 17) shift: -1.78 0.43 ...... Frame ( 18) shift: -1.75 0.46 ...... Frame ( 19) shift: -1.67 0.44 ...... Frame ( 20) shift: -1.59 0.43 ...... Frame ( 21) shift: -1.55 0.42 ...... Frame ( 22) shift: -1.57 0.41 ...... Frame ( 23) shift: -1.58 0.40 ...... Frame ( 24) shift: -1.58 0.40 ...... Frame ( 25) shift: -1.56 0.39 ...... Frame ( 26) shift: -1.54 0.39 ...... Frame ( 27) shift: -1.52 0.38 ...... Frame ( 28) shift: -1.52 0.36 ...... Frame ( 29) shift: -1.52 0.35 ...... Frame ( 30) shift: -1.53 0.36 ...... Frame ( 31) shift: -1.57 0.39 ...... Frame ( 32) shift: -1.61 0.42 ...... Frame ( 33) shift: -1.63 0.44 ...... Frame ( 34) shift: -1.62 0.45 ...... Frame ( 35) shift: -1.61 0.46 ...... Frame ( 36) shift: -1.60 0.48 ...... Frame ( 37) shift: -1.59 0.50 ...... Frame ( 38) shift: -1.59 0.52 ...... Frame ( 39) shift: -1.58 0.54 ...... Frame ( 40) shift: -1.58 0.56 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.177986 Iteration 2 Error: 0.161359 Iteration 3 Error: 0.041991 Align patch 2 23 left Iteration 1 Error: 1.016955 Iteration 2 Error: 0.149603 Iteration 3 Error: 0.026471 Align patch 3 22 left Iteration 1 Error: 1.153458 Iteration 2 Error: 0.192256 Iteration 3 Error: 0.034152 Align patch 4 21 left Iteration 1 Error: 0.713317 Iteration 2 Error: 0.085813 Iteration 3 Error: 0.020620 Align patch 5 20 left Iteration 1 Error: 0.934790 Iteration 2 Error: 0.137738 Iteration 3 Error: 0.033505 Align patch 6 19 left Iteration 1 Error: 0.906251 Iteration 2 Error: 0.125122 Iteration 3 Error: 0.043688 Align patch 7 18 left Iteration 1 Error: 0.641085 Iteration 2 Error: 0.207132 Iteration 3 Error: 0.055880 Iteration 4 Error: 0.028657 Align patch 8 17 left Iteration 1 Error: 0.796245 Iteration 2 Error: 0.171490 Iteration 3 Error: 0.056088 Iteration 4 Error: 0.018186 Align patch 9 16 left Iteration 1 Error: 0.627209 Iteration 2 Error: 0.066059 Iteration 3 Error: 0.016286 Align patch 10 15 left Iteration 1 Error: 0.554619 Iteration 2 Error: 0.091121 Iteration 3 Error: 0.016786 Align patch 11 14 left Iteration 1 Error: 0.894077 Iteration 2 Error: 0.146145 Iteration 3 Error: 0.044569 Align patch 12 13 left Iteration 1 Error: 0.634621 Iteration 2 Error: 0.093481 Iteration 3 Error: 0.020170 Align patch 13 12 left Iteration 1 Error: 0.491722 Iteration 2 Error: 0.070463 Iteration 3 Error: 0.014919 Align patch 14 11 left Iteration 1 Error: 0.652930 Iteration 2 Error: 0.130652 Iteration 3 Error: 0.022510 Align patch 15 10 left Iteration 1 Error: 0.680039 Iteration 2 Error: 0.117899 Iteration 3 Error: 0.036559 Align patch 16 9 left Iteration 1 Error: 0.841049 Iteration 2 Error: 0.129541 Iteration 3 Error: 0.047414 Align patch 17 8 left Iteration 1 Error: 0.562954 Iteration 2 Error: 0.139857 Iteration 3 Error: 0.045526 Align patch 18 7 left Iteration 1 Error: 0.644047 Iteration 2 Error: 0.230031 Iteration 3 Error: 0.059888 Iteration 4 Error: 0.021044 Align patch 19 6 left Iteration 1 Error: 0.512561 Iteration 2 Error: 0.078572 Iteration 3 Error: 0.020474 Align patch 20 5 left Iteration 1 Error: 0.567998 Iteration 2 Error: 0.091460 Iteration 3 Error: 0.023497 Align patch 21 4 left Iteration 1 Error: 1.227678 Iteration 2 Error: 0.170573 Iteration 3 Error: 0.040081 Align patch 22 3 left Iteration 1 Error: 1.130890 Iteration 2 Error: 0.174928 Iteration 3 Error: 0.048005 Align patch 23 2 left Iteration 1 Error: 0.936731 Iteration 2 Error: 0.078419 Iteration 3 Error: 0.023020 Align patch 24 1 left Iteration 1 Error: 0.643236 Iteration 2 Error: 0.082091 Iteration 3 Error: 0.020825 Align patch 25 0 left Iteration 1 Error: 0.827640 Iteration 2 Error: 0.119495 Iteration 3 Error: 0.030847 3D Fitting completed. Patch alignment time: 15.43(sec) Local motion has been corrected. Process thread exits. Computational time: 24.097359 sec Total time: 29.739838 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00007hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00007hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.566189s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00007hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.167310s ........................................ >>>>>>TIME<<<<<< FFT: 0.934020s Defocus_U Defocus_V Angle CCC 14261.73 13640.61 83.20 0.050978 Final Values Defocus_U Defocus_V Angle CCC 14264.85 13646.88 84.77 0.088299 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00008hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00008hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 45.00 7.89 Num Hot pixels: 184 Hot pixel threshold: 92.35 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.760085 Iteration 2 Error: 0.113808 Iteration 3 Error: 0.025963 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.37 -0.03 ...... Frame ( 3) shift: -0.73 -0.06 ...... Frame ( 4) shift: -1.10 -0.09 ...... Frame ( 5) shift: -1.47 -0.12 ...... Frame ( 6) shift: -1.66 -0.14 ...... Frame ( 7) shift: -1.68 -0.15 ...... Frame ( 8) shift: -1.70 -0.15 ...... Frame ( 9) shift: -1.70 -0.11 ...... Frame ( 10) shift: -1.69 -0.03 ...... Frame ( 11) shift: -1.67 0.06 ...... Frame ( 12) shift: -1.63 0.11 ...... Frame ( 13) shift: -1.56 0.12 ...... Frame ( 14) shift: -1.49 0.13 ...... Frame ( 15) shift: -1.47 0.14 ...... Frame ( 16) shift: -1.51 0.15 ...... Frame ( 17) shift: -1.54 0.16 ...... Frame ( 18) shift: -1.52 0.20 ...... Frame ( 19) shift: -1.44 0.26 ...... Frame ( 20) shift: -1.36 0.32 ...... Frame ( 21) shift: -1.28 0.38 ...... Frame ( 22) shift: -1.21 0.45 ...... Frame ( 23) shift: -1.14 0.51 ...... Frame ( 24) shift: -1.09 0.53 ...... Frame ( 25) shift: -1.06 0.51 ...... Frame ( 26) shift: -1.03 0.49 ...... Frame ( 27) shift: -1.00 0.48 ...... Frame ( 28) shift: -0.98 0.50 ...... Frame ( 29) shift: -0.95 0.51 ...... Frame ( 30) shift: -0.92 0.53 ...... Frame ( 31) shift: -0.87 0.54 ...... Frame ( 32) shift: -0.81 0.55 ...... Frame ( 33) shift: -0.78 0.57 ...... Frame ( 34) shift: -0.76 0.58 ...... Frame ( 35) shift: -0.75 0.60 ...... Frame ( 36) shift: -0.70 0.61 ...... Frame ( 37) shift: -0.63 0.62 ...... Frame ( 38) shift: -0.56 0.63 ...... Frame ( 39) shift: -0.48 0.63 ...... Frame ( 40) shift: -0.41 0.64 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.632329 Iteration 2 Error: 0.113732 Iteration 3 Error: 0.043325 Align patch 2 23 left Iteration 1 Error: 1.106781 Iteration 2 Error: 0.156256 Iteration 3 Error: 0.046967 Align patch 3 22 left Iteration 1 Error: 1.013155 Iteration 2 Error: 0.223072 Iteration 3 Error: 0.043421 Align patch 4 21 left Iteration 1 Error: 0.824572 Iteration 2 Error: 0.139153 Iteration 3 Error: 0.040883 Align patch 5 20 left Iteration 1 Error: 0.807285 Iteration 2 Error: 0.216300 Iteration 3 Error: 0.056586 Iteration 4 Error: 0.019376 Align patch 6 19 left Iteration 1 Error: 1.484083 Iteration 2 Error: 0.224593 Iteration 3 Error: 0.072937 Iteration 4 Error: 0.027308 Align patch 7 18 left Iteration 1 Error: 0.664605 Iteration 2 Error: 0.145940 Iteration 3 Error: 0.031266 Align patch 8 17 left Iteration 1 Error: 0.613987 Iteration 2 Error: 0.097867 Iteration 3 Error: 0.048663 Align patch 9 16 left Iteration 1 Error: 0.867634 Iteration 2 Error: 0.142540 Iteration 3 Error: 0.024933 Align patch 10 15 left Iteration 1 Error: 0.700643 Iteration 2 Error: 0.154928 Iteration 3 Error: 0.031233 Align patch 11 14 left Iteration 1 Error: 0.807861 Iteration 2 Error: 0.258103 Iteration 3 Error: 0.077456 Iteration 4 Error: 0.027752 Align patch 12 13 left Iteration 1 Error: 0.944697 Iteration 2 Error: 0.117403 Iteration 3 Error: 0.024583 Align patch 13 12 left Iteration 1 Error: 0.766805 Iteration 2 Error: 0.159826 Iteration 3 Error: 0.037753 Align patch 14 11 left Iteration 1 Error: 0.661173 Iteration 2 Error: 0.118980 Iteration 3 Error: 0.038166 Align patch 15 10 left Iteration 1 Error: 0.714029 Iteration 2 Error: 0.135108 Iteration 3 Error: 0.028562 Align patch 16 9 left Iteration 1 Error: 1.208271 Iteration 2 Error: 0.167472 Iteration 3 Error: 0.041017 Align patch 17 8 left Iteration 1 Error: 1.136109 Iteration 2 Error: 0.228194 Iteration 3 Error: 0.048935 Align patch 18 7 left Iteration 1 Error: 0.651861 Iteration 2 Error: 0.100364 Iteration 3 Error: 0.027412 Align patch 19 6 left Iteration 1 Error: 0.994159 Iteration 2 Error: 0.136146 Iteration 3 Error: 0.030745 Align patch 20 5 left Iteration 1 Error: 0.512527 Iteration 2 Error: 0.094474 Iteration 3 Error: 0.025924 Align patch 21 4 left Iteration 1 Error: 0.847647 Iteration 2 Error: 0.210585 Iteration 3 Error: 0.077344 Iteration 4 Error: 0.039028 Align patch 22 3 left Iteration 1 Error: 0.790705 Iteration 2 Error: 0.253416 Iteration 3 Error: 0.060620 Iteration 4 Error: 0.032957 Align patch 23 2 left Iteration 1 Error: 0.881179 Iteration 2 Error: 0.121156 Iteration 3 Error: 0.027509 Align patch 24 1 left Iteration 1 Error: 0.785255 Iteration 2 Error: 0.174855 Iteration 3 Error: 0.038079 Align patch 25 0 left Iteration 1 Error: 1.088583 Iteration 2 Error: 0.195130 Iteration 3 Error: 0.072850 Iteration 4 Error: 0.023154 3D Fitting completed. Patch alignment time: 15.62(sec) Local motion has been corrected. Process thread exits. Computational time: 24.844376 sec Total time: 30.566133 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00008hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00008hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.565207s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00008hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.076758s ........................................ >>>>>>TIME<<<<<< FFT: 0.935448s Defocus_U Defocus_V Angle CCC 8291.02 9119.15 14.71 0.030309 Final Values Defocus_U Defocus_V Angle CCC 8291.03 9106.64 14.71 0.066585 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00008hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00008hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.329e-01 9.899e-02 CC threshold: 0.727 Mean Std: 45.29 7.72 Num Hot pixels: 196 Hot pixel threshold: 91.64 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.505803 Iteration 2 Error: 0.122863 Iteration 3 Error: 0.030955 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.24 0.10 ...... Frame ( 3) shift: -0.48 0.19 ...... Frame ( 4) shift: -0.73 0.29 ...... Frame ( 5) shift: -0.97 0.38 ...... Frame ( 6) shift: -1.14 0.43 ...... Frame ( 7) shift: -1.23 0.43 ...... Frame ( 8) shift: -1.33 0.43 ...... Frame ( 9) shift: -1.40 0.44 ...... Frame ( 10) shift: -1.46 0.44 ...... Frame ( 11) shift: -1.51 0.45 ...... Frame ( 12) shift: -1.56 0.48 ...... Frame ( 13) shift: -1.60 0.55 ...... Frame ( 14) shift: -1.65 0.61 ...... Frame ( 15) shift: -1.72 0.67 ...... Frame ( 16) shift: -1.84 0.72 ...... Frame ( 17) shift: -1.95 0.78 ...... Frame ( 18) shift: -2.00 0.83 ...... Frame ( 19) shift: -1.98 0.88 ...... Frame ( 20) shift: -1.96 0.94 ...... Frame ( 21) shift: -1.97 0.95 ...... Frame ( 22) shift: -2.02 0.93 ...... Frame ( 23) shift: -2.06 0.92 ...... Frame ( 24) shift: -2.10 0.92 ...... Frame ( 25) shift: -2.12 0.96 ...... Frame ( 26) shift: -2.14 1.00 ...... Frame ( 27) shift: -2.17 0.99 ...... Frame ( 28) shift: -2.21 0.92 ...... Frame ( 29) shift: -2.24 0.85 ...... Frame ( 30) shift: -2.25 0.83 ...... Frame ( 31) shift: -2.21 0.87 ...... Frame ( 32) shift: -2.18 0.91 ...... Frame ( 33) shift: -2.18 0.94 ...... Frame ( 34) shift: -2.21 0.96 ...... Frame ( 35) shift: -2.25 0.98 ...... Frame ( 36) shift: -2.27 0.97 ...... Frame ( 37) shift: -2.27 0.95 ...... Frame ( 38) shift: -2.28 0.93 ...... Frame ( 39) shift: -2.29 0.91 ...... Frame ( 40) shift: -2.30 0.89 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.756577 Iteration 2 Error: 0.337515 Iteration 3 Error: 0.103636 Iteration 4 Error: 0.024951 Align patch 2 23 left Iteration 1 Error: 2.076745 Iteration 2 Error: 0.505167 Iteration 3 Error: 0.218111 Iteration 4 Error: 0.068147 Iteration 5 Error: 0.040537 Align patch 3 22 left Iteration 1 Error: 1.013137 Iteration 2 Error: 0.146818 Iteration 3 Error: 0.045058 Align patch 4 21 left Iteration 1 Error: 0.569117 Iteration 2 Error: 0.113887 Iteration 3 Error: 0.029941 Align patch 5 20 left Iteration 1 Error: 1.010439 Iteration 2 Error: 0.193216 Iteration 3 Error: 0.039492 Align patch 6 19 left Iteration 1 Error: 2.054721 Iteration 2 Error: 0.642925 Iteration 3 Error: 0.154182 Iteration 4 Error: 0.139750 Iteration 5 Error: 0.034018 Align patch 7 18 left Iteration 1 Error: 0.869473 Iteration 2 Error: 0.260736 Iteration 3 Error: 0.046877 Align patch 8 17 left Iteration 1 Error: 1.414849 Iteration 2 Error: 0.238804 Iteration 3 Error: 0.102766 Iteration 4 Error: 0.028375 Align patch 9 16 left Iteration 1 Error: 0.712394 Iteration 2 Error: 0.089939 Iteration 3 Error: 0.017653 Align patch 10 15 left Iteration 1 Error: 0.822989 Iteration 2 Error: 0.120783 Iteration 3 Error: 0.040780 Align patch 11 14 left Iteration 1 Error: 1.572664 Iteration 2 Error: 0.313069 Iteration 3 Error: 0.196279 Iteration 4 Error: 0.127952 Iteration 5 Error: 0.064053 Align patch 11 14 left Iteration 1 Error: 2.101637 Iteration 2 Error: 0.298539 Iteration 3 Error: 0.073938 Iteration 4 Error: 0.029435 Align patch 12 13 left Iteration 1 Error: 1.097023 Iteration 2 Error: 0.169296 Iteration 3 Error: 0.076969 Iteration 4 Error: 0.038754 Align patch 13 12 left Iteration 1 Error: 0.920132 Iteration 2 Error: 0.211159 Iteration 3 Error: 0.092257 Iteration 4 Error: 0.021141 Align patch 14 11 left Iteration 1 Error: 0.462670 Iteration 2 Error: 0.106707 Iteration 3 Error: 0.029296 Align patch 15 10 left Iteration 1 Error: 1.027868 Iteration 2 Error: 0.098452 Iteration 3 Error: 0.027249 Align patch 16 9 left Iteration 1 Error: 1.331760 Iteration 2 Error: 0.298730 Iteration 3 Error: 0.179796 Iteration 4 Error: 0.078597 Iteration 5 Error: 0.056013 Align patch 16 9 left Iteration 1 Error: 2.158264 Iteration 2 Error: 0.304948 Iteration 3 Error: 0.065321 Iteration 4 Error: 0.033409 Align patch 17 8 left Iteration 1 Error: 1.670099 Iteration 2 Error: 0.436585 Iteration 3 Error: 0.151378 Iteration 4 Error: 0.104774 Iteration 5 Error: 0.049584 Align patch 18 7 left Iteration 1 Error: 1.065472 Iteration 2 Error: 0.094472 Iteration 3 Error: 0.019511 Align patch 19 6 left Iteration 1 Error: 1.081079 Iteration 2 Error: 0.168280 Iteration 3 Error: 0.041837 Align patch 20 5 left Iteration 1 Error: 0.646262 Iteration 2 Error: 0.107537 Iteration 3 Error: 0.021042 Align patch 21 4 left Iteration 1 Error: 1.298114 Iteration 2 Error: 0.277737 Iteration 3 Error: 0.120649 Iteration 4 Error: 0.060892 Iteration 5 Error: 0.029228 Align patch 22 3 left Iteration 1 Error: 1.529252 Iteration 2 Error: 0.365857 Iteration 3 Error: 0.090598 Iteration 4 Error: 0.034550 Align patch 23 2 left Iteration 1 Error: 0.557413 Iteration 2 Error: 0.079983 Iteration 3 Error: 0.036411 Align patch 24 1 left Iteration 1 Error: 0.597006 Iteration 2 Error: 0.094619 Iteration 3 Error: 0.022283 Align patch 25 0 left Iteration 1 Error: 0.922330 Iteration 2 Error: 0.120328 Iteration 3 Error: 0.025509 3D Fitting completed. Patch alignment time: 17.72(sec) Local motion has been corrected. Process thread exits. Computational time: 25.837526 sec Total time: 32.033707 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00008hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00008hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.567507s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00008hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.637265s ........................................ >>>>>>TIME<<<<<< FFT: 0.922610s Defocus_U Defocus_V Angle CCC 10734.45 11214.78 4.86 0.018359 Final Values Defocus_U Defocus_V Angle CCC 10764.10 11228.91 3.30 -0.018897 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00008hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00008hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.001e-01 CC threshold: 0.735 Mean Std: 47.22 7.59 Num Hot pixels: 205 Hot pixel threshold: 92.75 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.138086 Iteration 2 Error: 0.084402 Iteration 3 Error: 0.021637 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.37 0.02 ...... Frame ( 3) shift: -0.74 0.04 ...... Frame ( 4) shift: -1.12 0.06 ...... Frame ( 5) shift: -1.49 0.09 ...... Frame ( 6) shift: -1.70 0.10 ...... Frame ( 7) shift: -1.77 0.10 ...... Frame ( 8) shift: -1.83 0.11 ...... Frame ( 9) shift: -1.83 0.13 ...... Frame ( 10) shift: -1.76 0.18 ...... Frame ( 11) shift: -1.69 0.22 ...... Frame ( 12) shift: -1.66 0.24 ...... Frame ( 13) shift: -1.65 0.23 ...... Frame ( 14) shift: -1.65 0.22 ...... Frame ( 15) shift: -1.65 0.25 ...... Frame ( 16) shift: -1.66 0.31 ...... Frame ( 17) shift: -1.67 0.37 ...... Frame ( 18) shift: -1.65 0.42 ...... Frame ( 19) shift: -1.62 0.44 ...... Frame ( 20) shift: -1.60 0.46 ...... Frame ( 21) shift: -1.57 0.48 ...... Frame ( 22) shift: -1.56 0.50 ...... Frame ( 23) shift: -1.55 0.53 ...... Frame ( 24) shift: -1.57 0.56 ...... Frame ( 25) shift: -1.63 0.60 ...... Frame ( 26) shift: -1.69 0.63 ...... Frame ( 27) shift: -1.69 0.68 ...... Frame ( 28) shift: -1.64 0.74 ...... Frame ( 29) shift: -1.60 0.80 ...... Frame ( 30) shift: -1.56 0.83 ...... Frame ( 31) shift: -1.53 0.83 ...... Frame ( 32) shift: -1.51 0.83 ...... Frame ( 33) shift: -1.51 0.86 ...... Frame ( 34) shift: -1.53 0.92 ...... Frame ( 35) shift: -1.54 0.98 ...... Frame ( 36) shift: -1.55 1.01 ...... Frame ( 37) shift: -1.53 1.03 ...... Frame ( 38) shift: -1.51 1.04 ...... Frame ( 39) shift: -1.49 1.06 ...... Frame ( 40) shift: -1.48 1.07 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.666393 Iteration 2 Error: 0.181875 Iteration 3 Error: 0.067144 Iteration 4 Error: 0.024759 Align patch 2 23 left Iteration 1 Error: 1.643311 Iteration 2 Error: 0.220046 Iteration 3 Error: 0.062030 Iteration 4 Error: 0.035703 Align patch 3 22 left Iteration 1 Error: 1.784254 Iteration 2 Error: 0.145951 Iteration 3 Error: 0.059361 Iteration 4 Error: 0.020639 Align patch 4 21 left Iteration 1 Error: 0.960115 Iteration 2 Error: 0.129583 Iteration 3 Error: 0.031902 Align patch 5 20 left Iteration 1 Error: 0.539831 Iteration 2 Error: 0.056522 Iteration 3 Error: 0.012078 Align patch 6 19 left Iteration 1 Error: 0.823564 Iteration 2 Error: 0.172524 Iteration 3 Error: 0.064677 Iteration 4 Error: 0.031672 Align patch 7 18 left Iteration 1 Error: 0.823767 Iteration 2 Error: 0.183154 Iteration 3 Error: 0.064467 Iteration 4 Error: 0.028595 Align patch 8 17 left Iteration 1 Error: 0.713977 Iteration 2 Error: 0.149986 Iteration 3 Error: 0.031690 Align patch 9 16 left Iteration 1 Error: 0.741725 Iteration 2 Error: 0.088399 Iteration 3 Error: 0.018833 Align patch 10 15 left Iteration 1 Error: 0.593815 Iteration 2 Error: 0.109508 Iteration 3 Error: 0.024942 Align patch 11 14 left Iteration 1 Error: 0.584715 Iteration 2 Error: 0.116621 Iteration 3 Error: 0.031306 Align patch 12 13 left Iteration 1 Error: 0.595971 Iteration 2 Error: 0.098470 Iteration 3 Error: 0.021235 Align patch 13 12 left Iteration 1 Error: 0.847947 Iteration 2 Error: 0.071309 Iteration 3 Error: 0.015828 Align patch 14 11 left Iteration 1 Error: 0.703574 Iteration 2 Error: 0.147028 Iteration 3 Error: 0.037318 Align patch 15 10 left Iteration 1 Error: 0.598243 Iteration 2 Error: 0.098803 Iteration 3 Error: 0.024491 Align patch 16 9 left Iteration 1 Error: 1.027337 Iteration 2 Error: 0.254847 Iteration 3 Error: 0.070342 Iteration 4 Error: 0.026183 Align patch 17 8 left Iteration 1 Error: 0.791093 Iteration 2 Error: 0.138236 Iteration 3 Error: 0.031478 Align patch 18 7 left Iteration 1 Error: 1.272925 Iteration 2 Error: 0.136341 Iteration 3 Error: 0.047014 Align patch 19 6 left Iteration 1 Error: 0.944515 Iteration 2 Error: 0.134659 Iteration 3 Error: 0.035482 Align patch 20 5 left Iteration 1 Error: 0.654130 Iteration 2 Error: 0.115880 Iteration 3 Error: 0.025825 Align patch 21 4 left Iteration 1 Error: 1.019159 Iteration 2 Error: 0.179328 Iteration 3 Error: 0.031229 Align patch 22 3 left Iteration 1 Error: 1.641138 Iteration 2 Error: 0.183481 Iteration 3 Error: 0.041602 Align patch 23 2 left Iteration 1 Error: 1.230476 Iteration 2 Error: 0.128610 Iteration 3 Error: 0.021713 Align patch 24 1 left Iteration 1 Error: 1.175187 Iteration 2 Error: 0.135838 Iteration 3 Error: 0.034591 Align patch 25 0 left Iteration 1 Error: 0.577842 Iteration 2 Error: 0.079326 Iteration 3 Error: 0.020299 3D Fitting completed. Patch alignment time: 15.72(sec) Local motion has been corrected. Process thread exits. Computational time: 24.367540 sec Total time: 30.329048 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00008hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00008hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.704685s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00008hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.994258s ........................................ >>>>>>TIME<<<<<< FFT: 0.926617s Defocus_U Defocus_V Angle CCC 13281.25 14164.07 7.36 0.053210 Final Values Defocus_U Defocus_V Angle CCC 13281.25 14154.69 7.36 0.093065 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00008hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00008hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.000e-01 CC threshold: 0.735 Mean Std: 46.55 7.63 Num Hot pixels: 211 Hot pixel threshold: 92.30 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.081661 Iteration 2 Error: 0.037935 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.34 0.00 ...... Frame ( 3) shift: -0.69 0.00 ...... Frame ( 4) shift: -1.03 0.00 ...... Frame ( 5) shift: -1.38 0.00 ...... Frame ( 6) shift: -1.55 -0.02 ...... Frame ( 7) shift: -1.56 -0.05 ...... Frame ( 8) shift: -1.56 -0.09 ...... Frame ( 9) shift: -1.58 -0.12 ...... Frame ( 10) shift: -1.60 -0.15 ...... Frame ( 11) shift: -1.62 -0.17 ...... Frame ( 12) shift: -1.65 -0.18 ...... Frame ( 13) shift: -1.69 -0.15 ...... Frame ( 14) shift: -1.73 -0.13 ...... Frame ( 15) shift: -1.73 -0.11 ...... Frame ( 16) shift: -1.68 -0.11 ...... Frame ( 17) shift: -1.63 -0.12 ...... Frame ( 18) shift: -1.61 -0.13 ...... Frame ( 19) shift: -1.62 -0.16 ...... Frame ( 20) shift: -1.63 -0.19 ...... Frame ( 21) shift: -1.61 -0.22 ...... Frame ( 22) shift: -1.57 -0.24 ...... Frame ( 23) shift: -1.54 -0.26 ...... Frame ( 24) shift: -1.53 -0.25 ...... Frame ( 25) shift: -1.56 -0.20 ...... Frame ( 26) shift: -1.59 -0.15 ...... Frame ( 27) shift: -1.60 -0.11 ...... Frame ( 28) shift: -1.57 -0.09 ...... Frame ( 29) shift: -1.54 -0.07 ...... Frame ( 30) shift: -1.59 -0.04 ...... Frame ( 31) shift: -1.70 -0.02 ...... Frame ( 32) shift: -1.81 0.01 ...... Frame ( 33) shift: -1.84 0.02 ...... Frame ( 34) shift: -1.78 0.02 ...... Frame ( 35) shift: -1.72 0.01 ...... Frame ( 36) shift: -1.68 0.02 ...... Frame ( 37) shift: -1.67 0.04 ...... Frame ( 38) shift: -1.66 0.07 ...... Frame ( 39) shift: -1.65 0.09 ...... Frame ( 40) shift: -1.64 0.12 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.114534 Iteration 2 Error: 0.229957 Iteration 3 Error: 0.056014 Iteration 4 Error: 0.022367 Align patch 2 23 left Iteration 1 Error: 1.029928 Iteration 2 Error: 0.151664 Iteration 3 Error: 0.028954 Align patch 3 22 left Iteration 1 Error: 1.049666 Iteration 2 Error: 0.164307 Iteration 3 Error: 0.020550 Align patch 4 21 left Iteration 1 Error: 0.510497 Iteration 2 Error: 0.078907 Iteration 3 Error: 0.012311 Align patch 5 20 left Iteration 1 Error: 0.498718 Iteration 2 Error: 0.045348 Align patch 6 19 left Iteration 1 Error: 0.655562 Iteration 2 Error: 0.074338 Iteration 3 Error: 0.030498 Align patch 7 18 left Iteration 1 Error: 0.644557 Iteration 2 Error: 0.101902 Iteration 3 Error: 0.020772 Align patch 8 17 left Iteration 1 Error: 0.657208 Iteration 2 Error: 0.078961 Iteration 3 Error: 0.023425 Align patch 9 16 left Iteration 1 Error: 0.749327 Iteration 2 Error: 0.147763 Iteration 3 Error: 0.040990 Align patch 10 15 left Iteration 1 Error: 0.714759 Iteration 2 Error: 0.108382 Iteration 3 Error: 0.022599 Align patch 11 14 left Iteration 1 Error: 0.851416 Iteration 2 Error: 0.143050 Iteration 3 Error: 0.039090 Align patch 12 13 left Iteration 1 Error: 0.809148 Iteration 2 Error: 0.095310 Iteration 3 Error: 0.025594 Align patch 13 12 left Iteration 1 Error: 0.909103 Iteration 2 Error: 0.156412 Iteration 3 Error: 0.033176 Align patch 14 11 left Iteration 1 Error: 0.484872 Iteration 2 Error: 0.128115 Iteration 3 Error: 0.032094 Align patch 15 10 left Iteration 1 Error: 0.657248 Iteration 2 Error: 0.109504 Iteration 3 Error: 0.043119 Align patch 16 9 left Iteration 1 Error: 1.845900 Iteration 2 Error: 0.442703 Iteration 3 Error: 0.076043 Iteration 4 Error: 0.053062 Iteration 5 Error: 0.022367 Align patch 17 8 left Iteration 1 Error: 1.866920 Iteration 2 Error: 0.328875 Iteration 3 Error: 0.097033 Iteration 4 Error: 0.037177 Align patch 18 7 left Iteration 1 Error: 0.962651 Iteration 2 Error: 0.177858 Iteration 3 Error: 0.033493 Align patch 19 6 left Iteration 1 Error: 0.766195 Iteration 2 Error: 0.138833 Iteration 3 Error: 0.035206 Align patch 20 5 left Iteration 1 Error: 0.808450 Iteration 2 Error: 0.131913 Iteration 3 Error: 0.035692 Align patch 21 4 left Iteration 1 Error: 1.366428 Iteration 2 Error: 0.226035 Iteration 3 Error: 0.046247 Align patch 22 3 left Iteration 1 Error: 1.793267 Iteration 2 Error: 0.345211 Iteration 3 Error: 0.070029 Iteration 4 Error: 0.025528 Align patch 23 2 left Iteration 1 Error: 0.778737 Iteration 2 Error: 0.155584 Iteration 3 Error: 0.059131 Iteration 4 Error: 0.015848 Align patch 24 1 left Iteration 1 Error: 0.711509 Iteration 2 Error: 0.139911 Iteration 3 Error: 0.028428 Align patch 25 0 left Iteration 1 Error: 0.651448 Iteration 2 Error: 0.110325 Iteration 3 Error: 0.036208 3D Fitting completed. Patch alignment time: 14.63(sec) Local motion has been corrected. Process thread exits. Computational time: 23.676611 sec Total time: 29.705715 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00008hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00008hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.596017s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00008hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.718505s ........................................ >>>>>>TIME<<<<<< FFT: 0.963285s Defocus_U Defocus_V Angle CCC 13525.40 13564.48 36.82 0.041697 Final Values Defocus_U Defocus_V Angle CCC 13854.56 13207.33 83.45 0.088778 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00009hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00009hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 45.35 7.80 Num Hot pixels: 199 Hot pixel threshold: 92.15 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.143779 Iteration 2 Error: 0.196002 Iteration 3 Error: 0.043705 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.40 -0.01 ...... Frame ( 3) shift: -0.80 -0.02 ...... Frame ( 4) shift: -1.20 -0.03 ...... Frame ( 5) shift: -1.60 -0.04 ...... Frame ( 6) shift: -1.79 -0.01 ...... Frame ( 7) shift: -1.75 0.06 ...... Frame ( 8) shift: -1.72 0.14 ...... Frame ( 9) shift: -1.68 0.23 ...... Frame ( 10) shift: -1.64 0.35 ...... Frame ( 11) shift: -1.60 0.46 ...... Frame ( 12) shift: -1.59 0.53 ...... Frame ( 13) shift: -1.61 0.56 ...... Frame ( 14) shift: -1.63 0.60 ...... Frame ( 15) shift: -1.63 0.63 ...... Frame ( 16) shift: -1.61 0.68 ...... Frame ( 17) shift: -1.59 0.72 ...... Frame ( 18) shift: -1.55 0.77 ...... Frame ( 19) shift: -1.50 0.83 ...... Frame ( 20) shift: -1.45 0.89 ...... Frame ( 21) shift: -1.43 0.93 ...... Frame ( 22) shift: -1.46 0.97 ...... Frame ( 23) shift: -1.48 1.00 ...... Frame ( 24) shift: -1.50 1.01 ...... Frame ( 25) shift: -1.50 1.01 ...... Frame ( 26) shift: -1.51 1.01 ...... Frame ( 27) shift: -1.50 1.05 ...... Frame ( 28) shift: -1.48 1.13 ...... Frame ( 29) shift: -1.45 1.22 ...... Frame ( 30) shift: -1.45 1.31 ...... Frame ( 31) shift: -1.46 1.39 ...... Frame ( 32) shift: -1.46 1.47 ...... Frame ( 33) shift: -1.46 1.50 ...... Frame ( 34) shift: -1.44 1.48 ...... Frame ( 35) shift: -1.42 1.45 ...... Frame ( 36) shift: -1.38 1.49 ...... Frame ( 37) shift: -1.32 1.60 ...... Frame ( 38) shift: -1.27 1.71 ...... Frame ( 39) shift: -1.21 1.82 ...... Frame ( 40) shift: -1.15 1.93 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.116462 Iteration 2 Error: 0.225168 Iteration 3 Error: 0.046948 Align patch 2 23 left Iteration 1 Error: 1.512633 Iteration 2 Error: 0.217152 Iteration 3 Error: 0.126605 Iteration 4 Error: 0.024390 Align patch 3 22 left Iteration 1 Error: 0.963416 Iteration 2 Error: 0.269022 Iteration 3 Error: 0.069769 Iteration 4 Error: 0.018116 Align patch 4 21 left Iteration 1 Error: 1.083767 Iteration 2 Error: 0.134568 Iteration 3 Error: 0.025083 Align patch 5 20 left Iteration 1 Error: 1.132203 Iteration 2 Error: 0.143693 Iteration 3 Error: 0.045052 Align patch 6 19 left Iteration 1 Error: 0.724165 Iteration 2 Error: 0.141319 Iteration 3 Error: 0.031021 Align patch 7 18 left Iteration 1 Error: 0.996397 Iteration 2 Error: 0.269631 Iteration 3 Error: 0.118362 Iteration 4 Error: 0.037179 Align patch 8 17 left Iteration 1 Error: 0.569441 Iteration 2 Error: 0.071919 Iteration 3 Error: 0.025223 Align patch 9 16 left Iteration 1 Error: 0.583148 Iteration 2 Error: 0.093511 Iteration 3 Error: 0.027981 Align patch 10 15 left Iteration 1 Error: 0.751713 Iteration 2 Error: 0.142192 Iteration 3 Error: 0.027216 Align patch 11 14 left Iteration 1 Error: 0.961048 Iteration 2 Error: 0.160479 Iteration 3 Error: 0.039385 Align patch 12 13 left Iteration 1 Error: 0.848030 Iteration 2 Error: 0.151313 Iteration 3 Error: 0.055132 Iteration 4 Error: 0.013391 Align patch 13 12 left Iteration 1 Error: 0.606085 Iteration 2 Error: 0.105017 Iteration 3 Error: 0.028988 Align patch 14 11 left Iteration 1 Error: 0.937193 Iteration 2 Error: 0.128929 Iteration 3 Error: 0.036788 Align patch 15 10 left Iteration 1 Error: 1.029415 Iteration 2 Error: 0.175009 Iteration 3 Error: 0.047096 Align patch 16 9 left Iteration 1 Error: 0.824080 Iteration 2 Error: 0.090701 Iteration 3 Error: 0.026265 Align patch 17 8 left Iteration 1 Error: 1.803510 Iteration 2 Error: 0.255096 Iteration 3 Error: 0.068902 Iteration 4 Error: 0.020812 Align patch 18 7 left Iteration 1 Error: 0.871676 Iteration 2 Error: 0.196933 Iteration 3 Error: 0.042077 Align patch 19 6 left Iteration 1 Error: 0.937483 Iteration 2 Error: 0.096346 Iteration 3 Error: 0.018503 Align patch 20 5 left Iteration 1 Error: 0.673899 Iteration 2 Error: 0.089105 Iteration 3 Error: 0.023500 Align patch 21 4 left Iteration 1 Error: 0.684562 Iteration 2 Error: 0.130098 Iteration 3 Error: 0.027833 Align patch 22 3 left Iteration 1 Error: 0.806693 Iteration 2 Error: 0.218213 Iteration 3 Error: 0.041735 Align patch 23 2 left Iteration 1 Error: 1.377233 Iteration 2 Error: 0.110957 Iteration 3 Error: 0.018309 Align patch 24 1 left Iteration 1 Error: 0.742353 Iteration 2 Error: 0.091844 Iteration 3 Error: 0.019987 Align patch 25 0 left Iteration 1 Error: 0.585271 Iteration 2 Error: 0.107580 Iteration 3 Error: 0.027144 3D Fitting completed. Patch alignment time: 14.91(sec) Local motion has been corrected. Process thread exits. Computational time: 23.917927 sec Total time: 29.585976 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00009hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00009hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.583047s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00009hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.087355s ........................................ >>>>>>TIME<<<<<< FFT: 0.794694s Defocus_U Defocus_V Angle CCC 13046.88 13929.69 11.65 0.053750 Final Values Defocus_U Defocus_V Angle CCC 13057.82 13931.25 11.03 0.093111 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00009hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00009hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.001e-01 CC threshold: 0.735 Mean Std: 46.25 7.73 Num Hot pixels: 217 Hot pixel threshold: 92.64 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.831854 Iteration 2 Error: 0.106982 Iteration 3 Error: 0.025386 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.30 0.05 ...... Frame ( 3) shift: -0.61 0.11 ...... Frame ( 4) shift: -0.91 0.16 ...... Frame ( 5) shift: -1.22 0.22 ...... Frame ( 6) shift: -1.34 0.25 ...... Frame ( 7) shift: -1.29 0.24 ...... Frame ( 8) shift: -1.23 0.24 ...... Frame ( 9) shift: -1.20 0.27 ...... Frame ( 10) shift: -1.18 0.33 ...... Frame ( 11) shift: -1.17 0.39 ...... Frame ( 12) shift: -1.13 0.47 ...... Frame ( 13) shift: -1.06 0.58 ...... Frame ( 14) shift: -1.00 0.70 ...... Frame ( 15) shift: -0.98 0.76 ...... Frame ( 16) shift: -1.00 0.78 ...... Frame ( 17) shift: -1.03 0.79 ...... Frame ( 18) shift: -1.05 0.83 ...... Frame ( 19) shift: -1.05 0.89 ...... Frame ( 20) shift: -1.06 0.94 ...... Frame ( 21) shift: -1.05 1.01 ...... Frame ( 22) shift: -1.03 1.09 ...... Frame ( 23) shift: -1.01 1.16 ...... Frame ( 24) shift: -1.00 1.17 ...... Frame ( 25) shift: -1.02 1.10 ...... Frame ( 26) shift: -1.04 1.04 ...... Frame ( 27) shift: -1.00 1.00 ...... Frame ( 28) shift: -0.91 0.99 ...... Frame ( 29) shift: -0.81 0.98 ...... Frame ( 30) shift: -0.76 0.99 ...... Frame ( 31) shift: -0.77 1.03 ...... Frame ( 32) shift: -0.77 1.07 ...... Frame ( 33) shift: -0.78 1.14 ...... Frame ( 34) shift: -0.79 1.26 ...... Frame ( 35) shift: -0.81 1.38 ...... Frame ( 36) shift: -0.81 1.45 ...... Frame ( 37) shift: -0.81 1.48 ...... Frame ( 38) shift: -0.81 1.51 ...... Frame ( 39) shift: -0.80 1.54 ...... Frame ( 40) shift: -0.80 1.58 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.660888 Iteration 2 Error: 0.191063 Iteration 3 Error: 0.058156 Iteration 4 Error: 0.013745 Align patch 2 23 left Iteration 1 Error: 1.387373 Iteration 2 Error: 0.152602 Iteration 3 Error: 0.035987 Align patch 3 22 left Iteration 1 Error: 0.856452 Iteration 2 Error: 0.071945 Iteration 3 Error: 0.015710 Align patch 4 21 left Iteration 1 Error: 0.764725 Iteration 2 Error: 0.127921 Iteration 3 Error: 0.018019 Align patch 5 20 left Iteration 1 Error: 0.625455 Iteration 2 Error: 0.076853 Iteration 3 Error: 0.012971 Align patch 6 19 left Iteration 1 Error: 2.429927 Iteration 2 Error: 0.955364 Iteration 3 Error: 0.520874 Iteration 4 Error: 0.443275 Iteration 5 Error: 0.197417 Align patch 6 19 left Iteration 1 Error: 2.124514 Iteration 2 Error: 0.270302 Iteration 3 Error: 0.057067 Iteration 4 Error: 0.019255 Align patch 7 18 left Iteration 1 Error: 1.292003 Iteration 2 Error: 0.200986 Iteration 3 Error: 0.056866 Iteration 4 Error: 0.032847 Align patch 8 17 left Iteration 1 Error: 1.034782 Iteration 2 Error: 0.106465 Iteration 3 Error: 0.032229 Align patch 9 16 left Iteration 1 Error: 0.650818 Iteration 2 Error: 0.094694 Iteration 3 Error: 0.028234 Align patch 10 15 left Iteration 1 Error: 0.900896 Iteration 2 Error: 0.113128 Iteration 3 Error: 0.026075 Align patch 11 14 left Iteration 1 Error: 0.944235 Iteration 2 Error: 0.377426 Iteration 3 Error: 0.127545 Iteration 4 Error: 0.052711 Iteration 5 Error: 0.023175 Align patch 12 13 left Iteration 1 Error: 0.849461 Iteration 2 Error: 0.212305 Iteration 3 Error: 0.061876 Iteration 4 Error: 0.034430 Align patch 13 12 left Iteration 1 Error: 0.981252 Iteration 2 Error: 0.100688 Iteration 3 Error: 0.031680 Align patch 14 11 left Iteration 1 Error: 0.639349 Iteration 2 Error: 0.106755 Iteration 3 Error: 0.031737 Align patch 15 10 left Iteration 1 Error: 0.965941 Iteration 2 Error: 0.113878 Iteration 3 Error: 0.034275 Align patch 16 9 left Iteration 1 Error: 1.514032 Iteration 2 Error: 0.176236 Iteration 3 Error: 0.053458 Iteration 4 Error: 0.020235 Align patch 17 8 left Iteration 1 Error: 0.833122 Iteration 2 Error: 0.143531 Iteration 3 Error: 0.037805 Align patch 18 7 left Iteration 1 Error: 0.896127 Iteration 2 Error: 0.187350 Iteration 3 Error: 0.047035 Align patch 19 6 left Iteration 1 Error: 0.700439 Iteration 2 Error: 0.149596 Iteration 3 Error: 0.038535 Align patch 20 5 left Iteration 1 Error: 0.758098 Iteration 2 Error: 0.169144 Iteration 3 Error: 0.034069 Align patch 21 4 left Iteration 1 Error: 1.711754 Iteration 2 Error: 0.233153 Iteration 3 Error: 0.039005 Align patch 22 3 left Iteration 1 Error: 0.893981 Iteration 2 Error: 0.119532 Iteration 3 Error: 0.038048 Align patch 23 2 left Iteration 1 Error: 0.719967 Iteration 2 Error: 0.147329 Iteration 3 Error: 0.043985 Align patch 24 1 left Iteration 1 Error: 0.654342 Iteration 2 Error: 0.105956 Iteration 3 Error: 0.024955 Align patch 25 0 left Iteration 1 Error: 0.710772 Iteration 2 Error: 0.107102 Iteration 3 Error: 0.040833 3D Fitting completed. Patch alignment time: 17.26(sec) Local motion has been corrected. Process thread exits. Computational time: 26.018164 sec Total time: 31.901628 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00009hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00009hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.763535s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00009hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.702206s ........................................ >>>>>>TIME<<<<<< FFT: 1.041959s Defocus_U Defocus_V Angle CCC 12394.93 11937.25 87.28 0.049117 Final Values Defocus_U Defocus_V Angle CCC 12423.06 11927.88 86.96 0.089348 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00009hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00009hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 47.52 7.63 Num Hot pixels: 235 Hot pixel threshold: 93.28 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.538385 Iteration 2 Error: 0.187222 Iteration 3 Error: 0.054189 Iteration 4 Error: 0.024570 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.39 0.11 ...... Frame ( 3) shift: -0.78 0.23 ...... Frame ( 4) shift: -1.18 0.34 ...... Frame ( 5) shift: -1.57 0.45 ...... Frame ( 6) shift: -1.76 0.57 ...... Frame ( 7) shift: -1.74 0.69 ...... Frame ( 8) shift: -1.73 0.81 ...... Frame ( 9) shift: -1.70 0.95 ...... Frame ( 10) shift: -1.66 1.09 ...... Frame ( 11) shift: -1.62 1.23 ...... Frame ( 12) shift: -1.56 1.33 ...... Frame ( 13) shift: -1.50 1.38 ...... Frame ( 14) shift: -1.43 1.43 ...... Frame ( 15) shift: -1.39 1.50 ...... Frame ( 16) shift: -1.37 1.59 ...... Frame ( 17) shift: -1.36 1.67 ...... Frame ( 18) shift: -1.30 1.76 ...... Frame ( 19) shift: -1.20 1.84 ...... Frame ( 20) shift: -1.10 1.92 ...... Frame ( 21) shift: -1.05 1.92 ...... Frame ( 22) shift: -1.03 1.84 ...... Frame ( 23) shift: -1.02 1.76 ...... Frame ( 24) shift: -1.03 1.77 ...... Frame ( 25) shift: -1.07 1.86 ...... Frame ( 26) shift: -1.12 1.96 ...... Frame ( 27) shift: -1.14 2.06 ...... Frame ( 28) shift: -1.12 2.18 ...... Frame ( 29) shift: -1.11 2.30 ...... Frame ( 30) shift: -1.13 2.37 ...... Frame ( 31) shift: -1.17 2.40 ...... Frame ( 32) shift: -1.21 2.43 ...... Frame ( 33) shift: -1.23 2.44 ...... Frame ( 34) shift: -1.23 2.41 ...... Frame ( 35) shift: -1.23 2.39 ...... Frame ( 36) shift: -1.24 2.39 ...... Frame ( 37) shift: -1.25 2.41 ...... Frame ( 38) shift: -1.26 2.43 ...... Frame ( 39) shift: -1.28 2.45 ...... Frame ( 40) shift: -1.29 2.47 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.839514 Iteration 2 Error: 0.302885 Iteration 3 Error: 0.073062 Iteration 4 Error: 0.038422 Align patch 2 23 left Iteration 1 Error: 2.346873 Iteration 2 Error: 0.233036 Iteration 3 Error: 0.156287 Iteration 4 Error: 0.063911 Iteration 5 Error: 0.050001 Align patch 2 23 left Iteration 1 Error: 2.715631 Iteration 2 Error: 0.173328 Iteration 3 Error: 0.031900 Align patch 3 22 left Iteration 1 Error: 1.471289 Iteration 2 Error: 0.259107 Iteration 3 Error: 0.050126 Iteration 4 Error: 0.023255 Align patch 4 21 left Iteration 1 Error: 0.918390 Iteration 2 Error: 0.126169 Iteration 3 Error: 0.049485 Align patch 5 20 left Iteration 1 Error: 0.535905 Iteration 2 Error: 0.137716 Iteration 3 Error: 0.039701 Align patch 6 19 left Iteration 1 Error: 0.743049 Iteration 2 Error: 0.250056 Iteration 3 Error: 0.070053 Iteration 4 Error: 0.050086 Iteration 5 Error: 0.025129 Align patch 7 18 left Iteration 1 Error: 0.998223 Iteration 2 Error: 0.282618 Iteration 3 Error: 0.136186 Iteration 4 Error: 0.052896 Iteration 5 Error: 0.028578 Align patch 8 17 left Iteration 1 Error: 1.915013 Iteration 2 Error: 0.162039 Iteration 3 Error: 0.036377 Align patch 9 16 left Iteration 1 Error: 0.893596 Iteration 2 Error: 0.147680 Iteration 3 Error: 0.044975 Align patch 10 15 left Iteration 1 Error: 0.728856 Iteration 2 Error: 0.191645 Iteration 3 Error: 0.045375 Align patch 11 14 left Iteration 1 Error: 0.811876 Iteration 2 Error: 0.180654 Iteration 3 Error: 0.057346 Iteration 4 Error: 0.022413 Align patch 12 13 left Iteration 1 Error: 0.875339 Iteration 2 Error: 0.153262 Iteration 3 Error: 0.083934 Iteration 4 Error: 0.022312 Align patch 13 12 left Iteration 1 Error: 0.882157 Iteration 2 Error: 0.114040 Iteration 3 Error: 0.025416 Align patch 14 11 left Iteration 1 Error: 1.169575 Iteration 2 Error: 0.092494 Iteration 3 Error: 0.038212 Align patch 15 10 left Iteration 1 Error: 0.963527 Iteration 2 Error: 0.197912 Iteration 3 Error: 0.053377 Iteration 4 Error: 0.018288 Align patch 16 9 left Iteration 1 Error: 1.388216 Iteration 2 Error: 0.383702 Iteration 3 Error: 0.096704 Iteration 4 Error: 0.035875 Align patch 17 8 left Iteration 1 Error: 1.203762 Iteration 2 Error: 0.152053 Iteration 3 Error: 0.030376 Align patch 18 7 left Iteration 1 Error: 0.626997 Iteration 2 Error: 0.113324 Iteration 3 Error: 0.055098 Iteration 4 Error: 0.026635 Align patch 19 6 left Iteration 1 Error: 1.154406 Iteration 2 Error: 0.336947 Iteration 3 Error: 0.098723 Iteration 4 Error: 0.035839 Align patch 20 5 left Iteration 1 Error: 1.260507 Iteration 2 Error: 0.191927 Iteration 3 Error: 0.043476 Align patch 21 4 left Iteration 1 Error: 2.141551 Iteration 2 Error: 0.364109 Iteration 3 Error: 0.073695 Iteration 4 Error: 0.011301 Align patch 22 3 left Iteration 1 Error: 1.921941 Iteration 2 Error: 0.358768 Iteration 3 Error: 0.120269 Iteration 4 Error: 0.041963 Align patch 23 2 left Iteration 1 Error: 1.154135 Iteration 2 Error: 0.241527 Iteration 3 Error: 0.052696 Iteration 4 Error: 0.014632 Align patch 24 1 left Iteration 1 Error: 0.966000 Iteration 2 Error: 0.154757 Iteration 3 Error: 0.045460 Align patch 25 0 left Iteration 1 Error: 0.929665 Iteration 2 Error: 0.216791 Iteration 3 Error: 0.088758 Iteration 4 Error: 0.047873 3D Fitting completed. Patch alignment time: 17.52(sec) Local motion has been corrected. Process thread exits. Computational time: 26.485498 sec Total time: 32.528801 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00009hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00009hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.787127s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00009hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.634150s ........................................ >>>>>>TIME<<<<<< FFT: 1.021156s Defocus_U Defocus_V Angle CCC 11916.06 12724.66 6.85 0.048472 Final Values Defocus_U Defocus_V Angle CCC 11939.50 12751.26 6.53 0.086895 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00009hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00009hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.998e-02 CC threshold: 0.734 Mean Std: 47.51 7.62 Num Hot pixels: 220 Hot pixel threshold: 93.23 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.099601 Iteration 2 Error: 0.171734 Iteration 3 Error: 0.047986 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.38 -0.03 ...... Frame ( 3) shift: -0.76 -0.05 ...... Frame ( 4) shift: -1.14 -0.08 ...... Frame ( 5) shift: -1.52 -0.10 ...... Frame ( 6) shift: -1.69 -0.16 ...... Frame ( 7) shift: -1.65 -0.23 ...... Frame ( 8) shift: -1.61 -0.31 ...... Frame ( 9) shift: -1.56 -0.27 ...... Frame ( 10) shift: -1.49 -0.14 ...... Frame ( 11) shift: -1.42 0.00 ...... Frame ( 12) shift: -1.38 0.12 ...... Frame ( 13) shift: -1.35 0.23 ...... Frame ( 14) shift: -1.33 0.33 ...... Frame ( 15) shift: -1.33 0.47 ...... Frame ( 16) shift: -1.34 0.65 ...... Frame ( 17) shift: -1.35 0.82 ...... Frame ( 18) shift: -1.31 0.96 ...... Frame ( 19) shift: -1.22 1.07 ...... Frame ( 20) shift: -1.13 1.18 ...... Frame ( 21) shift: -1.11 1.26 ...... Frame ( 22) shift: -1.15 1.30 ...... Frame ( 23) shift: -1.19 1.35 ...... Frame ( 24) shift: -1.19 1.35 ...... Frame ( 25) shift: -1.14 1.31 ...... Frame ( 26) shift: -1.09 1.26 ...... Frame ( 27) shift: -1.04 1.25 ...... Frame ( 28) shift: -1.00 1.27 ...... Frame ( 29) shift: -0.96 1.28 ...... Frame ( 30) shift: -0.93 1.29 ...... Frame ( 31) shift: -0.90 1.28 ...... Frame ( 32) shift: -0.88 1.27 ...... Frame ( 33) shift: -0.89 1.29 ...... Frame ( 34) shift: -0.92 1.32 ...... Frame ( 35) shift: -0.96 1.35 ...... Frame ( 36) shift: -0.90 1.40 ...... Frame ( 37) shift: -0.75 1.47 ...... Frame ( 38) shift: -0.59 1.53 ...... Frame ( 39) shift: -0.44 1.59 ...... Frame ( 40) shift: -0.29 1.65 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 3.484850 Iteration 2 Error: 0.554074 Iteration 3 Error: 0.120719 Iteration 4 Error: 0.036774 Align patch 2 23 left Iteration 1 Error: 1.266879 Iteration 2 Error: 0.204560 Iteration 3 Error: 0.095533 Iteration 4 Error: 0.037557 Align patch 3 22 left Iteration 1 Error: 1.389215 Iteration 2 Error: 0.178618 Iteration 3 Error: 0.034671 Align patch 4 21 left Iteration 1 Error: 0.647589 Iteration 2 Error: 0.129551 Iteration 3 Error: 0.039205 Align patch 5 20 left Iteration 1 Error: 0.596406 Iteration 2 Error: 0.081157 Iteration 3 Error: 0.016573 Align patch 6 19 left Iteration 1 Error: 1.058272 Iteration 2 Error: 0.252015 Iteration 3 Error: 0.073378 Iteration 4 Error: 0.037097 Align patch 7 18 left Iteration 1 Error: 0.651955 Iteration 2 Error: 0.175068 Iteration 3 Error: 0.056788 Iteration 4 Error: 0.035743 Align patch 8 17 left Iteration 1 Error: 0.919753 Iteration 2 Error: 0.091481 Iteration 3 Error: 0.020893 Align patch 9 16 left Iteration 1 Error: 0.614307 Iteration 2 Error: 0.109560 Iteration 3 Error: 0.027066 Align patch 10 15 left Iteration 1 Error: 0.742750 Iteration 2 Error: 0.109204 Iteration 3 Error: 0.024597 Align patch 11 14 left Iteration 1 Error: 0.871035 Iteration 2 Error: 0.153165 Iteration 3 Error: 0.043315 Align patch 12 13 left Iteration 1 Error: 0.759975 Iteration 2 Error: 0.119633 Iteration 3 Error: 0.037929 Align patch 13 12 left Iteration 1 Error: 0.708686 Iteration 2 Error: 0.168249 Iteration 3 Error: 0.046638 Align patch 14 11 left Iteration 1 Error: 0.659943 Iteration 2 Error: 0.186615 Iteration 3 Error: 0.058542 Iteration 4 Error: 0.029159 Align patch 15 10 left Iteration 1 Error: 0.714220 Iteration 2 Error: 0.142408 Iteration 3 Error: 0.039353 Align patch 16 9 left Iteration 1 Error: 1.318125 Iteration 2 Error: 0.176405 Iteration 3 Error: 0.052885 Iteration 4 Error: 0.029150 Align patch 17 8 left Iteration 1 Error: 0.845234 Iteration 2 Error: 0.133416 Iteration 3 Error: 0.044976 Align patch 18 7 left Iteration 1 Error: 1.501863 Iteration 2 Error: 0.219829 Iteration 3 Error: 0.070155 Iteration 4 Error: 0.024537 Align patch 19 6 left Iteration 1 Error: 0.710397 Iteration 2 Error: 0.242457 Iteration 3 Error: 0.061557 Iteration 4 Error: 0.028497 Align patch 20 5 left Iteration 1 Error: 0.781958 Iteration 2 Error: 0.099094 Iteration 3 Error: 0.037035 Align patch 21 4 left Iteration 1 Error: 1.542368 Iteration 2 Error: 0.238260 Iteration 3 Error: 0.062872 Iteration 4 Error: 0.014759 Align patch 22 3 left Iteration 1 Error: 1.340947 Iteration 2 Error: 0.367052 Iteration 3 Error: 0.093279 Iteration 4 Error: 0.052444 Iteration 5 Error: 0.016767 Align patch 23 2 left Iteration 1 Error: 0.953082 Iteration 2 Error: 0.181445 Iteration 3 Error: 0.056429 Iteration 4 Error: 0.012933 Align patch 24 1 left Iteration 1 Error: 0.706679 Iteration 2 Error: 0.096572 Iteration 3 Error: 0.031124 Align patch 25 0 left Iteration 1 Error: 0.592470 Iteration 2 Error: 0.077031 Iteration 3 Error: 0.026075 3D Fitting completed. Patch alignment time: 16.06(sec) Local motion has been corrected. Process thread exits. Computational time: 24.607685 sec Total time: 30.158524 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00009hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00009hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.650203s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00009hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.902148s ........................................ >>>>>>TIME<<<<<< FFT: 0.929629s Defocus_U Defocus_V Angle CCC 11535.18 10925.79 84.47 0.053381 Final Values Defocus_U Defocus_V Angle CCC 11549.25 10933.61 84.78 0.098217 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00010hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00010hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.001e-01 CC threshold: 0.735 Mean Std: 47.30 7.70 Num Hot pixels: 211 Hot pixel threshold: 93.49 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.687006 Iteration 2 Error: 0.067099 Iteration 3 Error: 0.017386 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.37 -0.15 ...... Frame ( 3) shift: -0.74 -0.30 ...... Frame ( 4) shift: -1.11 -0.44 ...... Frame ( 5) shift: -1.48 -0.59 ...... Frame ( 6) shift: -1.65 -0.65 ...... Frame ( 7) shift: -1.63 -0.61 ...... Frame ( 8) shift: -1.61 -0.57 ...... Frame ( 9) shift: -1.57 -0.52 ...... Frame ( 10) shift: -1.52 -0.45 ...... Frame ( 11) shift: -1.47 -0.38 ...... Frame ( 12) shift: -1.41 -0.33 ...... Frame ( 13) shift: -1.35 -0.28 ...... Frame ( 14) shift: -1.29 -0.23 ...... Frame ( 15) shift: -1.26 -0.19 ...... Frame ( 16) shift: -1.26 -0.18 ...... Frame ( 17) shift: -1.25 -0.17 ...... Frame ( 18) shift: -1.23 -0.17 ...... Frame ( 19) shift: -1.20 -0.19 ...... Frame ( 20) shift: -1.16 -0.22 ...... Frame ( 21) shift: -1.15 -0.20 ...... Frame ( 22) shift: -1.15 -0.15 ...... Frame ( 23) shift: -1.16 -0.10 ...... Frame ( 24) shift: -1.16 -0.06 ...... Frame ( 25) shift: -1.15 -0.04 ...... Frame ( 26) shift: -1.14 -0.02 ...... Frame ( 27) shift: -1.13 -0.02 ...... Frame ( 28) shift: -1.11 -0.02 ...... Frame ( 29) shift: -1.09 -0.03 ...... Frame ( 30) shift: -1.09 0.01 ...... Frame ( 31) shift: -1.11 0.09 ...... Frame ( 32) shift: -1.13 0.18 ...... Frame ( 33) shift: -1.13 0.23 ...... Frame ( 34) shift: -1.12 0.26 ...... Frame ( 35) shift: -1.11 0.29 ...... Frame ( 36) shift: -1.10 0.32 ...... Frame ( 37) shift: -1.10 0.36 ...... Frame ( 38) shift: -1.10 0.39 ...... Frame ( 39) shift: -1.10 0.43 ...... Frame ( 40) shift: -1.10 0.46 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.855328 Iteration 2 Error: 0.141096 Iteration 3 Error: 0.028953 Align patch 2 23 left Iteration 1 Error: 0.816844 Iteration 2 Error: 0.140894 Iteration 3 Error: 0.029107 Align patch 3 22 left Iteration 1 Error: 0.783587 Iteration 2 Error: 0.107561 Iteration 3 Error: 0.027395 Align patch 4 21 left Iteration 1 Error: 0.764351 Iteration 2 Error: 0.134650 Iteration 3 Error: 0.039739 Align patch 5 20 left Iteration 1 Error: 0.999194 Iteration 2 Error: 0.141812 Iteration 3 Error: 0.035348 Align patch 6 19 left Iteration 1 Error: 0.730452 Iteration 2 Error: 0.110587 Iteration 3 Error: 0.031754 Align patch 7 18 left Iteration 1 Error: 0.587027 Iteration 2 Error: 0.105490 Iteration 3 Error: 0.020542 Align patch 8 17 left Iteration 1 Error: 0.732246 Iteration 2 Error: 0.176333 Iteration 3 Error: 0.029605 Align patch 9 16 left Iteration 1 Error: 0.641501 Iteration 2 Error: 0.075940 Iteration 3 Error: 0.021948 Align patch 10 15 left Iteration 1 Error: 0.697125 Iteration 2 Error: 0.150439 Iteration 3 Error: 0.022679 Align patch 11 14 left Iteration 1 Error: 0.883673 Iteration 2 Error: 0.228570 Iteration 3 Error: 0.056996 Iteration 4 Error: 0.024626 Align patch 12 13 left Iteration 1 Error: 0.683426 Iteration 2 Error: 0.086607 Iteration 3 Error: 0.030407 Align patch 13 12 left Iteration 1 Error: 0.949061 Iteration 2 Error: 0.128493 Iteration 3 Error: 0.036756 Align patch 14 11 left Iteration 1 Error: 0.690276 Iteration 2 Error: 0.232652 Iteration 3 Error: 0.091766 Iteration 4 Error: 0.046017 Align patch 15 10 left Iteration 1 Error: 0.719125 Iteration 2 Error: 0.144405 Iteration 3 Error: 0.035536 Align patch 16 9 left Iteration 1 Error: 1.123503 Iteration 2 Error: 0.125889 Iteration 3 Error: 0.026684 Align patch 17 8 left Iteration 1 Error: 1.374947 Iteration 2 Error: 0.146551 Iteration 3 Error: 0.031978 Align patch 18 7 left Iteration 1 Error: 0.992537 Iteration 2 Error: 0.121134 Iteration 3 Error: 0.027898 Align patch 19 6 left Iteration 1 Error: 0.536935 Iteration 2 Error: 0.118572 Iteration 3 Error: 0.041624 Align patch 20 5 left Iteration 1 Error: 0.477093 Iteration 2 Error: 0.077675 Iteration 3 Error: 0.015241 Align patch 21 4 left Iteration 1 Error: 1.095472 Iteration 2 Error: 0.152146 Iteration 3 Error: 0.024620 Align patch 22 3 left Iteration 1 Error: 0.746462 Iteration 2 Error: 0.124462 Iteration 3 Error: 0.031592 Align patch 23 2 left Iteration 1 Error: 0.636056 Iteration 2 Error: 0.111682 Iteration 3 Error: 0.026037 Align patch 24 1 left Iteration 1 Error: 0.828848 Iteration 2 Error: 0.173154 Iteration 3 Error: 0.039912 Align patch 25 0 left Iteration 1 Error: 0.652703 Iteration 2 Error: 0.073061 Iteration 3 Error: 0.020345 3D Fitting completed. Patch alignment time: 14.63(sec) Local motion has been corrected. Process thread exits. Computational time: 22.761497 sec Total time: 29.023746 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00010hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00010hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.554134s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00010hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.845358s ........................................ >>>>>>TIME<<<<<< FFT: 1.107920s Defocus_U Defocus_V Angle CCC 12048.82 12966.81 12.72 0.046594 Final Values Defocus_U Defocus_V Angle CCC 12055.04 12966.84 13.35 0.086521 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00010hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00010hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 47.59 7.63 Num Hot pixels: 219 Hot pixel threshold: 93.37 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.835334 Iteration 2 Error: 0.082035 Iteration 3 Error: 0.026688 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.34 -0.18 ...... Frame ( 3) shift: -0.69 -0.36 ...... Frame ( 4) shift: -1.03 -0.54 ...... Frame ( 5) shift: -1.38 -0.72 ...... Frame ( 6) shift: -1.52 -0.75 ...... Frame ( 7) shift: -1.45 -0.61 ...... Frame ( 8) shift: -1.38 -0.48 ...... Frame ( 9) shift: -1.33 -0.39 ...... Frame ( 10) shift: -1.30 -0.35 ...... Frame ( 11) shift: -1.26 -0.32 ...... Frame ( 12) shift: -1.22 -0.31 ...... Frame ( 13) shift: -1.18 -0.33 ...... Frame ( 14) shift: -1.14 -0.35 ...... Frame ( 15) shift: -1.11 -0.31 ...... Frame ( 16) shift: -1.09 -0.21 ...... Frame ( 17) shift: -1.06 -0.11 ...... Frame ( 18) shift: -1.07 -0.06 ...... Frame ( 19) shift: -1.12 -0.07 ...... Frame ( 20) shift: -1.17 -0.07 ...... Frame ( 21) shift: -1.18 -0.05 ...... Frame ( 22) shift: -1.14 -0.01 ...... Frame ( 23) shift: -1.10 0.04 ...... Frame ( 24) shift: -1.07 0.08 ...... Frame ( 25) shift: -1.04 0.12 ...... Frame ( 26) shift: -1.01 0.15 ...... Frame ( 27) shift: -0.97 0.19 ...... Frame ( 28) shift: -0.92 0.24 ...... Frame ( 29) shift: -0.87 0.29 ...... Frame ( 30) shift: -0.85 0.29 ...... Frame ( 31) shift: -0.84 0.25 ...... Frame ( 32) shift: -0.83 0.21 ...... Frame ( 33) shift: -0.83 0.21 ...... Frame ( 34) shift: -0.82 0.25 ...... Frame ( 35) shift: -0.82 0.30 ...... Frame ( 36) shift: -0.78 0.31 ...... Frame ( 37) shift: -0.70 0.28 ...... Frame ( 38) shift: -0.62 0.25 ...... Frame ( 39) shift: -0.54 0.22 ...... Frame ( 40) shift: -0.46 0.20 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.264365 Iteration 2 Error: 0.321511 Iteration 3 Error: 0.062521 Iteration 4 Error: 0.011103 Align patch 2 23 left Iteration 1 Error: 1.174330 Iteration 2 Error: 0.175396 Iteration 3 Error: 0.061039 Iteration 4 Error: 0.017020 Align patch 3 22 left Iteration 1 Error: 1.271857 Iteration 2 Error: 0.177888 Iteration 3 Error: 0.049460 Align patch 4 21 left Iteration 1 Error: 1.300550 Iteration 2 Error: 0.135408 Iteration 3 Error: 0.061084 Iteration 4 Error: 0.014257 Align patch 5 20 left Iteration 1 Error: 0.804844 Iteration 2 Error: 0.182761 Iteration 3 Error: 0.023594 Align patch 6 19 left Iteration 1 Error: 1.088529 Iteration 2 Error: 0.144784 Iteration 3 Error: 0.042562 Align patch 7 18 left Iteration 1 Error: 0.957652 Iteration 2 Error: 0.113313 Iteration 3 Error: 0.023613 Align patch 8 17 left Iteration 1 Error: 1.270307 Iteration 2 Error: 0.144824 Iteration 3 Error: 0.074879 Iteration 4 Error: 0.020210 Align patch 9 16 left Iteration 1 Error: 0.751605 Iteration 2 Error: 0.095445 Iteration 3 Error: 0.023808 Align patch 10 15 left Iteration 1 Error: 0.667966 Iteration 2 Error: 0.075632 Iteration 3 Error: 0.022235 Align patch 11 14 left Iteration 1 Error: 1.103010 Iteration 2 Error: 0.181952 Iteration 3 Error: 0.047657 Align patch 12 13 left Iteration 1 Error: 0.962802 Iteration 2 Error: 0.177840 Iteration 3 Error: 0.057578 Iteration 4 Error: 0.017290 Align patch 13 12 left Iteration 1 Error: 0.736326 Iteration 2 Error: 0.125465 Iteration 3 Error: 0.032209 Align patch 14 11 left Iteration 1 Error: 0.832214 Iteration 2 Error: 0.134007 Iteration 3 Error: 0.024304 Align patch 15 10 left Iteration 1 Error: 0.767613 Iteration 2 Error: 0.095456 Iteration 3 Error: 0.022368 Align patch 16 9 left Iteration 1 Error: 1.415388 Iteration 2 Error: 0.170811 Iteration 3 Error: 0.045203 Align patch 17 8 left Iteration 1 Error: 0.683335 Iteration 2 Error: 0.103028 Iteration 3 Error: 0.028929 Align patch 18 7 left Iteration 1 Error: 1.118782 Iteration 2 Error: 0.245213 Iteration 3 Error: 0.060900 Iteration 4 Error: 0.024027 Align patch 19 6 left Iteration 1 Error: 0.924405 Iteration 2 Error: 0.232425 Iteration 3 Error: 0.063150 Iteration 4 Error: 0.025698 Align patch 20 5 left Iteration 1 Error: 0.694050 Iteration 2 Error: 0.096583 Iteration 3 Error: 0.021376 Align patch 21 4 left Iteration 1 Error: 1.793139 Iteration 2 Error: 0.410594 Iteration 3 Error: 0.098109 Iteration 4 Error: 0.032478 Align patch 22 3 left Iteration 1 Error: 0.659322 Iteration 2 Error: 0.107980 Iteration 3 Error: 0.028521 Align patch 23 2 left Iteration 1 Error: 0.570959 Iteration 2 Error: 0.122872 Iteration 3 Error: 0.038960 Align patch 24 1 left Iteration 1 Error: 1.048211 Iteration 2 Error: 0.120595 Iteration 3 Error: 0.026896 Align patch 25 0 left Iteration 1 Error: 0.834843 Iteration 2 Error: 0.196811 Iteration 3 Error: 0.031412 3D Fitting completed. Patch alignment time: 14.90(sec) Local motion has been corrected. Process thread exits. Computational time: 23.421335 sec Total time: 29.037611 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00010hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00010hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.701673s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00010hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.784774s ........................................ >>>>>>TIME<<<<<< FFT: 0.940150s Defocus_U Defocus_V Angle CCC 10917.64 10519.93 84.95 0.045258 Final Values Defocus_U Defocus_V Angle CCC 10931.70 10480.87 85.27 0.084746 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00010hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00010hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.996e-02 CC threshold: 0.734 Mean Std: 48.46 7.53 Num Hot pixels: 233 Hot pixel threshold: 93.64 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.818249 Iteration 2 Error: 0.076123 Iteration 3 Error: 0.019720 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.30 -0.17 ...... Frame ( 3) shift: -0.59 -0.33 ...... Frame ( 4) shift: -0.89 -0.50 ...... Frame ( 5) shift: -1.18 -0.66 ...... Frame ( 6) shift: -1.32 -0.68 ...... Frame ( 7) shift: -1.30 -0.55 ...... Frame ( 8) shift: -1.27 -0.42 ...... Frame ( 9) shift: -1.26 -0.31 ...... Frame ( 10) shift: -1.25 -0.22 ...... Frame ( 11) shift: -1.25 -0.13 ...... Frame ( 12) shift: -1.23 -0.08 ...... Frame ( 13) shift: -1.20 -0.07 ...... Frame ( 14) shift: -1.17 -0.06 ...... Frame ( 15) shift: -1.16 -0.02 ...... Frame ( 16) shift: -1.17 0.07 ...... Frame ( 17) shift: -1.18 0.15 ...... Frame ( 18) shift: -1.18 0.21 ...... Frame ( 19) shift: -1.17 0.24 ...... Frame ( 20) shift: -1.16 0.27 ...... Frame ( 21) shift: -1.17 0.28 ...... Frame ( 22) shift: -1.18 0.29 ...... Frame ( 23) shift: -1.19 0.30 ...... Frame ( 24) shift: -1.21 0.31 ...... Frame ( 25) shift: -1.24 0.32 ...... Frame ( 26) shift: -1.26 0.34 ...... Frame ( 27) shift: -1.27 0.34 ...... Frame ( 28) shift: -1.26 0.34 ...... Frame ( 29) shift: -1.24 0.34 ...... Frame ( 30) shift: -1.23 0.33 ...... Frame ( 31) shift: -1.22 0.32 ...... Frame ( 32) shift: -1.20 0.31 ...... Frame ( 33) shift: -1.19 0.31 ...... Frame ( 34) shift: -1.18 0.31 ...... Frame ( 35) shift: -1.18 0.30 ...... Frame ( 36) shift: -1.16 0.32 ...... Frame ( 37) shift: -1.13 0.37 ...... Frame ( 38) shift: -1.10 0.42 ...... Frame ( 39) shift: -1.07 0.47 ...... Frame ( 40) shift: -1.04 0.52 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.240024 Iteration 2 Error: 0.268805 Iteration 3 Error: 0.080042 Iteration 4 Error: 0.014559 Align patch 2 23 left Iteration 1 Error: 1.217294 Iteration 2 Error: 0.190360 Iteration 3 Error: 0.050224 Iteration 4 Error: 0.029312 Align patch 3 22 left Iteration 1 Error: 0.762793 Iteration 2 Error: 0.286811 Iteration 3 Error: 0.053697 Iteration 4 Error: 0.021057 Align patch 4 21 left Iteration 1 Error: 1.097339 Iteration 2 Error: 0.213228 Iteration 3 Error: 0.055347 Iteration 4 Error: 0.024633 Align patch 5 20 left Iteration 1 Error: 1.179568 Iteration 2 Error: 0.214760 Iteration 3 Error: 0.070605 Iteration 4 Error: 0.035095 Align patch 6 19 left Iteration 1 Error: 1.094624 Iteration 2 Error: 0.315026 Iteration 3 Error: 0.051007 Iteration 4 Error: 0.019777 Align patch 7 18 left Iteration 1 Error: 0.865283 Iteration 2 Error: 0.202244 Iteration 3 Error: 0.055821 Iteration 4 Error: 0.025467 Align patch 8 17 left Iteration 1 Error: 0.948354 Iteration 2 Error: 0.159636 Iteration 3 Error: 0.035961 Align patch 9 16 left Iteration 1 Error: 0.823157 Iteration 2 Error: 0.164545 Iteration 3 Error: 0.023721 Align patch 10 15 left Iteration 1 Error: 0.909992 Iteration 2 Error: 0.130525 Iteration 3 Error: 0.046716 Align patch 11 14 left Iteration 1 Error: 0.718452 Iteration 2 Error: 0.201623 Iteration 3 Error: 0.076499 Iteration 4 Error: 0.031641 Align patch 12 13 left Iteration 1 Error: 1.090544 Iteration 2 Error: 0.176234 Iteration 3 Error: 0.025716 Align patch 13 12 left Iteration 1 Error: 0.685274 Iteration 2 Error: 0.118227 Iteration 3 Error: 0.030730 Align patch 14 11 left Iteration 1 Error: 0.908142 Iteration 2 Error: 0.160312 Iteration 3 Error: 0.032186 Align patch 15 10 left Iteration 1 Error: 0.920612 Iteration 2 Error: 0.140440 Iteration 3 Error: 0.046709 Align patch 16 9 left Iteration 1 Error: 1.593072 Iteration 2 Error: 0.248157 Iteration 3 Error: 0.055390 Iteration 4 Error: 0.018051 Align patch 17 8 left Iteration 1 Error: 1.434908 Iteration 2 Error: 0.204842 Iteration 3 Error: 0.070971 Iteration 4 Error: 0.015601 Align patch 18 7 left Iteration 1 Error: 0.773773 Iteration 2 Error: 0.179584 Iteration 3 Error: 0.054076 Iteration 4 Error: 0.025010 Align patch 19 6 left Iteration 1 Error: 0.585029 Iteration 2 Error: 0.151053 Iteration 3 Error: 0.029788 Align patch 20 5 left Iteration 1 Error: 0.581482 Iteration 2 Error: 0.162307 Iteration 3 Error: 0.030653 Align patch 21 4 left Iteration 1 Error: 1.312105 Iteration 2 Error: 0.304892 Iteration 3 Error: 0.075348 Iteration 4 Error: 0.016119 Align patch 22 3 left Iteration 1 Error: 0.586001 Iteration 2 Error: 0.103426 Iteration 3 Error: 0.017081 Align patch 23 2 left Iteration 1 Error: 0.929846 Iteration 2 Error: 0.114289 Iteration 3 Error: 0.030559 Align patch 24 1 left Iteration 1 Error: 0.776686 Iteration 2 Error: 0.228167 Iteration 3 Error: 0.066480 Iteration 4 Error: 0.031305 Align patch 25 0 left Iteration 1 Error: 0.809531 Iteration 2 Error: 0.181650 Iteration 3 Error: 0.054388 Iteration 4 Error: 0.028645 3D Fitting completed. Patch alignment time: 16.62(sec) Local motion has been corrected. Process thread exits. Computational time: 25.242798 sec Total time: 31.906183 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00010hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00010hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.579742s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00010hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.797445s ........................................ >>>>>>TIME<<<<<< FFT: 0.947100s Defocus_U Defocus_V Angle CCC 11533.20 12353.52 4.33 0.048380 Final Values Defocus_U Defocus_V Angle CCC 11534.76 12370.71 4.64 0.089949 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00010hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00010hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 48.31 7.59 Num Hot pixels: 239 Hot pixel threshold: 93.83 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.285433 Iteration 2 Error: 0.084987 Iteration 3 Error: 0.022132 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.35 -0.09 ...... Frame ( 3) shift: -0.71 -0.19 ...... Frame ( 4) shift: -1.06 -0.28 ...... Frame ( 5) shift: -1.42 -0.38 ...... Frame ( 6) shift: -1.62 -0.38 ...... Frame ( 7) shift: -1.69 -0.30 ...... Frame ( 8) shift: -1.75 -0.21 ...... Frame ( 9) shift: -1.76 -0.12 ...... Frame ( 10) shift: -1.73 -0.02 ...... Frame ( 11) shift: -1.69 0.09 ...... Frame ( 12) shift: -1.69 0.17 ...... Frame ( 13) shift: -1.74 0.22 ...... Frame ( 14) shift: -1.79 0.28 ...... Frame ( 15) shift: -1.78 0.31 ...... Frame ( 16) shift: -1.72 0.33 ...... Frame ( 17) shift: -1.65 0.34 ...... Frame ( 18) shift: -1.63 0.41 ...... Frame ( 19) shift: -1.65 0.53 ...... Frame ( 20) shift: -1.67 0.65 ...... Frame ( 21) shift: -1.69 0.68 ...... Frame ( 22) shift: -1.70 0.60 ...... Frame ( 23) shift: -1.72 0.52 ...... Frame ( 24) shift: -1.76 0.50 ...... Frame ( 25) shift: -1.83 0.54 ...... Frame ( 26) shift: -1.90 0.57 ...... Frame ( 27) shift: -1.94 0.59 ...... Frame ( 28) shift: -1.96 0.59 ...... Frame ( 29) shift: -1.98 0.60 ...... Frame ( 30) shift: -1.98 0.62 ...... Frame ( 31) shift: -1.94 0.66 ...... Frame ( 32) shift: -1.90 0.71 ...... Frame ( 33) shift: -1.89 0.75 ...... Frame ( 34) shift: -1.92 0.80 ...... Frame ( 35) shift: -1.95 0.86 ...... Frame ( 36) shift: -1.98 0.89 ...... Frame ( 37) shift: -2.01 0.90 ...... Frame ( 38) shift: -2.04 0.91 ...... Frame ( 39) shift: -2.07 0.92 ...... Frame ( 40) shift: -2.11 0.93 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.546123 Iteration 2 Error: 0.382585 Iteration 3 Error: 0.181510 Iteration 4 Error: 0.096701 Iteration 5 Error: 0.047013 Align patch 2 23 left Iteration 1 Error: 1.501983 Iteration 2 Error: 0.174727 Iteration 3 Error: 0.063769 Iteration 4 Error: 0.016189 Align patch 3 22 left Iteration 1 Error: 1.900398 Iteration 2 Error: 0.549151 Iteration 3 Error: 0.193923 Iteration 4 Error: 0.122545 Iteration 5 Error: 0.050747 Align patch 3 22 left Iteration 1 Error: 1.783049 Iteration 2 Error: 0.260138 Iteration 3 Error: 0.033571 Align patch 4 21 left Iteration 1 Error: 0.649793 Iteration 2 Error: 0.146005 Iteration 3 Error: 0.066358 Iteration 4 Error: 0.025735 Align patch 5 20 left Iteration 1 Error: 1.229075 Iteration 2 Error: 0.319033 Iteration 3 Error: 0.055868 Iteration 4 Error: 0.045330 Align patch 6 19 left Iteration 1 Error: 1.402280 Iteration 2 Error: 0.263840 Iteration 3 Error: 0.054372 Iteration 4 Error: 0.015273 Align patch 7 18 left Iteration 1 Error: 0.715632 Iteration 2 Error: 0.098034 Iteration 3 Error: 0.016681 Align patch 8 17 left Iteration 1 Error: 0.973333 Iteration 2 Error: 0.213857 Iteration 3 Error: 0.047361 Align patch 9 16 left Iteration 1 Error: 0.734145 Iteration 2 Error: 0.170512 Iteration 3 Error: 0.031509 Align patch 10 15 left Iteration 1 Error: 0.893490 Iteration 2 Error: 0.152659 Iteration 3 Error: 0.037782 Align patch 11 14 left Iteration 1 Error: 1.415101 Iteration 2 Error: 0.272129 Iteration 3 Error: 0.057416 Iteration 4 Error: 0.024272 Align patch 12 13 left Iteration 1 Error: 1.276711 Iteration 2 Error: 0.088689 Iteration 3 Error: 0.019395 Align patch 13 12 left Iteration 1 Error: 0.718087 Iteration 2 Error: 0.116383 Iteration 3 Error: 0.029563 Align patch 14 11 left Iteration 1 Error: 0.710869 Iteration 2 Error: 0.144855 Iteration 3 Error: 0.049700 Align patch 15 10 left Iteration 1 Error: 0.653728 Iteration 2 Error: 0.094544 Iteration 3 Error: 0.026318 Align patch 16 9 left Iteration 1 Error: 1.139562 Iteration 2 Error: 0.190140 Iteration 3 Error: 0.042254 Align patch 17 8 left Iteration 1 Error: 0.911375 Iteration 2 Error: 0.139154 Iteration 3 Error: 0.053212 Iteration 4 Error: 0.009502 Align patch 18 7 left Iteration 1 Error: 0.741051 Iteration 2 Error: 0.115145 Iteration 3 Error: 0.029056 Align patch 19 6 left Iteration 1 Error: 0.594534 Iteration 2 Error: 0.116844 Iteration 3 Error: 0.041796 Align patch 20 5 left Iteration 1 Error: 0.625985 Iteration 2 Error: 0.118690 Iteration 3 Error: 0.042507 Align patch 21 4 left Iteration 1 Error: 1.126913 Iteration 2 Error: 0.148919 Iteration 3 Error: 0.026355 Align patch 22 3 left Iteration 1 Error: 1.404089 Iteration 2 Error: 0.328827 Iteration 3 Error: 0.080091 Iteration 4 Error: 0.041595 Align patch 23 2 left Iteration 1 Error: 1.123096 Iteration 2 Error: 0.120167 Iteration 3 Error: 0.028484 Align patch 24 1 left Iteration 1 Error: 0.656991 Iteration 2 Error: 0.112575 Iteration 3 Error: 0.016671 Align patch 25 0 left Iteration 1 Error: 0.858366 Iteration 2 Error: 0.080143 Iteration 3 Error: 0.017657 3D Fitting completed. Patch alignment time: 16.75(sec) Local motion has been corrected. Process thread exits. Computational time: 25.660477 sec Total time: 32.089859 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00010hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00010hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.580920s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00010hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.696931s ........................................ >>>>>>TIME<<<<<< FFT: 1.054556s Defocus_U Defocus_V Angle CCC 13027.39 12363.30 84.97 0.047845 Final Values Defocus_U Defocus_V Angle CCC 13032.07 12358.63 85.29 0.086031 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00011hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00011hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 44.93 7.66 Num Hot pixels: 186 Hot pixel threshold: 90.90 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.332336 Iteration 2 Error: 0.289585 Iteration 3 Error: 0.091949 Iteration 4 Error: 0.028412 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.46 -0.03 ...... Frame ( 3) shift: -0.91 -0.07 ...... Frame ( 4) shift: -1.37 -0.10 ...... Frame ( 5) shift: -1.82 -0.14 ...... Frame ( 6) shift: -2.05 -0.12 ...... Frame ( 7) shift: -2.04 -0.06 ...... Frame ( 8) shift: -2.03 0.01 ...... Frame ( 9) shift: -2.00 0.07 ...... Frame ( 10) shift: -1.95 0.14 ...... Frame ( 11) shift: -1.91 0.20 ...... Frame ( 12) shift: -1.87 0.29 ...... Frame ( 13) shift: -1.85 0.39 ...... Frame ( 14) shift: -1.83 0.49 ...... Frame ( 15) shift: -1.82 0.60 ...... Frame ( 16) shift: -1.83 0.71 ...... Frame ( 17) shift: -1.84 0.83 ...... Frame ( 18) shift: -1.83 0.94 ...... Frame ( 19) shift: -1.80 1.03 ...... Frame ( 20) shift: -1.76 1.13 ...... Frame ( 21) shift: -1.74 1.23 ...... Frame ( 22) shift: -1.72 1.31 ...... Frame ( 23) shift: -1.69 1.39 ...... Frame ( 24) shift: -1.65 1.48 ...... Frame ( 25) shift: -1.58 1.58 ...... Frame ( 26) shift: -1.52 1.68 ...... Frame ( 27) shift: -1.48 1.73 ...... Frame ( 28) shift: -1.47 1.74 ...... Frame ( 29) shift: -1.46 1.75 ...... Frame ( 30) shift: -1.45 1.82 ...... Frame ( 31) shift: -1.44 1.93 ...... Frame ( 32) shift: -1.44 2.05 ...... Frame ( 33) shift: -1.40 2.14 ...... Frame ( 34) shift: -1.33 2.22 ...... Frame ( 35) shift: -1.26 2.30 ...... Frame ( 36) shift: -1.22 2.35 ...... Frame ( 37) shift: -1.21 2.38 ...... Frame ( 38) shift: -1.20 2.40 ...... Frame ( 39) shift: -1.19 2.42 ...... Frame ( 40) shift: -1.18 2.44 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 5.930486 Iteration 2 Error: 1.535843 Iteration 3 Error: 0.871882 Iteration 4 Error: 0.425070 Iteration 5 Error: 0.303872 Align patch 1 24 left Iteration 1 Error: 3.384948 Iteration 2 Error: 0.989933 Iteration 3 Error: 0.347794 Iteration 4 Error: 0.141507 Iteration 5 Error: 0.067960 Align patch 2 23 left Iteration 1 Error: 2.310957 Iteration 2 Error: 0.687304 Iteration 3 Error: 0.369616 Iteration 4 Error: 0.166323 Iteration 5 Error: 0.081739 Align patch 2 23 left Iteration 1 Error: 2.694560 Iteration 2 Error: 0.660386 Iteration 3 Error: 0.256337 Iteration 4 Error: 0.097664 Iteration 5 Error: 0.041386 Align patch 3 22 left Iteration 1 Error: 1.166752 Iteration 2 Error: 0.278325 Iteration 3 Error: 0.130389 Iteration 4 Error: 0.043185 Align patch 4 21 left Iteration 1 Error: 0.785636 Iteration 2 Error: 0.091920 Iteration 3 Error: 0.030417 Align patch 5 20 left Iteration 1 Error: 0.895317 Iteration 2 Error: 0.163110 Iteration 3 Error: 0.041885 Align patch 6 19 left Iteration 1 Error: 2.206735 Iteration 2 Error: 0.429191 Iteration 3 Error: 0.188938 Iteration 4 Error: 0.105049 Iteration 5 Error: 0.062257 Align patch 6 19 left Iteration 1 Error: 3.273722 Iteration 2 Error: 0.765466 Iteration 3 Error: 0.225054 Iteration 4 Error: 0.074408 Iteration 5 Error: 0.039090 Align patch 7 18 left Iteration 1 Error: 2.255704 Iteration 2 Error: 1.106809 Iteration 3 Error: 0.499965 Iteration 4 Error: 0.193556 Iteration 5 Error: 0.149758 Align patch 7 18 left Iteration 1 Error: 3.115221 Iteration 2 Error: 0.596811 Iteration 3 Error: 0.175839 Iteration 4 Error: 0.063371 Iteration 5 Error: 0.040359 Align patch 8 17 left Iteration 1 Error: 0.855650 Iteration 2 Error: 0.182033 Iteration 3 Error: 0.083022 Iteration 4 Error: 0.030653 Align patch 9 16 left Iteration 1 Error: 0.696256 Iteration 2 Error: 0.120465 Iteration 3 Error: 0.016746 Align patch 10 15 left Iteration 1 Error: 0.605638 Iteration 2 Error: 0.129180 Iteration 3 Error: 0.038193 Align patch 11 14 left Iteration 1 Error: 0.987092 Iteration 2 Error: 0.399787 Iteration 3 Error: 0.160202 Iteration 4 Error: 0.115891 Iteration 5 Error: 0.054846 Align patch 11 14 left Iteration 1 Error: 1.546174 Iteration 2 Error: 0.269069 Iteration 3 Error: 0.071435 Iteration 4 Error: 0.047330 Align patch 12 13 left Iteration 1 Error: 2.472354 Iteration 2 Error: 0.224074 Iteration 3 Error: 0.121005 Iteration 4 Error: 0.034189 Align patch 13 12 left Iteration 1 Error: 1.233923 Iteration 2 Error: 0.179408 Iteration 3 Error: 0.047790 Align patch 14 11 left Iteration 1 Error: 1.218236 Iteration 2 Error: 0.149799 Iteration 3 Error: 0.047382 Align patch 15 10 left Iteration 1 Error: 0.789364 Iteration 2 Error: 0.122646 Iteration 3 Error: 0.026043 Align patch 16 9 left Iteration 1 Error: 0.529946 Iteration 2 Error: 0.133517 Iteration 3 Error: 0.065425 Iteration 4 Error: 0.018964 Align patch 17 8 left Iteration 1 Error: 0.983739 Iteration 2 Error: 0.144634 Iteration 3 Error: 0.042749 Align patch 18 7 left Iteration 1 Error: 1.259893 Iteration 2 Error: 0.175301 Iteration 3 Error: 0.056190 Iteration 4 Error: 0.022981 Align patch 19 6 left Iteration 1 Error: 1.502469 Iteration 2 Error: 0.353451 Iteration 3 Error: 0.102739 Iteration 4 Error: 0.031316 Align patch 20 5 left Iteration 1 Error: 0.882977 Iteration 2 Error: 0.162167 Iteration 3 Error: 0.026554 Align patch 21 4 left Iteration 1 Error: 1.608552 Iteration 2 Error: 0.273589 Iteration 3 Error: 0.063615 Iteration 4 Error: 0.023150 Align patch 22 3 left Iteration 1 Error: 1.680255 Iteration 2 Error: 0.264138 Iteration 3 Error: 0.054113 Iteration 4 Error: 0.018589 Align patch 23 2 left Iteration 1 Error: 1.007006 Iteration 2 Error: 0.174746 Iteration 3 Error: 0.041311 Align patch 24 1 left Iteration 1 Error: 1.044140 Iteration 2 Error: 0.154734 Iteration 3 Error: 0.025778 Align patch 25 0 left Iteration 1 Error: 1.079016 Iteration 2 Error: 0.236520 Iteration 3 Error: 0.037114 3D Fitting completed. Patch alignment time: 20.40(sec) Local motion has been corrected. Process thread exits. Computational time: 29.083445 sec Total time: 35.089977 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00011hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00011hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.743012s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00011hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.095086s ........................................ >>>>>>TIME<<<<<< FFT: 1.259445s Defocus_U Defocus_V Angle CCC 9578.13 10425.78 10.37 0.042620 Final Values Defocus_U Defocus_V Angle CCC 9585.94 10430.47 11.62 0.086116 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00011hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00011hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 46.20 7.71 Num Hot pixels: 194 Hot pixel threshold: 92.47 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.091197 Iteration 2 Error: 0.089102 Iteration 3 Error: 0.020252 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.28 -0.01 ...... Frame ( 3) shift: -0.56 -0.02 ...... Frame ( 4) shift: -0.83 -0.03 ...... Frame ( 5) shift: -1.11 -0.04 ...... Frame ( 6) shift: -1.26 0.00 ...... Frame ( 7) shift: -1.29 0.09 ...... Frame ( 8) shift: -1.31 0.18 ...... Frame ( 9) shift: -1.32 0.28 ...... Frame ( 10) shift: -1.32 0.37 ...... Frame ( 11) shift: -1.32 0.46 ...... Frame ( 12) shift: -1.31 0.55 ...... Frame ( 13) shift: -1.29 0.63 ...... Frame ( 14) shift: -1.28 0.72 ...... Frame ( 15) shift: -1.30 0.76 ...... Frame ( 16) shift: -1.36 0.76 ...... Frame ( 17) shift: -1.42 0.77 ...... Frame ( 18) shift: -1.45 0.78 ...... Frame ( 19) shift: -1.44 0.81 ...... Frame ( 20) shift: -1.43 0.85 ...... Frame ( 21) shift: -1.41 0.88 ...... Frame ( 22) shift: -1.38 0.91 ...... Frame ( 23) shift: -1.35 0.94 ...... Frame ( 24) shift: -1.33 0.95 ...... Frame ( 25) shift: -1.33 0.95 ...... Frame ( 26) shift: -1.33 0.95 ...... Frame ( 27) shift: -1.34 0.93 ...... Frame ( 28) shift: -1.36 0.88 ...... Frame ( 29) shift: -1.38 0.84 ...... Frame ( 30) shift: -1.38 0.82 ...... Frame ( 31) shift: -1.37 0.83 ...... Frame ( 32) shift: -1.36 0.84 ...... Frame ( 33) shift: -1.36 0.89 ...... Frame ( 34) shift: -1.38 0.96 ...... Frame ( 35) shift: -1.41 1.04 ...... Frame ( 36) shift: -1.45 1.09 ...... Frame ( 37) shift: -1.50 1.12 ...... Frame ( 38) shift: -1.55 1.16 ...... Frame ( 39) shift: -1.60 1.19 ...... Frame ( 40) shift: -1.65 1.22 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.511333 Iteration 2 Error: 0.198624 Iteration 3 Error: 0.043262 Align patch 2 23 left Iteration 1 Error: 1.051732 Iteration 2 Error: 0.155523 Iteration 3 Error: 0.036129 Align patch 3 22 left Iteration 1 Error: 1.186208 Iteration 2 Error: 0.192074 Iteration 3 Error: 0.059508 Iteration 4 Error: 0.028702 Align patch 4 21 left Iteration 1 Error: 0.985424 Iteration 2 Error: 0.121005 Iteration 3 Error: 0.033518 Align patch 5 20 left Iteration 1 Error: 0.862526 Iteration 2 Error: 0.109357 Iteration 3 Error: 0.021651 Align patch 6 19 left Iteration 1 Error: 0.684845 Iteration 2 Error: 0.094535 Iteration 3 Error: 0.016534 Align patch 7 18 left Iteration 1 Error: 0.964895 Iteration 2 Error: 0.291171 Iteration 3 Error: 0.068918 Iteration 4 Error: 0.035123 Align patch 8 17 left Iteration 1 Error: 1.361831 Iteration 2 Error: 0.174448 Iteration 3 Error: 0.078598 Iteration 4 Error: 0.017219 Align patch 9 16 left Iteration 1 Error: 0.936958 Iteration 2 Error: 0.202727 Iteration 3 Error: 0.069106 Iteration 4 Error: 0.024122 Align patch 10 15 left Iteration 1 Error: 0.939604 Iteration 2 Error: 0.136916 Iteration 3 Error: 0.026163 Align patch 11 14 left Iteration 1 Error: 1.446148 Iteration 2 Error: 0.175751 Iteration 3 Error: 0.047437 Align patch 12 13 left Iteration 1 Error: 0.918302 Iteration 2 Error: 0.156640 Iteration 3 Error: 0.036722 Align patch 13 12 left Iteration 1 Error: 0.859021 Iteration 2 Error: 0.092928 Iteration 3 Error: 0.029333 Align patch 14 11 left Iteration 1 Error: 0.597319 Iteration 2 Error: 0.088769 Iteration 3 Error: 0.024717 Align patch 15 10 left Iteration 1 Error: 0.626738 Iteration 2 Error: 0.116101 Iteration 3 Error: 0.027962 Align patch 16 9 left Iteration 1 Error: 1.328978 Iteration 2 Error: 0.167658 Iteration 3 Error: 0.047711 Align patch 17 8 left Iteration 1 Error: 0.658172 Iteration 2 Error: 0.121984 Iteration 3 Error: 0.033559 Align patch 18 7 left Iteration 1 Error: 0.618984 Iteration 2 Error: 0.130448 Iteration 3 Error: 0.046486 Align patch 19 6 left Iteration 1 Error: 0.948972 Iteration 2 Error: 0.132147 Iteration 3 Error: 0.021369 Align patch 20 5 left Iteration 1 Error: 0.683449 Iteration 2 Error: 0.059538 Iteration 3 Error: 0.015035 Align patch 21 4 left Iteration 1 Error: 0.994155 Iteration 2 Error: 0.177239 Iteration 3 Error: 0.033835 Align patch 22 3 left Iteration 1 Error: 0.992181 Iteration 2 Error: 0.217521 Iteration 3 Error: 0.095264 Iteration 4 Error: 0.039291 Align patch 23 2 left Iteration 1 Error: 0.754176 Iteration 2 Error: 0.127873 Iteration 3 Error: 0.025261 Align patch 24 1 left Iteration 1 Error: 1.405759 Iteration 2 Error: 0.161588 Iteration 3 Error: 0.031929 Align patch 25 0 left Iteration 1 Error: 0.542942 Iteration 2 Error: 0.073733 Iteration 3 Error: 0.014911 3D Fitting completed. Patch alignment time: 15.35(sec) Local motion has been corrected. Process thread exits. Computational time: 24.037392 sec Total time: 30.522404 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00011hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00011hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.605531s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00011hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.779466s ........................................ >>>>>>TIME<<<<<< FFT: 0.938486s Defocus_U Defocus_V Angle CCC 12910.15 13402.39 3.83 0.050935 Final Values Defocus_U Defocus_V Angle CCC 12907.02 13399.27 1.34 0.088191 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00011hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00011hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 9.999e-02 CC threshold: 0.734 Mean Std: 46.28 7.58 Num Hot pixels: 208 Hot pixel threshold: 91.75 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.450945 Iteration 2 Error: 0.088877 Iteration 3 Error: 0.024478 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.43 -0.05 ...... Frame ( 3) shift: -0.86 -0.09 ...... Frame ( 4) shift: -1.29 -0.14 ...... Frame ( 5) shift: -1.72 -0.19 ...... Frame ( 6) shift: -1.98 -0.20 ...... Frame ( 7) shift: -2.06 -0.19 ...... Frame ( 8) shift: -2.13 -0.18 ...... Frame ( 9) shift: -2.17 -0.14 ...... Frame ( 10) shift: -2.17 -0.07 ...... Frame ( 11) shift: -2.16 -0.00 ...... Frame ( 12) shift: -2.15 0.04 ...... Frame ( 13) shift: -2.13 0.05 ...... Frame ( 14) shift: -2.10 0.06 ...... Frame ( 15) shift: -2.10 0.09 ...... Frame ( 16) shift: -2.11 0.14 ...... Frame ( 17) shift: -2.13 0.19 ...... Frame ( 18) shift: -2.13 0.24 ...... Frame ( 19) shift: -2.11 0.27 ...... Frame ( 20) shift: -2.10 0.30 ...... Frame ( 21) shift: -2.08 0.34 ...... Frame ( 22) shift: -2.05 0.37 ...... Frame ( 23) shift: -2.02 0.41 ...... Frame ( 24) shift: -2.02 0.45 ...... Frame ( 25) shift: -2.04 0.48 ...... Frame ( 26) shift: -2.07 0.51 ...... Frame ( 27) shift: -2.08 0.51 ...... Frame ( 28) shift: -2.08 0.49 ...... Frame ( 29) shift: -2.08 0.47 ...... Frame ( 30) shift: -2.06 0.47 ...... Frame ( 31) shift: -2.03 0.48 ...... Frame ( 32) shift: -2.00 0.50 ...... Frame ( 33) shift: -2.01 0.51 ...... Frame ( 34) shift: -2.06 0.53 ...... Frame ( 35) shift: -2.12 0.55 ...... Frame ( 36) shift: -2.15 0.59 ...... Frame ( 37) shift: -2.17 0.64 ...... Frame ( 38) shift: -2.19 0.69 ...... Frame ( 39) shift: -2.20 0.74 ...... Frame ( 40) shift: -2.22 0.79 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.699147 Iteration 2 Error: 0.442492 Iteration 3 Error: 0.091132 Iteration 4 Error: 0.019501 Align patch 2 23 left Iteration 1 Error: 1.050779 Iteration 2 Error: 0.183392 Iteration 3 Error: 0.055013 Iteration 4 Error: 0.015647 Align patch 3 22 left Iteration 1 Error: 0.751864 Iteration 2 Error: 0.126682 Iteration 3 Error: 0.040955 Align patch 4 21 left Iteration 1 Error: 0.633325 Iteration 2 Error: 0.134201 Iteration 3 Error: 0.033295 Align patch 5 20 left Iteration 1 Error: 0.647154 Iteration 2 Error: 0.068644 Iteration 3 Error: 0.018126 Align patch 6 19 left Iteration 1 Error: 0.871053 Iteration 2 Error: 0.281764 Iteration 3 Error: 0.056214 Iteration 4 Error: 0.028967 Align patch 7 18 left Iteration 1 Error: 1.231153 Iteration 2 Error: 0.196397 Iteration 3 Error: 0.057060 Iteration 4 Error: 0.018235 Align patch 8 17 left Iteration 1 Error: 0.798162 Iteration 2 Error: 0.088640 Iteration 3 Error: 0.021734 Align patch 9 16 left Iteration 1 Error: 0.641001 Iteration 2 Error: 0.085119 Iteration 3 Error: 0.041136 Align patch 10 15 left Iteration 1 Error: 0.669748 Iteration 2 Error: 0.159997 Iteration 3 Error: 0.030144 Align patch 11 14 left Iteration 1 Error: 0.992937 Iteration 2 Error: 0.266100 Iteration 3 Error: 0.043248 Align patch 12 13 left Iteration 1 Error: 0.616581 Iteration 2 Error: 0.076098 Iteration 3 Error: 0.023746 Align patch 13 12 left Iteration 1 Error: 0.816441 Iteration 2 Error: 0.155824 Iteration 3 Error: 0.067180 Iteration 4 Error: 0.032211 Align patch 14 11 left Iteration 1 Error: 0.846913 Iteration 2 Error: 0.213565 Iteration 3 Error: 0.083866 Iteration 4 Error: 0.039070 Align patch 15 10 left Iteration 1 Error: 0.760114 Iteration 2 Error: 0.108379 Iteration 3 Error: 0.020602 Align patch 16 9 left Iteration 1 Error: 1.094470 Iteration 2 Error: 0.130125 Iteration 3 Error: 0.047123 Align patch 17 8 left Iteration 1 Error: 0.821458 Iteration 2 Error: 0.195175 Iteration 3 Error: 0.059527 Iteration 4 Error: 0.024464 Align patch 18 7 left Iteration 1 Error: 0.874964 Iteration 2 Error: 0.176488 Iteration 3 Error: 0.031643 Align patch 19 6 left Iteration 1 Error: 0.950503 Iteration 2 Error: 0.100770 Iteration 3 Error: 0.024327 Align patch 20 5 left Iteration 1 Error: 0.650644 Iteration 2 Error: 0.096143 Iteration 3 Error: 0.028033 Align patch 21 4 left Iteration 1 Error: 1.356971 Iteration 2 Error: 0.128057 Iteration 3 Error: 0.026156 Align patch 22 3 left Iteration 1 Error: 0.883237 Iteration 2 Error: 0.095739 Iteration 3 Error: 0.036616 Align patch 23 2 left Iteration 1 Error: 1.202324 Iteration 2 Error: 0.137331 Iteration 3 Error: 0.023843 Align patch 24 1 left Iteration 1 Error: 0.540562 Iteration 2 Error: 0.083385 Iteration 3 Error: 0.019914 Align patch 25 0 left Iteration 1 Error: 0.767957 Iteration 2 Error: 0.161290 Iteration 3 Error: 0.031341 3D Fitting completed. Patch alignment time: 15.64(sec) Local motion has been corrected. Process thread exits. Computational time: 24.077694 sec Total time: 29.916218 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00011hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00011hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.808680s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00011hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.122828s ........................................ >>>>>>TIME<<<<<< FFT: 1.049570s Defocus_U Defocus_V Angle CCC 11816.42 12699.30 6.18 0.046200 Final Values Defocus_U Defocus_V Angle CCC 11832.05 12702.44 6.18 0.083057 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00011hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00011hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 47.06 7.65 Num Hot pixels: 212 Hot pixel threshold: 92.94 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.071498 Iteration 2 Error: 0.065308 Iteration 3 Error: 0.016585 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.36 0.02 ...... Frame ( 3) shift: -0.71 0.05 ...... Frame ( 4) shift: -1.07 0.07 ...... Frame ( 5) shift: -1.42 0.09 ...... Frame ( 6) shift: -1.61 0.10 ...... Frame ( 7) shift: -1.64 0.09 ...... Frame ( 8) shift: -1.66 0.07 ...... Frame ( 9) shift: -1.65 0.14 ...... Frame ( 10) shift: -1.62 0.28 ...... Frame ( 11) shift: -1.58 0.42 ...... Frame ( 12) shift: -1.57 0.49 ...... Frame ( 13) shift: -1.58 0.49 ...... Frame ( 14) shift: -1.60 0.50 ...... Frame ( 15) shift: -1.59 0.47 ...... Frame ( 16) shift: -1.58 0.41 ...... Frame ( 17) shift: -1.56 0.35 ...... Frame ( 18) shift: -1.53 0.36 ...... Frame ( 19) shift: -1.49 0.44 ...... Frame ( 20) shift: -1.45 0.52 ...... Frame ( 21) shift: -1.42 0.59 ...... Frame ( 22) shift: -1.41 0.65 ...... Frame ( 23) shift: -1.40 0.70 ...... Frame ( 24) shift: -1.42 0.74 ...... Frame ( 25) shift: -1.46 0.74 ...... Frame ( 26) shift: -1.50 0.75 ...... Frame ( 27) shift: -1.49 0.74 ...... Frame ( 28) shift: -1.42 0.70 ...... Frame ( 29) shift: -1.36 0.66 ...... Frame ( 30) shift: -1.36 0.65 ...... Frame ( 31) shift: -1.44 0.67 ...... Frame ( 32) shift: -1.53 0.68 ...... Frame ( 33) shift: -1.56 0.70 ...... Frame ( 34) shift: -1.55 0.74 ...... Frame ( 35) shift: -1.53 0.78 ...... Frame ( 36) shift: -1.55 0.83 ...... Frame ( 37) shift: -1.58 0.87 ...... Frame ( 38) shift: -1.62 0.92 ...... Frame ( 39) shift: -1.66 0.97 ...... Frame ( 40) shift: -1.70 1.01 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.905434 Iteration 2 Error: 0.134874 Iteration 3 Error: 0.052562 Iteration 4 Error: 0.021327 Align patch 2 23 left Iteration 1 Error: 1.480699 Iteration 2 Error: 0.220277 Iteration 3 Error: 0.068968 Iteration 4 Error: 0.023708 Align patch 3 22 left Iteration 1 Error: 0.947411 Iteration 2 Error: 0.160641 Iteration 3 Error: 0.073734 Iteration 4 Error: 0.024973 Align patch 4 21 left Iteration 1 Error: 0.678707 Iteration 2 Error: 0.114964 Iteration 3 Error: 0.023883 Align patch 5 20 left Iteration 1 Error: 0.898090 Iteration 2 Error: 0.084752 Iteration 3 Error: 0.017988 Align patch 6 19 left Iteration 1 Error: 0.739557 Iteration 2 Error: 0.098351 Iteration 3 Error: 0.026961 Align patch 7 18 left Iteration 1 Error: 1.495371 Iteration 2 Error: 0.300055 Iteration 3 Error: 0.082805 Iteration 4 Error: 0.038805 Align patch 8 17 left Iteration 1 Error: 1.021494 Iteration 2 Error: 0.155319 Iteration 3 Error: 0.034601 Align patch 9 16 left Iteration 1 Error: 0.912673 Iteration 2 Error: 0.113956 Iteration 3 Error: 0.029366 Align patch 10 15 left Iteration 1 Error: 0.514115 Iteration 2 Error: 0.047024 Align patch 11 14 left Iteration 1 Error: 0.496568 Iteration 2 Error: 0.079802 Iteration 3 Error: 0.024423 Align patch 12 13 left Iteration 1 Error: 0.943340 Iteration 2 Error: 0.196621 Iteration 3 Error: 0.041527 Align patch 13 12 left Iteration 1 Error: 0.947040 Iteration 2 Error: 0.136177 Iteration 3 Error: 0.051515 Iteration 4 Error: 0.026254 Align patch 14 11 left Iteration 1 Error: 1.098067 Iteration 2 Error: 0.110810 Iteration 3 Error: 0.021390 Align patch 15 10 left Iteration 1 Error: 0.713750 Iteration 2 Error: 0.103500 Iteration 3 Error: 0.022593 Align patch 16 9 left Iteration 1 Error: 1.451462 Iteration 2 Error: 0.215040 Iteration 3 Error: 0.047697 Align patch 17 8 left Iteration 1 Error: 0.905941 Iteration 2 Error: 0.179315 Iteration 3 Error: 0.035197 Align patch 18 7 left Iteration 1 Error: 0.907987 Iteration 2 Error: 0.155371 Iteration 3 Error: 0.037748 Align patch 19 6 left Iteration 1 Error: 1.625013 Iteration 2 Error: 0.300016 Iteration 3 Error: 0.077648 Iteration 4 Error: 0.021680 Align patch 20 5 left Iteration 1 Error: 0.724143 Iteration 2 Error: 0.108465 Iteration 3 Error: 0.024928 Align patch 21 4 left Iteration 1 Error: 1.333468 Iteration 2 Error: 0.226853 Iteration 3 Error: 0.048096 Align patch 22 3 left Iteration 1 Error: 0.834291 Iteration 2 Error: 0.088922 Iteration 3 Error: 0.025606 Align patch 23 2 left Iteration 1 Error: 0.799267 Iteration 2 Error: 0.100148 Iteration 3 Error: 0.026799 Align patch 24 1 left Iteration 1 Error: 0.831792 Iteration 2 Error: 0.060885 Iteration 3 Error: 0.016175 Align patch 25 0 left Iteration 1 Error: 0.785347 Iteration 2 Error: 0.108194 Iteration 3 Error: 0.035933 3D Fitting completed. Patch alignment time: 15.85(sec) Local motion has been corrected. Process thread exits. Computational time: 25.353481 sec Total time: 31.227200 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00011hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00011hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.726261s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00011hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.956680s ........................................ >>>>>>TIME<<<<<< FFT: 0.972390s Defocus_U Defocus_V Angle CCC 11210.97 10570.28 82.29 0.049772 Final Values Defocus_U Defocus_V Angle CCC 11235.99 10579.72 82.61 0.092763 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00012hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00012hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.001e-01 CC threshold: 0.735 Mean Std: 46.15 7.64 Num Hot pixels: 216 Hot pixel threshold: 91.96 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.804504 Iteration 2 Error: 0.049888 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.34 -0.08 ...... Frame ( 3) shift: -0.69 -0.16 ...... Frame ( 4) shift: -1.03 -0.25 ...... Frame ( 5) shift: -1.37 -0.33 ...... Frame ( 6) shift: -1.53 -0.34 ...... Frame ( 7) shift: -1.49 -0.27 ...... Frame ( 8) shift: -1.46 -0.20 ...... Frame ( 9) shift: -1.43 -0.15 ...... Frame ( 10) shift: -1.40 -0.09 ...... Frame ( 11) shift: -1.36 -0.04 ...... Frame ( 12) shift: -1.36 -0.00 ...... Frame ( 13) shift: -1.40 0.02 ...... Frame ( 14) shift: -1.43 0.05 ...... Frame ( 15) shift: -1.44 0.05 ...... Frame ( 16) shift: -1.42 0.02 ...... Frame ( 17) shift: -1.41 -0.01 ...... Frame ( 18) shift: -1.42 -0.04 ...... Frame ( 19) shift: -1.44 -0.06 ...... Frame ( 20) shift: -1.47 -0.08 ...... Frame ( 21) shift: -1.47 -0.08 ...... Frame ( 22) shift: -1.43 -0.06 ...... Frame ( 23) shift: -1.40 -0.05 ...... Frame ( 24) shift: -1.39 -0.04 ...... Frame ( 25) shift: -1.42 -0.04 ...... Frame ( 26) shift: -1.45 -0.04 ...... Frame ( 27) shift: -1.43 -0.04 ...... Frame ( 28) shift: -1.36 -0.03 ...... Frame ( 29) shift: -1.29 -0.02 ...... Frame ( 30) shift: -1.23 -0.02 ...... Frame ( 31) shift: -1.17 -0.03 ...... Frame ( 32) shift: -1.12 -0.03 ...... Frame ( 33) shift: -1.07 -0.03 ...... Frame ( 34) shift: -1.02 -0.02 ...... Frame ( 35) shift: -0.97 -0.02 ...... Frame ( 36) shift: -0.95 0.02 ...... Frame ( 37) shift: -0.96 0.07 ...... Frame ( 38) shift: -0.96 0.13 ...... Frame ( 39) shift: -0.97 0.19 ...... Frame ( 40) shift: -0.98 0.25 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.640286 Iteration 2 Error: 0.081289 Iteration 3 Error: 0.022084 Align patch 2 23 left Iteration 1 Error: 0.726776 Iteration 2 Error: 0.105271 Iteration 3 Error: 0.030567 Align patch 3 22 left Iteration 1 Error: 0.968542 Iteration 2 Error: 0.165361 Iteration 3 Error: 0.039767 Align patch 4 21 left Iteration 1 Error: 0.770997 Iteration 2 Error: 0.106700 Iteration 3 Error: 0.036924 Align patch 5 20 left Iteration 1 Error: 1.087654 Iteration 2 Error: 0.222138 Iteration 3 Error: 0.063119 Iteration 4 Error: 0.030057 Align patch 6 19 left Iteration 1 Error: 1.233945 Iteration 2 Error: 0.407017 Iteration 3 Error: 0.188826 Iteration 4 Error: 0.091155 Iteration 5 Error: 0.026748 Align patch 7 18 left Iteration 1 Error: 1.074422 Iteration 2 Error: 0.134396 Iteration 3 Error: 0.027527 Align patch 8 17 left Iteration 1 Error: 0.855852 Iteration 2 Error: 0.161888 Iteration 3 Error: 0.033335 Align patch 9 16 left Iteration 1 Error: 0.925004 Iteration 2 Error: 0.153507 Iteration 3 Error: 0.051261 Iteration 4 Error: 0.020676 Align patch 10 15 left Iteration 1 Error: 0.637651 Iteration 2 Error: 0.135031 Iteration 3 Error: 0.038732 Align patch 11 14 left Iteration 1 Error: 0.841770 Iteration 2 Error: 0.114027 Iteration 3 Error: 0.032545 Align patch 12 13 left Iteration 1 Error: 1.641717 Iteration 2 Error: 0.277703 Iteration 3 Error: 0.046090 Align patch 13 12 left Iteration 1 Error: 1.363180 Iteration 2 Error: 0.214477 Iteration 3 Error: 0.069145 Iteration 4 Error: 0.015905 Align patch 14 11 left Iteration 1 Error: 0.788579 Iteration 2 Error: 0.178289 Iteration 3 Error: 0.044102 Align patch 15 10 left Iteration 1 Error: 0.489671 Iteration 2 Error: 0.074136 Iteration 3 Error: 0.014704 Align patch 16 9 left Iteration 1 Error: 0.894233 Iteration 2 Error: 0.158500 Iteration 3 Error: 0.054558 Iteration 4 Error: 0.030938 Align patch 17 8 left Iteration 1 Error: 1.090241 Iteration 2 Error: 0.145187 Iteration 3 Error: 0.026635 Align patch 18 7 left Iteration 1 Error: 0.844834 Iteration 2 Error: 0.202029 Iteration 3 Error: 0.042847 Align patch 19 6 left Iteration 1 Error: 0.738957 Iteration 2 Error: 0.080971 Iteration 3 Error: 0.019338 Align patch 20 5 left Iteration 1 Error: 0.555477 Iteration 2 Error: 0.093727 Iteration 3 Error: 0.023325 Align patch 21 4 left Iteration 1 Error: 0.704073 Iteration 2 Error: 0.168247 Iteration 3 Error: 0.070876 Iteration 4 Error: 0.014855 Align patch 22 3 left Iteration 1 Error: 1.006853 Iteration 2 Error: 0.132448 Iteration 3 Error: 0.033010 Align patch 23 2 left Iteration 1 Error: 0.602856 Iteration 2 Error: 0.116577 Iteration 3 Error: 0.021907 Align patch 24 1 left Iteration 1 Error: 0.687241 Iteration 2 Error: 0.126594 Iteration 3 Error: 0.035285 Align patch 25 0 left Iteration 1 Error: 0.708663 Iteration 2 Error: 0.099249 Iteration 3 Error: 0.017767 3D Fitting completed. Patch alignment time: 15.88(sec) Local motion has been corrected. Process thread exits. Computational time: 24.096027 sec Total time: 29.688168 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00012hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00012hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.557318s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00012hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.571373s ........................................ >>>>>>TIME<<<<<< FFT: 0.929534s Defocus_U Defocus_V Angle CCC 9349.62 10142.59 11.44 0.039870 Final Values Defocus_U Defocus_V Angle CCC 9344.93 10147.28 12.07 0.078480 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00012hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00012hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.319e-01 9.825e-02 CC threshold: 0.721 Mean Std: 43.66 7.55 Num Hot pixels: 188 Hot pixel threshold: 88.98 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.454072 Iteration 2 Error: 0.156775 Iteration 3 Error: 0.035057 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.14 0.14 ...... Frame ( 3) shift: -0.28 0.28 ...... Frame ( 4) shift: -0.42 0.42 ...... Frame ( 5) shift: -0.56 0.56 ...... Frame ( 6) shift: -0.68 0.64 ...... Frame ( 7) shift: -0.78 0.67 ...... Frame ( 8) shift: -0.88 0.71 ...... Frame ( 9) shift: -0.95 0.77 ...... Frame ( 10) shift: -0.98 0.85 ...... Frame ( 11) shift: -1.02 0.94 ...... Frame ( 12) shift: -1.06 1.01 ...... Frame ( 13) shift: -1.12 1.06 ...... Frame ( 14) shift: -1.18 1.12 ...... Frame ( 15) shift: -1.23 1.15 ...... Frame ( 16) shift: -1.27 1.15 ...... Frame ( 17) shift: -1.31 1.16 ...... Frame ( 18) shift: -1.34 1.18 ...... Frame ( 19) shift: -1.36 1.21 ...... Frame ( 20) shift: -1.39 1.25 ...... Frame ( 21) shift: -1.42 1.31 ...... Frame ( 22) shift: -1.48 1.40 ...... Frame ( 23) shift: -1.53 1.50 ...... Frame ( 24) shift: -1.59 1.53 ...... Frame ( 25) shift: -1.65 1.51 ...... Frame ( 26) shift: -1.70 1.49 ...... Frame ( 27) shift: -1.73 1.48 ...... Frame ( 28) shift: -1.74 1.48 ...... Frame ( 29) shift: -1.74 1.48 ...... Frame ( 30) shift: -1.75 1.51 ...... Frame ( 31) shift: -1.77 1.56 ...... Frame ( 32) shift: -1.79 1.61 ...... Frame ( 33) shift: -1.80 1.65 ...... Frame ( 34) shift: -1.80 1.67 ...... Frame ( 35) shift: -1.80 1.68 ...... Frame ( 36) shift: -1.80 1.69 ...... Frame ( 37) shift: -1.81 1.69 ...... Frame ( 38) shift: -1.81 1.69 ...... Frame ( 39) shift: -1.82 1.69 ...... Frame ( 40) shift: -1.82 1.69 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 3.019233 Iteration 2 Error: 0.574362 Iteration 3 Error: 0.278230 Iteration 4 Error: 0.105434 Iteration 5 Error: 0.049697 Align patch 2 23 left Iteration 1 Error: 1.011342 Iteration 2 Error: 0.198811 Iteration 3 Error: 0.069181 Iteration 4 Error: 0.028549 Align patch 3 22 left Iteration 1 Error: 0.788557 Iteration 2 Error: 0.112710 Iteration 3 Error: 0.020235 Align patch 4 21 left Iteration 1 Error: 0.928951 Iteration 2 Error: 0.148201 Iteration 3 Error: 0.031161 Align patch 5 20 left Iteration 1 Error: 1.524985 Iteration 2 Error: 0.193061 Iteration 3 Error: 0.033139 Align patch 6 19 left Iteration 1 Error: 3.483435 Iteration 2 Error: 1.005359 Iteration 3 Error: 0.447614 Iteration 4 Error: 0.228536 Iteration 5 Error: 0.133734 Align patch 6 19 left Iteration 1 Error: 2.535147 Iteration 2 Error: 0.582660 Iteration 3 Error: 0.139704 Iteration 4 Error: 0.057021 Iteration 5 Error: 0.040397 Align patch 7 18 left Iteration 1 Error: 1.019993 Iteration 2 Error: 0.161192 Iteration 3 Error: 0.063300 Iteration 4 Error: 0.031997 Align patch 8 17 left Iteration 1 Error: 0.965800 Iteration 2 Error: 0.099301 Iteration 3 Error: 0.039120 Align patch 9 16 left Iteration 1 Error: 0.939483 Iteration 2 Error: 0.203930 Iteration 3 Error: 0.048961 Align patch 10 15 left Iteration 1 Error: 0.844629 Iteration 2 Error: 0.142327 Iteration 3 Error: 0.029167 Align patch 11 14 left Iteration 1 Error: 1.753933 Iteration 2 Error: 0.391826 Iteration 3 Error: 0.180072 Iteration 4 Error: 0.087782 Iteration 5 Error: 0.048996 Align patch 12 13 left Iteration 1 Error: 3.035498 Iteration 2 Error: 0.576899 Iteration 3 Error: 0.214846 Iteration 4 Error: 0.081010 Iteration 5 Error: 0.027956 Align patch 13 12 left Iteration 1 Error: 1.329203 Iteration 2 Error: 0.191089 Iteration 3 Error: 0.058140 Iteration 4 Error: 0.015703 Align patch 14 11 left Iteration 1 Error: 0.786550 Iteration 2 Error: 0.124763 Iteration 3 Error: 0.049322 Align patch 15 10 left Iteration 1 Error: 0.886155 Iteration 2 Error: 0.151853 Iteration 3 Error: 0.024320 Align patch 16 9 left Iteration 1 Error: 2.500579 Iteration 2 Error: 0.429102 Iteration 3 Error: 0.340429 Iteration 4 Error: 0.129946 Iteration 5 Error: 0.067886 Align patch 16 9 left Iteration 1 Error: 2.445859 Iteration 2 Error: 0.283122 Iteration 3 Error: 0.098992 Iteration 4 Error: 0.037420 Align patch 17 8 left Iteration 1 Error: 1.574776 Iteration 2 Error: 0.356787 Iteration 3 Error: 0.198189 Iteration 4 Error: 0.146290 Iteration 5 Error: 0.086631 Align patch 17 8 left Iteration 1 Error: 2.520886 Iteration 2 Error: 0.379987 Iteration 3 Error: 0.115726 Iteration 4 Error: 0.034749 Align patch 18 7 left Iteration 1 Error: 2.191169 Iteration 2 Error: 0.305588 Iteration 3 Error: 0.077341 Iteration 4 Error: 0.031723 Align patch 19 6 left Iteration 1 Error: 0.946235 Iteration 2 Error: 0.282892 Iteration 3 Error: 0.059663 Iteration 4 Error: 0.019453 Align patch 20 5 left Iteration 1 Error: 0.782168 Iteration 2 Error: 0.143061 Iteration 3 Error: 0.035682 Align patch 21 4 left Iteration 1 Error: 2.840474 Iteration 2 Error: 0.659974 Iteration 3 Error: 0.220054 Iteration 4 Error: 0.115289 Iteration 5 Error: 0.054245 Align patch 21 4 left Iteration 1 Error: 2.756667 Iteration 2 Error: 0.330984 Iteration 3 Error: 0.086564 Iteration 4 Error: 0.056509 Iteration 5 Error: 0.022071 Align patch 22 3 left Iteration 1 Error: 2.025165 Iteration 2 Error: 0.441997 Iteration 3 Error: 0.208688 Iteration 4 Error: 0.064942 Iteration 5 Error: 0.023907 Align patch 23 2 left Iteration 1 Error: 1.233837 Iteration 2 Error: 0.194974 Iteration 3 Error: 0.071358 Iteration 4 Error: 0.028981 Align patch 24 1 left Iteration 1 Error: 0.790451 Iteration 2 Error: 0.112109 Iteration 3 Error: 0.025064 Align patch 25 0 left Iteration 1 Error: 1.074677 Iteration 2 Error: 0.099780 Iteration 3 Error: 0.019958 3D Fitting completed. Patch alignment time: 20.29(sec) Local motion has been corrected. Process thread exits. Computational time: 28.921358 sec Total time: 34.813286 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00012hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00012hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.748396s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00012hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.122353s ........................................ >>>>>>TIME<<<<<< FFT: 1.054277s Defocus_U Defocus_V Angle CCC 9468.81 8949.27 86.46 -0.016608 Final Values Defocus_U Defocus_V Angle CCC 9481.31 8936.77 86.46 -0.122393 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00012hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00012hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 45.59 7.63 Num Hot pixels: 189 Hot pixel threshold: 91.39 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.708559 Iteration 2 Error: 0.072813 Iteration 3 Error: 0.020802 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.33 -0.06 ...... Frame ( 3) shift: -0.67 -0.11 ...... Frame ( 4) shift: -1.00 -0.17 ...... Frame ( 5) shift: -1.34 -0.22 ...... Frame ( 6) shift: -1.50 -0.25 ...... Frame ( 7) shift: -1.48 -0.25 ...... Frame ( 8) shift: -1.46 -0.24 ...... Frame ( 9) shift: -1.42 -0.25 ...... Frame ( 10) shift: -1.35 -0.26 ...... Frame ( 11) shift: -1.28 -0.27 ...... Frame ( 12) shift: -1.25 -0.22 ...... Frame ( 13) shift: -1.28 -0.10 ...... Frame ( 14) shift: -1.31 0.02 ...... Frame ( 15) shift: -1.31 0.08 ...... Frame ( 16) shift: -1.29 0.07 ...... Frame ( 17) shift: -1.27 0.06 ...... Frame ( 18) shift: -1.24 0.06 ...... Frame ( 19) shift: -1.20 0.08 ...... Frame ( 20) shift: -1.16 0.09 ...... Frame ( 21) shift: -1.16 0.12 ...... Frame ( 22) shift: -1.18 0.15 ...... Frame ( 23) shift: -1.20 0.18 ...... Frame ( 24) shift: -1.20 0.23 ...... Frame ( 25) shift: -1.19 0.29 ...... Frame ( 26) shift: -1.17 0.35 ...... Frame ( 27) shift: -1.14 0.38 ...... Frame ( 28) shift: -1.11 0.40 ...... Frame ( 29) shift: -1.08 0.41 ...... Frame ( 30) shift: -1.08 0.40 ...... Frame ( 31) shift: -1.10 0.37 ...... Frame ( 32) shift: -1.12 0.33 ...... Frame ( 33) shift: -1.10 0.32 ...... Frame ( 34) shift: -1.02 0.31 ...... Frame ( 35) shift: -0.95 0.31 ...... Frame ( 36) shift: -0.93 0.34 ...... Frame ( 37) shift: -0.98 0.40 ...... Frame ( 38) shift: -1.02 0.45 ...... Frame ( 39) shift: -1.06 0.51 ...... Frame ( 40) shift: -1.11 0.57 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.463537 Iteration 2 Error: 0.241703 Iteration 3 Error: 0.083198 Iteration 4 Error: 0.022858 Align patch 2 23 left Iteration 1 Error: 1.210993 Iteration 2 Error: 0.094365 Iteration 3 Error: 0.029897 Align patch 3 22 left Iteration 1 Error: 0.760910 Iteration 2 Error: 0.142893 Iteration 3 Error: 0.035153 Align patch 4 21 left Iteration 1 Error: 0.848574 Iteration 2 Error: 0.187295 Iteration 3 Error: 0.033639 Align patch 5 20 left Iteration 1 Error: 0.722268 Iteration 2 Error: 0.084620 Iteration 3 Error: 0.014293 Align patch 6 19 left Iteration 1 Error: 1.137077 Iteration 2 Error: 0.232828 Iteration 3 Error: 0.052093 Iteration 4 Error: 0.022112 Align patch 7 18 left Iteration 1 Error: 0.734047 Iteration 2 Error: 0.178920 Iteration 3 Error: 0.072988 Iteration 4 Error: 0.027428 Align patch 8 17 left Iteration 1 Error: 0.598542 Iteration 2 Error: 0.087810 Iteration 3 Error: 0.022603 Align patch 9 16 left Iteration 1 Error: 1.113828 Iteration 2 Error: 0.154165 Iteration 3 Error: 0.042072 Align patch 10 15 left Iteration 1 Error: 0.512055 Iteration 2 Error: 0.080541 Iteration 3 Error: 0.015091 Align patch 11 14 left Iteration 1 Error: 0.719405 Iteration 2 Error: 0.105901 Iteration 3 Error: 0.035913 Align patch 12 13 left Iteration 1 Error: 0.947771 Iteration 2 Error: 0.092641 Iteration 3 Error: 0.032913 Align patch 13 12 left Iteration 1 Error: 0.776738 Iteration 2 Error: 0.122097 Iteration 3 Error: 0.042354 Align patch 14 11 left Iteration 1 Error: 0.497392 Iteration 2 Error: 0.062782 Iteration 3 Error: 0.013298 Align patch 15 10 left Iteration 1 Error: 0.646592 Iteration 2 Error: 0.111757 Iteration 3 Error: 0.028375 Align patch 16 9 left Iteration 1 Error: 0.897048 Iteration 2 Error: 0.118991 Iteration 3 Error: 0.045379 Align patch 17 8 left Iteration 1 Error: 0.784972 Iteration 2 Error: 0.169658 Iteration 3 Error: 0.057222 Iteration 4 Error: 0.014116 Align patch 18 7 left Iteration 1 Error: 0.648335 Iteration 2 Error: 0.062809 Iteration 3 Error: 0.013173 Align patch 19 6 left Iteration 1 Error: 0.581999 Iteration 2 Error: 0.100564 Iteration 3 Error: 0.027596 Align patch 20 5 left Iteration 1 Error: 0.780046 Iteration 2 Error: 0.093709 Iteration 3 Error: 0.028933 Align patch 21 4 left Iteration 1 Error: 0.906797 Iteration 2 Error: 0.128435 Iteration 3 Error: 0.023937 Align patch 22 3 left Iteration 1 Error: 0.816234 Iteration 2 Error: 0.214783 Iteration 3 Error: 0.066490 Iteration 4 Error: 0.025241 Align patch 23 2 left Iteration 1 Error: 0.990869 Iteration 2 Error: 0.153379 Iteration 3 Error: 0.022358 Align patch 24 1 left Iteration 1 Error: 1.119994 Iteration 2 Error: 0.117983 Iteration 3 Error: 0.037351 Align patch 25 0 left Iteration 1 Error: 0.617209 Iteration 2 Error: 0.081838 Iteration 3 Error: 0.013476 3D Fitting completed. Patch alignment time: 15.44(sec) Local motion has been corrected. Process thread exits. Computational time: 24.094997 sec Total time: 30.445683 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00012hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00012hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.675426s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00012hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.131393s ........................................ >>>>>>TIME<<<<<< FFT: 1.170772s Defocus_U Defocus_V Angle CCC 13084.01 13951.20 4.98 0.053851 Final Values Defocus_U Defocus_V Angle CCC 13082.47 13962.16 5.30 0.094032 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00012hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00012hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.325e-01 9.871e-02 CC threshold: 0.725 Mean Std: 43.72 7.36 Num Hot pixels: 189 Hot pixel threshold: 87.88 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.412724 Iteration 2 Error: 0.318299 Iteration 3 Error: 0.144629 Iteration 4 Error: 0.047431 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.19 0.16 ...... Frame ( 3) shift: -0.38 0.33 ...... Frame ( 4) shift: -0.56 0.49 ...... Frame ( 5) shift: -0.75 0.66 ...... Frame ( 6) shift: -0.98 0.81 ...... Frame ( 7) shift: -1.26 0.95 ...... Frame ( 8) shift: -1.53 1.09 ...... Frame ( 9) shift: -1.72 1.21 ...... Frame ( 10) shift: -1.82 1.33 ...... Frame ( 11) shift: -1.93 1.45 ...... Frame ( 12) shift: -2.04 1.56 ...... Frame ( 13) shift: -2.17 1.65 ...... Frame ( 14) shift: -2.29 1.73 ...... Frame ( 15) shift: -2.39 1.78 ...... Frame ( 16) shift: -2.45 1.79 ...... Frame ( 17) shift: -2.51 1.81 ...... Frame ( 18) shift: -2.58 1.86 ...... Frame ( 19) shift: -2.65 1.96 ...... Frame ( 20) shift: -2.73 2.05 ...... Frame ( 21) shift: -2.81 2.15 ...... Frame ( 22) shift: -2.91 2.23 ...... Frame ( 23) shift: -3.00 2.31 ...... Frame ( 24) shift: -3.07 2.35 ...... Frame ( 25) shift: -3.13 2.35 ...... Frame ( 26) shift: -3.18 2.34 ...... Frame ( 27) shift: -3.23 2.34 ...... Frame ( 28) shift: -3.28 2.33 ...... Frame ( 29) shift: -3.33 2.32 ...... Frame ( 30) shift: -3.40 2.31 ...... Frame ( 31) shift: -3.47 2.31 ...... Frame ( 32) shift: -3.54 2.30 ...... Frame ( 33) shift: -3.58 2.32 ...... Frame ( 34) shift: -3.59 2.39 ...... Frame ( 35) shift: -3.60 2.45 ...... Frame ( 36) shift: -3.62 2.46 ...... Frame ( 37) shift: -3.64 2.44 ...... Frame ( 38) shift: -3.66 2.41 ...... Frame ( 39) shift: -3.68 2.39 ...... Frame ( 40) shift: -3.71 2.36 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.983178 Iteration 2 Error: 0.442833 Iteration 3 Error: 0.090473 Iteration 4 Error: 0.047766 Align patch 2 23 left Iteration 1 Error: 0.929149 Iteration 2 Error: 0.206605 Iteration 3 Error: 0.108192 Iteration 4 Error: 0.058042 Iteration 5 Error: 0.027619 Align patch 3 22 left Iteration 1 Error: 0.914247 Iteration 2 Error: 0.167192 Iteration 3 Error: 0.078841 Iteration 4 Error: 0.028930 Align patch 4 21 left Iteration 1 Error: 0.732925 Iteration 2 Error: 0.164336 Iteration 3 Error: 0.044461 Align patch 5 20 left Iteration 1 Error: 1.884750 Iteration 2 Error: 0.181537 Iteration 3 Error: 0.041426 Align patch 6 19 left Iteration 1 Error: 3.875685 Iteration 2 Error: 0.819335 Iteration 3 Error: 0.387542 Iteration 4 Error: 0.147574 Iteration 5 Error: 0.070952 Align patch 6 19 left Iteration 1 Error: 3.278011 Iteration 2 Error: 0.485874 Iteration 3 Error: 0.148228 Iteration 4 Error: 0.068176 Iteration 5 Error: 0.059444 Align patch 7 18 left Iteration 1 Error: 2.038382 Iteration 2 Error: 0.754933 Iteration 3 Error: 0.419457 Iteration 4 Error: 0.263379 Iteration 5 Error: 0.131541 Align patch 7 18 left Iteration 1 Error: 2.852130 Iteration 2 Error: 0.325254 Iteration 3 Error: 0.067409 Iteration 4 Error: 0.022412 Align patch 8 17 left Iteration 1 Error: 1.038021 Iteration 2 Error: 0.134244 Iteration 3 Error: 0.030377 Align patch 9 16 left Iteration 1 Error: 0.641509 Iteration 2 Error: 0.115669 Iteration 3 Error: 0.030044 Align patch 10 15 left Iteration 1 Error: 1.309311 Iteration 2 Error: 0.225880 Iteration 3 Error: 0.074879 Iteration 4 Error: 0.023544 Align patch 11 14 left Iteration 1 Error: 5.984732 Iteration 2 Error: 1.380534 Iteration 3 Error: 0.557274 Iteration 4 Error: 0.258951 Iteration 5 Error: 0.163206 Align patch 11 14 left Iteration 1 Error: 3.890041 Iteration 2 Error: 0.927566 Iteration 3 Error: 0.277357 Iteration 4 Error: 0.089955 Iteration 5 Error: 0.048563 Align patch 12 13 left Iteration 1 Error: 2.447955 Iteration 2 Error: 0.839058 Iteration 3 Error: 0.447647 Iteration 4 Error: 0.251255 Iteration 5 Error: 0.181187 Align patch 12 13 left Iteration 1 Error: 3.435228 Iteration 2 Error: 0.632528 Iteration 3 Error: 0.180740 Iteration 4 Error: 0.071074 Iteration 5 Error: 0.030182 Align patch 13 12 left Iteration 1 Error: 1.188447 Iteration 2 Error: 0.292800 Iteration 3 Error: 0.075478 Iteration 4 Error: 0.048665 Align patch 14 11 left Iteration 1 Error: 0.926698 Iteration 2 Error: 0.190856 Iteration 3 Error: 0.051785 Iteration 4 Error: 0.018705 Align patch 15 10 left Iteration 1 Error: 0.907374 Iteration 2 Error: 0.236559 Iteration 3 Error: 0.079786 Iteration 4 Error: 0.014813 Align patch 16 9 left Iteration 1 Error: 4.074818 Iteration 2 Error: 0.727932 Iteration 3 Error: 0.317124 Iteration 4 Error: 0.172263 Iteration 5 Error: 0.080219 Align patch 16 9 left Iteration 1 Error: 3.168264 Iteration 2 Error: 0.497404 Iteration 3 Error: 0.179337 Iteration 4 Error: 0.063753 Iteration 5 Error: 0.024084 Align patch 17 8 left Iteration 1 Error: 3.074799 Iteration 2 Error: 0.656674 Iteration 3 Error: 0.213856 Iteration 4 Error: 0.102926 Iteration 5 Error: 0.052992 Align patch 17 8 left Iteration 1 Error: 2.714655 Iteration 2 Error: 0.444856 Iteration 3 Error: 0.130779 Iteration 4 Error: 0.056010 Iteration 5 Error: 0.030897 Align patch 18 7 left Iteration 1 Error: 1.283118 Iteration 2 Error: 0.620487 Iteration 3 Error: 0.237821 Iteration 4 Error: 0.125152 Iteration 5 Error: 0.056881 Align patch 18 7 left Iteration 1 Error: 1.316535 Iteration 2 Error: 0.229154 Iteration 3 Error: 0.060814 Iteration 4 Error: 0.018859 Align patch 19 6 left Iteration 1 Error: 0.594307 Iteration 2 Error: 0.159972 Iteration 3 Error: 0.054184 Iteration 4 Error: 0.025746 Align patch 20 5 left Iteration 1 Error: 1.282255 Iteration 2 Error: 0.171968 Iteration 3 Error: 0.045536 Align patch 21 4 left Iteration 1 Error: 3.458631 Iteration 2 Error: 0.564458 Iteration 3 Error: 0.217697 Iteration 4 Error: 0.084608 Iteration 5 Error: 0.041431 Align patch 22 3 left Iteration 1 Error: 2.064841 Iteration 2 Error: 0.475732 Iteration 3 Error: 0.197082 Iteration 4 Error: 0.117132 Iteration 5 Error: 0.060211 Align patch 22 3 left Iteration 1 Error: 2.653761 Iteration 2 Error: 0.350768 Iteration 3 Error: 0.104134 Iteration 4 Error: 0.040449 Align patch 23 2 left Iteration 1 Error: 1.243356 Iteration 2 Error: 0.244245 Iteration 3 Error: 0.079336 Iteration 4 Error: 0.023353 Align patch 24 1 left Iteration 1 Error: 0.885725 Iteration 2 Error: 0.103806 Iteration 3 Error: 0.029383 Align patch 25 0 left Iteration 1 Error: 1.652191 Iteration 2 Error: 0.139185 Iteration 3 Error: 0.023293 3D Fitting completed. Patch alignment time: 24.84(sec) Local motion has been corrected. Process thread exits. Computational time: 33.673824 sec Total time: 39.207748 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00012hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00012hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.550850s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00012hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.096310s ........................................ >>>>>>TIME<<<<<< FFT: 0.935044s Defocus_U Defocus_V Angle CCC 13550.86 12914.07 83.70 0.007643 Final Values Defocus_U Defocus_V Angle CCC 13561.80 12906.26 83.70 -0.088776 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00013hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00013hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 1.000e-01 CC threshold: 0.735 Mean Std: 46.55 7.70 Num Hot pixels: 225 Hot pixel threshold: 92.75 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.411085 Iteration 2 Error: 0.254160 Iteration 3 Error: 0.068853 Iteration 4 Error: 0.024692 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.24 -0.06 ...... Frame ( 3) shift: -0.49 -0.11 ...... Frame ( 4) shift: -0.73 -0.17 ...... Frame ( 5) shift: -0.98 -0.22 ...... Frame ( 6) shift: -1.11 -0.17 ...... Frame ( 7) shift: -1.14 -0.01 ...... Frame ( 8) shift: -1.16 0.15 ...... Frame ( 9) shift: -1.17 0.31 ...... Frame ( 10) shift: -1.16 0.46 ...... Frame ( 11) shift: -1.15 0.62 ...... Frame ( 12) shift: -1.14 0.77 ...... Frame ( 13) shift: -1.12 0.94 ...... Frame ( 14) shift: -1.10 1.10 ...... Frame ( 15) shift: -1.04 1.20 ...... Frame ( 16) shift: -0.93 1.24 ...... Frame ( 17) shift: -0.82 1.27 ...... Frame ( 18) shift: -0.73 1.31 ...... Frame ( 19) shift: -0.65 1.37 ...... Frame ( 20) shift: -0.58 1.43 ...... Frame ( 21) shift: -0.48 1.48 ...... Frame ( 22) shift: -0.38 1.51 ...... Frame ( 23) shift: -0.27 1.54 ...... Frame ( 24) shift: -0.16 1.57 ...... Frame ( 25) shift: -0.06 1.62 ...... Frame ( 26) shift: 0.05 1.66 ...... Frame ( 27) shift: 0.11 1.72 ...... Frame ( 28) shift: 0.13 1.81 ...... Frame ( 29) shift: 0.14 1.89 ...... Frame ( 30) shift: 0.16 1.93 ...... Frame ( 31) shift: 0.19 1.93 ...... Frame ( 32) shift: 0.23 1.92 ...... Frame ( 33) shift: 0.23 1.96 ...... Frame ( 34) shift: 0.20 2.04 ...... Frame ( 35) shift: 0.17 2.12 ...... Frame ( 36) shift: 0.13 2.16 ...... Frame ( 37) shift: 0.06 2.17 ...... Frame ( 38) shift: 0.00 2.17 ...... Frame ( 39) shift: -0.06 2.18 ...... Frame ( 40) shift: -0.12 2.18 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.822081 Iteration 2 Error: 0.192721 Iteration 3 Error: 0.066642 Iteration 4 Error: 0.030675 Align patch 2 23 left Iteration 1 Error: 0.715318 Iteration 2 Error: 0.140226 Iteration 3 Error: 0.046079 Align patch 3 22 left Iteration 1 Error: 0.732604 Iteration 2 Error: 0.166953 Iteration 3 Error: 0.080056 Iteration 4 Error: 0.035999 Align patch 4 21 left Iteration 1 Error: 0.658527 Iteration 2 Error: 0.113478 Iteration 3 Error: 0.025505 Align patch 5 20 left Iteration 1 Error: 0.725940 Iteration 2 Error: 0.154648 Iteration 3 Error: 0.046325 Align patch 6 19 left Iteration 1 Error: 1.183229 Iteration 2 Error: 0.248813 Iteration 3 Error: 0.181944 Iteration 4 Error: 0.056869 Iteration 5 Error: 0.040850 Align patch 7 18 left Iteration 1 Error: 1.104364 Iteration 2 Error: 0.287261 Iteration 3 Error: 0.087744 Iteration 4 Error: 0.025536 Align patch 8 17 left Iteration 1 Error: 0.571535 Iteration 2 Error: 0.112386 Iteration 3 Error: 0.037811 Align patch 9 16 left Iteration 1 Error: 0.784335 Iteration 2 Error: 0.120146 Iteration 3 Error: 0.044030 Align patch 10 15 left Iteration 1 Error: 0.565130 Iteration 2 Error: 0.088829 Iteration 3 Error: 0.023702 Align patch 11 14 left Iteration 1 Error: 0.742600 Iteration 2 Error: 0.151402 Iteration 3 Error: 0.063580 Iteration 4 Error: 0.019737 Align patch 12 13 left Iteration 1 Error: 2.178708 Iteration 2 Error: 0.291202 Iteration 3 Error: 0.073129 Iteration 4 Error: 0.026042 Align patch 13 12 left Iteration 1 Error: 0.705064 Iteration 2 Error: 0.172344 Iteration 3 Error: 0.034647 Align patch 14 11 left Iteration 1 Error: 0.782268 Iteration 2 Error: 0.146184 Iteration 3 Error: 0.045387 Align patch 15 10 left Iteration 1 Error: 0.945746 Iteration 2 Error: 0.136532 Iteration 3 Error: 0.025001 Align patch 16 9 left Iteration 1 Error: 1.385825 Iteration 2 Error: 0.235173 Iteration 3 Error: 0.087495 Iteration 4 Error: 0.029704 Align patch 17 8 left Iteration 1 Error: 0.905167 Iteration 2 Error: 0.257421 Iteration 3 Error: 0.054281 Iteration 4 Error: 0.011735 Align patch 18 7 left Iteration 1 Error: 1.027569 Iteration 2 Error: 0.182493 Iteration 3 Error: 0.064581 Iteration 4 Error: 0.040773 Align patch 19 6 left Iteration 1 Error: 0.673289 Iteration 2 Error: 0.094707 Iteration 3 Error: 0.041996 Align patch 20 5 left Iteration 1 Error: 0.692776 Iteration 2 Error: 0.111536 Iteration 3 Error: 0.024108 Align patch 21 4 left Iteration 1 Error: 1.788327 Iteration 2 Error: 0.243594 Iteration 3 Error: 0.089492 Iteration 4 Error: 0.037394 Align patch 22 3 left Iteration 1 Error: 1.217088 Iteration 2 Error: 0.220405 Iteration 3 Error: 0.113929 Iteration 4 Error: 0.044909 Align patch 23 2 left Iteration 1 Error: 1.404674 Iteration 2 Error: 0.260746 Iteration 3 Error: 0.075477 Iteration 4 Error: 0.032718 Align patch 24 1 left Iteration 1 Error: 0.733979 Iteration 2 Error: 0.124110 Iteration 3 Error: 0.036840 Align patch 25 0 left Iteration 1 Error: 0.652488 Iteration 2 Error: 0.094323 Iteration 3 Error: 0.037704 3D Fitting completed. Patch alignment time: 15.91(sec) Local motion has been corrected. Process thread exits. Computational time: 24.306892 sec Total time: 29.995596 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00013hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00013hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.817878s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00013hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.108013s ........................................ >>>>>>TIME<<<<<< FFT: 1.054345s Defocus_U Defocus_V Angle CCC 11388.67 12302.77 14.25 0.047003 Final Values Defocus_U Defocus_V Angle CCC 11396.48 12298.08 14.25 0.086157 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00013hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00013hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 45.80 7.75 Num Hot pixels: 204 Hot pixel threshold: 92.32 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.355121 Iteration 2 Error: 0.112245 Iteration 3 Error: 0.020245 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.35 0.11 ...... Frame ( 3) shift: -0.70 0.23 ...... Frame ( 4) shift: -1.04 0.34 ...... Frame ( 5) shift: -1.39 0.45 ...... Frame ( 6) shift: -1.59 0.53 ...... Frame ( 7) shift: -1.65 0.56 ...... Frame ( 8) shift: -1.71 0.60 ...... Frame ( 9) shift: -1.74 0.67 ...... Frame ( 10) shift: -1.73 0.76 ...... Frame ( 11) shift: -1.71 0.85 ...... Frame ( 12) shift: -1.71 0.89 ...... Frame ( 13) shift: -1.71 0.87 ...... Frame ( 14) shift: -1.70 0.85 ...... Frame ( 15) shift: -1.71 0.84 ...... Frame ( 16) shift: -1.71 0.84 ...... Frame ( 17) shift: -1.72 0.84 ...... Frame ( 18) shift: -1.70 0.88 ...... Frame ( 19) shift: -1.64 0.96 ...... Frame ( 20) shift: -1.59 1.04 ...... Frame ( 21) shift: -1.55 1.10 ...... Frame ( 22) shift: -1.54 1.12 ...... Frame ( 23) shift: -1.53 1.15 ...... Frame ( 24) shift: -1.51 1.16 ...... Frame ( 25) shift: -1.46 1.16 ...... Frame ( 26) shift: -1.42 1.16 ...... Frame ( 27) shift: -1.43 1.17 ...... Frame ( 28) shift: -1.48 1.20 ...... Frame ( 29) shift: -1.53 1.22 ...... Frame ( 30) shift: -1.56 1.28 ...... Frame ( 31) shift: -1.56 1.37 ...... Frame ( 32) shift: -1.55 1.45 ...... Frame ( 33) shift: -1.57 1.51 ...... Frame ( 34) shift: -1.61 1.54 ...... Frame ( 35) shift: -1.65 1.57 ...... Frame ( 36) shift: -1.66 1.59 ...... Frame ( 37) shift: -1.64 1.58 ...... Frame ( 38) shift: -1.63 1.57 ...... Frame ( 39) shift: -1.61 1.57 ...... Frame ( 40) shift: -1.60 1.56 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.294121 Iteration 2 Error: 0.087978 Iteration 3 Error: 0.025663 Align patch 2 23 left Iteration 1 Error: 0.924806 Iteration 2 Error: 0.197291 Iteration 3 Error: 0.086079 Iteration 4 Error: 0.018624 Align patch 3 22 left Iteration 1 Error: 1.277380 Iteration 2 Error: 0.198570 Iteration 3 Error: 0.041444 Align patch 4 21 left Iteration 1 Error: 0.555225 Iteration 2 Error: 0.113854 Iteration 3 Error: 0.034543 Align patch 5 20 left Iteration 1 Error: 1.653345 Iteration 2 Error: 0.119296 Iteration 3 Error: 0.018602 Align patch 6 19 left Iteration 1 Error: 0.952284 Iteration 2 Error: 0.185147 Iteration 3 Error: 0.041652 Align patch 7 18 left Iteration 1 Error: 1.019602 Iteration 2 Error: 0.245715 Iteration 3 Error: 0.051085 Iteration 4 Error: 0.026284 Align patch 8 17 left Iteration 1 Error: 0.864719 Iteration 2 Error: 0.235916 Iteration 3 Error: 0.058029 Iteration 4 Error: 0.027454 Align patch 9 16 left Iteration 1 Error: 0.977411 Iteration 2 Error: 0.218151 Iteration 3 Error: 0.061593 Iteration 4 Error: 0.019998 Align patch 10 15 left Iteration 1 Error: 0.607372 Iteration 2 Error: 0.135475 Iteration 3 Error: 0.029849 Align patch 11 14 left Iteration 1 Error: 0.782832 Iteration 2 Error: 0.128048 Iteration 3 Error: 0.046173 Align patch 12 13 left Iteration 1 Error: 1.488040 Iteration 2 Error: 0.273576 Iteration 3 Error: 0.090177 Iteration 4 Error: 0.024581 Align patch 13 12 left Iteration 1 Error: 1.678135 Iteration 2 Error: 0.197760 Iteration 3 Error: 0.038328 Align patch 14 11 left Iteration 1 Error: 0.546325 Iteration 2 Error: 0.121036 Iteration 3 Error: 0.037735 Align patch 15 10 left Iteration 1 Error: 0.607744 Iteration 2 Error: 0.134696 Iteration 3 Error: 0.036823 Align patch 16 9 left Iteration 1 Error: 0.826796 Iteration 2 Error: 0.172772 Iteration 3 Error: 0.076204 Iteration 4 Error: 0.022201 Align patch 17 8 left Iteration 1 Error: 1.639521 Iteration 2 Error: 0.306322 Iteration 3 Error: 0.073266 Iteration 4 Error: 0.030434 Align patch 18 7 left Iteration 1 Error: 0.980808 Iteration 2 Error: 0.138698 Iteration 3 Error: 0.038603 Align patch 19 6 left Iteration 1 Error: 0.634523 Iteration 2 Error: 0.094770 Iteration 3 Error: 0.017982 Align patch 20 5 left Iteration 1 Error: 0.641478 Iteration 2 Error: 0.085347 Iteration 3 Error: 0.013335 Align patch 21 4 left Iteration 1 Error: 0.775200 Iteration 2 Error: 0.119984 Iteration 3 Error: 0.041133 Align patch 22 3 left Iteration 1 Error: 0.770812 Iteration 2 Error: 0.200967 Iteration 3 Error: 0.052898 Iteration 4 Error: 0.020505 Align patch 23 2 left Iteration 1 Error: 1.019714 Iteration 2 Error: 0.191913 Iteration 3 Error: 0.041873 Align patch 24 1 left Iteration 1 Error: 0.641926 Iteration 2 Error: 0.098512 Iteration 3 Error: 0.011650 Align patch 25 0 left Iteration 1 Error: 0.589687 Iteration 2 Error: 0.097415 Iteration 3 Error: 0.027032 3D Fitting completed. Patch alignment time: 15.98(sec) Local motion has been corrected. Process thread exits. Computational time: 24.111099 sec Total time: 29.548145 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00013hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00013hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.533608s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00013hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.875097s ........................................ >>>>>>TIME<<<<<< FFT: 0.926307s Defocus_U Defocus_V Angle CCC 11061.46 10548.16 88.49 0.044828 Final Values Defocus_U Defocus_V Angle CCC 11084.91 10552.86 88.17 0.084720 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00013hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00013hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 47.24 7.58 Num Hot pixels: 205 Hot pixel threshold: 92.73 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.247894 Iteration 2 Error: 0.159180 Iteration 3 Error: 0.025745 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.41 0.11 ...... Frame ( 3) shift: -0.82 0.22 ...... Frame ( 4) shift: -1.23 0.33 ...... Frame ( 5) shift: -1.64 0.44 ...... Frame ( 6) shift: -1.82 0.51 ...... Frame ( 7) shift: -1.78 0.53 ...... Frame ( 8) shift: -1.73 0.55 ...... Frame ( 9) shift: -1.69 0.58 ...... Frame ( 10) shift: -1.66 0.62 ...... Frame ( 11) shift: -1.62 0.66 ...... Frame ( 12) shift: -1.60 0.73 ...... Frame ( 13) shift: -1.59 0.83 ...... Frame ( 14) shift: -1.59 0.92 ...... Frame ( 15) shift: -1.60 1.00 ...... Frame ( 16) shift: -1.64 1.06 ...... Frame ( 17) shift: -1.67 1.12 ...... Frame ( 18) shift: -1.67 1.18 ...... Frame ( 19) shift: -1.64 1.23 ...... Frame ( 20) shift: -1.61 1.28 ...... Frame ( 21) shift: -1.60 1.32 ...... Frame ( 22) shift: -1.61 1.36 ...... Frame ( 23) shift: -1.62 1.40 ...... Frame ( 24) shift: -1.62 1.41 ...... Frame ( 25) shift: -1.63 1.39 ...... Frame ( 26) shift: -1.63 1.36 ...... Frame ( 27) shift: -1.62 1.40 ...... Frame ( 28) shift: -1.60 1.50 ...... Frame ( 29) shift: -1.57 1.60 ...... Frame ( 30) shift: -1.54 1.66 ...... Frame ( 31) shift: -1.52 1.67 ...... Frame ( 32) shift: -1.50 1.69 ...... Frame ( 33) shift: -1.50 1.71 ...... Frame ( 34) shift: -1.54 1.73 ...... Frame ( 35) shift: -1.58 1.76 ...... Frame ( 36) shift: -1.58 1.79 ...... Frame ( 37) shift: -1.55 1.83 ...... Frame ( 38) shift: -1.52 1.87 ...... Frame ( 39) shift: -1.50 1.91 ...... Frame ( 40) shift: -1.47 1.95 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 3.743732 Iteration 2 Error: 0.370628 Iteration 3 Error: 0.123261 Iteration 4 Error: 0.056402 Iteration 5 Error: 0.013834 Align patch 2 23 left Iteration 1 Error: 1.506067 Iteration 2 Error: 0.213257 Iteration 3 Error: 0.089051 Iteration 4 Error: 0.017224 Align patch 3 22 left Iteration 1 Error: 0.923177 Iteration 2 Error: 0.246399 Iteration 3 Error: 0.093106 Iteration 4 Error: 0.036839 Align patch 4 21 left Iteration 1 Error: 0.895368 Iteration 2 Error: 0.169797 Iteration 3 Error: 0.035445 Align patch 5 20 left Iteration 1 Error: 1.071663 Iteration 2 Error: 0.158120 Iteration 3 Error: 0.035724 Align patch 6 19 left Iteration 1 Error: 1.241982 Iteration 2 Error: 0.162231 Iteration 3 Error: 0.046482 Align patch 7 18 left Iteration 1 Error: 1.034235 Iteration 2 Error: 0.253060 Iteration 3 Error: 0.112520 Iteration 4 Error: 0.044884 Align patch 8 17 left Iteration 1 Error: 0.873168 Iteration 2 Error: 0.183356 Iteration 3 Error: 0.047156 Align patch 9 16 left Iteration 1 Error: 0.802841 Iteration 2 Error: 0.077439 Iteration 3 Error: 0.018090 Align patch 10 15 left Iteration 1 Error: 0.531863 Iteration 2 Error: 0.082747 Iteration 3 Error: 0.020665 Align patch 11 14 left Iteration 1 Error: 0.757027 Iteration 2 Error: 0.177362 Iteration 3 Error: 0.049170 Align patch 12 13 left Iteration 1 Error: 0.794026 Iteration 2 Error: 0.177781 Iteration 3 Error: 0.042085 Align patch 13 12 left Iteration 1 Error: 0.610202 Iteration 2 Error: 0.209934 Iteration 3 Error: 0.093870 Iteration 4 Error: 0.045601 Align patch 14 11 left Iteration 1 Error: 0.909994 Iteration 2 Error: 0.175734 Iteration 3 Error: 0.053258 Iteration 4 Error: 0.017968 Align patch 15 10 left Iteration 1 Error: 0.518312 Iteration 2 Error: 0.087232 Iteration 3 Error: 0.019067 Align patch 16 9 left Iteration 1 Error: 1.204694 Iteration 2 Error: 0.179155 Iteration 3 Error: 0.031877 Align patch 17 8 left Iteration 1 Error: 1.095557 Iteration 2 Error: 0.146507 Iteration 3 Error: 0.028064 Align patch 18 7 left Iteration 1 Error: 1.712477 Iteration 2 Error: 0.195394 Iteration 3 Error: 0.140818 Iteration 4 Error: 0.031711 Align patch 19 6 left Iteration 1 Error: 0.977879 Iteration 2 Error: 0.250069 Iteration 3 Error: 0.065078 Iteration 4 Error: 0.023672 Align patch 20 5 left Iteration 1 Error: 0.715423 Iteration 2 Error: 0.133014 Iteration 3 Error: 0.034569 Align patch 21 4 left Iteration 1 Error: 1.307979 Iteration 2 Error: 0.234650 Iteration 3 Error: 0.040004 Align patch 22 3 left Iteration 1 Error: 1.531651 Iteration 2 Error: 0.197337 Iteration 3 Error: 0.054570 Iteration 4 Error: 0.013660 Align patch 23 2 left Iteration 1 Error: 1.164887 Iteration 2 Error: 0.214308 Iteration 3 Error: 0.083714 Iteration 4 Error: 0.021623 Align patch 24 1 left Iteration 1 Error: 0.987600 Iteration 2 Error: 0.150161 Iteration 3 Error: 0.057561 Iteration 4 Error: 0.016845 Align patch 25 0 left Iteration 1 Error: 0.834688 Iteration 2 Error: 0.101172 Iteration 3 Error: 0.021782 3D Fitting completed. Patch alignment time: 15.67(sec) Local motion has been corrected. Process thread exits. Computational time: 24.508577 sec Total time: 30.453478 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00013hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00013hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.559988s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00013hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.093523s ........................................ >>>>>>TIME<<<<<< FFT: 0.939499s Defocus_U Defocus_V Angle CCC 14556.64 15400.39 2.14 0.057738 Final Values Defocus_U Defocus_V Angle CCC 14558.20 15392.58 3.40 0.097954 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00013hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00013hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.001e-01 CC threshold: 0.735 Mean Std: 46.53 7.66 Num Hot pixels: 194 Hot pixel threshold: 92.51 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.446032 Iteration 2 Error: 0.108256 Iteration 3 Error: 0.030343 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.47 -0.01 ...... Frame ( 3) shift: -0.95 -0.01 ...... Frame ( 4) shift: -1.42 -0.02 ...... Frame ( 5) shift: -1.90 -0.03 ...... Frame ( 6) shift: -2.16 -0.01 ...... Frame ( 7) shift: -2.20 0.03 ...... Frame ( 8) shift: -2.24 0.07 ...... Frame ( 9) shift: -2.20 0.14 ...... Frame ( 10) shift: -2.09 0.24 ...... Frame ( 11) shift: -1.98 0.33 ...... Frame ( 12) shift: -1.95 0.41 ...... Frame ( 13) shift: -1.99 0.47 ...... Frame ( 14) shift: -2.03 0.54 ...... Frame ( 15) shift: -2.03 0.57 ...... Frame ( 16) shift: -1.99 0.57 ...... Frame ( 17) shift: -1.96 0.57 ...... Frame ( 18) shift: -1.95 0.62 ...... Frame ( 19) shift: -1.96 0.72 ...... Frame ( 20) shift: -1.97 0.83 ...... Frame ( 21) shift: -1.97 0.88 ...... Frame ( 22) shift: -1.98 0.88 ...... Frame ( 23) shift: -1.99 0.89 ...... Frame ( 24) shift: -2.02 0.91 ...... Frame ( 25) shift: -2.07 0.95 ...... Frame ( 26) shift: -2.12 1.00 ...... Frame ( 27) shift: -2.12 1.04 ...... Frame ( 28) shift: -2.07 1.07 ...... Frame ( 29) shift: -2.03 1.11 ...... Frame ( 30) shift: -2.02 1.12 ...... Frame ( 31) shift: -2.03 1.12 ...... Frame ( 32) shift: -2.05 1.11 ...... Frame ( 33) shift: -2.05 1.09 ...... Frame ( 34) shift: -2.04 1.04 ...... Frame ( 35) shift: -2.02 1.00 ...... Frame ( 36) shift: -2.03 0.99 ...... Frame ( 37) shift: -2.06 0.99 ...... Frame ( 38) shift: -2.09 1.00 ...... Frame ( 39) shift: -2.11 1.01 ...... Frame ( 40) shift: -2.14 1.02 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.296580 Iteration 2 Error: 0.354352 Iteration 3 Error: 0.143485 Iteration 4 Error: 0.070029 Iteration 5 Error: 0.032445 Align patch 2 23 left Iteration 1 Error: 1.193193 Iteration 2 Error: 0.266390 Iteration 3 Error: 0.096341 Iteration 4 Error: 0.057691 Iteration 5 Error: 0.027516 Align patch 3 22 left Iteration 1 Error: 0.743553 Iteration 2 Error: 0.112679 Iteration 3 Error: 0.036140 Align patch 4 21 left Iteration 1 Error: 0.841828 Iteration 2 Error: 0.092601 Iteration 3 Error: 0.024099 Align patch 5 20 left Iteration 1 Error: 0.628118 Iteration 2 Error: 0.090923 Iteration 3 Error: 0.031836 Align patch 6 19 left Iteration 1 Error: 0.693696 Iteration 2 Error: 0.180788 Iteration 3 Error: 0.058001 Iteration 4 Error: 0.022816 Align patch 7 18 left Iteration 1 Error: 0.724408 Iteration 2 Error: 0.267366 Iteration 3 Error: 0.118542 Iteration 4 Error: 0.053332 Iteration 5 Error: 0.029877 Align patch 8 17 left Iteration 1 Error: 1.092650 Iteration 2 Error: 0.118999 Iteration 3 Error: 0.021757 Align patch 9 16 left Iteration 1 Error: 0.551064 Iteration 2 Error: 0.078448 Iteration 3 Error: 0.017440 Align patch 10 15 left Iteration 1 Error: 0.701792 Iteration 2 Error: 0.120377 Iteration 3 Error: 0.038111 Align patch 11 14 left Iteration 1 Error: 0.957942 Iteration 2 Error: 0.152246 Iteration 3 Error: 0.047945 Align patch 12 13 left Iteration 1 Error: 1.060534 Iteration 2 Error: 0.232649 Iteration 3 Error: 0.080400 Iteration 4 Error: 0.027816 Align patch 13 12 left Iteration 1 Error: 0.652110 Iteration 2 Error: 0.163230 Iteration 3 Error: 0.044860 Align patch 14 11 left Iteration 1 Error: 0.639730 Iteration 2 Error: 0.107333 Iteration 3 Error: 0.027224 Align patch 15 10 left Iteration 1 Error: 0.802036 Iteration 2 Error: 0.091344 Iteration 3 Error: 0.026431 Align patch 16 9 left Iteration 1 Error: 1.157961 Iteration 2 Error: 0.178230 Iteration 3 Error: 0.041701 Align patch 17 8 left Iteration 1 Error: 0.772970 Iteration 2 Error: 0.184232 Iteration 3 Error: 0.059975 Iteration 4 Error: 0.016407 Align patch 18 7 left Iteration 1 Error: 1.501613 Iteration 2 Error: 0.120036 Iteration 3 Error: 0.051257 Iteration 4 Error: 0.023634 Align patch 19 6 left Iteration 1 Error: 0.815978 Iteration 2 Error: 0.129714 Iteration 3 Error: 0.026043 Align patch 20 5 left Iteration 1 Error: 0.486085 Iteration 2 Error: 0.041586 Align patch 21 4 left Iteration 1 Error: 1.159085 Iteration 2 Error: 0.230583 Iteration 3 Error: 0.074276 Iteration 4 Error: 0.049066 Align patch 22 3 left Iteration 1 Error: 0.780713 Iteration 2 Error: 0.168643 Iteration 3 Error: 0.044439 Align patch 23 2 left Iteration 1 Error: 2.162835 Iteration 2 Error: 0.129206 Iteration 3 Error: 0.048053 Align patch 24 1 left Iteration 1 Error: 1.001768 Iteration 2 Error: 0.106226 Iteration 3 Error: 0.031681 Align patch 25 0 left Iteration 1 Error: 0.457460 Iteration 2 Error: 0.074753 Iteration 3 Error: 0.019226 3D Fitting completed. Patch alignment time: 15.20(sec) Local motion has been corrected. Process thread exits. Computational time: 23.115677 sec Total time: 29.006748 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00013hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00013hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.747461s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00013hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.223592s ........................................ >>>>>>TIME<<<<<< FFT: 1.064391s Defocus_U Defocus_V Angle CCC 12584.03 11908.19 82.92 0.050889 Final Values Defocus_U Defocus_V Angle CCC 12577.78 11926.94 83.85 0.089270 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00014hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00014hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 46.25 7.73 Num Hot pixels: 203 Hot pixel threshold: 92.62 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.359630 Iteration 2 Error: 0.172932 Iteration 3 Error: 0.055297 Iteration 4 Error: 0.016313 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.21 0.06 ...... Frame ( 3) shift: -0.41 0.13 ...... Frame ( 4) shift: -0.62 0.19 ...... Frame ( 5) shift: -0.82 0.26 ...... Frame ( 6) shift: -0.93 0.38 ...... Frame ( 7) shift: -0.94 0.57 ...... Frame ( 8) shift: -0.94 0.75 ...... Frame ( 9) shift: -0.91 0.91 ...... Frame ( 10) shift: -0.85 1.03 ...... Frame ( 11) shift: -0.78 1.16 ...... Frame ( 12) shift: -0.73 1.27 ...... Frame ( 13) shift: -0.70 1.36 ...... Frame ( 14) shift: -0.67 1.45 ...... Frame ( 15) shift: -0.66 1.52 ...... Frame ( 16) shift: -0.66 1.55 ...... Frame ( 17) shift: -0.67 1.59 ...... Frame ( 18) shift: -0.67 1.66 ...... Frame ( 19) shift: -0.66 1.77 ...... Frame ( 20) shift: -0.64 1.88 ...... Frame ( 21) shift: -0.66 1.92 ...... Frame ( 22) shift: -0.70 1.90 ...... Frame ( 23) shift: -0.74 1.87 ...... Frame ( 24) shift: -0.70 1.88 ...... Frame ( 25) shift: -0.58 1.92 ...... Frame ( 26) shift: -0.46 1.95 ...... Frame ( 27) shift: -0.39 1.97 ...... Frame ( 28) shift: -0.37 1.97 ...... Frame ( 29) shift: -0.35 1.97 ...... Frame ( 30) shift: -0.34 1.99 ...... Frame ( 31) shift: -0.33 2.04 ...... Frame ( 32) shift: -0.32 2.09 ...... Frame ( 33) shift: -0.27 2.17 ...... Frame ( 34) shift: -0.17 2.27 ...... Frame ( 35) shift: -0.07 2.37 ...... Frame ( 36) shift: 0.00 2.43 ...... Frame ( 37) shift: 0.04 2.43 ...... Frame ( 38) shift: 0.07 2.44 ...... Frame ( 39) shift: 0.11 2.45 ...... Frame ( 40) shift: 0.15 2.46 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.089216 Iteration 2 Error: 0.233605 Iteration 3 Error: 0.076260 Iteration 4 Error: 0.033532 Align patch 2 23 left Iteration 1 Error: 1.002006 Iteration 2 Error: 0.428465 Iteration 3 Error: 0.183554 Iteration 4 Error: 0.096947 Iteration 5 Error: 0.046000 Align patch 3 22 left Iteration 1 Error: 0.884593 Iteration 2 Error: 0.129502 Iteration 3 Error: 0.023939 Align patch 4 21 left Iteration 1 Error: 0.781401 Iteration 2 Error: 0.079263 Iteration 3 Error: 0.020958 Align patch 5 20 left Iteration 1 Error: 0.797993 Iteration 2 Error: 0.094968 Iteration 3 Error: 0.043156 Align patch 6 19 left Iteration 1 Error: 1.553220 Iteration 2 Error: 0.198122 Iteration 3 Error: 0.067044 Iteration 4 Error: 0.021730 Align patch 7 18 left Iteration 1 Error: 1.296460 Iteration 2 Error: 0.270975 Iteration 3 Error: 0.044539 Align patch 8 17 left Iteration 1 Error: 0.825174 Iteration 2 Error: 0.190508 Iteration 3 Error: 0.102708 Iteration 4 Error: 0.031107 Align patch 9 16 left Iteration 1 Error: 0.628570 Iteration 2 Error: 0.100243 Iteration 3 Error: 0.039740 Align patch 10 15 left Iteration 1 Error: 0.784741 Iteration 2 Error: 0.091632 Iteration 3 Error: 0.024372 Align patch 11 14 left Iteration 1 Error: 1.419789 Iteration 2 Error: 0.305852 Iteration 3 Error: 0.174908 Iteration 4 Error: 0.062616 Iteration 5 Error: 0.055573 Align patch 11 14 left Iteration 1 Error: 0.982161 Iteration 2 Error: 0.118931 Iteration 3 Error: 0.040494 Align patch 12 13 left Iteration 1 Error: 0.984250 Iteration 2 Error: 0.296864 Iteration 3 Error: 0.101410 Iteration 4 Error: 0.028878 Align patch 13 12 left Iteration 1 Error: 0.739951 Iteration 2 Error: 0.140044 Iteration 3 Error: 0.053727 Iteration 4 Error: 0.011433 Align patch 14 11 left Iteration 1 Error: 0.537273 Iteration 2 Error: 0.119214 Iteration 3 Error: 0.038578 Align patch 15 10 left Iteration 1 Error: 0.446764 Iteration 2 Error: 0.125151 Iteration 3 Error: 0.047919 Align patch 16 9 left Iteration 1 Error: 0.835077 Iteration 2 Error: 0.156768 Iteration 3 Error: 0.033839 Align patch 17 8 left Iteration 1 Error: 1.011567 Iteration 2 Error: 0.160016 Iteration 3 Error: 0.050230 Iteration 4 Error: 0.021400 Align patch 18 7 left Iteration 1 Error: 0.791321 Iteration 2 Error: 0.151787 Iteration 3 Error: 0.038763 Align patch 19 6 left Iteration 1 Error: 0.777102 Iteration 2 Error: 0.102145 Iteration 3 Error: 0.029697 Align patch 20 5 left Iteration 1 Error: 0.662996 Iteration 2 Error: 0.101125 Iteration 3 Error: 0.022815 Align patch 21 4 left Iteration 1 Error: 1.100907 Iteration 2 Error: 0.096103 Iteration 3 Error: 0.021660 Align patch 22 3 left Iteration 1 Error: 1.022541 Iteration 2 Error: 0.222122 Iteration 3 Error: 0.064746 Iteration 4 Error: 0.018581 Align patch 23 2 left Iteration 1 Error: 0.794013 Iteration 2 Error: 0.155011 Iteration 3 Error: 0.024453 Align patch 24 1 left Iteration 1 Error: 1.132747 Iteration 2 Error: 0.166815 Iteration 3 Error: 0.049427 Align patch 25 0 left Iteration 1 Error: 0.732123 Iteration 2 Error: 0.104616 Iteration 3 Error: 0.036243 3D Fitting completed. Patch alignment time: 17.18(sec) Local motion has been corrected. Process thread exits. Computational time: 25.869493 sec Total time: 31.428116 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00014hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00014hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.615997s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00014hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.200229s ........................................ >>>>>>TIME<<<<<< FFT: 1.268905s Defocus_U Defocus_V Angle CCC 10738.29 11582.04 10.63 0.052035 Final Values Defocus_U Defocus_V Angle CCC 10757.04 11588.29 10.95 0.097449 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00014hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00014hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 46.51 7.69 Num Hot pixels: 220 Hot pixel threshold: 92.62 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.007986 Iteration 2 Error: 0.148789 Iteration 3 Error: 0.029866 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.29 0.04 ...... Frame ( 3) shift: -0.57 0.07 ...... Frame ( 4) shift: -0.86 0.11 ...... Frame ( 5) shift: -1.15 0.14 ...... Frame ( 6) shift: -1.30 0.22 ...... Frame ( 7) shift: -1.31 0.33 ...... Frame ( 8) shift: -1.33 0.44 ...... Frame ( 9) shift: -1.31 0.55 ...... Frame ( 10) shift: -1.25 0.65 ...... Frame ( 11) shift: -1.18 0.76 ...... Frame ( 12) shift: -1.17 0.84 ...... Frame ( 13) shift: -1.21 0.88 ...... Frame ( 14) shift: -1.25 0.93 ...... Frame ( 15) shift: -1.24 0.98 ...... Frame ( 16) shift: -1.18 1.04 ...... Frame ( 17) shift: -1.12 1.09 ...... Frame ( 18) shift: -1.09 1.13 ...... Frame ( 19) shift: -1.08 1.15 ...... Frame ( 20) shift: -1.07 1.17 ...... Frame ( 21) shift: -1.08 1.21 ...... Frame ( 22) shift: -1.10 1.28 ...... Frame ( 23) shift: -1.12 1.36 ...... Frame ( 24) shift: -1.10 1.40 ...... Frame ( 25) shift: -1.05 1.42 ...... Frame ( 26) shift: -1.00 1.45 ...... Frame ( 27) shift: -0.97 1.49 ...... Frame ( 28) shift: -0.96 1.56 ...... Frame ( 29) shift: -0.95 1.63 ...... Frame ( 30) shift: -0.94 1.66 ...... Frame ( 31) shift: -0.92 1.65 ...... Frame ( 32) shift: -0.91 1.64 ...... Frame ( 33) shift: -0.90 1.57 ...... Frame ( 34) shift: -0.91 1.43 ...... Frame ( 35) shift: -0.93 1.30 ...... Frame ( 36) shift: -0.91 1.25 ...... Frame ( 37) shift: -0.86 1.28 ...... Frame ( 38) shift: -0.82 1.32 ...... Frame ( 39) shift: -0.77 1.35 ...... Frame ( 40) shift: -0.73 1.38 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.229159 Iteration 2 Error: 0.249037 Iteration 3 Error: 0.061819 Iteration 4 Error: 0.022085 Align patch 2 23 left Iteration 1 Error: 1.268368 Iteration 2 Error: 0.261176 Iteration 3 Error: 0.061134 Iteration 4 Error: 0.028316 Align patch 3 22 left Iteration 1 Error: 2.469806 Iteration 2 Error: 0.224626 Iteration 3 Error: 0.066921 Iteration 4 Error: 0.016984 Align patch 4 21 left Iteration 1 Error: 0.917908 Iteration 2 Error: 0.123420 Iteration 3 Error: 0.042947 Align patch 5 20 left Iteration 1 Error: 0.713348 Iteration 2 Error: 0.145106 Iteration 3 Error: 0.026340 Align patch 6 19 left Iteration 1 Error: 1.407332 Iteration 2 Error: 0.466247 Iteration 3 Error: 0.114308 Iteration 4 Error: 0.094487 Iteration 5 Error: 0.031439 Align patch 7 18 left Iteration 1 Error: 1.721141 Iteration 2 Error: 0.188816 Iteration 3 Error: 0.048890 Align patch 8 17 left Iteration 1 Error: 1.764801 Iteration 2 Error: 0.212788 Iteration 3 Error: 0.048177 Align patch 9 16 left Iteration 1 Error: 0.618491 Iteration 2 Error: 0.101212 Iteration 3 Error: 0.026055 Align patch 10 15 left Iteration 1 Error: 0.646711 Iteration 2 Error: 0.088252 Iteration 3 Error: 0.018940 Align patch 11 14 left Iteration 1 Error: 0.856133 Iteration 2 Error: 0.309082 Iteration 3 Error: 0.069227 Iteration 4 Error: 0.033916 Align patch 12 13 left Iteration 1 Error: 1.859823 Iteration 2 Error: 0.374701 Iteration 3 Error: 0.089337 Iteration 4 Error: 0.030640 Align patch 13 12 left Iteration 1 Error: 0.807784 Iteration 2 Error: 0.208168 Iteration 3 Error: 0.052715 Iteration 4 Error: 0.028049 Align patch 14 11 left Iteration 1 Error: 0.701719 Iteration 2 Error: 0.070389 Iteration 3 Error: 0.019772 Align patch 15 10 left Iteration 1 Error: 0.801314 Iteration 2 Error: 0.134805 Iteration 3 Error: 0.035731 Align patch 16 9 left Iteration 1 Error: 0.830137 Iteration 2 Error: 0.192586 Iteration 3 Error: 0.043233 Align patch 17 8 left Iteration 1 Error: 0.430903 Iteration 2 Error: 0.051255 Iteration 3 Error: 0.015903 Align patch 18 7 left Iteration 1 Error: 1.160449 Iteration 2 Error: 0.183382 Iteration 3 Error: 0.058714 Iteration 4 Error: 0.012870 Align patch 19 6 left Iteration 1 Error: 1.052523 Iteration 2 Error: 0.125450 Iteration 3 Error: 0.029890 Align patch 20 5 left Iteration 1 Error: 0.755585 Iteration 2 Error: 0.092943 Iteration 3 Error: 0.030889 Align patch 21 4 left Iteration 1 Error: 0.992428 Iteration 2 Error: 0.171986 Iteration 3 Error: 0.048893 Align patch 22 3 left Iteration 1 Error: 1.341897 Iteration 2 Error: 0.183912 Iteration 3 Error: 0.061441 Iteration 4 Error: 0.024404 Align patch 23 2 left Iteration 1 Error: 0.987901 Iteration 2 Error: 0.145330 Iteration 3 Error: 0.039419 Align patch 24 1 left Iteration 1 Error: 1.060495 Iteration 2 Error: 0.140600 Iteration 3 Error: 0.028436 Align patch 25 0 left Iteration 1 Error: 0.610510 Iteration 2 Error: 0.067229 Iteration 3 Error: 0.009990 3D Fitting completed. Patch alignment time: 15.65(sec) Local motion has been corrected. Process thread exits. Computational time: 24.221069 sec Total time: 30.278172 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00014hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00014hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.577147s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00014hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.081310s ........................................ >>>>>>TIME<<<<<< FFT: 0.834930s Defocus_U Defocus_V Angle CCC 10611.33 10076.17 88.10 0.044942 Final Values Defocus_U Defocus_V Angle CCC 10622.27 10087.11 89.68 0.085753 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00014hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00014hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 46.94 7.60 Num Hot pixels: 227 Hot pixel threshold: 92.52 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.103079 Iteration 2 Error: 0.102960 Iteration 3 Error: 0.019800 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.25 0.04 ...... Frame ( 3) shift: -0.50 0.08 ...... Frame ( 4) shift: -0.75 0.12 ...... Frame ( 5) shift: -1.00 0.17 ...... Frame ( 6) shift: -1.08 0.24 ...... Frame ( 7) shift: -1.00 0.35 ...... Frame ( 8) shift: -0.91 0.45 ...... Frame ( 9) shift: -0.86 0.58 ...... Frame ( 10) shift: -0.84 0.73 ...... Frame ( 11) shift: -0.83 0.88 ...... Frame ( 12) shift: -0.85 1.03 ...... Frame ( 13) shift: -0.93 1.19 ...... Frame ( 14) shift: -1.00 1.36 ...... Frame ( 15) shift: -1.00 1.46 ...... Frame ( 16) shift: -0.93 1.50 ...... Frame ( 17) shift: -0.86 1.54 ...... Frame ( 18) shift: -0.85 1.57 ...... Frame ( 19) shift: -0.90 1.60 ...... Frame ( 20) shift: -0.96 1.62 ...... Frame ( 21) shift: -1.00 1.63 ...... Frame ( 22) shift: -1.02 1.62 ...... Frame ( 23) shift: -1.05 1.62 ...... Frame ( 24) shift: -1.04 1.63 ...... Frame ( 25) shift: -0.98 1.66 ...... Frame ( 26) shift: -0.93 1.69 ...... Frame ( 27) shift: -0.86 1.63 ...... Frame ( 28) shift: -0.76 1.49 ...... Frame ( 29) shift: -0.67 1.35 ...... Frame ( 30) shift: -0.60 1.24 ...... Frame ( 31) shift: -0.56 1.18 ...... Frame ( 32) shift: -0.52 1.12 ...... Frame ( 33) shift: -0.51 1.07 ...... Frame ( 34) shift: -0.54 1.05 ...... Frame ( 35) shift: -0.57 1.03 ...... Frame ( 36) shift: -0.61 1.04 ...... Frame ( 37) shift: -0.66 1.07 ...... Frame ( 38) shift: -0.72 1.11 ...... Frame ( 39) shift: -0.77 1.14 ...... Frame ( 40) shift: -0.82 1.17 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.924494 Iteration 2 Error: 0.162084 Iteration 3 Error: 0.091626 Iteration 4 Error: 0.014207 Align patch 2 23 left Iteration 1 Error: 2.403975 Iteration 2 Error: 0.232876 Iteration 3 Error: 0.134199 Iteration 4 Error: 0.042342 Align patch 3 22 left Iteration 1 Error: 1.128312 Iteration 2 Error: 0.319956 Iteration 3 Error: 0.075076 Iteration 4 Error: 0.032283 Align patch 4 21 left Iteration 1 Error: 0.917753 Iteration 2 Error: 0.101831 Iteration 3 Error: 0.033627 Align patch 5 20 left Iteration 1 Error: 0.608857 Iteration 2 Error: 0.077430 Iteration 3 Error: 0.020721 Align patch 6 19 left Iteration 1 Error: 0.920624 Iteration 2 Error: 0.157580 Iteration 3 Error: 0.023634 Align patch 7 18 left Iteration 1 Error: 1.508344 Iteration 2 Error: 0.197092 Iteration 3 Error: 0.021194 Align patch 8 17 left Iteration 1 Error: 1.042091 Iteration 2 Error: 0.203745 Iteration 3 Error: 0.081207 Iteration 4 Error: 0.029958 Align patch 9 16 left Iteration 1 Error: 0.947751 Iteration 2 Error: 0.130076 Iteration 3 Error: 0.037157 Align patch 10 15 left Iteration 1 Error: 0.601981 Iteration 2 Error: 0.118177 Iteration 3 Error: 0.014769 Align patch 11 14 left Iteration 1 Error: 1.054862 Iteration 2 Error: 0.215746 Iteration 3 Error: 0.085345 Iteration 4 Error: 0.022419 Align patch 12 13 left Iteration 1 Error: 0.916499 Iteration 2 Error: 0.159425 Iteration 3 Error: 0.044195 Align patch 13 12 left Iteration 1 Error: 1.267912 Iteration 2 Error: 0.077078 Iteration 3 Error: 0.018617 Align patch 14 11 left Iteration 1 Error: 0.829540 Iteration 2 Error: 0.152393 Iteration 3 Error: 0.045105 Align patch 15 10 left Iteration 1 Error: 0.797496 Iteration 2 Error: 0.141677 Iteration 3 Error: 0.037154 Align patch 16 9 left Iteration 1 Error: 1.263089 Iteration 2 Error: 0.326154 Iteration 3 Error: 0.054891 Iteration 4 Error: 0.046089 Align patch 17 8 left Iteration 1 Error: 0.813163 Iteration 2 Error: 0.179761 Iteration 3 Error: 0.030431 Align patch 18 7 left Iteration 1 Error: 1.519863 Iteration 2 Error: 0.181014 Iteration 3 Error: 0.044778 Align patch 19 6 left Iteration 1 Error: 0.669590 Iteration 2 Error: 0.094248 Iteration 3 Error: 0.022306 Align patch 20 5 left Iteration 1 Error: 0.732448 Iteration 2 Error: 0.087845 Iteration 3 Error: 0.021941 Align patch 21 4 left Iteration 1 Error: 0.895350 Iteration 2 Error: 0.154997 Iteration 3 Error: 0.042905 Align patch 22 3 left Iteration 1 Error: 1.378306 Iteration 2 Error: 0.134855 Iteration 3 Error: 0.044228 Align patch 23 2 left Iteration 1 Error: 1.379570 Iteration 2 Error: 0.165191 Iteration 3 Error: 0.029222 Align patch 24 1 left Iteration 1 Error: 0.669741 Iteration 2 Error: 0.128638 Iteration 3 Error: 0.051608 Iteration 4 Error: 0.016648 Align patch 25 0 left Iteration 1 Error: 0.560687 Iteration 2 Error: 0.073019 Iteration 3 Error: 0.024025 3D Fitting completed. Patch alignment time: 16.07(sec) Local motion has been corrected. Process thread exits. Computational time: 25.157696 sec Total time: 31.046474 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00014hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00014hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.863644s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00014hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.443059s ........................................ >>>>>>TIME<<<<<< FFT: 0.787874s Defocus_U Defocus_V Angle CCC 11068.36 11900.39 6.12 0.051871 Final Values Defocus_U Defocus_V Angle CCC 11079.30 11911.33 6.75 0.094438 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00014hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00014hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 47.15 7.63 Num Hot pixels: 224 Hot pixel threshold: 92.95 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.758390 Iteration 2 Error: 0.090146 Iteration 3 Error: 0.018310 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.44 -0.06 ...... Frame ( 3) shift: -0.87 -0.11 ...... Frame ( 4) shift: -1.31 -0.17 ...... Frame ( 5) shift: -1.75 -0.23 ...... Frame ( 6) shift: -1.96 -0.28 ...... Frame ( 7) shift: -1.97 -0.32 ...... Frame ( 8) shift: -1.97 -0.36 ...... Frame ( 9) shift: -1.91 -0.37 ...... Frame ( 10) shift: -1.80 -0.33 ...... Frame ( 11) shift: -1.69 -0.29 ...... Frame ( 12) shift: -1.60 -0.25 ...... Frame ( 13) shift: -1.52 -0.20 ...... Frame ( 14) shift: -1.45 -0.15 ...... Frame ( 15) shift: -1.41 -0.14 ...... Frame ( 16) shift: -1.39 -0.18 ...... Frame ( 17) shift: -1.38 -0.22 ...... Frame ( 18) shift: -1.36 -0.26 ...... Frame ( 19) shift: -1.32 -0.31 ...... Frame ( 20) shift: -1.29 -0.36 ...... Frame ( 21) shift: -1.29 -0.37 ...... Frame ( 22) shift: -1.32 -0.36 ...... Frame ( 23) shift: -1.35 -0.35 ...... Frame ( 24) shift: -1.30 -0.31 ...... Frame ( 25) shift: -1.17 -0.23 ...... Frame ( 26) shift: -1.04 -0.16 ...... Frame ( 27) shift: -0.96 -0.14 ...... Frame ( 28) shift: -0.95 -0.17 ...... Frame ( 29) shift: -0.93 -0.20 ...... Frame ( 30) shift: -0.95 -0.24 ...... Frame ( 31) shift: -1.00 -0.29 ...... Frame ( 32) shift: -1.06 -0.34 ...... Frame ( 33) shift: -1.06 -0.37 ...... Frame ( 34) shift: -1.03 -0.39 ...... Frame ( 35) shift: -0.99 -0.41 ...... Frame ( 36) shift: -0.98 -0.39 ...... Frame ( 37) shift: -1.00 -0.33 ...... Frame ( 38) shift: -1.02 -0.27 ...... Frame ( 39) shift: -1.04 -0.21 ...... Frame ( 40) shift: -1.06 -0.15 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.870031 Iteration 2 Error: 0.277913 Iteration 3 Error: 0.091621 Iteration 4 Error: 0.028043 Align patch 2 23 left Iteration 1 Error: 1.589436 Iteration 2 Error: 0.161871 Iteration 3 Error: 0.047172 Align patch 3 22 left Iteration 1 Error: 0.814985 Iteration 2 Error: 0.112545 Iteration 3 Error: 0.023763 Align patch 4 21 left Iteration 1 Error: 0.625937 Iteration 2 Error: 0.103093 Iteration 3 Error: 0.014637 Align patch 5 20 left Iteration 1 Error: 0.745001 Iteration 2 Error: 0.138175 Iteration 3 Error: 0.026162 Align patch 6 19 left Iteration 1 Error: 1.066403 Iteration 2 Error: 0.154684 Iteration 3 Error: 0.032223 Align patch 7 18 left Iteration 1 Error: 0.819831 Iteration 2 Error: 0.170464 Iteration 3 Error: 0.032886 Align patch 8 17 left Iteration 1 Error: 0.853814 Iteration 2 Error: 0.116286 Iteration 3 Error: 0.018444 Align patch 9 16 left Iteration 1 Error: 0.762620 Iteration 2 Error: 0.165941 Iteration 3 Error: 0.049400 Align patch 10 15 left Iteration 1 Error: 0.716862 Iteration 2 Error: 0.056277 Iteration 3 Error: 0.020542 Align patch 11 14 left Iteration 1 Error: 1.060004 Iteration 2 Error: 0.195094 Iteration 3 Error: 0.044414 Align patch 12 13 left Iteration 1 Error: 0.584583 Iteration 2 Error: 0.079041 Iteration 3 Error: 0.034340 Align patch 13 12 left Iteration 1 Error: 0.883712 Iteration 2 Error: 0.134140 Iteration 3 Error: 0.037521 Align patch 14 11 left Iteration 1 Error: 0.781388 Iteration 2 Error: 0.177470 Iteration 3 Error: 0.040482 Align patch 15 10 left Iteration 1 Error: 0.706896 Iteration 2 Error: 0.112651 Iteration 3 Error: 0.024793 Align patch 16 9 left Iteration 1 Error: 1.501628 Iteration 2 Error: 0.148673 Iteration 3 Error: 0.039098 Align patch 17 8 left Iteration 1 Error: 0.885126 Iteration 2 Error: 0.081023 Iteration 3 Error: 0.019936 Align patch 18 7 left Iteration 1 Error: 0.921242 Iteration 2 Error: 0.161369 Iteration 3 Error: 0.063218 Iteration 4 Error: 0.034339 Align patch 19 6 left Iteration 1 Error: 0.694859 Iteration 2 Error: 0.096053 Iteration 3 Error: 0.027927 Align patch 20 5 left Iteration 1 Error: 0.913384 Iteration 2 Error: 0.174832 Iteration 3 Error: 0.051032 Iteration 4 Error: 0.014159 Align patch 21 4 left Iteration 1 Error: 1.233189 Iteration 2 Error: 0.262433 Iteration 3 Error: 0.074705 Iteration 4 Error: 0.040617 Align patch 22 3 left Iteration 1 Error: 0.847249 Iteration 2 Error: 0.125662 Iteration 3 Error: 0.023707 Align patch 23 2 left Iteration 1 Error: 1.187410 Iteration 2 Error: 0.148647 Iteration 3 Error: 0.032654 Align patch 24 1 left Iteration 1 Error: 0.709466 Iteration 2 Error: 0.164627 Iteration 3 Error: 0.071668 Iteration 4 Error: 0.022346 Align patch 25 0 left Iteration 1 Error: 0.750777 Iteration 2 Error: 0.124400 Iteration 3 Error: 0.020791 3D Fitting completed. Patch alignment time: 15.63(sec) Local motion has been corrected. Process thread exits. Computational time: 24.137163 sec Total time: 30.502764 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00014hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00014hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.834820s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00014hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.112803s ........................................ >>>>>>TIME<<<<<< FFT: 1.052720s Defocus_U Defocus_V Angle CCC 11081.25 10453.96 82.40 0.048263 Final Values Defocus_U Defocus_V Angle CCC 11175.03 10510.25 83.35 0.092501 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00015hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00015hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 1.000e-01 CC threshold: 0.734 Mean Std: 45.35 7.57 Num Hot pixels: 190 Hot pixel threshold: 90.75 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.348815 Iteration 2 Error: 0.291235 Iteration 3 Error: 0.067993 Iteration 4 Error: 0.026766 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.40 0.01 ...... Frame ( 3) shift: -0.80 0.02 ...... Frame ( 4) shift: -1.20 0.03 ...... Frame ( 5) shift: -1.59 0.04 ...... Frame ( 6) shift: -1.77 0.05 ...... Frame ( 7) shift: -1.74 0.06 ...... Frame ( 8) shift: -1.70 0.08 ...... Frame ( 9) shift: -1.67 0.14 ...... Frame ( 10) shift: -1.64 0.27 ...... Frame ( 11) shift: -1.62 0.39 ...... Frame ( 12) shift: -1.59 0.52 ...... Frame ( 13) shift: -1.55 0.65 ...... Frame ( 14) shift: -1.50 0.78 ...... Frame ( 15) shift: -1.47 0.92 ...... Frame ( 16) shift: -1.46 1.06 ...... Frame ( 17) shift: -1.44 1.21 ...... Frame ( 18) shift: -1.43 1.31 ...... Frame ( 19) shift: -1.41 1.36 ...... Frame ( 20) shift: -1.40 1.41 ...... Frame ( 21) shift: -1.43 1.51 ...... Frame ( 22) shift: -1.52 1.66 ...... Frame ( 23) shift: -1.60 1.80 ...... Frame ( 24) shift: -1.61 1.91 ...... Frame ( 25) shift: -1.54 1.98 ...... Frame ( 26) shift: -1.47 2.05 ...... Frame ( 27) shift: -1.41 2.12 ...... Frame ( 28) shift: -1.37 2.20 ...... Frame ( 29) shift: -1.33 2.27 ...... Frame ( 30) shift: -1.33 2.34 ...... Frame ( 31) shift: -1.36 2.39 ...... Frame ( 32) shift: -1.39 2.44 ...... Frame ( 33) shift: -1.38 2.46 ...... Frame ( 34) shift: -1.31 2.46 ...... Frame ( 35) shift: -1.25 2.46 ...... Frame ( 36) shift: -1.21 2.51 ...... Frame ( 37) shift: -1.19 2.61 ...... Frame ( 38) shift: -1.16 2.71 ...... Frame ( 39) shift: -1.14 2.80 ...... Frame ( 40) shift: -1.12 2.90 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.488115 Iteration 2 Error: 0.294870 Iteration 3 Error: 0.150142 Iteration 4 Error: 0.046034 Align patch 2 23 left Iteration 1 Error: 1.630641 Iteration 2 Error: 0.184423 Iteration 3 Error: 0.062209 Iteration 4 Error: 0.022305 Align patch 3 22 left Iteration 1 Error: 0.766821 Iteration 2 Error: 0.227986 Iteration 3 Error: 0.137542 Iteration 4 Error: 0.070828 Iteration 5 Error: 0.039143 Align patch 4 21 left Iteration 1 Error: 0.683559 Iteration 2 Error: 0.095350 Iteration 3 Error: 0.023016 Align patch 5 20 left Iteration 1 Error: 0.679516 Iteration 2 Error: 0.122620 Iteration 3 Error: 0.037748 Align patch 6 19 left Iteration 1 Error: 1.575147 Iteration 2 Error: 0.196408 Iteration 3 Error: 0.053142 Iteration 4 Error: 0.026678 Align patch 7 18 left Iteration 1 Error: 0.978063 Iteration 2 Error: 0.207036 Iteration 3 Error: 0.062770 Iteration 4 Error: 0.022936 Align patch 8 17 left Iteration 1 Error: 1.298258 Iteration 2 Error: 0.187915 Iteration 3 Error: 0.061655 Iteration 4 Error: 0.015060 Align patch 9 16 left Iteration 1 Error: 0.508703 Iteration 2 Error: 0.104870 Iteration 3 Error: 0.041217 Align patch 10 15 left Iteration 1 Error: 0.622690 Iteration 2 Error: 0.133895 Iteration 3 Error: 0.049949 Align patch 11 14 left Iteration 1 Error: 1.663111 Iteration 2 Error: 0.308840 Iteration 3 Error: 0.077548 Iteration 4 Error: 0.038278 Align patch 12 13 left Iteration 1 Error: 0.744536 Iteration 2 Error: 0.083512 Iteration 3 Error: 0.019092 Align patch 13 12 left Iteration 1 Error: 0.753072 Iteration 2 Error: 0.092000 Iteration 3 Error: 0.014526 Align patch 14 11 left Iteration 1 Error: 0.823729 Iteration 2 Error: 0.132458 Iteration 3 Error: 0.042782 Align patch 15 10 left Iteration 1 Error: 0.546331 Iteration 2 Error: 0.135371 Iteration 3 Error: 0.042699 Align patch 16 9 left Iteration 1 Error: 0.731045 Iteration 2 Error: 0.241104 Iteration 3 Error: 0.037135 Align patch 17 8 left Iteration 1 Error: 0.976712 Iteration 2 Error: 0.157130 Iteration 3 Error: 0.052822 Iteration 4 Error: 0.023306 Align patch 18 7 left Iteration 1 Error: 1.176318 Iteration 2 Error: 0.181389 Iteration 3 Error: 0.064055 Iteration 4 Error: 0.022020 Align patch 19 6 left Iteration 1 Error: 0.718292 Iteration 2 Error: 0.098196 Iteration 3 Error: 0.029833 Align patch 20 5 left Iteration 1 Error: 0.517789 Iteration 2 Error: 0.092090 Iteration 3 Error: 0.012794 Align patch 21 4 left Iteration 1 Error: 1.769690 Iteration 2 Error: 0.537648 Iteration 3 Error: 0.112426 Iteration 4 Error: 0.036153 Align patch 22 3 left Iteration 1 Error: 1.161887 Iteration 2 Error: 0.143841 Iteration 3 Error: 0.037437 Align patch 23 2 left Iteration 1 Error: 1.183094 Iteration 2 Error: 0.240386 Iteration 3 Error: 0.056079 Iteration 4 Error: 0.013825 Align patch 24 1 left Iteration 1 Error: 0.908758 Iteration 2 Error: 0.112480 Iteration 3 Error: 0.028468 Align patch 25 0 left Iteration 1 Error: 0.692365 Iteration 2 Error: 0.090401 Iteration 3 Error: 0.018706 3D Fitting completed. Patch alignment time: 16.32(sec) Local motion has been corrected. Process thread exits. Computational time: 25.116386 sec Total time: 30.581398 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00015hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00015hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.726194s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00015hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.031615s ........................................ >>>>>>TIME<<<<<< FFT: 0.948410s Defocus_U Defocus_V Angle CCC 9818.40 10650.43 12.37 0.046106 Final Values Defocus_U Defocus_V Angle CCC 9824.63 10653.58 12.06 0.086593 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00015hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00015hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 45.04 7.66 Num Hot pixels: 202 Hot pixel threshold: 91.01 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.625723 Iteration 2 Error: 0.138408 Iteration 3 Error: 0.028219 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.29 0.04 ...... Frame ( 3) shift: -0.57 0.09 ...... Frame ( 4) shift: -0.86 0.13 ...... Frame ( 5) shift: -1.14 0.18 ...... Frame ( 6) shift: -1.36 0.24 ...... Frame ( 7) shift: -1.51 0.33 ...... Frame ( 8) shift: -1.65 0.41 ...... Frame ( 9) shift: -1.75 0.50 ...... Frame ( 10) shift: -1.79 0.60 ...... Frame ( 11) shift: -1.84 0.69 ...... Frame ( 12) shift: -1.89 0.77 ...... Frame ( 13) shift: -1.95 0.83 ...... Frame ( 14) shift: -2.01 0.89 ...... Frame ( 15) shift: -2.03 0.90 ...... Frame ( 16) shift: -2.02 0.87 ...... Frame ( 17) shift: -2.01 0.83 ...... Frame ( 18) shift: -2.01 0.87 ...... Frame ( 19) shift: -2.01 0.97 ...... Frame ( 20) shift: -2.02 1.08 ...... Frame ( 21) shift: -2.02 1.14 ...... Frame ( 22) shift: -2.02 1.17 ...... Frame ( 23) shift: -2.03 1.19 ...... Frame ( 24) shift: -2.02 1.21 ...... Frame ( 25) shift: -2.01 1.21 ...... Frame ( 26) shift: -2.00 1.21 ...... Frame ( 27) shift: -1.99 1.25 ...... Frame ( 28) shift: -2.00 1.34 ...... Frame ( 29) shift: -2.00 1.42 ...... Frame ( 30) shift: -2.02 1.49 ...... Frame ( 31) shift: -2.06 1.55 ...... Frame ( 32) shift: -2.10 1.60 ...... Frame ( 33) shift: -2.08 1.65 ...... Frame ( 34) shift: -1.99 1.68 ...... Frame ( 35) shift: -1.91 1.71 ...... Frame ( 36) shift: -1.87 1.73 ...... Frame ( 37) shift: -1.87 1.73 ...... Frame ( 38) shift: -1.87 1.73 ...... Frame ( 39) shift: -1.88 1.73 ...... Frame ( 40) shift: -1.88 1.73 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.252474 Iteration 2 Error: 0.372824 Iteration 3 Error: 0.196612 Iteration 4 Error: 0.123565 Iteration 5 Error: 0.057056 Align patch 1 24 left Iteration 1 Error: 1.958257 Iteration 2 Error: 0.112287 Iteration 3 Error: 0.029727 Align patch 2 23 left Iteration 1 Error: 2.224840 Iteration 2 Error: 0.277759 Iteration 3 Error: 0.091483 Iteration 4 Error: 0.029057 Align patch 3 22 left Iteration 1 Error: 0.683793 Iteration 2 Error: 0.276251 Iteration 3 Error: 0.087866 Iteration 4 Error: 0.038384 Align patch 4 21 left Iteration 1 Error: 0.775591 Iteration 2 Error: 0.149774 Iteration 3 Error: 0.049637 Align patch 5 20 left Iteration 1 Error: 0.545110 Iteration 2 Error: 0.177145 Iteration 3 Error: 0.053908 Iteration 4 Error: 0.024515 Align patch 6 19 left Iteration 1 Error: 0.823947 Iteration 2 Error: 0.325200 Iteration 3 Error: 0.218304 Iteration 4 Error: 0.186866 Iteration 5 Error: 0.111754 Align patch 6 19 left Iteration 1 Error: 1.605538 Iteration 2 Error: 0.291636 Iteration 3 Error: 0.038798 Align patch 7 18 left Iteration 1 Error: 2.007460 Iteration 2 Error: 0.232269 Iteration 3 Error: 0.029696 Align patch 8 17 left Iteration 1 Error: 0.745578 Iteration 2 Error: 0.126743 Iteration 3 Error: 0.049589 Align patch 9 16 left Iteration 1 Error: 0.884108 Iteration 2 Error: 0.169462 Iteration 3 Error: 0.035081 Align patch 10 15 left Iteration 1 Error: 0.380233 Iteration 2 Error: 0.071287 Iteration 3 Error: 0.009081 Align patch 11 14 left Iteration 1 Error: 0.905833 Iteration 2 Error: 0.118028 Iteration 3 Error: 0.038271 Align patch 12 13 left Iteration 1 Error: 1.196191 Iteration 2 Error: 0.215556 Iteration 3 Error: 0.044620 Align patch 13 12 left Iteration 1 Error: 0.800470 Iteration 2 Error: 0.159950 Iteration 3 Error: 0.045939 Align patch 14 11 left Iteration 1 Error: 0.667652 Iteration 2 Error: 0.173034 Iteration 3 Error: 0.057786 Iteration 4 Error: 0.014046 Align patch 15 10 left Iteration 1 Error: 0.598204 Iteration 2 Error: 0.071770 Iteration 3 Error: 0.017309 Align patch 16 9 left Iteration 1 Error: 0.708734 Iteration 2 Error: 0.185373 Iteration 3 Error: 0.043576 Align patch 17 8 left Iteration 1 Error: 0.682363 Iteration 2 Error: 0.119953 Iteration 3 Error: 0.027133 Align patch 18 7 left Iteration 1 Error: 0.724895 Iteration 2 Error: 0.082729 Iteration 3 Error: 0.018882 Align patch 19 6 left Iteration 1 Error: 0.917951 Iteration 2 Error: 0.102589 Iteration 3 Error: 0.027924 Align patch 20 5 left Iteration 1 Error: 0.680809 Iteration 2 Error: 0.094819 Iteration 3 Error: 0.026880 Align patch 21 4 left Iteration 1 Error: 0.889504 Iteration 2 Error: 0.158984 Iteration 3 Error: 0.039877 Align patch 22 3 left Iteration 1 Error: 1.221878 Iteration 2 Error: 0.178021 Iteration 3 Error: 0.047751 Align patch 23 2 left Iteration 1 Error: 1.051244 Iteration 2 Error: 0.204638 Iteration 3 Error: 0.049371 Align patch 24 1 left Iteration 1 Error: 0.824338 Iteration 2 Error: 0.153940 Iteration 3 Error: 0.023516 Align patch 25 0 left Iteration 1 Error: 0.991366 Iteration 2 Error: 0.130403 Iteration 3 Error: 0.034587 3D Fitting completed. Patch alignment time: 17.79(sec) Local motion has been corrected. Process thread exits. Computational time: 26.330711 sec Total time: 31.989609 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00015hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00015hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.613737s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00015hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.598933s ........................................ >>>>>>TIME<<<<<< FFT: 0.942942s Defocus_U Defocus_V Angle CCC 12208.98 12728.52 0.08 0.043648 Final Values Defocus_U Defocus_V Angle CCC 12726.95 12229.31 89.76 0.079998 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00015hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00015hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.996e-02 CC threshold: 0.734 Mean Std: 44.05 7.30 Num Hot pixels: 203 Hot pixel threshold: 87.84 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.995090 Iteration 2 Error: 0.184330 Iteration 3 Error: 0.042039 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.29 0.01 ...... Frame ( 3) shift: -0.57 0.02 ...... Frame ( 4) shift: -0.86 0.02 ...... Frame ( 5) shift: -1.15 0.03 ...... Frame ( 6) shift: -1.31 0.03 ...... Frame ( 7) shift: -1.34 0.01 ...... Frame ( 8) shift: -1.37 -0.00 ...... Frame ( 9) shift: -1.37 0.07 ...... Frame ( 10) shift: -1.34 0.23 ...... Frame ( 11) shift: -1.30 0.40 ...... Frame ( 12) shift: -1.30 0.53 ...... Frame ( 13) shift: -1.33 0.62 ...... Frame ( 14) shift: -1.35 0.72 ...... Frame ( 15) shift: -1.36 0.79 ...... Frame ( 16) shift: -1.35 0.83 ...... Frame ( 17) shift: -1.33 0.87 ...... Frame ( 18) shift: -1.30 0.88 ...... Frame ( 19) shift: -1.25 0.86 ...... Frame ( 20) shift: -1.20 0.84 ...... Frame ( 21) shift: -1.13 0.90 ...... Frame ( 22) shift: -1.03 1.02 ...... Frame ( 23) shift: -0.94 1.13 ...... Frame ( 24) shift: -0.87 1.21 ...... Frame ( 25) shift: -0.82 1.25 ...... Frame ( 26) shift: -0.78 1.28 ...... Frame ( 27) shift: -0.77 1.31 ...... Frame ( 28) shift: -0.79 1.35 ...... Frame ( 29) shift: -0.82 1.39 ...... Frame ( 30) shift: -0.85 1.45 ...... Frame ( 31) shift: -0.89 1.52 ...... Frame ( 32) shift: -0.93 1.60 ...... Frame ( 33) shift: -0.95 1.64 ...... Frame ( 34) shift: -0.93 1.63 ...... Frame ( 35) shift: -0.91 1.63 ...... Frame ( 36) shift: -0.89 1.63 ...... Frame ( 37) shift: -0.85 1.64 ...... Frame ( 38) shift: -0.81 1.64 ...... Frame ( 39) shift: -0.78 1.65 ...... Frame ( 40) shift: -0.74 1.65 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.198242 Iteration 2 Error: 0.413275 Iteration 3 Error: 0.093953 Iteration 4 Error: 0.037673 Align patch 2 23 left Iteration 1 Error: 2.173089 Iteration 2 Error: 0.437142 Iteration 3 Error: 0.132254 Iteration 4 Error: 0.053717 Iteration 5 Error: 0.030730 Align patch 3 22 left Iteration 1 Error: 2.142576 Iteration 2 Error: 0.772609 Iteration 3 Error: 0.420633 Iteration 4 Error: 0.288998 Iteration 5 Error: 0.210611 Align patch 3 22 left Iteration 1 Error: 2.444997 Iteration 2 Error: 0.606686 Iteration 3 Error: 0.159559 Iteration 4 Error: 0.068602 Iteration 5 Error: 0.027108 Align patch 4 21 left Iteration 1 Error: 1.354081 Iteration 2 Error: 0.134321 Iteration 3 Error: 0.053767 Iteration 4 Error: 0.025586 Align patch 5 20 left Iteration 1 Error: 0.955599 Iteration 2 Error: 0.162553 Iteration 3 Error: 0.037746 Align patch 6 19 left Iteration 1 Error: 1.484027 Iteration 2 Error: 0.240728 Iteration 3 Error: 0.113110 Iteration 4 Error: 0.026496 Align patch 7 18 left Iteration 1 Error: 1.759175 Iteration 2 Error: 0.338067 Iteration 3 Error: 0.082272 Iteration 4 Error: 0.043134 Align patch 8 17 left Iteration 1 Error: 1.045754 Iteration 2 Error: 0.360804 Iteration 3 Error: 0.121187 Iteration 4 Error: 0.060051 Iteration 5 Error: 0.026818 Align patch 9 16 left Iteration 1 Error: 0.896951 Iteration 2 Error: 0.108357 Iteration 3 Error: 0.034669 Align patch 10 15 left Iteration 1 Error: 0.758950 Iteration 2 Error: 0.107126 Iteration 3 Error: 0.027953 Align patch 11 14 left Iteration 1 Error: 0.995049 Iteration 2 Error: 0.151664 Iteration 3 Error: 0.036173 Align patch 12 13 left Iteration 1 Error: 0.725378 Iteration 2 Error: 0.170921 Iteration 3 Error: 0.045747 Align patch 13 12 left Iteration 1 Error: 0.775628 Iteration 2 Error: 0.110098 Iteration 3 Error: 0.032072 Align patch 14 11 left Iteration 1 Error: 0.653851 Iteration 2 Error: 0.116166 Iteration 3 Error: 0.022822 Align patch 15 10 left Iteration 1 Error: 0.670331 Iteration 2 Error: 0.122225 Iteration 3 Error: 0.030999 Align patch 16 9 left Iteration 1 Error: 0.944616 Iteration 2 Error: 0.167778 Iteration 3 Error: 0.031350 Align patch 17 8 left Iteration 1 Error: 0.916499 Iteration 2 Error: 0.248946 Iteration 3 Error: 0.037245 Align patch 18 7 left Iteration 1 Error: 1.052577 Iteration 2 Error: 0.124335 Iteration 3 Error: 0.035121 Align patch 19 6 left Iteration 1 Error: 0.677352 Iteration 2 Error: 0.120562 Iteration 3 Error: 0.040085 Align patch 20 5 left Iteration 1 Error: 0.991250 Iteration 2 Error: 0.174208 Iteration 3 Error: 0.036988 Align patch 21 4 left Iteration 1 Error: 2.066207 Iteration 2 Error: 0.220319 Iteration 3 Error: 0.063489 Iteration 4 Error: 0.026535 Align patch 22 3 left Iteration 1 Error: 1.563265 Iteration 2 Error: 0.214110 Iteration 3 Error: 0.059909 Iteration 4 Error: 0.016066 Align patch 23 2 left Iteration 1 Error: 0.700741 Iteration 2 Error: 0.127097 Iteration 3 Error: 0.031417 Align patch 24 1 left Iteration 1 Error: 0.707461 Iteration 2 Error: 0.099733 Iteration 3 Error: 0.031526 Align patch 25 0 left Iteration 1 Error: 0.662375 Iteration 2 Error: 0.112849 Iteration 3 Error: 0.023893 3D Fitting completed. Patch alignment time: 16.51(sec) Local motion has been corrected. Process thread exits. Computational time: 24.911030 sec Total time: 30.456640 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00015hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00015hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.717488s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00015hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.032228s ........................................ >>>>>>TIME<<<<<< FFT: 0.934273s Defocus_U Defocus_V Angle CCC 10751.96 11580.08 5.90 0.046341 Final Values Defocus_U Defocus_V Angle CCC 10750.39 11591.03 5.90 0.084984 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00015hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00015hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 44.34 7.47 Num Hot pixels: 207 Hot pixel threshold: 89.16 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.826243 Iteration 2 Error: 0.101268 Iteration 3 Error: 0.019216 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.29 0.05 ...... Frame ( 3) shift: -0.58 0.09 ...... Frame ( 4) shift: -0.88 0.14 ...... Frame ( 5) shift: -1.17 0.18 ...... Frame ( 6) shift: -1.32 0.17 ...... Frame ( 7) shift: -1.32 0.11 ...... Frame ( 8) shift: -1.32 0.04 ...... Frame ( 9) shift: -1.31 0.06 ...... Frame ( 10) shift: -1.29 0.15 ...... Frame ( 11) shift: -1.27 0.24 ...... Frame ( 12) shift: -1.26 0.30 ...... Frame ( 13) shift: -1.26 0.33 ...... Frame ( 14) shift: -1.26 0.36 ...... Frame ( 15) shift: -1.23 0.41 ...... Frame ( 16) shift: -1.18 0.49 ...... Frame ( 17) shift: -1.13 0.57 ...... Frame ( 18) shift: -1.09 0.62 ...... Frame ( 19) shift: -1.08 0.65 ...... Frame ( 20) shift: -1.06 0.67 ...... Frame ( 21) shift: -1.06 0.69 ...... Frame ( 22) shift: -1.10 0.70 ...... Frame ( 23) shift: -1.13 0.71 ...... Frame ( 24) shift: -1.15 0.73 ...... Frame ( 25) shift: -1.15 0.76 ...... Frame ( 26) shift: -1.15 0.79 ...... Frame ( 27) shift: -1.16 0.80 ...... Frame ( 28) shift: -1.16 0.79 ...... Frame ( 29) shift: -1.17 0.78 ...... Frame ( 30) shift: -1.15 0.81 ...... Frame ( 31) shift: -1.10 0.88 ...... Frame ( 32) shift: -1.05 0.94 ...... Frame ( 33) shift: -1.02 0.99 ...... Frame ( 34) shift: -1.00 1.04 ...... Frame ( 35) shift: -0.98 1.08 ...... Frame ( 36) shift: -0.97 1.08 ...... Frame ( 37) shift: -0.95 1.05 ...... Frame ( 38) shift: -0.94 1.02 ...... Frame ( 39) shift: -0.92 0.99 ...... Frame ( 40) shift: -0.91 0.95 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.199023 Iteration 2 Error: 0.237695 Iteration 3 Error: 0.048017 Align patch 2 23 left Iteration 1 Error: 0.830296 Iteration 2 Error: 0.118719 Iteration 3 Error: 0.048441 Align patch 3 22 left Iteration 1 Error: 0.668416 Iteration 2 Error: 0.135550 Iteration 3 Error: 0.023927 Align patch 4 21 left Iteration 1 Error: 0.511928 Iteration 2 Error: 0.104820 Iteration 3 Error: 0.030891 Align patch 5 20 left Iteration 1 Error: 0.888978 Iteration 2 Error: 0.069189 Iteration 3 Error: 0.016632 Align patch 6 19 left Iteration 1 Error: 0.972061 Iteration 2 Error: 0.161480 Iteration 3 Error: 0.048295 Align patch 7 18 left Iteration 1 Error: 0.764064 Iteration 2 Error: 0.112075 Iteration 3 Error: 0.034514 Align patch 8 17 left Iteration 1 Error: 0.754249 Iteration 2 Error: 0.141244 Iteration 3 Error: 0.037858 Align patch 9 16 left Iteration 1 Error: 0.528867 Iteration 2 Error: 0.092481 Iteration 3 Error: 0.016444 Align patch 10 15 left Iteration 1 Error: 0.732910 Iteration 2 Error: 0.102597 Iteration 3 Error: 0.026026 Align patch 11 14 left Iteration 1 Error: 0.762412 Iteration 2 Error: 0.111325 Iteration 3 Error: 0.026101 Align patch 12 13 left Iteration 1 Error: 0.623098 Iteration 2 Error: 0.145135 Iteration 3 Error: 0.043199 Align patch 13 12 left Iteration 1 Error: 0.773480 Iteration 2 Error: 0.114672 Iteration 3 Error: 0.020977 Align patch 14 11 left Iteration 1 Error: 0.681185 Iteration 2 Error: 0.097166 Iteration 3 Error: 0.019235 Align patch 15 10 left Iteration 1 Error: 1.006995 Iteration 2 Error: 0.196658 Iteration 3 Error: 0.044605 Align patch 16 9 left Iteration 1 Error: 0.542228 Iteration 2 Error: 0.123552 Iteration 3 Error: 0.016348 Align patch 17 8 left Iteration 1 Error: 0.792442 Iteration 2 Error: 0.152072 Iteration 3 Error: 0.032066 Align patch 18 7 left Iteration 1 Error: 0.888153 Iteration 2 Error: 0.149947 Iteration 3 Error: 0.028288 Align patch 19 6 left Iteration 1 Error: 0.712633 Iteration 2 Error: 0.096321 Iteration 3 Error: 0.042865 Align patch 20 5 left Iteration 1 Error: 0.868104 Iteration 2 Error: 0.108014 Iteration 3 Error: 0.023234 Align patch 21 4 left Iteration 1 Error: 0.756645 Iteration 2 Error: 0.090939 Iteration 3 Error: 0.017422 Align patch 22 3 left Iteration 1 Error: 1.141520 Iteration 2 Error: 0.164315 Iteration 3 Error: 0.040459 Align patch 23 2 left Iteration 1 Error: 1.107642 Iteration 2 Error: 0.125148 Iteration 3 Error: 0.031051 Align patch 24 1 left Iteration 1 Error: 1.021405 Iteration 2 Error: 0.172813 Iteration 3 Error: 0.027541 Align patch 25 0 left Iteration 1 Error: 0.579051 Iteration 2 Error: 0.125550 Iteration 3 Error: 0.023792 3D Fitting completed. Patch alignment time: 14.81(sec) Local motion has been corrected. Process thread exits. Computational time: 23.206223 sec Total time: 28.594177 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00015hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00015hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.567377s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00015hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.025626s ........................................ >>>>>>TIME<<<<<< FFT: 0.945916s Defocus_U Defocus_V Angle CCC 12689.50 12029.25 85.67 0.043987 Final Values Defocus_U Defocus_V Angle CCC 12702.00 12038.64 84.42 0.078184 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00016hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00016hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.314e-01 9.795e-02 CC threshold: 0.719 Mean Std: 41.55 7.25 Num Hot pixels: 181 Hot pixel threshold: 85.05 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.706098 Iteration 2 Error: 0.192811 Iteration 3 Error: 0.036920 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.06 0.20 ...... Frame ( 3) shift: -0.12 0.39 ...... Frame ( 4) shift: -0.19 0.59 ...... Frame ( 5) shift: -0.25 0.79 ...... Frame ( 6) shift: -0.35 0.94 ...... Frame ( 7) shift: -0.50 1.04 ...... Frame ( 8) shift: -0.65 1.15 ...... Frame ( 9) shift: -0.74 1.26 ...... Frame ( 10) shift: -0.78 1.38 ...... Frame ( 11) shift: -0.82 1.49 ...... Frame ( 12) shift: -0.85 1.60 ...... Frame ( 13) shift: -0.87 1.69 ...... Frame ( 14) shift: -0.89 1.78 ...... Frame ( 15) shift: -0.94 1.85 ...... Frame ( 16) shift: -1.02 1.90 ...... Frame ( 17) shift: -1.10 1.95 ...... Frame ( 18) shift: -1.12 2.02 ...... Frame ( 19) shift: -1.09 2.10 ...... Frame ( 20) shift: -1.05 2.18 ...... Frame ( 21) shift: -1.02 2.24 ...... Frame ( 22) shift: -1.00 2.27 ...... Frame ( 23) shift: -0.99 2.31 ...... Frame ( 24) shift: -0.98 2.36 ...... Frame ( 25) shift: -0.99 2.43 ...... Frame ( 26) shift: -1.00 2.49 ...... Frame ( 27) shift: -1.01 2.52 ...... Frame ( 28) shift: -1.02 2.52 ...... Frame ( 29) shift: -1.03 2.51 ...... Frame ( 30) shift: -1.02 2.51 ...... Frame ( 31) shift: -1.01 2.52 ...... Frame ( 32) shift: -0.99 2.52 ...... Frame ( 33) shift: -0.96 2.58 ...... Frame ( 34) shift: -0.90 2.70 ...... Frame ( 35) shift: -0.85 2.81 ...... Frame ( 36) shift: -0.81 2.88 ...... Frame ( 37) shift: -0.79 2.90 ...... Frame ( 38) shift: -0.77 2.92 ...... Frame ( 39) shift: -0.75 2.94 ...... Frame ( 40) shift: -0.73 2.96 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.858274 Iteration 2 Error: 0.179023 Iteration 3 Error: 0.073471 Iteration 4 Error: 0.042007 Align patch 2 23 left Iteration 1 Error: 1.387075 Iteration 2 Error: 0.135076 Iteration 3 Error: 0.025623 Align patch 3 22 left Iteration 1 Error: 1.127502 Iteration 2 Error: 0.143544 Iteration 3 Error: 0.056831 Iteration 4 Error: 0.014669 Align patch 4 21 left Iteration 1 Error: 0.812596 Iteration 2 Error: 0.144043 Iteration 3 Error: 0.041369 Align patch 5 20 left Iteration 1 Error: 1.244702 Iteration 2 Error: 0.353792 Iteration 3 Error: 0.040773 Align patch 6 19 left Iteration 1 Error: 0.865260 Iteration 2 Error: 0.208233 Iteration 3 Error: 0.081165 Iteration 4 Error: 0.045277 Align patch 7 18 left Iteration 1 Error: 0.501466 Iteration 2 Error: 0.126527 Iteration 3 Error: 0.032971 Align patch 8 17 left Iteration 1 Error: 0.660075 Iteration 2 Error: 0.105161 Iteration 3 Error: 0.033642 Align patch 9 16 left Iteration 1 Error: 0.786634 Iteration 2 Error: 0.122286 Iteration 3 Error: 0.028274 Align patch 10 15 left Iteration 1 Error: 1.157271 Iteration 2 Error: 0.133488 Iteration 3 Error: 0.035226 Align patch 11 14 left Iteration 1 Error: 1.497762 Iteration 2 Error: 0.634685 Iteration 3 Error: 0.183109 Iteration 4 Error: 0.116402 Iteration 5 Error: 0.045684 Align patch 12 13 left Iteration 1 Error: 1.060032 Iteration 2 Error: 0.204595 Iteration 3 Error: 0.066329 Iteration 4 Error: 0.016618 Align patch 13 12 left Iteration 1 Error: 0.975648 Iteration 2 Error: 0.171013 Iteration 3 Error: 0.032059 Align patch 14 11 left Iteration 1 Error: 0.621805 Iteration 2 Error: 0.118157 Iteration 3 Error: 0.020289 Align patch 15 10 left Iteration 1 Error: 1.433558 Iteration 2 Error: 0.241118 Iteration 3 Error: 0.053100 Iteration 4 Error: 0.015656 Align patch 16 9 left Iteration 1 Error: 2.078705 Iteration 2 Error: 0.465225 Iteration 3 Error: 0.234327 Iteration 4 Error: 0.091356 Iteration 5 Error: 0.033451 Align patch 17 8 left Iteration 1 Error: 0.976658 Iteration 2 Error: 0.172453 Iteration 3 Error: 0.041184 Align patch 18 7 left Iteration 1 Error: 0.851678 Iteration 2 Error: 0.116813 Iteration 3 Error: 0.020673 Align patch 19 6 left Iteration 1 Error: 0.762827 Iteration 2 Error: 0.092133 Iteration 3 Error: 0.021649 Align patch 20 5 left Iteration 1 Error: 0.934843 Iteration 2 Error: 0.260578 Iteration 3 Error: 0.034132 Align patch 21 4 left Iteration 1 Error: 2.300579 Iteration 2 Error: 0.393833 Iteration 3 Error: 0.171286 Iteration 4 Error: 0.055335 Iteration 5 Error: 0.022918 Align patch 22 3 left Iteration 1 Error: 1.896157 Iteration 2 Error: 0.175947 Iteration 3 Error: 0.046154 Align patch 23 2 left Iteration 1 Error: 1.380835 Iteration 2 Error: 0.112800 Iteration 3 Error: 0.015955 Align patch 24 1 left Iteration 1 Error: 0.549591 Iteration 2 Error: 0.113606 Iteration 3 Error: 0.020591 Align patch 25 0 left Iteration 1 Error: 1.283776 Iteration 2 Error: 0.238332 Iteration 3 Error: 0.048676 3D Fitting completed. Patch alignment time: 15.79(sec) Local motion has been corrected. Process thread exits. Computational time: 24.597666 sec Total time: 30.530388 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00016hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00016hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.731078s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00016hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.234686s ........................................ >>>>>>TIME<<<<<< FFT: 1.173648s Defocus_U Defocus_V Angle CCC 13037.11 13849.61 12.72 -0.018198 Final Values Defocus_U Defocus_V Angle CCC 13037.11 13852.74 12.40 -0.168244 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00016hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00016hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.301e-01 9.707e-02 CC threshold: 0.712 Mean Std: 30.48 6.22 Num Hot pixels: 176 Hot pixel threshold: 67.79 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.957255 Iteration 2 Error: 0.278243 Iteration 3 Error: 0.057319 Iteration 4 Error: 0.015615 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.07 0.15 ...... Frame ( 3) shift: 0.14 0.31 ...... Frame ( 4) shift: 0.21 0.46 ...... Frame ( 5) shift: 0.28 0.61 ...... Frame ( 6) shift: 0.37 0.75 ...... Frame ( 7) shift: 0.46 0.86 ...... Frame ( 8) shift: 0.55 0.97 ...... Frame ( 9) shift: 0.64 1.08 ...... Frame ( 10) shift: 0.74 1.21 ...... Frame ( 11) shift: 0.83 1.33 ...... Frame ( 12) shift: 0.93 1.42 ...... Frame ( 13) shift: 1.02 1.49 ...... Frame ( 14) shift: 1.12 1.55 ...... Frame ( 15) shift: 1.19 1.59 ...... Frame ( 16) shift: 1.25 1.62 ...... Frame ( 17) shift: 1.31 1.64 ...... Frame ( 18) shift: 1.39 1.69 ...... Frame ( 19) shift: 1.49 1.77 ...... Frame ( 20) shift: 1.59 1.84 ...... Frame ( 21) shift: 1.64 1.90 ...... Frame ( 22) shift: 1.66 1.94 ...... Frame ( 23) shift: 1.67 1.98 ...... Frame ( 24) shift: 1.73 1.99 ...... Frame ( 25) shift: 1.83 1.98 ...... Frame ( 26) shift: 1.94 1.97 ...... Frame ( 27) shift: 2.04 2.01 ...... Frame ( 28) shift: 2.14 2.12 ...... Frame ( 29) shift: 2.24 2.22 ...... Frame ( 30) shift: 2.31 2.30 ...... Frame ( 31) shift: 2.36 2.36 ...... Frame ( 32) shift: 2.42 2.43 ...... Frame ( 33) shift: 2.47 2.42 ...... Frame ( 34) shift: 2.52 2.33 ...... Frame ( 35) shift: 2.57 2.25 ...... Frame ( 36) shift: 2.65 2.26 ...... Frame ( 37) shift: 2.77 2.37 ...... Frame ( 38) shift: 2.89 2.47 ...... Frame ( 39) shift: 3.00 2.58 ...... Frame ( 40) shift: 3.12 2.68 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.700847 Iteration 2 Error: 0.105215 Iteration 3 Error: 0.025203 Align patch 2 23 left Iteration 1 Error: 0.565325 Iteration 2 Error: 0.124794 Iteration 3 Error: 0.027992 Align patch 3 22 left Iteration 1 Error: 0.936711 Iteration 2 Error: 0.117721 Iteration 3 Error: 0.024318 Align patch 4 21 left Iteration 1 Error: 0.529099 Iteration 2 Error: 0.114751 Iteration 3 Error: 0.028784 Align patch 5 20 left Iteration 1 Error: 0.670057 Iteration 2 Error: 0.081191 Iteration 3 Error: 0.018541 Align patch 6 19 left Iteration 1 Error: 0.662301 Iteration 2 Error: 0.138497 Iteration 3 Error: 0.049858 Align patch 7 18 left Iteration 1 Error: 0.843653 Iteration 2 Error: 0.129982 Iteration 3 Error: 0.028980 Align patch 8 17 left Iteration 1 Error: 0.619798 Iteration 2 Error: 0.106166 Iteration 3 Error: 0.013420 Align patch 9 16 left Iteration 1 Error: 0.572046 Iteration 2 Error: 0.103656 Iteration 3 Error: 0.024287 Align patch 10 15 left Iteration 1 Error: 0.620832 Iteration 2 Error: 0.169236 Iteration 3 Error: 0.026858 Align patch 11 14 left Iteration 1 Error: 0.937949 Iteration 2 Error: 0.167918 Iteration 3 Error: 0.039729 Align patch 12 13 left Iteration 1 Error: 0.622123 Iteration 2 Error: 0.106613 Iteration 3 Error: 0.027098 Align patch 13 12 left Iteration 1 Error: 0.472721 Iteration 2 Error: 0.093141 Iteration 3 Error: 0.015925 Align patch 14 11 left Iteration 1 Error: 0.509688 Iteration 2 Error: 0.065964 Iteration 3 Error: 0.015656 Align patch 15 10 left Iteration 1 Error: 0.732929 Iteration 2 Error: 0.114858 Iteration 3 Error: 0.024347 Align patch 16 9 left Iteration 1 Error: 0.709707 Iteration 2 Error: 0.182223 Iteration 3 Error: 0.058905 Iteration 4 Error: 0.014452 Align patch 17 8 left Iteration 1 Error: 0.795247 Iteration 2 Error: 0.076256 Iteration 3 Error: 0.021359 Align patch 18 7 left Iteration 1 Error: 0.478180 Iteration 2 Error: 0.098632 Iteration 3 Error: 0.030360 Align patch 19 6 left Iteration 1 Error: 0.644509 Iteration 2 Error: 0.190625 Iteration 3 Error: 0.050178 Iteration 4 Error: 0.014448 Align patch 20 5 left Iteration 1 Error: 0.773930 Iteration 2 Error: 0.160106 Iteration 3 Error: 0.044116 Align patch 21 4 left Iteration 1 Error: 0.691261 Iteration 2 Error: 0.139207 Iteration 3 Error: 0.038392 Align patch 22 3 left Iteration 1 Error: 0.749386 Iteration 2 Error: 0.137226 Iteration 3 Error: 0.036284 Align patch 23 2 left Iteration 1 Error: 0.695382 Iteration 2 Error: 0.167092 Iteration 3 Error: 0.044455 Align patch 24 1 left Iteration 1 Error: 0.681980 Iteration 2 Error: 0.103755 Iteration 3 Error: 0.033889 Align patch 25 0 left Iteration 1 Error: 1.207474 Iteration 2 Error: 0.122462 Iteration 3 Error: 0.021167 3D Fitting completed. Patch alignment time: 15.45(sec) Local motion has been corrected. Process thread exits. Computational time: 23.706882 sec Total time: 29.863585 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00016hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00016hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.704900s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00016hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.709409s ........................................ >>>>>>TIME<<<<<< FFT: 0.931821s Defocus_U Defocus_V Angle CCC 12652.31 13003.92 7.70 -0.070744 Final Values Defocus_U Defocus_V Angle CCC 12650.75 12958.63 3.66 -0.307660 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00016hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00016hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.301e-01 9.706e-02 CC threshold: 0.712 Mean Std: 40.22 7.11 Num Hot pixels: 206 Hot pixel threshold: 82.88 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.085787 Iteration 2 Error: 0.151479 Iteration 3 Error: 0.029931 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.16 0.11 ...... Frame ( 3) shift: 0.32 0.21 ...... Frame ( 4) shift: 0.49 0.32 ...... Frame ( 5) shift: 0.65 0.42 ...... Frame ( 6) shift: 0.72 0.49 ...... Frame ( 7) shift: 0.71 0.52 ...... Frame ( 8) shift: 0.70 0.55 ...... Frame ( 9) shift: 0.71 0.57 ...... Frame ( 10) shift: 0.73 0.58 ...... Frame ( 11) shift: 0.74 0.59 ...... Frame ( 12) shift: 0.78 0.64 ...... Frame ( 13) shift: 0.83 0.72 ...... Frame ( 14) shift: 0.89 0.80 ...... Frame ( 15) shift: 0.95 0.84 ...... Frame ( 16) shift: 1.01 0.85 ...... Frame ( 17) shift: 1.07 0.86 ...... Frame ( 18) shift: 1.09 0.88 ...... Frame ( 19) shift: 1.06 0.93 ...... Frame ( 20) shift: 1.03 0.98 ...... Frame ( 21) shift: 1.06 1.02 ...... Frame ( 22) shift: 1.14 1.05 ...... Frame ( 23) shift: 1.22 1.09 ...... Frame ( 24) shift: 1.26 1.13 ...... Frame ( 25) shift: 1.26 1.18 ...... Frame ( 26) shift: 1.27 1.22 ...... Frame ( 27) shift: 1.29 1.27 ...... Frame ( 28) shift: 1.33 1.30 ...... Frame ( 29) shift: 1.37 1.34 ...... Frame ( 30) shift: 1.41 1.36 ...... Frame ( 31) shift: 1.44 1.37 ...... Frame ( 32) shift: 1.47 1.38 ...... Frame ( 33) shift: 1.51 1.40 ...... Frame ( 34) shift: 1.55 1.41 ...... Frame ( 35) shift: 1.58 1.42 ...... Frame ( 36) shift: 1.65 1.43 ...... Frame ( 37) shift: 1.73 1.46 ...... Frame ( 38) shift: 1.81 1.48 ...... Frame ( 39) shift: 1.90 1.51 ...... Frame ( 40) shift: 1.98 1.54 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.825289 Iteration 2 Error: 0.117984 Iteration 3 Error: 0.054063 Iteration 4 Error: 0.021688 Align patch 2 23 left Iteration 1 Error: 0.697272 Iteration 2 Error: 0.125120 Iteration 3 Error: 0.045024 Align patch 3 22 left Iteration 1 Error: 0.710441 Iteration 2 Error: 0.079828 Iteration 3 Error: 0.014870 Align patch 4 21 left Iteration 1 Error: 0.595900 Iteration 2 Error: 0.121835 Iteration 3 Error: 0.021645 Align patch 5 20 left Iteration 1 Error: 0.737919 Iteration 2 Error: 0.119357 Iteration 3 Error: 0.030360 Align patch 6 19 left Iteration 1 Error: 0.747691 Iteration 2 Error: 0.170635 Iteration 3 Error: 0.038772 Align patch 7 18 left Iteration 1 Error: 0.673313 Iteration 2 Error: 0.110555 Iteration 3 Error: 0.041759 Align patch 8 17 left Iteration 1 Error: 0.433737 Iteration 2 Error: 0.080127 Iteration 3 Error: 0.027139 Align patch 9 16 left Iteration 1 Error: 0.588969 Iteration 2 Error: 0.071199 Iteration 3 Error: 0.012455 Align patch 10 15 left Iteration 1 Error: 0.715510 Iteration 2 Error: 0.132639 Iteration 3 Error: 0.030279 Align patch 11 14 left Iteration 1 Error: 0.617930 Iteration 2 Error: 0.124067 Iteration 3 Error: 0.020625 Align patch 12 13 left Iteration 1 Error: 0.682319 Iteration 2 Error: 0.082124 Iteration 3 Error: 0.015561 Align patch 13 12 left Iteration 1 Error: 0.604546 Iteration 2 Error: 0.074668 Iteration 3 Error: 0.019017 Align patch 14 11 left Iteration 1 Error: 0.593954 Iteration 2 Error: 0.139993 Iteration 3 Error: 0.018305 Align patch 15 10 left Iteration 1 Error: 0.602160 Iteration 2 Error: 0.091403 Iteration 3 Error: 0.022812 Align patch 16 9 left Iteration 1 Error: 0.730270 Iteration 2 Error: 0.123930 Iteration 3 Error: 0.027287 Align patch 17 8 left Iteration 1 Error: 0.662431 Iteration 2 Error: 0.073771 Iteration 3 Error: 0.013791 Align patch 18 7 left Iteration 1 Error: 0.384277 Iteration 2 Error: 0.090115 Iteration 3 Error: 0.018172 Align patch 19 6 left Iteration 1 Error: 0.739062 Iteration 2 Error: 0.123637 Iteration 3 Error: 0.019930 Align patch 20 5 left Iteration 1 Error: 0.630781 Iteration 2 Error: 0.133865 Iteration 3 Error: 0.027757 Align patch 21 4 left Iteration 1 Error: 0.430804 Iteration 2 Error: 0.065410 Iteration 3 Error: 0.008131 Align patch 22 3 left Iteration 1 Error: 0.731026 Iteration 2 Error: 0.130121 Iteration 3 Error: 0.021112 Align patch 23 2 left Iteration 1 Error: 0.538233 Iteration 2 Error: 0.132826 Iteration 3 Error: 0.041248 Align patch 24 1 left Iteration 1 Error: 0.690522 Iteration 2 Error: 0.084300 Iteration 3 Error: 0.022561 Align patch 25 0 left Iteration 1 Error: 0.637299 Iteration 2 Error: 0.118405 Iteration 3 Error: 0.040477 3D Fitting completed. Patch alignment time: 15.03(sec) Local motion has been corrected. Process thread exits. Computational time: 23.445185 sec Total time: 29.862621 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00016hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00016hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.686109s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00016hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.508680s ........................................ >>>>>>TIME<<<<<< FFT: 1.013654s Defocus_U Defocus_V Angle CCC 10994.09 11841.88 5.77 -0.039688 Final Values Defocus_U Defocus_V Angle CCC 11017.53 11887.20 5.14 -0.229040 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00017hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00017hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 43.76 7.61 Num Hot pixels: 181 Hot pixel threshold: 89.42 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.461799 Iteration 2 Error: 0.206034 Iteration 3 Error: 0.044123 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.28 -0.14 ...... Frame ( 3) shift: -0.57 -0.28 ...... Frame ( 4) shift: -0.85 -0.42 ...... Frame ( 5) shift: -1.14 -0.56 ...... Frame ( 6) shift: -1.29 -0.64 ...... Frame ( 7) shift: -1.30 -0.67 ...... Frame ( 8) shift: -1.31 -0.70 ...... Frame ( 9) shift: -1.28 -0.70 ...... Frame ( 10) shift: -1.20 -0.66 ...... Frame ( 11) shift: -1.11 -0.63 ...... Frame ( 12) shift: -1.03 -0.59 ...... Frame ( 13) shift: -0.94 -0.56 ...... Frame ( 14) shift: -0.85 -0.53 ...... Frame ( 15) shift: -0.74 -0.50 ...... Frame ( 16) shift: -0.61 -0.47 ...... Frame ( 17) shift: -0.48 -0.45 ...... Frame ( 18) shift: -0.39 -0.42 ...... Frame ( 19) shift: -0.34 -0.39 ...... Frame ( 20) shift: -0.29 -0.37 ...... Frame ( 21) shift: -0.22 -0.32 ...... Frame ( 22) shift: -0.13 -0.24 ...... Frame ( 23) shift: -0.05 -0.16 ...... Frame ( 24) shift: 0.01 -0.13 ...... Frame ( 25) shift: 0.03 -0.13 ...... Frame ( 26) shift: 0.05 -0.14 ...... Frame ( 27) shift: 0.11 -0.13 ...... Frame ( 28) shift: 0.20 -0.10 ...... Frame ( 29) shift: 0.30 -0.07 ...... Frame ( 30) shift: 0.38 -0.03 ...... Frame ( 31) shift: 0.44 0.03 ...... Frame ( 32) shift: 0.51 0.08 ...... Frame ( 33) shift: 0.60 0.15 ...... Frame ( 34) shift: 0.72 0.23 ...... Frame ( 35) shift: 0.85 0.31 ...... Frame ( 36) shift: 0.94 0.38 ...... Frame ( 37) shift: 1.02 0.45 ...... Frame ( 38) shift: 1.09 0.52 ...... Frame ( 39) shift: 1.16 0.59 ...... Frame ( 40) shift: 1.23 0.66 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.796716 Iteration 2 Error: 0.203710 Iteration 3 Error: 0.064518 Iteration 4 Error: 0.020625 Align patch 2 23 left Iteration 1 Error: 0.928831 Iteration 2 Error: 0.185800 Iteration 3 Error: 0.044743 Align patch 3 22 left Iteration 1 Error: 1.477209 Iteration 2 Error: 0.312800 Iteration 3 Error: 0.102014 Iteration 4 Error: 0.047020 Align patch 4 21 left Iteration 1 Error: 0.607767 Iteration 2 Error: 0.144589 Iteration 3 Error: 0.037708 Align patch 5 20 left Iteration 1 Error: 1.710430 Iteration 2 Error: 0.103853 Iteration 3 Error: 0.019408 Align patch 6 19 left Iteration 1 Error: 0.583283 Iteration 2 Error: 0.133136 Iteration 3 Error: 0.043677 Align patch 7 18 left Iteration 1 Error: 0.924007 Iteration 2 Error: 0.263285 Iteration 3 Error: 0.070454 Iteration 4 Error: 0.034299 Align patch 8 17 left Iteration 1 Error: 1.325316 Iteration 2 Error: 0.117964 Iteration 3 Error: 0.032539 Align patch 9 16 left Iteration 1 Error: 1.385199 Iteration 2 Error: 0.110547 Iteration 3 Error: 0.012917 Align patch 10 15 left Iteration 1 Error: 1.563633 Iteration 2 Error: 0.072018 Iteration 3 Error: 0.007129 Align patch 11 14 left Iteration 1 Error: 1.593046 Iteration 2 Error: 0.257879 Iteration 3 Error: 0.056338 Iteration 4 Error: 0.021420 Align patch 12 13 left Iteration 1 Error: 1.035889 Iteration 2 Error: 0.221964 Iteration 3 Error: 0.073252 Iteration 4 Error: 0.024671 Align patch 13 12 left Iteration 1 Error: 0.995445 Iteration 2 Error: 0.243500 Iteration 3 Error: 0.049016 Align patch 14 11 left Iteration 1 Error: 0.956901 Iteration 2 Error: 0.095317 Iteration 3 Error: 0.010158 Align patch 15 10 left Iteration 1 Error: 1.133271 Iteration 2 Error: 0.238471 Iteration 3 Error: 0.061866 Iteration 4 Error: 0.015690 Align patch 16 9 left Iteration 1 Error: 0.984873 Iteration 2 Error: 0.168741 Iteration 3 Error: 0.045383 Align patch 17 8 left Iteration 1 Error: 1.552488 Iteration 2 Error: 0.301115 Iteration 3 Error: 0.070963 Iteration 4 Error: 0.024381 Align patch 18 7 left Iteration 1 Error: 0.741727 Iteration 2 Error: 0.152488 Iteration 3 Error: 0.031065 Align patch 19 6 left Iteration 1 Error: 1.736558 Iteration 2 Error: 0.283322 Iteration 3 Error: 0.060937 Iteration 4 Error: 0.019120 Align patch 20 5 left Iteration 1 Error: 0.821449 Iteration 2 Error: 0.112480 Iteration 3 Error: 0.036178 Align patch 21 4 left Iteration 1 Error: 1.824206 Iteration 2 Error: 0.280693 Iteration 3 Error: 0.051889 Iteration 4 Error: 0.024206 Align patch 22 3 left Iteration 1 Error: 2.054102 Iteration 2 Error: 0.280186 Iteration 3 Error: 0.051216 Iteration 4 Error: 0.019453 Align patch 23 2 left Iteration 1 Error: 0.984536 Iteration 2 Error: 0.102912 Iteration 3 Error: 0.033267 Align patch 24 1 left Iteration 1 Error: 0.635293 Iteration 2 Error: 0.120414 Iteration 3 Error: 0.017461 Align patch 25 0 left Iteration 1 Error: 0.660604 Iteration 2 Error: 0.088664 Iteration 3 Error: 0.017798 3D Fitting completed. Patch alignment time: 16.25(sec) Local motion has been corrected. Process thread exits. Computational time: 24.554018 sec Total time: 30.294275 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00017hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00017hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.843940s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00017hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.938157s ........................................ >>>>>>TIME<<<<<< FFT: 1.064131s Defocus_U Defocus_V Angle CCC 9394.53 10191.41 11.91 0.050033 Final Values Defocus_U Defocus_V Angle CCC 9399.22 10202.35 12.22 0.095263 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00017hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00017hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 1.000e-01 CC threshold: 0.735 Mean Std: 43.11 7.26 Num Hot pixels: 198 Hot pixel threshold: 86.69 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.803238 Iteration 2 Error: 0.121956 Iteration 3 Error: 0.035037 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.18 -0.01 ...... Frame ( 3) shift: -0.37 -0.03 ...... Frame ( 4) shift: -0.55 -0.04 ...... Frame ( 5) shift: -0.74 -0.06 ...... Frame ( 6) shift: -0.83 -0.01 ...... Frame ( 7) shift: -0.84 0.09 ...... Frame ( 8) shift: -0.84 0.20 ...... Frame ( 9) shift: -0.85 0.28 ...... Frame ( 10) shift: -0.85 0.34 ...... Frame ( 11) shift: -0.85 0.40 ...... Frame ( 12) shift: -0.85 0.44 ...... Frame ( 13) shift: -0.84 0.46 ...... Frame ( 14) shift: -0.83 0.47 ...... Frame ( 15) shift: -0.87 0.49 ...... Frame ( 16) shift: -0.94 0.53 ...... Frame ( 17) shift: -1.01 0.56 ...... Frame ( 18) shift: -1.03 0.59 ...... Frame ( 19) shift: -0.98 0.63 ...... Frame ( 20) shift: -0.94 0.67 ...... Frame ( 21) shift: -0.88 0.73 ...... Frame ( 22) shift: -0.82 0.82 ...... Frame ( 23) shift: -0.76 0.90 ...... Frame ( 24) shift: -0.71 0.97 ...... Frame ( 25) shift: -0.68 1.03 ...... Frame ( 26) shift: -0.65 1.08 ...... Frame ( 27) shift: -0.64 1.12 ...... Frame ( 28) shift: -0.65 1.15 ...... Frame ( 29) shift: -0.66 1.18 ...... Frame ( 30) shift: -0.69 1.23 ...... Frame ( 31) shift: -0.75 1.31 ...... Frame ( 32) shift: -0.80 1.38 ...... Frame ( 33) shift: -0.77 1.44 ...... Frame ( 34) shift: -0.63 1.48 ...... Frame ( 35) shift: -0.50 1.52 ...... Frame ( 36) shift: -0.45 1.50 ...... Frame ( 37) shift: -0.48 1.44 ...... Frame ( 38) shift: -0.50 1.37 ...... Frame ( 39) shift: -0.52 1.30 ...... Frame ( 40) shift: -0.55 1.24 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.915336 Iteration 2 Error: 0.183577 Iteration 3 Error: 0.053944 Iteration 4 Error: 0.028999 Align patch 2 23 left Iteration 1 Error: 1.205185 Iteration 2 Error: 0.117083 Iteration 3 Error: 0.029294 Align patch 3 22 left Iteration 1 Error: 0.826480 Iteration 2 Error: 0.139514 Iteration 3 Error: 0.033977 Align patch 4 21 left Iteration 1 Error: 1.209379 Iteration 2 Error: 0.227579 Iteration 3 Error: 0.082129 Iteration 4 Error: 0.027490 Align patch 5 20 left Iteration 1 Error: 0.753421 Iteration 2 Error: 0.126009 Iteration 3 Error: 0.024314 Align patch 6 19 left Iteration 1 Error: 1.087559 Iteration 2 Error: 0.133615 Iteration 3 Error: 0.036777 Align patch 7 18 left Iteration 1 Error: 0.979033 Iteration 2 Error: 0.100084 Iteration 3 Error: 0.044969 Align patch 8 17 left Iteration 1 Error: 0.822245 Iteration 2 Error: 0.127860 Iteration 3 Error: 0.020688 Align patch 9 16 left Iteration 1 Error: 0.938758 Iteration 2 Error: 0.150653 Iteration 3 Error: 0.025424 Align patch 10 15 left Iteration 1 Error: 0.681640 Iteration 2 Error: 0.141011 Iteration 3 Error: 0.025397 Align patch 11 14 left Iteration 1 Error: 0.545405 Iteration 2 Error: 0.097910 Iteration 3 Error: 0.023533 Align patch 12 13 left Iteration 1 Error: 0.715452 Iteration 2 Error: 0.123938 Iteration 3 Error: 0.019926 Align patch 13 12 left Iteration 1 Error: 0.988068 Iteration 2 Error: 0.185048 Iteration 3 Error: 0.044117 Align patch 14 11 left Iteration 1 Error: 0.598957 Iteration 2 Error: 0.083888 Iteration 3 Error: 0.023312 Align patch 15 10 left Iteration 1 Error: 0.648375 Iteration 2 Error: 0.115424 Iteration 3 Error: 0.060042 Iteration 4 Error: 0.013694 Align patch 16 9 left Iteration 1 Error: 0.631085 Iteration 2 Error: 0.211584 Iteration 3 Error: 0.068479 Iteration 4 Error: 0.021445 Align patch 17 8 left Iteration 1 Error: 0.745569 Iteration 2 Error: 0.199745 Iteration 3 Error: 0.063221 Iteration 4 Error: 0.019808 Align patch 18 7 left Iteration 1 Error: 0.654905 Iteration 2 Error: 0.087868 Iteration 3 Error: 0.027502 Align patch 19 6 left Iteration 1 Error: 0.442391 Iteration 2 Error: 0.062022 Iteration 3 Error: 0.015787 Align patch 20 5 left Iteration 1 Error: 0.744809 Iteration 2 Error: 0.181868 Iteration 3 Error: 0.036020 Align patch 21 4 left Iteration 1 Error: 1.603225 Iteration 2 Error: 0.125964 Iteration 3 Error: 0.032758 Align patch 22 3 left Iteration 1 Error: 0.995856 Iteration 2 Error: 0.121738 Iteration 3 Error: 0.026891 Align patch 23 2 left Iteration 1 Error: 1.213007 Iteration 2 Error: 0.160072 Iteration 3 Error: 0.042354 Align patch 24 1 left Iteration 1 Error: 0.575586 Iteration 2 Error: 0.083452 Iteration 3 Error: 0.015745 Align patch 25 0 left Iteration 1 Error: 0.897379 Iteration 2 Error: 0.161693 Iteration 3 Error: 0.041982 3D Fitting completed. Patch alignment time: 16.01(sec) Local motion has been corrected. Process thread exits. Computational time: 24.165854 sec Total time: 30.670908 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00017hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00017hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.574272s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00017hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.906431s ........................................ >>>>>>TIME<<<<<< FFT: 0.915712s Defocus_U Defocus_V Angle CCC 9521.03 9014.16 86.98 0.034907 Final Values Defocus_U Defocus_V Angle CCC 9522.56 9025.13 86.35 0.067550 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00017hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00017hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.001e-01 CC threshold: 0.735 Mean Std: 44.03 7.38 Num Hot pixels: 194 Hot pixel threshold: 88.29 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.668796 Iteration 2 Error: 0.107174 Iteration 3 Error: 0.023705 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.30 -0.13 ...... Frame ( 3) shift: -0.61 -0.27 ...... Frame ( 4) shift: -0.91 -0.40 ...... Frame ( 5) shift: -1.22 -0.53 ...... Frame ( 6) shift: -1.41 -0.60 ...... Frame ( 7) shift: -1.48 -0.59 ...... Frame ( 8) shift: -1.56 -0.57 ...... Frame ( 9) shift: -1.55 -0.55 ...... Frame ( 10) shift: -1.47 -0.52 ...... Frame ( 11) shift: -1.39 -0.49 ...... Frame ( 12) shift: -1.35 -0.45 ...... Frame ( 13) shift: -1.36 -0.40 ...... Frame ( 14) shift: -1.37 -0.35 ...... Frame ( 15) shift: -1.37 -0.31 ...... Frame ( 16) shift: -1.37 -0.27 ...... Frame ( 17) shift: -1.37 -0.24 ...... Frame ( 18) shift: -1.31 -0.19 ...... Frame ( 19) shift: -1.20 -0.13 ...... Frame ( 20) shift: -1.09 -0.07 ...... Frame ( 21) shift: -1.05 -0.02 ...... Frame ( 22) shift: -1.08 0.02 ...... Frame ( 23) shift: -1.12 0.06 ...... Frame ( 24) shift: -1.09 0.06 ...... Frame ( 25) shift: -1.00 0.02 ...... Frame ( 26) shift: -0.91 -0.02 ...... Frame ( 27) shift: -0.87 -0.01 ...... Frame ( 28) shift: -0.87 0.07 ...... Frame ( 29) shift: -0.88 0.14 ...... Frame ( 30) shift: -0.88 0.18 ...... Frame ( 31) shift: -0.85 0.18 ...... Frame ( 32) shift: -0.83 0.19 ...... Frame ( 33) shift: -0.80 0.20 ...... Frame ( 34) shift: -0.77 0.21 ...... Frame ( 35) shift: -0.74 0.22 ...... Frame ( 36) shift: -0.71 0.24 ...... Frame ( 37) shift: -0.68 0.25 ...... Frame ( 38) shift: -0.66 0.27 ...... Frame ( 39) shift: -0.63 0.29 ...... Frame ( 40) shift: -0.60 0.30 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.865483 Iteration 2 Error: 0.104820 Iteration 3 Error: 0.030159 Align patch 2 23 left Iteration 1 Error: 1.298729 Iteration 2 Error: 0.153563 Iteration 3 Error: 0.029324 Align patch 3 22 left Iteration 1 Error: 0.798970 Iteration 2 Error: 0.104419 Iteration 3 Error: 0.025115 Align patch 4 21 left Iteration 1 Error: 0.720564 Iteration 2 Error: 0.078592 Iteration 3 Error: 0.013049 Align patch 5 20 left Iteration 1 Error: 0.714983 Iteration 2 Error: 0.115689 Iteration 3 Error: 0.033849 Align patch 6 19 left Iteration 1 Error: 1.114132 Iteration 2 Error: 0.155817 Iteration 3 Error: 0.033757 Align patch 7 18 left Iteration 1 Error: 1.001159 Iteration 2 Error: 0.145796 Iteration 3 Error: 0.047835 Align patch 8 17 left Iteration 1 Error: 0.874256 Iteration 2 Error: 0.155099 Iteration 3 Error: 0.046435 Align patch 9 16 left Iteration 1 Error: 0.493816 Iteration 2 Error: 0.069146 Iteration 3 Error: 0.018086 Align patch 10 15 left Iteration 1 Error: 0.861315 Iteration 2 Error: 0.106666 Iteration 3 Error: 0.017411 Align patch 11 14 left Iteration 1 Error: 0.665848 Iteration 2 Error: 0.122461 Iteration 3 Error: 0.030096 Align patch 12 13 left Iteration 1 Error: 0.637523 Iteration 2 Error: 0.142627 Iteration 3 Error: 0.042611 Align patch 13 12 left Iteration 1 Error: 0.717805 Iteration 2 Error: 0.090622 Iteration 3 Error: 0.022099 Align patch 14 11 left Iteration 1 Error: 0.836335 Iteration 2 Error: 0.119244 Iteration 3 Error: 0.038793 Align patch 15 10 left Iteration 1 Error: 0.669512 Iteration 2 Error: 0.095965 Iteration 3 Error: 0.031508 Align patch 16 9 left Iteration 1 Error: 0.951791 Iteration 2 Error: 0.124601 Iteration 3 Error: 0.025308 Align patch 17 8 left Iteration 1 Error: 0.466583 Iteration 2 Error: 0.081807 Iteration 3 Error: 0.032013 Align patch 18 7 left Iteration 1 Error: 0.996785 Iteration 2 Error: 0.168667 Iteration 3 Error: 0.032180 Align patch 19 6 left Iteration 1 Error: 0.720560 Iteration 2 Error: 0.150535 Iteration 3 Error: 0.027686 Align patch 20 5 left Iteration 1 Error: 0.992786 Iteration 2 Error: 0.128591 Iteration 3 Error: 0.027709 Align patch 21 4 left Iteration 1 Error: 1.655755 Iteration 2 Error: 0.262703 Iteration 3 Error: 0.056269 Iteration 4 Error: 0.020091 Align patch 22 3 left Iteration 1 Error: 0.731853 Iteration 2 Error: 0.169451 Iteration 3 Error: 0.045485 Align patch 23 2 left Iteration 1 Error: 0.837025 Iteration 2 Error: 0.083000 Iteration 3 Error: 0.016329 Align patch 24 1 left Iteration 1 Error: 0.954789 Iteration 2 Error: 0.171693 Iteration 3 Error: 0.034847 Align patch 25 0 left Iteration 1 Error: 0.819849 Iteration 2 Error: 0.092677 Iteration 3 Error: 0.014924 3D Fitting completed. Patch alignment time: 15.78(sec) Local motion has been corrected. Process thread exits. Computational time: 24.285023 sec Total time: 30.271435 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00017hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00017hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.573109s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00017hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.129345s ........................................ >>>>>>TIME<<<<<< FFT: 0.967256s Defocus_U Defocus_V Angle CCC 11422.95 12243.23 6.01 0.048370 Final Values Defocus_U Defocus_V Angle CCC 11429.20 12258.87 5.69 0.086970 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00017hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00017hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.335e-01 9.934e-02 CC threshold: 0.730 Mean Std: 41.26 7.03 Num Hot pixels: 210 Hot pixel threshold: 83.46 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.966711 Iteration 2 Error: 0.320990 Iteration 3 Error: 0.100604 Iteration 4 Error: 0.037624 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.38 0.35 ...... Frame ( 3) shift: -0.75 0.69 ...... Frame ( 4) shift: -1.13 1.04 ...... Frame ( 5) shift: -1.51 1.38 ...... Frame ( 6) shift: -1.78 1.62 ...... Frame ( 7) shift: -1.96 1.74 ...... Frame ( 8) shift: -2.13 1.86 ...... Frame ( 9) shift: -2.29 2.00 ...... Frame ( 10) shift: -2.44 2.15 ...... Frame ( 11) shift: -2.58 2.31 ...... Frame ( 12) shift: -2.70 2.44 ...... Frame ( 13) shift: -2.80 2.54 ...... Frame ( 14) shift: -2.89 2.65 ...... Frame ( 15) shift: -2.96 2.73 ...... Frame ( 16) shift: -3.02 2.81 ...... Frame ( 17) shift: -3.07 2.88 ...... Frame ( 18) shift: -3.11 2.93 ...... Frame ( 19) shift: -3.14 2.95 ...... Frame ( 20) shift: -3.18 2.97 ...... Frame ( 21) shift: -3.21 3.02 ...... Frame ( 22) shift: -3.24 3.10 ...... Frame ( 23) shift: -3.27 3.18 ...... Frame ( 24) shift: -3.33 3.23 ...... Frame ( 25) shift: -3.41 3.26 ...... Frame ( 26) shift: -3.50 3.28 ...... Frame ( 27) shift: -3.56 3.34 ...... Frame ( 28) shift: -3.59 3.42 ...... Frame ( 29) shift: -3.62 3.51 ...... Frame ( 30) shift: -3.60 3.55 ...... Frame ( 31) shift: -3.55 3.56 ...... Frame ( 32) shift: -3.49 3.57 ...... Frame ( 33) shift: -3.49 3.62 ...... Frame ( 34) shift: -3.53 3.72 ...... Frame ( 35) shift: -3.57 3.82 ...... Frame ( 36) shift: -3.59 3.88 ...... Frame ( 37) shift: -3.59 3.90 ...... Frame ( 38) shift: -3.58 3.92 ...... Frame ( 39) shift: -3.58 3.94 ...... Frame ( 40) shift: -3.57 3.97 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.243920 Iteration 2 Error: 0.297409 Iteration 3 Error: 0.091083 Iteration 4 Error: 0.024951 Align patch 2 23 left Iteration 1 Error: 1.919651 Iteration 2 Error: 0.477597 Iteration 3 Error: 0.162949 Iteration 4 Error: 0.062113 Iteration 5 Error: 0.043801 Align patch 3 22 left Iteration 1 Error: 0.958229 Iteration 2 Error: 0.330160 Iteration 3 Error: 0.129456 Iteration 4 Error: 0.052774 Iteration 5 Error: 0.027162 Align patch 4 21 left Iteration 1 Error: 0.694983 Iteration 2 Error: 0.207496 Iteration 3 Error: 0.069530 Iteration 4 Error: 0.016588 Align patch 5 20 left Iteration 1 Error: 0.912855 Iteration 2 Error: 0.190546 Iteration 3 Error: 0.041130 Align patch 6 19 left Iteration 1 Error: 0.862733 Iteration 2 Error: 0.196472 Iteration 3 Error: 0.032769 Align patch 7 18 left Iteration 1 Error: 1.131328 Iteration 2 Error: 0.222839 Iteration 3 Error: 0.081304 Iteration 4 Error: 0.027285 Align patch 8 17 left Iteration 1 Error: 1.790579 Iteration 2 Error: 0.319379 Iteration 3 Error: 0.101886 Iteration 4 Error: 0.036395 Align patch 9 16 left Iteration 1 Error: 0.656559 Iteration 2 Error: 0.173336 Iteration 3 Error: 0.030499 Align patch 10 15 left Iteration 1 Error: 0.806502 Iteration 2 Error: 0.169924 Iteration 3 Error: 0.042292 Align patch 11 14 left Iteration 1 Error: 0.787862 Iteration 2 Error: 0.202563 Iteration 3 Error: 0.070190 Iteration 4 Error: 0.035325 Align patch 12 13 left Iteration 1 Error: 0.533047 Iteration 2 Error: 0.193316 Iteration 3 Error: 0.083219 Iteration 4 Error: 0.027911 Align patch 13 12 left Iteration 1 Error: 1.036735 Iteration 2 Error: 0.259146 Iteration 3 Error: 0.111927 Iteration 4 Error: 0.053238 Iteration 5 Error: 0.036890 Align patch 14 11 left Iteration 1 Error: 1.537858 Iteration 2 Error: 0.262604 Iteration 3 Error: 0.036857 Align patch 15 10 left Iteration 1 Error: 0.918658 Iteration 2 Error: 0.100622 Iteration 3 Error: 0.035071 Align patch 16 9 left Iteration 1 Error: 1.193923 Iteration 2 Error: 0.198453 Iteration 3 Error: 0.044700 Align patch 17 8 left Iteration 1 Error: 0.601620 Iteration 2 Error: 0.096026 Iteration 3 Error: 0.023965 Align patch 18 7 left Iteration 1 Error: 0.798649 Iteration 2 Error: 0.183802 Iteration 3 Error: 0.094655 Iteration 4 Error: 0.041458 Align patch 19 6 left Iteration 1 Error: 0.783621 Iteration 2 Error: 0.170446 Iteration 3 Error: 0.075658 Iteration 4 Error: 0.029596 Align patch 20 5 left Iteration 1 Error: 0.749476 Iteration 2 Error: 0.119140 Iteration 3 Error: 0.036295 Align patch 21 4 left Iteration 1 Error: 1.839907 Iteration 2 Error: 0.214774 Iteration 3 Error: 0.042481 Align patch 22 3 left Iteration 1 Error: 1.187950 Iteration 2 Error: 0.224297 Iteration 3 Error: 0.061778 Iteration 4 Error: 0.021017 Align patch 23 2 left Iteration 1 Error: 0.721521 Iteration 2 Error: 0.139238 Iteration 3 Error: 0.043759 Align patch 24 1 left Iteration 1 Error: 1.062917 Iteration 2 Error: 0.193352 Iteration 3 Error: 0.041765 Align patch 25 0 left Iteration 1 Error: 0.833101 Iteration 2 Error: 0.202101 Iteration 3 Error: 0.049767 3D Fitting completed. Patch alignment time: 15.95(sec) Local motion has been corrected. Process thread exits. Computational time: 24.767262 sec Total time: 30.709751 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00017hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00017hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.655051s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00017hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.666207s ........................................ >>>>>>TIME<<<<<< FFT: 0.960157s Defocus_U Defocus_V Angle CCC 14324.52 13699.31 78.38 0.020553 Final Values Defocus_U Defocus_V Angle CCC 14326.04 13691.55 79.01 -0.022340 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00018hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00018hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 44.93 7.58 Num Hot pixels: 200 Hot pixel threshold: 90.38 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.917322 Iteration 2 Error: 0.155998 Iteration 3 Error: 0.022402 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.30 0.04 ...... Frame ( 3) shift: -0.59 0.07 ...... Frame ( 4) shift: -0.89 0.11 ...... Frame ( 5) shift: -1.18 0.15 ...... Frame ( 6) shift: -1.31 0.18 ...... Frame ( 7) shift: -1.28 0.22 ...... Frame ( 8) shift: -1.24 0.26 ...... Frame ( 9) shift: -1.21 0.31 ...... Frame ( 10) shift: -1.19 0.39 ...... Frame ( 11) shift: -1.16 0.46 ...... Frame ( 12) shift: -1.14 0.50 ...... Frame ( 13) shift: -1.13 0.51 ...... Frame ( 14) shift: -1.12 0.53 ...... Frame ( 15) shift: -1.11 0.58 ...... Frame ( 16) shift: -1.11 0.67 ...... Frame ( 17) shift: -1.12 0.76 ...... Frame ( 18) shift: -1.11 0.84 ...... Frame ( 19) shift: -1.10 0.93 ...... Frame ( 20) shift: -1.08 1.02 ...... Frame ( 21) shift: -1.07 1.06 ...... Frame ( 22) shift: -1.07 1.07 ...... Frame ( 23) shift: -1.06 1.07 ...... Frame ( 24) shift: -1.04 1.09 ...... Frame ( 25) shift: -1.01 1.13 ...... Frame ( 26) shift: -0.97 1.17 ...... Frame ( 27) shift: -0.94 1.23 ...... Frame ( 28) shift: -0.91 1.30 ...... Frame ( 29) shift: -0.88 1.38 ...... Frame ( 30) shift: -0.85 1.40 ...... Frame ( 31) shift: -0.82 1.37 ...... Frame ( 32) shift: -0.79 1.34 ...... Frame ( 33) shift: -0.76 1.33 ...... Frame ( 34) shift: -0.73 1.34 ...... Frame ( 35) shift: -0.70 1.36 ...... Frame ( 36) shift: -0.69 1.42 ...... Frame ( 37) shift: -0.71 1.52 ...... Frame ( 38) shift: -0.72 1.63 ...... Frame ( 39) shift: -0.73 1.73 ...... Frame ( 40) shift: -0.74 1.84 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.781567 Iteration 2 Error: 0.234912 Iteration 3 Error: 0.071177 Iteration 4 Error: 0.035107 Align patch 2 23 left Iteration 1 Error: 2.051422 Iteration 2 Error: 0.189531 Iteration 3 Error: 0.063328 Iteration 4 Error: 0.018579 Align patch 3 22 left Iteration 1 Error: 0.638586 Iteration 2 Error: 0.091424 Iteration 3 Error: 0.016259 Align patch 4 21 left Iteration 1 Error: 0.830526 Iteration 2 Error: 0.119574 Iteration 3 Error: 0.029365 Align patch 5 20 left Iteration 1 Error: 0.852665 Iteration 2 Error: 0.156400 Iteration 3 Error: 0.027073 Align patch 6 19 left Iteration 1 Error: 4.175574 Iteration 2 Error: 0.348280 Iteration 3 Error: 0.145460 Iteration 4 Error: 0.041361 Align patch 7 18 left Iteration 1 Error: 0.906804 Iteration 2 Error: 0.270536 Iteration 3 Error: 0.083627 Iteration 4 Error: 0.042917 Align patch 8 17 left Iteration 1 Error: 0.683632 Iteration 2 Error: 0.142487 Iteration 3 Error: 0.041329 Align patch 9 16 left Iteration 1 Error: 0.485679 Iteration 2 Error: 0.116288 Iteration 3 Error: 0.023746 Align patch 10 15 left Iteration 1 Error: 1.001639 Iteration 2 Error: 0.193874 Iteration 3 Error: 0.031036 Align patch 11 14 left Iteration 1 Error: 1.236826 Iteration 2 Error: 0.181496 Iteration 3 Error: 0.038601 Align patch 12 13 left Iteration 1 Error: 0.632623 Iteration 2 Error: 0.074382 Iteration 3 Error: 0.018739 Align patch 13 12 left Iteration 1 Error: 0.691158 Iteration 2 Error: 0.116887 Iteration 3 Error: 0.026707 Align patch 14 11 left Iteration 1 Error: 0.650689 Iteration 2 Error: 0.143983 Iteration 3 Error: 0.035480 Align patch 15 10 left Iteration 1 Error: 0.962561 Iteration 2 Error: 0.218588 Iteration 3 Error: 0.033532 Align patch 16 9 left Iteration 1 Error: 0.853178 Iteration 2 Error: 0.154423 Iteration 3 Error: 0.029850 Align patch 17 8 left Iteration 1 Error: 1.050936 Iteration 2 Error: 0.173925 Iteration 3 Error: 0.029489 Align patch 18 7 left Iteration 1 Error: 1.142873 Iteration 2 Error: 0.105066 Iteration 3 Error: 0.026271 Align patch 19 6 left Iteration 1 Error: 0.648673 Iteration 2 Error: 0.166199 Iteration 3 Error: 0.029243 Align patch 20 5 left Iteration 1 Error: 0.612425 Iteration 2 Error: 0.187580 Iteration 3 Error: 0.041388 Align patch 21 4 left Iteration 1 Error: 1.269535 Iteration 2 Error: 0.185584 Iteration 3 Error: 0.054832 Iteration 4 Error: 0.021110 Align patch 22 3 left Iteration 1 Error: 0.816683 Iteration 2 Error: 0.108174 Iteration 3 Error: 0.021159 Align patch 23 2 left Iteration 1 Error: 1.102342 Iteration 2 Error: 0.127847 Iteration 3 Error: 0.046433 Align patch 24 1 left Iteration 1 Error: 1.144555 Iteration 2 Error: 0.109344 Iteration 3 Error: 0.021331 Align patch 25 0 left Iteration 1 Error: 0.582151 Iteration 2 Error: 0.112101 Iteration 3 Error: 0.017081 3D Fitting completed. Patch alignment time: 15.95(sec) Local motion has been corrected. Process thread exits. Computational time: 24.748949 sec Total time: 30.955498 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00018hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00018hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.609009s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00018hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.606653s ........................................ >>>>>>TIME<<<<<< FFT: 0.930785s Defocus_U Defocus_V Angle CCC 12093.75 12906.25 13.37 0.045976 Final Values Defocus_U Defocus_V Angle CCC 12092.17 12914.10 13.37 0.083412 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00018hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00018hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 44.56 7.56 Num Hot pixels: 191 Hot pixel threshold: 89.91 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.947639 Iteration 2 Error: 0.127674 Iteration 3 Error: 0.031601 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.30 -0.02 ...... Frame ( 3) shift: -0.60 -0.04 ...... Frame ( 4) shift: -0.90 -0.06 ...... Frame ( 5) shift: -1.20 -0.08 ...... Frame ( 6) shift: -1.37 -0.07 ...... Frame ( 7) shift: -1.41 -0.02 ...... Frame ( 8) shift: -1.45 0.02 ...... Frame ( 9) shift: -1.46 0.09 ...... Frame ( 10) shift: -1.45 0.16 ...... Frame ( 11) shift: -1.45 0.24 ...... Frame ( 12) shift: -1.43 0.29 ...... Frame ( 13) shift: -1.41 0.32 ...... Frame ( 14) shift: -1.39 0.36 ...... Frame ( 15) shift: -1.39 0.41 ...... Frame ( 16) shift: -1.39 0.49 ...... Frame ( 17) shift: -1.39 0.57 ...... Frame ( 18) shift: -1.35 0.64 ...... Frame ( 19) shift: -1.26 0.70 ...... Frame ( 20) shift: -1.17 0.75 ...... Frame ( 21) shift: -1.12 0.81 ...... Frame ( 22) shift: -1.11 0.87 ...... Frame ( 23) shift: -1.09 0.93 ...... Frame ( 24) shift: -1.07 0.97 ...... Frame ( 25) shift: -1.05 1.00 ...... Frame ( 26) shift: -1.02 1.03 ...... Frame ( 27) shift: -0.98 1.08 ...... Frame ( 28) shift: -0.91 1.14 ...... Frame ( 29) shift: -0.85 1.21 ...... Frame ( 30) shift: -0.83 1.22 ...... Frame ( 31) shift: -0.85 1.18 ...... Frame ( 32) shift: -0.87 1.14 ...... Frame ( 33) shift: -0.88 1.13 ...... Frame ( 34) shift: -0.88 1.14 ...... Frame ( 35) shift: -0.87 1.16 ...... Frame ( 36) shift: -0.86 1.18 ...... Frame ( 37) shift: -0.85 1.21 ...... Frame ( 38) shift: -0.84 1.25 ...... Frame ( 39) shift: -0.82 1.28 ...... Frame ( 40) shift: -0.81 1.31 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.675746 Iteration 2 Error: 0.177840 Iteration 3 Error: 0.069959 Iteration 4 Error: 0.030030 Align patch 2 23 left Iteration 1 Error: 1.317174 Iteration 2 Error: 0.284293 Iteration 3 Error: 0.153332 Iteration 4 Error: 0.053043 Iteration 5 Error: 0.023196 Align patch 3 22 left Iteration 1 Error: 0.899781 Iteration 2 Error: 0.110064 Iteration 3 Error: 0.037789 Align patch 4 21 left Iteration 1 Error: 0.607350 Iteration 2 Error: 0.070818 Iteration 3 Error: 0.019581 Align patch 5 20 left Iteration 1 Error: 1.253530 Iteration 2 Error: 0.157758 Iteration 3 Error: 0.048298 Align patch 6 19 left Iteration 1 Error: 1.399631 Iteration 2 Error: 0.330847 Iteration 3 Error: 0.150876 Iteration 4 Error: 0.049061 Align patch 7 18 left Iteration 1 Error: 0.812840 Iteration 2 Error: 0.220907 Iteration 3 Error: 0.052110 Iteration 4 Error: 0.022172 Align patch 8 17 left Iteration 1 Error: 0.621223 Iteration 2 Error: 0.191568 Iteration 3 Error: 0.044302 Align patch 9 16 left Iteration 1 Error: 0.830057 Iteration 2 Error: 0.104111 Iteration 3 Error: 0.029002 Align patch 10 15 left Iteration 1 Error: 0.967455 Iteration 2 Error: 0.134055 Iteration 3 Error: 0.033920 Align patch 11 14 left Iteration 1 Error: 1.393202 Iteration 2 Error: 0.261848 Iteration 3 Error: 0.066655 Iteration 4 Error: 0.019550 Align patch 12 13 left Iteration 1 Error: 1.037469 Iteration 2 Error: 0.152202 Iteration 3 Error: 0.056800 Iteration 4 Error: 0.012492 Align patch 13 12 left Iteration 1 Error: 0.700917 Iteration 2 Error: 0.098851 Iteration 3 Error: 0.024383 Align patch 14 11 left Iteration 1 Error: 0.759095 Iteration 2 Error: 0.083127 Iteration 3 Error: 0.024922 Align patch 15 10 left Iteration 1 Error: 0.733241 Iteration 2 Error: 0.122968 Iteration 3 Error: 0.031768 Align patch 16 9 left Iteration 1 Error: 0.816495 Iteration 2 Error: 0.094808 Iteration 3 Error: 0.020383 Align patch 17 8 left Iteration 1 Error: 0.990631 Iteration 2 Error: 0.129134 Iteration 3 Error: 0.027199 Align patch 18 7 left Iteration 1 Error: 0.904809 Iteration 2 Error: 0.158570 Iteration 3 Error: 0.033636 Align patch 19 6 left Iteration 1 Error: 0.462998 Iteration 2 Error: 0.065975 Iteration 3 Error: 0.014295 Align patch 20 5 left Iteration 1 Error: 0.797327 Iteration 2 Error: 0.129852 Iteration 3 Error: 0.032567 Align patch 21 4 left Iteration 1 Error: 1.543240 Iteration 2 Error: 0.162175 Iteration 3 Error: 0.048369 Align patch 22 3 left Iteration 1 Error: 1.082307 Iteration 2 Error: 0.154661 Iteration 3 Error: 0.035460 Align patch 23 2 left Iteration 1 Error: 0.687573 Iteration 2 Error: 0.097307 Iteration 3 Error: 0.020461 Align patch 24 1 left Iteration 1 Error: 1.488605 Iteration 2 Error: 0.162012 Iteration 3 Error: 0.060420 Iteration 4 Error: 0.016835 Align patch 25 0 left Iteration 1 Error: 0.788431 Iteration 2 Error: 0.120157 Iteration 3 Error: 0.023398 3D Fitting completed. Patch alignment time: 15.99(sec) Local motion has been corrected. Process thread exits. Computational time: 24.365925 sec Total time: 31.805054 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00018hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00018hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 2.168021s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00018hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.570156s ........................................ >>>>>>TIME<<<<<< FFT: 1.003801s Defocus_U Defocus_V Angle CCC 9597.62 9957.08 2.76 0.044781 Final Values Defocus_U Defocus_V Angle CCC 9594.49 9969.58 2.45 0.086704 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00018hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00018hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 43.08 7.21 Num Hot pixels: 186 Hot pixel threshold: 86.35 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.240134 Iteration 2 Error: 0.151254 Iteration 3 Error: 0.029782 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.37 -0.18 ...... Frame ( 3) shift: -0.74 -0.37 ...... Frame ( 4) shift: -1.10 -0.55 ...... Frame ( 5) shift: -1.47 -0.73 ...... Frame ( 6) shift: -1.68 -0.81 ...... Frame ( 7) shift: -1.72 -0.78 ...... Frame ( 8) shift: -1.77 -0.76 ...... Frame ( 9) shift: -1.80 -0.70 ...... Frame ( 10) shift: -1.83 -0.60 ...... Frame ( 11) shift: -1.86 -0.51 ...... Frame ( 12) shift: -1.88 -0.42 ...... Frame ( 13) shift: -1.87 -0.34 ...... Frame ( 14) shift: -1.87 -0.26 ...... Frame ( 15) shift: -1.85 -0.20 ...... Frame ( 16) shift: -1.81 -0.15 ...... Frame ( 17) shift: -1.78 -0.10 ...... Frame ( 18) shift: -1.74 -0.04 ...... Frame ( 19) shift: -1.69 0.05 ...... Frame ( 20) shift: -1.65 0.14 ...... Frame ( 21) shift: -1.66 0.17 ...... Frame ( 22) shift: -1.71 0.13 ...... Frame ( 23) shift: -1.77 0.09 ...... Frame ( 24) shift: -1.82 0.13 ...... Frame ( 25) shift: -1.85 0.25 ...... Frame ( 26) shift: -1.88 0.36 ...... Frame ( 27) shift: -1.86 0.43 ...... Frame ( 28) shift: -1.80 0.44 ...... Frame ( 29) shift: -1.74 0.46 ...... Frame ( 30) shift: -1.71 0.45 ...... Frame ( 31) shift: -1.73 0.42 ...... Frame ( 32) shift: -1.75 0.39 ...... Frame ( 33) shift: -1.77 0.43 ...... Frame ( 34) shift: -1.80 0.53 ...... Frame ( 35) shift: -1.82 0.63 ...... Frame ( 36) shift: -1.85 0.70 ...... Frame ( 37) shift: -1.88 0.74 ...... Frame ( 38) shift: -1.91 0.79 ...... Frame ( 39) shift: -1.94 0.83 ...... Frame ( 40) shift: -1.97 0.88 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.545395 Iteration 2 Error: 0.164448 Iteration 3 Error: 0.069954 Iteration 4 Error: 0.022445 Align patch 2 23 left Iteration 1 Error: 1.198068 Iteration 2 Error: 0.173156 Iteration 3 Error: 0.033141 Align patch 3 22 left Iteration 1 Error: 1.136533 Iteration 2 Error: 0.226788 Iteration 3 Error: 0.040646 Align patch 4 21 left Iteration 1 Error: 0.791159 Iteration 2 Error: 0.096930 Iteration 3 Error: 0.036159 Align patch 5 20 left Iteration 1 Error: 0.714906 Iteration 2 Error: 0.077588 Iteration 3 Error: 0.022508 Align patch 6 19 left Iteration 1 Error: 0.910314 Iteration 2 Error: 0.209755 Iteration 3 Error: 0.049021 Align patch 7 18 left Iteration 1 Error: 1.256974 Iteration 2 Error: 0.177625 Iteration 3 Error: 0.028211 Align patch 8 17 left Iteration 1 Error: 0.863295 Iteration 2 Error: 0.129680 Iteration 3 Error: 0.041251 Align patch 9 16 left Iteration 1 Error: 0.920576 Iteration 2 Error: 0.230554 Iteration 3 Error: 0.091027 Iteration 4 Error: 0.031943 Align patch 10 15 left Iteration 1 Error: 0.553839 Iteration 2 Error: 0.119420 Iteration 3 Error: 0.021584 Align patch 11 14 left Iteration 1 Error: 0.853745 Iteration 2 Error: 0.136042 Iteration 3 Error: 0.033772 Align patch 12 13 left Iteration 1 Error: 0.956563 Iteration 2 Error: 0.132128 Iteration 3 Error: 0.034456 Align patch 13 12 left Iteration 1 Error: 0.753761 Iteration 2 Error: 0.059123 Iteration 3 Error: 0.017968 Align patch 14 11 left Iteration 1 Error: 0.976379 Iteration 2 Error: 0.122850 Iteration 3 Error: 0.035806 Align patch 15 10 left Iteration 1 Error: 1.378840 Iteration 2 Error: 0.155935 Iteration 3 Error: 0.024464 Align patch 16 9 left Iteration 1 Error: 0.836096 Iteration 2 Error: 0.178585 Iteration 3 Error: 0.055956 Iteration 4 Error: 0.026196 Align patch 17 8 left Iteration 1 Error: 0.758770 Iteration 2 Error: 0.162649 Iteration 3 Error: 0.069359 Iteration 4 Error: 0.014879 Align patch 18 7 left Iteration 1 Error: 0.686348 Iteration 2 Error: 0.082465 Iteration 3 Error: 0.020490 Align patch 19 6 left Iteration 1 Error: 0.870872 Iteration 2 Error: 0.131369 Iteration 3 Error: 0.037806 Align patch 20 5 left Iteration 1 Error: 0.650424 Iteration 2 Error: 0.076122 Iteration 3 Error: 0.013162 Align patch 21 4 left Iteration 1 Error: 1.281155 Iteration 2 Error: 0.113769 Iteration 3 Error: 0.034759 Align patch 22 3 left Iteration 1 Error: 0.733459 Iteration 2 Error: 0.164951 Iteration 3 Error: 0.041495 Align patch 23 2 left Iteration 1 Error: 0.935500 Iteration 2 Error: 0.174246 Iteration 3 Error: 0.045914 Align patch 24 1 left Iteration 1 Error: 0.706331 Iteration 2 Error: 0.094101 Iteration 3 Error: 0.029065 Align patch 25 0 left Iteration 1 Error: 0.764628 Iteration 2 Error: 0.135197 Iteration 3 Error: 0.035826 3D Fitting completed. Patch alignment time: 15.04(sec) Local motion has been corrected. Process thread exits. Computational time: 23.751652 sec Total time: 29.456120 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00018hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00018hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.553324s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00018hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.694871s ........................................ >>>>>>TIME<<<<<< FFT: 0.977303s Defocus_U Defocus_V Angle CCC 9955.08 10818.36 6.48 0.045050 Final Values Defocus_U Defocus_V Angle CCC 9962.89 10835.55 6.80 0.083673 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00018hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00018hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 42.93 7.20 Num Hot pixels: 211 Hot pixel threshold: 86.13 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.802372 Iteration 2 Error: 0.151554 Iteration 3 Error: 0.026303 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.29 -0.17 ...... Frame ( 3) shift: -0.58 -0.34 ...... Frame ( 4) shift: -0.87 -0.51 ...... Frame ( 5) shift: -1.16 -0.68 ...... Frame ( 6) shift: -1.30 -0.78 ...... Frame ( 7) shift: -1.30 -0.80 ...... Frame ( 8) shift: -1.29 -0.83 ...... Frame ( 9) shift: -1.25 -0.81 ...... Frame ( 10) shift: -1.17 -0.75 ...... Frame ( 11) shift: -1.08 -0.69 ...... Frame ( 12) shift: -1.02 -0.64 ...... Frame ( 13) shift: -0.97 -0.59 ...... Frame ( 14) shift: -0.93 -0.55 ...... Frame ( 15) shift: -0.90 -0.50 ...... Frame ( 16) shift: -0.91 -0.46 ...... Frame ( 17) shift: -0.91 -0.42 ...... Frame ( 18) shift: -0.89 -0.40 ...... Frame ( 19) shift: -0.83 -0.40 ...... Frame ( 20) shift: -0.77 -0.40 ...... Frame ( 21) shift: -0.69 -0.36 ...... Frame ( 22) shift: -0.57 -0.30 ...... Frame ( 23) shift: -0.46 -0.23 ...... Frame ( 24) shift: -0.37 -0.18 ...... Frame ( 25) shift: -0.28 -0.15 ...... Frame ( 26) shift: -0.20 -0.11 ...... Frame ( 27) shift: -0.19 -0.07 ...... Frame ( 28) shift: -0.26 -0.01 ...... Frame ( 29) shift: -0.33 0.04 ...... Frame ( 30) shift: -0.32 0.09 ...... Frame ( 31) shift: -0.22 0.12 ...... Frame ( 32) shift: -0.12 0.16 ...... Frame ( 33) shift: -0.09 0.17 ...... Frame ( 34) shift: -0.15 0.16 ...... Frame ( 35) shift: -0.20 0.15 ...... Frame ( 36) shift: -0.22 0.18 ...... Frame ( 37) shift: -0.21 0.26 ...... Frame ( 38) shift: -0.20 0.33 ...... Frame ( 39) shift: -0.19 0.41 ...... Frame ( 40) shift: -0.17 0.48 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.586646 Iteration 2 Error: 0.267606 Iteration 3 Error: 0.063397 Iteration 4 Error: 0.021535 Align patch 2 23 left Iteration 1 Error: 0.533254 Iteration 2 Error: 0.086018 Iteration 3 Error: 0.028699 Align patch 3 22 left Iteration 1 Error: 0.864179 Iteration 2 Error: 0.162684 Iteration 3 Error: 0.047839 Align patch 4 21 left Iteration 1 Error: 0.816966 Iteration 2 Error: 0.193684 Iteration 3 Error: 0.042101 Align patch 5 20 left Iteration 1 Error: 0.777714 Iteration 2 Error: 0.106766 Iteration 3 Error: 0.028026 Align patch 6 19 left Iteration 1 Error: 1.676033 Iteration 2 Error: 0.246074 Iteration 3 Error: 0.092313 Iteration 4 Error: 0.024046 Align patch 7 18 left Iteration 1 Error: 0.529794 Iteration 2 Error: 0.143533 Iteration 3 Error: 0.030379 Align patch 8 17 left Iteration 1 Error: 0.703730 Iteration 2 Error: 0.162753 Iteration 3 Error: 0.059072 Iteration 4 Error: 0.022321 Align patch 9 16 left Iteration 1 Error: 0.682692 Iteration 2 Error: 0.134641 Iteration 3 Error: 0.050206 Iteration 4 Error: 0.013514 Align patch 10 15 left Iteration 1 Error: 0.648444 Iteration 2 Error: 0.120330 Iteration 3 Error: 0.035512 Align patch 11 14 left Iteration 1 Error: 1.116852 Iteration 2 Error: 0.198787 Iteration 3 Error: 0.032841 Align patch 12 13 left Iteration 1 Error: 0.640968 Iteration 2 Error: 0.116153 Iteration 3 Error: 0.029181 Align patch 13 12 left Iteration 1 Error: 0.698107 Iteration 2 Error: 0.107685 Iteration 3 Error: 0.029011 Align patch 14 11 left Iteration 1 Error: 0.482292 Iteration 2 Error: 0.073054 Iteration 3 Error: 0.022592 Align patch 15 10 left Iteration 1 Error: 0.522864 Iteration 2 Error: 0.086906 Iteration 3 Error: 0.023460 Align patch 16 9 left Iteration 1 Error: 0.998836 Iteration 2 Error: 0.138728 Iteration 3 Error: 0.047573 Align patch 17 8 left Iteration 1 Error: 0.938321 Iteration 2 Error: 0.180432 Iteration 3 Error: 0.024413 Align patch 18 7 left Iteration 1 Error: 0.661999 Iteration 2 Error: 0.081611 Iteration 3 Error: 0.020331 Align patch 19 6 left Iteration 1 Error: 0.722676 Iteration 2 Error: 0.156381 Iteration 3 Error: 0.033287 Align patch 20 5 left Iteration 1 Error: 1.042974 Iteration 2 Error: 0.141681 Iteration 3 Error: 0.036204 Align patch 21 4 left Iteration 1 Error: 0.342725 Iteration 2 Error: 0.070034 Iteration 3 Error: 0.020997 Align patch 22 3 left Iteration 1 Error: 0.631466 Iteration 2 Error: 0.148880 Iteration 3 Error: 0.031325 Align patch 23 2 left Iteration 1 Error: 0.779907 Iteration 2 Error: 0.097933 Iteration 3 Error: 0.023703 Align patch 24 1 left Iteration 1 Error: 0.790226 Iteration 2 Error: 0.160097 Iteration 3 Error: 0.031630 Align patch 25 0 left Iteration 1 Error: 0.753078 Iteration 2 Error: 0.111656 Iteration 3 Error: 0.031389 3D Fitting completed. Patch alignment time: 15.09(sec) Local motion has been corrected. Process thread exits. Computational time: 23.385687 sec Total time: 28.956457 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00018hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00018hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.722296s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00018hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.906456s ........................................ >>>>>>TIME<<<<<< FFT: 0.889859s Defocus_U Defocus_V Angle CCC 10584.09 10001.95 84.36 0.040852 Final Values Defocus_U Defocus_V Angle CCC 10598.15 9991.01 84.68 0.076613 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00019hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00019hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 1.000e-01 CC threshold: 0.734 Mean Std: 41.09 7.07 Num Hot pixels: 193 Hot pixel threshold: 83.48 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.978499 Iteration 2 Error: 0.170101 Iteration 3 Error: 0.040921 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.23 0.03 ...... Frame ( 3) shift: -0.46 0.06 ...... Frame ( 4) shift: -0.68 0.09 ...... Frame ( 5) shift: -0.91 0.12 ...... Frame ( 6) shift: -1.00 0.13 ...... Frame ( 7) shift: -0.94 0.11 ...... Frame ( 8) shift: -0.88 0.10 ...... Frame ( 9) shift: -0.83 0.12 ...... Frame ( 10) shift: -0.79 0.18 ...... Frame ( 11) shift: -0.75 0.24 ...... Frame ( 12) shift: -0.74 0.31 ...... Frame ( 13) shift: -0.76 0.39 ...... Frame ( 14) shift: -0.79 0.46 ...... Frame ( 15) shift: -0.77 0.52 ...... Frame ( 16) shift: -0.72 0.54 ...... Frame ( 17) shift: -0.66 0.57 ...... Frame ( 18) shift: -0.62 0.61 ...... Frame ( 19) shift: -0.59 0.66 ...... Frame ( 20) shift: -0.57 0.72 ...... Frame ( 21) shift: -0.53 0.78 ...... Frame ( 22) shift: -0.48 0.86 ...... Frame ( 23) shift: -0.44 0.93 ...... Frame ( 24) shift: -0.36 0.96 ...... Frame ( 25) shift: -0.24 0.93 ...... Frame ( 26) shift: -0.13 0.91 ...... Frame ( 27) shift: -0.06 0.89 ...... Frame ( 28) shift: -0.04 0.89 ...... Frame ( 29) shift: -0.02 0.88 ...... Frame ( 30) shift: 0.04 0.90 ...... Frame ( 31) shift: 0.16 0.94 ...... Frame ( 32) shift: 0.28 0.99 ...... Frame ( 33) shift: 0.35 1.03 ...... Frame ( 34) shift: 0.36 1.06 ...... Frame ( 35) shift: 0.37 1.10 ...... Frame ( 36) shift: 0.41 1.12 ...... Frame ( 37) shift: 0.50 1.13 ...... Frame ( 38) shift: 0.58 1.14 ...... Frame ( 39) shift: 0.66 1.15 ...... Frame ( 40) shift: 0.75 1.16 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.813863 Iteration 2 Error: 0.203801 Iteration 3 Error: 0.055375 Iteration 4 Error: 0.038433 Align patch 2 23 left Iteration 1 Error: 0.699102 Iteration 2 Error: 0.179243 Iteration 3 Error: 0.035866 Align patch 3 22 left Iteration 1 Error: 0.727059 Iteration 2 Error: 0.171562 Iteration 3 Error: 0.046795 Align patch 4 21 left Iteration 1 Error: 0.511074 Iteration 2 Error: 0.070848 Iteration 3 Error: 0.013771 Align patch 5 20 left Iteration 1 Error: 1.032876 Iteration 2 Error: 0.194240 Iteration 3 Error: 0.055319 Iteration 4 Error: 0.010603 Align patch 6 19 left Iteration 1 Error: 1.107387 Iteration 2 Error: 0.382405 Iteration 3 Error: 0.109817 Iteration 4 Error: 0.068137 Iteration 5 Error: 0.026900 Align patch 7 18 left Iteration 1 Error: 0.789258 Iteration 2 Error: 0.256036 Iteration 3 Error: 0.104737 Iteration 4 Error: 0.056705 Iteration 5 Error: 0.030093 Align patch 8 17 left Iteration 1 Error: 0.762754 Iteration 2 Error: 0.129258 Iteration 3 Error: 0.041640 Align patch 9 16 left Iteration 1 Error: 0.587106 Iteration 2 Error: 0.101703 Iteration 3 Error: 0.032533 Align patch 10 15 left Iteration 1 Error: 0.659025 Iteration 2 Error: 0.168616 Iteration 3 Error: 0.046776 Align patch 11 14 left Iteration 1 Error: 1.260746 Iteration 2 Error: 0.159979 Iteration 3 Error: 0.033013 Align patch 12 13 left Iteration 1 Error: 0.992247 Iteration 2 Error: 0.207543 Iteration 3 Error: 0.066471 Iteration 4 Error: 0.029447 Align patch 13 12 left Iteration 1 Error: 1.090955 Iteration 2 Error: 0.102539 Iteration 3 Error: 0.027144 Align patch 14 11 left Iteration 1 Error: 0.753670 Iteration 2 Error: 0.164915 Iteration 3 Error: 0.032519 Align patch 15 10 left Iteration 1 Error: 0.790166 Iteration 2 Error: 0.096256 Iteration 3 Error: 0.028641 Align patch 16 9 left Iteration 1 Error: 0.797661 Iteration 2 Error: 0.121078 Iteration 3 Error: 0.020438 Align patch 17 8 left Iteration 1 Error: 0.658640 Iteration 2 Error: 0.165576 Iteration 3 Error: 0.050708 Iteration 4 Error: 0.014063 Align patch 18 7 left Iteration 1 Error: 0.961806 Iteration 2 Error: 0.134910 Iteration 3 Error: 0.032535 Align patch 19 6 left Iteration 1 Error: 0.661008 Iteration 2 Error: 0.092687 Iteration 3 Error: 0.028625 Align patch 20 5 left Iteration 1 Error: 0.854860 Iteration 2 Error: 0.197239 Iteration 3 Error: 0.056341 Iteration 4 Error: 0.022337 Align patch 21 4 left Iteration 1 Error: 1.294014 Iteration 2 Error: 0.102956 Iteration 3 Error: 0.040250 Align patch 22 3 left Iteration 1 Error: 1.746161 Iteration 2 Error: 0.281309 Iteration 3 Error: 0.097940 Iteration 4 Error: 0.033671 Align patch 23 2 left Iteration 1 Error: 0.682044 Iteration 2 Error: 0.119341 Iteration 3 Error: 0.029558 Align patch 24 1 left Iteration 1 Error: 0.687940 Iteration 2 Error: 0.073829 Iteration 3 Error: 0.017170 Align patch 25 0 left Iteration 1 Error: 0.638446 Iteration 2 Error: 0.102689 Iteration 3 Error: 0.032481 3D Fitting completed. Patch alignment time: 16.22(sec) Local motion has been corrected. Process thread exits. Computational time: 24.898710 sec Total time: 31.053619 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00019hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00019hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.693261s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00019hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.511153s ........................................ >>>>>>TIME<<<<<< FFT: 0.945340s Defocus_U Defocus_V Angle CCC 13513.67 14259.77 10.63 0.044907 Final Values Defocus_U Defocus_V Angle CCC 13479.31 14297.34 10.95 0.069383 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00019hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00019hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 41.14 7.07 Num Hot pixels: 196 Hot pixel threshold: 83.58 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.894385 Iteration 2 Error: 0.101647 Iteration 3 Error: 0.021242 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.26 0.09 ...... Frame ( 3) shift: -0.52 0.18 ...... Frame ( 4) shift: -0.78 0.26 ...... Frame ( 5) shift: -1.04 0.35 ...... Frame ( 6) shift: -1.20 0.41 ...... Frame ( 7) shift: -1.26 0.45 ...... Frame ( 8) shift: -1.32 0.48 ...... Frame ( 9) shift: -1.31 0.51 ...... Frame ( 10) shift: -1.23 0.53 ...... Frame ( 11) shift: -1.15 0.55 ...... Frame ( 12) shift: -1.08 0.57 ...... Frame ( 13) shift: -1.02 0.59 ...... Frame ( 14) shift: -0.97 0.61 ...... Frame ( 15) shift: -0.95 0.66 ...... Frame ( 16) shift: -0.95 0.75 ...... Frame ( 17) shift: -0.96 0.83 ...... Frame ( 18) shift: -0.99 0.91 ...... Frame ( 19) shift: -1.03 0.99 ...... Frame ( 20) shift: -1.08 1.07 ...... Frame ( 21) shift: -1.08 1.09 ...... Frame ( 22) shift: -1.02 1.04 ...... Frame ( 23) shift: -0.97 1.00 ...... Frame ( 24) shift: -0.93 0.99 ...... Frame ( 25) shift: -0.92 1.02 ...... Frame ( 26) shift: -0.91 1.04 ...... Frame ( 27) shift: -0.88 1.08 ...... Frame ( 28) shift: -0.81 1.13 ...... Frame ( 29) shift: -0.75 1.18 ...... Frame ( 30) shift: -0.75 1.21 ...... Frame ( 31) shift: -0.81 1.21 ...... Frame ( 32) shift: -0.88 1.22 ...... Frame ( 33) shift: -0.86 1.25 ...... Frame ( 34) shift: -0.77 1.31 ...... Frame ( 35) shift: -0.67 1.36 ...... Frame ( 36) shift: -0.63 1.40 ...... Frame ( 37) shift: -0.62 1.41 ...... Frame ( 38) shift: -0.62 1.42 ...... Frame ( 39) shift: -0.61 1.44 ...... Frame ( 40) shift: -0.61 1.45 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.974773 Iteration 2 Error: 0.273408 Iteration 3 Error: 0.076103 Iteration 4 Error: 0.029941 Align patch 2 23 left Iteration 1 Error: 0.901804 Iteration 2 Error: 0.134241 Iteration 3 Error: 0.040368 Align patch 3 22 left Iteration 1 Error: 0.712042 Iteration 2 Error: 0.114645 Iteration 3 Error: 0.019516 Align patch 4 21 left Iteration 1 Error: 0.660553 Iteration 2 Error: 0.179913 Iteration 3 Error: 0.039160 Align patch 5 20 left Iteration 1 Error: 0.705228 Iteration 2 Error: 0.072546 Iteration 3 Error: 0.017425 Align patch 6 19 left Iteration 1 Error: 0.738586 Iteration 2 Error: 0.100396 Iteration 3 Error: 0.026431 Align patch 7 18 left Iteration 1 Error: 0.686638 Iteration 2 Error: 0.112236 Iteration 3 Error: 0.027156 Align patch 8 17 left Iteration 1 Error: 0.719850 Iteration 2 Error: 0.114424 Iteration 3 Error: 0.025701 Align patch 9 16 left Iteration 1 Error: 1.217425 Iteration 2 Error: 0.135763 Iteration 3 Error: 0.030068 Align patch 10 15 left Iteration 1 Error: 0.753257 Iteration 2 Error: 0.098730 Iteration 3 Error: 0.016664 Align patch 11 14 left Iteration 1 Error: 0.781385 Iteration 2 Error: 0.179026 Iteration 3 Error: 0.037241 Align patch 12 13 left Iteration 1 Error: 0.738443 Iteration 2 Error: 0.135765 Iteration 3 Error: 0.043778 Align patch 13 12 left Iteration 1 Error: 0.777692 Iteration 2 Error: 0.166197 Iteration 3 Error: 0.045377 Align patch 14 11 left Iteration 1 Error: 0.959650 Iteration 2 Error: 0.192667 Iteration 3 Error: 0.043673 Align patch 15 10 left Iteration 1 Error: 0.766382 Iteration 2 Error: 0.126519 Iteration 3 Error: 0.028511 Align patch 16 9 left Iteration 1 Error: 0.758732 Iteration 2 Error: 0.129246 Iteration 3 Error: 0.029338 Align patch 17 8 left Iteration 1 Error: 0.713047 Iteration 2 Error: 0.161931 Iteration 3 Error: 0.046516 Align patch 18 7 left Iteration 1 Error: 0.689762 Iteration 2 Error: 0.260346 Iteration 3 Error: 0.050125 Iteration 4 Error: 0.033276 Align patch 19 6 left Iteration 1 Error: 0.770753 Iteration 2 Error: 0.086413 Iteration 3 Error: 0.016079 Align patch 20 5 left Iteration 1 Error: 0.493863 Iteration 2 Error: 0.082064 Iteration 3 Error: 0.026343 Align patch 21 4 left Iteration 1 Error: 0.705243 Iteration 2 Error: 0.212779 Iteration 3 Error: 0.042510 Align patch 22 3 left Iteration 1 Error: 0.678284 Iteration 2 Error: 0.126272 Iteration 3 Error: 0.040409 Align patch 23 2 left Iteration 1 Error: 0.533132 Iteration 2 Error: 0.103981 Iteration 3 Error: 0.029054 Align patch 24 1 left Iteration 1 Error: 0.938379 Iteration 2 Error: 0.157277 Iteration 3 Error: 0.032792 Align patch 25 0 left Iteration 1 Error: 0.812946 Iteration 2 Error: 0.166098 Iteration 3 Error: 0.027189 3D Fitting completed. Patch alignment time: 15.79(sec) Local motion has been corrected. Process thread exits. Computational time: 24.387493 sec Total time: 31.457111 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00019hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00019hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.780610s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00019hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.711952s ........................................ >>>>>>TIME<<<<<< FFT: 0.992481s Defocus_U Defocus_V Angle CCC 9291.03 8869.15 88.99 0.030987 Final Values Defocus_U Defocus_V Angle CCC 8881.66 9300.41 0.56 0.061512 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00019hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00019hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.994e-02 CC threshold: 0.734 Mean Std: 31.44 6.00 Num Hot pixels: 204 Hot pixel threshold: 67.41 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.832874 Iteration 2 Error: 0.183244 Iteration 3 Error: 0.037184 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.33 0.18 ...... Frame ( 3) shift: 0.67 0.37 ...... Frame ( 4) shift: 1.00 0.55 ...... Frame ( 5) shift: 1.34 0.73 ...... Frame ( 6) shift: 1.49 0.87 ...... Frame ( 7) shift: 1.47 0.97 ...... Frame ( 8) shift: 1.44 1.06 ...... Frame ( 9) shift: 1.48 1.14 ...... Frame ( 10) shift: 1.56 1.20 ...... Frame ( 11) shift: 1.65 1.25 ...... Frame ( 12) shift: 1.71 1.31 ...... Frame ( 13) shift: 1.72 1.37 ...... Frame ( 14) shift: 1.74 1.43 ...... Frame ( 15) shift: 1.75 1.48 ...... Frame ( 16) shift: 1.77 1.51 ...... Frame ( 17) shift: 1.78 1.54 ...... Frame ( 18) shift: 1.77 1.59 ...... Frame ( 19) shift: 1.74 1.65 ...... Frame ( 20) shift: 1.70 1.71 ...... Frame ( 21) shift: 1.70 1.76 ...... Frame ( 22) shift: 1.73 1.79 ...... Frame ( 23) shift: 1.75 1.82 ...... Frame ( 24) shift: 1.81 1.84 ...... Frame ( 25) shift: 1.88 1.84 ...... Frame ( 26) shift: 1.96 1.84 ...... Frame ( 27) shift: 1.99 1.84 ...... Frame ( 28) shift: 1.97 1.85 ...... Frame ( 29) shift: 1.95 1.85 ...... Frame ( 30) shift: 1.92 1.90 ...... Frame ( 31) shift: 1.89 1.98 ...... Frame ( 32) shift: 1.86 2.07 ...... Frame ( 33) shift: 1.83 2.09 ...... Frame ( 34) shift: 1.81 2.04 ...... Frame ( 35) shift: 1.79 2.00 ...... Frame ( 36) shift: 1.86 1.97 ...... Frame ( 37) shift: 2.02 1.97 ...... Frame ( 38) shift: 2.18 1.96 ...... Frame ( 39) shift: 2.33 1.95 ...... Frame ( 40) shift: 2.49 1.94 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.933491 Iteration 2 Error: 0.186351 Iteration 3 Error: 0.040960 Align patch 2 23 left Iteration 1 Error: 0.515754 Iteration 2 Error: 0.149381 Iteration 3 Error: 0.043410 Align patch 3 22 left Iteration 1 Error: 1.572778 Iteration 2 Error: 0.202226 Iteration 3 Error: 0.065792 Iteration 4 Error: 0.019838 Align patch 4 21 left Iteration 1 Error: 0.660667 Iteration 2 Error: 0.116636 Iteration 3 Error: 0.028459 Align patch 5 20 left Iteration 1 Error: 1.130096 Iteration 2 Error: 0.193869 Iteration 3 Error: 0.052943 Iteration 4 Error: 0.017559 Align patch 6 19 left Iteration 1 Error: 1.440916 Iteration 2 Error: 0.194534 Iteration 3 Error: 0.060551 Iteration 4 Error: 0.022668 Align patch 7 18 left Iteration 1 Error: 0.931518 Iteration 2 Error: 0.207102 Iteration 3 Error: 0.052130 Iteration 4 Error: 0.013433 Align patch 8 17 left Iteration 1 Error: 1.167087 Iteration 2 Error: 0.266836 Iteration 3 Error: 0.146675 Iteration 4 Error: 0.053516 Iteration 5 Error: 0.032709 Align patch 9 16 left Iteration 1 Error: 1.243966 Iteration 2 Error: 0.283221 Iteration 3 Error: 0.119451 Iteration 4 Error: 0.033341 Align patch 10 15 left Iteration 1 Error: 0.825258 Iteration 2 Error: 0.259940 Iteration 3 Error: 0.099686 Iteration 4 Error: 0.039502 Align patch 11 14 left Iteration 1 Error: 2.243510 Iteration 2 Error: 0.217532 Iteration 3 Error: 0.065503 Iteration 4 Error: 0.019924 Align patch 12 13 left Iteration 1 Error: 1.080375 Iteration 2 Error: 0.145232 Iteration 3 Error: 0.033450 Align patch 13 12 left Iteration 1 Error: 1.372152 Iteration 2 Error: 0.269301 Iteration 3 Error: 0.144219 Iteration 4 Error: 0.053291 Iteration 5 Error: 0.024341 Align patch 14 11 left Iteration 1 Error: 0.856146 Iteration 2 Error: 0.159866 Iteration 3 Error: 0.062275 Iteration 4 Error: 0.018453 Align patch 15 10 left Iteration 1 Error: 1.394469 Iteration 2 Error: 0.239129 Iteration 3 Error: 0.105935 Iteration 4 Error: 0.024587 Align patch 16 9 left Iteration 1 Error: 0.999556 Iteration 2 Error: 0.264600 Iteration 3 Error: 0.070377 Iteration 4 Error: 0.028050 Align patch 17 8 left Iteration 1 Error: 1.183625 Iteration 2 Error: 0.202218 Iteration 3 Error: 0.060732 Iteration 4 Error: 0.023227 Align patch 18 7 left Iteration 1 Error: 0.876572 Iteration 2 Error: 0.198233 Iteration 3 Error: 0.062153 Iteration 4 Error: 0.044180 Align patch 19 6 left Iteration 1 Error: 1.546509 Iteration 2 Error: 0.182220 Iteration 3 Error: 0.056516 Iteration 4 Error: 0.020097 Align patch 20 5 left Iteration 1 Error: 1.346968 Iteration 2 Error: 0.249559 Iteration 3 Error: 0.047736 Align patch 21 4 left Iteration 1 Error: 0.931069 Iteration 2 Error: 0.167997 Iteration 3 Error: 0.050018 Iteration 4 Error: 0.017507 Align patch 22 3 left Iteration 1 Error: 1.019229 Iteration 2 Error: 0.171250 Iteration 3 Error: 0.054043 Iteration 4 Error: 0.019981 Align patch 23 2 left Iteration 1 Error: 1.042209 Iteration 2 Error: 0.201023 Iteration 3 Error: 0.052062 Iteration 4 Error: 0.021338 Align patch 24 1 left Iteration 1 Error: 1.190463 Iteration 2 Error: 0.282399 Iteration 3 Error: 0.110452 Iteration 4 Error: 0.035249 Align patch 25 0 left Iteration 1 Error: 0.955384 Iteration 2 Error: 0.167053 Iteration 3 Error: 0.053089 Iteration 4 Error: 0.013196 3D Fitting completed. Patch alignment time: 16.77(sec) Local motion has been corrected. Process thread exits. Computational time: 25.315020 sec Total time: 31.477678 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00019hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00019hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.687679s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00019hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.665315s ........................................ >>>>>>TIME<<<<<< FFT: 0.948262s Defocus_U Defocus_V Angle CCC 10056.64 10947.27 9.90 0.013126 Final Values Defocus_U Defocus_V Angle CCC 10023.83 10911.33 8.96 0.021954 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00009sq_v01_00019hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00019hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 36.97 6.51 Num Hot pixels: 186 Hot pixel threshold: 76.01 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.633633 Iteration 2 Error: 0.116059 Iteration 3 Error: 0.029632 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.06 -0.06 ...... Frame ( 3) shift: -0.12 -0.11 ...... Frame ( 4) shift: -0.18 -0.17 ...... Frame ( 5) shift: -0.24 -0.23 ...... Frame ( 6) shift: -0.28 -0.27 ...... Frame ( 7) shift: -0.30 -0.30 ...... Frame ( 8) shift: -0.32 -0.33 ...... Frame ( 9) shift: -0.30 -0.31 ...... Frame ( 10) shift: -0.23 -0.23 ...... Frame ( 11) shift: -0.16 -0.15 ...... Frame ( 12) shift: -0.08 -0.08 ...... Frame ( 13) shift: 0.00 -0.02 ...... Frame ( 14) shift: 0.09 0.04 ...... Frame ( 15) shift: 0.14 0.08 ...... Frame ( 16) shift: 0.15 0.10 ...... Frame ( 17) shift: 0.16 0.12 ...... Frame ( 18) shift: 0.15 0.16 ...... Frame ( 19) shift: 0.13 0.22 ...... Frame ( 20) shift: 0.12 0.27 ...... Frame ( 21) shift: 0.15 0.32 ...... Frame ( 22) shift: 0.21 0.34 ...... Frame ( 23) shift: 0.28 0.36 ...... Frame ( 24) shift: 0.30 0.38 ...... Frame ( 25) shift: 0.26 0.39 ...... Frame ( 26) shift: 0.22 0.41 ...... Frame ( 27) shift: 0.19 0.42 ...... Frame ( 28) shift: 0.16 0.41 ...... Frame ( 29) shift: 0.14 0.41 ...... Frame ( 30) shift: 0.17 0.45 ...... Frame ( 31) shift: 0.27 0.52 ...... Frame ( 32) shift: 0.37 0.60 ...... Frame ( 33) shift: 0.39 0.62 ...... Frame ( 34) shift: 0.33 0.58 ...... Frame ( 35) shift: 0.27 0.53 ...... Frame ( 36) shift: 0.29 0.54 ...... Frame ( 37) shift: 0.40 0.59 ...... Frame ( 38) shift: 0.51 0.65 ...... Frame ( 39) shift: 0.62 0.70 ...... Frame ( 40) shift: 0.73 0.76 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.855800 Iteration 2 Error: 0.146739 Iteration 3 Error: 0.064187 Iteration 4 Error: 0.019900 Align patch 2 23 left Iteration 1 Error: 0.963220 Iteration 2 Error: 0.182610 Iteration 3 Error: 0.039394 Align patch 3 22 left Iteration 1 Error: 0.723511 Iteration 2 Error: 0.117594 Iteration 3 Error: 0.025392 Align patch 4 21 left Iteration 1 Error: 0.600730 Iteration 2 Error: 0.148344 Iteration 3 Error: 0.036124 Align patch 5 20 left Iteration 1 Error: 1.163010 Iteration 2 Error: 0.162897 Iteration 3 Error: 0.040140 Align patch 6 19 left Iteration 1 Error: 0.952250 Iteration 2 Error: 0.216919 Iteration 3 Error: 0.027596 Align patch 7 18 left Iteration 1 Error: 0.534224 Iteration 2 Error: 0.130597 Iteration 3 Error: 0.040122 Align patch 8 17 left Iteration 1 Error: 0.830435 Iteration 2 Error: 0.155557 Iteration 3 Error: 0.059652 Iteration 4 Error: 0.017780 Align patch 9 16 left Iteration 1 Error: 0.834788 Iteration 2 Error: 0.187554 Iteration 3 Error: 0.044615 Align patch 10 15 left Iteration 1 Error: 1.401201 Iteration 2 Error: 0.276532 Iteration 3 Error: 0.048328 Align patch 11 14 left Iteration 1 Error: 1.157534 Iteration 2 Error: 0.227726 Iteration 3 Error: 0.045066 Align patch 12 13 left Iteration 1 Error: 0.706183 Iteration 2 Error: 0.149764 Iteration 3 Error: 0.040300 Align patch 13 12 left Iteration 1 Error: 0.630945 Iteration 2 Error: 0.069084 Iteration 3 Error: 0.015244 Align patch 14 11 left Iteration 1 Error: 0.759534 Iteration 2 Error: 0.159072 Iteration 3 Error: 0.056238 Iteration 4 Error: 0.015826 Align patch 15 10 left Iteration 1 Error: 1.012057 Iteration 2 Error: 0.237446 Iteration 3 Error: 0.048145 Align patch 16 9 left Iteration 1 Error: 0.699901 Iteration 2 Error: 0.105954 Iteration 3 Error: 0.033587 Align patch 17 8 left Iteration 1 Error: 0.594219 Iteration 2 Error: 0.107188 Iteration 3 Error: 0.042028 Align patch 18 7 left Iteration 1 Error: 0.776709 Iteration 2 Error: 0.153957 Iteration 3 Error: 0.035015 Align patch 19 6 left Iteration 1 Error: 0.781324 Iteration 2 Error: 0.105441 Iteration 3 Error: 0.022675 Align patch 20 5 left Iteration 1 Error: 0.537734 Iteration 2 Error: 0.065967 Iteration 3 Error: 0.016128 Align patch 21 4 left Iteration 1 Error: 0.707565 Iteration 2 Error: 0.130624 Iteration 3 Error: 0.066117 Iteration 4 Error: 0.011929 Align patch 22 3 left Iteration 1 Error: 0.627491 Iteration 2 Error: 0.094283 Iteration 3 Error: 0.023860 Align patch 23 2 left Iteration 1 Error: 0.811212 Iteration 2 Error: 0.180244 Iteration 3 Error: 0.050151 Iteration 4 Error: 0.016084 Align patch 24 1 left Iteration 1 Error: 0.441173 Iteration 2 Error: 0.096095 Iteration 3 Error: 0.026587 Align patch 25 0 left Iteration 1 Error: 0.689431 Iteration 2 Error: 0.149286 Iteration 3 Error: 0.047516 3D Fitting completed. Patch alignment time: 14.76(sec) Local motion has been corrected. Process thread exits. Computational time: 23.375465 sec Total time: 29.108097 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00019hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00019hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.553410s Reading file: gc_18feb27f_CTD_g1_00012gr_00009sq_v01_00019hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.725938s ........................................ >>>>>>TIME<<<<<< FFT: 0.895868s Defocus_U Defocus_V Angle CCC 12750.01 12003.90 85.98 0.028903 Final Values Defocus_U Defocus_V Angle CCC 12789.07 12064.85 88.83 0.041829 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00002hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00002hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 40.57 6.82 Num Hot pixels: 224 Hot pixel threshold: 81.50 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.529489 Iteration 2 Error: 0.435003 Iteration 3 Error: 0.122593 Iteration 4 Error: 0.039981 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.03 0.30 ...... Frame ( 3) shift: 0.06 0.61 ...... Frame ( 4) shift: 0.09 0.91 ...... Frame ( 5) shift: 0.12 1.22 ...... Frame ( 6) shift: 0.15 1.48 ...... Frame ( 7) shift: 0.20 1.69 ...... Frame ( 8) shift: 0.24 1.90 ...... Frame ( 9) shift: 0.28 2.08 ...... Frame ( 10) shift: 0.32 2.22 ...... Frame ( 11) shift: 0.35 2.36 ...... Frame ( 12) shift: 0.39 2.49 ...... Frame ( 13) shift: 0.42 2.59 ...... Frame ( 14) shift: 0.45 2.69 ...... Frame ( 15) shift: 0.47 2.80 ...... Frame ( 16) shift: 0.47 2.93 ...... Frame ( 17) shift: 0.46 3.05 ...... Frame ( 18) shift: 0.46 3.20 ...... Frame ( 19) shift: 0.46 3.38 ...... Frame ( 20) shift: 0.46 3.55 ...... Frame ( 21) shift: 0.49 3.69 ...... Frame ( 22) shift: 0.55 3.79 ...... Frame ( 23) shift: 0.60 3.89 ...... Frame ( 24) shift: 0.64 4.03 ...... Frame ( 25) shift: 0.66 4.20 ...... Frame ( 26) shift: 0.67 4.38 ...... Frame ( 27) shift: 0.68 4.51 ...... Frame ( 28) shift: 0.68 4.61 ...... Frame ( 29) shift: 0.68 4.70 ...... Frame ( 30) shift: 0.72 4.79 ...... Frame ( 31) shift: 0.81 4.87 ...... Frame ( 32) shift: 0.90 4.96 ...... Frame ( 33) shift: 0.98 5.05 ...... Frame ( 34) shift: 1.03 5.16 ...... Frame ( 35) shift: 1.09 5.27 ...... Frame ( 36) shift: 1.11 5.37 ...... Frame ( 37) shift: 1.11 5.45 ...... Frame ( 38) shift: 1.11 5.53 ...... Frame ( 39) shift: 1.11 5.62 ...... Frame ( 40) shift: 1.11 5.70 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.701220 Iteration 2 Error: 0.202424 Iteration 3 Error: 0.065447 Iteration 4 Error: 0.026596 Align patch 2 23 left Iteration 1 Error: 0.775998 Iteration 2 Error: 0.121196 Iteration 3 Error: 0.036288 Align patch 3 22 left Iteration 1 Error: 1.089569 Iteration 2 Error: 0.177328 Iteration 3 Error: 0.034082 Align patch 4 21 left Iteration 1 Error: 0.878458 Iteration 2 Error: 0.206497 Iteration 3 Error: 0.063223 Iteration 4 Error: 0.025487 Align patch 5 20 left Iteration 1 Error: 0.700463 Iteration 2 Error: 0.137679 Iteration 3 Error: 0.029120 Align patch 6 19 left Iteration 1 Error: 0.546921 Iteration 2 Error: 0.134377 Iteration 3 Error: 0.030116 Align patch 7 18 left Iteration 1 Error: 0.383057 Iteration 2 Error: 0.061792 Iteration 3 Error: 0.022170 Align patch 8 17 left Iteration 1 Error: 0.495240 Iteration 2 Error: 0.083735 Iteration 3 Error: 0.015297 Align patch 9 16 left Iteration 1 Error: 0.826696 Iteration 2 Error: 0.052486 Iteration 3 Error: 0.010950 Align patch 10 15 left Iteration 1 Error: 0.670458 Iteration 2 Error: 0.084180 Iteration 3 Error: 0.020815 Align patch 11 14 left Iteration 1 Error: 0.802271 Iteration 2 Error: 0.130220 Iteration 3 Error: 0.051592 Iteration 4 Error: 0.014956 Align patch 12 13 left Iteration 1 Error: 0.770003 Iteration 2 Error: 0.179469 Iteration 3 Error: 0.046332 Align patch 13 12 left Iteration 1 Error: 0.594506 Iteration 2 Error: 0.116045 Iteration 3 Error: 0.039429 Align patch 14 11 left Iteration 1 Error: 0.534101 Iteration 2 Error: 0.147290 Iteration 3 Error: 0.040945 Align patch 15 10 left Iteration 1 Error: 0.991579 Iteration 2 Error: 0.180359 Iteration 3 Error: 0.030176 Align patch 16 9 left Iteration 1 Error: 1.486637 Iteration 2 Error: 0.212202 Iteration 3 Error: 0.086163 Iteration 4 Error: 0.024612 Align patch 17 8 left Iteration 1 Error: 0.925974 Iteration 2 Error: 0.105158 Iteration 3 Error: 0.027609 Align patch 18 7 left Iteration 1 Error: 0.722425 Iteration 2 Error: 0.079302 Iteration 3 Error: 0.019597 Align patch 19 6 left Iteration 1 Error: 0.819619 Iteration 2 Error: 0.129965 Iteration 3 Error: 0.028120 Align patch 20 5 left Iteration 1 Error: 0.552275 Iteration 2 Error: 0.096543 Iteration 3 Error: 0.033716 Align patch 21 4 left Iteration 1 Error: 1.417653 Iteration 2 Error: 0.282467 Iteration 3 Error: 0.128815 Iteration 4 Error: 0.041857 Align patch 22 3 left Iteration 1 Error: 1.209215 Iteration 2 Error: 0.160829 Iteration 3 Error: 0.057747 Iteration 4 Error: 0.014680 Align patch 23 2 left Iteration 1 Error: 0.609653 Iteration 2 Error: 0.107152 Iteration 3 Error: 0.024638 Align patch 24 1 left Iteration 1 Error: 0.634290 Iteration 2 Error: 0.123993 Iteration 3 Error: 0.028366 Align patch 25 0 left Iteration 1 Error: 0.608191 Iteration 2 Error: 0.171428 Iteration 3 Error: 0.034202 3D Fitting completed. Patch alignment time: 15.96(sec) Local motion has been corrected. Process thread exits. Computational time: 24.642418 sec Total time: 30.915310 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00002hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00002hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.784653s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00002hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.012548s ........................................ >>>>>>TIME<<<<<< FFT: 1.070465s Defocus_U Defocus_V Angle CCC 10271.49 11091.80 13.78 0.057717 Final Values Defocus_U Defocus_V Angle CCC 10282.42 11112.14 13.78 0.096467 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00002hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00002hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.004e-01 CC threshold: 0.737 Mean Std: 39.12 6.75 Num Hot pixels: 216 Hot pixel threshold: 79.60 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.029435 Iteration 2 Error: 0.284690 Iteration 3 Error: 0.062037 Iteration 4 Error: 0.015558 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.07 0.19 ...... Frame ( 3) shift: -0.14 0.38 ...... Frame ( 4) shift: -0.20 0.57 ...... Frame ( 5) shift: -0.27 0.76 ...... Frame ( 6) shift: -0.27 0.94 ...... Frame ( 7) shift: -0.21 1.13 ...... Frame ( 8) shift: -0.16 1.31 ...... Frame ( 9) shift: -0.12 1.46 ...... Frame ( 10) shift: -0.11 1.57 ...... Frame ( 11) shift: -0.10 1.69 ...... Frame ( 12) shift: -0.11 1.77 ...... Frame ( 13) shift: -0.16 1.84 ...... Frame ( 14) shift: -0.20 1.90 ...... Frame ( 15) shift: -0.22 2.00 ...... Frame ( 16) shift: -0.22 2.13 ...... Frame ( 17) shift: -0.21 2.27 ...... Frame ( 18) shift: -0.21 2.40 ...... Frame ( 19) shift: -0.21 2.52 ...... Frame ( 20) shift: -0.20 2.64 ...... Frame ( 21) shift: -0.20 2.75 ...... Frame ( 22) shift: -0.18 2.84 ...... Frame ( 23) shift: -0.17 2.93 ...... Frame ( 24) shift: -0.15 3.02 ...... Frame ( 25) shift: -0.13 3.12 ...... Frame ( 26) shift: -0.11 3.22 ...... Frame ( 27) shift: -0.10 3.33 ...... Frame ( 28) shift: -0.13 3.48 ...... Frame ( 29) shift: -0.15 3.62 ...... Frame ( 30) shift: -0.16 3.70 ...... Frame ( 31) shift: -0.14 3.71 ...... Frame ( 32) shift: -0.13 3.73 ...... Frame ( 33) shift: -0.12 3.79 ...... Frame ( 34) shift: -0.11 3.87 ...... Frame ( 35) shift: -0.11 3.96 ...... Frame ( 36) shift: -0.11 4.05 ...... Frame ( 37) shift: -0.12 4.13 ...... Frame ( 38) shift: -0.13 4.22 ...... Frame ( 39) shift: -0.14 4.31 ...... Frame ( 40) shift: -0.15 4.40 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.859342 Iteration 2 Error: 0.136398 Iteration 3 Error: 0.029460 Align patch 2 23 left Iteration 1 Error: 1.112694 Iteration 2 Error: 0.194403 Iteration 3 Error: 0.034133 Align patch 3 22 left Iteration 1 Error: 0.837686 Iteration 2 Error: 0.195460 Iteration 3 Error: 0.045503 Align patch 4 21 left Iteration 1 Error: 0.589509 Iteration 2 Error: 0.129207 Iteration 3 Error: 0.041397 Align patch 5 20 left Iteration 1 Error: 0.849742 Iteration 2 Error: 0.146649 Iteration 3 Error: 0.027833 Align patch 6 19 left Iteration 1 Error: 0.930794 Iteration 2 Error: 0.218707 Iteration 3 Error: 0.044399 Align patch 7 18 left Iteration 1 Error: 0.632952 Iteration 2 Error: 0.138426 Iteration 3 Error: 0.027733 Align patch 8 17 left Iteration 1 Error: 0.475878 Iteration 2 Error: 0.104544 Iteration 3 Error: 0.034496 Align patch 9 16 left Iteration 1 Error: 0.467948 Iteration 2 Error: 0.094659 Iteration 3 Error: 0.019100 Align patch 10 15 left Iteration 1 Error: 0.311320 Iteration 2 Error: 0.039881 Align patch 11 14 left Iteration 1 Error: 0.628973 Iteration 2 Error: 0.098932 Iteration 3 Error: 0.019620 Align patch 12 13 left Iteration 1 Error: 0.746489 Iteration 2 Error: 0.082985 Iteration 3 Error: 0.030210 Align patch 13 12 left Iteration 1 Error: 0.707695 Iteration 2 Error: 0.110628 Iteration 3 Error: 0.026460 Align patch 14 11 left Iteration 1 Error: 0.820921 Iteration 2 Error: 0.109810 Iteration 3 Error: 0.034704 Align patch 15 10 left Iteration 1 Error: 0.515891 Iteration 2 Error: 0.073398 Iteration 3 Error: 0.022277 Align patch 16 9 left Iteration 1 Error: 0.676309 Iteration 2 Error: 0.172006 Iteration 3 Error: 0.050360 Iteration 4 Error: 0.021035 Align patch 17 8 left Iteration 1 Error: 0.845194 Iteration 2 Error: 0.150972 Iteration 3 Error: 0.035491 Align patch 18 7 left Iteration 1 Error: 0.620344 Iteration 2 Error: 0.135676 Iteration 3 Error: 0.028676 Align patch 19 6 left Iteration 1 Error: 0.697054 Iteration 2 Error: 0.095259 Iteration 3 Error: 0.026750 Align patch 20 5 left Iteration 1 Error: 0.489384 Iteration 2 Error: 0.075493 Iteration 3 Error: 0.025588 Align patch 21 4 left Iteration 1 Error: 1.356354 Iteration 2 Error: 0.250052 Iteration 3 Error: 0.054324 Iteration 4 Error: 0.019866 Align patch 22 3 left Iteration 1 Error: 0.942063 Iteration 2 Error: 0.094890 Iteration 3 Error: 0.016259 Align patch 23 2 left Iteration 1 Error: 0.930789 Iteration 2 Error: 0.150685 Iteration 3 Error: 0.029572 Align patch 24 1 left Iteration 1 Error: 0.882252 Iteration 2 Error: 0.120624 Iteration 3 Error: 0.029942 Align patch 25 0 left Iteration 1 Error: 0.726113 Iteration 2 Error: 0.103025 Iteration 3 Error: 0.024068 3D Fitting completed. Patch alignment time: 15.50(sec) Local motion has been corrected. Process thread exits. Computational time: 24.156248 sec Total time: 30.161295 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00002hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00002hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.735182s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00002hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.518596s ........................................ >>>>>>TIME<<<<<< FFT: 1.030991s Defocus_U Defocus_V Angle CCC 8619.13 9083.99 3.46 0.040400 Final Values Defocus_U Defocus_V Angle CCC 8597.28 9087.14 2.84 0.077079 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00002hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00002hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.350e-01 1.004e-01 CC threshold: 0.737 Mean Std: 39.51 6.83 Num Hot pixels: 226 Hot pixel threshold: 80.51 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.431129 Iteration 2 Error: 0.163417 Iteration 3 Error: 0.029510 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.21 0.09 ...... Frame ( 3) shift: -0.41 0.18 ...... Frame ( 4) shift: -0.62 0.26 ...... Frame ( 5) shift: -0.82 0.35 ...... Frame ( 6) shift: -0.93 0.46 ...... Frame ( 7) shift: -0.94 0.57 ...... Frame ( 8) shift: -0.94 0.69 ...... Frame ( 9) shift: -0.92 0.82 ...... Frame ( 10) shift: -0.86 0.96 ...... Frame ( 11) shift: -0.80 1.10 ...... Frame ( 12) shift: -0.77 1.20 ...... Frame ( 13) shift: -0.76 1.26 ...... Frame ( 14) shift: -0.76 1.33 ...... Frame ( 15) shift: -0.79 1.40 ...... Frame ( 16) shift: -0.84 1.48 ...... Frame ( 17) shift: -0.89 1.56 ...... Frame ( 18) shift: -0.92 1.63 ...... Frame ( 19) shift: -0.93 1.70 ...... Frame ( 20) shift: -0.94 1.76 ...... Frame ( 21) shift: -0.96 1.85 ...... Frame ( 22) shift: -0.99 1.95 ...... Frame ( 23) shift: -1.02 2.06 ...... Frame ( 24) shift: -1.03 2.09 ...... Frame ( 25) shift: -1.02 2.04 ...... Frame ( 26) shift: -1.02 2.00 ...... Frame ( 27) shift: -1.01 1.98 ...... Frame ( 28) shift: -1.01 1.99 ...... Frame ( 29) shift: -1.01 2.00 ...... Frame ( 30) shift: -1.01 2.00 ...... Frame ( 31) shift: -1.00 1.99 ...... Frame ( 32) shift: -0.99 1.99 ...... Frame ( 33) shift: -0.99 2.03 ...... Frame ( 34) shift: -0.99 2.11 ...... Frame ( 35) shift: -0.99 2.19 ...... Frame ( 36) shift: -1.00 2.25 ...... Frame ( 37) shift: -1.02 2.27 ...... Frame ( 38) shift: -1.03 2.30 ...... Frame ( 39) shift: -1.05 2.33 ...... Frame ( 40) shift: -1.06 2.35 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.544917 Iteration 2 Error: 0.138052 Iteration 3 Error: 0.052052 Iteration 4 Error: 0.014316 Align patch 2 23 left Iteration 1 Error: 0.557386 Iteration 2 Error: 0.110963 Iteration 3 Error: 0.034706 Align patch 3 22 left Iteration 1 Error: 0.367781 Iteration 2 Error: 0.063570 Iteration 3 Error: 0.018945 Align patch 4 21 left Iteration 1 Error: 0.449794 Iteration 2 Error: 0.060274 Iteration 3 Error: 0.012558 Align patch 5 20 left Iteration 1 Error: 0.505273 Iteration 2 Error: 0.088085 Iteration 3 Error: 0.021267 Align patch 6 19 left Iteration 1 Error: 1.052014 Iteration 2 Error: 0.182499 Iteration 3 Error: 0.048694 Align patch 7 18 left Iteration 1 Error: 0.614965 Iteration 2 Error: 0.060892 Iteration 3 Error: 0.011753 Align patch 8 17 left Iteration 1 Error: 0.571262 Iteration 2 Error: 0.069086 Iteration 3 Error: 0.012489 Align patch 9 16 left Iteration 1 Error: 0.474252 Iteration 2 Error: 0.076445 Iteration 3 Error: 0.016396 Align patch 10 15 left Iteration 1 Error: 0.497257 Iteration 2 Error: 0.091586 Iteration 3 Error: 0.014812 Align patch 11 14 left Iteration 1 Error: 0.918860 Iteration 2 Error: 0.151148 Iteration 3 Error: 0.036847 Align patch 12 13 left Iteration 1 Error: 0.530312 Iteration 2 Error: 0.088544 Iteration 3 Error: 0.012358 Align patch 13 12 left Iteration 1 Error: 0.635996 Iteration 2 Error: 0.118319 Iteration 3 Error: 0.025147 Align patch 14 11 left Iteration 1 Error: 0.373792 Iteration 2 Error: 0.035868 Align patch 15 10 left Iteration 1 Error: 0.454417 Iteration 2 Error: 0.055186 Iteration 3 Error: 0.017818 Align patch 16 9 left Iteration 1 Error: 0.629100 Iteration 2 Error: 0.092262 Iteration 3 Error: 0.021351 Align patch 17 8 left Iteration 1 Error: 0.672422 Iteration 2 Error: 0.107179 Iteration 3 Error: 0.021628 Align patch 18 7 left Iteration 1 Error: 0.597867 Iteration 2 Error: 0.105004 Iteration 3 Error: 0.025030 Align patch 19 6 left Iteration 1 Error: 0.526995 Iteration 2 Error: 0.054518 Iteration 3 Error: 0.014127 Align patch 20 5 left Iteration 1 Error: 0.438198 Iteration 2 Error: 0.059133 Iteration 3 Error: 0.008280 Align patch 21 4 left Iteration 1 Error: 0.441120 Iteration 2 Error: 0.094584 Iteration 3 Error: 0.020448 Align patch 22 3 left Iteration 1 Error: 0.642852 Iteration 2 Error: 0.111227 Iteration 3 Error: 0.021136 Align patch 23 2 left Iteration 1 Error: 0.609390 Iteration 2 Error: 0.128060 Iteration 3 Error: 0.020032 Align patch 24 1 left Iteration 1 Error: 0.590063 Iteration 2 Error: 0.132484 Iteration 3 Error: 0.022142 Align patch 25 0 left Iteration 1 Error: 0.871411 Iteration 2 Error: 0.109273 Iteration 3 Error: 0.022552 3D Fitting completed. Patch alignment time: 15.26(sec) Local motion has been corrected. Process thread exits. Computational time: 23.242451 sec Total time: 28.884188 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00002hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00002hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.532786s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00002hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.911344s ........................................ >>>>>>TIME<<<<<< FFT: 0.950532s Defocus_U Defocus_V Angle CCC 10175.80 11023.45 6.04 0.057355 Final Values Defocus_U Defocus_V Angle CCC 10199.26 11056.29 5.73 0.093080 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00002hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00002hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.004e-01 CC threshold: 0.737 Mean Std: 39.43 6.75 Num Hot pixels: 203 Hot pixel threshold: 79.95 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.875231 Iteration 2 Error: 0.206139 Iteration 3 Error: 0.037773 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.09 0.25 ...... Frame ( 3) shift: 0.17 0.50 ...... Frame ( 4) shift: 0.26 0.75 ...... Frame ( 5) shift: 0.35 1.00 ...... Frame ( 6) shift: 0.37 1.18 ...... Frame ( 7) shift: 0.32 1.28 ...... Frame ( 8) shift: 0.28 1.38 ...... Frame ( 9) shift: 0.26 1.49 ...... Frame ( 10) shift: 0.27 1.60 ...... Frame ( 11) shift: 0.28 1.72 ...... Frame ( 12) shift: 0.30 1.80 ...... Frame ( 13) shift: 0.34 1.85 ...... Frame ( 14) shift: 0.38 1.90 ...... Frame ( 15) shift: 0.42 2.00 ...... Frame ( 16) shift: 0.44 2.15 ...... Frame ( 17) shift: 0.47 2.30 ...... Frame ( 18) shift: 0.51 2.42 ...... Frame ( 19) shift: 0.55 2.49 ...... Frame ( 20) shift: 0.60 2.57 ...... Frame ( 21) shift: 0.62 2.63 ...... Frame ( 22) shift: 0.63 2.68 ...... Frame ( 23) shift: 0.63 2.72 ...... Frame ( 24) shift: 0.62 2.76 ...... Frame ( 25) shift: 0.58 2.78 ...... Frame ( 26) shift: 0.54 2.81 ...... Frame ( 27) shift: 0.55 2.85 ...... Frame ( 28) shift: 0.60 2.90 ...... Frame ( 29) shift: 0.65 2.96 ...... Frame ( 30) shift: 0.69 3.00 ...... Frame ( 31) shift: 0.73 3.04 ...... Frame ( 32) shift: 0.76 3.08 ...... Frame ( 33) shift: 0.78 3.14 ...... Frame ( 34) shift: 0.79 3.23 ...... Frame ( 35) shift: 0.79 3.31 ...... Frame ( 36) shift: 0.80 3.38 ...... Frame ( 37) shift: 0.82 3.43 ...... Frame ( 38) shift: 0.84 3.49 ...... Frame ( 39) shift: 0.86 3.54 ...... Frame ( 40) shift: 0.88 3.60 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.211967 Iteration 2 Error: 0.157159 Iteration 3 Error: 0.022364 Align patch 2 23 left Iteration 1 Error: 0.906352 Iteration 2 Error: 0.121413 Iteration 3 Error: 0.036933 Align patch 3 22 left Iteration 1 Error: 0.562095 Iteration 2 Error: 0.115515 Iteration 3 Error: 0.027907 Align patch 4 21 left Iteration 1 Error: 0.597887 Iteration 2 Error: 0.077571 Iteration 3 Error: 0.017099 Align patch 5 20 left Iteration 1 Error: 0.674197 Iteration 2 Error: 0.072764 Iteration 3 Error: 0.015405 Align patch 6 19 left Iteration 1 Error: 0.586866 Iteration 2 Error: 0.087715 Iteration 3 Error: 0.023116 Align patch 7 18 left Iteration 1 Error: 0.830637 Iteration 2 Error: 0.178693 Iteration 3 Error: 0.052652 Iteration 4 Error: 0.015470 Align patch 8 17 left Iteration 1 Error: 0.449109 Iteration 2 Error: 0.073700 Iteration 3 Error: 0.017619 Align patch 9 16 left Iteration 1 Error: 0.748472 Iteration 2 Error: 0.090915 Iteration 3 Error: 0.016916 Align patch 10 15 left Iteration 1 Error: 0.492693 Iteration 2 Error: 0.076043 Iteration 3 Error: 0.018365 Align patch 11 14 left Iteration 1 Error: 0.583364 Iteration 2 Error: 0.115351 Iteration 3 Error: 0.040878 Align patch 12 13 left Iteration 1 Error: 0.590955 Iteration 2 Error: 0.087724 Iteration 3 Error: 0.031247 Align patch 13 12 left Iteration 1 Error: 0.424067 Iteration 2 Error: 0.073561 Iteration 3 Error: 0.010145 Align patch 14 11 left Iteration 1 Error: 0.400316 Iteration 2 Error: 0.054031 Iteration 3 Error: 0.013804 Align patch 15 10 left Iteration 1 Error: 0.628274 Iteration 2 Error: 0.101155 Iteration 3 Error: 0.024391 Align patch 16 9 left Iteration 1 Error: 0.450181 Iteration 2 Error: 0.078157 Iteration 3 Error: 0.014553 Align patch 17 8 left Iteration 1 Error: 0.618545 Iteration 2 Error: 0.133072 Iteration 3 Error: 0.031856 Align patch 18 7 left Iteration 1 Error: 0.599023 Iteration 2 Error: 0.110380 Iteration 3 Error: 0.013886 Align patch 19 6 left Iteration 1 Error: 0.656346 Iteration 2 Error: 0.059093 Iteration 3 Error: 0.007944 Align patch 20 5 left Iteration 1 Error: 0.730699 Iteration 2 Error: 0.132030 Iteration 3 Error: 0.023442 Align patch 21 4 left Iteration 1 Error: 0.828138 Iteration 2 Error: 0.079559 Iteration 3 Error: 0.016860 Align patch 22 3 left Iteration 1 Error: 0.807781 Iteration 2 Error: 0.104057 Iteration 3 Error: 0.033845 Align patch 23 2 left Iteration 1 Error: 0.834202 Iteration 2 Error: 0.114847 Iteration 3 Error: 0.030490 Align patch 24 1 left Iteration 1 Error: 0.765388 Iteration 2 Error: 0.129128 Iteration 3 Error: 0.021755 Align patch 25 0 left Iteration 1 Error: 0.551946 Iteration 2 Error: 0.113323 Iteration 3 Error: 0.017544 3D Fitting completed. Patch alignment time: 15.03(sec) Local motion has been corrected. Process thread exits. Computational time: 23.473894 sec Total time: 30.998566 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00002hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00002hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.609092s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00002hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.774789s ........................................ >>>>>>TIME<<<<<< FFT: 0.951487s Defocus_U Defocus_V Angle CCC 15065.03 14392.08 83.70 0.064412 Final Values Defocus_U Defocus_V Angle CCC 15065.03 14398.33 83.70 0.096833 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00003hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00003hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.305e-01 9.738e-02 CC threshold: 0.715 Mean Std: 38.51 6.98 Num Hot pixels: 200 Hot pixel threshold: 80.42 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.226428 Iteration 2 Error: 0.157501 Iteration 3 Error: 0.032744 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.06 0.12 ...... Frame ( 3) shift: 0.12 0.24 ...... Frame ( 4) shift: 0.18 0.36 ...... Frame ( 5) shift: 0.24 0.48 ...... Frame ( 6) shift: 0.30 0.57 ...... Frame ( 7) shift: 0.35 0.64 ...... Frame ( 8) shift: 0.41 0.71 ...... Frame ( 9) shift: 0.44 0.77 ...... Frame ( 10) shift: 0.44 0.82 ...... Frame ( 11) shift: 0.45 0.88 ...... Frame ( 12) shift: 0.42 0.96 ...... Frame ( 13) shift: 0.38 1.06 ...... Frame ( 14) shift: 0.33 1.17 ...... Frame ( 15) shift: 0.34 1.27 ...... Frame ( 16) shift: 0.41 1.38 ...... Frame ( 17) shift: 0.48 1.49 ...... Frame ( 18) shift: 0.52 1.54 ...... Frame ( 19) shift: 0.52 1.52 ...... Frame ( 20) shift: 0.53 1.51 ...... Frame ( 21) shift: 0.53 1.52 ...... Frame ( 22) shift: 0.53 1.57 ...... Frame ( 23) shift: 0.54 1.62 ...... Frame ( 24) shift: 0.55 1.68 ...... Frame ( 25) shift: 0.57 1.74 ...... Frame ( 26) shift: 0.59 1.80 ...... Frame ( 27) shift: 0.60 1.86 ...... Frame ( 28) shift: 0.61 1.92 ...... Frame ( 29) shift: 0.62 1.99 ...... Frame ( 30) shift: 0.67 2.02 ...... Frame ( 31) shift: 0.76 2.04 ...... Frame ( 32) shift: 0.85 2.05 ...... Frame ( 33) shift: 0.89 2.06 ...... Frame ( 34) shift: 0.89 2.09 ...... Frame ( 35) shift: 0.89 2.11 ...... Frame ( 36) shift: 0.89 2.15 ...... Frame ( 37) shift: 0.90 2.21 ...... Frame ( 38) shift: 0.90 2.27 ...... Frame ( 39) shift: 0.91 2.33 ...... Frame ( 40) shift: 0.92 2.40 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.906382 Iteration 2 Error: 0.178862 Iteration 3 Error: 0.033655 Align patch 2 23 left Iteration 1 Error: 0.853915 Iteration 2 Error: 0.183653 Iteration 3 Error: 0.042907 Align patch 3 22 left Iteration 1 Error: 0.823320 Iteration 2 Error: 0.097591 Iteration 3 Error: 0.019561 Align patch 4 21 left Iteration 1 Error: 0.745144 Iteration 2 Error: 0.091218 Iteration 3 Error: 0.021031 Align patch 5 20 left Iteration 1 Error: 0.631673 Iteration 2 Error: 0.155930 Iteration 3 Error: 0.021034 Align patch 6 19 left Iteration 1 Error: 1.017243 Iteration 2 Error: 0.141569 Iteration 3 Error: 0.021908 Align patch 7 18 left Iteration 1 Error: 0.998664 Iteration 2 Error: 0.135880 Iteration 3 Error: 0.043451 Align patch 8 17 left Iteration 1 Error: 0.596073 Iteration 2 Error: 0.118922 Iteration 3 Error: 0.031272 Align patch 9 16 left Iteration 1 Error: 0.917617 Iteration 2 Error: 0.112600 Iteration 3 Error: 0.036243 Align patch 10 15 left Iteration 1 Error: 0.696657 Iteration 2 Error: 0.121720 Iteration 3 Error: 0.032062 Align patch 11 14 left Iteration 1 Error: 1.111344 Iteration 2 Error: 0.155985 Iteration 3 Error: 0.029318 Align patch 12 13 left Iteration 1 Error: 0.846605 Iteration 2 Error: 0.151506 Iteration 3 Error: 0.030560 Align patch 13 12 left Iteration 1 Error: 0.693251 Iteration 2 Error: 0.149600 Iteration 3 Error: 0.031984 Align patch 14 11 left Iteration 1 Error: 0.904196 Iteration 2 Error: 0.173538 Iteration 3 Error: 0.052848 Iteration 4 Error: 0.020730 Align patch 15 10 left Iteration 1 Error: 1.190225 Iteration 2 Error: 0.167839 Iteration 3 Error: 0.029892 Align patch 16 9 left Iteration 1 Error: 0.749451 Iteration 2 Error: 0.146682 Iteration 3 Error: 0.047774 Align patch 17 8 left Iteration 1 Error: 0.747151 Iteration 2 Error: 0.114587 Iteration 3 Error: 0.044594 Align patch 18 7 left Iteration 1 Error: 0.783070 Iteration 2 Error: 0.146555 Iteration 3 Error: 0.024585 Align patch 19 6 left Iteration 1 Error: 0.922949 Iteration 2 Error: 0.168286 Iteration 3 Error: 0.043246 Align patch 20 5 left Iteration 1 Error: 1.171717 Iteration 2 Error: 0.169835 Iteration 3 Error: 0.032829 Align patch 21 4 left Iteration 1 Error: 0.764152 Iteration 2 Error: 0.153138 Iteration 3 Error: 0.027650 Align patch 22 3 left Iteration 1 Error: 0.893009 Iteration 2 Error: 0.121467 Iteration 3 Error: 0.025067 Align patch 23 2 left Iteration 1 Error: 1.056701 Iteration 2 Error: 0.157192 Iteration 3 Error: 0.049689 Align patch 24 1 left Iteration 1 Error: 1.163782 Iteration 2 Error: 0.137262 Iteration 3 Error: 0.033754 Align patch 25 0 left Iteration 1 Error: 0.641158 Iteration 2 Error: 0.137049 Iteration 3 Error: 0.040661 3D Fitting completed. Patch alignment time: 14.84(sec) Local motion has been corrected. Process thread exits. Computational time: 23.172647 sec Total time: 29.065014 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00003hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00003hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.566531s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00003hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.736766s ........................................ >>>>>>TIME<<<<<< FFT: 0.962811s Defocus_U Defocus_V Angle CCC 9667.99 10542.99 10.11 0.004920 Final Values Defocus_U Defocus_V Angle CCC 9660.18 10697.84 7.97 -0.028446 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00003hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00003hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.002e-01 CC threshold: 0.736 Mean Std: 39.42 6.84 Num Hot pixels: 219 Hot pixel threshold: 80.49 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.843452 Iteration 2 Error: 0.448021 Iteration 3 Error: 0.125949 Iteration 4 Error: 0.044474 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.11 -0.09 ...... Frame ( 3) shift: -0.21 -0.17 ...... Frame ( 4) shift: -0.32 -0.26 ...... Frame ( 5) shift: -0.43 -0.34 ...... Frame ( 6) shift: -0.44 -0.34 ...... Frame ( 7) shift: -0.36 -0.26 ...... Frame ( 8) shift: -0.29 -0.17 ...... Frame ( 9) shift: -0.17 -0.04 ...... Frame ( 10) shift: -0.02 0.14 ...... Frame ( 11) shift: 0.13 0.31 ...... Frame ( 12) shift: 0.22 0.45 ...... Frame ( 13) shift: 0.25 0.56 ...... Frame ( 14) shift: 0.27 0.67 ...... Frame ( 15) shift: 0.35 0.80 ...... Frame ( 16) shift: 0.47 0.95 ...... Frame ( 17) shift: 0.59 1.11 ...... Frame ( 18) shift: 0.67 1.25 ...... Frame ( 19) shift: 0.73 1.39 ...... Frame ( 20) shift: 0.78 1.52 ...... Frame ( 21) shift: 0.85 1.65 ...... Frame ( 22) shift: 0.92 1.77 ...... Frame ( 23) shift: 1.00 1.90 ...... Frame ( 24) shift: 1.10 1.99 ...... Frame ( 25) shift: 1.22 2.04 ...... Frame ( 26) shift: 1.35 2.09 ...... Frame ( 27) shift: 1.41 2.16 ...... Frame ( 28) shift: 1.41 2.24 ...... Frame ( 29) shift: 1.40 2.33 ...... Frame ( 30) shift: 1.43 2.41 ...... Frame ( 31) shift: 1.50 2.49 ...... Frame ( 32) shift: 1.56 2.58 ...... Frame ( 33) shift: 1.63 2.61 ...... Frame ( 34) shift: 1.72 2.60 ...... Frame ( 35) shift: 1.80 2.59 ...... Frame ( 36) shift: 1.86 2.61 ...... Frame ( 37) shift: 1.89 2.67 ...... Frame ( 38) shift: 1.92 2.73 ...... Frame ( 39) shift: 1.96 2.79 ...... Frame ( 40) shift: 1.99 2.85 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.238868 Iteration 2 Error: 0.694067 Iteration 3 Error: 0.171020 Iteration 4 Error: 0.074754 Iteration 5 Error: 0.018908 Align patch 2 23 left Iteration 1 Error: 1.469134 Iteration 2 Error: 0.391307 Iteration 3 Error: 0.158998 Iteration 4 Error: 0.079504 Iteration 5 Error: 0.035027 Align patch 3 22 left Iteration 1 Error: 1.098327 Iteration 2 Error: 0.334859 Iteration 3 Error: 0.138262 Iteration 4 Error: 0.060325 Iteration 5 Error: 0.036476 Align patch 4 21 left Iteration 1 Error: 0.804640 Iteration 2 Error: 0.127323 Iteration 3 Error: 0.037163 Align patch 5 20 left Iteration 1 Error: 0.622518 Iteration 2 Error: 0.112593 Iteration 3 Error: 0.021696 Align patch 6 19 left Iteration 1 Error: 2.195448 Iteration 2 Error: 0.482045 Iteration 3 Error: 0.171331 Iteration 4 Error: 0.066812 Iteration 5 Error: 0.022761 Align patch 7 18 left Iteration 1 Error: 1.334417 Iteration 2 Error: 0.413481 Iteration 3 Error: 0.161594 Iteration 4 Error: 0.060818 Iteration 5 Error: 0.023582 Align patch 8 17 left Iteration 1 Error: 0.751697 Iteration 2 Error: 0.185570 Iteration 3 Error: 0.065694 Iteration 4 Error: 0.017666 Align patch 9 16 left Iteration 1 Error: 0.613619 Iteration 2 Error: 0.126428 Iteration 3 Error: 0.045974 Align patch 10 15 left Iteration 1 Error: 0.874415 Iteration 2 Error: 0.179973 Iteration 3 Error: 0.026000 Align patch 11 14 left Iteration 1 Error: 1.869064 Iteration 2 Error: 0.479247 Iteration 3 Error: 0.167067 Iteration 4 Error: 0.063552 Iteration 5 Error: 0.026027 Align patch 12 13 left Iteration 1 Error: 0.987882 Iteration 2 Error: 0.327946 Iteration 3 Error: 0.116725 Iteration 4 Error: 0.048360 Align patch 13 12 left Iteration 1 Error: 0.774278 Iteration 2 Error: 0.125557 Iteration 3 Error: 0.021854 Align patch 14 11 left Iteration 1 Error: 0.473859 Iteration 2 Error: 0.091897 Iteration 3 Error: 0.022342 Align patch 15 10 left Iteration 1 Error: 0.863400 Iteration 2 Error: 0.223341 Iteration 3 Error: 0.058223 Iteration 4 Error: 0.015628 Align patch 16 9 left Iteration 1 Error: 0.738542 Iteration 2 Error: 0.338671 Iteration 3 Error: 0.216722 Iteration 4 Error: 0.127396 Iteration 5 Error: 0.062407 Align patch 16 9 left Iteration 1 Error: 1.266822 Iteration 2 Error: 0.290941 Iteration 3 Error: 0.079101 Iteration 4 Error: 0.024282 Align patch 17 8 left Iteration 1 Error: 1.018668 Iteration 2 Error: 0.300431 Iteration 3 Error: 0.117831 Iteration 4 Error: 0.046884 Align patch 18 7 left Iteration 1 Error: 0.539746 Iteration 2 Error: 0.126601 Iteration 3 Error: 0.043506 Align patch 19 6 left Iteration 1 Error: 0.793979 Iteration 2 Error: 0.120797 Iteration 3 Error: 0.040960 Align patch 20 5 left Iteration 1 Error: 1.130900 Iteration 2 Error: 0.221791 Iteration 3 Error: 0.052349 Iteration 4 Error: 0.012941 Align patch 21 4 left Iteration 1 Error: 1.032831 Iteration 2 Error: 0.228016 Iteration 3 Error: 0.073885 Iteration 4 Error: 0.028983 Align patch 22 3 left Iteration 1 Error: 1.040641 Iteration 2 Error: 0.195415 Iteration 3 Error: 0.045817 Align patch 23 2 left Iteration 1 Error: 0.513705 Iteration 2 Error: 0.066731 Iteration 3 Error: 0.020011 Align patch 24 1 left Iteration 1 Error: 0.724784 Iteration 2 Error: 0.200482 Iteration 3 Error: 0.062166 Iteration 4 Error: 0.027817 Align patch 25 0 left Iteration 1 Error: 0.974409 Iteration 2 Error: 0.170689 Iteration 3 Error: 0.065444 Iteration 4 Error: 0.019478 3D Fitting completed. Patch alignment time: 16.84(sec) Local motion has been corrected. Process thread exits. Computational time: 25.549868 sec Total time: 31.233362 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00003hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00003hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.684005s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00003hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.604474s ........................................ >>>>>>TIME<<<<<< FFT: 1.026178s Defocus_U Defocus_V Angle CCC 10166.06 9791.06 88.89 0.041277 Final Values Defocus_U Defocus_V Angle CCC 10183.25 9789.50 89.52 0.071175 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00003hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00003hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.322e-01 9.852e-02 CC threshold: 0.723 Mean Std: 39.81 6.89 Num Hot pixels: 222 Hot pixel threshold: 81.12 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 7.855038 Iteration 2 Error: 0.637607 Iteration 3 Error: 0.145154 Iteration 4 Error: 0.049978 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.64 -1.02 ...... Frame ( 3) shift: 1.28 -2.05 ...... Frame ( 4) shift: 1.92 -3.07 ...... Frame ( 5) shift: 2.55 -4.09 ...... Frame ( 6) shift: 3.13 -4.87 ...... Frame ( 7) shift: 3.63 -5.41 ...... Frame ( 8) shift: 4.14 -5.95 ...... Frame ( 9) shift: 4.62 -6.27 ...... Frame ( 10) shift: 5.09 -6.39 ...... Frame ( 11) shift: 5.55 -6.50 ...... Frame ( 12) shift: 5.89 -6.65 ...... Frame ( 13) shift: 6.11 -6.83 ...... Frame ( 14) shift: 6.32 -7.01 ...... Frame ( 15) shift: 6.47 -7.17 ...... Frame ( 16) shift: 6.54 -7.32 ...... Frame ( 17) shift: 6.62 -7.47 ...... Frame ( 18) shift: 6.70 -7.60 ...... Frame ( 19) shift: 6.79 -7.70 ...... Frame ( 20) shift: 6.89 -7.80 ...... Frame ( 21) shift: 6.98 -7.88 ...... Frame ( 22) shift: 7.08 -7.94 ...... Frame ( 23) shift: 7.17 -8.00 ...... Frame ( 24) shift: 7.24 -8.09 ...... Frame ( 25) shift: 7.28 -8.21 ...... Frame ( 26) shift: 7.32 -8.32 ...... Frame ( 27) shift: 7.36 -8.41 ...... Frame ( 28) shift: 7.40 -8.48 ...... Frame ( 29) shift: 7.43 -8.55 ...... Frame ( 30) shift: 7.42 -8.59 ...... Frame ( 31) shift: 7.37 -8.60 ...... Frame ( 32) shift: 7.31 -8.61 ...... Frame ( 33) shift: 7.31 -8.62 ...... Frame ( 34) shift: 7.37 -8.64 ...... Frame ( 35) shift: 7.42 -8.66 ...... Frame ( 36) shift: 7.50 -8.71 ...... Frame ( 37) shift: 7.62 -8.79 ...... Frame ( 38) shift: 7.73 -8.87 ...... Frame ( 39) shift: 7.84 -8.96 ...... Frame ( 40) shift: 7.95 -9.04 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.381293 Iteration 2 Error: 0.200768 Iteration 3 Error: 0.037990 Align patch 2 23 left Iteration 1 Error: 2.449678 Iteration 2 Error: 0.160599 Iteration 3 Error: 0.031179 Align patch 3 22 left Iteration 1 Error: 2.141251 Iteration 2 Error: 0.206411 Iteration 3 Error: 0.045289 Align patch 4 21 left Iteration 1 Error: 1.744636 Iteration 2 Error: 0.139437 Iteration 3 Error: 0.032277 Align patch 5 20 left Iteration 1 Error: 0.955326 Iteration 2 Error: 0.094807 Iteration 3 Error: 0.028228 Align patch 6 19 left Iteration 1 Error: 0.808881 Iteration 2 Error: 0.107176 Iteration 3 Error: 0.023680 Align patch 7 18 left Iteration 1 Error: 1.368100 Iteration 2 Error: 0.169945 Iteration 3 Error: 0.037549 Align patch 8 17 left Iteration 1 Error: 0.996632 Iteration 2 Error: 0.118943 Iteration 3 Error: 0.024675 Align patch 9 16 left Iteration 1 Error: 1.364883 Iteration 2 Error: 0.189478 Iteration 3 Error: 0.037629 Align patch 10 15 left Iteration 1 Error: 1.791372 Iteration 2 Error: 0.175574 Iteration 3 Error: 0.027759 Align patch 11 14 left Iteration 1 Error: 0.853694 Iteration 2 Error: 0.156781 Iteration 3 Error: 0.040141 Align patch 12 13 left Iteration 1 Error: 0.933475 Iteration 2 Error: 0.173532 Iteration 3 Error: 0.053824 Iteration 4 Error: 0.017795 Align patch 13 12 left Iteration 1 Error: 0.650878 Iteration 2 Error: 0.081961 Iteration 3 Error: 0.020366 Align patch 14 11 left Iteration 1 Error: 0.540593 Iteration 2 Error: 0.112219 Iteration 3 Error: 0.023547 Align patch 15 10 left Iteration 1 Error: 0.953103 Iteration 2 Error: 0.273833 Iteration 3 Error: 0.105315 Iteration 4 Error: 0.033121 Align patch 16 9 left Iteration 1 Error: 1.768489 Iteration 2 Error: 0.225348 Iteration 3 Error: 0.053753 Iteration 4 Error: 0.019200 Align patch 17 8 left Iteration 1 Error: 1.450440 Iteration 2 Error: 0.268723 Iteration 3 Error: 0.068512 Iteration 4 Error: 0.019227 Align patch 18 7 left Iteration 1 Error: 1.568014 Iteration 2 Error: 0.302488 Iteration 3 Error: 0.061673 Iteration 4 Error: 0.017447 Align patch 19 6 left Iteration 1 Error: 1.381372 Iteration 2 Error: 0.169551 Iteration 3 Error: 0.038009 Align patch 20 5 left Iteration 1 Error: 2.119465 Iteration 2 Error: 0.199067 Iteration 3 Error: 0.042594 Align patch 21 4 left Iteration 1 Error: 2.650423 Iteration 2 Error: 0.321556 Iteration 3 Error: 0.068613 Iteration 4 Error: 0.020782 Align patch 22 3 left Iteration 1 Error: 2.488390 Iteration 2 Error: 0.211131 Iteration 3 Error: 0.033429 Align patch 23 2 left Iteration 1 Error: 2.429587 Iteration 2 Error: 0.276417 Iteration 3 Error: 0.053650 Iteration 4 Error: 0.013552 Align patch 24 1 left Iteration 1 Error: 3.190078 Iteration 2 Error: 0.329851 Iteration 3 Error: 0.069685 Iteration 4 Error: 0.025241 Align patch 25 0 left Iteration 1 Error: 3.660542 Iteration 2 Error: 0.406423 Iteration 3 Error: 0.047645 3D Fitting completed. Patch alignment time: 15.99(sec) Local motion has been corrected. Process thread exits. Computational time: 25.054136 sec Total time: 30.759193 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00003hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00003hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.672694s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00003hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.859688s ........................................ >>>>>>TIME<<<<<< FFT: 0.953630s Defocus_U Defocus_V Angle CCC 12091.80 12923.83 5.55 0.056193 Final Values Defocus_U Defocus_V Angle CCC 12102.74 12928.52 4.93 0.055393 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00003hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00003hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.003e-01 CC threshold: 0.736 Mean Std: 38.10 6.70 Num Hot pixels: 206 Hot pixel threshold: 78.28 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.665698 Iteration 2 Error: 0.351637 Iteration 3 Error: 0.097395 Iteration 4 Error: 0.022254 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.01 -0.22 ...... Frame ( 3) shift: 0.02 -0.45 ...... Frame ( 4) shift: 0.03 -0.67 ...... Frame ( 5) shift: 0.04 -0.90 ...... Frame ( 6) shift: 0.08 -0.96 ...... Frame ( 7) shift: 0.14 -0.87 ...... Frame ( 8) shift: 0.21 -0.77 ...... Frame ( 9) shift: 0.23 -0.68 ...... Frame ( 10) shift: 0.21 -0.59 ...... Frame ( 11) shift: 0.19 -0.49 ...... Frame ( 12) shift: 0.22 -0.37 ...... Frame ( 13) shift: 0.30 -0.20 ...... Frame ( 14) shift: 0.38 -0.03 ...... Frame ( 15) shift: 0.45 0.13 ...... Frame ( 16) shift: 0.51 0.29 ...... Frame ( 17) shift: 0.56 0.44 ...... Frame ( 18) shift: 0.66 0.61 ...... Frame ( 19) shift: 0.82 0.79 ...... Frame ( 20) shift: 0.98 0.97 ...... Frame ( 21) shift: 1.09 1.13 ...... Frame ( 22) shift: 1.14 1.27 ...... Frame ( 23) shift: 1.19 1.40 ...... Frame ( 24) shift: 1.24 1.50 ...... Frame ( 25) shift: 1.29 1.56 ...... Frame ( 26) shift: 1.34 1.63 ...... Frame ( 27) shift: 1.37 1.70 ...... Frame ( 28) shift: 1.40 1.78 ...... Frame ( 29) shift: 1.42 1.86 ...... Frame ( 30) shift: 1.47 1.95 ...... Frame ( 31) shift: 1.56 2.04 ...... Frame ( 32) shift: 1.65 2.14 ...... Frame ( 33) shift: 1.72 2.18 ...... Frame ( 34) shift: 1.75 2.18 ...... Frame ( 35) shift: 1.79 2.17 ...... Frame ( 36) shift: 1.81 2.15 ...... Frame ( 37) shift: 1.82 2.09 ...... Frame ( 38) shift: 1.83 2.04 ...... Frame ( 39) shift: 1.84 1.99 ...... Frame ( 40) shift: 1.85 1.94 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.839958 Iteration 2 Error: 0.094579 Iteration 3 Error: 0.022955 Align patch 2 23 left Iteration 1 Error: 0.694672 Iteration 2 Error: 0.072535 Iteration 3 Error: 0.026610 Align patch 3 22 left Iteration 1 Error: 0.555505 Iteration 2 Error: 0.083878 Iteration 3 Error: 0.019988 Align patch 4 21 left Iteration 1 Error: 0.719353 Iteration 2 Error: 0.221298 Iteration 3 Error: 0.043740 Align patch 5 20 left Iteration 1 Error: 0.764442 Iteration 2 Error: 0.156851 Iteration 3 Error: 0.040803 Align patch 6 19 left Iteration 1 Error: 1.276225 Iteration 2 Error: 0.249198 Iteration 3 Error: 0.071438 Iteration 4 Error: 0.023130 Align patch 7 18 left Iteration 1 Error: 0.827333 Iteration 2 Error: 0.142508 Iteration 3 Error: 0.042881 Align patch 8 17 left Iteration 1 Error: 0.613543 Iteration 2 Error: 0.078564 Iteration 3 Error: 0.022004 Align patch 9 16 left Iteration 1 Error: 0.629063 Iteration 2 Error: 0.086551 Iteration 3 Error: 0.019062 Align patch 10 15 left Iteration 1 Error: 0.773805 Iteration 2 Error: 0.065917 Iteration 3 Error: 0.014102 Align patch 11 14 left Iteration 1 Error: 1.146296 Iteration 2 Error: 0.261308 Iteration 3 Error: 0.110571 Iteration 4 Error: 0.041399 Align patch 12 13 left Iteration 1 Error: 0.703067 Iteration 2 Error: 0.152980 Iteration 3 Error: 0.040415 Align patch 13 12 left Iteration 1 Error: 0.810764 Iteration 2 Error: 0.125794 Iteration 3 Error: 0.032821 Align patch 14 11 left Iteration 1 Error: 0.547962 Iteration 2 Error: 0.104132 Iteration 3 Error: 0.024451 Align patch 15 10 left Iteration 1 Error: 0.692884 Iteration 2 Error: 0.169669 Iteration 3 Error: 0.030771 Align patch 16 9 left Iteration 1 Error: 1.010202 Iteration 2 Error: 0.194898 Iteration 3 Error: 0.044938 Align patch 17 8 left Iteration 1 Error: 0.657935 Iteration 2 Error: 0.142504 Iteration 3 Error: 0.043711 Align patch 18 7 left Iteration 1 Error: 0.540504 Iteration 2 Error: 0.057012 Iteration 3 Error: 0.014656 Align patch 19 6 left Iteration 1 Error: 0.732633 Iteration 2 Error: 0.109639 Iteration 3 Error: 0.032998 Align patch 20 5 left Iteration 1 Error: 1.187251 Iteration 2 Error: 0.181130 Iteration 3 Error: 0.034903 Align patch 21 4 left Iteration 1 Error: 0.622477 Iteration 2 Error: 0.088455 Iteration 3 Error: 0.041739 Align patch 22 3 left Iteration 1 Error: 0.875615 Iteration 2 Error: 0.127392 Iteration 3 Error: 0.021183 Align patch 23 2 left Iteration 1 Error: 0.718656 Iteration 2 Error: 0.134250 Iteration 3 Error: 0.033270 Align patch 24 1 left Iteration 1 Error: 0.410623 Iteration 2 Error: 0.046224 Align patch 25 0 left Iteration 1 Error: 0.518469 Iteration 2 Error: 0.062201 Iteration 3 Error: 0.019116 3D Fitting completed. Patch alignment time: 14.53(sec) Local motion has been corrected. Process thread exits. Computational time: 23.355848 sec Total time: 28.974083 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00003hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00003hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.742118s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00003hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.124469s ........................................ >>>>>>TIME<<<<<< FFT: 1.024263s Defocus_U Defocus_V Angle CCC 14050.68 13394.68 87.43 0.061101 Final Values Defocus_U Defocus_V Angle CCC 14056.92 13435.33 89.63 0.087286 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00004hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00004hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.337e-01 9.948e-02 CC threshold: 0.731 Mean Std: 39.31 6.77 Num Hot pixels: 200 Hot pixel threshold: 79.94 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.769483 Iteration 2 Error: 0.144516 Iteration 3 Error: 0.022533 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.27 -0.19 ...... Frame ( 3) shift: -0.54 -0.39 ...... Frame ( 4) shift: -0.81 -0.58 ...... Frame ( 5) shift: -1.08 -0.78 ...... Frame ( 6) shift: -1.31 -0.94 ...... Frame ( 7) shift: -1.51 -1.08 ...... Frame ( 8) shift: -1.71 -1.22 ...... Frame ( 9) shift: -1.83 -1.35 ...... Frame ( 10) shift: -1.88 -1.46 ...... Frame ( 11) shift: -1.92 -1.57 ...... Frame ( 12) shift: -1.95 -1.59 ...... Frame ( 13) shift: -1.97 -1.51 ...... Frame ( 14) shift: -1.99 -1.44 ...... Frame ( 15) shift: -2.03 -1.40 ...... Frame ( 16) shift: -2.09 -1.39 ...... Frame ( 17) shift: -2.15 -1.39 ...... Frame ( 18) shift: -2.19 -1.38 ...... Frame ( 19) shift: -2.20 -1.37 ...... Frame ( 20) shift: -2.21 -1.36 ...... Frame ( 21) shift: -2.22 -1.31 ...... Frame ( 22) shift: -2.23 -1.21 ...... Frame ( 23) shift: -2.23 -1.12 ...... Frame ( 24) shift: -2.25 -1.05 ...... Frame ( 25) shift: -2.28 -1.01 ...... Frame ( 26) shift: -2.32 -0.96 ...... Frame ( 27) shift: -2.34 -0.95 ...... Frame ( 28) shift: -2.35 -0.95 ...... Frame ( 29) shift: -2.36 -0.96 ...... Frame ( 30) shift: -2.35 -0.95 ...... Frame ( 31) shift: -2.33 -0.91 ...... Frame ( 32) shift: -2.31 -0.87 ...... Frame ( 33) shift: -2.31 -0.83 ...... Frame ( 34) shift: -2.35 -0.80 ...... Frame ( 35) shift: -2.38 -0.76 ...... Frame ( 36) shift: -2.40 -0.75 ...... Frame ( 37) shift: -2.42 -0.75 ...... Frame ( 38) shift: -2.43 -0.76 ...... Frame ( 39) shift: -2.44 -0.76 ...... Frame ( 40) shift: -2.46 -0.77 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.820992 Iteration 2 Error: 0.110356 Iteration 3 Error: 0.028646 Align patch 2 23 left Iteration 1 Error: 1.212535 Iteration 2 Error: 0.204944 Iteration 3 Error: 0.023906 Align patch 3 22 left Iteration 1 Error: 1.265258 Iteration 2 Error: 0.252454 Iteration 3 Error: 0.038902 Align patch 4 21 left Iteration 1 Error: 0.991932 Iteration 2 Error: 0.101291 Iteration 3 Error: 0.027516 Align patch 5 20 left Iteration 1 Error: 0.718293 Iteration 2 Error: 0.139433 Iteration 3 Error: 0.023765 Align patch 6 19 left Iteration 1 Error: 0.727649 Iteration 2 Error: 0.138717 Iteration 3 Error: 0.037543 Align patch 7 18 left Iteration 1 Error: 0.601181 Iteration 2 Error: 0.114936 Iteration 3 Error: 0.025542 Align patch 8 17 left Iteration 1 Error: 0.525264 Iteration 2 Error: 0.149623 Iteration 3 Error: 0.050122 Iteration 4 Error: 0.021689 Align patch 9 16 left Iteration 1 Error: 0.742849 Iteration 2 Error: 0.185395 Iteration 3 Error: 0.064596 Iteration 4 Error: 0.022813 Align patch 10 15 left Iteration 1 Error: 0.726713 Iteration 2 Error: 0.131702 Iteration 3 Error: 0.028849 Align patch 11 14 left Iteration 1 Error: 1.406795 Iteration 2 Error: 0.118868 Iteration 3 Error: 0.031871 Align patch 12 13 left Iteration 1 Error: 1.149955 Iteration 2 Error: 0.129686 Iteration 3 Error: 0.047221 Align patch 13 12 left Iteration 1 Error: 0.808566 Iteration 2 Error: 0.252189 Iteration 3 Error: 0.065347 Iteration 4 Error: 0.036864 Align patch 14 11 left Iteration 1 Error: 0.664272 Iteration 2 Error: 0.142801 Iteration 3 Error: 0.032761 Align patch 15 10 left Iteration 1 Error: 1.194038 Iteration 2 Error: 0.151145 Iteration 3 Error: 0.016007 Align patch 16 9 left Iteration 1 Error: 1.396831 Iteration 2 Error: 0.174231 Iteration 3 Error: 0.047892 Align patch 17 8 left Iteration 1 Error: 0.878957 Iteration 2 Error: 0.199750 Iteration 3 Error: 0.034262 Align patch 18 7 left Iteration 1 Error: 0.785058 Iteration 2 Error: 0.116261 Iteration 3 Error: 0.048119 Align patch 19 6 left Iteration 1 Error: 0.671526 Iteration 2 Error: 0.096366 Iteration 3 Error: 0.029120 Align patch 20 5 left Iteration 1 Error: 0.739571 Iteration 2 Error: 0.163161 Iteration 3 Error: 0.064219 Iteration 4 Error: 0.023506 Align patch 21 4 left Iteration 1 Error: 1.868089 Iteration 2 Error: 0.215835 Iteration 3 Error: 0.066390 Iteration 4 Error: 0.019945 Align patch 22 3 left Iteration 1 Error: 1.486618 Iteration 2 Error: 0.163990 Iteration 3 Error: 0.069138 Iteration 4 Error: 0.019226 Align patch 23 2 left Iteration 1 Error: 0.923400 Iteration 2 Error: 0.257110 Iteration 3 Error: 0.059736 Iteration 4 Error: 0.020218 Align patch 24 1 left Iteration 1 Error: 0.659483 Iteration 2 Error: 0.140466 Iteration 3 Error: 0.029481 Align patch 25 0 left Iteration 1 Error: 1.157338 Iteration 2 Error: 0.421002 Iteration 3 Error: 0.140769 Iteration 4 Error: 0.059197 Iteration 5 Error: 0.029409 3D Fitting completed. Patch alignment time: 16.09(sec) Local motion has been corrected. Process thread exits. Computational time: 24.689552 sec Total time: 30.327036 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00004hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00004hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.648012s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00004hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.155803s ........................................ >>>>>>TIME<<<<<< FFT: 1.048080s Defocus_U Defocus_V Angle CCC 13548.85 12908.22 80.89 0.018289 Final Values Defocus_U Defocus_V Angle CCC 13622.30 12903.55 81.84 -0.015588 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00004hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00004hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.303e-01 9.719e-02 CC threshold: 0.713 Mean Std: 35.56 6.61 Num Hot pixels: 188 Hot pixel threshold: 75.23 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.904068 Iteration 2 Error: 0.203253 Iteration 3 Error: 0.050827 Iteration 4 Error: 0.016645 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.07 0.09 ...... Frame ( 3) shift: 0.14 0.18 ...... Frame ( 4) shift: 0.21 0.26 ...... Frame ( 5) shift: 0.29 0.35 ...... Frame ( 6) shift: 0.30 0.41 ...... Frame ( 7) shift: 0.26 0.45 ...... Frame ( 8) shift: 0.22 0.48 ...... Frame ( 9) shift: 0.15 0.51 ...... Frame ( 10) shift: 0.07 0.53 ...... Frame ( 11) shift: -0.02 0.56 ...... Frame ( 12) shift: -0.13 0.60 ...... Frame ( 13) shift: -0.27 0.66 ...... Frame ( 14) shift: -0.40 0.73 ...... Frame ( 15) shift: -0.49 0.79 ...... Frame ( 16) shift: -0.54 0.84 ...... Frame ( 17) shift: -0.58 0.89 ...... Frame ( 18) shift: -0.64 0.92 ...... Frame ( 19) shift: -0.71 0.93 ...... Frame ( 20) shift: -0.78 0.95 ...... Frame ( 21) shift: -0.83 0.96 ...... Frame ( 22) shift: -0.84 0.97 ...... Frame ( 23) shift: -0.86 0.98 ...... Frame ( 24) shift: -0.91 1.02 ...... Frame ( 25) shift: -0.99 1.10 ...... Frame ( 26) shift: -1.07 1.17 ...... Frame ( 27) shift: -1.13 1.23 ...... Frame ( 28) shift: -1.17 1.25 ...... Frame ( 29) shift: -1.22 1.28 ...... Frame ( 30) shift: -1.21 1.27 ...... Frame ( 31) shift: -1.16 1.23 ...... Frame ( 32) shift: -1.11 1.19 ...... Frame ( 33) shift: -1.13 1.22 ...... Frame ( 34) shift: -1.22 1.33 ...... Frame ( 35) shift: -1.31 1.43 ...... Frame ( 36) shift: -1.36 1.49 ...... Frame ( 37) shift: -1.37 1.50 ...... Frame ( 38) shift: -1.38 1.51 ...... Frame ( 39) shift: -1.39 1.52 ...... Frame ( 40) shift: -1.40 1.53 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.393734 Iteration 2 Error: 0.414271 Iteration 3 Error: 0.193849 Iteration 4 Error: 0.085496 Iteration 5 Error: 0.041001 Align patch 2 23 left Iteration 1 Error: 1.235909 Iteration 2 Error: 0.386560 Iteration 3 Error: 0.094977 Iteration 4 Error: 0.053707 Iteration 5 Error: 0.022319 Align patch 3 22 left Iteration 1 Error: 0.882619 Iteration 2 Error: 0.304647 Iteration 3 Error: 0.127654 Iteration 4 Error: 0.057816 Iteration 5 Error: 0.026124 Align patch 4 21 left Iteration 1 Error: 0.986595 Iteration 2 Error: 0.226818 Iteration 3 Error: 0.079453 Iteration 4 Error: 0.038247 Align patch 5 20 left Iteration 1 Error: 1.376012 Iteration 2 Error: 0.324771 Iteration 3 Error: 0.073240 Iteration 4 Error: 0.021434 Align patch 6 19 left Iteration 1 Error: 1.224780 Iteration 2 Error: 0.469650 Iteration 3 Error: 0.178046 Iteration 4 Error: 0.107409 Iteration 5 Error: 0.046240 Align patch 7 18 left Iteration 1 Error: 0.600171 Iteration 2 Error: 0.112875 Iteration 3 Error: 0.031857 Align patch 8 17 left Iteration 1 Error: 0.833624 Iteration 2 Error: 0.127144 Iteration 3 Error: 0.039034 Align patch 9 16 left Iteration 1 Error: 0.874765 Iteration 2 Error: 0.110159 Iteration 3 Error: 0.039901 Align patch 10 15 left Iteration 1 Error: 1.913378 Iteration 2 Error: 0.284912 Iteration 3 Error: 0.080683 Iteration 4 Error: 0.024676 Align patch 11 14 left Iteration 1 Error: 1.326424 Iteration 2 Error: 0.253280 Iteration 3 Error: 0.135985 Iteration 4 Error: 0.038621 Align patch 12 13 left Iteration 1 Error: 0.935719 Iteration 2 Error: 0.158106 Iteration 3 Error: 0.041634 Align patch 13 12 left Iteration 1 Error: 0.757704 Iteration 2 Error: 0.082294 Iteration 3 Error: 0.022785 Align patch 14 11 left Iteration 1 Error: 1.247539 Iteration 2 Error: 0.243360 Iteration 3 Error: 0.070726 Iteration 4 Error: 0.034562 Align patch 15 10 left Iteration 1 Error: 0.937041 Iteration 2 Error: 0.209460 Iteration 3 Error: 0.086373 Iteration 4 Error: 0.030338 Align patch 16 9 left Iteration 1 Error: 1.929018 Iteration 2 Error: 0.186630 Iteration 3 Error: 0.039761 Align patch 17 8 left Iteration 1 Error: 0.751338 Iteration 2 Error: 0.175178 Iteration 3 Error: 0.049901 Align patch 18 7 left Iteration 1 Error: 1.083219 Iteration 2 Error: 0.160215 Iteration 3 Error: 0.045001 Align patch 19 6 left Iteration 1 Error: 0.769247 Iteration 2 Error: 0.117449 Iteration 3 Error: 0.048283 Align patch 20 5 left Iteration 1 Error: 1.085307 Iteration 2 Error: 0.147686 Iteration 3 Error: 0.035402 Align patch 21 4 left Iteration 1 Error: 1.502112 Iteration 2 Error: 0.300142 Iteration 3 Error: 0.047398 Align patch 22 3 left Iteration 1 Error: 1.181328 Iteration 2 Error: 0.183912 Iteration 3 Error: 0.029638 Align patch 23 2 left Iteration 1 Error: 1.154182 Iteration 2 Error: 0.133247 Iteration 3 Error: 0.033253 Align patch 24 1 left Iteration 1 Error: 1.047726 Iteration 2 Error: 0.146736 Iteration 3 Error: 0.027253 Align patch 25 0 left Iteration 1 Error: 1.522092 Iteration 2 Error: 0.257495 Iteration 3 Error: 0.074605 Iteration 4 Error: 0.017273 3D Fitting completed. Patch alignment time: 16.77(sec) Local motion has been corrected. Process thread exits. Computational time: 25.741388 sec Total time: 32.081013 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00004hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00004hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.595823s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00004hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.049719s ........................................ >>>>>>TIME<<<<<< FFT: 0.946965s Defocus_U Defocus_V Angle CCC 9556.69 9564.49 26.32 -0.065540 Final Values Defocus_U Defocus_V Angle CCC 9617.57 9475.53 3.15 -0.283019 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00005hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00005hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.352e-01 1.005e-01 CC threshold: 0.738 Mean Std: 39.51 6.80 Num Hot pixels: 219 Hot pixel threshold: 80.31 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.798647 Iteration 2 Error: 0.117681 Iteration 3 Error: 0.019579 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.02 -0.06 ...... Frame ( 3) shift: -0.05 -0.13 ...... Frame ( 4) shift: -0.07 -0.19 ...... Frame ( 5) shift: -0.10 -0.26 ...... Frame ( 6) shift: -0.10 -0.27 ...... Frame ( 7) shift: -0.09 -0.24 ...... Frame ( 8) shift: -0.07 -0.20 ...... Frame ( 9) shift: -0.05 -0.20 ...... Frame ( 10) shift: -0.01 -0.23 ...... Frame ( 11) shift: 0.03 -0.26 ...... Frame ( 12) shift: 0.06 -0.26 ...... Frame ( 13) shift: 0.08 -0.23 ...... Frame ( 14) shift: 0.11 -0.20 ...... Frame ( 15) shift: 0.13 -0.17 ...... Frame ( 16) shift: 0.14 -0.14 ...... Frame ( 17) shift: 0.16 -0.11 ...... Frame ( 18) shift: 0.20 -0.09 ...... Frame ( 19) shift: 0.26 -0.07 ...... Frame ( 20) shift: 0.33 -0.05 ...... Frame ( 21) shift: 0.38 -0.01 ...... Frame ( 22) shift: 0.43 0.04 ...... Frame ( 23) shift: 0.47 0.09 ...... Frame ( 24) shift: 0.50 0.13 ...... Frame ( 25) shift: 0.51 0.16 ...... Frame ( 26) shift: 0.52 0.19 ...... Frame ( 27) shift: 0.56 0.22 ...... Frame ( 28) shift: 0.62 0.26 ...... Frame ( 29) shift: 0.68 0.29 ...... Frame ( 30) shift: 0.69 0.34 ...... Frame ( 31) shift: 0.64 0.40 ...... Frame ( 32) shift: 0.60 0.45 ...... Frame ( 33) shift: 0.59 0.51 ...... Frame ( 34) shift: 0.61 0.58 ...... Frame ( 35) shift: 0.63 0.64 ...... Frame ( 36) shift: 0.66 0.69 ...... Frame ( 37) shift: 0.70 0.73 ...... Frame ( 38) shift: 0.74 0.77 ...... Frame ( 39) shift: 0.78 0.82 ...... Frame ( 40) shift: 0.82 0.86 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.816124 Iteration 2 Error: 0.080292 Iteration 3 Error: 0.016975 Align patch 2 23 left Iteration 1 Error: 0.769143 Iteration 2 Error: 0.095809 Iteration 3 Error: 0.019245 Align patch 3 22 left Iteration 1 Error: 0.875966 Iteration 2 Error: 0.143527 Iteration 3 Error: 0.033303 Align patch 4 21 left Iteration 1 Error: 0.713079 Iteration 2 Error: 0.135615 Iteration 3 Error: 0.038373 Align patch 5 20 left Iteration 1 Error: 0.877258 Iteration 2 Error: 0.124811 Iteration 3 Error: 0.019434 Align patch 6 19 left Iteration 1 Error: 0.444311 Iteration 2 Error: 0.065447 Iteration 3 Error: 0.015928 Align patch 7 18 left Iteration 1 Error: 0.542810 Iteration 2 Error: 0.035400 Align patch 8 17 left Iteration 1 Error: 0.446444 Iteration 2 Error: 0.053097 Iteration 3 Error: 0.010871 Align patch 9 16 left Iteration 1 Error: 0.511654 Iteration 2 Error: 0.069367 Iteration 3 Error: 0.013856 Align patch 10 15 left Iteration 1 Error: 0.934100 Iteration 2 Error: 0.093168 Iteration 3 Error: 0.022350 Align patch 11 14 left Iteration 1 Error: 0.465119 Iteration 2 Error: 0.084077 Iteration 3 Error: 0.012311 Align patch 12 13 left Iteration 1 Error: 0.418261 Iteration 2 Error: 0.031871 Align patch 13 12 left Iteration 1 Error: 0.523600 Iteration 2 Error: 0.078206 Iteration 3 Error: 0.018294 Align patch 14 11 left Iteration 1 Error: 0.414252 Iteration 2 Error: 0.053824 Iteration 3 Error: 0.010908 Align patch 15 10 left Iteration 1 Error: 0.512632 Iteration 2 Error: 0.054436 Iteration 3 Error: 0.008253 Align patch 16 9 left Iteration 1 Error: 0.541624 Iteration 2 Error: 0.079655 Iteration 3 Error: 0.013554 Align patch 17 8 left Iteration 1 Error: 0.408148 Iteration 2 Error: 0.051746 Iteration 3 Error: 0.006244 Align patch 18 7 left Iteration 1 Error: 0.639289 Iteration 2 Error: 0.087510 Iteration 3 Error: 0.025749 Align patch 19 6 left Iteration 1 Error: 0.627671 Iteration 2 Error: 0.080489 Iteration 3 Error: 0.013423 Align patch 20 5 left Iteration 1 Error: 0.438264 Iteration 2 Error: 0.057701 Iteration 3 Error: 0.009733 Align patch 21 4 left Iteration 1 Error: 0.825118 Iteration 2 Error: 0.095602 Iteration 3 Error: 0.014399 Align patch 22 3 left Iteration 1 Error: 0.648501 Iteration 2 Error: 0.094040 Iteration 3 Error: 0.023005 Align patch 23 2 left Iteration 1 Error: 0.784558 Iteration 2 Error: 0.101369 Iteration 3 Error: 0.017646 Align patch 24 1 left Iteration 1 Error: 0.565780 Iteration 2 Error: 0.050270 Iteration 3 Error: 0.012643 Align patch 25 0 left Iteration 1 Error: 0.450403 Iteration 2 Error: 0.064849 Iteration 3 Error: 0.011899 3D Fitting completed. Patch alignment time: 15.23(sec) Local motion has been corrected. Process thread exits. Computational time: 23.744501 sec Total time: 29.484430 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00005hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00005hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.739407s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00005hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.817739s ........................................ >>>>>>TIME<<<<<< FFT: 0.987609s Defocus_U Defocus_V Angle CCC 12083.98 12916.02 12.86 0.066386 Final Values Defocus_U Defocus_V Angle CCC 12094.92 12930.08 13.18 0.106309 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00005hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00005hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 38.70 6.72 Num Hot pixels: 221 Hot pixel threshold: 79.05 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.604280 Iteration 2 Error: 0.120383 Iteration 3 Error: 0.028075 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.01 0.05 ...... Frame ( 3) shift: -0.02 0.09 ...... Frame ( 4) shift: -0.03 0.14 ...... Frame ( 5) shift: -0.03 0.18 ...... Frame ( 6) shift: -0.03 0.22 ...... Frame ( 7) shift: -0.02 0.27 ...... Frame ( 8) shift: -0.01 0.31 ...... Frame ( 9) shift: -0.00 0.32 ...... Frame ( 10) shift: 0.02 0.32 ...... Frame ( 11) shift: 0.03 0.31 ...... Frame ( 12) shift: 0.04 0.35 ...... Frame ( 13) shift: 0.04 0.44 ...... Frame ( 14) shift: 0.04 0.53 ...... Frame ( 15) shift: 0.07 0.57 ...... Frame ( 16) shift: 0.12 0.57 ...... Frame ( 17) shift: 0.17 0.56 ...... Frame ( 18) shift: 0.21 0.58 ...... Frame ( 19) shift: 0.24 0.63 ...... Frame ( 20) shift: 0.28 0.67 ...... Frame ( 21) shift: 0.30 0.72 ...... Frame ( 22) shift: 0.33 0.78 ...... Frame ( 23) shift: 0.35 0.83 ...... Frame ( 24) shift: 0.38 0.90 ...... Frame ( 25) shift: 0.42 0.98 ...... Frame ( 26) shift: 0.45 1.05 ...... Frame ( 27) shift: 0.49 1.09 ...... Frame ( 28) shift: 0.53 1.07 ...... Frame ( 29) shift: 0.57 1.06 ...... Frame ( 30) shift: 0.61 1.06 ...... Frame ( 31) shift: 0.63 1.08 ...... Frame ( 32) shift: 0.65 1.09 ...... Frame ( 33) shift: 0.68 1.11 ...... Frame ( 34) shift: 0.71 1.13 ...... Frame ( 35) shift: 0.74 1.15 ...... Frame ( 36) shift: 0.77 1.15 ...... Frame ( 37) shift: 0.81 1.13 ...... Frame ( 38) shift: 0.85 1.11 ...... Frame ( 39) shift: 0.88 1.10 ...... Frame ( 40) shift: 0.92 1.08 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.831891 Iteration 2 Error: 0.146735 Iteration 3 Error: 0.041651 Align patch 2 23 left Iteration 1 Error: 0.643296 Iteration 2 Error: 0.077993 Iteration 3 Error: 0.018458 Align patch 3 22 left Iteration 1 Error: 0.532299 Iteration 2 Error: 0.073088 Iteration 3 Error: 0.020851 Align patch 4 21 left Iteration 1 Error: 0.560926 Iteration 2 Error: 0.061727 Iteration 3 Error: 0.019678 Align patch 5 20 left Iteration 1 Error: 0.603993 Iteration 2 Error: 0.096047 Iteration 3 Error: 0.024170 Align patch 6 19 left Iteration 1 Error: 0.789490 Iteration 2 Error: 0.187415 Iteration 3 Error: 0.053061 Iteration 4 Error: 0.020936 Align patch 7 18 left Iteration 1 Error: 0.704472 Iteration 2 Error: 0.170935 Iteration 3 Error: 0.047383 Align patch 8 17 left Iteration 1 Error: 0.639402 Iteration 2 Error: 0.127313 Iteration 3 Error: 0.037837 Align patch 9 16 left Iteration 1 Error: 0.886281 Iteration 2 Error: 0.112229 Iteration 3 Error: 0.019585 Align patch 10 15 left Iteration 1 Error: 0.549615 Iteration 2 Error: 0.074947 Iteration 3 Error: 0.018425 Align patch 11 14 left Iteration 1 Error: 0.797380 Iteration 2 Error: 0.159870 Iteration 3 Error: 0.034714 Align patch 12 13 left Iteration 1 Error: 0.673810 Iteration 2 Error: 0.134394 Iteration 3 Error: 0.039713 Align patch 13 12 left Iteration 1 Error: 0.542678 Iteration 2 Error: 0.138257 Iteration 3 Error: 0.035018 Align patch 14 11 left Iteration 1 Error: 0.578754 Iteration 2 Error: 0.143731 Iteration 3 Error: 0.061694 Iteration 4 Error: 0.015612 Align patch 15 10 left Iteration 1 Error: 0.570451 Iteration 2 Error: 0.122099 Iteration 3 Error: 0.029257 Align patch 16 9 left Iteration 1 Error: 0.564282 Iteration 2 Error: 0.100061 Iteration 3 Error: 0.023248 Align patch 17 8 left Iteration 1 Error: 0.642300 Iteration 2 Error: 0.102136 Iteration 3 Error: 0.032392 Align patch 18 7 left Iteration 1 Error: 0.565098 Iteration 2 Error: 0.098447 Iteration 3 Error: 0.024624 Align patch 19 6 left Iteration 1 Error: 0.719010 Iteration 2 Error: 0.167046 Iteration 3 Error: 0.040944 Align patch 20 5 left Iteration 1 Error: 0.646332 Iteration 2 Error: 0.082937 Iteration 3 Error: 0.016476 Align patch 21 4 left Iteration 1 Error: 0.781072 Iteration 2 Error: 0.105276 Iteration 3 Error: 0.019290 Align patch 22 3 left Iteration 1 Error: 0.932398 Iteration 2 Error: 0.161695 Iteration 3 Error: 0.019411 Align patch 23 2 left Iteration 1 Error: 0.833871 Iteration 2 Error: 0.247151 Iteration 3 Error: 0.067468 Iteration 4 Error: 0.020551 Align patch 24 1 left Iteration 1 Error: 0.691001 Iteration 2 Error: 0.127985 Iteration 3 Error: 0.028638 Align patch 25 0 left Iteration 1 Error: 0.977784 Iteration 2 Error: 0.107168 Iteration 3 Error: 0.023086 3D Fitting completed. Patch alignment time: 15.39(sec) Local motion has been corrected. Process thread exits. Computational time: 24.320074 sec Total time: 30.527168 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00005hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00005hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.639809s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00005hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.565864s ........................................ >>>>>>TIME<<<<<< FFT: 0.960117s Defocus_U Defocus_V Angle CCC 14420.81 13915.15 88.89 0.039008 Final Values Defocus_U Defocus_V Angle CCC 14436.44 13918.28 88.27 0.058331 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00005hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00005hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 40.76 6.86 Num Hot pixels: 233 Hot pixel threshold: 81.92 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.439622 Iteration 2 Error: 0.080400 Iteration 3 Error: 0.013580 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.01 0.05 ...... Frame ( 3) shift: -0.02 0.10 ...... Frame ( 4) shift: -0.03 0.15 ...... Frame ( 5) shift: -0.03 0.20 ...... Frame ( 6) shift: -0.03 0.23 ...... Frame ( 7) shift: -0.01 0.25 ...... Frame ( 8) shift: 0.00 0.26 ...... Frame ( 9) shift: 0.01 0.27 ...... Frame ( 10) shift: 0.02 0.28 ...... Frame ( 11) shift: 0.03 0.29 ...... Frame ( 12) shift: 0.05 0.32 ...... Frame ( 13) shift: 0.08 0.36 ...... Frame ( 14) shift: 0.12 0.40 ...... Frame ( 15) shift: 0.15 0.41 ...... Frame ( 16) shift: 0.18 0.38 ...... Frame ( 17) shift: 0.21 0.35 ...... Frame ( 18) shift: 0.24 0.33 ...... Frame ( 19) shift: 0.27 0.34 ...... Frame ( 20) shift: 0.30 0.34 ...... Frame ( 21) shift: 0.34 0.36 ...... Frame ( 22) shift: 0.39 0.39 ...... Frame ( 23) shift: 0.45 0.43 ...... Frame ( 24) shift: 0.48 0.45 ...... Frame ( 25) shift: 0.48 0.46 ...... Frame ( 26) shift: 0.48 0.46 ...... Frame ( 27) shift: 0.48 0.47 ...... Frame ( 28) shift: 0.48 0.49 ...... Frame ( 29) shift: 0.49 0.50 ...... Frame ( 30) shift: 0.51 0.52 ...... Frame ( 31) shift: 0.56 0.55 ...... Frame ( 32) shift: 0.60 0.58 ...... Frame ( 33) shift: 0.63 0.59 ...... Frame ( 34) shift: 0.64 0.59 ...... Frame ( 35) shift: 0.66 0.59 ...... Frame ( 36) shift: 0.67 0.60 ...... Frame ( 37) shift: 0.69 0.61 ...... Frame ( 38) shift: 0.71 0.62 ...... Frame ( 39) shift: 0.72 0.64 ...... Frame ( 40) shift: 0.74 0.65 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.799774 Iteration 2 Error: 0.103000 Iteration 3 Error: 0.025015 Align patch 2 23 left Iteration 1 Error: 1.042551 Iteration 2 Error: 0.110574 Iteration 3 Error: 0.021454 Align patch 3 22 left Iteration 1 Error: 0.845497 Iteration 2 Error: 0.107978 Iteration 3 Error: 0.024726 Align patch 4 21 left Iteration 1 Error: 0.795090 Iteration 2 Error: 0.112011 Iteration 3 Error: 0.022618 Align patch 5 20 left Iteration 1 Error: 0.438537 Iteration 2 Error: 0.052742 Iteration 3 Error: 0.010704 Align patch 6 19 left Iteration 1 Error: 1.147229 Iteration 2 Error: 0.090393 Iteration 3 Error: 0.018167 Align patch 7 18 left Iteration 1 Error: 0.722703 Iteration 2 Error: 0.054600 Iteration 3 Error: 0.012280 Align patch 8 17 left Iteration 1 Error: 0.630828 Iteration 2 Error: 0.094659 Iteration 3 Error: 0.021528 Align patch 9 16 left Iteration 1 Error: 0.540934 Iteration 2 Error: 0.089118 Iteration 3 Error: 0.021254 Align patch 10 15 left Iteration 1 Error: 0.448913 Iteration 2 Error: 0.069353 Iteration 3 Error: 0.014506 Align patch 11 14 left Iteration 1 Error: 0.468940 Iteration 2 Error: 0.034979 Align patch 12 13 left Iteration 1 Error: 0.593758 Iteration 2 Error: 0.064846 Iteration 3 Error: 0.016154 Align patch 13 12 left Iteration 1 Error: 0.592416 Iteration 2 Error: 0.051966 Iteration 3 Error: 0.013978 Align patch 14 11 left Iteration 1 Error: 0.825549 Iteration 2 Error: 0.119328 Iteration 3 Error: 0.017830 Align patch 15 10 left Iteration 1 Error: 0.431797 Iteration 2 Error: 0.061250 Iteration 3 Error: 0.009458 Align patch 16 9 left Iteration 1 Error: 0.634735 Iteration 2 Error: 0.060381 Iteration 3 Error: 0.014971 Align patch 17 8 left Iteration 1 Error: 0.581336 Iteration 2 Error: 0.091629 Iteration 3 Error: 0.014842 Align patch 18 7 left Iteration 1 Error: 0.727753 Iteration 2 Error: 0.110860 Iteration 3 Error: 0.030454 Align patch 19 6 left Iteration 1 Error: 0.707332 Iteration 2 Error: 0.087390 Iteration 3 Error: 0.022623 Align patch 20 5 left Iteration 1 Error: 0.524831 Iteration 2 Error: 0.050744 Iteration 3 Error: 0.008225 Align patch 21 4 left Iteration 1 Error: 1.101286 Iteration 2 Error: 0.100558 Iteration 3 Error: 0.017804 Align patch 22 3 left Iteration 1 Error: 0.737531 Iteration 2 Error: 0.110466 Iteration 3 Error: 0.035292 Align patch 23 2 left Iteration 1 Error: 0.979428 Iteration 2 Error: 0.126423 Iteration 3 Error: 0.019775 Align patch 24 1 left Iteration 1 Error: 0.730835 Iteration 2 Error: 0.110385 Iteration 3 Error: 0.016826 Align patch 25 0 left Iteration 1 Error: 0.484569 Iteration 2 Error: 0.089059 Iteration 3 Error: 0.017379 3D Fitting completed. Patch alignment time: 14.33(sec) Local motion has been corrected. Process thread exits. Computational time: 23.258398 sec Total time: 28.982822 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00005hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00005hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.535406s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00005hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.540471s ........................................ >>>>>>TIME<<<<<< FFT: 0.946381s Defocus_U Defocus_V Angle CCC 13691.43 14601.59 5.11 0.062044 Final Values Defocus_U Defocus_V Angle CCC 13691.43 14601.59 5.11 0.099222 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00005hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00005hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.350e-01 1.004e-01 CC threshold: 0.737 Mean Std: 39.83 6.80 Num Hot pixels: 210 Hot pixel threshold: 80.62 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.743867 Iteration 2 Error: 0.153978 Iteration 3 Error: 0.030492 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.06 -0.05 ...... Frame ( 3) shift: -0.12 -0.10 ...... Frame ( 4) shift: -0.17 -0.15 ...... Frame ( 5) shift: -0.23 -0.20 ...... Frame ( 6) shift: -0.25 -0.22 ...... Frame ( 7) shift: -0.22 -0.22 ...... Frame ( 8) shift: -0.19 -0.22 ...... Frame ( 9) shift: -0.17 -0.22 ...... Frame ( 10) shift: -0.18 -0.22 ...... Frame ( 11) shift: -0.18 -0.22 ...... Frame ( 12) shift: -0.17 -0.21 ...... Frame ( 13) shift: -0.14 -0.19 ...... Frame ( 14) shift: -0.11 -0.16 ...... Frame ( 15) shift: -0.02 -0.13 ...... Frame ( 16) shift: 0.11 -0.10 ...... Frame ( 17) shift: 0.24 -0.07 ...... Frame ( 18) shift: 0.31 -0.03 ...... Frame ( 19) shift: 0.32 -0.00 ...... Frame ( 20) shift: 0.33 0.03 ...... Frame ( 21) shift: 0.37 0.02 ...... Frame ( 22) shift: 0.45 -0.02 ...... Frame ( 23) shift: 0.53 -0.06 ...... Frame ( 24) shift: 0.62 -0.07 ...... Frame ( 25) shift: 0.72 -0.05 ...... Frame ( 26) shift: 0.82 -0.02 ...... Frame ( 27) shift: 0.90 0.02 ...... Frame ( 28) shift: 0.96 0.07 ...... Frame ( 29) shift: 1.01 0.11 ...... Frame ( 30) shift: 1.03 0.17 ...... Frame ( 31) shift: 1.02 0.23 ...... Frame ( 32) shift: 1.00 0.28 ...... Frame ( 33) shift: 1.00 0.32 ...... Frame ( 34) shift: 1.01 0.34 ...... Frame ( 35) shift: 1.02 0.36 ...... Frame ( 36) shift: 1.04 0.38 ...... Frame ( 37) shift: 1.06 0.42 ...... Frame ( 38) shift: 1.08 0.45 ...... Frame ( 39) shift: 1.10 0.49 ...... Frame ( 40) shift: 1.12 0.52 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.754364 Iteration 2 Error: 0.110206 Iteration 3 Error: 0.017229 Align patch 2 23 left Iteration 1 Error: 0.738674 Iteration 2 Error: 0.159211 Iteration 3 Error: 0.030199 Align patch 3 22 left Iteration 1 Error: 0.922959 Iteration 2 Error: 0.132151 Iteration 3 Error: 0.038251 Align patch 4 21 left Iteration 1 Error: 0.827523 Iteration 2 Error: 0.141290 Iteration 3 Error: 0.037957 Align patch 5 20 left Iteration 1 Error: 0.587216 Iteration 2 Error: 0.106951 Iteration 3 Error: 0.024429 Align patch 6 19 left Iteration 1 Error: 0.860086 Iteration 2 Error: 0.107682 Iteration 3 Error: 0.029636 Align patch 7 18 left Iteration 1 Error: 0.670108 Iteration 2 Error: 0.148246 Iteration 3 Error: 0.036159 Align patch 8 17 left Iteration 1 Error: 0.603996 Iteration 2 Error: 0.090628 Iteration 3 Error: 0.019659 Align patch 9 16 left Iteration 1 Error: 0.656738 Iteration 2 Error: 0.122742 Iteration 3 Error: 0.028941 Align patch 10 15 left Iteration 1 Error: 0.572125 Iteration 2 Error: 0.065350 Iteration 3 Error: 0.015773 Align patch 11 14 left Iteration 1 Error: 0.429571 Iteration 2 Error: 0.049510 Align patch 12 13 left Iteration 1 Error: 0.725222 Iteration 2 Error: 0.076196 Iteration 3 Error: 0.011588 Align patch 13 12 left Iteration 1 Error: 0.405361 Iteration 2 Error: 0.052521 Iteration 3 Error: 0.009002 Align patch 14 11 left Iteration 1 Error: 0.717468 Iteration 2 Error: 0.085255 Iteration 3 Error: 0.020385 Align patch 15 10 left Iteration 1 Error: 0.714381 Iteration 2 Error: 0.098248 Iteration 3 Error: 0.026620 Align patch 16 9 left Iteration 1 Error: 0.795073 Iteration 2 Error: 0.075813 Iteration 3 Error: 0.011245 Align patch 17 8 left Iteration 1 Error: 0.761474 Iteration 2 Error: 0.120133 Iteration 3 Error: 0.022023 Align patch 18 7 left Iteration 1 Error: 0.406911 Iteration 2 Error: 0.066372 Iteration 3 Error: 0.015182 Align patch 19 6 left Iteration 1 Error: 0.522815 Iteration 2 Error: 0.054497 Iteration 3 Error: 0.010396 Align patch 20 5 left Iteration 1 Error: 0.683788 Iteration 2 Error: 0.087687 Iteration 3 Error: 0.022251 Align patch 21 4 left Iteration 1 Error: 0.819679 Iteration 2 Error: 0.059164 Iteration 3 Error: 0.009422 Align patch 22 3 left Iteration 1 Error: 0.600084 Iteration 2 Error: 0.097386 Iteration 3 Error: 0.019317 Align patch 23 2 left Iteration 1 Error: 0.811483 Iteration 2 Error: 0.179549 Iteration 3 Error: 0.052441 Iteration 4 Error: 0.020676 Align patch 24 1 left Iteration 1 Error: 0.612745 Iteration 2 Error: 0.102412 Iteration 3 Error: 0.022327 Align patch 25 0 left Iteration 1 Error: 0.476071 Iteration 2 Error: 0.066994 Iteration 3 Error: 0.013712 3D Fitting completed. Patch alignment time: 14.67(sec) Local motion has been corrected. Process thread exits. Computational time: 23.428701 sec Total time: 29.091166 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00005hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00005hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.741268s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00005hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.003241s ........................................ >>>>>>TIME<<<<<< FFT: 1.032329s Defocus_U Defocus_V Angle CCC 11550.79 10941.41 84.96 0.055544 Final Values Defocus_U Defocus_V Angle CCC 11558.60 10958.60 86.22 0.093601 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00006hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00006hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 39.41 6.79 Num Hot pixels: 221 Hot pixel threshold: 80.14 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.879285 Iteration 2 Error: 0.287106 Iteration 3 Error: 0.078669 Iteration 4 Error: 0.021759 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.09 0.15 ...... Frame ( 3) shift: 0.17 0.31 ...... Frame ( 4) shift: 0.26 0.46 ...... Frame ( 5) shift: 0.34 0.62 ...... Frame ( 6) shift: 0.42 0.75 ...... Frame ( 7) shift: 0.50 0.86 ...... Frame ( 8) shift: 0.57 0.97 ...... Frame ( 9) shift: 0.65 1.05 ...... Frame ( 10) shift: 0.74 1.10 ...... Frame ( 11) shift: 0.82 1.15 ...... Frame ( 12) shift: 0.94 1.23 ...... Frame ( 13) shift: 1.08 1.35 ...... Frame ( 14) shift: 1.23 1.47 ...... Frame ( 15) shift: 1.32 1.58 ...... Frame ( 16) shift: 1.37 1.69 ...... Frame ( 17) shift: 1.41 1.81 ...... Frame ( 18) shift: 1.44 1.87 ...... Frame ( 19) shift: 1.46 1.87 ...... Frame ( 20) shift: 1.48 1.88 ...... Frame ( 21) shift: 1.51 1.93 ...... Frame ( 22) shift: 1.55 2.03 ...... Frame ( 23) shift: 1.60 2.12 ...... Frame ( 24) shift: 1.64 2.21 ...... Frame ( 25) shift: 1.67 2.30 ...... Frame ( 26) shift: 1.71 2.39 ...... Frame ( 27) shift: 1.77 2.44 ...... Frame ( 28) shift: 1.88 2.47 ...... Frame ( 29) shift: 1.98 2.50 ...... Frame ( 30) shift: 2.03 2.53 ...... Frame ( 31) shift: 2.02 2.57 ...... Frame ( 32) shift: 2.01 2.60 ...... Frame ( 33) shift: 2.02 2.64 ...... Frame ( 34) shift: 2.05 2.69 ...... Frame ( 35) shift: 2.08 2.74 ...... Frame ( 36) shift: 2.15 2.78 ...... Frame ( 37) shift: 2.26 2.80 ...... Frame ( 38) shift: 2.37 2.82 ...... Frame ( 39) shift: 2.48 2.84 ...... Frame ( 40) shift: 2.59 2.86 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.973242 Iteration 2 Error: 0.205942 Iteration 3 Error: 0.056874 Iteration 4 Error: 0.025557 Align patch 2 23 left Iteration 1 Error: 0.832363 Iteration 2 Error: 0.219477 Iteration 3 Error: 0.080413 Iteration 4 Error: 0.031453 Align patch 3 22 left Iteration 1 Error: 0.593729 Iteration 2 Error: 0.110638 Iteration 3 Error: 0.018589 Align patch 4 21 left Iteration 1 Error: 0.523399 Iteration 2 Error: 0.084261 Iteration 3 Error: 0.019414 Align patch 5 20 left Iteration 1 Error: 0.667398 Iteration 2 Error: 0.130645 Iteration 3 Error: 0.026475 Align patch 6 19 left Iteration 1 Error: 0.573140 Iteration 2 Error: 0.187595 Iteration 3 Error: 0.062842 Iteration 4 Error: 0.025288 Align patch 7 18 left Iteration 1 Error: 0.638230 Iteration 2 Error: 0.191135 Iteration 3 Error: 0.053932 Iteration 4 Error: 0.027640 Align patch 8 17 left Iteration 1 Error: 0.636199 Iteration 2 Error: 0.118913 Iteration 3 Error: 0.022674 Align patch 9 16 left Iteration 1 Error: 0.570137 Iteration 2 Error: 0.091345 Iteration 3 Error: 0.016292 Align patch 10 15 left Iteration 1 Error: 0.592195 Iteration 2 Error: 0.097128 Iteration 3 Error: 0.033153 Align patch 11 14 left Iteration 1 Error: 0.637575 Iteration 2 Error: 0.097025 Iteration 3 Error: 0.025946 Align patch 12 13 left Iteration 1 Error: 0.924908 Iteration 2 Error: 0.116472 Iteration 3 Error: 0.041291 Align patch 13 12 left Iteration 1 Error: 0.664671 Iteration 2 Error: 0.108578 Iteration 3 Error: 0.022026 Align patch 14 11 left Iteration 1 Error: 0.663029 Iteration 2 Error: 0.141689 Iteration 3 Error: 0.048574 Align patch 15 10 left Iteration 1 Error: 0.683894 Iteration 2 Error: 0.066012 Iteration 3 Error: 0.020695 Align patch 16 9 left Iteration 1 Error: 0.786638 Iteration 2 Error: 0.162409 Iteration 3 Error: 0.047467 Align patch 17 8 left Iteration 1 Error: 0.610210 Iteration 2 Error: 0.157346 Iteration 3 Error: 0.058895 Iteration 4 Error: 0.021033 Align patch 18 7 left Iteration 1 Error: 0.628469 Iteration 2 Error: 0.064279 Iteration 3 Error: 0.017217 Align patch 19 6 left Iteration 1 Error: 0.665045 Iteration 2 Error: 0.123477 Iteration 3 Error: 0.029694 Align patch 20 5 left Iteration 1 Error: 0.567084 Iteration 2 Error: 0.090938 Iteration 3 Error: 0.022971 Align patch 21 4 left Iteration 1 Error: 0.781360 Iteration 2 Error: 0.147002 Iteration 3 Error: 0.033730 Align patch 22 3 left Iteration 1 Error: 0.854597 Iteration 2 Error: 0.074388 Iteration 3 Error: 0.020230 Align patch 23 2 left Iteration 1 Error: 0.628540 Iteration 2 Error: 0.074729 Iteration 3 Error: 0.015861 Align patch 24 1 left Iteration 1 Error: 0.854468 Iteration 2 Error: 0.119651 Iteration 3 Error: 0.033418 Align patch 25 0 left Iteration 1 Error: 0.563112 Iteration 2 Error: 0.061306 Iteration 3 Error: 0.008417 3D Fitting completed. Patch alignment time: 15.06(sec) Local motion has been corrected. Process thread exits. Computational time: 23.530607 sec Total time: 30.201805 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00006hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00006hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.737125s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00006hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.387893s ........................................ >>>>>>TIME<<<<<< FFT: 1.063118s Defocus_U Defocus_V Angle CCC 8988.28 9785.16 13.70 0.041452 Final Values Defocus_U Defocus_V Angle CCC 9010.17 9807.04 14.64 0.073362 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00006hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00006hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.003e-01 CC threshold: 0.736 Mean Std: 39.95 6.77 Num Hot pixels: 212 Hot pixel threshold: 80.57 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.262780 Iteration 2 Error: 0.265522 Iteration 3 Error: 0.068854 Iteration 4 Error: 0.020864 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.06 0.02 ...... Frame ( 3) shift: 0.13 0.04 ...... Frame ( 4) shift: 0.19 0.07 ...... Frame ( 5) shift: 0.26 0.09 ...... Frame ( 6) shift: 0.33 0.13 ...... Frame ( 7) shift: 0.42 0.20 ...... Frame ( 8) shift: 0.51 0.28 ...... Frame ( 9) shift: 0.58 0.32 ...... Frame ( 10) shift: 0.64 0.34 ...... Frame ( 11) shift: 0.70 0.36 ...... Frame ( 12) shift: 0.77 0.41 ...... Frame ( 13) shift: 0.85 0.48 ...... Frame ( 14) shift: 0.92 0.55 ...... Frame ( 15) shift: 0.98 0.61 ...... Frame ( 16) shift: 1.00 0.66 ...... Frame ( 17) shift: 1.03 0.72 ...... Frame ( 18) shift: 1.06 0.79 ...... Frame ( 19) shift: 1.09 0.89 ...... Frame ( 20) shift: 1.13 0.98 ...... Frame ( 21) shift: 1.17 1.08 ...... Frame ( 22) shift: 1.23 1.19 ...... Frame ( 23) shift: 1.29 1.30 ...... Frame ( 24) shift: 1.34 1.38 ...... Frame ( 25) shift: 1.39 1.42 ...... Frame ( 26) shift: 1.44 1.46 ...... Frame ( 27) shift: 1.51 1.51 ...... Frame ( 28) shift: 1.60 1.57 ...... Frame ( 29) shift: 1.68 1.64 ...... Frame ( 30) shift: 1.77 1.70 ...... Frame ( 31) shift: 1.85 1.78 ...... Frame ( 32) shift: 1.92 1.85 ...... Frame ( 33) shift: 1.97 1.89 ...... Frame ( 34) shift: 1.97 1.90 ...... Frame ( 35) shift: 1.97 1.90 ...... Frame ( 36) shift: 2.00 1.94 ...... Frame ( 37) shift: 2.06 1.99 ...... Frame ( 38) shift: 2.12 2.05 ...... Frame ( 39) shift: 2.19 2.11 ...... Frame ( 40) shift: 2.25 2.16 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.944297 Iteration 2 Error: 0.168180 Iteration 3 Error: 0.080073 Iteration 4 Error: 0.042903 Align patch 2 23 left Iteration 1 Error: 0.835776 Iteration 2 Error: 0.141318 Iteration 3 Error: 0.046024 Align patch 3 22 left Iteration 1 Error: 0.721483 Iteration 2 Error: 0.129964 Iteration 3 Error: 0.040996 Align patch 4 21 left Iteration 1 Error: 0.669641 Iteration 2 Error: 0.102614 Iteration 3 Error: 0.029161 Align patch 5 20 left Iteration 1 Error: 0.559408 Iteration 2 Error: 0.116487 Iteration 3 Error: 0.023577 Align patch 6 19 left Iteration 1 Error: 1.143885 Iteration 2 Error: 0.322953 Iteration 3 Error: 0.169175 Iteration 4 Error: 0.087443 Iteration 5 Error: 0.049352 Align patch 7 18 left Iteration 1 Error: 0.928055 Iteration 2 Error: 0.187699 Iteration 3 Error: 0.063738 Iteration 4 Error: 0.020118 Align patch 8 17 left Iteration 1 Error: 0.922411 Iteration 2 Error: 0.105315 Iteration 3 Error: 0.022967 Align patch 9 16 left Iteration 1 Error: 0.502490 Iteration 2 Error: 0.115485 Iteration 3 Error: 0.020624 Align patch 10 15 left Iteration 1 Error: 0.595096 Iteration 2 Error: 0.109995 Iteration 3 Error: 0.023975 Align patch 11 14 left Iteration 1 Error: 0.817142 Iteration 2 Error: 0.285563 Iteration 3 Error: 0.124367 Iteration 4 Error: 0.059657 Iteration 5 Error: 0.024822 Align patch 12 13 left Iteration 1 Error: 0.453882 Iteration 2 Error: 0.164742 Iteration 3 Error: 0.075693 Iteration 4 Error: 0.031069 Align patch 13 12 left Iteration 1 Error: 0.502657 Iteration 2 Error: 0.080098 Iteration 3 Error: 0.024030 Align patch 14 11 left Iteration 1 Error: 0.401463 Iteration 2 Error: 0.091517 Iteration 3 Error: 0.018197 Align patch 15 10 left Iteration 1 Error: 0.811180 Iteration 2 Error: 0.088597 Iteration 3 Error: 0.015043 Align patch 16 9 left Iteration 1 Error: 0.920616 Iteration 2 Error: 0.092390 Iteration 3 Error: 0.015393 Align patch 17 8 left Iteration 1 Error: 0.736859 Iteration 2 Error: 0.108699 Iteration 3 Error: 0.015454 Align patch 18 7 left Iteration 1 Error: 0.649599 Iteration 2 Error: 0.141767 Iteration 3 Error: 0.042213 Align patch 19 6 left Iteration 1 Error: 0.804951 Iteration 2 Error: 0.205022 Iteration 3 Error: 0.037227 Align patch 20 5 left Iteration 1 Error: 0.692590 Iteration 2 Error: 0.129290 Iteration 3 Error: 0.020258 Align patch 21 4 left Iteration 1 Error: 0.896478 Iteration 2 Error: 0.117926 Iteration 3 Error: 0.039204 Align patch 22 3 left Iteration 1 Error: 0.819226 Iteration 2 Error: 0.198945 Iteration 3 Error: 0.045142 Align patch 23 2 left Iteration 1 Error: 1.027025 Iteration 2 Error: 0.123527 Iteration 3 Error: 0.029865 Align patch 24 1 left Iteration 1 Error: 1.489365 Iteration 2 Error: 0.175543 Iteration 3 Error: 0.028220 Align patch 25 0 left Iteration 1 Error: 1.119418 Iteration 2 Error: 0.175812 Iteration 3 Error: 0.035008 3D Fitting completed. Patch alignment time: 15.48(sec) Local motion has been corrected. Process thread exits. Computational time: 24.101385 sec Total time: 30.334732 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00006hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00006hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.569412s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00006hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.132367s ........................................ >>>>>>TIME<<<<<< FFT: 1.042325s Defocus_U Defocus_V Angle CCC 12683.59 13203.13 4.40 0.049947 Final Values Defocus_U Defocus_V Angle CCC 12702.32 13200.05 3.78 0.079888 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00006hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00006hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.002e-01 CC threshold: 0.736 Mean Std: 39.29 6.72 Num Hot pixels: 220 Hot pixel threshold: 79.62 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.060184 Iteration 2 Error: 0.180305 Iteration 3 Error: 0.034562 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.09 -0.11 ...... Frame ( 3) shift: -0.19 -0.22 ...... Frame ( 4) shift: -0.28 -0.32 ...... Frame ( 5) shift: -0.37 -0.43 ...... Frame ( 6) shift: -0.41 -0.44 ...... Frame ( 7) shift: -0.39 -0.36 ...... Frame ( 8) shift: -0.37 -0.27 ...... Frame ( 9) shift: -0.32 -0.18 ...... Frame ( 10) shift: -0.26 -0.09 ...... Frame ( 11) shift: -0.20 0.00 ...... Frame ( 12) shift: -0.15 0.08 ...... Frame ( 13) shift: -0.12 0.15 ...... Frame ( 14) shift: -0.09 0.21 ...... Frame ( 15) shift: -0.02 0.29 ...... Frame ( 16) shift: 0.10 0.39 ...... Frame ( 17) shift: 0.21 0.48 ...... Frame ( 18) shift: 0.28 0.57 ...... Frame ( 19) shift: 0.30 0.64 ...... Frame ( 20) shift: 0.32 0.72 ...... Frame ( 21) shift: 0.33 0.75 ...... Frame ( 22) shift: 0.33 0.75 ...... Frame ( 23) shift: 0.32 0.75 ...... Frame ( 24) shift: 0.34 0.76 ...... Frame ( 25) shift: 0.39 0.79 ...... Frame ( 26) shift: 0.44 0.81 ...... Frame ( 27) shift: 0.46 0.84 ...... Frame ( 28) shift: 0.47 0.87 ...... Frame ( 29) shift: 0.47 0.89 ...... Frame ( 30) shift: 0.50 0.94 ...... Frame ( 31) shift: 0.58 1.00 ...... Frame ( 32) shift: 0.65 1.06 ...... Frame ( 33) shift: 0.68 1.13 ...... Frame ( 34) shift: 0.67 1.21 ...... Frame ( 35) shift: 0.67 1.28 ...... Frame ( 36) shift: 0.68 1.34 ...... Frame ( 37) shift: 0.71 1.37 ...... Frame ( 38) shift: 0.74 1.40 ...... Frame ( 39) shift: 0.77 1.43 ...... Frame ( 40) shift: 0.80 1.46 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.842979 Iteration 2 Error: 0.122225 Iteration 3 Error: 0.028796 Align patch 2 23 left Iteration 1 Error: 0.959701 Iteration 2 Error: 0.132103 Iteration 3 Error: 0.027698 Align patch 3 22 left Iteration 1 Error: 0.561657 Iteration 2 Error: 0.058616 Iteration 3 Error: 0.014148 Align patch 4 21 left Iteration 1 Error: 0.560996 Iteration 2 Error: 0.089311 Iteration 3 Error: 0.019671 Align patch 5 20 left Iteration 1 Error: 0.532089 Iteration 2 Error: 0.054702 Iteration 3 Error: 0.017202 Align patch 6 19 left Iteration 1 Error: 0.849203 Iteration 2 Error: 0.133899 Iteration 3 Error: 0.042512 Align patch 7 18 left Iteration 1 Error: 1.006375 Iteration 2 Error: 0.181718 Iteration 3 Error: 0.044321 Align patch 8 17 left Iteration 1 Error: 0.694275 Iteration 2 Error: 0.073451 Iteration 3 Error: 0.016663 Align patch 9 16 left Iteration 1 Error: 0.574842 Iteration 2 Error: 0.098777 Iteration 3 Error: 0.011770 Align patch 10 15 left Iteration 1 Error: 0.514198 Iteration 2 Error: 0.078264 Iteration 3 Error: 0.017989 Align patch 11 14 left Iteration 1 Error: 0.711863 Iteration 2 Error: 0.064131 Iteration 3 Error: 0.021362 Align patch 12 13 left Iteration 1 Error: 0.680756 Iteration 2 Error: 0.155287 Iteration 3 Error: 0.026356 Align patch 13 12 left Iteration 1 Error: 0.348970 Iteration 2 Error: 0.054153 Iteration 3 Error: 0.007142 Align patch 14 11 left Iteration 1 Error: 0.523901 Iteration 2 Error: 0.110742 Iteration 3 Error: 0.024928 Align patch 15 10 left Iteration 1 Error: 0.573671 Iteration 2 Error: 0.142609 Iteration 3 Error: 0.030885 Align patch 16 9 left Iteration 1 Error: 0.830299 Iteration 2 Error: 0.135873 Iteration 3 Error: 0.037858 Align patch 17 8 left Iteration 1 Error: 0.883061 Iteration 2 Error: 0.127061 Iteration 3 Error: 0.029313 Align patch 18 7 left Iteration 1 Error: 0.631689 Iteration 2 Error: 0.102662 Iteration 3 Error: 0.020711 Align patch 19 6 left Iteration 1 Error: 0.467130 Iteration 2 Error: 0.087288 Iteration 3 Error: 0.022652 Align patch 20 5 left Iteration 1 Error: 0.717480 Iteration 2 Error: 0.104759 Iteration 3 Error: 0.027520 Align patch 21 4 left Iteration 1 Error: 0.797348 Iteration 2 Error: 0.112224 Iteration 3 Error: 0.031323 Align patch 22 3 left Iteration 1 Error: 0.559997 Iteration 2 Error: 0.098838 Iteration 3 Error: 0.018792 Align patch 23 2 left Iteration 1 Error: 0.609023 Iteration 2 Error: 0.075583 Iteration 3 Error: 0.013940 Align patch 24 1 left Iteration 1 Error: 0.537366 Iteration 2 Error: 0.108127 Iteration 3 Error: 0.015880 Align patch 25 0 left Iteration 1 Error: 0.604376 Iteration 2 Error: 0.107956 Iteration 3 Error: 0.018529 3D Fitting completed. Patch alignment time: 15.21(sec) Local motion has been corrected. Process thread exits. Computational time: 24.113415 sec Total time: 31.877338 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00006hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00006hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.861317s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00006hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.245106s ........................................ >>>>>>TIME<<<<<< FFT: 1.081485s Defocus_U Defocus_V Angle CCC 14132.82 14933.60 5.79 0.059097 Final Values Defocus_U Defocus_V Angle CCC 14142.20 14927.36 5.48 0.085094 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00006hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00006hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.350e-01 1.004e-01 CC threshold: 0.737 Mean Std: 38.14 6.64 Num Hot pixels: 209 Hot pixel threshold: 78.01 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.755790 Iteration 2 Error: 0.083091 Iteration 3 Error: 0.017978 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.01 0.12 ...... Frame ( 3) shift: 0.01 0.24 ...... Frame ( 4) shift: 0.02 0.37 ...... Frame ( 5) shift: 0.02 0.49 ...... Frame ( 6) shift: 0.04 0.55 ...... Frame ( 7) shift: 0.08 0.56 ...... Frame ( 8) shift: 0.11 0.57 ...... Frame ( 9) shift: 0.15 0.60 ...... Frame ( 10) shift: 0.19 0.64 ...... Frame ( 11) shift: 0.23 0.69 ...... Frame ( 12) shift: 0.25 0.74 ...... Frame ( 13) shift: 0.24 0.79 ...... Frame ( 14) shift: 0.23 0.84 ...... Frame ( 15) shift: 0.24 0.87 ...... Frame ( 16) shift: 0.28 0.88 ...... Frame ( 17) shift: 0.32 0.90 ...... Frame ( 18) shift: 0.33 0.93 ...... Frame ( 19) shift: 0.31 0.98 ...... Frame ( 20) shift: 0.29 1.03 ...... Frame ( 21) shift: 0.26 1.10 ...... Frame ( 22) shift: 0.23 1.18 ...... Frame ( 23) shift: 0.21 1.27 ...... Frame ( 24) shift: 0.22 1.29 ...... Frame ( 25) shift: 0.25 1.24 ...... Frame ( 26) shift: 0.29 1.20 ...... Frame ( 27) shift: 0.30 1.18 ...... Frame ( 28) shift: 0.29 1.21 ...... Frame ( 29) shift: 0.27 1.23 ...... Frame ( 30) shift: 0.28 1.25 ...... Frame ( 31) shift: 0.33 1.26 ...... Frame ( 32) shift: 0.37 1.27 ...... Frame ( 33) shift: 0.38 1.30 ...... Frame ( 34) shift: 0.36 1.36 ...... Frame ( 35) shift: 0.33 1.41 ...... Frame ( 36) shift: 0.34 1.43 ...... Frame ( 37) shift: 0.39 1.42 ...... Frame ( 38) shift: 0.44 1.41 ...... Frame ( 39) shift: 0.50 1.39 ...... Frame ( 40) shift: 0.55 1.38 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.438432 Iteration 2 Error: 0.258674 Iteration 3 Error: 0.075894 Iteration 4 Error: 0.029540 Align patch 2 23 left Iteration 1 Error: 1.070594 Iteration 2 Error: 0.099388 Iteration 3 Error: 0.032851 Align patch 3 22 left Iteration 1 Error: 0.651509 Iteration 2 Error: 0.130906 Iteration 3 Error: 0.024896 Align patch 4 21 left Iteration 1 Error: 0.708588 Iteration 2 Error: 0.093564 Iteration 3 Error: 0.015094 Align patch 5 20 left Iteration 1 Error: 0.625111 Iteration 2 Error: 0.071757 Iteration 3 Error: 0.016570 Align patch 6 19 left Iteration 1 Error: 1.232006 Iteration 2 Error: 0.252111 Iteration 3 Error: 0.055666 Iteration 4 Error: 0.015774 Align patch 7 18 left Iteration 1 Error: 0.949110 Iteration 2 Error: 0.158927 Iteration 3 Error: 0.033659 Align patch 8 17 left Iteration 1 Error: 0.438808 Iteration 2 Error: 0.060355 Iteration 3 Error: 0.008769 Align patch 9 16 left Iteration 1 Error: 0.732333 Iteration 2 Error: 0.106740 Iteration 3 Error: 0.015175 Align patch 10 15 left Iteration 1 Error: 0.385601 Iteration 2 Error: 0.039500 Align patch 11 14 left Iteration 1 Error: 0.633937 Iteration 2 Error: 0.119099 Iteration 3 Error: 0.042801 Align patch 12 13 left Iteration 1 Error: 0.595420 Iteration 2 Error: 0.121855 Iteration 3 Error: 0.025609 Align patch 13 12 left Iteration 1 Error: 0.616330 Iteration 2 Error: 0.077237 Iteration 3 Error: 0.018529 Align patch 14 11 left Iteration 1 Error: 0.705525 Iteration 2 Error: 0.149764 Iteration 3 Error: 0.036740 Align patch 15 10 left Iteration 1 Error: 0.436799 Iteration 2 Error: 0.054459 Iteration 3 Error: 0.012667 Align patch 16 9 left Iteration 1 Error: 0.455776 Iteration 2 Error: 0.054841 Iteration 3 Error: 0.014692 Align patch 17 8 left Iteration 1 Error: 0.503119 Iteration 2 Error: 0.102551 Iteration 3 Error: 0.021615 Align patch 18 7 left Iteration 1 Error: 0.600205 Iteration 2 Error: 0.108052 Iteration 3 Error: 0.022572 Align patch 19 6 left Iteration 1 Error: 0.640938 Iteration 2 Error: 0.119987 Iteration 3 Error: 0.024305 Align patch 20 5 left Iteration 1 Error: 0.566693 Iteration 2 Error: 0.130682 Iteration 3 Error: 0.016765 Align patch 21 4 left Iteration 1 Error: 0.820200 Iteration 2 Error: 0.086971 Iteration 3 Error: 0.010982 Align patch 22 3 left Iteration 1 Error: 0.717315 Iteration 2 Error: 0.172920 Iteration 3 Error: 0.057206 Iteration 4 Error: 0.021238 Align patch 23 2 left Iteration 1 Error: 1.002972 Iteration 2 Error: 0.148652 Iteration 3 Error: 0.029334 Align patch 24 1 left Iteration 1 Error: 0.573608 Iteration 2 Error: 0.081602 Iteration 3 Error: 0.012950 Align patch 25 0 left Iteration 1 Error: 0.653016 Iteration 2 Error: 0.101661 Iteration 3 Error: 0.020551 3D Fitting completed. Patch alignment time: 15.63(sec) Local motion has been corrected. Process thread exits. Computational time: 24.159615 sec Total time: 30.610531 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00006hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00006hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.734026s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00006hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.042672s ........................................ >>>>>>TIME<<<<<< FFT: 1.016317s Defocus_U Defocus_V Angle CCC 11521.52 11013.71 84.63 0.043524 Final Values Defocus_U Defocus_V Angle CCC 11529.34 11071.55 87.15 0.067177 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00007hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00007hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.002e-01 CC threshold: 0.736 Mean Std: 39.22 6.73 Num Hot pixels: 215 Hot pixel threshold: 79.60 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.022379 Iteration 2 Error: 0.186096 Iteration 3 Error: 0.041061 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.09 -0.09 ...... Frame ( 3) shift: -0.19 -0.17 ...... Frame ( 4) shift: -0.28 -0.26 ...... Frame ( 5) shift: -0.38 -0.34 ...... Frame ( 6) shift: -0.39 -0.36 ...... Frame ( 7) shift: -0.32 -0.31 ...... Frame ( 8) shift: -0.25 -0.25 ...... Frame ( 9) shift: -0.17 -0.19 ...... Frame ( 10) shift: -0.09 -0.12 ...... Frame ( 11) shift: -0.00 -0.05 ...... Frame ( 12) shift: 0.04 0.03 ...... Frame ( 13) shift: 0.06 0.12 ...... Frame ( 14) shift: 0.07 0.21 ...... Frame ( 15) shift: 0.08 0.29 ...... Frame ( 16) shift: 0.08 0.35 ...... Frame ( 17) shift: 0.09 0.41 ...... Frame ( 18) shift: 0.10 0.47 ...... Frame ( 19) shift: 0.14 0.54 ...... Frame ( 20) shift: 0.17 0.62 ...... Frame ( 21) shift: 0.20 0.68 ...... Frame ( 22) shift: 0.23 0.75 ...... Frame ( 23) shift: 0.26 0.81 ...... Frame ( 24) shift: 0.30 0.89 ...... Frame ( 25) shift: 0.35 0.97 ...... Frame ( 26) shift: 0.41 1.06 ...... Frame ( 27) shift: 0.46 1.11 ...... Frame ( 28) shift: 0.51 1.15 ...... Frame ( 29) shift: 0.56 1.18 ...... Frame ( 30) shift: 0.57 1.18 ...... Frame ( 31) shift: 0.55 1.16 ...... Frame ( 32) shift: 0.53 1.14 ...... Frame ( 33) shift: 0.55 1.19 ...... Frame ( 34) shift: 0.62 1.30 ...... Frame ( 35) shift: 0.69 1.41 ...... Frame ( 36) shift: 0.75 1.47 ...... Frame ( 37) shift: 0.81 1.49 ...... Frame ( 38) shift: 0.86 1.50 ...... Frame ( 39) shift: 0.92 1.51 ...... Frame ( 40) shift: 0.97 1.53 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.953168 Iteration 2 Error: 0.108425 Iteration 3 Error: 0.022090 Align patch 2 23 left Iteration 1 Error: 0.587994 Iteration 2 Error: 0.082953 Iteration 3 Error: 0.017258 Align patch 3 22 left Iteration 1 Error: 0.606640 Iteration 2 Error: 0.130797 Iteration 3 Error: 0.024918 Align patch 4 21 left Iteration 1 Error: 0.537675 Iteration 2 Error: 0.074990 Iteration 3 Error: 0.020147 Align patch 5 20 left Iteration 1 Error: 0.479278 Iteration 2 Error: 0.071730 Iteration 3 Error: 0.021503 Align patch 6 19 left Iteration 1 Error: 0.864451 Iteration 2 Error: 0.129146 Iteration 3 Error: 0.037579 Align patch 7 18 left Iteration 1 Error: 0.486924 Iteration 2 Error: 0.074341 Iteration 3 Error: 0.020397 Align patch 8 17 left Iteration 1 Error: 0.484541 Iteration 2 Error: 0.069099 Iteration 3 Error: 0.015970 Align patch 9 16 left Iteration 1 Error: 0.439685 Iteration 2 Error: 0.086070 Iteration 3 Error: 0.015088 Align patch 10 15 left Iteration 1 Error: 0.674261 Iteration 2 Error: 0.108429 Iteration 3 Error: 0.032596 Align patch 11 14 left Iteration 1 Error: 0.757073 Iteration 2 Error: 0.122080 Iteration 3 Error: 0.030184 Align patch 12 13 left Iteration 1 Error: 0.542373 Iteration 2 Error: 0.095892 Iteration 3 Error: 0.025370 Align patch 13 12 left Iteration 1 Error: 0.659332 Iteration 2 Error: 0.084061 Iteration 3 Error: 0.022364 Align patch 14 11 left Iteration 1 Error: 0.577390 Iteration 2 Error: 0.066082 Iteration 3 Error: 0.024756 Align patch 15 10 left Iteration 1 Error: 0.446816 Iteration 2 Error: 0.085359 Iteration 3 Error: 0.020898 Align patch 16 9 left Iteration 1 Error: 0.769716 Iteration 2 Error: 0.131660 Iteration 3 Error: 0.030949 Align patch 17 8 left Iteration 1 Error: 0.752529 Iteration 2 Error: 0.086151 Iteration 3 Error: 0.024814 Align patch 18 7 left Iteration 1 Error: 0.518443 Iteration 2 Error: 0.119491 Iteration 3 Error: 0.021063 Align patch 19 6 left Iteration 1 Error: 0.845321 Iteration 2 Error: 0.113091 Iteration 3 Error: 0.031954 Align patch 20 5 left Iteration 1 Error: 0.716237 Iteration 2 Error: 0.122654 Iteration 3 Error: 0.019659 Align patch 21 4 left Iteration 1 Error: 0.722028 Iteration 2 Error: 0.126432 Iteration 3 Error: 0.021100 Align patch 22 3 left Iteration 1 Error: 0.611606 Iteration 2 Error: 0.081916 Iteration 3 Error: 0.021135 Align patch 23 2 left Iteration 1 Error: 0.808071 Iteration 2 Error: 0.115780 Iteration 3 Error: 0.022106 Align patch 24 1 left Iteration 1 Error: 0.579826 Iteration 2 Error: 0.109222 Iteration 3 Error: 0.021128 Align patch 25 0 left Iteration 1 Error: 0.601526 Iteration 2 Error: 0.071644 Iteration 3 Error: 0.016860 3D Fitting completed. Patch alignment time: 15.01(sec) Local motion has been corrected. Process thread exits. Computational time: 23.246489 sec Total time: 29.943089 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00007hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00007hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.715266s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00007hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.956907s ........................................ >>>>>>TIME<<<<<< FFT: 1.043271s Defocus_U Defocus_V Angle CCC 12826.13 13752.00 11.89 0.057343 Final Values Defocus_U Defocus_V Angle CCC 12824.56 13759.82 11.26 0.087788 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00007hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00007hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 38.52 6.68 Num Hot pixels: 222 Hot pixel threshold: 78.63 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.717650 Iteration 2 Error: 0.138077 Iteration 3 Error: 0.028931 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.19 -0.12 ...... Frame ( 3) shift: -0.39 -0.24 ...... Frame ( 4) shift: -0.58 -0.35 ...... Frame ( 5) shift: -0.78 -0.47 ...... Frame ( 6) shift: -0.89 -0.52 ...... Frame ( 7) shift: -0.91 -0.50 ...... Frame ( 8) shift: -0.93 -0.48 ...... Frame ( 9) shift: -0.93 -0.44 ...... Frame ( 10) shift: -0.90 -0.36 ...... Frame ( 11) shift: -0.88 -0.29 ...... Frame ( 12) shift: -0.81 -0.24 ...... Frame ( 13) shift: -0.70 -0.21 ...... Frame ( 14) shift: -0.59 -0.19 ...... Frame ( 15) shift: -0.52 -0.15 ...... Frame ( 16) shift: -0.50 -0.09 ...... Frame ( 17) shift: -0.48 -0.04 ...... Frame ( 18) shift: -0.49 0.01 ...... Frame ( 19) shift: -0.51 0.06 ...... Frame ( 20) shift: -0.53 0.11 ...... Frame ( 21) shift: -0.53 0.17 ...... Frame ( 22) shift: -0.51 0.26 ...... Frame ( 23) shift: -0.48 0.34 ...... Frame ( 24) shift: -0.49 0.44 ...... Frame ( 25) shift: -0.52 0.54 ...... Frame ( 26) shift: -0.55 0.64 ...... Frame ( 27) shift: -0.53 0.69 ...... Frame ( 28) shift: -0.46 0.68 ...... Frame ( 29) shift: -0.39 0.68 ...... Frame ( 30) shift: -0.34 0.69 ...... Frame ( 31) shift: -0.31 0.70 ...... Frame ( 32) shift: -0.28 0.72 ...... Frame ( 33) shift: -0.25 0.77 ...... Frame ( 34) shift: -0.22 0.85 ...... Frame ( 35) shift: -0.19 0.94 ...... Frame ( 36) shift: -0.20 0.97 ...... Frame ( 37) shift: -0.23 0.97 ...... Frame ( 38) shift: -0.26 0.97 ...... Frame ( 39) shift: -0.29 0.96 ...... Frame ( 40) shift: -0.32 0.96 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.686999 Iteration 2 Error: 0.140818 Iteration 3 Error: 0.022264 Align patch 2 23 left Iteration 1 Error: 0.602718 Iteration 2 Error: 0.064349 Iteration 3 Error: 0.012811 Align patch 3 22 left Iteration 1 Error: 0.677893 Iteration 2 Error: 0.087922 Iteration 3 Error: 0.023208 Align patch 4 21 left Iteration 1 Error: 0.450523 Iteration 2 Error: 0.049150 Align patch 5 20 left Iteration 1 Error: 0.349221 Iteration 2 Error: 0.057344 Iteration 3 Error: 0.009973 Align patch 6 19 left Iteration 1 Error: 0.635529 Iteration 2 Error: 0.105464 Iteration 3 Error: 0.018891 Align patch 7 18 left Iteration 1 Error: 0.493324 Iteration 2 Error: 0.059445 Iteration 3 Error: 0.013409 Align patch 8 17 left Iteration 1 Error: 0.580079 Iteration 2 Error: 0.085997 Iteration 3 Error: 0.009805 Align patch 9 16 left Iteration 1 Error: 0.444408 Iteration 2 Error: 0.048248 Align patch 10 15 left Iteration 1 Error: 0.438404 Iteration 2 Error: 0.053741 Iteration 3 Error: 0.008394 Align patch 11 14 left Iteration 1 Error: 0.973701 Iteration 2 Error: 0.119832 Iteration 3 Error: 0.033034 Align patch 12 13 left Iteration 1 Error: 0.480245 Iteration 2 Error: 0.107749 Iteration 3 Error: 0.040569 Align patch 13 12 left Iteration 1 Error: 0.478623 Iteration 2 Error: 0.080824 Iteration 3 Error: 0.013416 Align patch 14 11 left Iteration 1 Error: 0.302146 Iteration 2 Error: 0.035211 Align patch 15 10 left Iteration 1 Error: 0.510654 Iteration 2 Error: 0.049136 Align patch 16 9 left Iteration 1 Error: 0.694622 Iteration 2 Error: 0.218885 Iteration 3 Error: 0.043513 Align patch 17 8 left Iteration 1 Error: 0.691737 Iteration 2 Error: 0.130612 Iteration 3 Error: 0.036433 Align patch 18 7 left Iteration 1 Error: 0.576072 Iteration 2 Error: 0.066343 Iteration 3 Error: 0.021017 Align patch 19 6 left Iteration 1 Error: 0.473569 Iteration 2 Error: 0.081244 Iteration 3 Error: 0.012173 Align patch 20 5 left Iteration 1 Error: 0.455664 Iteration 2 Error: 0.062797 Iteration 3 Error: 0.013937 Align patch 21 4 left Iteration 1 Error: 0.565557 Iteration 2 Error: 0.085387 Iteration 3 Error: 0.018920 Align patch 22 3 left Iteration 1 Error: 0.418518 Iteration 2 Error: 0.049116 Align patch 23 2 left Iteration 1 Error: 0.457858 Iteration 2 Error: 0.051577 Iteration 3 Error: 0.009873 Align patch 24 1 left Iteration 1 Error: 0.441030 Iteration 2 Error: 0.090264 Iteration 3 Error: 0.015321 Align patch 25 0 left Iteration 1 Error: 0.836624 Iteration 2 Error: 0.110348 Iteration 3 Error: 0.032143 3D Fitting completed. Patch alignment time: 13.89(sec) Local motion has been corrected. Process thread exits. Computational time: 22.750393 sec Total time: 29.126797 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00007hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00007hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.526086s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00007hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.216293s ........................................ >>>>>>TIME<<<<<< FFT: 0.995908s Defocus_U Defocus_V Angle CCC 13005.85 13638.68 0.71 0.052545 Final Values Defocus_U Defocus_V Angle CCC 13059.00 13648.07 0.08 0.077727 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00007hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00007hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 38.92 6.69 Num Hot pixels: 209 Hot pixel threshold: 79.03 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.436230 Iteration 2 Error: 0.028636 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.02 -0.06 ...... Frame ( 3) shift: 0.04 -0.13 ...... Frame ( 4) shift: 0.06 -0.19 ...... Frame ( 5) shift: 0.08 -0.25 ...... Frame ( 6) shift: 0.11 -0.31 ...... Frame ( 7) shift: 0.15 -0.36 ...... Frame ( 8) shift: 0.19 -0.40 ...... Frame ( 9) shift: 0.19 -0.45 ...... Frame ( 10) shift: 0.14 -0.50 ...... Frame ( 11) shift: 0.10 -0.55 ...... Frame ( 12) shift: 0.10 -0.56 ...... Frame ( 13) shift: 0.15 -0.54 ...... Frame ( 14) shift: 0.20 -0.53 ...... Frame ( 15) shift: 0.22 -0.51 ...... Frame ( 16) shift: 0.21 -0.50 ...... Frame ( 17) shift: 0.20 -0.49 ...... Frame ( 18) shift: 0.20 -0.49 ...... Frame ( 19) shift: 0.20 -0.49 ...... Frame ( 20) shift: 0.19 -0.50 ...... Frame ( 21) shift: 0.22 -0.52 ...... Frame ( 22) shift: 0.27 -0.57 ...... Frame ( 23) shift: 0.32 -0.61 ...... Frame ( 24) shift: 0.34 -0.65 ...... Frame ( 25) shift: 0.32 -0.68 ...... Frame ( 26) shift: 0.29 -0.71 ...... Frame ( 27) shift: 0.31 -0.73 ...... Frame ( 28) shift: 0.35 -0.75 ...... Frame ( 29) shift: 0.40 -0.77 ...... Frame ( 30) shift: 0.39 -0.76 ...... Frame ( 31) shift: 0.34 -0.72 ...... Frame ( 32) shift: 0.29 -0.67 ...... Frame ( 33) shift: 0.25 -0.63 ...... Frame ( 34) shift: 0.21 -0.58 ...... Frame ( 35) shift: 0.17 -0.54 ...... Frame ( 36) shift: 0.15 -0.51 ...... Frame ( 37) shift: 0.15 -0.50 ...... Frame ( 38) shift: 0.14 -0.48 ...... Frame ( 39) shift: 0.13 -0.47 ...... Frame ( 40) shift: 0.13 -0.45 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.703319 Iteration 2 Error: 0.069017 Iteration 3 Error: 0.009678 Align patch 2 23 left Iteration 1 Error: 0.930086 Iteration 2 Error: 0.087742 Iteration 3 Error: 0.018357 Align patch 3 22 left Iteration 1 Error: 0.827724 Iteration 2 Error: 0.096010 Iteration 3 Error: 0.014784 Align patch 4 21 left Iteration 1 Error: 0.554328 Iteration 2 Error: 0.104530 Iteration 3 Error: 0.023782 Align patch 5 20 left Iteration 1 Error: 0.397094 Iteration 2 Error: 0.064656 Iteration 3 Error: 0.012145 Align patch 6 19 left Iteration 1 Error: 0.571872 Iteration 2 Error: 0.059676 Iteration 3 Error: 0.017429 Align patch 7 18 left Iteration 1 Error: 0.617764 Iteration 2 Error: 0.100457 Iteration 3 Error: 0.019028 Align patch 8 17 left Iteration 1 Error: 0.589067 Iteration 2 Error: 0.058333 Iteration 3 Error: 0.010710 Align patch 9 16 left Iteration 1 Error: 0.506349 Iteration 2 Error: 0.085656 Iteration 3 Error: 0.016833 Align patch 10 15 left Iteration 1 Error: 0.906320 Iteration 2 Error: 0.099906 Iteration 3 Error: 0.022601 Align patch 11 14 left Iteration 1 Error: 0.519409 Iteration 2 Error: 0.079980 Iteration 3 Error: 0.010813 Align patch 12 13 left Iteration 1 Error: 0.395727 Iteration 2 Error: 0.078493 Iteration 3 Error: 0.017119 Align patch 13 12 left Iteration 1 Error: 0.400206 Iteration 2 Error: 0.077553 Iteration 3 Error: 0.021813 Align patch 14 11 left Iteration 1 Error: 0.573821 Iteration 2 Error: 0.068383 Iteration 3 Error: 0.010451 Align patch 15 10 left Iteration 1 Error: 0.695232 Iteration 2 Error: 0.095929 Iteration 3 Error: 0.022554 Align patch 16 9 left Iteration 1 Error: 0.643838 Iteration 2 Error: 0.106642 Iteration 3 Error: 0.021559 Align patch 17 8 left Iteration 1 Error: 0.756519 Iteration 2 Error: 0.073135 Iteration 3 Error: 0.017380 Align patch 18 7 left Iteration 1 Error: 0.586450 Iteration 2 Error: 0.083215 Iteration 3 Error: 0.012160 Align patch 19 6 left Iteration 1 Error: 0.783865 Iteration 2 Error: 0.110724 Iteration 3 Error: 0.020821 Align patch 20 5 left Iteration 1 Error: 0.481984 Iteration 2 Error: 0.078378 Iteration 3 Error: 0.023955 Align patch 21 4 left Iteration 1 Error: 0.846003 Iteration 2 Error: 0.087011 Iteration 3 Error: 0.015667 Align patch 22 3 left Iteration 1 Error: 0.616568 Iteration 2 Error: 0.101939 Iteration 3 Error: 0.023393 Align patch 23 2 left Iteration 1 Error: 0.451723 Iteration 2 Error: 0.063494 Iteration 3 Error: 0.009356 Align patch 24 1 left Iteration 1 Error: 0.592255 Iteration 2 Error: 0.058766 Iteration 3 Error: 0.013050 Align patch 25 0 left Iteration 1 Error: 0.383458 Iteration 2 Error: 0.049240 3D Fitting completed. Patch alignment time: 14.29(sec) Local motion has been corrected. Process thread exits. Computational time: 22.675520 sec Total time: 28.855314 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00007hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00007hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.562261s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00007hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.651370s ........................................ >>>>>>TIME<<<<<< FFT: 0.957920s Defocus_U Defocus_V Angle CCC 13410.16 14316.41 7.81 0.059125 Final Values Defocus_U Defocus_V Angle CCC 13432.04 14313.29 7.49 0.086863 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00007hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00007hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 39.19 6.69 Num Hot pixels: 224 Hot pixel threshold: 79.30 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.484634 Iteration 2 Error: 0.067697 Iteration 3 Error: 0.007549 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.01 -0.20 ...... Frame ( 3) shift: -0.03 -0.39 ...... Frame ( 4) shift: -0.04 -0.59 ...... Frame ( 5) shift: -0.05 -0.78 ...... Frame ( 6) shift: -0.04 -0.92 ...... Frame ( 7) shift: -0.01 -0.99 ...... Frame ( 8) shift: 0.02 -1.07 ...... Frame ( 9) shift: 0.08 -1.08 ...... Frame ( 10) shift: 0.15 -1.03 ...... Frame ( 11) shift: 0.22 -0.98 ...... Frame ( 12) shift: 0.27 -0.90 ...... Frame ( 13) shift: 0.31 -0.80 ...... Frame ( 14) shift: 0.34 -0.70 ...... Frame ( 15) shift: 0.34 -0.64 ...... Frame ( 16) shift: 0.30 -0.61 ...... Frame ( 17) shift: 0.27 -0.59 ...... Frame ( 18) shift: 0.26 -0.59 ...... Frame ( 19) shift: 0.28 -0.63 ...... Frame ( 20) shift: 0.31 -0.67 ...... Frame ( 21) shift: 0.29 -0.68 ...... Frame ( 22) shift: 0.22 -0.68 ...... Frame ( 23) shift: 0.16 -0.67 ...... Frame ( 24) shift: 0.15 -0.64 ...... Frame ( 25) shift: 0.19 -0.59 ...... Frame ( 26) shift: 0.24 -0.54 ...... Frame ( 27) shift: 0.24 -0.50 ...... Frame ( 28) shift: 0.20 -0.47 ...... Frame ( 29) shift: 0.15 -0.43 ...... Frame ( 30) shift: 0.12 -0.40 ...... Frame ( 31) shift: 0.10 -0.38 ...... Frame ( 32) shift: 0.08 -0.36 ...... Frame ( 33) shift: 0.04 -0.35 ...... Frame ( 34) shift: -0.01 -0.36 ...... Frame ( 35) shift: -0.06 -0.37 ...... Frame ( 36) shift: -0.08 -0.38 ...... Frame ( 37) shift: -0.08 -0.39 ...... Frame ( 38) shift: -0.07 -0.40 ...... Frame ( 39) shift: -0.07 -0.42 ...... Frame ( 40) shift: -0.07 -0.43 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.695411 Iteration 2 Error: 0.086553 Iteration 3 Error: 0.014421 Align patch 2 23 left Iteration 1 Error: 1.040010 Iteration 2 Error: 0.118687 Iteration 3 Error: 0.019302 Align patch 3 22 left Iteration 1 Error: 0.610418 Iteration 2 Error: 0.080725 Iteration 3 Error: 0.018870 Align patch 4 21 left Iteration 1 Error: 0.452841 Iteration 2 Error: 0.073473 Iteration 3 Error: 0.025936 Align patch 5 20 left Iteration 1 Error: 0.672768 Iteration 2 Error: 0.071929 Iteration 3 Error: 0.019801 Align patch 6 19 left Iteration 1 Error: 0.564355 Iteration 2 Error: 0.091377 Iteration 3 Error: 0.025872 Align patch 7 18 left Iteration 1 Error: 0.614648 Iteration 2 Error: 0.063250 Iteration 3 Error: 0.013732 Align patch 8 17 left Iteration 1 Error: 0.518193 Iteration 2 Error: 0.068559 Iteration 3 Error: 0.020382 Align patch 9 16 left Iteration 1 Error: 0.478700 Iteration 2 Error: 0.063637 Iteration 3 Error: 0.016666 Align patch 10 15 left Iteration 1 Error: 0.491927 Iteration 2 Error: 0.046955 Align patch 11 14 left Iteration 1 Error: 0.671211 Iteration 2 Error: 0.155178 Iteration 3 Error: 0.044500 Align patch 12 13 left Iteration 1 Error: 0.572307 Iteration 2 Error: 0.132955 Iteration 3 Error: 0.030008 Align patch 13 12 left Iteration 1 Error: 0.667410 Iteration 2 Error: 0.100809 Iteration 3 Error: 0.025671 Align patch 14 11 left Iteration 1 Error: 0.458801 Iteration 2 Error: 0.071334 Iteration 3 Error: 0.016339 Align patch 15 10 left Iteration 1 Error: 0.905943 Iteration 2 Error: 0.112080 Iteration 3 Error: 0.035563 Align patch 16 9 left Iteration 1 Error: 0.482943 Iteration 2 Error: 0.073448 Iteration 3 Error: 0.016542 Align patch 17 8 left Iteration 1 Error: 0.492355 Iteration 2 Error: 0.049037 Align patch 18 7 left Iteration 1 Error: 0.539434 Iteration 2 Error: 0.053919 Iteration 3 Error: 0.009557 Align patch 19 6 left Iteration 1 Error: 0.719563 Iteration 2 Error: 0.064303 Iteration 3 Error: 0.014073 Align patch 20 5 left Iteration 1 Error: 0.701105 Iteration 2 Error: 0.105206 Iteration 3 Error: 0.025020 Align patch 21 4 left Iteration 1 Error: 0.838485 Iteration 2 Error: 0.158376 Iteration 3 Error: 0.045598 Align patch 22 3 left Iteration 1 Error: 0.496202 Iteration 2 Error: 0.061019 Iteration 3 Error: 0.011426 Align patch 23 2 left Iteration 1 Error: 0.680675 Iteration 2 Error: 0.092963 Iteration 3 Error: 0.013688 Align patch 24 1 left Iteration 1 Error: 0.754997 Iteration 2 Error: 0.110350 Iteration 3 Error: 0.016426 Align patch 25 0 left Iteration 1 Error: 0.591248 Iteration 2 Error: 0.066575 Iteration 3 Error: 0.014365 3D Fitting completed. Patch alignment time: 15.39(sec) Local motion has been corrected. Process thread exits. Computational time: 23.368450 sec Total time: 29.228907 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00007hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00007hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.552876s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00007hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.269220s ........................................ >>>>>>TIME<<<<<< FFT: 0.779784s Defocus_U Defocus_V Angle CCC 12068.36 11400.39 85.73 0.050180 Final Values Defocus_U Defocus_V Angle CCC 12124.61 11394.15 86.04 0.080594 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00008hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00008hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.350e-01 1.004e-01 CC threshold: 0.737 Mean Std: 39.17 6.76 Num Hot pixels: 223 Hot pixel threshold: 79.71 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.911416 Iteration 2 Error: 0.285560 Iteration 3 Error: 0.065027 Iteration 4 Error: 0.018823 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.07 0.22 ...... Frame ( 3) shift: 0.13 0.45 ...... Frame ( 4) shift: 0.20 0.67 ...... Frame ( 5) shift: 0.27 0.89 ...... Frame ( 6) shift: 0.29 1.08 ...... Frame ( 7) shift: 0.25 1.24 ...... Frame ( 8) shift: 0.22 1.39 ...... Frame ( 9) shift: 0.22 1.52 ...... Frame ( 10) shift: 0.26 1.63 ...... Frame ( 11) shift: 0.30 1.73 ...... Frame ( 12) shift: 0.36 1.84 ...... Frame ( 13) shift: 0.45 1.94 ...... Frame ( 14) shift: 0.53 2.05 ...... Frame ( 15) shift: 0.58 2.13 ...... Frame ( 16) shift: 0.59 2.18 ...... Frame ( 17) shift: 0.59 2.24 ...... Frame ( 18) shift: 0.61 2.30 ...... Frame ( 19) shift: 0.65 2.36 ...... Frame ( 20) shift: 0.69 2.43 ...... Frame ( 21) shift: 0.74 2.50 ...... Frame ( 22) shift: 0.80 2.57 ...... Frame ( 23) shift: 0.86 2.64 ...... Frame ( 24) shift: 0.90 2.71 ...... Frame ( 25) shift: 0.91 2.75 ...... Frame ( 26) shift: 0.92 2.80 ...... Frame ( 27) shift: 0.94 2.87 ...... Frame ( 28) shift: 0.97 2.97 ...... Frame ( 29) shift: 0.99 3.07 ...... Frame ( 30) shift: 1.07 3.14 ...... Frame ( 31) shift: 1.21 3.20 ...... Frame ( 32) shift: 1.34 3.25 ...... Frame ( 33) shift: 1.42 3.32 ...... Frame ( 34) shift: 1.44 3.40 ...... Frame ( 35) shift: 1.46 3.48 ...... Frame ( 36) shift: 1.50 3.54 ...... Frame ( 37) shift: 1.57 3.58 ...... Frame ( 38) shift: 1.63 3.61 ...... Frame ( 39) shift: 1.69 3.65 ...... Frame ( 40) shift: 1.75 3.69 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.564502 Iteration 2 Error: 0.123404 Iteration 3 Error: 0.031025 Align patch 2 23 left Iteration 1 Error: 0.716287 Iteration 2 Error: 0.108213 Iteration 3 Error: 0.027398 Align patch 3 22 left Iteration 1 Error: 0.699860 Iteration 2 Error: 0.101629 Iteration 3 Error: 0.022793 Align patch 4 21 left Iteration 1 Error: 0.615326 Iteration 2 Error: 0.116014 Iteration 3 Error: 0.019346 Align patch 5 20 left Iteration 1 Error: 0.608598 Iteration 2 Error: 0.074885 Iteration 3 Error: 0.014200 Align patch 6 19 left Iteration 1 Error: 0.897675 Iteration 2 Error: 0.169324 Iteration 3 Error: 0.052844 Iteration 4 Error: 0.013329 Align patch 7 18 left Iteration 1 Error: 0.520965 Iteration 2 Error: 0.059111 Iteration 3 Error: 0.013744 Align patch 8 17 left Iteration 1 Error: 0.559917 Iteration 2 Error: 0.135962 Iteration 3 Error: 0.034769 Align patch 9 16 left Iteration 1 Error: 0.366813 Iteration 2 Error: 0.045359 Align patch 10 15 left Iteration 1 Error: 0.348628 Iteration 2 Error: 0.058330 Iteration 3 Error: 0.015819 Align patch 11 14 left Iteration 1 Error: 0.696069 Iteration 2 Error: 0.096784 Iteration 3 Error: 0.029213 Align patch 12 13 left Iteration 1 Error: 0.391748 Iteration 2 Error: 0.030470 Align patch 13 12 left Iteration 1 Error: 0.672311 Iteration 2 Error: 0.087856 Iteration 3 Error: 0.022028 Align patch 14 11 left Iteration 1 Error: 0.446570 Iteration 2 Error: 0.049064 Align patch 15 10 left Iteration 1 Error: 0.455126 Iteration 2 Error: 0.042364 Align patch 16 9 left Iteration 1 Error: 0.764442 Iteration 2 Error: 0.135966 Iteration 3 Error: 0.030064 Align patch 17 8 left Iteration 1 Error: 0.614493 Iteration 2 Error: 0.064346 Iteration 3 Error: 0.018737 Align patch 18 7 left Iteration 1 Error: 0.560162 Iteration 2 Error: 0.060787 Iteration 3 Error: 0.012659 Align patch 19 6 left Iteration 1 Error: 0.636439 Iteration 2 Error: 0.065363 Iteration 3 Error: 0.014322 Align patch 20 5 left Iteration 1 Error: 0.728142 Iteration 2 Error: 0.122040 Iteration 3 Error: 0.015573 Align patch 21 4 left Iteration 1 Error: 0.751158 Iteration 2 Error: 0.145335 Iteration 3 Error: 0.030022 Align patch 22 3 left Iteration 1 Error: 0.503609 Iteration 2 Error: 0.086039 Iteration 3 Error: 0.017247 Align patch 23 2 left Iteration 1 Error: 0.565149 Iteration 2 Error: 0.075284 Iteration 3 Error: 0.019106 Align patch 24 1 left Iteration 1 Error: 0.650643 Iteration 2 Error: 0.086348 Iteration 3 Error: 0.023825 Align patch 25 0 left Iteration 1 Error: 0.583500 Iteration 2 Error: 0.069761 Iteration 3 Error: 0.013683 3D Fitting completed. Patch alignment time: 14.35(sec) Local motion has been corrected. Process thread exits. Computational time: 23.245773 sec Total time: 29.811481 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00008hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00008hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.554338s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00008hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.749276s ........................................ >>>>>>TIME<<<<<< FFT: 1.013980s Defocus_U Defocus_V Angle CCC 9048.83 9916.02 13.71 0.053385 Final Values Defocus_U Defocus_V Angle CCC 9041.00 9926.97 13.71 0.092651 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00008hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00008hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 40.15 6.81 Num Hot pixels: 227 Hot pixel threshold: 81.01 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.329270 Iteration 2 Error: 0.172604 Iteration 3 Error: 0.041128 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.05 0.18 ...... Frame ( 3) shift: 0.10 0.37 ...... Frame ( 4) shift: 0.15 0.55 ...... Frame ( 5) shift: 0.21 0.73 ...... Frame ( 6) shift: 0.24 0.84 ...... Frame ( 7) shift: 0.25 0.87 ...... Frame ( 8) shift: 0.26 0.89 ...... Frame ( 9) shift: 0.28 0.95 ...... Frame ( 10) shift: 0.30 1.02 ...... Frame ( 11) shift: 0.32 1.09 ...... Frame ( 12) shift: 0.32 1.15 ...... Frame ( 13) shift: 0.31 1.18 ...... Frame ( 14) shift: 0.30 1.22 ...... Frame ( 15) shift: 0.30 1.30 ...... Frame ( 16) shift: 0.31 1.41 ...... Frame ( 17) shift: 0.32 1.53 ...... Frame ( 18) shift: 0.35 1.60 ...... Frame ( 19) shift: 0.39 1.64 ...... Frame ( 20) shift: 0.43 1.67 ...... Frame ( 21) shift: 0.48 1.70 ...... Frame ( 22) shift: 0.54 1.74 ...... Frame ( 23) shift: 0.59 1.78 ...... Frame ( 24) shift: 0.68 1.86 ...... Frame ( 25) shift: 0.79 1.99 ...... Frame ( 26) shift: 0.90 2.11 ...... Frame ( 27) shift: 0.97 2.21 ...... Frame ( 28) shift: 1.00 2.27 ...... Frame ( 29) shift: 1.02 2.33 ...... Frame ( 30) shift: 0.97 2.36 ...... Frame ( 31) shift: 0.84 2.35 ...... Frame ( 32) shift: 0.72 2.35 ...... Frame ( 33) shift: 0.68 2.34 ...... Frame ( 34) shift: 0.72 2.32 ...... Frame ( 35) shift: 0.77 2.30 ...... Frame ( 36) shift: 0.81 2.33 ...... Frame ( 37) shift: 0.83 2.42 ...... Frame ( 38) shift: 0.86 2.51 ...... Frame ( 39) shift: 0.89 2.60 ...... Frame ( 40) shift: 0.91 2.68 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.013180 Iteration 2 Error: 0.160041 Iteration 3 Error: 0.037190 Align patch 2 23 left Iteration 1 Error: 1.042738 Iteration 2 Error: 0.151672 Iteration 3 Error: 0.033929 Align patch 3 22 left Iteration 1 Error: 0.686688 Iteration 2 Error: 0.084575 Iteration 3 Error: 0.023031 Align patch 4 21 left Iteration 1 Error: 0.509950 Iteration 2 Error: 0.120963 Iteration 3 Error: 0.019444 Align patch 5 20 left Iteration 1 Error: 0.460046 Iteration 2 Error: 0.097709 Iteration 3 Error: 0.017512 Align patch 6 19 left Iteration 1 Error: 0.885729 Iteration 2 Error: 0.143337 Iteration 3 Error: 0.037257 Align patch 7 18 left Iteration 1 Error: 0.765257 Iteration 2 Error: 0.179575 Iteration 3 Error: 0.023732 Align patch 8 17 left Iteration 1 Error: 0.736430 Iteration 2 Error: 0.069441 Iteration 3 Error: 0.014916 Align patch 9 16 left Iteration 1 Error: 0.651041 Iteration 2 Error: 0.101135 Iteration 3 Error: 0.027878 Align patch 10 15 left Iteration 1 Error: 0.955541 Iteration 2 Error: 0.145576 Iteration 3 Error: 0.032032 Align patch 11 14 left Iteration 1 Error: 0.599172 Iteration 2 Error: 0.101743 Iteration 3 Error: 0.021503 Align patch 12 13 left Iteration 1 Error: 0.470263 Iteration 2 Error: 0.042739 Align patch 13 12 left Iteration 1 Error: 0.662547 Iteration 2 Error: 0.153617 Iteration 3 Error: 0.038620 Align patch 14 11 left Iteration 1 Error: 0.502404 Iteration 2 Error: 0.104814 Iteration 3 Error: 0.025323 Align patch 15 10 left Iteration 1 Error: 0.729134 Iteration 2 Error: 0.120333 Iteration 3 Error: 0.019412 Align patch 16 9 left Iteration 1 Error: 0.446903 Iteration 2 Error: 0.051725 Iteration 3 Error: 0.013796 Align patch 17 8 left Iteration 1 Error: 0.492969 Iteration 2 Error: 0.071472 Iteration 3 Error: 0.010701 Align patch 18 7 left Iteration 1 Error: 0.665582 Iteration 2 Error: 0.118950 Iteration 3 Error: 0.027394 Align patch 19 6 left Iteration 1 Error: 0.709401 Iteration 2 Error: 0.124553 Iteration 3 Error: 0.023000 Align patch 20 5 left Iteration 1 Error: 0.631080 Iteration 2 Error: 0.140082 Iteration 3 Error: 0.021299 Align patch 21 4 left Iteration 1 Error: 0.599228 Iteration 2 Error: 0.115829 Iteration 3 Error: 0.024196 Align patch 22 3 left Iteration 1 Error: 0.538958 Iteration 2 Error: 0.062415 Iteration 3 Error: 0.012563 Align patch 23 2 left Iteration 1 Error: 0.796748 Iteration 2 Error: 0.072186 Iteration 3 Error: 0.010834 Align patch 24 1 left Iteration 1 Error: 0.829644 Iteration 2 Error: 0.101469 Iteration 3 Error: 0.019124 Align patch 25 0 left Iteration 1 Error: 0.697014 Iteration 2 Error: 0.132375 Iteration 3 Error: 0.031824 3D Fitting completed. Patch alignment time: 14.20(sec) Local motion has been corrected. Process thread exits. Computational time: 22.497223 sec Total time: 29.622084 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00008hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00008hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.571052s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00008hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.083313s ........................................ >>>>>>TIME<<<<<< FFT: 0.912959s Defocus_U Defocus_V Angle CCC 11007.16 11504.59 0.91 0.060924 Final Values Defocus_U Defocus_V Angle CCC 11052.48 11521.80 0.61 0.099447 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00008hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00008hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 40.26 6.85 Num Hot pixels: 236 Hot pixel threshold: 81.34 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.598349 Iteration 2 Error: 0.079647 Iteration 3 Error: 0.016775 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.01 -0.09 ...... Frame ( 3) shift: -0.01 -0.18 ...... Frame ( 4) shift: -0.02 -0.27 ...... Frame ( 5) shift: -0.03 -0.36 ...... Frame ( 6) shift: -0.02 -0.38 ...... Frame ( 7) shift: -0.01 -0.33 ...... Frame ( 8) shift: 0.00 -0.28 ...... Frame ( 9) shift: 0.01 -0.27 ...... Frame ( 10) shift: 0.00 -0.30 ...... Frame ( 11) shift: -0.00 -0.34 ...... Frame ( 12) shift: 0.02 -0.34 ...... Frame ( 13) shift: 0.07 -0.31 ...... Frame ( 14) shift: 0.11 -0.29 ...... Frame ( 15) shift: 0.16 -0.25 ...... Frame ( 16) shift: 0.19 -0.21 ...... Frame ( 17) shift: 0.23 -0.18 ...... Frame ( 18) shift: 0.27 -0.14 ...... Frame ( 19) shift: 0.32 -0.12 ...... Frame ( 20) shift: 0.36 -0.10 ...... Frame ( 21) shift: 0.37 -0.06 ...... Frame ( 22) shift: 0.35 -0.02 ...... Frame ( 23) shift: 0.33 0.02 ...... Frame ( 24) shift: 0.33 0.08 ...... Frame ( 25) shift: 0.35 0.17 ...... Frame ( 26) shift: 0.37 0.26 ...... Frame ( 27) shift: 0.41 0.29 ...... Frame ( 28) shift: 0.46 0.27 ...... Frame ( 29) shift: 0.51 0.24 ...... Frame ( 30) shift: 0.52 0.27 ...... Frame ( 31) shift: 0.48 0.34 ...... Frame ( 32) shift: 0.45 0.41 ...... Frame ( 33) shift: 0.45 0.44 ...... Frame ( 34) shift: 0.48 0.42 ...... Frame ( 35) shift: 0.51 0.40 ...... Frame ( 36) shift: 0.54 0.42 ...... Frame ( 37) shift: 0.55 0.47 ...... Frame ( 38) shift: 0.56 0.53 ...... Frame ( 39) shift: 0.58 0.59 ...... Frame ( 40) shift: 0.59 0.64 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.248569 Iteration 2 Error: 0.104352 Iteration 3 Error: 0.026940 Align patch 2 23 left Iteration 1 Error: 0.568062 Iteration 2 Error: 0.132440 Iteration 3 Error: 0.025493 Align patch 3 22 left Iteration 1 Error: 0.460040 Iteration 2 Error: 0.088917 Iteration 3 Error: 0.017740 Align patch 4 21 left Iteration 1 Error: 0.559787 Iteration 2 Error: 0.055746 Iteration 3 Error: 0.020379 Align patch 5 20 left Iteration 1 Error: 0.549930 Iteration 2 Error: 0.124760 Iteration 3 Error: 0.031115 Align patch 6 19 left Iteration 1 Error: 0.854235 Iteration 2 Error: 0.132411 Iteration 3 Error: 0.030354 Align patch 7 18 left Iteration 1 Error: 0.430031 Iteration 2 Error: 0.096911 Iteration 3 Error: 0.015380 Align patch 8 17 left Iteration 1 Error: 0.548061 Iteration 2 Error: 0.041641 Align patch 9 16 left Iteration 1 Error: 0.429645 Iteration 2 Error: 0.043898 Align patch 10 15 left Iteration 1 Error: 0.448528 Iteration 2 Error: 0.057626 Iteration 3 Error: 0.010275 Align patch 11 14 left Iteration 1 Error: 0.854499 Iteration 2 Error: 0.089064 Iteration 3 Error: 0.016985 Align patch 12 13 left Iteration 1 Error: 0.598273 Iteration 2 Error: 0.105437 Iteration 3 Error: 0.019111 Align patch 13 12 left Iteration 1 Error: 0.399744 Iteration 2 Error: 0.073679 Iteration 3 Error: 0.013209 Align patch 14 11 left Iteration 1 Error: 0.835064 Iteration 2 Error: 0.093503 Iteration 3 Error: 0.013868 Align patch 15 10 left Iteration 1 Error: 1.049277 Iteration 2 Error: 0.141198 Iteration 3 Error: 0.022942 Align patch 16 9 left Iteration 1 Error: 0.674709 Iteration 2 Error: 0.131761 Iteration 3 Error: 0.030900 Align patch 17 8 left Iteration 1 Error: 0.590667 Iteration 2 Error: 0.133274 Iteration 3 Error: 0.018868 Align patch 18 7 left Iteration 1 Error: 0.658822 Iteration 2 Error: 0.098864 Iteration 3 Error: 0.027651 Align patch 19 6 left Iteration 1 Error: 0.671690 Iteration 2 Error: 0.108993 Iteration 3 Error: 0.011872 Align patch 20 5 left Iteration 1 Error: 0.594223 Iteration 2 Error: 0.092527 Iteration 3 Error: 0.017059 Align patch 21 4 left Iteration 1 Error: 1.179922 Iteration 2 Error: 0.136993 Iteration 3 Error: 0.020382 Align patch 22 3 left Iteration 1 Error: 0.637391 Iteration 2 Error: 0.065749 Iteration 3 Error: 0.009399 Align patch 23 2 left Iteration 1 Error: 0.577832 Iteration 2 Error: 0.051288 Iteration 3 Error: 0.008403 Align patch 24 1 left Iteration 1 Error: 0.785546 Iteration 2 Error: 0.092089 Iteration 3 Error: 0.024451 Align patch 25 0 left Iteration 1 Error: 0.572322 Iteration 2 Error: 0.079231 Iteration 3 Error: 0.017371 3D Fitting completed. Patch alignment time: 15.17(sec) Local motion has been corrected. Process thread exits. Computational time: 24.120674 sec Total time: 30.486605 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00008hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00008hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.750034s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00008hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.601725s ........................................ >>>>>>TIME<<<<<< FFT: 1.354272s Defocus_U Defocus_V Angle CCC 13998.05 14904.30 4.75 0.061069 Final Values Defocus_U Defocus_V Angle CCC 13991.79 14926.19 4.75 0.095836 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00008hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00008hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.350e-01 1.004e-01 CC threshold: 0.737 Mean Std: 40.27 6.82 Num Hot pixels: 230 Hot pixel threshold: 81.21 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.894472 Iteration 2 Error: 0.069916 Iteration 3 Error: 0.016730 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.03 0.15 ...... Frame ( 3) shift: 0.05 0.30 ...... Frame ( 4) shift: 0.08 0.45 ...... Frame ( 5) shift: 0.11 0.60 ...... Frame ( 6) shift: 0.14 0.73 ...... Frame ( 7) shift: 0.19 0.83 ...... Frame ( 8) shift: 0.24 0.94 ...... Frame ( 9) shift: 0.28 0.98 ...... Frame ( 10) shift: 0.31 0.95 ...... Frame ( 11) shift: 0.35 0.92 ...... Frame ( 12) shift: 0.39 0.92 ...... Frame ( 13) shift: 0.44 0.95 ...... Frame ( 14) shift: 0.49 0.97 ...... Frame ( 15) shift: 0.50 1.02 ...... Frame ( 16) shift: 0.48 1.08 ...... Frame ( 17) shift: 0.46 1.14 ...... Frame ( 18) shift: 0.46 1.17 ...... Frame ( 19) shift: 0.50 1.17 ...... Frame ( 20) shift: 0.53 1.17 ...... Frame ( 21) shift: 0.56 1.16 ...... Frame ( 22) shift: 0.58 1.16 ...... Frame ( 23) shift: 0.60 1.15 ...... Frame ( 24) shift: 0.61 1.16 ...... Frame ( 25) shift: 0.60 1.19 ...... Frame ( 26) shift: 0.60 1.22 ...... Frame ( 27) shift: 0.59 1.24 ...... Frame ( 28) shift: 0.58 1.25 ...... Frame ( 29) shift: 0.58 1.26 ...... Frame ( 30) shift: 0.57 1.29 ...... Frame ( 31) shift: 0.56 1.32 ...... Frame ( 32) shift: 0.54 1.36 ...... Frame ( 33) shift: 0.55 1.36 ...... Frame ( 34) shift: 0.56 1.34 ...... Frame ( 35) shift: 0.58 1.32 ...... Frame ( 36) shift: 0.58 1.33 ...... Frame ( 37) shift: 0.56 1.38 ...... Frame ( 38) shift: 0.55 1.42 ...... Frame ( 39) shift: 0.53 1.47 ...... Frame ( 40) shift: 0.51 1.51 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.590418 Iteration 2 Error: 0.091567 Iteration 3 Error: 0.011563 Align patch 2 23 left Iteration 1 Error: 0.681709 Iteration 2 Error: 0.068218 Iteration 3 Error: 0.013750 Align patch 3 22 left Iteration 1 Error: 0.574427 Iteration 2 Error: 0.089433 Iteration 3 Error: 0.022926 Align patch 4 21 left Iteration 1 Error: 0.532334 Iteration 2 Error: 0.066263 Iteration 3 Error: 0.015589 Align patch 5 20 left Iteration 1 Error: 0.404221 Iteration 2 Error: 0.076641 Iteration 3 Error: 0.023167 Align patch 6 19 left Iteration 1 Error: 0.491005 Iteration 2 Error: 0.082974 Iteration 3 Error: 0.016745 Align patch 7 18 left Iteration 1 Error: 0.426541 Iteration 2 Error: 0.044944 Align patch 8 17 left Iteration 1 Error: 0.570655 Iteration 2 Error: 0.097665 Iteration 3 Error: 0.018845 Align patch 9 16 left Iteration 1 Error: 0.687427 Iteration 2 Error: 0.113965 Iteration 3 Error: 0.019600 Align patch 10 15 left Iteration 1 Error: 0.687949 Iteration 2 Error: 0.080358 Iteration 3 Error: 0.020481 Align patch 11 14 left Iteration 1 Error: 0.483688 Iteration 2 Error: 0.088211 Iteration 3 Error: 0.012274 Align patch 12 13 left Iteration 1 Error: 0.402283 Iteration 2 Error: 0.062327 Iteration 3 Error: 0.011516 Align patch 13 12 left Iteration 1 Error: 0.450549 Iteration 2 Error: 0.053451 Iteration 3 Error: 0.014136 Align patch 14 11 left Iteration 1 Error: 0.573597 Iteration 2 Error: 0.089789 Iteration 3 Error: 0.018860 Align patch 15 10 left Iteration 1 Error: 0.635378 Iteration 2 Error: 0.069943 Iteration 3 Error: 0.020026 Align patch 16 9 left Iteration 1 Error: 0.466735 Iteration 2 Error: 0.063676 Iteration 3 Error: 0.012912 Align patch 17 8 left Iteration 1 Error: 0.668319 Iteration 2 Error: 0.070664 Iteration 3 Error: 0.013979 Align patch 18 7 left Iteration 1 Error: 0.767994 Iteration 2 Error: 0.094466 Iteration 3 Error: 0.020496 Align patch 19 6 left Iteration 1 Error: 0.826058 Iteration 2 Error: 0.115223 Iteration 3 Error: 0.024632 Align patch 20 5 left Iteration 1 Error: 0.999699 Iteration 2 Error: 0.131124 Iteration 3 Error: 0.027828 Align patch 21 4 left Iteration 1 Error: 0.452307 Iteration 2 Error: 0.059724 Iteration 3 Error: 0.011175 Align patch 22 3 left Iteration 1 Error: 0.597697 Iteration 2 Error: 0.047809 Align patch 23 2 left Iteration 1 Error: 0.815653 Iteration 2 Error: 0.090808 Iteration 3 Error: 0.018385 Align patch 24 1 left Iteration 1 Error: 0.707647 Iteration 2 Error: 0.074321 Iteration 3 Error: 0.018137 Align patch 25 0 left Iteration 1 Error: 0.499905 Iteration 2 Error: 0.076564 Iteration 3 Error: 0.013727 3D Fitting completed. Patch alignment time: 15.38(sec) Local motion has been corrected. Process thread exits. Computational time: 24.009092 sec Total time: 29.725266 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00008hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00008hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.837305s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00008hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.517081s ........................................ >>>>>>TIME<<<<<< FFT: 1.017753s Defocus_U Defocus_V Angle CCC 11595.71 11005.86 84.97 0.054405 Final Values Defocus_U Defocus_V Angle CCC 11614.45 11055.88 85.29 0.089130 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00009hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00009hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 39.72 6.79 Num Hot pixels: 237 Hot pixel threshold: 80.45 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.038561 Iteration 2 Error: 0.220866 Iteration 3 Error: 0.072259 Iteration 4 Error: 0.022941 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.05 0.05 ...... Frame ( 3) shift: 0.09 0.09 ...... Frame ( 4) shift: 0.14 0.14 ...... Frame ( 5) shift: 0.18 0.18 ...... Frame ( 6) shift: 0.18 0.22 ...... Frame ( 7) shift: 0.13 0.25 ...... Frame ( 8) shift: 0.09 0.29 ...... Frame ( 9) shift: 0.11 0.32 ...... Frame ( 10) shift: 0.19 0.36 ...... Frame ( 11) shift: 0.28 0.39 ...... Frame ( 12) shift: 0.39 0.44 ...... Frame ( 13) shift: 0.53 0.51 ...... Frame ( 14) shift: 0.67 0.58 ...... Frame ( 15) shift: 0.76 0.64 ...... Frame ( 16) shift: 0.80 0.70 ...... Frame ( 17) shift: 0.84 0.76 ...... Frame ( 18) shift: 0.85 0.83 ...... Frame ( 19) shift: 0.82 0.92 ...... Frame ( 20) shift: 0.79 1.02 ...... Frame ( 21) shift: 0.82 1.09 ...... Frame ( 22) shift: 0.90 1.16 ...... Frame ( 23) shift: 0.98 1.22 ...... Frame ( 24) shift: 1.04 1.27 ...... Frame ( 25) shift: 1.07 1.31 ...... Frame ( 26) shift: 1.11 1.35 ...... Frame ( 27) shift: 1.16 1.39 ...... Frame ( 28) shift: 1.21 1.43 ...... Frame ( 29) shift: 1.27 1.47 ...... Frame ( 30) shift: 1.34 1.52 ...... Frame ( 31) shift: 1.43 1.57 ...... Frame ( 32) shift: 1.52 1.63 ...... Frame ( 33) shift: 1.59 1.69 ...... Frame ( 34) shift: 1.64 1.74 ...... Frame ( 35) shift: 1.69 1.80 ...... Frame ( 36) shift: 1.72 1.84 ...... Frame ( 37) shift: 1.72 1.88 ...... Frame ( 38) shift: 1.73 1.91 ...... Frame ( 39) shift: 1.73 1.95 ...... Frame ( 40) shift: 1.74 1.99 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.127520 Iteration 2 Error: 0.218265 Iteration 3 Error: 0.064787 Iteration 4 Error: 0.023437 Align patch 2 23 left Iteration 1 Error: 0.403934 Iteration 2 Error: 0.078110 Iteration 3 Error: 0.021997 Align patch 3 22 left Iteration 1 Error: 0.580464 Iteration 2 Error: 0.087376 Iteration 3 Error: 0.011330 Align patch 4 21 left Iteration 1 Error: 0.862469 Iteration 2 Error: 0.197495 Iteration 3 Error: 0.041103 Align patch 5 20 left Iteration 1 Error: 0.514106 Iteration 2 Error: 0.093856 Iteration 3 Error: 0.014829 Align patch 6 19 left Iteration 1 Error: 0.859168 Iteration 2 Error: 0.170057 Iteration 3 Error: 0.053427 Iteration 4 Error: 0.013817 Align patch 7 18 left Iteration 1 Error: 0.667317 Iteration 2 Error: 0.208999 Iteration 3 Error: 0.035609 Align patch 8 17 left Iteration 1 Error: 0.549689 Iteration 2 Error: 0.094187 Iteration 3 Error: 0.018809 Align patch 9 16 left Iteration 1 Error: 0.842397 Iteration 2 Error: 0.246380 Iteration 3 Error: 0.102678 Iteration 4 Error: 0.034958 Align patch 10 15 left Iteration 1 Error: 0.544443 Iteration 2 Error: 0.109123 Iteration 3 Error: 0.024425 Align patch 11 14 left Iteration 1 Error: 0.557526 Iteration 2 Error: 0.109683 Iteration 3 Error: 0.016917 Align patch 12 13 left Iteration 1 Error: 0.698292 Iteration 2 Error: 0.147991 Iteration 3 Error: 0.032327 Align patch 13 12 left Iteration 1 Error: 0.662911 Iteration 2 Error: 0.098128 Iteration 3 Error: 0.030342 Align patch 14 11 left Iteration 1 Error: 0.779930 Iteration 2 Error: 0.162583 Iteration 3 Error: 0.045370 Align patch 15 10 left Iteration 1 Error: 0.796066 Iteration 2 Error: 0.115233 Iteration 3 Error: 0.030243 Align patch 16 9 left Iteration 1 Error: 1.102803 Iteration 2 Error: 0.168084 Iteration 3 Error: 0.024437 Align patch 17 8 left Iteration 1 Error: 0.663303 Iteration 2 Error: 0.078384 Iteration 3 Error: 0.017558 Align patch 18 7 left Iteration 1 Error: 0.783633 Iteration 2 Error: 0.065861 Iteration 3 Error: 0.014646 Align patch 19 6 left Iteration 1 Error: 0.631784 Iteration 2 Error: 0.077741 Iteration 3 Error: 0.018427 Align patch 20 5 left Iteration 1 Error: 0.478590 Iteration 2 Error: 0.088785 Iteration 3 Error: 0.014426 Align patch 21 4 left Iteration 1 Error: 0.577032 Iteration 2 Error: 0.087299 Iteration 3 Error: 0.025694 Align patch 22 3 left Iteration 1 Error: 0.785088 Iteration 2 Error: 0.099386 Iteration 3 Error: 0.022670 Align patch 23 2 left Iteration 1 Error: 0.660685 Iteration 2 Error: 0.086158 Iteration 3 Error: 0.014932 Align patch 24 1 left Iteration 1 Error: 0.606963 Iteration 2 Error: 0.115953 Iteration 3 Error: 0.032774 Align patch 25 0 left Iteration 1 Error: 0.603680 Iteration 2 Error: 0.070865 Iteration 3 Error: 0.018459 3D Fitting completed. Patch alignment time: 15.53(sec) Local motion has been corrected. Process thread exits. Computational time: 24.741823 sec Total time: 31.017475 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00009hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00009hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.810408s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00009hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.467093s ........................................ >>>>>>TIME<<<<<< FFT: 1.136855s Defocus_U Defocus_V Angle CCC 11900.37 12826.21 14.19 0.054544 Final Values Defocus_U Defocus_V Angle CCC 11917.56 12834.03 14.81 0.086863 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00009hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00009hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 40.25 6.81 Num Hot pixels: 235 Hot pixel threshold: 81.13 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.544051 Iteration 2 Error: 0.331500 Iteration 3 Error: 0.066911 Iteration 4 Error: 0.019606 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.08 0.02 ...... Frame ( 3) shift: 0.16 0.04 ...... Frame ( 4) shift: 0.24 0.06 ...... Frame ( 5) shift: 0.32 0.08 ...... Frame ( 6) shift: 0.40 0.14 ...... Frame ( 7) shift: 0.48 0.24 ...... Frame ( 8) shift: 0.56 0.33 ...... Frame ( 9) shift: 0.63 0.41 ...... Frame ( 10) shift: 0.68 0.48 ...... Frame ( 11) shift: 0.74 0.55 ...... Frame ( 12) shift: 0.80 0.60 ...... Frame ( 13) shift: 0.85 0.65 ...... Frame ( 14) shift: 0.90 0.69 ...... Frame ( 15) shift: 0.98 0.75 ...... Frame ( 16) shift: 1.09 0.81 ...... Frame ( 17) shift: 1.21 0.87 ...... Frame ( 18) shift: 1.27 0.91 ...... Frame ( 19) shift: 1.29 0.92 ...... Frame ( 20) shift: 1.30 0.94 ...... Frame ( 21) shift: 1.35 0.97 ...... Frame ( 22) shift: 1.44 1.04 ...... Frame ( 23) shift: 1.53 1.11 ...... Frame ( 24) shift: 1.59 1.14 ...... Frame ( 25) shift: 1.62 1.15 ...... Frame ( 26) shift: 1.65 1.15 ...... Frame ( 27) shift: 1.72 1.20 ...... Frame ( 28) shift: 1.83 1.30 ...... Frame ( 29) shift: 1.94 1.40 ...... Frame ( 30) shift: 2.04 1.48 ...... Frame ( 31) shift: 2.14 1.56 ...... Frame ( 32) shift: 2.24 1.64 ...... Frame ( 33) shift: 2.31 1.68 ...... Frame ( 34) shift: 2.33 1.68 ...... Frame ( 35) shift: 2.35 1.69 ...... Frame ( 36) shift: 2.40 1.74 ...... Frame ( 37) shift: 2.46 1.83 ...... Frame ( 38) shift: 2.53 1.92 ...... Frame ( 39) shift: 2.59 2.01 ...... Frame ( 40) shift: 2.66 2.10 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.075748 Iteration 2 Error: 0.153402 Iteration 3 Error: 0.050945 Iteration 4 Error: 0.023066 Align patch 2 23 left Iteration 1 Error: 1.074263 Iteration 2 Error: 0.122233 Iteration 3 Error: 0.040634 Align patch 3 22 left Iteration 1 Error: 0.727291 Iteration 2 Error: 0.085790 Iteration 3 Error: 0.018634 Align patch 4 21 left Iteration 1 Error: 0.757624 Iteration 2 Error: 0.090349 Iteration 3 Error: 0.021941 Align patch 5 20 left Iteration 1 Error: 0.617266 Iteration 2 Error: 0.113590 Iteration 3 Error: 0.022298 Align patch 6 19 left Iteration 1 Error: 0.538435 Iteration 2 Error: 0.138803 Iteration 3 Error: 0.055551 Iteration 4 Error: 0.018462 Align patch 7 18 left Iteration 1 Error: 0.578189 Iteration 2 Error: 0.204876 Iteration 3 Error: 0.041599 Align patch 8 17 left Iteration 1 Error: 0.522794 Iteration 2 Error: 0.072604 Iteration 3 Error: 0.016150 Align patch 9 16 left Iteration 1 Error: 0.570618 Iteration 2 Error: 0.088333 Iteration 3 Error: 0.033215 Align patch 10 15 left Iteration 1 Error: 0.536942 Iteration 2 Error: 0.056426 Iteration 3 Error: 0.017212 Align patch 11 14 left Iteration 1 Error: 0.590242 Iteration 2 Error: 0.125065 Iteration 3 Error: 0.038851 Align patch 12 13 left Iteration 1 Error: 0.456279 Iteration 2 Error: 0.077093 Iteration 3 Error: 0.015074 Align patch 13 12 left Iteration 1 Error: 0.651327 Iteration 2 Error: 0.192335 Iteration 3 Error: 0.053512 Iteration 4 Error: 0.014367 Align patch 14 11 left Iteration 1 Error: 0.495739 Iteration 2 Error: 0.110842 Iteration 3 Error: 0.022143 Align patch 15 10 left Iteration 1 Error: 0.398920 Iteration 2 Error: 0.042542 Align patch 16 9 left Iteration 1 Error: 0.643797 Iteration 2 Error: 0.067159 Iteration 3 Error: 0.011879 Align patch 17 8 left Iteration 1 Error: 0.687786 Iteration 2 Error: 0.128127 Iteration 3 Error: 0.026252 Align patch 18 7 left Iteration 1 Error: 0.479719 Iteration 2 Error: 0.063956 Iteration 3 Error: 0.019096 Align patch 19 6 left Iteration 1 Error: 0.593749 Iteration 2 Error: 0.086039 Iteration 3 Error: 0.018905 Align patch 20 5 left Iteration 1 Error: 0.604454 Iteration 2 Error: 0.084565 Iteration 3 Error: 0.015848 Align patch 21 4 left Iteration 1 Error: 1.249318 Iteration 2 Error: 0.131294 Iteration 3 Error: 0.026646 Align patch 22 3 left Iteration 1 Error: 0.711995 Iteration 2 Error: 0.117571 Iteration 3 Error: 0.038883 Align patch 23 2 left Iteration 1 Error: 0.555309 Iteration 2 Error: 0.089400 Iteration 3 Error: 0.027723 Align patch 24 1 left Iteration 1 Error: 0.470048 Iteration 2 Error: 0.060519 Iteration 3 Error: 0.011986 Align patch 25 0 left Iteration 1 Error: 0.397387 Iteration 2 Error: 0.074533 Iteration 3 Error: 0.011461 3D Fitting completed. Patch alignment time: 15.58(sec) Local motion has been corrected. Process thread exits. Computational time: 24.335880 sec Total time: 29.962841 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00009hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00009hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.772770s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00009hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.428887s ........................................ >>>>>>TIME<<<<<< FFT: 1.028418s Defocus_U Defocus_V Angle CCC 9041.02 9494.14 3.09 0.044361 Final Values Defocus_U Defocus_V Angle CCC 9042.57 9505.08 3.09 0.084996 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00009hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00009hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.002e-01 CC threshold: 0.736 Mean Std: 39.79 6.77 Num Hot pixels: 230 Hot pixel threshold: 80.41 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.288144 Iteration 2 Error: 0.192402 Iteration 3 Error: 0.039955 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.01 0.25 ...... Frame ( 3) shift: 0.03 0.49 ...... Frame ( 4) shift: 0.04 0.74 ...... Frame ( 5) shift: 0.05 0.99 ...... Frame ( 6) shift: 0.09 1.16 ...... Frame ( 7) shift: 0.17 1.24 ...... Frame ( 8) shift: 0.24 1.33 ...... Frame ( 9) shift: 0.30 1.36 ...... Frame ( 10) shift: 0.35 1.33 ...... Frame ( 11) shift: 0.39 1.31 ...... Frame ( 12) shift: 0.43 1.30 ...... Frame ( 13) shift: 0.47 1.32 ...... Frame ( 14) shift: 0.51 1.34 ...... Frame ( 15) shift: 0.56 1.37 ...... Frame ( 16) shift: 0.61 1.40 ...... Frame ( 17) shift: 0.65 1.44 ...... Frame ( 18) shift: 0.71 1.47 ...... Frame ( 19) shift: 0.77 1.50 ...... Frame ( 20) shift: 0.83 1.54 ...... Frame ( 21) shift: 0.85 1.57 ...... Frame ( 22) shift: 0.83 1.61 ...... Frame ( 23) shift: 0.80 1.64 ...... Frame ( 24) shift: 0.83 1.69 ...... Frame ( 25) shift: 0.93 1.75 ...... Frame ( 26) shift: 1.02 1.81 ...... Frame ( 27) shift: 1.09 1.84 ...... Frame ( 28) shift: 1.14 1.85 ...... Frame ( 29) shift: 1.18 1.86 ...... Frame ( 30) shift: 1.26 1.87 ...... Frame ( 31) shift: 1.36 1.89 ...... Frame ( 32) shift: 1.46 1.91 ...... Frame ( 33) shift: 1.50 1.96 ...... Frame ( 34) shift: 1.48 2.04 ...... Frame ( 35) shift: 1.46 2.13 ...... Frame ( 36) shift: 1.47 2.15 ...... Frame ( 37) shift: 1.52 2.13 ...... Frame ( 38) shift: 1.56 2.10 ...... Frame ( 39) shift: 1.60 2.07 ...... Frame ( 40) shift: 1.64 2.05 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.887166 Iteration 2 Error: 0.279380 Iteration 3 Error: 0.076581 Iteration 4 Error: 0.020547 Align patch 2 23 left Iteration 1 Error: 1.276920 Iteration 2 Error: 0.161967 Iteration 3 Error: 0.059794 Iteration 4 Error: 0.016511 Align patch 3 22 left Iteration 1 Error: 0.747368 Iteration 2 Error: 0.066345 Iteration 3 Error: 0.016021 Align patch 4 21 left Iteration 1 Error: 0.522001 Iteration 2 Error: 0.068645 Iteration 3 Error: 0.021331 Align patch 5 20 left Iteration 1 Error: 0.528938 Iteration 2 Error: 0.141679 Iteration 3 Error: 0.037504 Align patch 6 19 left Iteration 1 Error: 0.924274 Iteration 2 Error: 0.196347 Iteration 3 Error: 0.066266 Iteration 4 Error: 0.018905 Align patch 7 18 left Iteration 1 Error: 0.655583 Iteration 2 Error: 0.167822 Iteration 3 Error: 0.030104 Align patch 8 17 left Iteration 1 Error: 0.493090 Iteration 2 Error: 0.053190 Iteration 3 Error: 0.009877 Align patch 9 16 left Iteration 1 Error: 1.179111 Iteration 2 Error: 0.162332 Iteration 3 Error: 0.029301 Align patch 10 15 left Iteration 1 Error: 1.012210 Iteration 2 Error: 0.140694 Iteration 3 Error: 0.032280 Align patch 11 14 left Iteration 1 Error: 0.653671 Iteration 2 Error: 0.154380 Iteration 3 Error: 0.042195 Align patch 12 13 left Iteration 1 Error: 0.464631 Iteration 2 Error: 0.074829 Iteration 3 Error: 0.024762 Align patch 13 12 left Iteration 1 Error: 0.662612 Iteration 2 Error: 0.159140 Iteration 3 Error: 0.060316 Iteration 4 Error: 0.024831 Align patch 14 11 left Iteration 1 Error: 0.664226 Iteration 2 Error: 0.139752 Iteration 3 Error: 0.038006 Align patch 15 10 left Iteration 1 Error: 0.908803 Iteration 2 Error: 0.142889 Iteration 3 Error: 0.029392 Align patch 16 9 left Iteration 1 Error: 0.625132 Iteration 2 Error: 0.101457 Iteration 3 Error: 0.036411 Align patch 17 8 left Iteration 1 Error: 0.703479 Iteration 2 Error: 0.130559 Iteration 3 Error: 0.025519 Align patch 18 7 left Iteration 1 Error: 1.005606 Iteration 2 Error: 0.118914 Iteration 3 Error: 0.019321 Align patch 19 6 left Iteration 1 Error: 0.770308 Iteration 2 Error: 0.157013 Iteration 3 Error: 0.044569 Align patch 20 5 left Iteration 1 Error: 0.767670 Iteration 2 Error: 0.118546 Iteration 3 Error: 0.032201 Align patch 21 4 left Iteration 1 Error: 0.668409 Iteration 2 Error: 0.111826 Iteration 3 Error: 0.018309 Align patch 22 3 left Iteration 1 Error: 0.812872 Iteration 2 Error: 0.117771 Iteration 3 Error: 0.029514 Align patch 23 2 left Iteration 1 Error: 0.896717 Iteration 2 Error: 0.127128 Iteration 3 Error: 0.023360 Align patch 24 1 left Iteration 1 Error: 1.086095 Iteration 2 Error: 0.254546 Iteration 3 Error: 0.044517 Align patch 25 0 left Iteration 1 Error: 1.159525 Iteration 2 Error: 0.123164 Iteration 3 Error: 0.019119 3D Fitting completed. Patch alignment time: 15.73(sec) Local motion has been corrected. Process thread exits. Computational time: 24.451075 sec Total time: 31.993073 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00009hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00009hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.776263s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00009hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.755470s ........................................ >>>>>>TIME<<<<<< FFT: 1.049381s Defocus_U Defocus_V Angle CCC 13230.46 14050.81 5.43 0.058178 Final Values Defocus_U Defocus_V Angle CCC 13266.40 14046.22 6.05 0.090405 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00009hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00009hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.003e-01 CC threshold: 0.736 Mean Std: 40.58 6.86 Num Hot pixels: 230 Hot pixel threshold: 81.75 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.752901 Iteration 2 Error: 0.136894 Iteration 3 Error: 0.025252 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.02 0.03 ...... Frame ( 3) shift: -0.03 0.06 ...... Frame ( 4) shift: -0.05 0.09 ...... Frame ( 5) shift: -0.07 0.12 ...... Frame ( 6) shift: -0.06 0.14 ...... Frame ( 7) shift: -0.01 0.15 ...... Frame ( 8) shift: 0.03 0.16 ...... Frame ( 9) shift: 0.07 0.19 ...... Frame ( 10) shift: 0.11 0.26 ...... Frame ( 11) shift: 0.15 0.33 ...... Frame ( 12) shift: 0.22 0.41 ...... Frame ( 13) shift: 0.32 0.50 ...... Frame ( 14) shift: 0.42 0.59 ...... Frame ( 15) shift: 0.47 0.66 ...... Frame ( 16) shift: 0.46 0.71 ...... Frame ( 17) shift: 0.45 0.76 ...... Frame ( 18) shift: 0.45 0.82 ...... Frame ( 19) shift: 0.44 0.90 ...... Frame ( 20) shift: 0.43 0.98 ...... Frame ( 21) shift: 0.48 1.01 ...... Frame ( 22) shift: 0.57 1.01 ...... Frame ( 23) shift: 0.66 1.00 ...... Frame ( 24) shift: 0.72 0.99 ...... Frame ( 25) shift: 0.73 0.98 ...... Frame ( 26) shift: 0.75 0.96 ...... Frame ( 27) shift: 0.76 1.01 ...... Frame ( 28) shift: 0.78 1.11 ...... Frame ( 29) shift: 0.79 1.21 ...... Frame ( 30) shift: 0.80 1.25 ...... Frame ( 31) shift: 0.80 1.23 ...... Frame ( 32) shift: 0.80 1.20 ...... Frame ( 33) shift: 0.80 1.17 ...... Frame ( 34) shift: 0.79 1.13 ...... Frame ( 35) shift: 0.78 1.09 ...... Frame ( 36) shift: 0.77 1.11 ...... Frame ( 37) shift: 0.78 1.19 ...... Frame ( 38) shift: 0.78 1.27 ...... Frame ( 39) shift: 0.78 1.35 ...... Frame ( 40) shift: 0.78 1.43 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.866250 Iteration 2 Error: 0.149079 Iteration 3 Error: 0.053207 Iteration 4 Error: 0.021822 Align patch 2 23 left Iteration 1 Error: 0.885689 Iteration 2 Error: 0.130642 Iteration 3 Error: 0.044023 Align patch 3 22 left Iteration 1 Error: 0.600325 Iteration 2 Error: 0.068220 Iteration 3 Error: 0.009775 Align patch 4 21 left Iteration 1 Error: 0.390308 Iteration 2 Error: 0.045679 Align patch 5 20 left Iteration 1 Error: 0.551896 Iteration 2 Error: 0.109075 Iteration 3 Error: 0.035676 Align patch 6 19 left Iteration 1 Error: 0.795182 Iteration 2 Error: 0.094322 Iteration 3 Error: 0.029436 Align patch 7 18 left Iteration 1 Error: 0.749593 Iteration 2 Error: 0.076487 Iteration 3 Error: 0.024315 Align patch 8 17 left Iteration 1 Error: 0.808964 Iteration 2 Error: 0.153330 Iteration 3 Error: 0.036290 Align patch 9 16 left Iteration 1 Error: 0.651322 Iteration 2 Error: 0.122956 Iteration 3 Error: 0.049780 Align patch 10 15 left Iteration 1 Error: 0.669996 Iteration 2 Error: 0.111302 Iteration 3 Error: 0.022041 Align patch 11 14 left Iteration 1 Error: 0.592301 Iteration 2 Error: 0.099839 Iteration 3 Error: 0.022130 Align patch 12 13 left Iteration 1 Error: 0.490034 Iteration 2 Error: 0.076764 Iteration 3 Error: 0.021414 Align patch 13 12 left Iteration 1 Error: 0.893579 Iteration 2 Error: 0.107529 Iteration 3 Error: 0.030270 Align patch 14 11 left Iteration 1 Error: 0.738592 Iteration 2 Error: 0.098948 Iteration 3 Error: 0.020948 Align patch 15 10 left Iteration 1 Error: 0.513496 Iteration 2 Error: 0.096704 Iteration 3 Error: 0.027513 Align patch 16 9 left Iteration 1 Error: 0.594722 Iteration 2 Error: 0.101141 Iteration 3 Error: 0.022565 Align patch 17 8 left Iteration 1 Error: 0.518303 Iteration 2 Error: 0.097451 Iteration 3 Error: 0.021606 Align patch 18 7 left Iteration 1 Error: 1.028260 Iteration 2 Error: 0.131255 Iteration 3 Error: 0.030066 Align patch 19 6 left Iteration 1 Error: 0.478842 Iteration 2 Error: 0.051614 Iteration 3 Error: 0.014864 Align patch 20 5 left Iteration 1 Error: 0.632234 Iteration 2 Error: 0.100704 Iteration 3 Error: 0.021276 Align patch 21 4 left Iteration 1 Error: 0.665334 Iteration 2 Error: 0.068774 Iteration 3 Error: 0.018252 Align patch 22 3 left Iteration 1 Error: 0.731628 Iteration 2 Error: 0.069534 Iteration 3 Error: 0.013415 Align patch 23 2 left Iteration 1 Error: 0.763122 Iteration 2 Error: 0.092483 Iteration 3 Error: 0.017019 Align patch 24 1 left Iteration 1 Error: 0.663056 Iteration 2 Error: 0.074625 Iteration 3 Error: 0.015054 Align patch 25 0 left Iteration 1 Error: 0.552985 Iteration 2 Error: 0.081761 Iteration 3 Error: 0.022127 3D Fitting completed. Patch alignment time: 15.49(sec) Local motion has been corrected. Process thread exits. Computational time: 24.494598 sec Total time: 31.125942 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00009hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00009hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.718032s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00009hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.932606s ........................................ >>>>>>TIME<<<<<< FFT: 1.058426s Defocus_U Defocus_V Angle CCC 12898.45 12230.48 81.98 0.054980 Final Values Defocus_U Defocus_V Angle CCC 12907.83 12236.74 81.66 0.090792 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00010hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00010hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 38.79 6.65 Num Hot pixels: 216 Hot pixel threshold: 78.67 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.746338 Iteration 2 Error: 0.412108 Iteration 3 Error: 0.093761 Iteration 4 Error: 0.040626 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.07 0.06 ...... Frame ( 3) shift: 0.13 0.12 ...... Frame ( 4) shift: 0.20 0.18 ...... Frame ( 5) shift: 0.27 0.24 ...... Frame ( 6) shift: 0.34 0.31 ...... Frame ( 7) shift: 0.43 0.39 ...... Frame ( 8) shift: 0.52 0.48 ...... Frame ( 9) shift: 0.62 0.58 ...... Frame ( 10) shift: 0.74 0.71 ...... Frame ( 11) shift: 0.86 0.83 ...... Frame ( 12) shift: 0.98 0.91 ...... Frame ( 13) shift: 1.10 0.95 ...... Frame ( 14) shift: 1.21 0.98 ...... Frame ( 15) shift: 1.30 1.06 ...... Frame ( 16) shift: 1.36 1.17 ...... Frame ( 17) shift: 1.42 1.27 ...... Frame ( 18) shift: 1.46 1.35 ...... Frame ( 19) shift: 1.48 1.40 ...... Frame ( 20) shift: 1.50 1.44 ...... Frame ( 21) shift: 1.58 1.47 ...... Frame ( 22) shift: 1.71 1.50 ...... Frame ( 23) shift: 1.84 1.52 ...... Frame ( 24) shift: 1.92 1.59 ...... Frame ( 25) shift: 1.94 1.70 ...... Frame ( 26) shift: 1.96 1.81 ...... Frame ( 27) shift: 2.04 1.91 ...... Frame ( 28) shift: 2.16 2.00 ...... Frame ( 29) shift: 2.29 2.09 ...... Frame ( 30) shift: 2.40 2.16 ...... Frame ( 31) shift: 2.48 2.22 ...... Frame ( 32) shift: 2.57 2.28 ...... Frame ( 33) shift: 2.62 2.32 ...... Frame ( 34) shift: 2.64 2.36 ...... Frame ( 35) shift: 2.66 2.39 ...... Frame ( 36) shift: 2.72 2.43 ...... Frame ( 37) shift: 2.81 2.47 ...... Frame ( 38) shift: 2.90 2.51 ...... Frame ( 39) shift: 2.99 2.55 ...... Frame ( 40) shift: 3.08 2.59 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.271926 Iteration 2 Error: 0.355329 Iteration 3 Error: 0.160541 Iteration 4 Error: 0.078630 Iteration 5 Error: 0.036103 Align patch 2 23 left Iteration 1 Error: 0.811547 Iteration 2 Error: 0.191154 Iteration 3 Error: 0.066532 Iteration 4 Error: 0.022236 Align patch 3 22 left Iteration 1 Error: 1.151201 Iteration 2 Error: 0.225338 Iteration 3 Error: 0.037350 Align patch 4 21 left Iteration 1 Error: 0.747176 Iteration 2 Error: 0.216126 Iteration 3 Error: 0.090317 Iteration 4 Error: 0.039233 Align patch 5 20 left Iteration 1 Error: 0.854122 Iteration 2 Error: 0.147255 Iteration 3 Error: 0.028222 Align patch 6 19 left Iteration 1 Error: 1.196672 Iteration 2 Error: 0.429191 Iteration 3 Error: 0.229722 Iteration 4 Error: 0.106158 Iteration 5 Error: 0.054150 Align patch 6 19 left Iteration 1 Error: 1.128659 Iteration 2 Error: 0.277866 Iteration 3 Error: 0.059918 Iteration 4 Error: 0.016461 Align patch 7 18 left Iteration 1 Error: 0.931202 Iteration 2 Error: 0.197789 Iteration 3 Error: 0.084333 Iteration 4 Error: 0.037224 Align patch 8 17 left Iteration 1 Error: 0.862997 Iteration 2 Error: 0.322080 Iteration 3 Error: 0.114538 Iteration 4 Error: 0.039645 Align patch 9 16 left Iteration 1 Error: 0.525632 Iteration 2 Error: 0.083977 Iteration 3 Error: 0.020438 Align patch 10 15 left Iteration 1 Error: 0.899450 Iteration 2 Error: 0.152950 Iteration 3 Error: 0.028011 Align patch 11 14 left Iteration 1 Error: 0.882501 Iteration 2 Error: 0.217105 Iteration 3 Error: 0.120157 Iteration 4 Error: 0.045226 Align patch 12 13 left Iteration 1 Error: 0.445228 Iteration 2 Error: 0.123719 Iteration 3 Error: 0.043211 Align patch 13 12 left Iteration 1 Error: 0.487633 Iteration 2 Error: 0.076320 Iteration 3 Error: 0.015788 Align patch 14 11 left Iteration 1 Error: 0.685377 Iteration 2 Error: 0.080678 Iteration 3 Error: 0.024287 Align patch 15 10 left Iteration 1 Error: 0.479775 Iteration 2 Error: 0.151724 Iteration 3 Error: 0.033760 Align patch 16 9 left Iteration 1 Error: 0.837345 Iteration 2 Error: 0.245340 Iteration 3 Error: 0.049320 Align patch 17 8 left Iteration 1 Error: 0.649523 Iteration 2 Error: 0.080930 Iteration 3 Error: 0.014167 Align patch 18 7 left Iteration 1 Error: 0.974938 Iteration 2 Error: 0.140631 Iteration 3 Error: 0.023471 Align patch 19 6 left Iteration 1 Error: 0.706261 Iteration 2 Error: 0.188929 Iteration 3 Error: 0.026844 Align patch 20 5 left Iteration 1 Error: 1.034106 Iteration 2 Error: 0.153646 Iteration 3 Error: 0.031552 Align patch 21 4 left Iteration 1 Error: 0.743092 Iteration 2 Error: 0.124521 Iteration 3 Error: 0.041783 Align patch 22 3 left Iteration 1 Error: 0.991193 Iteration 2 Error: 0.164519 Iteration 3 Error: 0.029308 Align patch 23 2 left Iteration 1 Error: 0.454287 Iteration 2 Error: 0.062275 Iteration 3 Error: 0.017656 Align patch 24 1 left Iteration 1 Error: 0.746227 Iteration 2 Error: 0.191285 Iteration 3 Error: 0.043206 Align patch 25 0 left Iteration 1 Error: 0.718593 Iteration 2 Error: 0.174922 Iteration 3 Error: 0.038039 3D Fitting completed. Patch alignment time: 15.94(sec) Local motion has been corrected. Process thread exits. Computational time: 24.543785 sec Total time: 31.438995 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00010hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00010hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.604891s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00010hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.033063s ........................................ >>>>>>TIME<<<<<< FFT: 1.035906s Defocus_U Defocus_V Angle CCC 9626.95 10365.23 11.60 0.039764 Final Values Defocus_U Defocus_V Angle CCC 9641.02 10376.18 11.28 0.065239 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00010hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00010hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.002e-01 CC threshold: 0.736 Mean Std: 39.16 6.71 Num Hot pixels: 205 Hot pixel threshold: 79.45 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.970535 Iteration 2 Error: 0.314261 Iteration 3 Error: 0.078635 Iteration 4 Error: 0.029232 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.10 0.22 ...... Frame ( 3) shift: 0.21 0.45 ...... Frame ( 4) shift: 0.31 0.67 ...... Frame ( 5) shift: 0.41 0.90 ...... Frame ( 6) shift: 0.50 1.08 ...... Frame ( 7) shift: 0.56 1.22 ...... Frame ( 8) shift: 0.63 1.36 ...... Frame ( 9) shift: 0.71 1.46 ...... Frame ( 10) shift: 0.80 1.52 ...... Frame ( 11) shift: 0.89 1.59 ...... Frame ( 12) shift: 0.97 1.65 ...... Frame ( 13) shift: 1.05 1.70 ...... Frame ( 14) shift: 1.12 1.75 ...... Frame ( 15) shift: 1.20 1.78 ...... Frame ( 16) shift: 1.27 1.79 ...... Frame ( 17) shift: 1.35 1.80 ...... Frame ( 18) shift: 1.40 1.85 ...... Frame ( 19) shift: 1.43 1.92 ...... Frame ( 20) shift: 1.46 2.00 ...... Frame ( 21) shift: 1.52 2.08 ...... Frame ( 22) shift: 1.61 2.15 ...... Frame ( 23) shift: 1.70 2.23 ...... Frame ( 24) shift: 1.77 2.28 ...... Frame ( 25) shift: 1.79 2.31 ...... Frame ( 26) shift: 1.82 2.35 ...... Frame ( 27) shift: 1.85 2.41 ...... Frame ( 28) shift: 1.87 2.49 ...... Frame ( 29) shift: 1.89 2.58 ...... Frame ( 30) shift: 1.96 2.65 ...... Frame ( 31) shift: 2.08 2.70 ...... Frame ( 32) shift: 2.20 2.75 ...... Frame ( 33) shift: 2.32 2.76 ...... Frame ( 34) shift: 2.43 2.72 ...... Frame ( 35) shift: 2.54 2.68 ...... Frame ( 36) shift: 2.62 2.71 ...... Frame ( 37) shift: 2.66 2.79 ...... Frame ( 38) shift: 2.70 2.87 ...... Frame ( 39) shift: 2.74 2.95 ...... Frame ( 40) shift: 2.78 3.04 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.820077 Iteration 2 Error: 0.350698 Iteration 3 Error: 0.136224 Iteration 4 Error: 0.054138 Iteration 5 Error: 0.025553 Align patch 2 23 left Iteration 1 Error: 1.170607 Iteration 2 Error: 0.303650 Iteration 3 Error: 0.111556 Iteration 4 Error: 0.036082 Align patch 3 22 left Iteration 1 Error: 0.658752 Iteration 2 Error: 0.213883 Iteration 3 Error: 0.047614 Align patch 4 21 left Iteration 1 Error: 0.657200 Iteration 2 Error: 0.089676 Iteration 3 Error: 0.027182 Align patch 5 20 left Iteration 1 Error: 1.065290 Iteration 2 Error: 0.090727 Iteration 3 Error: 0.019141 Align patch 6 19 left Iteration 1 Error: 1.806639 Iteration 2 Error: 0.343256 Iteration 3 Error: 0.128463 Iteration 4 Error: 0.044791 Align patch 7 18 left Iteration 1 Error: 0.775301 Iteration 2 Error: 0.164468 Iteration 3 Error: 0.078600 Iteration 4 Error: 0.022224 Align patch 8 17 left Iteration 1 Error: 0.477150 Iteration 2 Error: 0.174795 Iteration 3 Error: 0.049219 Align patch 9 16 left Iteration 1 Error: 0.412224 Iteration 2 Error: 0.070389 Iteration 3 Error: 0.013513 Align patch 10 15 left Iteration 1 Error: 0.659278 Iteration 2 Error: 0.078166 Iteration 3 Error: 0.019386 Align patch 11 14 left Iteration 1 Error: 0.792852 Iteration 2 Error: 0.189386 Iteration 3 Error: 0.076604 Iteration 4 Error: 0.035386 Align patch 12 13 left Iteration 1 Error: 0.682148 Iteration 2 Error: 0.098065 Iteration 3 Error: 0.022204 Align patch 13 12 left Iteration 1 Error: 0.507586 Iteration 2 Error: 0.103409 Iteration 3 Error: 0.020108 Align patch 14 11 left Iteration 1 Error: 0.469743 Iteration 2 Error: 0.075837 Iteration 3 Error: 0.018777 Align patch 15 10 left Iteration 1 Error: 0.455563 Iteration 2 Error: 0.084053 Iteration 3 Error: 0.018356 Align patch 16 9 left Iteration 1 Error: 0.588562 Iteration 2 Error: 0.141336 Iteration 3 Error: 0.029720 Align patch 17 8 left Iteration 1 Error: 0.489443 Iteration 2 Error: 0.092306 Iteration 3 Error: 0.042169 Align patch 18 7 left Iteration 1 Error: 0.821756 Iteration 2 Error: 0.108357 Iteration 3 Error: 0.035175 Align patch 19 6 left Iteration 1 Error: 0.687996 Iteration 2 Error: 0.119631 Iteration 3 Error: 0.039854 Align patch 20 5 left Iteration 1 Error: 0.568284 Iteration 2 Error: 0.098924 Iteration 3 Error: 0.018447 Align patch 21 4 left Iteration 1 Error: 0.935919 Iteration 2 Error: 0.120893 Iteration 3 Error: 0.026432 Align patch 22 3 left Iteration 1 Error: 0.492742 Iteration 2 Error: 0.096886 Iteration 3 Error: 0.025670 Align patch 23 2 left Iteration 1 Error: 0.685856 Iteration 2 Error: 0.160179 Iteration 3 Error: 0.045120 Align patch 24 1 left Iteration 1 Error: 0.659944 Iteration 2 Error: 0.150094 Iteration 3 Error: 0.030130 Align patch 25 0 left Iteration 1 Error: 1.023715 Iteration 2 Error: 0.173049 Iteration 3 Error: 0.040547 3D Fitting completed. Patch alignment time: 15.45(sec) Local motion has been corrected. Process thread exits. Computational time: 24.171043 sec Total time: 32.160137 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00010hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00010hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.577246s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00010hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.905338s ........................................ >>>>>>TIME<<<<<< FFT: 0.924306s Defocus_U Defocus_V Angle CCC 9863.29 10328.14 2.17 0.042757 Final Values Defocus_U Defocus_V Angle CCC 9866.44 10356.30 2.17 0.072330 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00010hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00010hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.002e-01 CC threshold: 0.736 Mean Std: 38.59 6.68 Num Hot pixels: 234 Hot pixel threshold: 78.68 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.731225 Iteration 2 Error: 0.130044 Iteration 3 Error: 0.026601 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.10 -0.28 ...... Frame ( 3) shift: -0.21 -0.56 ...... Frame ( 4) shift: -0.31 -0.84 ...... Frame ( 5) shift: -0.41 -1.12 ...... Frame ( 6) shift: -0.47 -1.25 ...... Frame ( 7) shift: -0.49 -1.24 ...... Frame ( 8) shift: -0.50 -1.22 ...... Frame ( 9) shift: -0.49 -1.18 ...... Frame ( 10) shift: -0.45 -1.12 ...... Frame ( 11) shift: -0.41 -1.06 ...... Frame ( 12) shift: -0.37 -1.00 ...... Frame ( 13) shift: -0.33 -0.94 ...... Frame ( 14) shift: -0.29 -0.89 ...... Frame ( 15) shift: -0.23 -0.82 ...... Frame ( 16) shift: -0.16 -0.74 ...... Frame ( 17) shift: -0.09 -0.66 ...... Frame ( 18) shift: -0.05 -0.63 ...... Frame ( 19) shift: -0.04 -0.63 ...... Frame ( 20) shift: -0.03 -0.64 ...... Frame ( 21) shift: 0.00 -0.62 ...... Frame ( 22) shift: 0.04 -0.57 ...... Frame ( 23) shift: 0.09 -0.51 ...... Frame ( 24) shift: 0.11 -0.43 ...... Frame ( 25) shift: 0.11 -0.33 ...... Frame ( 26) shift: 0.11 -0.22 ...... Frame ( 27) shift: 0.14 -0.19 ...... Frame ( 28) shift: 0.20 -0.24 ...... Frame ( 29) shift: 0.26 -0.29 ...... Frame ( 30) shift: 0.30 -0.30 ...... Frame ( 31) shift: 0.33 -0.25 ...... Frame ( 32) shift: 0.36 -0.21 ...... Frame ( 33) shift: 0.37 -0.16 ...... Frame ( 34) shift: 0.38 -0.11 ...... Frame ( 35) shift: 0.38 -0.06 ...... Frame ( 36) shift: 0.39 -0.03 ...... Frame ( 37) shift: 0.41 -0.02 ...... Frame ( 38) shift: 0.42 -0.02 ...... Frame ( 39) shift: 0.44 -0.02 ...... Frame ( 40) shift: 0.45 -0.02 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.667550 Iteration 2 Error: 0.117467 Iteration 3 Error: 0.031877 Align patch 2 23 left Iteration 1 Error: 0.623981 Iteration 2 Error: 0.091428 Iteration 3 Error: 0.030149 Align patch 3 22 left Iteration 1 Error: 0.510766 Iteration 2 Error: 0.074705 Iteration 3 Error: 0.019028 Align patch 4 21 left Iteration 1 Error: 0.624002 Iteration 2 Error: 0.091050 Iteration 3 Error: 0.016585 Align patch 5 20 left Iteration 1 Error: 0.688254 Iteration 2 Error: 0.111855 Iteration 3 Error: 0.022743 Align patch 6 19 left Iteration 1 Error: 0.886736 Iteration 2 Error: 0.087273 Iteration 3 Error: 0.018687 Align patch 7 18 left Iteration 1 Error: 0.988584 Iteration 2 Error: 0.135245 Iteration 3 Error: 0.039057 Align patch 8 17 left Iteration 1 Error: 0.883043 Iteration 2 Error: 0.115091 Iteration 3 Error: 0.016386 Align patch 9 16 left Iteration 1 Error: 0.727566 Iteration 2 Error: 0.096554 Iteration 3 Error: 0.020813 Align patch 10 15 left Iteration 1 Error: 0.752121 Iteration 2 Error: 0.100377 Iteration 3 Error: 0.020926 Align patch 11 14 left Iteration 1 Error: 0.773243 Iteration 2 Error: 0.201592 Iteration 3 Error: 0.032563 Align patch 12 13 left Iteration 1 Error: 0.634989 Iteration 2 Error: 0.106508 Iteration 3 Error: 0.018418 Align patch 13 12 left Iteration 1 Error: 0.706108 Iteration 2 Error: 0.123493 Iteration 3 Error: 0.028187 Align patch 14 11 left Iteration 1 Error: 0.641947 Iteration 2 Error: 0.078078 Iteration 3 Error: 0.014439 Align patch 15 10 left Iteration 1 Error: 0.554666 Iteration 2 Error: 0.076266 Iteration 3 Error: 0.014680 Align patch 16 9 left Iteration 1 Error: 0.445553 Iteration 2 Error: 0.105441 Iteration 3 Error: 0.018780 Align patch 17 8 left Iteration 1 Error: 0.643918 Iteration 2 Error: 0.086779 Iteration 3 Error: 0.018339 Align patch 18 7 left Iteration 1 Error: 0.584838 Iteration 2 Error: 0.080498 Iteration 3 Error: 0.021939 Align patch 19 6 left Iteration 1 Error: 0.829720 Iteration 2 Error: 0.115678 Iteration 3 Error: 0.017236 Align patch 20 5 left Iteration 1 Error: 0.837601 Iteration 2 Error: 0.102950 Iteration 3 Error: 0.024980 Align patch 21 4 left Iteration 1 Error: 0.709337 Iteration 2 Error: 0.100991 Iteration 3 Error: 0.025369 Align patch 22 3 left Iteration 1 Error: 0.629135 Iteration 2 Error: 0.109757 Iteration 3 Error: 0.023141 Align patch 23 2 left Iteration 1 Error: 0.518332 Iteration 2 Error: 0.094031 Iteration 3 Error: 0.021569 Align patch 24 1 left Iteration 1 Error: 0.536234 Iteration 2 Error: 0.107021 Iteration 3 Error: 0.013983 Align patch 25 0 left Iteration 1 Error: 0.535138 Iteration 2 Error: 0.066599 Iteration 3 Error: 0.011032 3D Fitting completed. Patch alignment time: 14.28(sec) Local motion has been corrected. Process thread exits. Computational time: 22.743046 sec Total time: 28.537994 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00010hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00010hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.567239s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00010hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.971079s ........................................ >>>>>>TIME<<<<<< FFT: 1.050479s Defocus_U Defocus_V Angle CCC 14962.87 15857.44 3.68 0.050710 Final Values Defocus_U Defocus_V Angle CCC 15000.37 15816.83 4.00 0.075260 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00010hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00010hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 39.28 6.71 Num Hot pixels: 214 Hot pixel threshold: 79.57 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.008678 Iteration 2 Error: 0.169902 Iteration 3 Error: 0.045297 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.05 0.05 ...... Frame ( 3) shift: 0.10 0.10 ...... Frame ( 4) shift: 0.14 0.15 ...... Frame ( 5) shift: 0.19 0.20 ...... Frame ( 6) shift: 0.26 0.26 ...... Frame ( 7) shift: 0.34 0.32 ...... Frame ( 8) shift: 0.43 0.39 ...... Frame ( 9) shift: 0.50 0.46 ...... Frame ( 10) shift: 0.56 0.53 ...... Frame ( 11) shift: 0.62 0.60 ...... Frame ( 12) shift: 0.67 0.65 ...... Frame ( 13) shift: 0.71 0.69 ...... Frame ( 14) shift: 0.76 0.73 ...... Frame ( 15) shift: 0.80 0.76 ...... Frame ( 16) shift: 0.82 0.78 ...... Frame ( 17) shift: 0.85 0.80 ...... Frame ( 18) shift: 0.88 0.82 ...... Frame ( 19) shift: 0.92 0.85 ...... Frame ( 20) shift: 0.95 0.88 ...... Frame ( 21) shift: 1.00 0.92 ...... Frame ( 22) shift: 1.05 0.96 ...... Frame ( 23) shift: 1.11 1.00 ...... Frame ( 24) shift: 1.15 1.03 ...... Frame ( 25) shift: 1.18 1.06 ...... Frame ( 26) shift: 1.21 1.08 ...... Frame ( 27) shift: 1.23 1.11 ...... Frame ( 28) shift: 1.24 1.14 ...... Frame ( 29) shift: 1.26 1.17 ...... Frame ( 30) shift: 1.30 1.19 ...... Frame ( 31) shift: 1.39 1.22 ...... Frame ( 32) shift: 1.47 1.25 ...... Frame ( 33) shift: 1.54 1.29 ...... Frame ( 34) shift: 1.59 1.35 ...... Frame ( 35) shift: 1.65 1.41 ...... Frame ( 36) shift: 1.65 1.43 ...... Frame ( 37) shift: 1.60 1.42 ...... Frame ( 38) shift: 1.55 1.41 ...... Frame ( 39) shift: 1.51 1.40 ...... Frame ( 40) shift: 1.46 1.38 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.045632 Iteration 2 Error: 0.209074 Iteration 3 Error: 0.069631 Iteration 4 Error: 0.031272 Align patch 2 23 left Iteration 1 Error: 0.479897 Iteration 2 Error: 0.109853 Iteration 3 Error: 0.033782 Align patch 3 22 left Iteration 1 Error: 0.839830 Iteration 2 Error: 0.138006 Iteration 3 Error: 0.042502 Align patch 4 21 left Iteration 1 Error: 0.554889 Iteration 2 Error: 0.060239 Iteration 3 Error: 0.010359 Align patch 5 20 left Iteration 1 Error: 0.546602 Iteration 2 Error: 0.112411 Iteration 3 Error: 0.020784 Align patch 6 19 left Iteration 1 Error: 0.884602 Iteration 2 Error: 0.201498 Iteration 3 Error: 0.109722 Iteration 4 Error: 0.045173 Align patch 7 18 left Iteration 1 Error: 0.631211 Iteration 2 Error: 0.107651 Iteration 3 Error: 0.029997 Align patch 8 17 left Iteration 1 Error: 0.641514 Iteration 2 Error: 0.158612 Iteration 3 Error: 0.035605 Align patch 9 16 left Iteration 1 Error: 0.611334 Iteration 2 Error: 0.070742 Iteration 3 Error: 0.012833 Align patch 10 15 left Iteration 1 Error: 1.096991 Iteration 2 Error: 0.128065 Iteration 3 Error: 0.037095 Align patch 11 14 left Iteration 1 Error: 0.485170 Iteration 2 Error: 0.131513 Iteration 3 Error: 0.058111 Iteration 4 Error: 0.023774 Align patch 12 13 left Iteration 1 Error: 0.811009 Iteration 2 Error: 0.102935 Iteration 3 Error: 0.029445 Align patch 13 12 left Iteration 1 Error: 0.450541 Iteration 2 Error: 0.066544 Iteration 3 Error: 0.015385 Align patch 14 11 left Iteration 1 Error: 0.454448 Iteration 2 Error: 0.094435 Iteration 3 Error: 0.017827 Align patch 15 10 left Iteration 1 Error: 0.503713 Iteration 2 Error: 0.096571 Iteration 3 Error: 0.026644 Align patch 16 9 left Iteration 1 Error: 0.625818 Iteration 2 Error: 0.184047 Iteration 3 Error: 0.078241 Iteration 4 Error: 0.033138 Align patch 17 8 left Iteration 1 Error: 0.730116 Iteration 2 Error: 0.223377 Iteration 3 Error: 0.046589 Align patch 18 7 left Iteration 1 Error: 0.856779 Iteration 2 Error: 0.140095 Iteration 3 Error: 0.037572 Align patch 19 6 left Iteration 1 Error: 0.467900 Iteration 2 Error: 0.097021 Iteration 3 Error: 0.017027 Align patch 20 5 left Iteration 1 Error: 0.551802 Iteration 2 Error: 0.074953 Iteration 3 Error: 0.013066 Align patch 21 4 left Iteration 1 Error: 1.033647 Iteration 2 Error: 0.136891 Iteration 3 Error: 0.034705 Align patch 22 3 left Iteration 1 Error: 0.759036 Iteration 2 Error: 0.169670 Iteration 3 Error: 0.045117 Align patch 23 2 left Iteration 1 Error: 0.726756 Iteration 2 Error: 0.144320 Iteration 3 Error: 0.036867 Align patch 24 1 left Iteration 1 Error: 0.540518 Iteration 2 Error: 0.064667 Iteration 3 Error: 0.020745 Align patch 25 0 left Iteration 1 Error: 0.541616 Iteration 2 Error: 0.061473 Iteration 3 Error: 0.008441 3D Fitting completed. Patch alignment time: 15.51(sec) Local motion has been corrected. Process thread exits. Computational time: 24.617046 sec Total time: 30.144585 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00010hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00010hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.685868s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00010hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.238137s ........................................ >>>>>>TIME<<<<<< FFT: 1.046921s Defocus_U Defocus_V Angle CCC 10669.93 10080.07 79.70 0.036230 Final Values Defocus_U Defocus_V Angle CCC 10710.57 10089.46 80.01 0.060699 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00011hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00011hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.002e-01 CC threshold: 0.736 Mean Std: 38.79 6.67 Num Hot pixels: 209 Hot pixel threshold: 78.79 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.976636 Iteration 2 Error: 0.152747 Iteration 3 Error: 0.033449 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.07 -0.04 ...... Frame ( 3) shift: 0.14 -0.08 ...... Frame ( 4) shift: 0.21 -0.12 ...... Frame ( 5) shift: 0.28 -0.16 ...... Frame ( 6) shift: 0.36 -0.15 ...... Frame ( 7) shift: 0.43 -0.09 ...... Frame ( 8) shift: 0.51 -0.02 ...... Frame ( 9) shift: 0.61 0.05 ...... Frame ( 10) shift: 0.74 0.13 ...... Frame ( 11) shift: 0.86 0.21 ...... Frame ( 12) shift: 0.91 0.28 ...... Frame ( 13) shift: 0.87 0.34 ...... Frame ( 14) shift: 0.83 0.41 ...... Frame ( 15) shift: 0.84 0.46 ...... Frame ( 16) shift: 0.92 0.50 ...... Frame ( 17) shift: 0.99 0.55 ...... Frame ( 18) shift: 1.05 0.61 ...... Frame ( 19) shift: 1.08 0.69 ...... Frame ( 20) shift: 1.12 0.77 ...... Frame ( 21) shift: 1.15 0.85 ...... Frame ( 22) shift: 1.18 0.93 ...... Frame ( 23) shift: 1.21 1.01 ...... Frame ( 24) shift: 1.21 1.04 ...... Frame ( 25) shift: 1.17 1.02 ...... Frame ( 26) shift: 1.13 1.01 ...... Frame ( 27) shift: 1.13 1.00 ...... Frame ( 28) shift: 1.17 1.01 ...... Frame ( 29) shift: 1.21 1.02 ...... Frame ( 30) shift: 1.23 1.01 ...... Frame ( 31) shift: 1.23 1.00 ...... Frame ( 32) shift: 1.23 0.99 ...... Frame ( 33) shift: 1.28 0.97 ...... Frame ( 34) shift: 1.37 0.95 ...... Frame ( 35) shift: 1.47 0.92 ...... Frame ( 36) shift: 1.56 0.94 ...... Frame ( 37) shift: 1.65 1.00 ...... Frame ( 38) shift: 1.73 1.06 ...... Frame ( 39) shift: 1.82 1.13 ...... Frame ( 40) shift: 1.91 1.19 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.641943 Iteration 2 Error: 0.179453 Iteration 3 Error: 0.031425 Align patch 2 23 left Iteration 1 Error: 0.867797 Iteration 2 Error: 0.108506 Iteration 3 Error: 0.034564 Align patch 3 22 left Iteration 1 Error: 0.648922 Iteration 2 Error: 0.127591 Iteration 3 Error: 0.042272 Align patch 4 21 left Iteration 1 Error: 0.527975 Iteration 2 Error: 0.116109 Iteration 3 Error: 0.025364 Align patch 5 20 left Iteration 1 Error: 0.563539 Iteration 2 Error: 0.090781 Iteration 3 Error: 0.018970 Align patch 6 19 left Iteration 1 Error: 0.642391 Iteration 2 Error: 0.114498 Iteration 3 Error: 0.015871 Align patch 7 18 left Iteration 1 Error: 0.473775 Iteration 2 Error: 0.054153 Iteration 3 Error: 0.014079 Align patch 8 17 left Iteration 1 Error: 0.944698 Iteration 2 Error: 0.106203 Iteration 3 Error: 0.015292 Align patch 9 16 left Iteration 1 Error: 0.489490 Iteration 2 Error: 0.095583 Iteration 3 Error: 0.015615 Align patch 10 15 left Iteration 1 Error: 0.651574 Iteration 2 Error: 0.062782 Iteration 3 Error: 0.009577 Align patch 11 14 left Iteration 1 Error: 0.576860 Iteration 2 Error: 0.096356 Iteration 3 Error: 0.028235 Align patch 12 13 left Iteration 1 Error: 0.658576 Iteration 2 Error: 0.100929 Iteration 3 Error: 0.035074 Align patch 13 12 left Iteration 1 Error: 0.687420 Iteration 2 Error: 0.131606 Iteration 3 Error: 0.028368 Align patch 14 11 left Iteration 1 Error: 0.516431 Iteration 2 Error: 0.101135 Iteration 3 Error: 0.017927 Align patch 15 10 left Iteration 1 Error: 0.910030 Iteration 2 Error: 0.183412 Iteration 3 Error: 0.032266 Align patch 16 9 left Iteration 1 Error: 0.579372 Iteration 2 Error: 0.072108 Iteration 3 Error: 0.019176 Align patch 17 8 left Iteration 1 Error: 0.888913 Iteration 2 Error: 0.093820 Iteration 3 Error: 0.031285 Align patch 18 7 left Iteration 1 Error: 0.396292 Iteration 2 Error: 0.062261 Iteration 3 Error: 0.015742 Align patch 19 6 left Iteration 1 Error: 0.512756 Iteration 2 Error: 0.072086 Iteration 3 Error: 0.028492 Align patch 20 5 left Iteration 1 Error: 0.520296 Iteration 2 Error: 0.130485 Iteration 3 Error: 0.027528 Align patch 21 4 left Iteration 1 Error: 0.821756 Iteration 2 Error: 0.144332 Iteration 3 Error: 0.036372 Align patch 22 3 left Iteration 1 Error: 0.538227 Iteration 2 Error: 0.050167 Iteration 3 Error: 0.010446 Align patch 23 2 left Iteration 1 Error: 1.033094 Iteration 2 Error: 0.142258 Iteration 3 Error: 0.028734 Align patch 24 1 left Iteration 1 Error: 0.676943 Iteration 2 Error: 0.173223 Iteration 3 Error: 0.026294 Align patch 25 0 left Iteration 1 Error: 1.021720 Iteration 2 Error: 0.134816 Iteration 3 Error: 0.032400 3D Fitting completed. Patch alignment time: 15.18(sec) Local motion has been corrected. Process thread exits. Computational time: 24.425850 sec Total time: 31.444832 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00011hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00011hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.697680s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00011hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.968503s ........................................ >>>>>>TIME<<<<<< FFT: 1.053309s Defocus_U Defocus_V Angle CCC 12207.05 13089.86 11.70 0.046532 Final Values Defocus_U Defocus_V Angle CCC 12205.48 13103.95 12.02 0.071776 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00011hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00011hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.003e-01 CC threshold: 0.736 Mean Std: 39.04 7.01 Num Hot pixels: 197 Hot pixel threshold: 81.10 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.594038 Iteration 2 Error: 0.105896 Iteration 3 Error: 0.020716 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.01 -0.12 ...... Frame ( 3) shift: -0.03 -0.24 ...... Frame ( 4) shift: -0.04 -0.35 ...... Frame ( 5) shift: -0.05 -0.47 ...... Frame ( 6) shift: -0.06 -0.55 ...... Frame ( 7) shift: -0.05 -0.58 ...... Frame ( 8) shift: -0.04 -0.62 ...... Frame ( 9) shift: 0.01 -0.59 ...... Frame ( 10) shift: 0.10 -0.49 ...... Frame ( 11) shift: 0.19 -0.38 ...... Frame ( 12) shift: 0.24 -0.29 ...... Frame ( 13) shift: 0.25 -0.21 ...... Frame ( 14) shift: 0.27 -0.13 ...... Frame ( 15) shift: 0.30 -0.08 ...... Frame ( 16) shift: 0.34 -0.07 ...... Frame ( 17) shift: 0.39 -0.06 ...... Frame ( 18) shift: 0.41 -0.04 ...... Frame ( 19) shift: 0.40 -0.02 ...... Frame ( 20) shift: 0.40 -0.00 ...... Frame ( 21) shift: 0.40 0.03 ...... Frame ( 22) shift: 0.41 0.07 ...... Frame ( 23) shift: 0.41 0.12 ...... Frame ( 24) shift: 0.40 0.13 ...... Frame ( 25) shift: 0.37 0.11 ...... Frame ( 26) shift: 0.34 0.10 ...... Frame ( 27) shift: 0.34 0.08 ...... Frame ( 28) shift: 0.38 0.06 ...... Frame ( 29) shift: 0.42 0.04 ...... Frame ( 30) shift: 0.46 0.07 ...... Frame ( 31) shift: 0.50 0.14 ...... Frame ( 32) shift: 0.53 0.21 ...... Frame ( 33) shift: 0.56 0.27 ...... Frame ( 34) shift: 0.58 0.31 ...... Frame ( 35) shift: 0.60 0.35 ...... Frame ( 36) shift: 0.59 0.37 ...... Frame ( 37) shift: 0.57 0.39 ...... Frame ( 38) shift: 0.54 0.40 ...... Frame ( 39) shift: 0.52 0.41 ...... Frame ( 40) shift: 0.49 0.42 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.563573 Iteration 2 Error: 0.110445 Iteration 3 Error: 0.025930 Align patch 2 23 left Iteration 1 Error: 0.603819 Iteration 2 Error: 0.079502 Iteration 3 Error: 0.022408 Align patch 3 22 left Iteration 1 Error: 0.785794 Iteration 2 Error: 0.159014 Iteration 3 Error: 0.037890 Align patch 4 21 left Iteration 1 Error: 0.592818 Iteration 2 Error: 0.113369 Iteration 3 Error: 0.017635 Align patch 5 20 left Iteration 1 Error: 0.204097 Iteration 2 Error: 0.067566 Iteration 3 Error: 0.024003 Align patch 6 19 left Iteration 1 Error: 0.780599 Iteration 2 Error: 0.105278 Iteration 3 Error: 0.021596 Align patch 7 18 left Iteration 1 Error: 0.672617 Iteration 2 Error: 0.127672 Iteration 3 Error: 0.035193 Align patch 8 17 left Iteration 1 Error: 0.647964 Iteration 2 Error: 0.100469 Iteration 3 Error: 0.018080 Align patch 9 16 left Iteration 1 Error: 0.727910 Iteration 2 Error: 0.089004 Iteration 3 Error: 0.015433 Align patch 10 15 left Iteration 1 Error: 0.539797 Iteration 2 Error: 0.044710 Align patch 11 14 left Iteration 1 Error: 0.604015 Iteration 2 Error: 0.087719 Iteration 3 Error: 0.017593 Align patch 12 13 left Iteration 1 Error: 0.647094 Iteration 2 Error: 0.102815 Iteration 3 Error: 0.019054 Align patch 13 12 left Iteration 1 Error: 0.423070 Iteration 2 Error: 0.047335 Align patch 14 11 left Iteration 1 Error: 0.440392 Iteration 2 Error: 0.060469 Iteration 3 Error: 0.010525 Align patch 15 10 left Iteration 1 Error: 0.714306 Iteration 2 Error: 0.108012 Iteration 3 Error: 0.017672 Align patch 16 9 left Iteration 1 Error: 0.779434 Iteration 2 Error: 0.102352 Iteration 3 Error: 0.027355 Align patch 17 8 left Iteration 1 Error: 0.561162 Iteration 2 Error: 0.085710 Iteration 3 Error: 0.019640 Align patch 18 7 left Iteration 1 Error: 0.556129 Iteration 2 Error: 0.168320 Iteration 3 Error: 0.035710 Align patch 19 6 left Iteration 1 Error: 0.669643 Iteration 2 Error: 0.103536 Iteration 3 Error: 0.022055 Align patch 20 5 left Iteration 1 Error: 0.616601 Iteration 2 Error: 0.113287 Iteration 3 Error: 0.029041 Align patch 21 4 left Iteration 1 Error: 0.616174 Iteration 2 Error: 0.110517 Iteration 3 Error: 0.031068 Align patch 22 3 left Iteration 1 Error: 0.576993 Iteration 2 Error: 0.066616 Iteration 3 Error: 0.008775 Align patch 23 2 left Iteration 1 Error: 0.678725 Iteration 2 Error: 0.103002 Iteration 3 Error: 0.014501 Align patch 24 1 left Iteration 1 Error: 0.916636 Iteration 2 Error: 0.137644 Iteration 3 Error: 0.022843 Align patch 25 0 left Iteration 1 Error: 0.711150 Iteration 2 Error: 0.097336 Iteration 3 Error: 0.022209 3D Fitting completed. Patch alignment time: 15.09(sec) Local motion has been corrected. Process thread exits. Computational time: 23.302111 sec Total time: 29.474487 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00011hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00011hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.728621s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00011hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.781167s ........................................ >>>>>>TIME<<<<<< FFT: 1.044277s Defocus_U Defocus_V Angle CCC 10587.89 10048.83 89.55 0.034833 Final Values Defocus_U Defocus_V Angle CCC 10628.54 10064.48 88.30 0.060652 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00011hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00011hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 38.90 6.68 Num Hot pixels: 228 Hot pixel threshold: 79.00 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.814633 Iteration 2 Error: 0.129623 Iteration 3 Error: 0.025517 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.12 0.07 ...... Frame ( 3) shift: 0.24 0.15 ...... Frame ( 4) shift: 0.36 0.22 ...... Frame ( 5) shift: 0.48 0.29 ...... Frame ( 6) shift: 0.53 0.36 ...... Frame ( 7) shift: 0.50 0.43 ...... Frame ( 8) shift: 0.48 0.50 ...... Frame ( 9) shift: 0.45 0.54 ...... Frame ( 10) shift: 0.42 0.56 ...... Frame ( 11) shift: 0.40 0.59 ...... Frame ( 12) shift: 0.39 0.62 ...... Frame ( 13) shift: 0.39 0.67 ...... Frame ( 14) shift: 0.40 0.73 ...... Frame ( 15) shift: 0.41 0.78 ...... Frame ( 16) shift: 0.43 0.83 ...... Frame ( 17) shift: 0.45 0.88 ...... Frame ( 18) shift: 0.43 0.90 ...... Frame ( 19) shift: 0.38 0.90 ...... Frame ( 20) shift: 0.34 0.90 ...... Frame ( 21) shift: 0.34 0.93 ...... Frame ( 22) shift: 0.38 0.99 ...... Frame ( 23) shift: 0.43 1.06 ...... Frame ( 24) shift: 0.45 1.11 ...... Frame ( 25) shift: 0.42 1.15 ...... Frame ( 26) shift: 0.40 1.18 ...... Frame ( 27) shift: 0.39 1.23 ...... Frame ( 28) shift: 0.40 1.29 ...... Frame ( 29) shift: 0.41 1.35 ...... Frame ( 30) shift: 0.40 1.40 ...... Frame ( 31) shift: 0.38 1.45 ...... Frame ( 32) shift: 0.36 1.50 ...... Frame ( 33) shift: 0.33 1.53 ...... Frame ( 34) shift: 0.29 1.53 ...... Frame ( 35) shift: 0.25 1.54 ...... Frame ( 36) shift: 0.23 1.58 ...... Frame ( 37) shift: 0.24 1.66 ...... Frame ( 38) shift: 0.26 1.74 ...... Frame ( 39) shift: 0.27 1.81 ...... Frame ( 40) shift: 0.28 1.89 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.597798 Iteration 2 Error: 0.077917 Iteration 3 Error: 0.018747 Align patch 2 23 left Iteration 1 Error: 0.513311 Iteration 2 Error: 0.092271 Iteration 3 Error: 0.024502 Align patch 3 22 left Iteration 1 Error: 0.469368 Iteration 2 Error: 0.062675 Iteration 3 Error: 0.016970 Align patch 4 21 left Iteration 1 Error: 0.808982 Iteration 2 Error: 0.084680 Iteration 3 Error: 0.021525 Align patch 5 20 left Iteration 1 Error: 0.747142 Iteration 2 Error: 0.102406 Iteration 3 Error: 0.021368 Align patch 6 19 left Iteration 1 Error: 0.558212 Iteration 2 Error: 0.085278 Iteration 3 Error: 0.022082 Align patch 7 18 left Iteration 1 Error: 0.725439 Iteration 2 Error: 0.082271 Iteration 3 Error: 0.017245 Align patch 8 17 left Iteration 1 Error: 0.534169 Iteration 2 Error: 0.067199 Iteration 3 Error: 0.017986 Align patch 9 16 left Iteration 1 Error: 0.892269 Iteration 2 Error: 0.065956 Iteration 3 Error: 0.017925 Align patch 10 15 left Iteration 1 Error: 0.631704 Iteration 2 Error: 0.103183 Iteration 3 Error: 0.022535 Align patch 11 14 left Iteration 1 Error: 0.425668 Iteration 2 Error: 0.048360 Align patch 12 13 left Iteration 1 Error: 0.714192 Iteration 2 Error: 0.136513 Iteration 3 Error: 0.034688 Align patch 13 12 left Iteration 1 Error: 0.577959 Iteration 2 Error: 0.082335 Iteration 3 Error: 0.016062 Align patch 14 11 left Iteration 1 Error: 0.664408 Iteration 2 Error: 0.061622 Iteration 3 Error: 0.007701 Align patch 15 10 left Iteration 1 Error: 1.015536 Iteration 2 Error: 0.124782 Iteration 3 Error: 0.028442 Align patch 16 9 left Iteration 1 Error: 0.885880 Iteration 2 Error: 0.083590 Iteration 3 Error: 0.022132 Align patch 17 8 left Iteration 1 Error: 0.467493 Iteration 2 Error: 0.068589 Iteration 3 Error: 0.014765 Align patch 18 7 left Iteration 1 Error: 0.669004 Iteration 2 Error: 0.094074 Iteration 3 Error: 0.021237 Align patch 19 6 left Iteration 1 Error: 0.726792 Iteration 2 Error: 0.067872 Iteration 3 Error: 0.024117 Align patch 20 5 left Iteration 1 Error: 0.831914 Iteration 2 Error: 0.096085 Iteration 3 Error: 0.019394 Align patch 21 4 left Iteration 1 Error: 0.712057 Iteration 2 Error: 0.056321 Iteration 3 Error: 0.019418 Align patch 22 3 left Iteration 1 Error: 0.636856 Iteration 2 Error: 0.072099 Iteration 3 Error: 0.008247 Align patch 23 2 left Iteration 1 Error: 0.339217 Iteration 2 Error: 0.044830 Align patch 24 1 left Iteration 1 Error: 0.574062 Iteration 2 Error: 0.074860 Iteration 3 Error: 0.022764 Align patch 25 0 left Iteration 1 Error: 0.518812 Iteration 2 Error: 0.077241 Iteration 3 Error: 0.020504 3D Fitting completed. Patch alignment time: 14.42(sec) Local motion has been corrected. Process thread exits. Computational time: 22.670618 sec Total time: 28.635441 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00011hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00011hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.698594s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00011hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.776924s ........................................ >>>>>>TIME<<<<<< FFT: 1.089427s Defocus_U Defocus_V Angle CCC 9763.68 10646.50 6.28 0.042842 Final Values Defocus_U Defocus_V Angle CCC 9755.86 10669.95 6.91 0.072934 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00011hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00011hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.002e-01 CC threshold: 0.736 Mean Std: 38.73 6.64 Num Hot pixels: 229 Hot pixel threshold: 78.59 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.259036 Iteration 2 Error: 0.223774 Iteration 3 Error: 0.057613 Iteration 4 Error: 0.015209 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.29 -0.06 ...... Frame ( 3) shift: 0.58 -0.11 ...... Frame ( 4) shift: 0.87 -0.17 ...... Frame ( 5) shift: 1.16 -0.23 ...... Frame ( 6) shift: 1.46 -0.21 ...... Frame ( 7) shift: 1.77 -0.13 ...... Frame ( 8) shift: 2.08 -0.04 ...... Frame ( 9) shift: 2.34 0.03 ...... Frame ( 10) shift: 2.55 0.10 ...... Frame ( 11) shift: 2.75 0.16 ...... Frame ( 12) shift: 2.84 0.22 ...... Frame ( 13) shift: 2.80 0.28 ...... Frame ( 14) shift: 2.76 0.34 ...... Frame ( 15) shift: 2.73 0.37 ...... Frame ( 16) shift: 2.72 0.37 ...... Frame ( 17) shift: 2.71 0.37 ...... Frame ( 18) shift: 2.73 0.38 ...... Frame ( 19) shift: 2.80 0.40 ...... Frame ( 20) shift: 2.87 0.42 ...... Frame ( 21) shift: 2.92 0.37 ...... Frame ( 22) shift: 2.97 0.26 ...... Frame ( 23) shift: 3.02 0.14 ...... Frame ( 24) shift: 3.08 0.07 ...... Frame ( 25) shift: 3.17 0.02 ...... Frame ( 26) shift: 3.26 -0.02 ...... Frame ( 27) shift: 3.34 -0.03 ...... Frame ( 28) shift: 3.40 -0.01 ...... Frame ( 29) shift: 3.46 0.01 ...... Frame ( 30) shift: 3.53 0.05 ...... Frame ( 31) shift: 3.61 0.10 ...... Frame ( 32) shift: 3.68 0.16 ...... Frame ( 33) shift: 3.77 0.18 ...... Frame ( 34) shift: 3.86 0.16 ...... Frame ( 35) shift: 3.95 0.15 ...... Frame ( 36) shift: 3.99 0.11 ...... Frame ( 37) shift: 3.99 0.05 ...... Frame ( 38) shift: 3.99 -0.00 ...... Frame ( 39) shift: 3.99 -0.06 ...... Frame ( 40) shift: 3.99 -0.11 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.449851 Iteration 2 Error: 0.113317 Iteration 3 Error: 0.018085 Align patch 2 23 left Iteration 1 Error: 0.562937 Iteration 2 Error: 0.060438 Iteration 3 Error: 0.016946 Align patch 3 22 left Iteration 1 Error: 0.454661 Iteration 2 Error: 0.045627 Align patch 4 21 left Iteration 1 Error: 0.563354 Iteration 2 Error: 0.082663 Iteration 3 Error: 0.015977 Align patch 5 20 left Iteration 1 Error: 0.827918 Iteration 2 Error: 0.137102 Iteration 3 Error: 0.023698 Align patch 6 19 left Iteration 1 Error: 0.666023 Iteration 2 Error: 0.170457 Iteration 3 Error: 0.041135 Align patch 7 18 left Iteration 1 Error: 0.574360 Iteration 2 Error: 0.085401 Iteration 3 Error: 0.021735 Align patch 8 17 left Iteration 1 Error: 0.659056 Iteration 2 Error: 0.077883 Iteration 3 Error: 0.017054 Align patch 9 16 left Iteration 1 Error: 0.655738 Iteration 2 Error: 0.127772 Iteration 3 Error: 0.029948 Align patch 10 15 left Iteration 1 Error: 0.725796 Iteration 2 Error: 0.090226 Iteration 3 Error: 0.034547 Align patch 11 14 left Iteration 1 Error: 0.878097 Iteration 2 Error: 0.190978 Iteration 3 Error: 0.035881 Align patch 12 13 left Iteration 1 Error: 0.777279 Iteration 2 Error: 0.111877 Iteration 3 Error: 0.016409 Align patch 13 12 left Iteration 1 Error: 0.742489 Iteration 2 Error: 0.145506 Iteration 3 Error: 0.032705 Align patch 14 11 left Iteration 1 Error: 0.570237 Iteration 2 Error: 0.091165 Iteration 3 Error: 0.023274 Align patch 15 10 left Iteration 1 Error: 0.752308 Iteration 2 Error: 0.114302 Iteration 3 Error: 0.032554 Align patch 16 9 left Iteration 1 Error: 0.436231 Iteration 2 Error: 0.077106 Iteration 3 Error: 0.019529 Align patch 17 8 left Iteration 1 Error: 0.568624 Iteration 2 Error: 0.073809 Iteration 3 Error: 0.026768 Align patch 18 7 left Iteration 1 Error: 0.402301 Iteration 2 Error: 0.054418 Iteration 3 Error: 0.016000 Align patch 19 6 left Iteration 1 Error: 0.596079 Iteration 2 Error: 0.108216 Iteration 3 Error: 0.016990 Align patch 20 5 left Iteration 1 Error: 0.624259 Iteration 2 Error: 0.103872 Iteration 3 Error: 0.020579 Align patch 21 4 left Iteration 1 Error: 0.622754 Iteration 2 Error: 0.093681 Iteration 3 Error: 0.024657 Align patch 22 3 left Iteration 1 Error: 0.611293 Iteration 2 Error: 0.144827 Iteration 3 Error: 0.055510 Iteration 4 Error: 0.012393 Align patch 23 2 left Iteration 1 Error: 1.173320 Iteration 2 Error: 0.344861 Iteration 3 Error: 0.070040 Iteration 4 Error: 0.027226 Align patch 24 1 left Iteration 1 Error: 0.884135 Iteration 2 Error: 0.208303 Iteration 3 Error: 0.075973 Iteration 4 Error: 0.032274 Align patch 25 0 left Iteration 1 Error: 0.635901 Iteration 2 Error: 0.085482 Iteration 3 Error: 0.017345 3D Fitting completed. Patch alignment time: 15.52(sec) Local motion has been corrected. Process thread exits. Computational time: 24.742571 sec Total time: 31.084126 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00011hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00011hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.822754s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00011hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.801352s ........................................ >>>>>>TIME<<<<<< FFT: 1.042059s Defocus_U Defocus_V Angle CCC 11527.35 10910.17 82.22 0.040865 Final Values Defocus_U Defocus_V Angle CCC 11553.93 10930.50 81.28 0.064109 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00012hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00012hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.002e-01 CC threshold: 0.736 Mean Std: 40.05 6.83 Num Hot pixels: 223 Hot pixel threshold: 81.04 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.449087 Iteration 2 Error: 0.395821 Iteration 3 Error: 0.098981 Iteration 4 Error: 0.030107 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.01 0.16 ...... Frame ( 3) shift: -0.01 0.33 ...... Frame ( 4) shift: -0.02 0.49 ...... Frame ( 5) shift: -0.03 0.65 ...... Frame ( 6) shift: 0.03 0.79 ...... Frame ( 7) shift: 0.15 0.90 ...... Frame ( 8) shift: 0.26 1.02 ...... Frame ( 9) shift: 0.41 1.11 ...... Frame ( 10) shift: 0.58 1.20 ...... Frame ( 11) shift: 0.75 1.28 ...... Frame ( 12) shift: 0.84 1.35 ...... Frame ( 13) shift: 0.84 1.39 ...... Frame ( 14) shift: 0.84 1.43 ...... Frame ( 15) shift: 0.88 1.49 ...... Frame ( 16) shift: 0.97 1.55 ...... Frame ( 17) shift: 1.06 1.62 ...... Frame ( 18) shift: 1.15 1.68 ...... Frame ( 19) shift: 1.24 1.73 ...... Frame ( 20) shift: 1.33 1.79 ...... Frame ( 21) shift: 1.40 1.88 ...... Frame ( 22) shift: 1.44 2.02 ...... Frame ( 23) shift: 1.47 2.16 ...... Frame ( 24) shift: 1.53 2.32 ...... Frame ( 25) shift: 1.61 2.49 ...... Frame ( 26) shift: 1.69 2.66 ...... Frame ( 27) shift: 1.75 2.75 ...... Frame ( 28) shift: 1.81 2.76 ...... Frame ( 29) shift: 1.87 2.76 ...... Frame ( 30) shift: 1.95 2.80 ...... Frame ( 31) shift: 2.03 2.88 ...... Frame ( 32) shift: 2.12 2.95 ...... Frame ( 33) shift: 2.28 3.01 ...... Frame ( 34) shift: 2.52 3.04 ...... Frame ( 35) shift: 2.76 3.08 ...... Frame ( 36) shift: 2.97 3.15 ...... Frame ( 37) shift: 3.14 3.27 ...... Frame ( 38) shift: 3.31 3.39 ...... Frame ( 39) shift: 3.49 3.51 ...... Frame ( 40) shift: 3.66 3.63 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.717758 Iteration 2 Error: 0.180593 Iteration 3 Error: 0.051423 Iteration 4 Error: 0.022593 Align patch 2 23 left Iteration 1 Error: 0.797926 Iteration 2 Error: 0.227379 Iteration 3 Error: 0.085934 Iteration 4 Error: 0.028702 Align patch 3 22 left Iteration 1 Error: 0.585997 Iteration 2 Error: 0.075693 Iteration 3 Error: 0.022458 Align patch 4 21 left Iteration 1 Error: 0.950369 Iteration 2 Error: 0.118117 Iteration 3 Error: 0.024490 Align patch 5 20 left Iteration 1 Error: 0.583841 Iteration 2 Error: 0.072873 Iteration 3 Error: 0.014817 Align patch 6 19 left Iteration 1 Error: 0.604769 Iteration 2 Error: 0.142442 Iteration 3 Error: 0.051696 Iteration 4 Error: 0.020684 Align patch 7 18 left Iteration 1 Error: 0.502741 Iteration 2 Error: 0.076007 Iteration 3 Error: 0.030583 Align patch 8 17 left Iteration 1 Error: 0.538668 Iteration 2 Error: 0.059784 Iteration 3 Error: 0.015848 Align patch 9 16 left Iteration 1 Error: 0.701827 Iteration 2 Error: 0.102196 Iteration 3 Error: 0.040826 Align patch 10 15 left Iteration 1 Error: 0.755770 Iteration 2 Error: 0.189547 Iteration 3 Error: 0.051137 Iteration 4 Error: 0.010204 Align patch 11 14 left Iteration 1 Error: 0.920395 Iteration 2 Error: 0.192513 Iteration 3 Error: 0.040939 Align patch 12 13 left Iteration 1 Error: 0.587173 Iteration 2 Error: 0.175699 Iteration 3 Error: 0.060770 Iteration 4 Error: 0.023209 Align patch 13 12 left Iteration 1 Error: 0.610289 Iteration 2 Error: 0.136379 Iteration 3 Error: 0.031994 Align patch 14 11 left Iteration 1 Error: 0.565259 Iteration 2 Error: 0.069407 Iteration 3 Error: 0.013871 Align patch 15 10 left Iteration 1 Error: 0.699788 Iteration 2 Error: 0.095112 Iteration 3 Error: 0.015945 Align patch 16 9 left Iteration 1 Error: 0.800243 Iteration 2 Error: 0.185099 Iteration 3 Error: 0.053362 Iteration 4 Error: 0.021125 Align patch 17 8 left Iteration 1 Error: 0.623167 Iteration 2 Error: 0.208459 Iteration 3 Error: 0.081383 Iteration 4 Error: 0.038137 Align patch 18 7 left Iteration 1 Error: 0.575775 Iteration 2 Error: 0.107296 Iteration 3 Error: 0.029410 Align patch 19 6 left Iteration 1 Error: 0.507299 Iteration 2 Error: 0.085313 Iteration 3 Error: 0.019061 Align patch 20 5 left Iteration 1 Error: 0.471677 Iteration 2 Error: 0.110776 Iteration 3 Error: 0.024758 Align patch 21 4 left Iteration 1 Error: 0.491428 Iteration 2 Error: 0.113581 Iteration 3 Error: 0.020657 Align patch 22 3 left Iteration 1 Error: 0.693071 Iteration 2 Error: 0.105624 Iteration 3 Error: 0.029124 Align patch 23 2 left Iteration 1 Error: 0.690570 Iteration 2 Error: 0.174030 Iteration 3 Error: 0.034578 Align patch 24 1 left Iteration 1 Error: 0.858972 Iteration 2 Error: 0.108116 Iteration 3 Error: 0.024484 Align patch 25 0 left Iteration 1 Error: 0.940107 Iteration 2 Error: 0.106661 Iteration 3 Error: 0.028685 3D Fitting completed. Patch alignment time: 15.42(sec) Local motion has been corrected. Process thread exits. Computational time: 24.555809 sec Total time: 30.856266 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00012hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00012hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.767946s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00012hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.775663s ........................................ >>>>>>TIME<<<<<< FFT: 0.939143s Defocus_U Defocus_V Angle CCC 11232.45 12064.48 10.02 0.060801 Final Values Defocus_U Defocus_V Angle CCC 11259.03 12078.56 9.70 0.100378 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00012hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00012hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.003e-01 CC threshold: 0.736 Mean Std: 39.45 6.72 Num Hot pixels: 218 Hot pixel threshold: 79.77 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.372323 Iteration 2 Error: 0.182855 Iteration 3 Error: 0.034475 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.24 0.29 ...... Frame ( 3) shift: 0.47 0.58 ...... Frame ( 4) shift: 0.71 0.86 ...... Frame ( 5) shift: 0.94 1.15 ...... Frame ( 6) shift: 1.12 1.40 ...... Frame ( 7) shift: 1.23 1.62 ...... Frame ( 8) shift: 1.34 1.84 ...... Frame ( 9) shift: 1.41 2.00 ...... Frame ( 10) shift: 1.43 2.11 ...... Frame ( 11) shift: 1.45 2.22 ...... Frame ( 12) shift: 1.44 2.30 ...... Frame ( 13) shift: 1.40 2.34 ...... Frame ( 14) shift: 1.35 2.38 ...... Frame ( 15) shift: 1.35 2.43 ...... Frame ( 16) shift: 1.40 2.49 ...... Frame ( 17) shift: 1.44 2.55 ...... Frame ( 18) shift: 1.48 2.63 ...... Frame ( 19) shift: 1.50 2.71 ...... Frame ( 20) shift: 1.52 2.79 ...... Frame ( 21) shift: 1.55 2.85 ...... Frame ( 22) shift: 1.60 2.90 ...... Frame ( 23) shift: 1.64 2.96 ...... Frame ( 24) shift: 1.65 3.00 ...... Frame ( 25) shift: 1.60 3.03 ...... Frame ( 26) shift: 1.56 3.06 ...... Frame ( 27) shift: 1.57 3.11 ...... Frame ( 28) shift: 1.62 3.18 ...... Frame ( 29) shift: 1.68 3.25 ...... Frame ( 30) shift: 1.74 3.30 ...... Frame ( 31) shift: 1.80 3.33 ...... Frame ( 32) shift: 1.85 3.36 ...... Frame ( 33) shift: 1.86 3.35 ...... Frame ( 34) shift: 1.83 3.29 ...... Frame ( 35) shift: 1.79 3.24 ...... Frame ( 36) shift: 1.80 3.18 ...... Frame ( 37) shift: 1.84 3.13 ...... Frame ( 38) shift: 1.88 3.08 ...... Frame ( 39) shift: 1.92 3.03 ...... Frame ( 40) shift: 1.96 2.99 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.769020 Iteration 2 Error: 0.097249 Iteration 3 Error: 0.018514 Align patch 2 23 left Iteration 1 Error: 0.448571 Iteration 2 Error: 0.073124 Iteration 3 Error: 0.020112 Align patch 3 22 left Iteration 1 Error: 0.567434 Iteration 2 Error: 0.082976 Iteration 3 Error: 0.018457 Align patch 4 21 left Iteration 1 Error: 0.531303 Iteration 2 Error: 0.089687 Iteration 3 Error: 0.022473 Align patch 5 20 left Iteration 1 Error: 0.478714 Iteration 2 Error: 0.046399 Align patch 6 19 left Iteration 1 Error: 0.700495 Iteration 2 Error: 0.141213 Iteration 3 Error: 0.032134 Align patch 7 18 left Iteration 1 Error: 0.594869 Iteration 2 Error: 0.108451 Iteration 3 Error: 0.026242 Align patch 8 17 left Iteration 1 Error: 0.497819 Iteration 2 Error: 0.087482 Iteration 3 Error: 0.018159 Align patch 9 16 left Iteration 1 Error: 0.649181 Iteration 2 Error: 0.198661 Iteration 3 Error: 0.066827 Iteration 4 Error: 0.019778 Align patch 10 15 left Iteration 1 Error: 0.608275 Iteration 2 Error: 0.108139 Iteration 3 Error: 0.033167 Align patch 11 14 left Iteration 1 Error: 0.513478 Iteration 2 Error: 0.051051 Iteration 3 Error: 0.010183 Align patch 12 13 left Iteration 1 Error: 0.590714 Iteration 2 Error: 0.068145 Iteration 3 Error: 0.010937 Align patch 13 12 left Iteration 1 Error: 0.556217 Iteration 2 Error: 0.077775 Iteration 3 Error: 0.016260 Align patch 14 11 left Iteration 1 Error: 0.611859 Iteration 2 Error: 0.166980 Iteration 3 Error: 0.042747 Align patch 15 10 left Iteration 1 Error: 0.612301 Iteration 2 Error: 0.087230 Iteration 3 Error: 0.017154 Align patch 16 9 left Iteration 1 Error: 0.466649 Iteration 2 Error: 0.086971 Iteration 3 Error: 0.013119 Align patch 17 8 left Iteration 1 Error: 0.920395 Iteration 2 Error: 0.109594 Iteration 3 Error: 0.021074 Align patch 18 7 left Iteration 1 Error: 0.678874 Iteration 2 Error: 0.083697 Iteration 3 Error: 0.023020 Align patch 19 6 left Iteration 1 Error: 0.515067 Iteration 2 Error: 0.076951 Iteration 3 Error: 0.016061 Align patch 20 5 left Iteration 1 Error: 0.680169 Iteration 2 Error: 0.088643 Iteration 3 Error: 0.018678 Align patch 21 4 left Iteration 1 Error: 0.639636 Iteration 2 Error: 0.100237 Iteration 3 Error: 0.019270 Align patch 22 3 left Iteration 1 Error: 0.929304 Iteration 2 Error: 0.124670 Iteration 3 Error: 0.026570 Align patch 23 2 left Iteration 1 Error: 0.618941 Iteration 2 Error: 0.097285 Iteration 3 Error: 0.022175 Align patch 24 1 left Iteration 1 Error: 0.590517 Iteration 2 Error: 0.129547 Iteration 3 Error: 0.024531 Align patch 25 0 left Iteration 1 Error: 0.715223 Iteration 2 Error: 0.092024 Iteration 3 Error: 0.017369 3D Fitting completed. Patch alignment time: 15.64(sec) Local motion has been corrected. Process thread exits. Computational time: 24.385553 sec Total time: 30.054991 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00012hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00012hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.550039s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00012hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.725867s ........................................ >>>>>>TIME<<<<<< FFT: 1.027596s Defocus_U Defocus_V Angle CCC 10750.00 11164.06 2.25 0.048034 Final Values Defocus_U Defocus_V Angle CCC 10757.83 11237.53 3.20 0.077498 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00012hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00012hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 40.00 6.84 Num Hot pixels: 229 Hot pixel threshold: 81.07 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.157191 Iteration 2 Error: 0.359357 Iteration 3 Error: 0.090071 Iteration 4 Error: 0.025900 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.03 0.11 ...... Frame ( 3) shift: -0.06 0.22 ...... Frame ( 4) shift: -0.08 0.33 ...... Frame ( 5) shift: -0.11 0.44 ...... Frame ( 6) shift: -0.06 0.54 ...... Frame ( 7) shift: 0.08 0.63 ...... Frame ( 8) shift: 0.22 0.71 ...... Frame ( 9) shift: 0.27 0.80 ...... Frame ( 10) shift: 0.22 0.89 ...... Frame ( 11) shift: 0.17 0.98 ...... Frame ( 12) shift: 0.17 1.00 ...... Frame ( 13) shift: 0.21 0.97 ...... Frame ( 14) shift: 0.25 0.93 ...... Frame ( 15) shift: 0.37 0.91 ...... Frame ( 16) shift: 0.57 0.90 ...... Frame ( 17) shift: 0.78 0.88 ...... Frame ( 18) shift: 0.96 0.91 ...... Frame ( 19) shift: 1.13 0.98 ...... Frame ( 20) shift: 1.29 1.05 ...... Frame ( 21) shift: 1.46 1.12 ...... Frame ( 22) shift: 1.64 1.21 ...... Frame ( 23) shift: 1.83 1.29 ...... Frame ( 24) shift: 1.98 1.40 ...... Frame ( 25) shift: 2.10 1.55 ...... Frame ( 26) shift: 2.22 1.69 ...... Frame ( 27) shift: 2.34 1.78 ...... Frame ( 28) shift: 2.47 1.83 ...... Frame ( 29) shift: 2.60 1.88 ...... Frame ( 30) shift: 2.69 1.97 ...... Frame ( 31) shift: 2.75 2.09 ...... Frame ( 32) shift: 2.81 2.21 ...... Frame ( 33) shift: 2.87 2.32 ...... Frame ( 34) shift: 2.91 2.41 ...... Frame ( 35) shift: 2.96 2.50 ...... Frame ( 36) shift: 3.00 2.60 ...... Frame ( 37) shift: 3.04 2.71 ...... Frame ( 38) shift: 3.08 2.82 ...... Frame ( 39) shift: 3.11 2.93 ...... Frame ( 40) shift: 3.15 3.04 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.732103 Iteration 2 Error: 0.112860 Iteration 3 Error: 0.046793 Align patch 2 23 left Iteration 1 Error: 0.686049 Iteration 2 Error: 0.141261 Iteration 3 Error: 0.034161 Align patch 3 22 left Iteration 1 Error: 0.515857 Iteration 2 Error: 0.170180 Iteration 3 Error: 0.029020 Align patch 4 21 left Iteration 1 Error: 0.675336 Iteration 2 Error: 0.106089 Iteration 3 Error: 0.035764 Align patch 5 20 left Iteration 1 Error: 1.456031 Iteration 2 Error: 0.383523 Iteration 3 Error: 0.082107 Iteration 4 Error: 0.027413 Align patch 6 19 left Iteration 1 Error: 0.797226 Iteration 2 Error: 0.162725 Iteration 3 Error: 0.042537 Align patch 7 18 left Iteration 1 Error: 0.617503 Iteration 2 Error: 0.169673 Iteration 3 Error: 0.045725 Align patch 8 17 left Iteration 1 Error: 0.679829 Iteration 2 Error: 0.159093 Iteration 3 Error: 0.046658 Align patch 9 16 left Iteration 1 Error: 0.531680 Iteration 2 Error: 0.052184 Iteration 3 Error: 0.010254 Align patch 10 15 left Iteration 1 Error: 0.485085 Iteration 2 Error: 0.115357 Iteration 3 Error: 0.030076 Align patch 11 14 left Iteration 1 Error: 0.815044 Iteration 2 Error: 0.188427 Iteration 3 Error: 0.096909 Iteration 4 Error: 0.041995 Align patch 12 13 left Iteration 1 Error: 0.556412 Iteration 2 Error: 0.084737 Iteration 3 Error: 0.015824 Align patch 13 12 left Iteration 1 Error: 0.522326 Iteration 2 Error: 0.070784 Iteration 3 Error: 0.013559 Align patch 14 11 left Iteration 1 Error: 0.557850 Iteration 2 Error: 0.093804 Iteration 3 Error: 0.023502 Align patch 15 10 left Iteration 1 Error: 0.521188 Iteration 2 Error: 0.149140 Iteration 3 Error: 0.042362 Align patch 16 9 left Iteration 1 Error: 0.736241 Iteration 2 Error: 0.124709 Iteration 3 Error: 0.054354 Iteration 4 Error: 0.017542 Align patch 17 8 left Iteration 1 Error: 0.679121 Iteration 2 Error: 0.094877 Iteration 3 Error: 0.024711 Align patch 18 7 left Iteration 1 Error: 0.854813 Iteration 2 Error: 0.136490 Iteration 3 Error: 0.030454 Align patch 19 6 left Iteration 1 Error: 0.383176 Iteration 2 Error: 0.081354 Iteration 3 Error: 0.014265 Align patch 20 5 left Iteration 1 Error: 0.652182 Iteration 2 Error: 0.141560 Iteration 3 Error: 0.030733 Align patch 21 4 left Iteration 1 Error: 1.002562 Iteration 2 Error: 0.112873 Iteration 3 Error: 0.025305 Align patch 22 3 left Iteration 1 Error: 0.726952 Iteration 2 Error: 0.171708 Iteration 3 Error: 0.043284 Align patch 23 2 left Iteration 1 Error: 0.607914 Iteration 2 Error: 0.116734 Iteration 3 Error: 0.033414 Align patch 24 1 left Iteration 1 Error: 0.685010 Iteration 2 Error: 0.070277 Iteration 3 Error: 0.015265 Align patch 25 0 left Iteration 1 Error: 0.667886 Iteration 2 Error: 0.098035 Iteration 3 Error: 0.023469 3D Fitting completed. Patch alignment time: 14.75(sec) Local motion has been corrected. Process thread exits. Computational time: 23.157450 sec Total time: 28.688631 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00012hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00012hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.556287s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00012hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.548500s ........................................ >>>>>>TIME<<<<<< FFT: 0.946572s Defocus_U Defocus_V Angle CCC 13042.97 13906.25 4.72 0.067374 Final Values Defocus_U Defocus_V Angle CCC 13049.21 13903.14 5.04 0.104589 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00012hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00012hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 39.55 6.72 Num Hot pixels: 237 Hot pixel threshold: 79.90 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.851045 Iteration 2 Error: 0.126351 Iteration 3 Error: 0.028353 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.09 0.31 ...... Frame ( 3) shift: 0.19 0.62 ...... Frame ( 4) shift: 0.28 0.92 ...... Frame ( 5) shift: 0.37 1.23 ...... Frame ( 6) shift: 0.45 1.45 ...... Frame ( 7) shift: 0.51 1.57 ...... Frame ( 8) shift: 0.57 1.70 ...... Frame ( 9) shift: 0.58 1.81 ...... Frame ( 10) shift: 0.53 1.90 ...... Frame ( 11) shift: 0.48 1.99 ...... Frame ( 12) shift: 0.46 2.08 ...... Frame ( 13) shift: 0.47 2.16 ...... Frame ( 14) shift: 0.49 2.24 ...... Frame ( 15) shift: 0.49 2.29 ...... Frame ( 16) shift: 0.48 2.31 ...... Frame ( 17) shift: 0.46 2.34 ...... Frame ( 18) shift: 0.43 2.37 ...... Frame ( 19) shift: 0.36 2.41 ...... Frame ( 20) shift: 0.30 2.45 ...... Frame ( 21) shift: 0.29 2.47 ...... Frame ( 22) shift: 0.34 2.48 ...... Frame ( 23) shift: 0.39 2.50 ...... Frame ( 24) shift: 0.40 2.52 ...... Frame ( 25) shift: 0.38 2.57 ...... Frame ( 26) shift: 0.36 2.61 ...... Frame ( 27) shift: 0.35 2.65 ...... Frame ( 28) shift: 0.34 2.68 ...... Frame ( 29) shift: 0.33 2.72 ...... Frame ( 30) shift: 0.33 2.80 ...... Frame ( 31) shift: 0.34 2.91 ...... Frame ( 32) shift: 0.34 3.02 ...... Frame ( 33) shift: 0.31 3.09 ...... Frame ( 34) shift: 0.24 3.13 ...... Frame ( 35) shift: 0.16 3.16 ...... Frame ( 36) shift: 0.15 3.18 ...... Frame ( 37) shift: 0.19 3.19 ...... Frame ( 38) shift: 0.23 3.20 ...... Frame ( 39) shift: 0.27 3.21 ...... Frame ( 40) shift: 0.31 3.22 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.614298 Iteration 2 Error: 0.091044 Iteration 3 Error: 0.016761 Align patch 2 23 left Iteration 1 Error: 0.719349 Iteration 2 Error: 0.179344 Iteration 3 Error: 0.024064 Align patch 3 22 left Iteration 1 Error: 0.784569 Iteration 2 Error: 0.100256 Iteration 3 Error: 0.023107 Align patch 4 21 left Iteration 1 Error: 0.575346 Iteration 2 Error: 0.113016 Iteration 3 Error: 0.019302 Align patch 5 20 left Iteration 1 Error: 0.648195 Iteration 2 Error: 0.102174 Iteration 3 Error: 0.017358 Align patch 6 19 left Iteration 1 Error: 0.836212 Iteration 2 Error: 0.133227 Iteration 3 Error: 0.044166 Align patch 7 18 left Iteration 1 Error: 0.664976 Iteration 2 Error: 0.136007 Iteration 3 Error: 0.031447 Align patch 8 17 left Iteration 1 Error: 0.488988 Iteration 2 Error: 0.072221 Iteration 3 Error: 0.023165 Align patch 9 16 left Iteration 1 Error: 0.523585 Iteration 2 Error: 0.086366 Iteration 3 Error: 0.015292 Align patch 10 15 left Iteration 1 Error: 0.999839 Iteration 2 Error: 0.117730 Iteration 3 Error: 0.014930 Align patch 11 14 left Iteration 1 Error: 0.637287 Iteration 2 Error: 0.095100 Iteration 3 Error: 0.024951 Align patch 12 13 left Iteration 1 Error: 0.530095 Iteration 2 Error: 0.068457 Iteration 3 Error: 0.017770 Align patch 13 12 left Iteration 1 Error: 0.650460 Iteration 2 Error: 0.073629 Iteration 3 Error: 0.017718 Align patch 14 11 left Iteration 1 Error: 0.689339 Iteration 2 Error: 0.087155 Iteration 3 Error: 0.021937 Align patch 15 10 left Iteration 1 Error: 0.792711 Iteration 2 Error: 0.157022 Iteration 3 Error: 0.026680 Align patch 16 9 left Iteration 1 Error: 0.642982 Iteration 2 Error: 0.148862 Iteration 3 Error: 0.022267 Align patch 17 8 left Iteration 1 Error: 0.542248 Iteration 2 Error: 0.055855 Iteration 3 Error: 0.011904 Align patch 18 7 left Iteration 1 Error: 0.586496 Iteration 2 Error: 0.033921 Align patch 19 6 left Iteration 1 Error: 0.645279 Iteration 2 Error: 0.099749 Iteration 3 Error: 0.012712 Align patch 20 5 left Iteration 1 Error: 0.749929 Iteration 2 Error: 0.065404 Iteration 3 Error: 0.011595 Align patch 21 4 left Iteration 1 Error: 0.721665 Iteration 2 Error: 0.114647 Iteration 3 Error: 0.024482 Align patch 22 3 left Iteration 1 Error: 0.882589 Iteration 2 Error: 0.096328 Iteration 3 Error: 0.019803 Align patch 23 2 left Iteration 1 Error: 0.615258 Iteration 2 Error: 0.057514 Iteration 3 Error: 0.014399 Align patch 24 1 left Iteration 1 Error: 0.767403 Iteration 2 Error: 0.104341 Iteration 3 Error: 0.017665 Align patch 25 0 left Iteration 1 Error: 0.948864 Iteration 2 Error: 0.101456 Iteration 3 Error: 0.023706 3D Fitting completed. Patch alignment time: 15.33(sec) Local motion has been corrected. Process thread exits. Computational time: 23.820391 sec Total time: 30.115744 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00012hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00012hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.612871s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00012hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.661849s ........................................ >>>>>>TIME<<<<<< FFT: 0.983865s Defocus_U Defocus_V Angle CCC 11957.05 11308.58 84.43 0.053716 Final Values Defocus_U Defocus_V Angle CCC 11958.61 11347.65 84.11 0.087503 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00013hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00013hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 39.88 6.80 Num Hot pixels: 238 Hot pixel threshold: 80.68 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.311756 Iteration 2 Error: 0.268781 Iteration 3 Error: 0.060457 Iteration 4 Error: 0.018284 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.05 0.11 ...... Frame ( 3) shift: -0.10 0.21 ...... Frame ( 4) shift: -0.15 0.32 ...... Frame ( 5) shift: -0.20 0.43 ...... Frame ( 6) shift: -0.17 0.51 ...... Frame ( 7) shift: -0.07 0.58 ...... Frame ( 8) shift: 0.03 0.65 ...... Frame ( 9) shift: 0.11 0.69 ...... Frame ( 10) shift: 0.17 0.70 ...... Frame ( 11) shift: 0.23 0.71 ...... Frame ( 12) shift: 0.30 0.75 ...... Frame ( 13) shift: 0.38 0.82 ...... Frame ( 14) shift: 0.46 0.88 ...... Frame ( 15) shift: 0.50 0.95 ...... Frame ( 16) shift: 0.50 1.02 ...... Frame ( 17) shift: 0.50 1.10 ...... Frame ( 18) shift: 0.54 1.18 ...... Frame ( 19) shift: 0.63 1.27 ...... Frame ( 20) shift: 0.71 1.37 ...... Frame ( 21) shift: 0.75 1.44 ...... Frame ( 22) shift: 0.74 1.50 ...... Frame ( 23) shift: 0.73 1.55 ...... Frame ( 24) shift: 0.78 1.58 ...... Frame ( 25) shift: 0.89 1.59 ...... Frame ( 26) shift: 0.99 1.60 ...... Frame ( 27) shift: 1.09 1.63 ...... Frame ( 28) shift: 1.17 1.67 ...... Frame ( 29) shift: 1.25 1.72 ...... Frame ( 30) shift: 1.29 1.77 ...... Frame ( 31) shift: 1.30 1.84 ...... Frame ( 32) shift: 1.30 1.90 ...... Frame ( 33) shift: 1.33 1.99 ...... Frame ( 34) shift: 1.37 2.11 ...... Frame ( 35) shift: 1.41 2.22 ...... Frame ( 36) shift: 1.46 2.31 ...... Frame ( 37) shift: 1.50 2.37 ...... Frame ( 38) shift: 1.54 2.42 ...... Frame ( 39) shift: 1.58 2.48 ...... Frame ( 40) shift: 1.62 2.54 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.911897 Iteration 2 Error: 0.200809 Iteration 3 Error: 0.067092 Iteration 4 Error: 0.019674 Align patch 2 23 left Iteration 1 Error: 0.644000 Iteration 2 Error: 0.232532 Iteration 3 Error: 0.102478 Iteration 4 Error: 0.041869 Align patch 3 22 left Iteration 1 Error: 0.690192 Iteration 2 Error: 0.119341 Iteration 3 Error: 0.044464 Align patch 4 21 left Iteration 1 Error: 0.481639 Iteration 2 Error: 0.070412 Iteration 3 Error: 0.017064 Align patch 5 20 left Iteration 1 Error: 0.549232 Iteration 2 Error: 0.105779 Iteration 3 Error: 0.019554 Align patch 6 19 left Iteration 1 Error: 0.988337 Iteration 2 Error: 0.199236 Iteration 3 Error: 0.070586 Iteration 4 Error: 0.020003 Align patch 7 18 left Iteration 1 Error: 0.945245 Iteration 2 Error: 0.213316 Iteration 3 Error: 0.086918 Iteration 4 Error: 0.032273 Align patch 8 17 left Iteration 1 Error: 0.677310 Iteration 2 Error: 0.142204 Iteration 3 Error: 0.033560 Align patch 9 16 left Iteration 1 Error: 0.723575 Iteration 2 Error: 0.092720 Iteration 3 Error: 0.019491 Align patch 10 15 left Iteration 1 Error: 0.529094 Iteration 2 Error: 0.102222 Iteration 3 Error: 0.020050 Align patch 11 14 left Iteration 1 Error: 0.733429 Iteration 2 Error: 0.117337 Iteration 3 Error: 0.071200 Iteration 4 Error: 0.017424 Align patch 12 13 left Iteration 1 Error: 0.571086 Iteration 2 Error: 0.084188 Iteration 3 Error: 0.030814 Align patch 13 12 left Iteration 1 Error: 0.564062 Iteration 2 Error: 0.124376 Iteration 3 Error: 0.035982 Align patch 14 11 left Iteration 1 Error: 0.411547 Iteration 2 Error: 0.082497 Iteration 3 Error: 0.020235 Align patch 15 10 left Iteration 1 Error: 0.426367 Iteration 2 Error: 0.086632 Iteration 3 Error: 0.022347 Align patch 16 9 left Iteration 1 Error: 0.612825 Iteration 2 Error: 0.102399 Iteration 3 Error: 0.035084 Align patch 17 8 left Iteration 1 Error: 0.499559 Iteration 2 Error: 0.083538 Iteration 3 Error: 0.026648 Align patch 18 7 left Iteration 1 Error: 0.558844 Iteration 2 Error: 0.139866 Iteration 3 Error: 0.039172 Align patch 19 6 left Iteration 1 Error: 0.702220 Iteration 2 Error: 0.186412 Iteration 3 Error: 0.042905 Align patch 20 5 left Iteration 1 Error: 0.847601 Iteration 2 Error: 0.137788 Iteration 3 Error: 0.033080 Align patch 21 4 left Iteration 1 Error: 0.555306 Iteration 2 Error: 0.134266 Iteration 3 Error: 0.044581 Align patch 22 3 left Iteration 1 Error: 0.491946 Iteration 2 Error: 0.133834 Iteration 3 Error: 0.067172 Iteration 4 Error: 0.015937 Align patch 23 2 left Iteration 1 Error: 0.485677 Iteration 2 Error: 0.087686 Iteration 3 Error: 0.021157 Align patch 24 1 left Iteration 1 Error: 1.041124 Iteration 2 Error: 0.089304 Iteration 3 Error: 0.016723 Align patch 25 0 left Iteration 1 Error: 0.513092 Iteration 2 Error: 0.117744 Iteration 3 Error: 0.019524 3D Fitting completed. Patch alignment time: 16.03(sec) Local motion has been corrected. Process thread exits. Computational time: 25.216097 sec Total time: 32.872524 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00013hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00013hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.534560s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00013hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.480405s ........................................ >>>>>>TIME<<<<<< FFT: 0.941449s Defocus_U Defocus_V Angle CCC 10828.15 11699.24 13.61 0.047998 Final Values Defocus_U Defocus_V Angle CCC 10846.90 11721.13 13.30 0.081494 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00013hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00013hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.004e-01 CC threshold: 0.737 Mean Std: 39.47 7.13 Num Hot pixels: 194 Hot pixel threshold: 82.23 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.877544 Iteration 2 Error: 0.183393 Iteration 3 Error: 0.045953 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.10 -0.04 ...... Frame ( 3) shift: -0.20 -0.07 ...... Frame ( 4) shift: -0.29 -0.11 ...... Frame ( 5) shift: -0.39 -0.15 ...... Frame ( 6) shift: -0.42 -0.15 ...... Frame ( 7) shift: -0.36 -0.13 ...... Frame ( 8) shift: -0.31 -0.10 ...... Frame ( 9) shift: -0.24 -0.04 ...... Frame ( 10) shift: -0.15 0.05 ...... Frame ( 11) shift: -0.07 0.15 ...... Frame ( 12) shift: 0.00 0.22 ...... Frame ( 13) shift: 0.07 0.27 ...... Frame ( 14) shift: 0.13 0.32 ...... Frame ( 15) shift: 0.14 0.39 ...... Frame ( 16) shift: 0.09 0.46 ...... Frame ( 17) shift: 0.05 0.54 ...... Frame ( 18) shift: 0.07 0.61 ...... Frame ( 19) shift: 0.15 0.65 ...... Frame ( 20) shift: 0.24 0.70 ...... Frame ( 21) shift: 0.30 0.76 ...... Frame ( 22) shift: 0.35 0.85 ...... Frame ( 23) shift: 0.40 0.94 ...... Frame ( 24) shift: 0.45 0.99 ...... Frame ( 25) shift: 0.50 1.03 ...... Frame ( 26) shift: 0.55 1.06 ...... Frame ( 27) shift: 0.58 1.09 ...... Frame ( 28) shift: 0.60 1.11 ...... Frame ( 29) shift: 0.62 1.14 ...... Frame ( 30) shift: 0.63 1.18 ...... Frame ( 31) shift: 0.63 1.22 ...... Frame ( 32) shift: 0.62 1.27 ...... Frame ( 33) shift: 0.64 1.30 ...... Frame ( 34) shift: 0.69 1.31 ...... Frame ( 35) shift: 0.73 1.33 ...... Frame ( 36) shift: 0.76 1.36 ...... Frame ( 37) shift: 0.78 1.40 ...... Frame ( 38) shift: 0.80 1.44 ...... Frame ( 39) shift: 0.81 1.48 ...... Frame ( 40) shift: 0.83 1.52 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.791697 Iteration 2 Error: 0.135983 Iteration 3 Error: 0.061312 Iteration 4 Error: 0.022679 Align patch 2 23 left Iteration 1 Error: 0.770476 Iteration 2 Error: 0.098502 Iteration 3 Error: 0.029294 Align patch 3 22 left Iteration 1 Error: 0.476628 Iteration 2 Error: 0.099261 Iteration 3 Error: 0.013716 Align patch 4 21 left Iteration 1 Error: 0.533639 Iteration 2 Error: 0.121982 Iteration 3 Error: 0.021453 Align patch 5 20 left Iteration 1 Error: 0.322129 Iteration 2 Error: 0.104202 Iteration 3 Error: 0.022829 Align patch 6 19 left Iteration 1 Error: 0.939503 Iteration 2 Error: 0.197934 Iteration 3 Error: 0.049283 Align patch 7 18 left Iteration 1 Error: 0.697575 Iteration 2 Error: 0.120884 Iteration 3 Error: 0.028897 Align patch 8 17 left Iteration 1 Error: 0.577458 Iteration 2 Error: 0.159118 Iteration 3 Error: 0.047190 Align patch 9 16 left Iteration 1 Error: 0.540751 Iteration 2 Error: 0.079347 Iteration 3 Error: 0.021710 Align patch 10 15 left Iteration 1 Error: 0.400868 Iteration 2 Error: 0.059198 Iteration 3 Error: 0.012127 Align patch 11 14 left Iteration 1 Error: 0.651572 Iteration 2 Error: 0.169093 Iteration 3 Error: 0.037204 Align patch 12 13 left Iteration 1 Error: 0.553210 Iteration 2 Error: 0.126680 Iteration 3 Error: 0.042600 Align patch 13 12 left Iteration 1 Error: 0.404798 Iteration 2 Error: 0.045277 Align patch 14 11 left Iteration 1 Error: 0.528983 Iteration 2 Error: 0.127379 Iteration 3 Error: 0.039536 Align patch 15 10 left Iteration 1 Error: 0.468224 Iteration 2 Error: 0.051110 Iteration 3 Error: 0.014915 Align patch 16 9 left Iteration 1 Error: 1.052520 Iteration 2 Error: 0.201774 Iteration 3 Error: 0.059422 Iteration 4 Error: 0.024686 Align patch 17 8 left Iteration 1 Error: 0.623036 Iteration 2 Error: 0.099930 Iteration 3 Error: 0.030747 Align patch 18 7 left Iteration 1 Error: 0.694633 Iteration 2 Error: 0.085231 Iteration 3 Error: 0.024230 Align patch 19 6 left Iteration 1 Error: 0.588297 Iteration 2 Error: 0.125930 Iteration 3 Error: 0.031002 Align patch 20 5 left Iteration 1 Error: 0.619643 Iteration 2 Error: 0.093691 Iteration 3 Error: 0.015506 Align patch 21 4 left Iteration 1 Error: 0.800086 Iteration 2 Error: 0.137246 Iteration 3 Error: 0.030324 Align patch 22 3 left Iteration 1 Error: 0.512722 Iteration 2 Error: 0.086317 Iteration 3 Error: 0.015061 Align patch 23 2 left Iteration 1 Error: 0.396779 Iteration 2 Error: 0.065107 Iteration 3 Error: 0.015337 Align patch 24 1 left Iteration 1 Error: 0.602210 Iteration 2 Error: 0.107036 Iteration 3 Error: 0.036572 Align patch 25 0 left Iteration 1 Error: 0.776334 Iteration 2 Error: 0.162202 Iteration 3 Error: 0.040147 3D Fitting completed. Patch alignment time: 14.79(sec) Local motion has been corrected. Process thread exits. Computational time: 22.862455 sec Total time: 29.224661 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00013hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00013hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.695406s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00013hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.101142s ........................................ >>>>>>TIME<<<<<< FFT: 1.056430s Defocus_U Defocus_V Angle CCC 10027.37 10539.09 2.90 0.042993 Final Values Defocus_U Defocus_V Angle CCC 10061.75 10573.47 2.27 0.076517 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00013hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00013hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.002e-01 CC threshold: 0.736 Mean Std: 40.09 6.80 Num Hot pixels: 212 Hot pixel threshold: 80.89 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.077048 Iteration 2 Error: 0.237014 Iteration 3 Error: 0.056122 Iteration 4 Error: 0.017034 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.03 0.19 ...... Frame ( 3) shift: -0.07 0.37 ...... Frame ( 4) shift: -0.10 0.56 ...... Frame ( 5) shift: -0.13 0.75 ...... Frame ( 6) shift: -0.13 0.83 ...... Frame ( 7) shift: -0.09 0.81 ...... Frame ( 8) shift: -0.05 0.79 ...... Frame ( 9) shift: 0.01 0.79 ...... Frame ( 10) shift: 0.10 0.79 ...... Frame ( 11) shift: 0.18 0.80 ...... Frame ( 12) shift: 0.26 0.80 ...... Frame ( 13) shift: 0.33 0.80 ...... Frame ( 14) shift: 0.40 0.81 ...... Frame ( 15) shift: 0.45 0.81 ...... Frame ( 16) shift: 0.48 0.81 ...... Frame ( 17) shift: 0.51 0.82 ...... Frame ( 18) shift: 0.54 0.83 ...... Frame ( 19) shift: 0.57 0.86 ...... Frame ( 20) shift: 0.60 0.88 ...... Frame ( 21) shift: 0.65 0.92 ...... Frame ( 22) shift: 0.71 0.98 ...... Frame ( 23) shift: 0.76 1.03 ...... Frame ( 24) shift: 0.82 1.10 ...... Frame ( 25) shift: 0.86 1.18 ...... Frame ( 26) shift: 0.91 1.26 ...... Frame ( 27) shift: 0.95 1.33 ...... Frame ( 28) shift: 1.00 1.38 ...... Frame ( 29) shift: 1.05 1.43 ...... Frame ( 30) shift: 1.12 1.48 ...... Frame ( 31) shift: 1.22 1.53 ...... Frame ( 32) shift: 1.31 1.58 ...... Frame ( 33) shift: 1.39 1.61 ...... Frame ( 34) shift: 1.45 1.64 ...... Frame ( 35) shift: 1.51 1.67 ...... Frame ( 36) shift: 1.55 1.72 ...... Frame ( 37) shift: 1.58 1.79 ...... Frame ( 38) shift: 1.61 1.86 ...... Frame ( 39) shift: 1.64 1.94 ...... Frame ( 40) shift: 1.67 2.01 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.916725 Iteration 2 Error: 0.519974 Iteration 3 Error: 0.149168 Iteration 4 Error: 0.060397 Iteration 5 Error: 0.021403 Align patch 2 23 left Iteration 1 Error: 1.645651 Iteration 2 Error: 0.329355 Iteration 3 Error: 0.067480 Iteration 4 Error: 0.024079 Align patch 3 22 left Iteration 1 Error: 1.172040 Iteration 2 Error: 0.209177 Iteration 3 Error: 0.066262 Iteration 4 Error: 0.026391 Align patch 4 21 left Iteration 1 Error: 0.765688 Iteration 2 Error: 0.178989 Iteration 3 Error: 0.047014 Align patch 5 20 left Iteration 1 Error: 0.674957 Iteration 2 Error: 0.116462 Iteration 3 Error: 0.026492 Align patch 6 19 left Iteration 1 Error: 1.046501 Iteration 2 Error: 0.260476 Iteration 3 Error: 0.074269 Iteration 4 Error: 0.028827 Align patch 7 18 left Iteration 1 Error: 1.689078 Iteration 2 Error: 0.350313 Iteration 3 Error: 0.158335 Iteration 4 Error: 0.063794 Iteration 5 Error: 0.026663 Align patch 8 17 left Iteration 1 Error: 0.790032 Iteration 2 Error: 0.106259 Iteration 3 Error: 0.036198 Align patch 9 16 left Iteration 1 Error: 0.420470 Iteration 2 Error: 0.067015 Iteration 3 Error: 0.008995 Align patch 10 15 left Iteration 1 Error: 0.534870 Iteration 2 Error: 0.086881 Iteration 3 Error: 0.021950 Align patch 11 14 left Iteration 1 Error: 0.695452 Iteration 2 Error: 0.194731 Iteration 3 Error: 0.056851 Iteration 4 Error: 0.023908 Align patch 12 13 left Iteration 1 Error: 0.565988 Iteration 2 Error: 0.142320 Iteration 3 Error: 0.053727 Iteration 4 Error: 0.025880 Align patch 13 12 left Iteration 1 Error: 0.745514 Iteration 2 Error: 0.105759 Iteration 3 Error: 0.025256 Align patch 14 11 left Iteration 1 Error: 0.417377 Iteration 2 Error: 0.088930 Iteration 3 Error: 0.026924 Align patch 15 10 left Iteration 1 Error: 0.566169 Iteration 2 Error: 0.097655 Iteration 3 Error: 0.028313 Align patch 16 9 left Iteration 1 Error: 0.715199 Iteration 2 Error: 0.105334 Iteration 3 Error: 0.028676 Align patch 17 8 left Iteration 1 Error: 0.642185 Iteration 2 Error: 0.146867 Iteration 3 Error: 0.032242 Align patch 18 7 left Iteration 1 Error: 0.780378 Iteration 2 Error: 0.097221 Iteration 3 Error: 0.035687 Align patch 19 6 left Iteration 1 Error: 0.840946 Iteration 2 Error: 0.109219 Iteration 3 Error: 0.029097 Align patch 20 5 left Iteration 1 Error: 0.864214 Iteration 2 Error: 0.097685 Iteration 3 Error: 0.030289 Align patch 21 4 left Iteration 1 Error: 0.596479 Iteration 2 Error: 0.139601 Iteration 3 Error: 0.041459 Align patch 22 3 left Iteration 1 Error: 0.810699 Iteration 2 Error: 0.161655 Iteration 3 Error: 0.029617 Align patch 23 2 left Iteration 1 Error: 0.887751 Iteration 2 Error: 0.230654 Iteration 3 Error: 0.038224 Align patch 24 1 left Iteration 1 Error: 1.281816 Iteration 2 Error: 0.140094 Iteration 3 Error: 0.026486 Align patch 25 0 left Iteration 1 Error: 1.476681 Iteration 2 Error: 0.158681 Iteration 3 Error: 0.029744 3D Fitting completed. Patch alignment time: 15.14(sec) Local motion has been corrected. Process thread exits. Computational time: 23.369644 sec Total time: 29.186874 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00013hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00013hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.772574s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00013hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.203826s ........................................ >>>>>>TIME<<<<<< FFT: 1.052584s Defocus_U Defocus_V Angle CCC 10757.85 11640.66 4.85 0.045415 Final Values Defocus_U Defocus_V Angle CCC 10762.58 11670.39 4.85 0.076122 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00013hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00013hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 39.13 6.80 Num Hot pixels: 235 Hot pixel threshold: 79.94 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.804482 Iteration 2 Error: 0.146793 Iteration 3 Error: 0.022325 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.16 0.02 ...... Frame ( 3) shift: -0.32 0.04 ...... Frame ( 4) shift: -0.48 0.06 ...... Frame ( 5) shift: -0.64 0.07 ...... Frame ( 6) shift: -0.74 0.10 ...... Frame ( 7) shift: -0.77 0.13 ...... Frame ( 8) shift: -0.80 0.15 ...... Frame ( 9) shift: -0.78 0.20 ...... Frame ( 10) shift: -0.73 0.26 ...... Frame ( 11) shift: -0.67 0.33 ...... Frame ( 12) shift: -0.62 0.37 ...... Frame ( 13) shift: -0.59 0.40 ...... Frame ( 14) shift: -0.56 0.43 ...... Frame ( 15) shift: -0.55 0.47 ...... Frame ( 16) shift: -0.56 0.52 ...... Frame ( 17) shift: -0.57 0.57 ...... Frame ( 18) shift: -0.56 0.64 ...... Frame ( 19) shift: -0.54 0.72 ...... Frame ( 20) shift: -0.52 0.80 ...... Frame ( 21) shift: -0.49 0.87 ...... Frame ( 22) shift: -0.45 0.92 ...... Frame ( 23) shift: -0.41 0.98 ...... Frame ( 24) shift: -0.39 1.01 ...... Frame ( 25) shift: -0.39 1.04 ...... Frame ( 26) shift: -0.38 1.06 ...... Frame ( 27) shift: -0.38 1.08 ...... Frame ( 28) shift: -0.39 1.10 ...... Frame ( 29) shift: -0.41 1.12 ...... Frame ( 30) shift: -0.39 1.17 ...... Frame ( 31) shift: -0.35 1.23 ...... Frame ( 32) shift: -0.32 1.30 ...... Frame ( 33) shift: -0.27 1.34 ...... Frame ( 34) shift: -0.23 1.35 ...... Frame ( 35) shift: -0.19 1.36 ...... Frame ( 36) shift: -0.16 1.39 ...... Frame ( 37) shift: -0.15 1.45 ...... Frame ( 38) shift: -0.13 1.51 ...... Frame ( 39) shift: -0.12 1.57 ...... Frame ( 40) shift: -0.11 1.63 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.016832 Iteration 2 Error: 0.084851 Iteration 3 Error: 0.017849 Align patch 2 23 left Iteration 1 Error: 0.644683 Iteration 2 Error: 0.062628 Iteration 3 Error: 0.013622 Align patch 3 22 left Iteration 1 Error: 0.646413 Iteration 2 Error: 0.084460 Iteration 3 Error: 0.019992 Align patch 4 21 left Iteration 1 Error: 0.681339 Iteration 2 Error: 0.110634 Iteration 3 Error: 0.025252 Align patch 5 20 left Iteration 1 Error: 0.944620 Iteration 2 Error: 0.107080 Iteration 3 Error: 0.019374 Align patch 6 19 left Iteration 1 Error: 1.160761 Iteration 2 Error: 0.239395 Iteration 3 Error: 0.052269 Iteration 4 Error: 0.018189 Align patch 7 18 left Iteration 1 Error: 0.748164 Iteration 2 Error: 0.152585 Iteration 3 Error: 0.033444 Align patch 8 17 left Iteration 1 Error: 0.570598 Iteration 2 Error: 0.055113 Iteration 3 Error: 0.014901 Align patch 9 16 left Iteration 1 Error: 0.455844 Iteration 2 Error: 0.074082 Iteration 3 Error: 0.019657 Align patch 10 15 left Iteration 1 Error: 0.446954 Iteration 2 Error: 0.064616 Iteration 3 Error: 0.010607 Align patch 11 14 left Iteration 1 Error: 1.115620 Iteration 2 Error: 0.172203 Iteration 3 Error: 0.061705 Iteration 4 Error: 0.015110 Align patch 12 13 left Iteration 1 Error: 0.916481 Iteration 2 Error: 0.097714 Iteration 3 Error: 0.021953 Align patch 13 12 left Iteration 1 Error: 0.543839 Iteration 2 Error: 0.059440 Iteration 3 Error: 0.009349 Align patch 14 11 left Iteration 1 Error: 0.446947 Iteration 2 Error: 0.073952 Iteration 3 Error: 0.011492 Align patch 15 10 left Iteration 1 Error: 0.712408 Iteration 2 Error: 0.104297 Iteration 3 Error: 0.022992 Align patch 16 9 left Iteration 1 Error: 0.976170 Iteration 2 Error: 0.120251 Iteration 3 Error: 0.028584 Align patch 17 8 left Iteration 1 Error: 0.457547 Iteration 2 Error: 0.087035 Iteration 3 Error: 0.032210 Align patch 18 7 left Iteration 1 Error: 0.451989 Iteration 2 Error: 0.048547 Align patch 19 6 left Iteration 1 Error: 0.491958 Iteration 2 Error: 0.084697 Iteration 3 Error: 0.017125 Align patch 20 5 left Iteration 1 Error: 0.728443 Iteration 2 Error: 0.185828 Iteration 3 Error: 0.043472 Align patch 21 4 left Iteration 1 Error: 0.692513 Iteration 2 Error: 0.107230 Iteration 3 Error: 0.024119 Align patch 22 3 left Iteration 1 Error: 0.822091 Iteration 2 Error: 0.103706 Iteration 3 Error: 0.017558 Align patch 23 2 left Iteration 1 Error: 0.690050 Iteration 2 Error: 0.103773 Iteration 3 Error: 0.027528 Align patch 24 1 left Iteration 1 Error: 0.845693 Iteration 2 Error: 0.153088 Iteration 3 Error: 0.047359 Align patch 25 0 left Iteration 1 Error: 0.748392 Iteration 2 Error: 0.187475 Iteration 3 Error: 0.046344 3D Fitting completed. Patch alignment time: 15.00(sec) Local motion has been corrected. Process thread exits. Computational time: 23.585264 sec Total time: 29.433571 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00013hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00013hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.575720s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00013hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.188724s ........................................ >>>>>>TIME<<<<<< FFT: 0.957411s Defocus_U Defocus_V Angle CCC 15359.71 14691.09 84.97 0.059648 Final Values Defocus_U Defocus_V Angle CCC 15392.54 14705.17 85.29 0.090597 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00014hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00014hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.001e-01 CC threshold: 0.736 Mean Std: 38.94 6.66 Num Hot pixels: 201 Hot pixel threshold: 78.91 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.867722 Iteration 2 Error: 0.420676 Iteration 3 Error: 0.105006 Iteration 4 Error: 0.035422 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.01 0.10 ...... Frame ( 3) shift: -0.01 0.19 ...... Frame ( 4) shift: -0.02 0.29 ...... Frame ( 5) shift: -0.03 0.38 ...... Frame ( 6) shift: 0.01 0.46 ...... Frame ( 7) shift: 0.10 0.52 ...... Frame ( 8) shift: 0.18 0.58 ...... Frame ( 9) shift: 0.28 0.66 ...... Frame ( 10) shift: 0.39 0.76 ...... Frame ( 11) shift: 0.50 0.86 ...... Frame ( 12) shift: 0.60 0.99 ...... Frame ( 13) shift: 0.71 1.15 ...... Frame ( 14) shift: 0.81 1.31 ...... Frame ( 15) shift: 0.87 1.45 ...... Frame ( 16) shift: 0.91 1.58 ...... Frame ( 17) shift: 0.95 1.71 ...... Frame ( 18) shift: 1.03 1.81 ...... Frame ( 19) shift: 1.14 1.88 ...... Frame ( 20) shift: 1.25 1.95 ...... Frame ( 21) shift: 1.35 2.03 ...... Frame ( 22) shift: 1.43 2.13 ...... Frame ( 23) shift: 1.51 2.22 ...... Frame ( 24) shift: 1.60 2.30 ...... Frame ( 25) shift: 1.69 2.36 ...... Frame ( 26) shift: 1.78 2.42 ...... Frame ( 27) shift: 1.84 2.50 ...... Frame ( 28) shift: 1.89 2.61 ...... Frame ( 29) shift: 1.94 2.72 ...... Frame ( 30) shift: 2.00 2.83 ...... Frame ( 31) shift: 2.07 2.93 ...... Frame ( 32) shift: 2.15 3.04 ...... Frame ( 33) shift: 2.21 3.09 ...... Frame ( 34) shift: 2.26 3.09 ...... Frame ( 35) shift: 2.32 3.10 ...... Frame ( 36) shift: 2.38 3.14 ...... Frame ( 37) shift: 2.45 3.24 ...... Frame ( 38) shift: 2.52 3.34 ...... Frame ( 39) shift: 2.59 3.43 ...... Frame ( 40) shift: 2.66 3.53 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.178206 Iteration 2 Error: 0.325657 Iteration 3 Error: 0.093051 Iteration 4 Error: 0.037522 Align patch 2 23 left Iteration 1 Error: 0.925673 Iteration 2 Error: 0.288842 Iteration 3 Error: 0.055950 Iteration 4 Error: 0.022745 Align patch 3 22 left Iteration 1 Error: 0.782554 Iteration 2 Error: 0.107237 Iteration 3 Error: 0.030262 Align patch 4 21 left Iteration 1 Error: 0.466733 Iteration 2 Error: 0.077726 Iteration 3 Error: 0.018506 Align patch 5 20 left Iteration 1 Error: 0.650351 Iteration 2 Error: 0.119787 Iteration 3 Error: 0.026651 Align patch 6 19 left Iteration 1 Error: 0.777012 Iteration 2 Error: 0.276051 Iteration 3 Error: 0.097743 Iteration 4 Error: 0.035410 Align patch 7 18 left Iteration 1 Error: 0.897939 Iteration 2 Error: 0.236320 Iteration 3 Error: 0.061237 Iteration 4 Error: 0.019242 Align patch 8 17 left Iteration 1 Error: 0.720529 Iteration 2 Error: 0.146478 Iteration 3 Error: 0.039941 Align patch 9 16 left Iteration 1 Error: 0.708794 Iteration 2 Error: 0.125160 Iteration 3 Error: 0.028851 Align patch 10 15 left Iteration 1 Error: 0.583387 Iteration 2 Error: 0.093196 Iteration 3 Error: 0.020287 Align patch 11 14 left Iteration 1 Error: 0.818838 Iteration 2 Error: 0.193060 Iteration 3 Error: 0.058770 Iteration 4 Error: 0.029274 Align patch 12 13 left Iteration 1 Error: 0.698896 Iteration 2 Error: 0.135183 Iteration 3 Error: 0.044080 Align patch 13 12 left Iteration 1 Error: 0.555744 Iteration 2 Error: 0.075399 Iteration 3 Error: 0.017170 Align patch 14 11 left Iteration 1 Error: 0.813616 Iteration 2 Error: 0.146452 Iteration 3 Error: 0.053854 Iteration 4 Error: 0.020009 Align patch 15 10 left Iteration 1 Error: 0.765104 Iteration 2 Error: 0.140819 Iteration 3 Error: 0.038354 Align patch 16 9 left Iteration 1 Error: 0.543719 Iteration 2 Error: 0.215674 Iteration 3 Error: 0.095146 Iteration 4 Error: 0.067097 Iteration 5 Error: 0.034314 Align patch 17 8 left Iteration 1 Error: 0.855671 Iteration 2 Error: 0.155605 Iteration 3 Error: 0.055005 Iteration 4 Error: 0.023301 Align patch 18 7 left Iteration 1 Error: 0.587293 Iteration 2 Error: 0.075206 Iteration 3 Error: 0.017539 Align patch 19 6 left Iteration 1 Error: 1.005871 Iteration 2 Error: 0.138123 Iteration 3 Error: 0.030847 Align patch 20 5 left Iteration 1 Error: 0.862990 Iteration 2 Error: 0.106214 Iteration 3 Error: 0.026118 Align patch 21 4 left Iteration 1 Error: 0.913533 Iteration 2 Error: 0.216382 Iteration 3 Error: 0.082960 Iteration 4 Error: 0.040039 Align patch 22 3 left Iteration 1 Error: 0.513389 Iteration 2 Error: 0.119151 Iteration 3 Error: 0.028993 Align patch 23 2 left Iteration 1 Error: 0.816674 Iteration 2 Error: 0.170991 Iteration 3 Error: 0.043063 Align patch 24 1 left Iteration 1 Error: 0.738557 Iteration 2 Error: 0.166772 Iteration 3 Error: 0.063009 Iteration 4 Error: 0.012044 Align patch 25 0 left Iteration 1 Error: 1.062642 Iteration 2 Error: 0.223404 Iteration 3 Error: 0.123981 Iteration 4 Error: 0.054713 Iteration 5 Error: 0.026105 3D Fitting completed. Patch alignment time: 15.95(sec) Local motion has been corrected. Process thread exits. Computational time: 24.825348 sec Total time: 30.765854 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00014hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00014hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.701479s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00014hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.321839s ........................................ >>>>>>TIME<<<<<< FFT: 0.986402s Defocus_U Defocus_V Angle CCC 12380.86 13220.70 11.20 0.050641 Final Values Defocus_U Defocus_V Angle CCC 12387.11 13217.58 11.20 0.077532 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00014hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00014hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 40.29 6.80 Num Hot pixels: 217 Hot pixel threshold: 81.12 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.585543 Iteration 2 Error: 0.262597 Iteration 3 Error: 0.057616 Iteration 4 Error: 0.020811 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.08 0.12 ...... Frame ( 3) shift: 0.15 0.23 ...... Frame ( 4) shift: 0.23 0.35 ...... Frame ( 5) shift: 0.30 0.47 ...... Frame ( 6) shift: 0.39 0.56 ...... Frame ( 7) shift: 0.49 0.63 ...... Frame ( 8) shift: 0.59 0.71 ...... Frame ( 9) shift: 0.66 0.77 ...... Frame ( 10) shift: 0.68 0.84 ...... Frame ( 11) shift: 0.71 0.91 ...... Frame ( 12) shift: 0.77 0.95 ...... Frame ( 13) shift: 0.86 0.98 ...... Frame ( 14) shift: 0.96 1.00 ...... Frame ( 15) shift: 1.04 1.05 ...... Frame ( 16) shift: 1.10 1.14 ...... Frame ( 17) shift: 1.16 1.22 ...... Frame ( 18) shift: 1.22 1.29 ...... Frame ( 19) shift: 1.28 1.34 ...... Frame ( 20) shift: 1.34 1.40 ...... Frame ( 21) shift: 1.41 1.47 ...... Frame ( 22) shift: 1.52 1.57 ...... Frame ( 23) shift: 1.62 1.67 ...... Frame ( 24) shift: 1.68 1.71 ...... Frame ( 25) shift: 1.71 1.69 ...... Frame ( 26) shift: 1.73 1.68 ...... Frame ( 27) shift: 1.77 1.67 ...... Frame ( 28) shift: 1.82 1.69 ...... Frame ( 29) shift: 1.86 1.70 ...... Frame ( 30) shift: 1.90 1.75 ...... Frame ( 31) shift: 1.91 1.83 ...... Frame ( 32) shift: 1.93 1.92 ...... Frame ( 33) shift: 2.00 1.99 ...... Frame ( 34) shift: 2.13 2.06 ...... Frame ( 35) shift: 2.25 2.12 ...... Frame ( 36) shift: 2.34 2.18 ...... Frame ( 37) shift: 2.39 2.24 ...... Frame ( 38) shift: 2.43 2.30 ...... Frame ( 39) shift: 2.48 2.36 ...... Frame ( 40) shift: 2.53 2.42 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.356749 Iteration 2 Error: 0.270892 Iteration 3 Error: 0.107725 Iteration 4 Error: 0.048684 Align patch 2 23 left Iteration 1 Error: 0.664270 Iteration 2 Error: 0.100481 Iteration 3 Error: 0.025688 Align patch 3 22 left Iteration 1 Error: 0.760266 Iteration 2 Error: 0.152673 Iteration 3 Error: 0.029546 Align patch 4 21 left Iteration 1 Error: 0.654154 Iteration 2 Error: 0.076411 Iteration 3 Error: 0.012437 Align patch 5 20 left Iteration 1 Error: 0.559265 Iteration 2 Error: 0.078366 Iteration 3 Error: 0.015409 Align patch 6 19 left Iteration 1 Error: 0.639206 Iteration 2 Error: 0.246146 Iteration 3 Error: 0.103357 Iteration 4 Error: 0.067595 Iteration 5 Error: 0.038966 Align patch 7 18 left Iteration 1 Error: 0.762879 Iteration 2 Error: 0.116176 Iteration 3 Error: 0.032150 Align patch 8 17 left Iteration 1 Error: 0.657068 Iteration 2 Error: 0.116372 Iteration 3 Error: 0.029773 Align patch 9 16 left Iteration 1 Error: 0.545974 Iteration 2 Error: 0.058944 Iteration 3 Error: 0.012892 Align patch 10 15 left Iteration 1 Error: 0.676275 Iteration 2 Error: 0.124735 Iteration 3 Error: 0.030997 Align patch 11 14 left Iteration 1 Error: 0.644406 Iteration 2 Error: 0.136819 Iteration 3 Error: 0.057302 Iteration 4 Error: 0.026898 Align patch 12 13 left Iteration 1 Error: 0.495782 Iteration 2 Error: 0.091595 Iteration 3 Error: 0.028971 Align patch 13 12 left Iteration 1 Error: 0.649207 Iteration 2 Error: 0.093313 Iteration 3 Error: 0.016838 Align patch 14 11 left Iteration 1 Error: 0.478428 Iteration 2 Error: 0.076932 Iteration 3 Error: 0.019002 Align patch 15 10 left Iteration 1 Error: 0.792989 Iteration 2 Error: 0.141925 Iteration 3 Error: 0.044832 Align patch 16 9 left Iteration 1 Error: 1.004060 Iteration 2 Error: 0.178649 Iteration 3 Error: 0.049556 Align patch 17 8 left Iteration 1 Error: 0.606934 Iteration 2 Error: 0.096085 Iteration 3 Error: 0.033829 Align patch 18 7 left Iteration 1 Error: 0.744535 Iteration 2 Error: 0.131713 Iteration 3 Error: 0.045561 Align patch 19 6 left Iteration 1 Error: 0.774029 Iteration 2 Error: 0.109561 Iteration 3 Error: 0.042512 Align patch 20 5 left Iteration 1 Error: 0.530803 Iteration 2 Error: 0.115100 Iteration 3 Error: 0.017913 Align patch 21 4 left Iteration 1 Error: 0.977094 Iteration 2 Error: 0.200069 Iteration 3 Error: 0.057228 Iteration 4 Error: 0.021482 Align patch 22 3 left Iteration 1 Error: 1.068417 Iteration 2 Error: 0.163399 Iteration 3 Error: 0.038289 Align patch 23 2 left Iteration 1 Error: 1.333596 Iteration 2 Error: 0.167140 Iteration 3 Error: 0.044322 Align patch 24 1 left Iteration 1 Error: 0.886254 Iteration 2 Error: 0.227140 Iteration 3 Error: 0.064435 Iteration 4 Error: 0.016014 Align patch 25 0 left Iteration 1 Error: 0.938925 Iteration 2 Error: 0.180502 Iteration 3 Error: 0.028985 3D Fitting completed. Patch alignment time: 16.00(sec) Local motion has been corrected. Process thread exits. Computational time: 25.005548 sec Total time: 31.842533 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00014hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00014hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.627079s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00014hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.130335s ........................................ >>>>>>TIME<<<<<< FFT: 0.952370s Defocus_U Defocus_V Angle CCC 12791.03 13353.53 1.22 0.054679 Final Values Defocus_U Defocus_V Angle CCC 13356.66 12806.66 89.97 0.086767 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00014hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00014hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.002e-01 CC threshold: 0.736 Mean Std: 38.99 6.69 Num Hot pixels: 204 Hot pixel threshold: 79.12 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.784368 Iteration 2 Error: 0.162572 Iteration 3 Error: 0.042922 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.05 -0.02 ...... Frame ( 3) shift: -0.09 -0.03 ...... Frame ( 4) shift: -0.14 -0.05 ...... Frame ( 5) shift: -0.18 -0.06 ...... Frame ( 6) shift: -0.18 -0.04 ...... Frame ( 7) shift: -0.14 0.01 ...... Frame ( 8) shift: -0.10 0.06 ...... Frame ( 9) shift: -0.06 0.10 ...... Frame ( 10) shift: -0.03 0.11 ...... Frame ( 11) shift: 0.00 0.12 ...... Frame ( 12) shift: 0.04 0.18 ...... Frame ( 13) shift: 0.08 0.28 ...... Frame ( 14) shift: 0.12 0.38 ...... Frame ( 15) shift: 0.17 0.44 ...... Frame ( 16) shift: 0.23 0.46 ...... Frame ( 17) shift: 0.29 0.47 ...... Frame ( 18) shift: 0.32 0.52 ...... Frame ( 19) shift: 0.31 0.60 ...... Frame ( 20) shift: 0.30 0.68 ...... Frame ( 21) shift: 0.31 0.77 ...... Frame ( 22) shift: 0.35 0.85 ...... Frame ( 23) shift: 0.38 0.93 ...... Frame ( 24) shift: 0.42 1.01 ...... Frame ( 25) shift: 0.44 1.10 ...... Frame ( 26) shift: 0.47 1.19 ...... Frame ( 27) shift: 0.50 1.24 ...... Frame ( 28) shift: 0.52 1.26 ...... Frame ( 29) shift: 0.54 1.27 ...... Frame ( 30) shift: 0.58 1.29 ...... Frame ( 31) shift: 0.64 1.32 ...... Frame ( 32) shift: 0.69 1.35 ...... Frame ( 33) shift: 0.70 1.40 ...... Frame ( 34) shift: 0.67 1.47 ...... Frame ( 35) shift: 0.63 1.54 ...... Frame ( 36) shift: 0.61 1.58 ...... Frame ( 37) shift: 0.60 1.59 ...... Frame ( 38) shift: 0.58 1.60 ...... Frame ( 39) shift: 0.57 1.61 ...... Frame ( 40) shift: 0.56 1.62 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.895860 Iteration 2 Error: 0.183184 Iteration 3 Error: 0.059326 Iteration 4 Error: 0.018038 Align patch 2 23 left Iteration 1 Error: 1.086117 Iteration 2 Error: 0.281736 Iteration 3 Error: 0.057131 Iteration 4 Error: 0.031723 Align patch 3 22 left Iteration 1 Error: 0.602927 Iteration 2 Error: 0.080674 Iteration 3 Error: 0.014563 Align patch 4 21 left Iteration 1 Error: 0.633529 Iteration 2 Error: 0.133392 Iteration 3 Error: 0.035988 Align patch 5 20 left Iteration 1 Error: 0.761416 Iteration 2 Error: 0.094615 Iteration 3 Error: 0.016303 Align patch 6 19 left Iteration 1 Error: 0.801631 Iteration 2 Error: 0.162634 Iteration 3 Error: 0.051681 Iteration 4 Error: 0.020144 Align patch 7 18 left Iteration 1 Error: 0.724084 Iteration 2 Error: 0.187197 Iteration 3 Error: 0.058578 Iteration 4 Error: 0.015246 Align patch 8 17 left Iteration 1 Error: 0.529515 Iteration 2 Error: 0.123282 Iteration 3 Error: 0.032302 Align patch 9 16 left Iteration 1 Error: 0.520723 Iteration 2 Error: 0.095055 Iteration 3 Error: 0.022639 Align patch 10 15 left Iteration 1 Error: 0.561755 Iteration 2 Error: 0.098677 Iteration 3 Error: 0.019973 Align patch 11 14 left Iteration 1 Error: 0.781470 Iteration 2 Error: 0.149511 Iteration 3 Error: 0.059463 Iteration 4 Error: 0.023019 Align patch 12 13 left Iteration 1 Error: 0.640058 Iteration 2 Error: 0.112200 Iteration 3 Error: 0.031384 Align patch 13 12 left Iteration 1 Error: 0.608874 Iteration 2 Error: 0.144837 Iteration 3 Error: 0.043575 Align patch 14 11 left Iteration 1 Error: 0.669506 Iteration 2 Error: 0.086707 Iteration 3 Error: 0.021939 Align patch 15 10 left Iteration 1 Error: 0.701876 Iteration 2 Error: 0.100226 Iteration 3 Error: 0.019953 Align patch 16 9 left Iteration 1 Error: 0.464515 Iteration 2 Error: 0.108184 Iteration 3 Error: 0.036541 Align patch 17 8 left Iteration 1 Error: 0.544358 Iteration 2 Error: 0.066734 Iteration 3 Error: 0.016444 Align patch 18 7 left Iteration 1 Error: 0.527510 Iteration 2 Error: 0.077831 Iteration 3 Error: 0.021430 Align patch 19 6 left Iteration 1 Error: 0.934798 Iteration 2 Error: 0.216540 Iteration 3 Error: 0.035240 Align patch 20 5 left Iteration 1 Error: 0.820540 Iteration 2 Error: 0.122659 Iteration 3 Error: 0.031622 Align patch 21 4 left Iteration 1 Error: 0.384746 Iteration 2 Error: 0.065712 Iteration 3 Error: 0.015753 Align patch 22 3 left Iteration 1 Error: 0.617929 Iteration 2 Error: 0.083509 Iteration 3 Error: 0.016256 Align patch 23 2 left Iteration 1 Error: 0.519256 Iteration 2 Error: 0.110526 Iteration 3 Error: 0.018724 Align patch 24 1 left Iteration 1 Error: 0.945108 Iteration 2 Error: 0.157948 Iteration 3 Error: 0.045364 Align patch 25 0 left Iteration 1 Error: 0.706407 Iteration 2 Error: 0.164706 Iteration 3 Error: 0.020734 3D Fitting completed. Patch alignment time: 14.28(sec) Local motion has been corrected. Process thread exits. Computational time: 23.098211 sec Total time: 29.328344 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00014hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00014hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.706904s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00014hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.119738s ........................................ >>>>>>TIME<<<<<< FFT: 1.049474s Defocus_U Defocus_V Angle CCC 14964.84 15792.97 3.18 0.046651 Final Values Defocus_U Defocus_V Angle CCC 14992.96 15802.37 4.78 0.070466 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00014hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00014hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 38.87 6.68 Num Hot pixels: 240 Hot pixel threshold: 78.93 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.592744 Iteration 2 Error: 0.129224 Iteration 3 Error: 0.031012 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.16 -0.02 ...... Frame ( 3) shift: -0.32 -0.03 ...... Frame ( 4) shift: -0.48 -0.05 ...... Frame ( 5) shift: -0.65 -0.07 ...... Frame ( 6) shift: -0.74 -0.06 ...... Frame ( 7) shift: -0.76 -0.03 ...... Frame ( 8) shift: -0.78 0.00 ...... Frame ( 9) shift: -0.77 0.04 ...... Frame ( 10) shift: -0.71 0.09 ...... Frame ( 11) shift: -0.66 0.14 ...... Frame ( 12) shift: -0.62 0.19 ...... Frame ( 13) shift: -0.61 0.23 ...... Frame ( 14) shift: -0.59 0.27 ...... Frame ( 15) shift: -0.59 0.33 ...... Frame ( 16) shift: -0.60 0.39 ...... Frame ( 17) shift: -0.61 0.45 ...... Frame ( 18) shift: -0.58 0.52 ...... Frame ( 19) shift: -0.52 0.61 ...... Frame ( 20) shift: -0.46 0.71 ...... Frame ( 21) shift: -0.43 0.77 ...... Frame ( 22) shift: -0.42 0.80 ...... Frame ( 23) shift: -0.41 0.83 ...... Frame ( 24) shift: -0.38 0.84 ...... Frame ( 25) shift: -0.35 0.84 ...... Frame ( 26) shift: -0.32 0.84 ...... Frame ( 27) shift: -0.32 0.87 ...... Frame ( 28) shift: -0.36 0.93 ...... Frame ( 29) shift: -0.40 1.00 ...... Frame ( 30) shift: -0.40 1.05 ...... Frame ( 31) shift: -0.37 1.08 ...... Frame ( 32) shift: -0.33 1.12 ...... Frame ( 33) shift: -0.28 1.14 ...... Frame ( 34) shift: -0.22 1.13 ...... Frame ( 35) shift: -0.16 1.12 ...... Frame ( 36) shift: -0.16 1.12 ...... Frame ( 37) shift: -0.21 1.13 ...... Frame ( 38) shift: -0.25 1.13 ...... Frame ( 39) shift: -0.30 1.14 ...... Frame ( 40) shift: -0.35 1.15 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.256507 Iteration 2 Error: 0.203772 Iteration 3 Error: 0.051389 Iteration 4 Error: 0.016184 Align patch 2 23 left Iteration 1 Error: 0.752205 Iteration 2 Error: 0.141957 Iteration 3 Error: 0.039286 Align patch 3 22 left Iteration 1 Error: 0.664743 Iteration 2 Error: 0.083486 Iteration 3 Error: 0.018590 Align patch 4 21 left Iteration 1 Error: 0.543202 Iteration 2 Error: 0.052334 Iteration 3 Error: 0.012629 Align patch 5 20 left Iteration 1 Error: 0.704420 Iteration 2 Error: 0.090540 Iteration 3 Error: 0.011451 Align patch 6 19 left Iteration 1 Error: 0.874268 Iteration 2 Error: 0.256073 Iteration 3 Error: 0.074845 Iteration 4 Error: 0.035892 Align patch 7 18 left Iteration 1 Error: 0.718142 Iteration 2 Error: 0.223521 Iteration 3 Error: 0.053959 Iteration 4 Error: 0.021775 Align patch 8 17 left Iteration 1 Error: 0.841304 Iteration 2 Error: 0.127615 Iteration 3 Error: 0.032134 Align patch 9 16 left Iteration 1 Error: 0.520967 Iteration 2 Error: 0.072156 Iteration 3 Error: 0.014971 Align patch 10 15 left Iteration 1 Error: 0.459444 Iteration 2 Error: 0.071768 Iteration 3 Error: 0.013280 Align patch 11 14 left Iteration 1 Error: 0.826950 Iteration 2 Error: 0.211949 Iteration 3 Error: 0.077686 Iteration 4 Error: 0.027239 Align patch 12 13 left Iteration 1 Error: 0.847402 Iteration 2 Error: 0.187360 Iteration 3 Error: 0.060485 Iteration 4 Error: 0.025413 Align patch 13 12 left Iteration 1 Error: 0.559602 Iteration 2 Error: 0.098181 Iteration 3 Error: 0.023984 Align patch 14 11 left Iteration 1 Error: 0.508465 Iteration 2 Error: 0.041383 Align patch 15 10 left Iteration 1 Error: 0.673286 Iteration 2 Error: 0.076627 Iteration 3 Error: 0.017414 Align patch 16 9 left Iteration 1 Error: 0.607235 Iteration 2 Error: 0.105414 Iteration 3 Error: 0.032814 Align patch 17 8 left Iteration 1 Error: 0.524350 Iteration 2 Error: 0.084376 Iteration 3 Error: 0.025409 Align patch 18 7 left Iteration 1 Error: 0.582032 Iteration 2 Error: 0.114659 Iteration 3 Error: 0.022525 Align patch 19 6 left Iteration 1 Error: 0.720418 Iteration 2 Error: 0.177550 Iteration 3 Error: 0.034568 Align patch 20 5 left Iteration 1 Error: 1.136120 Iteration 2 Error: 0.134562 Iteration 3 Error: 0.017392 Align patch 21 4 left Iteration 1 Error: 0.487912 Iteration 2 Error: 0.056958 Iteration 3 Error: 0.007397 Align patch 22 3 left Iteration 1 Error: 0.571763 Iteration 2 Error: 0.084460 Iteration 3 Error: 0.025636 Align patch 23 2 left Iteration 1 Error: 0.455555 Iteration 2 Error: 0.119462 Iteration 3 Error: 0.026820 Align patch 24 1 left Iteration 1 Error: 0.570407 Iteration 2 Error: 0.131633 Iteration 3 Error: 0.034528 Align patch 25 0 left Iteration 1 Error: 0.978979 Iteration 2 Error: 0.092469 Iteration 3 Error: 0.026224 3D Fitting completed. Patch alignment time: 14.62(sec) Local motion has been corrected. Process thread exits. Computational time: 23.026724 sec Total time: 28.846178 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00014hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00014hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.554487s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00014hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.032291s ........................................ >>>>>>TIME<<<<<< FFT: 1.332561s Defocus_U Defocus_V Angle CCC 12410.97 11780.50 76.92 0.043136 Final Values Defocus_U Defocus_V Angle CCC 12460.97 11780.50 77.23 0.066527 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00015hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00015hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 39.08 6.72 Num Hot pixels: 220 Hot pixel threshold: 79.39 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.868345 Iteration 2 Error: 0.183889 Iteration 3 Error: 0.042995 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.05 -0.07 ...... Frame ( 3) shift: 0.09 -0.14 ...... Frame ( 4) shift: 0.14 -0.21 ...... Frame ( 5) shift: 0.19 -0.28 ...... Frame ( 6) shift: 0.24 -0.29 ...... Frame ( 7) shift: 0.31 -0.25 ...... Frame ( 8) shift: 0.37 -0.21 ...... Frame ( 9) shift: 0.44 -0.16 ...... Frame ( 10) shift: 0.51 -0.09 ...... Frame ( 11) shift: 0.58 -0.02 ...... Frame ( 12) shift: 0.63 0.04 ...... Frame ( 13) shift: 0.65 0.09 ...... Frame ( 14) shift: 0.67 0.15 ...... Frame ( 15) shift: 0.69 0.19 ...... Frame ( 16) shift: 0.72 0.22 ...... Frame ( 17) shift: 0.76 0.25 ...... Frame ( 18) shift: 0.77 0.31 ...... Frame ( 19) shift: 0.77 0.39 ...... Frame ( 20) shift: 0.77 0.47 ...... Frame ( 21) shift: 0.80 0.51 ...... Frame ( 22) shift: 0.87 0.51 ...... Frame ( 23) shift: 0.94 0.50 ...... Frame ( 24) shift: 0.98 0.53 ...... Frame ( 25) shift: 1.01 0.59 ...... Frame ( 26) shift: 1.03 0.65 ...... Frame ( 27) shift: 1.07 0.72 ...... Frame ( 28) shift: 1.12 0.81 ...... Frame ( 29) shift: 1.17 0.90 ...... Frame ( 30) shift: 1.22 0.91 ...... Frame ( 31) shift: 1.25 0.85 ...... Frame ( 32) shift: 1.29 0.80 ...... Frame ( 33) shift: 1.31 0.81 ...... Frame ( 34) shift: 1.32 0.90 ...... Frame ( 35) shift: 1.34 0.98 ...... Frame ( 36) shift: 1.39 1.02 ...... Frame ( 37) shift: 1.48 1.01 ...... Frame ( 38) shift: 1.56 1.01 ...... Frame ( 39) shift: 1.65 1.00 ...... Frame ( 40) shift: 1.74 0.99 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.869769 Iteration 2 Error: 0.199579 Iteration 3 Error: 0.036317 Align patch 2 23 left Iteration 1 Error: 0.655688 Iteration 2 Error: 0.098074 Iteration 3 Error: 0.032417 Align patch 3 22 left Iteration 1 Error: 0.519122 Iteration 2 Error: 0.089481 Iteration 3 Error: 0.019975 Align patch 4 21 left Iteration 1 Error: 0.380445 Iteration 2 Error: 0.050092 Iteration 3 Error: 0.012551 Align patch 5 20 left Iteration 1 Error: 0.487619 Iteration 2 Error: 0.060772 Iteration 3 Error: 0.012615 Align patch 6 19 left Iteration 1 Error: 1.065774 Iteration 2 Error: 0.147351 Iteration 3 Error: 0.032799 Align patch 7 18 left Iteration 1 Error: 0.535990 Iteration 2 Error: 0.069771 Iteration 3 Error: 0.019693 Align patch 8 17 left Iteration 1 Error: 1.112849 Iteration 2 Error: 0.294213 Iteration 3 Error: 0.086345 Iteration 4 Error: 0.023934 Align patch 9 16 left Iteration 1 Error: 0.929112 Iteration 2 Error: 0.114643 Iteration 3 Error: 0.025554 Align patch 10 15 left Iteration 1 Error: 0.568686 Iteration 2 Error: 0.070748 Iteration 3 Error: 0.014757 Align patch 11 14 left Iteration 1 Error: 0.611427 Iteration 2 Error: 0.120863 Iteration 3 Error: 0.030951 Align patch 12 13 left Iteration 1 Error: 0.507843 Iteration 2 Error: 0.081663 Iteration 3 Error: 0.017688 Align patch 13 12 left Iteration 1 Error: 0.629138 Iteration 2 Error: 0.148930 Iteration 3 Error: 0.028918 Align patch 14 11 left Iteration 1 Error: 0.491639 Iteration 2 Error: 0.133068 Iteration 3 Error: 0.041632 Align patch 15 10 left Iteration 1 Error: 0.607015 Iteration 2 Error: 0.125027 Iteration 3 Error: 0.035369 Align patch 16 9 left Iteration 1 Error: 0.582559 Iteration 2 Error: 0.096345 Iteration 3 Error: 0.029513 Align patch 17 8 left Iteration 1 Error: 0.421224 Iteration 2 Error: 0.042089 Align patch 18 7 left Iteration 1 Error: 0.816438 Iteration 2 Error: 0.154566 Iteration 3 Error: 0.036756 Align patch 19 6 left Iteration 1 Error: 0.670808 Iteration 2 Error: 0.113255 Iteration 3 Error: 0.044888 Align patch 20 5 left Iteration 1 Error: 1.057735 Iteration 2 Error: 0.125539 Iteration 3 Error: 0.023505 Align patch 21 4 left Iteration 1 Error: 1.004795 Iteration 2 Error: 0.245589 Iteration 3 Error: 0.086068 Iteration 4 Error: 0.035419 Align patch 22 3 left Iteration 1 Error: 0.858590 Iteration 2 Error: 0.318383 Iteration 3 Error: 0.105526 Iteration 4 Error: 0.045079 Align patch 23 2 left Iteration 1 Error: 0.764573 Iteration 2 Error: 0.080127 Iteration 3 Error: 0.022081 Align patch 24 1 left Iteration 1 Error: 0.508316 Iteration 2 Error: 0.098803 Iteration 3 Error: 0.022558 Align patch 25 0 left Iteration 1 Error: 1.175180 Iteration 2 Error: 0.270144 Iteration 3 Error: 0.047802 3D Fitting completed. Patch alignment time: 15.61(sec) Local motion has been corrected. Process thread exits. Computational time: 24.560160 sec Total time: 31.120829 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00015hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00015hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.573955s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00015hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.204872s ........................................ >>>>>>TIME<<<<<< FFT: 0.933126s Defocus_U Defocus_V Angle CCC 11873.79 11309.86 89.71 0.046541 Final Values Defocus_U Defocus_V Angle CCC 11886.30 11322.37 88.78 0.076367 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00015hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00015hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.351e-01 1.004e-01 CC threshold: 0.738 Mean Std: 38.54 6.67 Num Hot pixels: 209 Hot pixel threshold: 78.55 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.534190 Iteration 2 Error: 0.028617 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.00 0.15 ...... Frame ( 3) shift: -0.01 0.30 ...... Frame ( 4) shift: -0.01 0.45 ...... Frame ( 5) shift: -0.01 0.60 ...... Frame ( 6) shift: 0.03 0.70 ...... Frame ( 7) shift: 0.11 0.76 ...... Frame ( 8) shift: 0.19 0.82 ...... Frame ( 9) shift: 0.24 0.85 ...... Frame ( 10) shift: 0.28 0.87 ...... Frame ( 11) shift: 0.31 0.89 ...... Frame ( 12) shift: 0.33 0.88 ...... Frame ( 13) shift: 0.32 0.83 ...... Frame ( 14) shift: 0.32 0.78 ...... Frame ( 15) shift: 0.30 0.77 ...... Frame ( 16) shift: 0.26 0.80 ...... Frame ( 17) shift: 0.22 0.83 ...... Frame ( 18) shift: 0.19 0.84 ...... Frame ( 19) shift: 0.17 0.81 ...... Frame ( 20) shift: 0.16 0.79 ...... Frame ( 21) shift: 0.17 0.77 ...... Frame ( 22) shift: 0.20 0.74 ...... Frame ( 23) shift: 0.24 0.72 ...... Frame ( 24) shift: 0.26 0.71 ...... Frame ( 25) shift: 0.25 0.71 ...... Frame ( 26) shift: 0.24 0.72 ...... Frame ( 27) shift: 0.27 0.70 ...... Frame ( 28) shift: 0.32 0.65 ...... Frame ( 29) shift: 0.38 0.60 ...... Frame ( 30) shift: 0.42 0.58 ...... Frame ( 31) shift: 0.44 0.60 ...... Frame ( 32) shift: 0.47 0.61 ...... Frame ( 33) shift: 0.46 0.61 ...... Frame ( 34) shift: 0.42 0.58 ...... Frame ( 35) shift: 0.39 0.55 ...... Frame ( 36) shift: 0.36 0.54 ...... Frame ( 37) shift: 0.35 0.54 ...... Frame ( 38) shift: 0.34 0.54 ...... Frame ( 39) shift: 0.33 0.54 ...... Frame ( 40) shift: 0.32 0.54 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.529452 Iteration 2 Error: 0.112133 Iteration 3 Error: 0.025635 Align patch 2 23 left Iteration 1 Error: 0.515911 Iteration 2 Error: 0.067778 Iteration 3 Error: 0.010364 Align patch 3 22 left Iteration 1 Error: 0.971297 Iteration 2 Error: 0.101459 Iteration 3 Error: 0.021142 Align patch 4 21 left Iteration 1 Error: 0.533164 Iteration 2 Error: 0.070834 Iteration 3 Error: 0.010097 Align patch 5 20 left Iteration 1 Error: 0.528093 Iteration 2 Error: 0.053865 Iteration 3 Error: 0.012924 Align patch 6 19 left Iteration 1 Error: 0.548214 Iteration 2 Error: 0.091363 Iteration 3 Error: 0.022125 Align patch 7 18 left Iteration 1 Error: 0.418943 Iteration 2 Error: 0.071591 Iteration 3 Error: 0.010655 Align patch 8 17 left Iteration 1 Error: 0.604740 Iteration 2 Error: 0.084631 Iteration 3 Error: 0.018594 Align patch 9 16 left Iteration 1 Error: 0.501772 Iteration 2 Error: 0.069785 Iteration 3 Error: 0.018062 Align patch 10 15 left Iteration 1 Error: 0.481806 Iteration 2 Error: 0.034360 Align patch 11 14 left Iteration 1 Error: 0.662192 Iteration 2 Error: 0.069022 Iteration 3 Error: 0.009425 Align patch 12 13 left Iteration 1 Error: 0.674552 Iteration 2 Error: 0.092423 Iteration 3 Error: 0.020520 Align patch 13 12 left Iteration 1 Error: 0.486371 Iteration 2 Error: 0.085927 Iteration 3 Error: 0.017413 Align patch 14 11 left Iteration 1 Error: 0.434048 Iteration 2 Error: 0.065005 Iteration 3 Error: 0.017955 Align patch 15 10 left Iteration 1 Error: 0.464391 Iteration 2 Error: 0.048791 Align patch 16 9 left Iteration 1 Error: 0.685893 Iteration 2 Error: 0.056729 Iteration 3 Error: 0.011351 Align patch 17 8 left Iteration 1 Error: 0.554522 Iteration 2 Error: 0.092218 Iteration 3 Error: 0.017210 Align patch 18 7 left Iteration 1 Error: 0.415985 Iteration 2 Error: 0.078267 Iteration 3 Error: 0.016085 Align patch 19 6 left Iteration 1 Error: 0.508957 Iteration 2 Error: 0.075674 Iteration 3 Error: 0.016482 Align patch 20 5 left Iteration 1 Error: 0.535909 Iteration 2 Error: 0.057563 Iteration 3 Error: 0.010748 Align patch 21 4 left Iteration 1 Error: 0.735585 Iteration 2 Error: 0.119889 Iteration 3 Error: 0.029120 Align patch 22 3 left Iteration 1 Error: 0.683696 Iteration 2 Error: 0.061224 Iteration 3 Error: 0.009382 Align patch 23 2 left Iteration 1 Error: 0.318722 Iteration 2 Error: 0.038216 Align patch 24 1 left Iteration 1 Error: 0.543782 Iteration 2 Error: 0.039037 Align patch 25 0 left Iteration 1 Error: 0.468836 Iteration 2 Error: 0.050853 Iteration 3 Error: 0.014020 3D Fitting completed. Patch alignment time: 14.65(sec) Local motion has been corrected. Process thread exits. Computational time: 22.761038 sec Total time: 28.777803 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00015hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00015hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.531956s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00015hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.145609s ........................................ >>>>>>TIME<<<<<< FFT: 1.048006s Defocus_U Defocus_V Angle CCC 10417.99 11175.79 6.94 0.046360 Final Values Defocus_U Defocus_V Angle CCC 10446.12 11216.43 6.00 0.072301 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00015hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00015hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 38.58 6.73 Num Hot pixels: 212 Hot pixel threshold: 78.95 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.624087 Iteration 2 Error: 0.116160 Iteration 3 Error: 0.025692 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.02 0.04 ...... Frame ( 3) shift: 0.03 0.09 ...... Frame ( 4) shift: 0.05 0.13 ...... Frame ( 5) shift: 0.07 0.17 ...... Frame ( 6) shift: 0.08 0.23 ...... Frame ( 7) shift: 0.08 0.29 ...... Frame ( 8) shift: 0.08 0.35 ...... Frame ( 9) shift: 0.07 0.38 ...... Frame ( 10) shift: 0.04 0.38 ...... Frame ( 11) shift: 0.01 0.39 ...... Frame ( 12) shift: -0.00 0.40 ...... Frame ( 13) shift: 0.01 0.41 ...... Frame ( 14) shift: 0.02 0.43 ...... Frame ( 15) shift: 0.02 0.47 ...... Frame ( 16) shift: 0.03 0.55 ...... Frame ( 17) shift: 0.04 0.62 ...... Frame ( 18) shift: 0.04 0.67 ...... Frame ( 19) shift: 0.03 0.70 ...... Frame ( 20) shift: 0.02 0.73 ...... Frame ( 21) shift: 0.02 0.77 ...... Frame ( 22) shift: 0.03 0.80 ...... Frame ( 23) shift: 0.04 0.84 ...... Frame ( 24) shift: 0.06 0.88 ...... Frame ( 25) shift: 0.10 0.92 ...... Frame ( 26) shift: 0.13 0.95 ...... Frame ( 27) shift: 0.14 0.99 ...... Frame ( 28) shift: 0.12 1.02 ...... Frame ( 29) shift: 0.11 1.05 ...... Frame ( 30) shift: 0.13 1.06 ...... Frame ( 31) shift: 0.20 1.06 ...... Frame ( 32) shift: 0.27 1.05 ...... Frame ( 33) shift: 0.30 1.10 ...... Frame ( 34) shift: 0.30 1.20 ...... Frame ( 35) shift: 0.30 1.29 ...... Frame ( 36) shift: 0.28 1.36 ...... Frame ( 37) shift: 0.26 1.38 ...... Frame ( 38) shift: 0.23 1.40 ...... Frame ( 39) shift: 0.21 1.43 ...... Frame ( 40) shift: 0.18 1.45 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.586761 Iteration 2 Error: 0.130742 Iteration 3 Error: 0.021917 Align patch 2 23 left Iteration 1 Error: 0.764508 Iteration 2 Error: 0.165487 Iteration 3 Error: 0.042907 Align patch 3 22 left Iteration 1 Error: 0.763081 Iteration 2 Error: 0.105514 Iteration 3 Error: 0.034704 Align patch 4 21 left Iteration 1 Error: 0.540578 Iteration 2 Error: 0.107540 Iteration 3 Error: 0.029441 Align patch 5 20 left Iteration 1 Error: 0.498812 Iteration 2 Error: 0.061208 Iteration 3 Error: 0.014395 Align patch 6 19 left Iteration 1 Error: 0.601026 Iteration 2 Error: 0.105381 Iteration 3 Error: 0.025210 Align patch 7 18 left Iteration 1 Error: 0.453699 Iteration 2 Error: 0.078832 Iteration 3 Error: 0.015597 Align patch 8 17 left Iteration 1 Error: 0.723576 Iteration 2 Error: 0.058993 Iteration 3 Error: 0.008993 Align patch 9 16 left Iteration 1 Error: 0.525268 Iteration 2 Error: 0.079994 Iteration 3 Error: 0.017273 Align patch 10 15 left Iteration 1 Error: 0.715098 Iteration 2 Error: 0.066687 Iteration 3 Error: 0.016951 Align patch 11 14 left Iteration 1 Error: 1.514269 Iteration 2 Error: 0.368477 Iteration 3 Error: 0.112093 Iteration 4 Error: 0.043499 Align patch 12 13 left Iteration 1 Error: 1.065822 Iteration 2 Error: 0.139861 Iteration 3 Error: 0.046411 Align patch 13 12 left Iteration 1 Error: 0.704987 Iteration 2 Error: 0.091882 Iteration 3 Error: 0.018236 Align patch 14 11 left Iteration 1 Error: 0.638444 Iteration 2 Error: 0.085796 Iteration 3 Error: 0.015029 Align patch 15 10 left Iteration 1 Error: 0.732038 Iteration 2 Error: 0.111036 Iteration 3 Error: 0.015828 Align patch 16 9 left Iteration 1 Error: 1.248200 Iteration 2 Error: 0.223773 Iteration 3 Error: 0.085521 Iteration 4 Error: 0.033296 Align patch 17 8 left Iteration 1 Error: 0.908487 Iteration 2 Error: 0.148893 Iteration 3 Error: 0.045891 Align patch 18 7 left Iteration 1 Error: 0.684055 Iteration 2 Error: 0.097005 Iteration 3 Error: 0.017532 Align patch 19 6 left Iteration 1 Error: 0.811166 Iteration 2 Error: 0.089457 Iteration 3 Error: 0.019215 Align patch 20 5 left Iteration 1 Error: 0.746083 Iteration 2 Error: 0.106563 Iteration 3 Error: 0.020150 Align patch 21 4 left Iteration 1 Error: 0.573411 Iteration 2 Error: 0.146696 Iteration 3 Error: 0.027701 Align patch 22 3 left Iteration 1 Error: 0.388473 Iteration 2 Error: 0.055575 Iteration 3 Error: 0.012578 Align patch 23 2 left Iteration 1 Error: 0.615224 Iteration 2 Error: 0.085545 Iteration 3 Error: 0.020661 Align patch 24 1 left Iteration 1 Error: 0.550139 Iteration 2 Error: 0.083251 Iteration 3 Error: 0.019177 Align patch 25 0 left Iteration 1 Error: 0.831079 Iteration 2 Error: 0.178168 Iteration 3 Error: 0.054217 Iteration 4 Error: 0.019766 3D Fitting completed. Patch alignment time: 14.67(sec) Local motion has been corrected. Process thread exits. Computational time: 23.291098 sec Total time: 29.103027 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00015hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00015hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.674161s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00015hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.141995s ........................................ >>>>>>TIME<<<<<< FFT: 1.060160s Defocus_U Defocus_V Angle CCC 11387.07 10726.44 83.63 0.040817 Final Values Defocus_U Defocus_V Angle CCC 11413.65 10749.90 84.25 0.066862 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00016hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00016hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.003e-01 CC threshold: 0.736 Mean Std: 39.10 6.76 Num Hot pixels: 211 Hot pixel threshold: 79.68 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.559008 Iteration 2 Error: 0.221752 Iteration 3 Error: 0.053427 Iteration 4 Error: 0.017341 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.09 0.11 ...... Frame ( 3) shift: -0.18 0.23 ...... Frame ( 4) shift: -0.26 0.34 ...... Frame ( 5) shift: -0.35 0.46 ...... Frame ( 6) shift: -0.42 0.55 ...... Frame ( 7) shift: -0.46 0.63 ...... Frame ( 8) shift: -0.51 0.71 ...... Frame ( 9) shift: -0.50 0.80 ...... Frame ( 10) shift: -0.44 0.90 ...... Frame ( 11) shift: -0.39 1.00 ...... Frame ( 12) shift: -0.27 1.14 ...... Frame ( 13) shift: -0.08 1.32 ...... Frame ( 14) shift: 0.10 1.50 ...... Frame ( 15) shift: 0.27 1.69 ...... Frame ( 16) shift: 0.41 1.89 ...... Frame ( 17) shift: 0.56 2.09 ...... Frame ( 18) shift: 0.64 2.23 ...... Frame ( 19) shift: 0.65 2.30 ...... Frame ( 20) shift: 0.66 2.38 ...... Frame ( 21) shift: 0.66 2.46 ...... Frame ( 22) shift: 0.63 2.55 ...... Frame ( 23) shift: 0.61 2.63 ...... Frame ( 24) shift: 0.61 2.65 ...... Frame ( 25) shift: 0.66 2.59 ...... Frame ( 26) shift: 0.70 2.54 ...... Frame ( 27) shift: 0.79 2.46 ...... Frame ( 28) shift: 0.92 2.37 ...... Frame ( 29) shift: 1.06 2.28 ...... Frame ( 30) shift: 1.21 2.22 ...... Frame ( 31) shift: 1.39 2.22 ...... Frame ( 32) shift: 1.56 2.21 ...... Frame ( 33) shift: 1.66 2.21 ...... Frame ( 34) shift: 1.68 2.21 ...... Frame ( 35) shift: 1.70 2.22 ...... Frame ( 36) shift: 1.74 2.23 ...... Frame ( 37) shift: 1.80 2.24 ...... Frame ( 38) shift: 1.86 2.25 ...... Frame ( 39) shift: 1.92 2.26 ...... Frame ( 40) shift: 1.98 2.27 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.913288 Iteration 2 Error: 0.189206 Iteration 3 Error: 0.053742 Iteration 4 Error: 0.019800 Align patch 2 23 left Iteration 1 Error: 0.341309 Iteration 2 Error: 0.045553 Align patch 3 22 left Iteration 1 Error: 0.680613 Iteration 2 Error: 0.120054 Iteration 3 Error: 0.035419 Align patch 4 21 left Iteration 1 Error: 0.443832 Iteration 2 Error: 0.066672 Iteration 3 Error: 0.018385 Align patch 5 20 left Iteration 1 Error: 0.894203 Iteration 2 Error: 0.134475 Iteration 3 Error: 0.032035 Align patch 6 19 left Iteration 1 Error: 0.447788 Iteration 2 Error: 0.097028 Iteration 3 Error: 0.022927 Align patch 7 18 left Iteration 1 Error: 0.375383 Iteration 2 Error: 0.052654 Iteration 3 Error: 0.013487 Align patch 8 17 left Iteration 1 Error: 0.763049 Iteration 2 Error: 0.068403 Iteration 3 Error: 0.012809 Align patch 9 16 left Iteration 1 Error: 0.565097 Iteration 2 Error: 0.056113 Iteration 3 Error: 0.014329 Align patch 10 15 left Iteration 1 Error: 0.473695 Iteration 2 Error: 0.119152 Iteration 3 Error: 0.029174 Align patch 11 14 left Iteration 1 Error: 0.814314 Iteration 2 Error: 0.089323 Iteration 3 Error: 0.011750 Align patch 12 13 left Iteration 1 Error: 0.687350 Iteration 2 Error: 0.188521 Iteration 3 Error: 0.073238 Iteration 4 Error: 0.021117 Align patch 13 12 left Iteration 1 Error: 0.666190 Iteration 2 Error: 0.076183 Iteration 3 Error: 0.012061 Align patch 14 11 left Iteration 1 Error: 0.670382 Iteration 2 Error: 0.091289 Iteration 3 Error: 0.021444 Align patch 15 10 left Iteration 1 Error: 0.504690 Iteration 2 Error: 0.081722 Iteration 3 Error: 0.021543 Align patch 16 9 left Iteration 1 Error: 0.544270 Iteration 2 Error: 0.139184 Iteration 3 Error: 0.020913 Align patch 17 8 left Iteration 1 Error: 0.653709 Iteration 2 Error: 0.116387 Iteration 3 Error: 0.016691 Align patch 18 7 left Iteration 1 Error: 0.497948 Iteration 2 Error: 0.099698 Iteration 3 Error: 0.020015 Align patch 19 6 left Iteration 1 Error: 0.551398 Iteration 2 Error: 0.081687 Iteration 3 Error: 0.025590 Align patch 20 5 left Iteration 1 Error: 0.506426 Iteration 2 Error: 0.059411 Iteration 3 Error: 0.017084 Align patch 21 4 left Iteration 1 Error: 0.765586 Iteration 2 Error: 0.112246 Iteration 3 Error: 0.019619 Align patch 22 3 left Iteration 1 Error: 0.505435 Iteration 2 Error: 0.045705 Align patch 23 2 left Iteration 1 Error: 0.564043 Iteration 2 Error: 0.079287 Iteration 3 Error: 0.014789 Align patch 24 1 left Iteration 1 Error: 0.792659 Iteration 2 Error: 0.112449 Iteration 3 Error: 0.022247 Align patch 25 0 left Iteration 1 Error: 0.424268 Iteration 2 Error: 0.056487 Iteration 3 Error: 0.010754 3D Fitting completed. Patch alignment time: 15.62(sec) Local motion has been corrected. Process thread exits. Computational time: 24.302607 sec Total time: 30.450596 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00016hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00016hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.754339s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00016hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.219397s ........................................ >>>>>>TIME<<<<<< FFT: 0.936667s Defocus_U Defocus_V Angle CCC 12253.92 13156.28 14.02 0.061096 Final Values Defocus_U Defocus_V Angle CCC 12263.29 13196.93 13.70 0.095978 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00016hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00016hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.002e-01 CC threshold: 0.736 Mean Std: 39.54 6.75 Num Hot pixels: 221 Hot pixel threshold: 80.03 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.433193 Iteration 2 Error: 0.118106 Iteration 3 Error: 0.023186 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.01 0.24 ...... Frame ( 3) shift: 0.03 0.47 ...... Frame ( 4) shift: 0.04 0.71 ...... Frame ( 5) shift: 0.05 0.94 ...... Frame ( 6) shift: 0.07 1.10 ...... Frame ( 7) shift: 0.09 1.18 ...... Frame ( 8) shift: 0.12 1.26 ...... Frame ( 9) shift: 0.09 1.34 ...... Frame ( 10) shift: 0.02 1.44 ...... Frame ( 11) shift: -0.06 1.53 ...... Frame ( 12) shift: -0.09 1.59 ...... Frame ( 13) shift: -0.07 1.63 ...... Frame ( 14) shift: -0.06 1.66 ...... Frame ( 15) shift: -0.04 1.73 ...... Frame ( 16) shift: -0.01 1.84 ...... Frame ( 17) shift: 0.01 1.95 ...... Frame ( 18) shift: 0.03 2.00 ...... Frame ( 19) shift: 0.04 2.01 ...... Frame ( 20) shift: 0.04 2.02 ...... Frame ( 21) shift: 0.05 2.02 ...... Frame ( 22) shift: 0.07 2.02 ...... Frame ( 23) shift: 0.09 2.02 ...... Frame ( 24) shift: 0.11 2.02 ...... Frame ( 25) shift: 0.13 2.01 ...... Frame ( 26) shift: 0.16 2.00 ...... Frame ( 27) shift: 0.18 2.03 ...... Frame ( 28) shift: 0.19 2.09 ...... Frame ( 29) shift: 0.21 2.15 ...... Frame ( 30) shift: 0.22 2.22 ...... Frame ( 31) shift: 0.22 2.29 ...... Frame ( 32) shift: 0.22 2.37 ...... Frame ( 33) shift: 0.26 2.39 ...... Frame ( 34) shift: 0.35 2.35 ...... Frame ( 35) shift: 0.44 2.32 ...... Frame ( 36) shift: 0.48 2.31 ...... Frame ( 37) shift: 0.48 2.35 ...... Frame ( 38) shift: 0.48 2.38 ...... Frame ( 39) shift: 0.48 2.41 ...... Frame ( 40) shift: 0.48 2.45 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.727465 Iteration 2 Error: 0.087552 Iteration 3 Error: 0.027988 Align patch 2 23 left Iteration 1 Error: 0.551689 Iteration 2 Error: 0.084022 Iteration 3 Error: 0.020203 Align patch 3 22 left Iteration 1 Error: 0.458643 Iteration 2 Error: 0.076440 Iteration 3 Error: 0.017675 Align patch 4 21 left Iteration 1 Error: 0.643567 Iteration 2 Error: 0.090626 Iteration 3 Error: 0.022099 Align patch 5 20 left Iteration 1 Error: 0.479138 Iteration 2 Error: 0.068647 Iteration 3 Error: 0.014985 Align patch 6 19 left Iteration 1 Error: 0.479142 Iteration 2 Error: 0.076921 Iteration 3 Error: 0.018137 Align patch 7 18 left Iteration 1 Error: 0.596040 Iteration 2 Error: 0.106808 Iteration 3 Error: 0.020594 Align patch 8 17 left Iteration 1 Error: 0.471270 Iteration 2 Error: 0.068680 Iteration 3 Error: 0.016036 Align patch 9 16 left Iteration 1 Error: 0.387447 Iteration 2 Error: 0.062565 Iteration 3 Error: 0.010837 Align patch 10 15 left Iteration 1 Error: 0.535241 Iteration 2 Error: 0.062231 Iteration 3 Error: 0.015122 Align patch 11 14 left Iteration 1 Error: 0.592683 Iteration 2 Error: 0.073173 Iteration 3 Error: 0.015019 Align patch 12 13 left Iteration 1 Error: 0.914555 Iteration 2 Error: 0.108576 Iteration 3 Error: 0.021000 Align patch 13 12 left Iteration 1 Error: 0.773665 Iteration 2 Error: 0.113012 Iteration 3 Error: 0.024832 Align patch 14 11 left Iteration 1 Error: 0.719285 Iteration 2 Error: 0.112731 Iteration 3 Error: 0.022783 Align patch 15 10 left Iteration 1 Error: 0.684842 Iteration 2 Error: 0.128406 Iteration 3 Error: 0.035092 Align patch 16 9 left Iteration 1 Error: 0.788499 Iteration 2 Error: 0.116378 Iteration 3 Error: 0.023428 Align patch 17 8 left Iteration 1 Error: 1.071272 Iteration 2 Error: 0.080736 Iteration 3 Error: 0.017283 Align patch 18 7 left Iteration 1 Error: 1.164007 Iteration 2 Error: 0.151107 Iteration 3 Error: 0.035792 Align patch 19 6 left Iteration 1 Error: 0.565409 Iteration 2 Error: 0.066889 Iteration 3 Error: 0.013693 Align patch 20 5 left Iteration 1 Error: 0.710987 Iteration 2 Error: 0.062317 Iteration 3 Error: 0.009141 Align patch 21 4 left Iteration 1 Error: 1.055344 Iteration 2 Error: 0.127798 Iteration 3 Error: 0.022100 Align patch 22 3 left Iteration 1 Error: 0.840711 Iteration 2 Error: 0.086961 Iteration 3 Error: 0.018638 Align patch 23 2 left Iteration 1 Error: 0.900045 Iteration 2 Error: 0.123840 Iteration 3 Error: 0.028918 Align patch 24 1 left Iteration 1 Error: 0.752065 Iteration 2 Error: 0.079087 Iteration 3 Error: 0.013722 Align patch 25 0 left Iteration 1 Error: 0.767805 Iteration 2 Error: 0.072842 Iteration 3 Error: 0.012807 3D Fitting completed. Patch alignment time: 15.20(sec) Local motion has been corrected. Process thread exits. Computational time: 23.692551 sec Total time: 29.252676 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00016hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00016hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.539391s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00016hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.349111s ........................................ >>>>>>TIME<<<<<< FFT: 0.967361s Defocus_U Defocus_V Angle CCC 10470.73 9955.10 88.44 0.045520 Final Values Defocus_U Defocus_V Angle CCC 10500.43 9966.06 88.13 0.077735 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00016hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00016hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.002e-01 CC threshold: 0.736 Mean Std: 40.79 6.86 Num Hot pixels: 234 Hot pixel threshold: 81.95 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.163569 Iteration 2 Error: 0.159623 Iteration 3 Error: 0.034093 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.09 -0.00 ...... Frame ( 3) shift: -0.17 -0.01 ...... Frame ( 4) shift: -0.26 -0.01 ...... Frame ( 5) shift: -0.35 -0.02 ...... Frame ( 6) shift: -0.33 0.03 ...... Frame ( 7) shift: -0.21 0.13 ...... Frame ( 8) shift: -0.09 0.24 ...... Frame ( 9) shift: 0.02 0.33 ...... Frame ( 10) shift: 0.11 0.43 ...... Frame ( 11) shift: 0.21 0.53 ...... Frame ( 12) shift: 0.31 0.63 ...... Frame ( 13) shift: 0.42 0.76 ...... Frame ( 14) shift: 0.53 0.88 ...... Frame ( 15) shift: 0.58 0.99 ...... Frame ( 16) shift: 0.59 1.09 ...... Frame ( 17) shift: 0.60 1.19 ...... Frame ( 18) shift: 0.63 1.26 ...... Frame ( 19) shift: 0.67 1.29 ...... Frame ( 20) shift: 0.71 1.33 ...... Frame ( 21) shift: 0.72 1.34 ...... Frame ( 22) shift: 0.69 1.32 ...... Frame ( 23) shift: 0.66 1.29 ...... Frame ( 24) shift: 0.64 1.30 ...... Frame ( 25) shift: 0.62 1.35 ...... Frame ( 26) shift: 0.61 1.39 ...... Frame ( 27) shift: 0.62 1.40 ...... Frame ( 28) shift: 0.64 1.39 ...... Frame ( 29) shift: 0.67 1.38 ...... Frame ( 30) shift: 0.65 1.38 ...... Frame ( 31) shift: 0.57 1.39 ...... Frame ( 32) shift: 0.50 1.40 ...... Frame ( 33) shift: 0.48 1.44 ...... Frame ( 34) shift: 0.52 1.52 ...... Frame ( 35) shift: 0.57 1.59 ...... Frame ( 36) shift: 0.60 1.66 ...... Frame ( 37) shift: 0.64 1.71 ...... Frame ( 38) shift: 0.68 1.76 ...... Frame ( 39) shift: 0.72 1.81 ...... Frame ( 40) shift: 0.76 1.87 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.908270 Iteration 2 Error: 0.270309 Iteration 3 Error: 0.097026 Iteration 4 Error: 0.038404 Align patch 2 23 left Iteration 1 Error: 0.810061 Iteration 2 Error: 0.162644 Iteration 3 Error: 0.052737 Iteration 4 Error: 0.016130 Align patch 3 22 left Iteration 1 Error: 0.761096 Iteration 2 Error: 0.093498 Iteration 3 Error: 0.028089 Align patch 4 21 left Iteration 1 Error: 0.498844 Iteration 2 Error: 0.091498 Iteration 3 Error: 0.026284 Align patch 5 20 left Iteration 1 Error: 0.557320 Iteration 2 Error: 0.081204 Iteration 3 Error: 0.014515 Align patch 6 19 left Iteration 1 Error: 0.883671 Iteration 2 Error: 0.178286 Iteration 3 Error: 0.046405 Align patch 7 18 left Iteration 1 Error: 0.477861 Iteration 2 Error: 0.122868 Iteration 3 Error: 0.032348 Align patch 8 17 left Iteration 1 Error: 0.588383 Iteration 2 Error: 0.066045 Iteration 3 Error: 0.014718 Align patch 9 16 left Iteration 1 Error: 0.474422 Iteration 2 Error: 0.059660 Iteration 3 Error: 0.014280 Align patch 10 15 left Iteration 1 Error: 0.546408 Iteration 2 Error: 0.046030 Align patch 11 14 left Iteration 1 Error: 0.865964 Iteration 2 Error: 0.175837 Iteration 3 Error: 0.036712 Align patch 12 13 left Iteration 1 Error: 0.538882 Iteration 2 Error: 0.101918 Iteration 3 Error: 0.025434 Align patch 13 12 left Iteration 1 Error: 0.555166 Iteration 2 Error: 0.056936 Iteration 3 Error: 0.009247 Align patch 14 11 left Iteration 1 Error: 0.826308 Iteration 2 Error: 0.090716 Iteration 3 Error: 0.012186 Align patch 15 10 left Iteration 1 Error: 0.783745 Iteration 2 Error: 0.079317 Iteration 3 Error: 0.021136 Align patch 16 9 left Iteration 1 Error: 0.667885 Iteration 2 Error: 0.078574 Iteration 3 Error: 0.016864 Align patch 17 8 left Iteration 1 Error: 0.721886 Iteration 2 Error: 0.169691 Iteration 3 Error: 0.082771 Iteration 4 Error: 0.042266 Align patch 18 7 left Iteration 1 Error: 0.517110 Iteration 2 Error: 0.097672 Iteration 3 Error: 0.029799 Align patch 19 6 left Iteration 1 Error: 0.620240 Iteration 2 Error: 0.082463 Iteration 3 Error: 0.014574 Align patch 20 5 left Iteration 1 Error: 0.742595 Iteration 2 Error: 0.139599 Iteration 3 Error: 0.020854 Align patch 21 4 left Iteration 1 Error: 0.716343 Iteration 2 Error: 0.079931 Iteration 3 Error: 0.018917 Align patch 22 3 left Iteration 1 Error: 0.843902 Iteration 2 Error: 0.084804 Iteration 3 Error: 0.016902 Align patch 23 2 left Iteration 1 Error: 0.484832 Iteration 2 Error: 0.071741 Iteration 3 Error: 0.015873 Align patch 24 1 left Iteration 1 Error: 0.581833 Iteration 2 Error: 0.134773 Iteration 3 Error: 0.037197 Align patch 25 0 left Iteration 1 Error: 1.220292 Iteration 2 Error: 0.111992 Iteration 3 Error: 0.035065 3D Fitting completed. Patch alignment time: 14.94(sec) Local motion has been corrected. Process thread exits. Computational time: 23.547733 sec Total time: 29.604321 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00016hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00016hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.793127s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00016hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.302343s ........................................ >>>>>>TIME<<<<<< FFT: 1.332881s Defocus_U Defocus_V Angle CCC 11859.43 12734.43 4.75 0.056821 Final Values Defocus_U Defocus_V Angle CCC 11867.23 12745.40 4.44 0.089740 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00016hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00016hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 39.04 6.74 Num Hot pixels: 215 Hot pixel threshold: 79.49 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.376268 Iteration 2 Error: 0.201609 Iteration 3 Error: 0.038734 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.08 0.21 ...... Frame ( 3) shift: -0.16 0.42 ...... Frame ( 4) shift: -0.24 0.63 ...... Frame ( 5) shift: -0.32 0.84 ...... Frame ( 6) shift: -0.32 0.96 ...... Frame ( 7) shift: -0.25 0.99 ...... Frame ( 8) shift: -0.19 1.01 ...... Frame ( 9) shift: -0.14 1.03 ...... Frame ( 10) shift: -0.12 1.02 ...... Frame ( 11) shift: -0.10 1.02 ...... Frame ( 12) shift: -0.06 0.97 ...... Frame ( 13) shift: 0.00 0.88 ...... Frame ( 14) shift: 0.06 0.78 ...... Frame ( 15) shift: 0.10 0.74 ...... Frame ( 16) shift: 0.12 0.75 ...... Frame ( 17) shift: 0.14 0.77 ...... Frame ( 18) shift: 0.19 0.84 ...... Frame ( 19) shift: 0.28 0.96 ...... Frame ( 20) shift: 0.36 1.09 ...... Frame ( 21) shift: 0.40 1.22 ...... Frame ( 22) shift: 0.40 1.36 ...... Frame ( 23) shift: 0.41 1.51 ...... Frame ( 24) shift: 0.44 1.64 ...... Frame ( 25) shift: 0.51 1.76 ...... Frame ( 26) shift: 0.58 1.88 ...... Frame ( 27) shift: 0.61 1.94 ...... Frame ( 28) shift: 0.61 1.93 ...... Frame ( 29) shift: 0.61 1.93 ...... Frame ( 30) shift: 0.62 1.97 ...... Frame ( 31) shift: 0.66 2.05 ...... Frame ( 32) shift: 0.70 2.14 ...... Frame ( 33) shift: 0.74 2.23 ...... Frame ( 34) shift: 0.77 2.31 ...... Frame ( 35) shift: 0.80 2.40 ...... Frame ( 36) shift: 0.84 2.48 ...... Frame ( 37) shift: 0.89 2.56 ...... Frame ( 38) shift: 0.94 2.63 ...... Frame ( 39) shift: 0.99 2.71 ...... Frame ( 40) shift: 1.03 2.78 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.639890 Iteration 2 Error: 0.125793 Iteration 3 Error: 0.028612 Align patch 2 23 left Iteration 1 Error: 0.541745 Iteration 2 Error: 0.079153 Iteration 3 Error: 0.022777 Align patch 3 22 left Iteration 1 Error: 0.554796 Iteration 2 Error: 0.078759 Iteration 3 Error: 0.015194 Align patch 4 21 left Iteration 1 Error: 0.714842 Iteration 2 Error: 0.063623 Iteration 3 Error: 0.012491 Align patch 5 20 left Iteration 1 Error: 0.600928 Iteration 2 Error: 0.066591 Iteration 3 Error: 0.011229 Align patch 6 19 left Iteration 1 Error: 0.625868 Iteration 2 Error: 0.137556 Iteration 3 Error: 0.024548 Align patch 7 18 left Iteration 1 Error: 0.388335 Iteration 2 Error: 0.064055 Iteration 3 Error: 0.014024 Align patch 8 17 left Iteration 1 Error: 0.653343 Iteration 2 Error: 0.080154 Iteration 3 Error: 0.012544 Align patch 9 16 left Iteration 1 Error: 0.593000 Iteration 2 Error: 0.113023 Iteration 3 Error: 0.027853 Align patch 10 15 left Iteration 1 Error: 0.446990 Iteration 2 Error: 0.043493 Align patch 11 14 left Iteration 1 Error: 0.639753 Iteration 2 Error: 0.114585 Iteration 3 Error: 0.021213 Align patch 12 13 left Iteration 1 Error: 0.496328 Iteration 2 Error: 0.105607 Iteration 3 Error: 0.022675 Align patch 13 12 left Iteration 1 Error: 0.573984 Iteration 2 Error: 0.070183 Iteration 3 Error: 0.013518 Align patch 14 11 left Iteration 1 Error: 0.465026 Iteration 2 Error: 0.049728 Align patch 15 10 left Iteration 1 Error: 0.520232 Iteration 2 Error: 0.068595 Iteration 3 Error: 0.014650 Align patch 16 9 left Iteration 1 Error: 0.464227 Iteration 2 Error: 0.114379 Iteration 3 Error: 0.021545 Align patch 17 8 left Iteration 1 Error: 0.514134 Iteration 2 Error: 0.054176 Iteration 3 Error: 0.018032 Align patch 18 7 left Iteration 1 Error: 0.509553 Iteration 2 Error: 0.046950 Align patch 19 6 left Iteration 1 Error: 0.550852 Iteration 2 Error: 0.088522 Iteration 3 Error: 0.014132 Align patch 20 5 left Iteration 1 Error: 0.852703 Iteration 2 Error: 0.096009 Iteration 3 Error: 0.026837 Align patch 21 4 left Iteration 1 Error: 0.584801 Iteration 2 Error: 0.064799 Iteration 3 Error: 0.019631 Align patch 22 3 left Iteration 1 Error: 0.786311 Iteration 2 Error: 0.102006 Iteration 3 Error: 0.023817 Align patch 23 2 left Iteration 1 Error: 0.632868 Iteration 2 Error: 0.057127 Iteration 3 Error: 0.012860 Align patch 24 1 left Iteration 1 Error: 0.671930 Iteration 2 Error: 0.083604 Iteration 3 Error: 0.026003 Align patch 25 0 left Iteration 1 Error: 0.805942 Iteration 2 Error: 0.146765 Iteration 3 Error: 0.054288 Iteration 4 Error: 0.016287 3D Fitting completed. Patch alignment time: 15.09(sec) Local motion has been corrected. Process thread exits. Computational time: 23.126762 sec Total time: 29.755684 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00016hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00016hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.777693s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00016hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.918255s ........................................ >>>>>>TIME<<<<<< FFT: 1.032229s Defocus_U Defocus_V Angle CCC 13562.56 12992.20 86.47 0.062181 Final Values Defocus_U Defocus_V Angle CCC 13600.07 12998.46 86.78 0.093040 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00017hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00017hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.004e-01 CC threshold: 0.737 Mean Std: 38.81 6.74 Num Hot pixels: 228 Hot pixel threshold: 79.26 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.829341 Iteration 2 Error: 0.469594 Iteration 3 Error: 0.101672 Iteration 4 Error: 0.034862 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.11 -0.00 ...... Frame ( 3) shift: -0.22 -0.01 ...... Frame ( 4) shift: -0.33 -0.01 ...... Frame ( 5) shift: -0.44 -0.02 ...... Frame ( 6) shift: -0.49 -0.01 ...... Frame ( 7) shift: -0.48 0.01 ...... Frame ( 8) shift: -0.47 0.04 ...... Frame ( 9) shift: -0.44 0.07 ...... Frame ( 10) shift: -0.40 0.12 ...... Frame ( 11) shift: -0.35 0.17 ...... Frame ( 12) shift: -0.27 0.26 ...... Frame ( 13) shift: -0.13 0.40 ...... Frame ( 14) shift: 0.00 0.54 ...... Frame ( 15) shift: 0.08 0.64 ...... Frame ( 16) shift: 0.09 0.70 ...... Frame ( 17) shift: 0.11 0.76 ...... Frame ( 18) shift: 0.17 0.81 ...... Frame ( 19) shift: 0.26 0.87 ...... Frame ( 20) shift: 0.35 0.92 ...... Frame ( 21) shift: 0.40 0.99 ...... Frame ( 22) shift: 0.41 1.08 ...... Frame ( 23) shift: 0.41 1.18 ...... Frame ( 24) shift: 0.46 1.28 ...... Frame ( 25) shift: 0.56 1.39 ...... Frame ( 26) shift: 0.65 1.50 ...... Frame ( 27) shift: 0.74 1.59 ...... Frame ( 28) shift: 0.80 1.67 ...... Frame ( 29) shift: 0.87 1.75 ...... Frame ( 30) shift: 0.95 1.83 ...... Frame ( 31) shift: 1.05 1.91 ...... Frame ( 32) shift: 1.15 1.99 ...... Frame ( 33) shift: 1.24 2.08 ...... Frame ( 34) shift: 1.30 2.18 ...... Frame ( 35) shift: 1.37 2.28 ...... Frame ( 36) shift: 1.42 2.38 ...... Frame ( 37) shift: 1.44 2.48 ...... Frame ( 38) shift: 1.47 2.58 ...... Frame ( 39) shift: 1.50 2.68 ...... Frame ( 40) shift: 1.53 2.77 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.683105 Iteration 2 Error: 0.385645 Iteration 3 Error: 0.113257 Iteration 4 Error: 0.041492 Align patch 2 23 left Iteration 1 Error: 0.961298 Iteration 2 Error: 0.277831 Iteration 3 Error: 0.084608 Iteration 4 Error: 0.032982 Align patch 3 22 left Iteration 1 Error: 0.645517 Iteration 2 Error: 0.163844 Iteration 3 Error: 0.052674 Iteration 4 Error: 0.011992 Align patch 4 21 left Iteration 1 Error: 0.508296 Iteration 2 Error: 0.123954 Iteration 3 Error: 0.033753 Align patch 5 20 left Iteration 1 Error: 0.764625 Iteration 2 Error: 0.086329 Iteration 3 Error: 0.015312 Align patch 6 19 left Iteration 1 Error: 0.830201 Iteration 2 Error: 0.183973 Iteration 3 Error: 0.033646 Align patch 7 18 left Iteration 1 Error: 0.709469 Iteration 2 Error: 0.164566 Iteration 3 Error: 0.058262 Iteration 4 Error: 0.014985 Align patch 8 17 left Iteration 1 Error: 0.555699 Iteration 2 Error: 0.155023 Iteration 3 Error: 0.064426 Iteration 4 Error: 0.030052 Align patch 9 16 left Iteration 1 Error: 0.495882 Iteration 2 Error: 0.083595 Iteration 3 Error: 0.021717 Align patch 10 15 left Iteration 1 Error: 0.759168 Iteration 2 Error: 0.136597 Iteration 3 Error: 0.037800 Align patch 11 14 left Iteration 1 Error: 0.577775 Iteration 2 Error: 0.143641 Iteration 3 Error: 0.045143 Align patch 12 13 left Iteration 1 Error: 0.584413 Iteration 2 Error: 0.090049 Iteration 3 Error: 0.026682 Align patch 13 12 left Iteration 1 Error: 0.631131 Iteration 2 Error: 0.130695 Iteration 3 Error: 0.040364 Align patch 14 11 left Iteration 1 Error: 1.116447 Iteration 2 Error: 0.114476 Iteration 3 Error: 0.037557 Align patch 15 10 left Iteration 1 Error: 0.669201 Iteration 2 Error: 0.130106 Iteration 3 Error: 0.034707 Align patch 16 9 left Iteration 1 Error: 0.772242 Iteration 2 Error: 0.093143 Iteration 3 Error: 0.038263 Align patch 17 8 left Iteration 1 Error: 0.674361 Iteration 2 Error: 0.090654 Iteration 3 Error: 0.018290 Align patch 18 7 left Iteration 1 Error: 0.982528 Iteration 2 Error: 0.135586 Iteration 3 Error: 0.053432 Iteration 4 Error: 0.023246 Align patch 19 6 left Iteration 1 Error: 0.774313 Iteration 2 Error: 0.135163 Iteration 3 Error: 0.052229 Iteration 4 Error: 0.015925 Align patch 20 5 left Iteration 1 Error: 0.637706 Iteration 2 Error: 0.155240 Iteration 3 Error: 0.044701 Align patch 21 4 left Iteration 1 Error: 0.838944 Iteration 2 Error: 0.172170 Iteration 3 Error: 0.061991 Iteration 4 Error: 0.026603 Align patch 22 3 left Iteration 1 Error: 0.635271 Iteration 2 Error: 0.129101 Iteration 3 Error: 0.046130 Align patch 23 2 left Iteration 1 Error: 0.517141 Iteration 2 Error: 0.205851 Iteration 3 Error: 0.063442 Iteration 4 Error: 0.024863 Align patch 24 1 left Iteration 1 Error: 0.758929 Iteration 2 Error: 0.107531 Iteration 3 Error: 0.019811 Align patch 25 0 left Iteration 1 Error: 0.569904 Iteration 2 Error: 0.093919 Iteration 3 Error: 0.016905 3D Fitting completed. Patch alignment time: 15.21(sec) Local motion has been corrected. Process thread exits. Computational time: 23.505865 sec Total time: 30.437792 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00017hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00017hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.587883s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00017hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.529747s ........................................ >>>>>>TIME<<<<<< FFT: 0.938093s Defocus_U Defocus_V Angle CCC 9236.35 10056.66 15.08 0.047669 Final Values Defocus_U Defocus_V Angle CCC 9236.36 10084.81 14.77 0.085509 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00017hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00017hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 38.52 6.68 Num Hot pixels: 212 Hot pixel threshold: 78.58 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.987676 Iteration 2 Error: 0.106844 Iteration 3 Error: 0.022607 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.24 -0.19 ...... Frame ( 3) shift: -0.47 -0.37 ...... Frame ( 4) shift: -0.71 -0.56 ...... Frame ( 5) shift: -0.95 -0.75 ...... Frame ( 6) shift: -1.07 -0.84 ...... Frame ( 7) shift: -1.09 -0.84 ...... Frame ( 8) shift: -1.11 -0.83 ...... Frame ( 9) shift: -1.07 -0.82 ...... Frame ( 10) shift: -0.98 -0.80 ...... Frame ( 11) shift: -0.89 -0.78 ...... Frame ( 12) shift: -0.83 -0.77 ...... Frame ( 13) shift: -0.81 -0.77 ...... Frame ( 14) shift: -0.79 -0.78 ...... Frame ( 15) shift: -0.79 -0.74 ...... Frame ( 16) shift: -0.82 -0.64 ...... Frame ( 17) shift: -0.84 -0.55 ...... Frame ( 18) shift: -0.84 -0.53 ...... Frame ( 19) shift: -0.79 -0.57 ...... Frame ( 20) shift: -0.75 -0.61 ...... Frame ( 21) shift: -0.69 -0.62 ...... Frame ( 22) shift: -0.61 -0.60 ...... Frame ( 23) shift: -0.54 -0.58 ...... Frame ( 24) shift: -0.50 -0.56 ...... Frame ( 25) shift: -0.49 -0.53 ...... Frame ( 26) shift: -0.49 -0.50 ...... Frame ( 27) shift: -0.45 -0.47 ...... Frame ( 28) shift: -0.38 -0.45 ...... Frame ( 29) shift: -0.31 -0.43 ...... Frame ( 30) shift: -0.27 -0.42 ...... Frame ( 31) shift: -0.26 -0.41 ...... Frame ( 32) shift: -0.26 -0.40 ...... Frame ( 33) shift: -0.24 -0.33 ...... Frame ( 34) shift: -0.22 -0.17 ...... Frame ( 35) shift: -0.20 -0.02 ...... Frame ( 36) shift: -0.15 0.10 ...... Frame ( 37) shift: -0.09 0.20 ...... Frame ( 38) shift: -0.03 0.29 ...... Frame ( 39) shift: 0.03 0.39 ...... Frame ( 40) shift: 0.09 0.49 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.542459 Iteration 2 Error: 0.078025 Iteration 3 Error: 0.012182 Align patch 2 23 left Iteration 1 Error: 0.756087 Iteration 2 Error: 0.103450 Iteration 3 Error: 0.018766 Align patch 3 22 left Iteration 1 Error: 0.873391 Iteration 2 Error: 0.096692 Iteration 3 Error: 0.022966 Align patch 4 21 left Iteration 1 Error: 0.698545 Iteration 2 Error: 0.170037 Iteration 3 Error: 0.028931 Align patch 5 20 left Iteration 1 Error: 0.754750 Iteration 2 Error: 0.114426 Iteration 3 Error: 0.035090 Align patch 6 19 left Iteration 1 Error: 0.638091 Iteration 2 Error: 0.097169 Iteration 3 Error: 0.016044 Align patch 7 18 left Iteration 1 Error: 0.702480 Iteration 2 Error: 0.087450 Iteration 3 Error: 0.023130 Align patch 8 17 left Iteration 1 Error: 0.615882 Iteration 2 Error: 0.091429 Iteration 3 Error: 0.022181 Align patch 9 16 left Iteration 1 Error: 0.558044 Iteration 2 Error: 0.061795 Iteration 3 Error: 0.013298 Align patch 10 15 left Iteration 1 Error: 0.814093 Iteration 2 Error: 0.075607 Iteration 3 Error: 0.016829 Align patch 11 14 left Iteration 1 Error: 0.499225 Iteration 2 Error: 0.051174 Iteration 3 Error: 0.010754 Align patch 12 13 left Iteration 1 Error: 0.546731 Iteration 2 Error: 0.070599 Iteration 3 Error: 0.014164 Align patch 13 12 left Iteration 1 Error: 0.752188 Iteration 2 Error: 0.091844 Iteration 3 Error: 0.011711 Align patch 14 11 left Iteration 1 Error: 0.809919 Iteration 2 Error: 0.114006 Iteration 3 Error: 0.027036 Align patch 15 10 left Iteration 1 Error: 0.847715 Iteration 2 Error: 0.186221 Iteration 3 Error: 0.036079 Align patch 16 9 left Iteration 1 Error: 0.653062 Iteration 2 Error: 0.099430 Iteration 3 Error: 0.023943 Align patch 17 8 left Iteration 1 Error: 1.082831 Iteration 2 Error: 0.127302 Iteration 3 Error: 0.024026 Align patch 18 7 left Iteration 1 Error: 0.558755 Iteration 2 Error: 0.081101 Iteration 3 Error: 0.011751 Align patch 19 6 left Iteration 1 Error: 0.667921 Iteration 2 Error: 0.140175 Iteration 3 Error: 0.026674 Align patch 20 5 left Iteration 1 Error: 0.716522 Iteration 2 Error: 0.106553 Iteration 3 Error: 0.033873 Align patch 21 4 left Iteration 1 Error: 0.429127 Iteration 2 Error: 0.076140 Iteration 3 Error: 0.017713 Align patch 22 3 left Iteration 1 Error: 0.894539 Iteration 2 Error: 0.162766 Iteration 3 Error: 0.046794 Align patch 23 2 left Iteration 1 Error: 0.912228 Iteration 2 Error: 0.147328 Iteration 3 Error: 0.043818 Align patch 24 1 left Iteration 1 Error: 0.836811 Iteration 2 Error: 0.134250 Iteration 3 Error: 0.030289 Align patch 25 0 left Iteration 1 Error: 0.819783 Iteration 2 Error: 0.214516 Iteration 3 Error: 0.047545 3D Fitting completed. Patch alignment time: 15.20(sec) Local motion has been corrected. Process thread exits. Computational time: 23.544785 sec Total time: 29.133369 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00017hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00017hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.736573s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00017hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.484788s ........................................ >>>>>>TIME<<<<<< FFT: 1.020255s Defocus_U Defocus_V Angle CCC 12234.35 12671.90 7.61 0.039512 Final Values Defocus_U Defocus_V Angle CCC 12246.86 12681.28 11.39 0.061834 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00017hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00017hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.736 Mean Std: 40.03 6.82 Num Hot pixels: 238 Hot pixel threshold: 80.94 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.955570 Iteration 2 Error: 0.162564 Iteration 3 Error: 0.037118 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.07 -0.04 ...... Frame ( 3) shift: -0.15 -0.08 ...... Frame ( 4) shift: -0.22 -0.12 ...... Frame ( 5) shift: -0.30 -0.15 ...... Frame ( 6) shift: -0.33 -0.17 ...... Frame ( 7) shift: -0.32 -0.18 ...... Frame ( 8) shift: -0.31 -0.18 ...... Frame ( 9) shift: -0.33 -0.13 ...... Frame ( 10) shift: -0.38 -0.03 ...... Frame ( 11) shift: -0.44 0.07 ...... Frame ( 12) shift: -0.46 0.16 ...... Frame ( 13) shift: -0.44 0.25 ...... Frame ( 14) shift: -0.43 0.33 ...... Frame ( 15) shift: -0.40 0.43 ...... Frame ( 16) shift: -0.35 0.54 ...... Frame ( 17) shift: -0.30 0.65 ...... Frame ( 18) shift: -0.26 0.73 ...... Frame ( 19) shift: -0.23 0.77 ...... Frame ( 20) shift: -0.20 0.80 ...... Frame ( 21) shift: -0.16 0.84 ...... Frame ( 22) shift: -0.10 0.87 ...... Frame ( 23) shift: -0.05 0.89 ...... Frame ( 24) shift: -0.01 0.94 ...... Frame ( 25) shift: 0.02 0.99 ...... Frame ( 26) shift: 0.04 1.05 ...... Frame ( 27) shift: 0.06 1.11 ...... Frame ( 28) shift: 0.08 1.17 ...... Frame ( 29) shift: 0.10 1.23 ...... Frame ( 30) shift: 0.12 1.31 ...... Frame ( 31) shift: 0.14 1.39 ...... Frame ( 32) shift: 0.17 1.47 ...... Frame ( 33) shift: 0.20 1.53 ...... Frame ( 34) shift: 0.24 1.57 ...... Frame ( 35) shift: 0.28 1.61 ...... Frame ( 36) shift: 0.31 1.64 ...... Frame ( 37) shift: 0.33 1.68 ...... Frame ( 38) shift: 0.35 1.72 ...... Frame ( 39) shift: 0.37 1.76 ...... Frame ( 40) shift: 0.39 1.80 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.578039 Iteration 2 Error: 0.203322 Iteration 3 Error: 0.056228 Iteration 4 Error: 0.020490 Align patch 2 23 left Iteration 1 Error: 0.628836 Iteration 2 Error: 0.100510 Iteration 3 Error: 0.037274 Align patch 3 22 left Iteration 1 Error: 0.615308 Iteration 2 Error: 0.077900 Iteration 3 Error: 0.028237 Align patch 4 21 left Iteration 1 Error: 0.772485 Iteration 2 Error: 0.098375 Iteration 3 Error: 0.035923 Align patch 5 20 left Iteration 1 Error: 0.419125 Iteration 2 Error: 0.065021 Iteration 3 Error: 0.016609 Align patch 6 19 left Iteration 1 Error: 1.239628 Iteration 2 Error: 0.220120 Iteration 3 Error: 0.067096 Iteration 4 Error: 0.026839 Align patch 7 18 left Iteration 1 Error: 1.122422 Iteration 2 Error: 0.136610 Iteration 3 Error: 0.036821 Align patch 8 17 left Iteration 1 Error: 0.712886 Iteration 2 Error: 0.080562 Iteration 3 Error: 0.018375 Align patch 9 16 left Iteration 1 Error: 0.605898 Iteration 2 Error: 0.078504 Iteration 3 Error: 0.018321 Align patch 10 15 left Iteration 1 Error: 0.734253 Iteration 2 Error: 0.069206 Iteration 3 Error: 0.015217 Align patch 11 14 left Iteration 1 Error: 0.716286 Iteration 2 Error: 0.082163 Iteration 3 Error: 0.021162 Align patch 12 13 left Iteration 1 Error: 0.448452 Iteration 2 Error: 0.080276 Iteration 3 Error: 0.015144 Align patch 13 12 left Iteration 1 Error: 0.415690 Iteration 2 Error: 0.059609 Iteration 3 Error: 0.013180 Align patch 14 11 left Iteration 1 Error: 0.629977 Iteration 2 Error: 0.083896 Iteration 3 Error: 0.013914 Align patch 15 10 left Iteration 1 Error: 0.496097 Iteration 2 Error: 0.083591 Iteration 3 Error: 0.025979 Align patch 16 9 left Iteration 1 Error: 0.751790 Iteration 2 Error: 0.090460 Iteration 3 Error: 0.020811 Align patch 17 8 left Iteration 1 Error: 0.683285 Iteration 2 Error: 0.068501 Iteration 3 Error: 0.012334 Align patch 18 7 left Iteration 1 Error: 0.895167 Iteration 2 Error: 0.124676 Iteration 3 Error: 0.022047 Align patch 19 6 left Iteration 1 Error: 1.131943 Iteration 2 Error: 0.155354 Iteration 3 Error: 0.044947 Align patch 20 5 left Iteration 1 Error: 0.587422 Iteration 2 Error: 0.142247 Iteration 3 Error: 0.040508 Align patch 21 4 left Iteration 1 Error: 0.539479 Iteration 2 Error: 0.125296 Iteration 3 Error: 0.052092 Iteration 4 Error: 0.018557 Align patch 22 3 left Iteration 1 Error: 0.908693 Iteration 2 Error: 0.117069 Iteration 3 Error: 0.040416 Align patch 23 2 left Iteration 1 Error: 0.741929 Iteration 2 Error: 0.103163 Iteration 3 Error: 0.024885 Align patch 24 1 left Iteration 1 Error: 0.686374 Iteration 2 Error: 0.104089 Iteration 3 Error: 0.025490 Align patch 25 0 left Iteration 1 Error: 0.833751 Iteration 2 Error: 0.110845 Iteration 3 Error: 0.021794 3D Fitting completed. Patch alignment time: 15.79(sec) Local motion has been corrected. Process thread exits. Computational time: 24.561024 sec Total time: 30.415621 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00017hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00017hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.736239s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00017hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.494739s ........................................ >>>>>>TIME<<<<<< FFT: 1.028831s Defocus_U Defocus_V Angle CCC 10345.74 11181.68 6.90 0.052714 Final Values Defocus_U Defocus_V Angle CCC 10362.95 11211.38 6.90 0.088920 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00017hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00017hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 1.000e-01 CC threshold: 0.734 Mean Std: 36.26 6.46 Num Hot pixels: 225 Hot pixel threshold: 75.00 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.394158 Iteration 2 Error: 0.052293 Iteration 3 Error: 0.017311 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.07 -0.03 ...... Frame ( 3) shift: -0.14 -0.07 ...... Frame ( 4) shift: -0.20 -0.10 ...... Frame ( 5) shift: -0.27 -0.13 ...... Frame ( 6) shift: -0.28 -0.21 ...... Frame ( 7) shift: -0.22 -0.33 ...... Frame ( 8) shift: -0.16 -0.44 ...... Frame ( 9) shift: -0.16 -0.50 ...... Frame ( 10) shift: -0.21 -0.50 ...... Frame ( 11) shift: -0.26 -0.49 ...... Frame ( 12) shift: -0.27 -0.47 ...... Frame ( 13) shift: -0.25 -0.43 ...... Frame ( 14) shift: -0.22 -0.39 ...... Frame ( 15) shift: -0.24 -0.37 ...... Frame ( 16) shift: -0.28 -0.39 ...... Frame ( 17) shift: -0.33 -0.40 ...... Frame ( 18) shift: -0.31 -0.37 ...... Frame ( 19) shift: -0.23 -0.28 ...... Frame ( 20) shift: -0.16 -0.20 ...... Frame ( 21) shift: -0.12 -0.19 ...... Frame ( 22) shift: -0.11 -0.23 ...... Frame ( 23) shift: -0.11 -0.28 ...... Frame ( 24) shift: -0.09 -0.27 ...... Frame ( 25) shift: -0.06 -0.20 ...... Frame ( 26) shift: -0.03 -0.13 ...... Frame ( 27) shift: -0.00 -0.07 ...... Frame ( 28) shift: 0.02 -0.01 ...... Frame ( 29) shift: 0.04 0.05 ...... Frame ( 30) shift: 0.05 0.06 ...... Frame ( 31) shift: 0.06 0.03 ...... Frame ( 32) shift: 0.08 0.01 ...... Frame ( 33) shift: 0.10 0.03 ...... Frame ( 34) shift: 0.12 0.11 ...... Frame ( 35) shift: 0.14 0.18 ...... Frame ( 36) shift: 0.15 0.22 ...... Frame ( 37) shift: 0.14 0.22 ...... Frame ( 38) shift: 0.12 0.23 ...... Frame ( 39) shift: 0.11 0.23 ...... Frame ( 40) shift: 0.10 0.23 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.785861 Iteration 2 Error: 0.278927 Iteration 3 Error: 0.074142 Iteration 4 Error: 0.028294 Align patch 2 23 left Iteration 1 Error: 1.008260 Iteration 2 Error: 0.182680 Iteration 3 Error: 0.051939 Iteration 4 Error: 0.023087 Align patch 3 22 left Iteration 1 Error: 0.807997 Iteration 2 Error: 0.145866 Iteration 3 Error: 0.034098 Align patch 4 21 left Iteration 1 Error: 1.209267 Iteration 2 Error: 0.125595 Iteration 3 Error: 0.030074 Align patch 5 20 left Iteration 1 Error: 0.789646 Iteration 2 Error: 0.155876 Iteration 3 Error: 0.044531 Align patch 6 19 left Iteration 1 Error: 0.820680 Iteration 2 Error: 0.104349 Iteration 3 Error: 0.044032 Align patch 7 18 left Iteration 1 Error: 0.827002 Iteration 2 Error: 0.134778 Iteration 3 Error: 0.052088 Iteration 4 Error: 0.014168 Align patch 8 17 left Iteration 1 Error: 0.754166 Iteration 2 Error: 0.107125 Iteration 3 Error: 0.025657 Align patch 9 16 left Iteration 1 Error: 0.926745 Iteration 2 Error: 0.179743 Iteration 3 Error: 0.039818 Align patch 10 15 left Iteration 1 Error: 0.859961 Iteration 2 Error: 0.174336 Iteration 3 Error: 0.023588 Align patch 11 14 left Iteration 1 Error: 0.637699 Iteration 2 Error: 0.136193 Iteration 3 Error: 0.027418 Align patch 12 13 left Iteration 1 Error: 0.921652 Iteration 2 Error: 0.127810 Iteration 3 Error: 0.049259 Align patch 13 12 left Iteration 1 Error: 0.866337 Iteration 2 Error: 0.211943 Iteration 3 Error: 0.061053 Iteration 4 Error: 0.017854 Align patch 14 11 left Iteration 1 Error: 0.781448 Iteration 2 Error: 0.107762 Iteration 3 Error: 0.026941 Align patch 15 10 left Iteration 1 Error: 0.738206 Iteration 2 Error: 0.157138 Iteration 3 Error: 0.054561 Iteration 4 Error: 0.025993 Align patch 16 9 left Iteration 1 Error: 0.642271 Iteration 2 Error: 0.101987 Iteration 3 Error: 0.023687 Align patch 17 8 left Iteration 1 Error: 0.522629 Iteration 2 Error: 0.092946 Iteration 3 Error: 0.029663 Align patch 18 7 left Iteration 1 Error: 0.673894 Iteration 2 Error: 0.093382 Iteration 3 Error: 0.021395 Align patch 19 6 left Iteration 1 Error: 0.417951 Iteration 2 Error: 0.071670 Iteration 3 Error: 0.026175 Align patch 20 5 left Iteration 1 Error: 0.746389 Iteration 2 Error: 0.178809 Iteration 3 Error: 0.061444 Iteration 4 Error: 0.018950 Align patch 21 4 left Iteration 1 Error: 0.786730 Iteration 2 Error: 0.139654 Iteration 3 Error: 0.027593 Align patch 22 3 left Iteration 1 Error: 0.851570 Iteration 2 Error: 0.282297 Iteration 3 Error: 0.078949 Iteration 4 Error: 0.031328 Align patch 23 2 left Iteration 1 Error: 0.700503 Iteration 2 Error: 0.149820 Iteration 3 Error: 0.037842 Align patch 24 1 left Iteration 1 Error: 0.701253 Iteration 2 Error: 0.190018 Iteration 3 Error: 0.065308 Iteration 4 Error: 0.018324 Align patch 25 0 left Iteration 1 Error: 0.861438 Iteration 2 Error: 0.102280 Iteration 3 Error: 0.032158 3D Fitting completed. Patch alignment time: 15.71(sec) Local motion has been corrected. Process thread exits. Computational time: 24.475916 sec Total time: 30.278418 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00017hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00017hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.747912s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00017hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.059321s ........................................ >>>>>>TIME<<<<<< FFT: 1.076038s Defocus_U Defocus_V Angle CCC 13626.90 13556.73 74.16 0.025059 Final Values Defocus_U Defocus_V Angle CCC 13915.88 13483.50 76.54 0.035490 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00018hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00018hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.003e-01 CC threshold: 0.736 Mean Std: 37.97 6.64 Num Hot pixels: 232 Hot pixel threshold: 77.82 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.062107 Iteration 2 Error: 0.433353 Iteration 3 Error: 0.115443 Iteration 4 Error: 0.048538 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.23 -0.10 ...... Frame ( 3) shift: -0.45 -0.21 ...... Frame ( 4) shift: -0.68 -0.31 ...... Frame ( 5) shift: -0.91 -0.41 ...... Frame ( 6) shift: -0.99 -0.45 ...... Frame ( 7) shift: -0.92 -0.41 ...... Frame ( 8) shift: -0.86 -0.38 ...... Frame ( 9) shift: -0.80 -0.31 ...... Frame ( 10) shift: -0.74 -0.21 ...... Frame ( 11) shift: -0.68 -0.10 ...... Frame ( 12) shift: -0.62 -0.03 ...... Frame ( 13) shift: -0.55 0.02 ...... Frame ( 14) shift: -0.48 0.06 ...... Frame ( 15) shift: -0.41 0.05 ...... Frame ( 16) shift: -0.34 -0.01 ...... Frame ( 17) shift: -0.27 -0.07 ...... Frame ( 18) shift: -0.13 -0.06 ...... Frame ( 19) shift: 0.08 0.00 ...... Frame ( 20) shift: 0.29 0.07 ...... Frame ( 21) shift: 0.47 0.13 ...... Frame ( 22) shift: 0.63 0.18 ...... Frame ( 23) shift: 0.78 0.24 ...... Frame ( 24) shift: 0.89 0.31 ...... Frame ( 25) shift: 0.95 0.41 ...... Frame ( 26) shift: 1.01 0.51 ...... Frame ( 27) shift: 1.06 0.66 ...... Frame ( 28) shift: 1.09 0.85 ...... Frame ( 29) shift: 1.13 1.05 ...... Frame ( 30) shift: 1.21 1.19 ...... Frame ( 31) shift: 1.33 1.27 ...... Frame ( 32) shift: 1.45 1.35 ...... Frame ( 33) shift: 1.55 1.44 ...... Frame ( 34) shift: 1.63 1.55 ...... Frame ( 35) shift: 1.71 1.66 ...... Frame ( 36) shift: 1.80 1.74 ...... Frame ( 37) shift: 1.90 1.80 ...... Frame ( 38) shift: 1.99 1.86 ...... Frame ( 39) shift: 2.09 1.93 ...... Frame ( 40) shift: 2.18 1.99 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.154215 Iteration 2 Error: 0.225641 Iteration 3 Error: 0.099084 Iteration 4 Error: 0.048523 Align patch 2 23 left Iteration 1 Error: 0.591732 Iteration 2 Error: 0.178430 Iteration 3 Error: 0.074103 Iteration 4 Error: 0.037756 Align patch 3 22 left Iteration 1 Error: 0.801280 Iteration 2 Error: 0.137104 Iteration 3 Error: 0.036528 Align patch 4 21 left Iteration 1 Error: 0.562729 Iteration 2 Error: 0.059462 Iteration 3 Error: 0.013196 Align patch 5 20 left Iteration 1 Error: 0.579857 Iteration 2 Error: 0.112844 Iteration 3 Error: 0.035034 Align patch 6 19 left Iteration 1 Error: 1.138531 Iteration 2 Error: 0.214771 Iteration 3 Error: 0.057564 Iteration 4 Error: 0.025232 Align patch 7 18 left Iteration 1 Error: 0.776567 Iteration 2 Error: 0.131927 Iteration 3 Error: 0.047409 Align patch 8 17 left Iteration 1 Error: 0.618141 Iteration 2 Error: 0.101591 Iteration 3 Error: 0.028025 Align patch 9 16 left Iteration 1 Error: 0.419991 Iteration 2 Error: 0.047166 Align patch 10 15 left Iteration 1 Error: 0.511626 Iteration 2 Error: 0.089893 Iteration 3 Error: 0.035102 Align patch 11 14 left Iteration 1 Error: 0.819309 Iteration 2 Error: 0.171725 Iteration 3 Error: 0.094876 Iteration 4 Error: 0.060492 Iteration 5 Error: 0.033161 Align patch 12 13 left Iteration 1 Error: 0.564098 Iteration 2 Error: 0.155025 Iteration 3 Error: 0.031671 Align patch 13 12 left Iteration 1 Error: 0.681400 Iteration 2 Error: 0.095725 Iteration 3 Error: 0.023985 Align patch 14 11 left Iteration 1 Error: 0.508713 Iteration 2 Error: 0.122249 Iteration 3 Error: 0.043742 Align patch 15 10 left Iteration 1 Error: 0.896303 Iteration 2 Error: 0.142621 Iteration 3 Error: 0.025506 Align patch 16 9 left Iteration 1 Error: 0.496736 Iteration 2 Error: 0.079340 Iteration 3 Error: 0.021670 Align patch 17 8 left Iteration 1 Error: 0.779044 Iteration 2 Error: 0.190018 Iteration 3 Error: 0.057560 Iteration 4 Error: 0.020914 Align patch 18 7 left Iteration 1 Error: 0.482485 Iteration 2 Error: 0.054452 Iteration 3 Error: 0.011457 Align patch 19 6 left Iteration 1 Error: 0.424900 Iteration 2 Error: 0.068442 Iteration 3 Error: 0.020890 Align patch 20 5 left Iteration 1 Error: 0.534637 Iteration 2 Error: 0.040371 Align patch 21 4 left Iteration 1 Error: 0.778995 Iteration 2 Error: 0.159893 Iteration 3 Error: 0.047454 Align patch 22 3 left Iteration 1 Error: 0.913413 Iteration 2 Error: 0.169179 Iteration 3 Error: 0.060556 Iteration 4 Error: 0.016244 Align patch 23 2 left Iteration 1 Error: 0.716218 Iteration 2 Error: 0.080484 Iteration 3 Error: 0.019993 Align patch 24 1 left Iteration 1 Error: 0.496659 Iteration 2 Error: 0.070728 Iteration 3 Error: 0.024381 Align patch 25 0 left Iteration 1 Error: 0.583014 Iteration 2 Error: 0.102955 Iteration 3 Error: 0.025631 3D Fitting completed. Patch alignment time: 14.94(sec) Local motion has been corrected. Process thread exits. Computational time: 23.528435 sec Total time: 29.350527 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00018hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00018hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.796718s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00018hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.849331s ........................................ >>>>>>TIME<<<<<< FFT: 1.071976s Defocus_U Defocus_V Angle CCC 9222.66 10035.16 10.97 0.041655 Final Values Defocus_U Defocus_V Angle CCC 9217.96 10052.36 11.29 0.070504 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00018hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00018hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 38.70 6.73 Num Hot pixels: 244 Hot pixel threshold: 79.10 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.832231 Iteration 2 Error: 0.420515 Iteration 3 Error: 0.091290 Iteration 4 Error: 0.041611 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.03 -0.01 ...... Frame ( 3) shift: 0.07 -0.03 ...... Frame ( 4) shift: 0.10 -0.04 ...... Frame ( 5) shift: 0.13 -0.05 ...... Frame ( 6) shift: 0.15 -0.05 ...... Frame ( 7) shift: 0.14 -0.03 ...... Frame ( 8) shift: 0.13 -0.02 ...... Frame ( 9) shift: 0.18 0.07 ...... Frame ( 10) shift: 0.30 0.23 ...... Frame ( 11) shift: 0.41 0.40 ...... Frame ( 12) shift: 0.50 0.50 ...... Frame ( 13) shift: 0.58 0.55 ...... Frame ( 14) shift: 0.65 0.60 ...... Frame ( 15) shift: 0.71 0.65 ...... Frame ( 16) shift: 0.75 0.72 ...... Frame ( 17) shift: 0.80 0.79 ...... Frame ( 18) shift: 0.87 0.88 ...... Frame ( 19) shift: 0.96 0.99 ...... Frame ( 20) shift: 1.05 1.09 ...... Frame ( 21) shift: 1.14 1.20 ...... Frame ( 22) shift: 1.24 1.32 ...... Frame ( 23) shift: 1.34 1.43 ...... Frame ( 24) shift: 1.41 1.50 ...... Frame ( 25) shift: 1.47 1.52 ...... Frame ( 26) shift: 1.52 1.54 ...... Frame ( 27) shift: 1.58 1.56 ...... Frame ( 28) shift: 1.64 1.57 ...... Frame ( 29) shift: 1.69 1.59 ...... Frame ( 30) shift: 1.79 1.66 ...... Frame ( 31) shift: 1.92 1.80 ...... Frame ( 32) shift: 2.05 1.94 ...... Frame ( 33) shift: 2.10 2.04 ...... Frame ( 34) shift: 2.07 2.09 ...... Frame ( 35) shift: 2.04 2.14 ...... Frame ( 36) shift: 2.08 2.22 ...... Frame ( 37) shift: 2.17 2.32 ...... Frame ( 38) shift: 2.27 2.42 ...... Frame ( 39) shift: 2.36 2.52 ...... Frame ( 40) shift: 2.46 2.62 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.775754 Iteration 2 Error: 0.427966 Iteration 3 Error: 0.135865 Iteration 4 Error: 0.068906 Iteration 5 Error: 0.030642 Align patch 2 23 left Iteration 1 Error: 0.769533 Iteration 2 Error: 0.205233 Iteration 3 Error: 0.089962 Iteration 4 Error: 0.037742 Align patch 3 22 left Iteration 1 Error: 0.560144 Iteration 2 Error: 0.089368 Iteration 3 Error: 0.022338 Align patch 4 21 left Iteration 1 Error: 0.457852 Iteration 2 Error: 0.082141 Iteration 3 Error: 0.022645 Align patch 5 20 left Iteration 1 Error: 0.723614 Iteration 2 Error: 0.190892 Iteration 3 Error: 0.059406 Iteration 4 Error: 0.016526 Align patch 6 19 left Iteration 1 Error: 1.043156 Iteration 2 Error: 0.331663 Iteration 3 Error: 0.107744 Iteration 4 Error: 0.045346 Align patch 7 18 left Iteration 1 Error: 0.893311 Iteration 2 Error: 0.267017 Iteration 3 Error: 0.132948 Iteration 4 Error: 0.073854 Iteration 5 Error: 0.033056 Align patch 8 17 left Iteration 1 Error: 0.556554 Iteration 2 Error: 0.151834 Iteration 3 Error: 0.043215 Align patch 9 16 left Iteration 1 Error: 0.459340 Iteration 2 Error: 0.050975 Iteration 3 Error: 0.009522 Align patch 10 15 left Iteration 1 Error: 0.515460 Iteration 2 Error: 0.072678 Iteration 3 Error: 0.013068 Align patch 11 14 left Iteration 1 Error: 0.734885 Iteration 2 Error: 0.159890 Iteration 3 Error: 0.072443 Iteration 4 Error: 0.032291 Align patch 12 13 left Iteration 1 Error: 0.574590 Iteration 2 Error: 0.264172 Iteration 3 Error: 0.117541 Iteration 4 Error: 0.045651 Align patch 13 12 left Iteration 1 Error: 0.570936 Iteration 2 Error: 0.164585 Iteration 3 Error: 0.066921 Iteration 4 Error: 0.033966 Align patch 14 11 left Iteration 1 Error: 0.524736 Iteration 2 Error: 0.129843 Iteration 3 Error: 0.041721 Align patch 15 10 left Iteration 1 Error: 0.664086 Iteration 2 Error: 0.139037 Iteration 3 Error: 0.028398 Align patch 16 9 left Iteration 1 Error: 0.999815 Iteration 2 Error: 0.190048 Iteration 3 Error: 0.067662 Iteration 4 Error: 0.026671 Align patch 17 8 left Iteration 1 Error: 0.627292 Iteration 2 Error: 0.128131 Iteration 3 Error: 0.044013 Align patch 18 7 left Iteration 1 Error: 0.844100 Iteration 2 Error: 0.123721 Iteration 3 Error: 0.037757 Align patch 19 6 left Iteration 1 Error: 0.483386 Iteration 2 Error: 0.081697 Iteration 3 Error: 0.022776 Align patch 20 5 left Iteration 1 Error: 0.427746 Iteration 2 Error: 0.140337 Iteration 3 Error: 0.030908 Align patch 21 4 left Iteration 1 Error: 1.402992 Iteration 2 Error: 0.161965 Iteration 3 Error: 0.036317 Align patch 22 3 left Iteration 1 Error: 0.646664 Iteration 2 Error: 0.080474 Iteration 3 Error: 0.024582 Align patch 23 2 left Iteration 1 Error: 0.744538 Iteration 2 Error: 0.236509 Iteration 3 Error: 0.090105 Iteration 4 Error: 0.037639 Align patch 24 1 left Iteration 1 Error: 0.576459 Iteration 2 Error: 0.078843 Iteration 3 Error: 0.024073 Align patch 25 0 left Iteration 1 Error: 0.828010 Iteration 2 Error: 0.121686 Iteration 3 Error: 0.026032 3D Fitting completed. Patch alignment time: 16.04(sec) Local motion has been corrected. Process thread exits. Computational time: 24.687458 sec Total time: 31.169252 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00018hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00018hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.572866s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00018hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.702818s ........................................ >>>>>>TIME<<<<<< FFT: 0.939561s Defocus_U Defocus_V Angle CCC 10748.09 10333.98 89.66 0.049440 Final Values Defocus_U Defocus_V Angle CCC 10771.53 10357.42 88.10 0.081569 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00018hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00018hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 39.26 6.75 Num Hot pixels: 235 Hot pixel threshold: 79.78 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.464121 Iteration 2 Error: 0.298054 Iteration 3 Error: 0.060627 Iteration 4 Error: 0.018288 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.26 -0.25 ...... Frame ( 3) shift: -0.53 -0.51 ...... Frame ( 4) shift: -0.79 -0.76 ...... Frame ( 5) shift: -1.05 -1.02 ...... Frame ( 6) shift: -1.20 -1.15 ...... Frame ( 7) shift: -1.23 -1.15 ...... Frame ( 8) shift: -1.26 -1.16 ...... Frame ( 9) shift: -1.26 -1.12 ...... Frame ( 10) shift: -1.23 -1.02 ...... Frame ( 11) shift: -1.20 -0.93 ...... Frame ( 12) shift: -1.18 -0.82 ...... Frame ( 13) shift: -1.16 -0.70 ...... Frame ( 14) shift: -1.15 -0.58 ...... Frame ( 15) shift: -1.14 -0.47 ...... Frame ( 16) shift: -1.13 -0.39 ...... Frame ( 17) shift: -1.12 -0.31 ...... Frame ( 18) shift: -1.13 -0.24 ...... Frame ( 19) shift: -1.14 -0.18 ...... Frame ( 20) shift: -1.16 -0.12 ...... Frame ( 21) shift: -1.16 -0.04 ...... Frame ( 22) shift: -1.15 0.05 ...... Frame ( 23) shift: -1.13 0.14 ...... Frame ( 24) shift: -1.11 0.27 ...... Frame ( 25) shift: -1.08 0.43 ...... Frame ( 26) shift: -1.05 0.60 ...... Frame ( 27) shift: -1.02 0.74 ...... Frame ( 28) shift: -1.00 0.85 ...... Frame ( 29) shift: -0.99 0.96 ...... Frame ( 30) shift: -0.96 1.04 ...... Frame ( 31) shift: -0.92 1.09 ...... Frame ( 32) shift: -0.88 1.13 ...... Frame ( 33) shift: -0.88 1.18 ...... Frame ( 34) shift: -0.93 1.24 ...... Frame ( 35) shift: -0.97 1.29 ...... Frame ( 36) shift: -0.94 1.37 ...... Frame ( 37) shift: -0.85 1.46 ...... Frame ( 38) shift: -0.75 1.55 ...... Frame ( 39) shift: -0.65 1.64 ...... Frame ( 40) shift: -0.56 1.73 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.151479 Iteration 2 Error: 0.219025 Iteration 3 Error: 0.081517 Iteration 4 Error: 0.043109 Align patch 2 23 left Iteration 1 Error: 1.140249 Iteration 2 Error: 0.215466 Iteration 3 Error: 0.080653 Iteration 4 Error: 0.041605 Align patch 3 22 left Iteration 1 Error: 0.947003 Iteration 2 Error: 0.176180 Iteration 3 Error: 0.057490 Iteration 4 Error: 0.017476 Align patch 4 21 left Iteration 1 Error: 0.720352 Iteration 2 Error: 0.145675 Iteration 3 Error: 0.042848 Align patch 5 20 left Iteration 1 Error: 0.590843 Iteration 2 Error: 0.123022 Iteration 3 Error: 0.024966 Align patch 6 19 left Iteration 1 Error: 1.094528 Iteration 2 Error: 0.236001 Iteration 3 Error: 0.105103 Iteration 4 Error: 0.027334 Align patch 7 18 left Iteration 1 Error: 0.930191 Iteration 2 Error: 0.143431 Iteration 3 Error: 0.050691 Iteration 4 Error: 0.015889 Align patch 8 17 left Iteration 1 Error: 0.595333 Iteration 2 Error: 0.069054 Iteration 3 Error: 0.013269 Align patch 9 16 left Iteration 1 Error: 0.831177 Iteration 2 Error: 0.095432 Iteration 3 Error: 0.017406 Align patch 10 15 left Iteration 1 Error: 0.989110 Iteration 2 Error: 0.110807 Iteration 3 Error: 0.027933 Align patch 11 14 left Iteration 1 Error: 0.606301 Iteration 2 Error: 0.178985 Iteration 3 Error: 0.045136 Align patch 12 13 left Iteration 1 Error: 1.080751 Iteration 2 Error: 0.207119 Iteration 3 Error: 0.053756 Iteration 4 Error: 0.021110 Align patch 13 12 left Iteration 1 Error: 0.791017 Iteration 2 Error: 0.109212 Iteration 3 Error: 0.035705 Align patch 14 11 left Iteration 1 Error: 0.528934 Iteration 2 Error: 0.053581 Iteration 3 Error: 0.011433 Align patch 15 10 left Iteration 1 Error: 0.760941 Iteration 2 Error: 0.119619 Iteration 3 Error: 0.022428 Align patch 16 9 left Iteration 1 Error: 0.502924 Iteration 2 Error: 0.095574 Iteration 3 Error: 0.036994 Align patch 17 8 left Iteration 1 Error: 0.613529 Iteration 2 Error: 0.107077 Iteration 3 Error: 0.033520 Align patch 18 7 left Iteration 1 Error: 0.966198 Iteration 2 Error: 0.122712 Iteration 3 Error: 0.014412 Align patch 19 6 left Iteration 1 Error: 0.675546 Iteration 2 Error: 0.090437 Iteration 3 Error: 0.031490 Align patch 20 5 left Iteration 1 Error: 1.426267 Iteration 2 Error: 0.115243 Iteration 3 Error: 0.025959 Align patch 21 4 left Iteration 1 Error: 0.789594 Iteration 2 Error: 0.079505 Iteration 3 Error: 0.027112 Align patch 22 3 left Iteration 1 Error: 0.555267 Iteration 2 Error: 0.100298 Iteration 3 Error: 0.026559 Align patch 23 2 left Iteration 1 Error: 0.764920 Iteration 2 Error: 0.128066 Iteration 3 Error: 0.023385 Align patch 24 1 left Iteration 1 Error: 0.535258 Iteration 2 Error: 0.079632 Iteration 3 Error: 0.021177 Align patch 25 0 left Iteration 1 Error: 0.538407 Iteration 2 Error: 0.113052 Iteration 3 Error: 0.019983 3D Fitting completed. Patch alignment time: 15.05(sec) Local motion has been corrected. Process thread exits. Computational time: 23.814358 sec Total time: 29.540222 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00018hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00018hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.760784s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00018hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.367574s ........................................ >>>>>>TIME<<<<<< FFT: 0.931114s Defocus_U Defocus_V Angle CCC 11009.77 11857.42 9.73 0.050915 Final Values Defocus_U Defocus_V Angle CCC 11036.33 11858.99 10.05 0.084097 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00018hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00018hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 39.69 6.81 Num Hot pixels: 222 Hot pixel threshold: 80.57 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.650252 Iteration 2 Error: 0.115723 Iteration 3 Error: 0.024698 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.14 -0.15 ...... Frame ( 3) shift: -0.27 -0.29 ...... Frame ( 4) shift: -0.41 -0.44 ...... Frame ( 5) shift: -0.54 -0.58 ...... Frame ( 6) shift: -0.63 -0.66 ...... Frame ( 7) shift: -0.66 -0.66 ...... Frame ( 8) shift: -0.69 -0.67 ...... Frame ( 9) shift: -0.66 -0.64 ...... Frame ( 10) shift: -0.57 -0.59 ...... Frame ( 11) shift: -0.47 -0.53 ...... Frame ( 12) shift: -0.40 -0.48 ...... Frame ( 13) shift: -0.36 -0.43 ...... Frame ( 14) shift: -0.31 -0.38 ...... Frame ( 15) shift: -0.27 -0.35 ...... Frame ( 16) shift: -0.24 -0.35 ...... Frame ( 17) shift: -0.20 -0.35 ...... Frame ( 18) shift: -0.16 -0.30 ...... Frame ( 19) shift: -0.11 -0.22 ...... Frame ( 20) shift: -0.06 -0.14 ...... Frame ( 21) shift: -0.02 -0.08 ...... Frame ( 22) shift: -0.00 -0.05 ...... Frame ( 23) shift: 0.02 -0.02 ...... Frame ( 24) shift: 0.01 0.01 ...... Frame ( 25) shift: -0.02 0.05 ...... Frame ( 26) shift: -0.05 0.08 ...... Frame ( 27) shift: -0.06 0.13 ...... Frame ( 28) shift: -0.05 0.20 ...... Frame ( 29) shift: -0.04 0.27 ...... Frame ( 30) shift: -0.01 0.29 ...... Frame ( 31) shift: 0.02 0.25 ...... Frame ( 32) shift: 0.05 0.21 ...... Frame ( 33) shift: 0.07 0.21 ...... Frame ( 34) shift: 0.08 0.25 ...... Frame ( 35) shift: 0.10 0.29 ...... Frame ( 36) shift: 0.12 0.31 ...... Frame ( 37) shift: 0.13 0.31 ...... Frame ( 38) shift: 0.15 0.32 ...... Frame ( 39) shift: 0.17 0.32 ...... Frame ( 40) shift: 0.19 0.33 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.057478 Iteration 2 Error: 0.204333 Iteration 3 Error: 0.070767 Iteration 4 Error: 0.030762 Align patch 2 23 left Iteration 1 Error: 1.076375 Iteration 2 Error: 0.225929 Iteration 3 Error: 0.098773 Iteration 4 Error: 0.023967 Align patch 3 22 left Iteration 1 Error: 0.728913 Iteration 2 Error: 0.082535 Iteration 3 Error: 0.024453 Align patch 4 21 left Iteration 1 Error: 0.886951 Iteration 2 Error: 0.190031 Iteration 3 Error: 0.066439 Iteration 4 Error: 0.021523 Align patch 5 20 left Iteration 1 Error: 0.638848 Iteration 2 Error: 0.084206 Iteration 3 Error: 0.014682 Align patch 6 19 left Iteration 1 Error: 1.399644 Iteration 2 Error: 0.363016 Iteration 3 Error: 0.156152 Iteration 4 Error: 0.091941 Iteration 5 Error: 0.051574 Align patch 6 19 left Iteration 1 Error: 1.916445 Iteration 2 Error: 0.288575 Iteration 3 Error: 0.068150 Iteration 4 Error: 0.026897 Align patch 7 18 left Iteration 1 Error: 0.852386 Iteration 2 Error: 0.283235 Iteration 3 Error: 0.104671 Iteration 4 Error: 0.047509 Align patch 8 17 left Iteration 1 Error: 0.790562 Iteration 2 Error: 0.142882 Iteration 3 Error: 0.042213 Align patch 9 16 left Iteration 1 Error: 0.685690 Iteration 2 Error: 0.068428 Iteration 3 Error: 0.012247 Align patch 10 15 left Iteration 1 Error: 0.752076 Iteration 2 Error: 0.116792 Iteration 3 Error: 0.033651 Align patch 11 14 left Iteration 1 Error: 0.896430 Iteration 2 Error: 0.120071 Iteration 3 Error: 0.033399 Align patch 12 13 left Iteration 1 Error: 0.909628 Iteration 2 Error: 0.153714 Iteration 3 Error: 0.036843 Align patch 13 12 left Iteration 1 Error: 0.834594 Iteration 2 Error: 0.290039 Iteration 3 Error: 0.080647 Iteration 4 Error: 0.037908 Align patch 14 11 left Iteration 1 Error: 0.463664 Iteration 2 Error: 0.056761 Iteration 3 Error: 0.020097 Align patch 15 10 left Iteration 1 Error: 0.559101 Iteration 2 Error: 0.097774 Iteration 3 Error: 0.020462 Align patch 16 9 left Iteration 1 Error: 0.760900 Iteration 2 Error: 0.137413 Iteration 3 Error: 0.055431 Iteration 4 Error: 0.015347 Align patch 17 8 left Iteration 1 Error: 0.424023 Iteration 2 Error: 0.117151 Iteration 3 Error: 0.022542 Align patch 18 7 left Iteration 1 Error: 0.568971 Iteration 2 Error: 0.073414 Iteration 3 Error: 0.020948 Align patch 19 6 left Iteration 1 Error: 0.715463 Iteration 2 Error: 0.115006 Iteration 3 Error: 0.019950 Align patch 20 5 left Iteration 1 Error: 0.668934 Iteration 2 Error: 0.091239 Iteration 3 Error: 0.017027 Align patch 21 4 left Iteration 1 Error: 0.622965 Iteration 2 Error: 0.090381 Iteration 3 Error: 0.022396 Align patch 22 3 left Iteration 1 Error: 0.477975 Iteration 2 Error: 0.109761 Iteration 3 Error: 0.030895 Align patch 23 2 left Iteration 1 Error: 0.457713 Iteration 2 Error: 0.056707 Iteration 3 Error: 0.012687 Align patch 24 1 left Iteration 1 Error: 0.787650 Iteration 2 Error: 0.128489 Iteration 3 Error: 0.033616 Align patch 25 0 left Iteration 1 Error: 0.681404 Iteration 2 Error: 0.103028 Iteration 3 Error: 0.019911 3D Fitting completed. Patch alignment time: 16.62(sec) Local motion has been corrected. Process thread exits. Computational time: 25.447210 sec Total time: 31.138712 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00018hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00018hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.639550s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00018hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.753083s ........................................ >>>>>>TIME<<<<<< FFT: 0.911879s Defocus_U Defocus_V Angle CCC 10400.41 9787.12 85.09 0.037858 Final Values Defocus_U Defocus_V Angle CCC 10433.21 9820.02 84.19 0.065815 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00019hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00019hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.004e-01 CC threshold: 0.737 Mean Std: 37.96 6.62 Num Hot pixels: 240 Hot pixel threshold: 77.69 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.199273 Iteration 2 Error: 0.154512 Iteration 3 Error: 0.039732 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.03 0.11 ...... Frame ( 3) shift: 0.06 0.21 ...... Frame ( 4) shift: 0.09 0.32 ...... Frame ( 5) shift: 0.12 0.42 ...... Frame ( 6) shift: 0.16 0.53 ...... Frame ( 7) shift: 0.20 0.63 ...... Frame ( 8) shift: 0.25 0.73 ...... Frame ( 9) shift: 0.27 0.82 ...... Frame ( 10) shift: 0.25 0.89 ...... Frame ( 11) shift: 0.24 0.96 ...... Frame ( 12) shift: 0.24 1.02 ...... Frame ( 13) shift: 0.24 1.06 ...... Frame ( 14) shift: 0.25 1.11 ...... Frame ( 15) shift: 0.27 1.16 ...... Frame ( 16) shift: 0.30 1.22 ...... Frame ( 17) shift: 0.33 1.28 ...... Frame ( 18) shift: 0.37 1.34 ...... Frame ( 19) shift: 0.42 1.42 ...... Frame ( 20) shift: 0.47 1.50 ...... Frame ( 21) shift: 0.47 1.55 ...... Frame ( 22) shift: 0.42 1.57 ...... Frame ( 23) shift: 0.38 1.59 ...... Frame ( 24) shift: 0.38 1.62 ...... Frame ( 25) shift: 0.42 1.66 ...... Frame ( 26) shift: 0.46 1.70 ...... Frame ( 27) shift: 0.50 1.76 ...... Frame ( 28) shift: 0.52 1.84 ...... Frame ( 29) shift: 0.55 1.93 ...... Frame ( 30) shift: 0.57 1.96 ...... Frame ( 31) shift: 0.59 1.95 ...... Frame ( 32) shift: 0.62 1.95 ...... Frame ( 33) shift: 0.64 1.98 ...... Frame ( 34) shift: 0.66 2.06 ...... Frame ( 35) shift: 0.68 2.14 ...... Frame ( 36) shift: 0.70 2.20 ...... Frame ( 37) shift: 0.74 2.24 ...... Frame ( 38) shift: 0.77 2.28 ...... Frame ( 39) shift: 0.81 2.32 ...... Frame ( 40) shift: 0.84 2.36 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.631237 Iteration 2 Error: 0.081487 Iteration 3 Error: 0.017683 Align patch 2 23 left Iteration 1 Error: 0.734701 Iteration 2 Error: 0.093971 Iteration 3 Error: 0.017225 Align patch 3 22 left Iteration 1 Error: 0.631090 Iteration 2 Error: 0.079254 Iteration 3 Error: 0.010818 Align patch 4 21 left Iteration 1 Error: 0.384075 Iteration 2 Error: 0.070062 Iteration 3 Error: 0.014408 Align patch 5 20 left Iteration 1 Error: 0.781353 Iteration 2 Error: 0.060242 Iteration 3 Error: 0.014009 Align patch 6 19 left Iteration 1 Error: 0.545074 Iteration 2 Error: 0.079510 Iteration 3 Error: 0.019104 Align patch 7 18 left Iteration 1 Error: 0.388805 Iteration 2 Error: 0.065178 Iteration 3 Error: 0.020550 Align patch 8 17 left Iteration 1 Error: 0.459375 Iteration 2 Error: 0.062172 Iteration 3 Error: 0.011755 Align patch 9 16 left Iteration 1 Error: 0.412899 Iteration 2 Error: 0.058145 Iteration 3 Error: 0.011536 Align patch 10 15 left Iteration 1 Error: 0.879290 Iteration 2 Error: 0.168781 Iteration 3 Error: 0.032365 Align patch 11 14 left Iteration 1 Error: 0.740959 Iteration 2 Error: 0.120346 Iteration 3 Error: 0.017009 Align patch 12 13 left Iteration 1 Error: 0.528670 Iteration 2 Error: 0.075203 Iteration 3 Error: 0.013385 Align patch 13 12 left Iteration 1 Error: 0.624849 Iteration 2 Error: 0.098071 Iteration 3 Error: 0.020087 Align patch 14 11 left Iteration 1 Error: 0.551093 Iteration 2 Error: 0.085063 Iteration 3 Error: 0.020078 Align patch 15 10 left Iteration 1 Error: 0.513723 Iteration 2 Error: 0.103072 Iteration 3 Error: 0.016504 Align patch 16 9 left Iteration 1 Error: 0.612752 Iteration 2 Error: 0.141085 Iteration 3 Error: 0.028158 Align patch 17 8 left Iteration 1 Error: 0.577701 Iteration 2 Error: 0.072770 Iteration 3 Error: 0.015252 Align patch 18 7 left Iteration 1 Error: 0.576652 Iteration 2 Error: 0.090424 Iteration 3 Error: 0.037332 Align patch 19 6 left Iteration 1 Error: 0.488333 Iteration 2 Error: 0.072949 Iteration 3 Error: 0.024907 Align patch 20 5 left Iteration 1 Error: 0.507662 Iteration 2 Error: 0.068824 Iteration 3 Error: 0.016273 Align patch 21 4 left Iteration 1 Error: 0.856036 Iteration 2 Error: 0.136082 Iteration 3 Error: 0.033606 Align patch 22 3 left Iteration 1 Error: 0.979356 Iteration 2 Error: 0.146631 Iteration 3 Error: 0.028885 Align patch 23 2 left Iteration 1 Error: 0.552720 Iteration 2 Error: 0.101022 Iteration 3 Error: 0.014991 Align patch 24 1 left Iteration 1 Error: 0.497839 Iteration 2 Error: 0.061081 Iteration 3 Error: 0.012019 Align patch 25 0 left Iteration 1 Error: 0.574698 Iteration 2 Error: 0.089818 Iteration 3 Error: 0.023425 3D Fitting completed. Patch alignment time: 14.44(sec) Local motion has been corrected. Process thread exits. Computational time: 22.656715 sec Total time: 28.671551 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00019hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00019hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.687983s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00019hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.153217s ........................................ >>>>>>TIME<<<<<< FFT: 0.959708s Defocus_U Defocus_V Angle CCC 9882.81 10617.19 14.91 0.040813 Final Values Defocus_U Defocus_V Angle CCC 9914.05 10660.96 16.19 0.065493 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00019hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00019hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 38.89 6.76 Num Hot pixels: 230 Hot pixel threshold: 79.47 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.780112 Iteration 2 Error: 0.149732 Iteration 3 Error: 0.028237 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.10 -0.11 ...... Frame ( 3) shift: -0.21 -0.22 ...... Frame ( 4) shift: -0.31 -0.32 ...... Frame ( 5) shift: -0.41 -0.43 ...... Frame ( 6) shift: -0.46 -0.48 ...... Frame ( 7) shift: -0.44 -0.47 ...... Frame ( 8) shift: -0.43 -0.46 ...... Frame ( 9) shift: -0.41 -0.41 ...... Frame ( 10) shift: -0.39 -0.33 ...... Frame ( 11) shift: -0.38 -0.24 ...... Frame ( 12) shift: -0.33 -0.14 ...... Frame ( 13) shift: -0.27 -0.04 ...... Frame ( 14) shift: -0.20 0.07 ...... Frame ( 15) shift: -0.16 0.13 ...... Frame ( 16) shift: -0.16 0.16 ...... Frame ( 17) shift: -0.15 0.19 ...... Frame ( 18) shift: -0.14 0.24 ...... Frame ( 19) shift: -0.13 0.32 ...... Frame ( 20) shift: -0.12 0.39 ...... Frame ( 21) shift: -0.10 0.45 ...... Frame ( 22) shift: -0.05 0.48 ...... Frame ( 23) shift: 0.01 0.52 ...... Frame ( 24) shift: 0.04 0.56 ...... Frame ( 25) shift: 0.05 0.60 ...... Frame ( 26) shift: 0.05 0.64 ...... Frame ( 27) shift: 0.04 0.67 ...... Frame ( 28) shift: -0.01 0.68 ...... Frame ( 29) shift: -0.06 0.68 ...... Frame ( 30) shift: -0.02 0.74 ...... Frame ( 31) shift: 0.09 0.83 ...... Frame ( 32) shift: 0.20 0.92 ...... Frame ( 33) shift: 0.25 0.97 ...... Frame ( 34) shift: 0.24 0.98 ...... Frame ( 35) shift: 0.23 0.98 ...... Frame ( 36) shift: 0.25 1.00 ...... Frame ( 37) shift: 0.29 1.03 ...... Frame ( 38) shift: 0.33 1.05 ...... Frame ( 39) shift: 0.37 1.08 ...... Frame ( 40) shift: 0.41 1.10 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.644962 Iteration 2 Error: 0.093743 Iteration 3 Error: 0.018890 Align patch 2 23 left Iteration 1 Error: 0.714463 Iteration 2 Error: 0.079442 Iteration 3 Error: 0.018972 Align patch 3 22 left Iteration 1 Error: 0.668526 Iteration 2 Error: 0.075216 Iteration 3 Error: 0.016451 Align patch 4 21 left Iteration 1 Error: 0.797588 Iteration 2 Error: 0.163195 Iteration 3 Error: 0.045155 Align patch 5 20 left Iteration 1 Error: 0.327583 Iteration 2 Error: 0.072172 Iteration 3 Error: 0.021646 Align patch 6 19 left Iteration 1 Error: 0.535336 Iteration 2 Error: 0.086950 Iteration 3 Error: 0.020739 Align patch 7 18 left Iteration 1 Error: 0.605756 Iteration 2 Error: 0.080322 Iteration 3 Error: 0.016624 Align patch 8 17 left Iteration 1 Error: 0.407083 Iteration 2 Error: 0.068394 Iteration 3 Error: 0.012645 Align patch 9 16 left Iteration 1 Error: 0.446534 Iteration 2 Error: 0.106569 Iteration 3 Error: 0.036144 Align patch 10 15 left Iteration 1 Error: 0.523092 Iteration 2 Error: 0.047287 Align patch 11 14 left Iteration 1 Error: 0.548055 Iteration 2 Error: 0.090523 Iteration 3 Error: 0.024251 Align patch 12 13 left Iteration 1 Error: 0.571145 Iteration 2 Error: 0.070002 Iteration 3 Error: 0.015706 Align patch 13 12 left Iteration 1 Error: 0.573263 Iteration 2 Error: 0.088851 Iteration 3 Error: 0.016980 Align patch 14 11 left Iteration 1 Error: 0.468686 Iteration 2 Error: 0.074425 Iteration 3 Error: 0.017164 Align patch 15 10 left Iteration 1 Error: 0.784422 Iteration 2 Error: 0.070577 Iteration 3 Error: 0.018844 Align patch 16 9 left Iteration 1 Error: 0.586226 Iteration 2 Error: 0.122256 Iteration 3 Error: 0.028579 Align patch 17 8 left Iteration 1 Error: 0.734413 Iteration 2 Error: 0.126524 Iteration 3 Error: 0.021487 Align patch 18 7 left Iteration 1 Error: 0.563529 Iteration 2 Error: 0.093339 Iteration 3 Error: 0.028686 Align patch 19 6 left Iteration 1 Error: 0.540212 Iteration 2 Error: 0.061385 Iteration 3 Error: 0.013200 Align patch 20 5 left Iteration 1 Error: 0.414975 Iteration 2 Error: 0.053910 Iteration 3 Error: 0.012056 Align patch 21 4 left Iteration 1 Error: 0.652737 Iteration 2 Error: 0.102264 Iteration 3 Error: 0.017849 Align patch 22 3 left Iteration 1 Error: 0.510820 Iteration 2 Error: 0.080301 Iteration 3 Error: 0.019214 Align patch 23 2 left Iteration 1 Error: 0.681199 Iteration 2 Error: 0.081660 Iteration 3 Error: 0.012513 Align patch 24 1 left Iteration 1 Error: 1.095013 Iteration 2 Error: 0.124901 Iteration 3 Error: 0.033091 Align patch 25 0 left Iteration 1 Error: 0.545892 Iteration 2 Error: 0.080723 Iteration 3 Error: 0.015540 3D Fitting completed. Patch alignment time: 14.89(sec) Local motion has been corrected. Process thread exits. Computational time: 23.865992 sec Total time: 30.631258 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00019hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00019hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.604902s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00019hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.265806s ........................................ >>>>>>TIME<<<<<< FFT: 0.936725s Defocus_U Defocus_V Angle CCC 9751.95 10189.45 0.48 0.042501 Final Values Defocus_U Defocus_V Angle CCC 9756.60 10203.57 0.17 0.074330 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00019hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00019hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.351e-01 1.004e-01 CC threshold: 0.738 Mean Std: 38.75 6.79 Num Hot pixels: 235 Hot pixel threshold: 79.48 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.307021 Iteration 2 Error: 0.035054 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.02 0.13 ...... Frame ( 3) shift: -0.05 0.25 ...... Frame ( 4) shift: -0.07 0.38 ...... Frame ( 5) shift: -0.10 0.51 ...... Frame ( 6) shift: -0.08 0.57 ...... Frame ( 7) shift: -0.03 0.58 ...... Frame ( 8) shift: 0.02 0.58 ...... Frame ( 9) shift: 0.03 0.54 ...... Frame ( 10) shift: -0.01 0.46 ...... Frame ( 11) shift: -0.04 0.37 ...... Frame ( 12) shift: -0.06 0.32 ...... Frame ( 13) shift: -0.06 0.30 ...... Frame ( 14) shift: -0.05 0.28 ...... Frame ( 15) shift: -0.03 0.26 ...... Frame ( 16) shift: 0.02 0.24 ...... Frame ( 17) shift: 0.07 0.22 ...... Frame ( 18) shift: 0.12 0.21 ...... Frame ( 19) shift: 0.17 0.21 ...... Frame ( 20) shift: 0.22 0.20 ...... Frame ( 21) shift: 0.24 0.20 ...... Frame ( 22) shift: 0.22 0.20 ...... Frame ( 23) shift: 0.21 0.20 ...... Frame ( 24) shift: 0.18 0.19 ...... Frame ( 25) shift: 0.16 0.17 ...... Frame ( 26) shift: 0.13 0.14 ...... Frame ( 27) shift: 0.11 0.17 ...... Frame ( 28) shift: 0.12 0.24 ...... Frame ( 29) shift: 0.12 0.32 ...... Frame ( 30) shift: 0.14 0.35 ...... Frame ( 31) shift: 0.17 0.35 ...... Frame ( 32) shift: 0.20 0.34 ...... Frame ( 33) shift: 0.21 0.36 ...... Frame ( 34) shift: 0.21 0.40 ...... Frame ( 35) shift: 0.21 0.43 ...... Frame ( 36) shift: 0.21 0.48 ...... Frame ( 37) shift: 0.21 0.52 ...... Frame ( 38) shift: 0.20 0.56 ...... Frame ( 39) shift: 0.20 0.61 ...... Frame ( 40) shift: 0.20 0.65 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.438003 Iteration 2 Error: 0.056488 Iteration 3 Error: 0.013932 Align patch 2 23 left Iteration 1 Error: 0.734677 Iteration 2 Error: 0.113485 Iteration 3 Error: 0.025815 Align patch 3 22 left Iteration 1 Error: 0.558962 Iteration 2 Error: 0.084725 Iteration 3 Error: 0.020441 Align patch 4 21 left Iteration 1 Error: 0.343935 Iteration 2 Error: 0.055072 Iteration 3 Error: 0.012312 Align patch 5 20 left Iteration 1 Error: 0.417636 Iteration 2 Error: 0.048890 Align patch 6 19 left Iteration 1 Error: 0.539589 Iteration 2 Error: 0.048593 Align patch 7 18 left Iteration 1 Error: 0.567694 Iteration 2 Error: 0.099578 Iteration 3 Error: 0.022143 Align patch 8 17 left Iteration 1 Error: 0.617361 Iteration 2 Error: 0.068261 Iteration 3 Error: 0.016558 Align patch 9 16 left Iteration 1 Error: 0.652441 Iteration 2 Error: 0.041581 Align patch 10 15 left Iteration 1 Error: 0.439738 Iteration 2 Error: 0.049413 Align patch 11 14 left Iteration 1 Error: 0.605064 Iteration 2 Error: 0.113922 Iteration 3 Error: 0.018908 Align patch 12 13 left Iteration 1 Error: 0.398465 Iteration 2 Error: 0.070692 Iteration 3 Error: 0.015060 Align patch 13 12 left Iteration 1 Error: 0.329388 Iteration 2 Error: 0.048410 Align patch 14 11 left Iteration 1 Error: 0.694421 Iteration 2 Error: 0.086221 Iteration 3 Error: 0.012911 Align patch 15 10 left Iteration 1 Error: 0.642997 Iteration 2 Error: 0.087331 Iteration 3 Error: 0.025355 Align patch 16 9 left Iteration 1 Error: 0.524788 Iteration 2 Error: 0.080221 Iteration 3 Error: 0.012839 Align patch 17 8 left Iteration 1 Error: 0.546762 Iteration 2 Error: 0.084028 Iteration 3 Error: 0.013911 Align patch 18 7 left Iteration 1 Error: 0.489570 Iteration 2 Error: 0.054386 Iteration 3 Error: 0.009801 Align patch 19 6 left Iteration 1 Error: 0.626956 Iteration 2 Error: 0.098167 Iteration 3 Error: 0.026090 Align patch 20 5 left Iteration 1 Error: 0.561165 Iteration 2 Error: 0.136029 Iteration 3 Error: 0.024115 Align patch 21 4 left Iteration 1 Error: 0.699091 Iteration 2 Error: 0.087735 Iteration 3 Error: 0.019220 Align patch 22 3 left Iteration 1 Error: 0.640453 Iteration 2 Error: 0.125612 Iteration 3 Error: 0.023991 Align patch 23 2 left Iteration 1 Error: 0.519924 Iteration 2 Error: 0.094899 Iteration 3 Error: 0.023280 Align patch 24 1 left Iteration 1 Error: 0.435423 Iteration 2 Error: 0.089765 Iteration 3 Error: 0.010082 Align patch 25 0 left Iteration 1 Error: 0.468757 Iteration 2 Error: 0.066137 Iteration 3 Error: 0.010941 3D Fitting completed. Patch alignment time: 14.06(sec) Local motion has been corrected. Process thread exits. Computational time: 22.449995 sec Total time: 28.517117 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00019hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00019hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.685817s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00019hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.219727s ........................................ >>>>>>TIME<<<<<< FFT: 0.919102s Defocus_U Defocus_V Angle CCC 11777.36 12683.61 6.15 0.052445 Final Values Defocus_U Defocus_V Angle CCC 11808.62 12696.12 6.47 0.082350 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00019hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00019hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.350e-01 1.004e-01 CC threshold: 0.737 Mean Std: 39.64 6.80 Num Hot pixels: 231 Hot pixel threshold: 80.46 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.661530 Iteration 2 Error: 0.059876 Iteration 3 Error: 0.010707 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.04 0.07 ...... Frame ( 3) shift: -0.08 0.14 ...... Frame ( 4) shift: -0.13 0.21 ...... Frame ( 5) shift: -0.17 0.28 ...... Frame ( 6) shift: -0.24 0.32 ...... Frame ( 7) shift: -0.34 0.34 ...... Frame ( 8) shift: -0.43 0.36 ...... Frame ( 9) shift: -0.47 0.40 ...... Frame ( 10) shift: -0.44 0.45 ...... Frame ( 11) shift: -0.41 0.50 ...... Frame ( 12) shift: -0.41 0.51 ...... Frame ( 13) shift: -0.44 0.48 ...... Frame ( 14) shift: -0.47 0.45 ...... Frame ( 15) shift: -0.51 0.47 ...... Frame ( 16) shift: -0.55 0.54 ...... Frame ( 17) shift: -0.60 0.61 ...... Frame ( 18) shift: -0.61 0.64 ...... Frame ( 19) shift: -0.61 0.63 ...... Frame ( 20) shift: -0.60 0.62 ...... Frame ( 21) shift: -0.60 0.64 ...... Frame ( 22) shift: -0.60 0.70 ...... Frame ( 23) shift: -0.60 0.76 ...... Frame ( 24) shift: -0.61 0.78 ...... Frame ( 25) shift: -0.62 0.75 ...... Frame ( 26) shift: -0.63 0.72 ...... Frame ( 27) shift: -0.64 0.71 ...... Frame ( 28) shift: -0.65 0.73 ...... Frame ( 29) shift: -0.66 0.76 ...... Frame ( 30) shift: -0.68 0.77 ...... Frame ( 31) shift: -0.72 0.78 ...... Frame ( 32) shift: -0.75 0.79 ...... Frame ( 33) shift: -0.78 0.81 ...... Frame ( 34) shift: -0.80 0.83 ...... Frame ( 35) shift: -0.83 0.86 ...... Frame ( 36) shift: -0.81 0.88 ...... Frame ( 37) shift: -0.77 0.89 ...... Frame ( 38) shift: -0.72 0.90 ...... Frame ( 39) shift: -0.67 0.90 ...... Frame ( 40) shift: -0.62 0.91 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.713421 Iteration 2 Error: 0.228100 Iteration 3 Error: 0.048276 Align patch 2 23 left Iteration 1 Error: 0.679108 Iteration 2 Error: 0.077620 Iteration 3 Error: 0.015612 Align patch 3 22 left Iteration 1 Error: 0.582573 Iteration 2 Error: 0.059763 Iteration 3 Error: 0.009639 Align patch 4 21 left Iteration 1 Error: 0.544675 Iteration 2 Error: 0.073417 Iteration 3 Error: 0.010837 Align patch 5 20 left Iteration 1 Error: 0.459110 Iteration 2 Error: 0.058152 Iteration 3 Error: 0.012288 Align patch 6 19 left Iteration 1 Error: 0.702513 Iteration 2 Error: 0.108066 Iteration 3 Error: 0.026250 Align patch 7 18 left Iteration 1 Error: 0.799382 Iteration 2 Error: 0.101005 Iteration 3 Error: 0.013839 Align patch 8 17 left Iteration 1 Error: 0.507588 Iteration 2 Error: 0.079374 Iteration 3 Error: 0.024586 Align patch 9 16 left Iteration 1 Error: 0.516484 Iteration 2 Error: 0.061294 Iteration 3 Error: 0.011807 Align patch 10 15 left Iteration 1 Error: 0.520203 Iteration 2 Error: 0.058519 Iteration 3 Error: 0.009177 Align patch 11 14 left Iteration 1 Error: 0.852641 Iteration 2 Error: 0.085712 Iteration 3 Error: 0.015389 Align patch 12 13 left Iteration 1 Error: 0.627256 Iteration 2 Error: 0.092765 Iteration 3 Error: 0.027072 Align patch 13 12 left Iteration 1 Error: 0.569383 Iteration 2 Error: 0.071260 Iteration 3 Error: 0.017246 Align patch 14 11 left Iteration 1 Error: 0.438474 Iteration 2 Error: 0.065251 Iteration 3 Error: 0.010581 Align patch 15 10 left Iteration 1 Error: 0.708835 Iteration 2 Error: 0.099787 Iteration 3 Error: 0.020207 Align patch 16 9 left Iteration 1 Error: 0.744605 Iteration 2 Error: 0.068005 Iteration 3 Error: 0.017317 Align patch 17 8 left Iteration 1 Error: 0.934288 Iteration 2 Error: 0.129897 Iteration 3 Error: 0.036145 Align patch 18 7 left Iteration 1 Error: 0.656532 Iteration 2 Error: 0.111629 Iteration 3 Error: 0.017756 Align patch 19 6 left Iteration 1 Error: 0.560236 Iteration 2 Error: 0.072554 Iteration 3 Error: 0.013074 Align patch 20 5 left Iteration 1 Error: 0.442088 Iteration 2 Error: 0.085508 Iteration 3 Error: 0.015164 Align patch 21 4 left Iteration 1 Error: 0.695221 Iteration 2 Error: 0.068964 Iteration 3 Error: 0.009449 Align patch 22 3 left Iteration 1 Error: 0.580591 Iteration 2 Error: 0.058771 Iteration 3 Error: 0.015191 Align patch 23 2 left Iteration 1 Error: 0.566487 Iteration 2 Error: 0.100065 Iteration 3 Error: 0.024858 Align patch 24 1 left Iteration 1 Error: 0.481959 Iteration 2 Error: 0.092291 Iteration 3 Error: 0.025596 Align patch 25 0 left Iteration 1 Error: 0.341005 Iteration 2 Error: 0.047387 3D Fitting completed. Patch alignment time: 14.71(sec) Local motion has been corrected. Process thread exits. Computational time: 22.967278 sec Total time: 29.685360 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00019hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00019hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.752187s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00019hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.177154s ........................................ >>>>>>TIME<<<<<< FFT: 1.076768s Defocus_U Defocus_V Angle CCC 12921.90 12261.71 81.16 0.053620 Final Values Defocus_U Defocus_V Angle CCC 12923.48 12275.79 80.85 0.085860 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00020hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00020hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.351e-01 1.004e-01 CC threshold: 0.737 Mean Std: 38.63 6.75 Num Hot pixels: 214 Hot pixel threshold: 79.11 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.375446 Iteration 2 Error: 0.227549 Iteration 3 Error: 0.052715 Iteration 4 Error: 0.013104 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.19 -0.07 ...... Frame ( 3) shift: -0.38 -0.15 ...... Frame ( 4) shift: -0.58 -0.22 ...... Frame ( 5) shift: -0.77 -0.29 ...... Frame ( 6) shift: -0.86 -0.29 ...... Frame ( 7) shift: -0.85 -0.21 ...... Frame ( 8) shift: -0.84 -0.13 ...... Frame ( 9) shift: -0.80 -0.02 ...... Frame ( 10) shift: -0.72 0.12 ...... Frame ( 11) shift: -0.65 0.26 ...... Frame ( 12) shift: -0.61 0.40 ...... Frame ( 13) shift: -0.61 0.54 ...... Frame ( 14) shift: -0.61 0.68 ...... Frame ( 15) shift: -0.58 0.79 ...... Frame ( 16) shift: -0.51 0.86 ...... Frame ( 17) shift: -0.44 0.92 ...... Frame ( 18) shift: -0.38 0.99 ...... Frame ( 19) shift: -0.31 1.06 ...... Frame ( 20) shift: -0.24 1.13 ...... Frame ( 21) shift: -0.22 1.21 ...... Frame ( 22) shift: -0.25 1.28 ...... Frame ( 23) shift: -0.27 1.36 ...... Frame ( 24) shift: -0.25 1.46 ...... Frame ( 25) shift: -0.17 1.57 ...... Frame ( 26) shift: -0.10 1.69 ...... Frame ( 27) shift: -0.05 1.78 ...... Frame ( 28) shift: -0.03 1.86 ...... Frame ( 29) shift: -0.01 1.94 ...... Frame ( 30) shift: 0.01 2.00 ...... Frame ( 31) shift: 0.02 2.06 ...... Frame ( 32) shift: 0.03 2.12 ...... Frame ( 33) shift: 0.02 2.18 ...... Frame ( 34) shift: -0.01 2.25 ...... Frame ( 35) shift: -0.04 2.32 ...... Frame ( 36) shift: -0.05 2.39 ...... Frame ( 37) shift: -0.02 2.45 ...... Frame ( 38) shift: 0.00 2.51 ...... Frame ( 39) shift: 0.03 2.58 ...... Frame ( 40) shift: 0.06 2.64 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.736332 Iteration 2 Error: 0.086663 Iteration 3 Error: 0.028844 Align patch 2 23 left Iteration 1 Error: 0.438537 Iteration 2 Error: 0.057299 Iteration 3 Error: 0.017033 Align patch 3 22 left Iteration 1 Error: 0.466043 Iteration 2 Error: 0.083216 Iteration 3 Error: 0.017705 Align patch 4 21 left Iteration 1 Error: 0.525244 Iteration 2 Error: 0.057739 Iteration 3 Error: 0.020740 Align patch 5 20 left Iteration 1 Error: 0.586586 Iteration 2 Error: 0.073447 Iteration 3 Error: 0.011474 Align patch 6 19 left Iteration 1 Error: 0.716217 Iteration 2 Error: 0.097039 Iteration 3 Error: 0.028548 Align patch 7 18 left Iteration 1 Error: 0.418231 Iteration 2 Error: 0.056571 Iteration 3 Error: 0.008554 Align patch 8 17 left Iteration 1 Error: 0.460869 Iteration 2 Error: 0.090524 Iteration 3 Error: 0.017081 Align patch 9 16 left Iteration 1 Error: 0.486506 Iteration 2 Error: 0.053960 Iteration 3 Error: 0.020586 Align patch 10 15 left Iteration 1 Error: 0.488231 Iteration 2 Error: 0.053059 Iteration 3 Error: 0.010565 Align patch 11 14 left Iteration 1 Error: 0.640284 Iteration 2 Error: 0.172871 Iteration 3 Error: 0.045844 Align patch 12 13 left Iteration 1 Error: 0.382632 Iteration 2 Error: 0.047216 Align patch 13 12 left Iteration 1 Error: 0.708465 Iteration 2 Error: 0.092178 Iteration 3 Error: 0.018859 Align patch 14 11 left Iteration 1 Error: 0.461344 Iteration 2 Error: 0.075813 Iteration 3 Error: 0.010012 Align patch 15 10 left Iteration 1 Error: 0.570141 Iteration 2 Error: 0.084370 Iteration 3 Error: 0.016633 Align patch 16 9 left Iteration 1 Error: 0.716792 Iteration 2 Error: 0.088849 Iteration 3 Error: 0.020311 Align patch 17 8 left Iteration 1 Error: 0.511487 Iteration 2 Error: 0.078943 Iteration 3 Error: 0.012682 Align patch 18 7 left Iteration 1 Error: 0.495092 Iteration 2 Error: 0.057950 Iteration 3 Error: 0.011208 Align patch 19 6 left Iteration 1 Error: 0.656114 Iteration 2 Error: 0.082293 Iteration 3 Error: 0.019486 Align patch 20 5 left Iteration 1 Error: 0.595441 Iteration 2 Error: 0.055497 Iteration 3 Error: 0.012010 Align patch 21 4 left Iteration 1 Error: 0.533735 Iteration 2 Error: 0.055033 Iteration 3 Error: 0.007911 Align patch 22 3 left Iteration 1 Error: 0.576292 Iteration 2 Error: 0.101487 Iteration 3 Error: 0.031410 Align patch 23 2 left Iteration 1 Error: 0.387183 Iteration 2 Error: 0.040858 Align patch 24 1 left Iteration 1 Error: 0.522341 Iteration 2 Error: 0.057463 Iteration 3 Error: 0.008702 Align patch 25 0 left Iteration 1 Error: 0.595752 Iteration 2 Error: 0.045627 3D Fitting completed. Patch alignment time: 15.31(sec) Local motion has been corrected. Process thread exits. Computational time: 24.313692 sec Total time: 29.822546 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00020hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00020hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.866731s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00020hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.180605s ........................................ >>>>>>TIME<<<<<< FFT: 1.053714s Defocus_U Defocus_V Angle CCC 12636.72 13515.65 14.16 0.073663 Final Values Defocus_U Defocus_V Angle CCC 12661.72 13503.15 14.47 0.109762 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00020hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00020hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.350e-01 1.004e-01 CC threshold: 0.738 Mean Std: 38.27 6.70 Num Hot pixels: 200 Hot pixel threshold: 78.47 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.827468 Iteration 2 Error: 0.090628 Iteration 3 Error: 0.023963 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.11 0.11 ...... Frame ( 3) shift: -0.22 0.22 ...... Frame ( 4) shift: -0.33 0.33 ...... Frame ( 5) shift: -0.44 0.43 ...... Frame ( 6) shift: -0.51 0.48 ...... Frame ( 7) shift: -0.53 0.47 ...... Frame ( 8) shift: -0.54 0.46 ...... Frame ( 9) shift: -0.53 0.49 ...... Frame ( 10) shift: -0.48 0.59 ...... Frame ( 11) shift: -0.43 0.68 ...... Frame ( 12) shift: -0.40 0.74 ...... Frame ( 13) shift: -0.39 0.77 ...... Frame ( 14) shift: -0.39 0.81 ...... Frame ( 15) shift: -0.40 0.85 ...... Frame ( 16) shift: -0.43 0.90 ...... Frame ( 17) shift: -0.47 0.95 ...... Frame ( 18) shift: -0.48 0.98 ...... Frame ( 19) shift: -0.48 0.99 ...... Frame ( 20) shift: -0.48 0.99 ...... Frame ( 21) shift: -0.48 1.02 ...... Frame ( 22) shift: -0.48 1.06 ...... Frame ( 23) shift: -0.48 1.10 ...... Frame ( 24) shift: -0.47 1.15 ...... Frame ( 25) shift: -0.45 1.22 ...... Frame ( 26) shift: -0.44 1.29 ...... Frame ( 27) shift: -0.43 1.32 ...... Frame ( 28) shift: -0.44 1.32 ...... Frame ( 29) shift: -0.45 1.33 ...... Frame ( 30) shift: -0.48 1.34 ...... Frame ( 31) shift: -0.52 1.38 ...... Frame ( 32) shift: -0.57 1.42 ...... Frame ( 33) shift: -0.59 1.47 ...... Frame ( 34) shift: -0.58 1.55 ...... Frame ( 35) shift: -0.58 1.63 ...... Frame ( 36) shift: -0.56 1.66 ...... Frame ( 37) shift: -0.54 1.65 ...... Frame ( 38) shift: -0.51 1.64 ...... Frame ( 39) shift: -0.48 1.63 ...... Frame ( 40) shift: -0.46 1.62 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.619677 Iteration 2 Error: 0.089306 Iteration 3 Error: 0.019024 Align patch 2 23 left Iteration 1 Error: 0.495601 Iteration 2 Error: 0.072630 Iteration 3 Error: 0.018664 Align patch 3 22 left Iteration 1 Error: 0.691103 Iteration 2 Error: 0.051881 Iteration 3 Error: 0.012130 Align patch 4 21 left Iteration 1 Error: 0.561235 Iteration 2 Error: 0.092364 Iteration 3 Error: 0.017853 Align patch 5 20 left Iteration 1 Error: 0.460960 Iteration 2 Error: 0.080076 Iteration 3 Error: 0.012559 Align patch 6 19 left Iteration 1 Error: 0.528651 Iteration 2 Error: 0.051255 Iteration 3 Error: 0.014692 Align patch 7 18 left Iteration 1 Error: 0.522130 Iteration 2 Error: 0.118308 Iteration 3 Error: 0.029266 Align patch 8 17 left Iteration 1 Error: 0.549808 Iteration 2 Error: 0.073442 Iteration 3 Error: 0.011947 Align patch 9 16 left Iteration 1 Error: 0.594368 Iteration 2 Error: 0.139534 Iteration 3 Error: 0.024880 Align patch 10 15 left Iteration 1 Error: 0.556483 Iteration 2 Error: 0.101848 Iteration 3 Error: 0.012087 Align patch 11 14 left Iteration 1 Error: 0.513319 Iteration 2 Error: 0.096072 Iteration 3 Error: 0.026339 Align patch 12 13 left Iteration 1 Error: 0.523431 Iteration 2 Error: 0.077532 Iteration 3 Error: 0.010375 Align patch 13 12 left Iteration 1 Error: 0.538624 Iteration 2 Error: 0.052430 Iteration 3 Error: 0.011180 Align patch 14 11 left Iteration 1 Error: 0.640192 Iteration 2 Error: 0.080760 Iteration 3 Error: 0.012927 Align patch 15 10 left Iteration 1 Error: 0.567520 Iteration 2 Error: 0.079792 Iteration 3 Error: 0.026437 Align patch 16 9 left Iteration 1 Error: 0.440548 Iteration 2 Error: 0.057257 Iteration 3 Error: 0.008972 Align patch 17 8 left Iteration 1 Error: 0.588549 Iteration 2 Error: 0.103244 Iteration 3 Error: 0.023416 Align patch 18 7 left Iteration 1 Error: 0.647965 Iteration 2 Error: 0.157155 Iteration 3 Error: 0.031798 Align patch 19 6 left Iteration 1 Error: 0.567720 Iteration 2 Error: 0.096122 Iteration 3 Error: 0.014582 Align patch 20 5 left Iteration 1 Error: 0.776422 Iteration 2 Error: 0.080305 Iteration 3 Error: 0.016167 Align patch 21 4 left Iteration 1 Error: 0.574403 Iteration 2 Error: 0.073275 Iteration 3 Error: 0.016083 Align patch 22 3 left Iteration 1 Error: 0.564678 Iteration 2 Error: 0.079039 Iteration 3 Error: 0.024645 Align patch 23 2 left Iteration 1 Error: 0.582751 Iteration 2 Error: 0.070826 Iteration 3 Error: 0.015245 Align patch 24 1 left Iteration 1 Error: 0.932401 Iteration 2 Error: 0.094810 Iteration 3 Error: 0.028337 Align patch 25 0 left Iteration 1 Error: 0.466318 Iteration 2 Error: 0.066883 Iteration 3 Error: 0.028897 3D Fitting completed. Patch alignment time: 15.12(sec) Local motion has been corrected. Process thread exits. Computational time: 23.464350 sec Total time: 30.187567 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00020hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00020hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.580337s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00020hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.683207s ........................................ >>>>>>TIME<<<<<< FFT: 1.046508s Defocus_U Defocus_V Angle CCC 8263.67 8736.33 9.29 0.028301 Final Values Defocus_U Defocus_V Angle CCC 8246.48 8756.66 11.81 0.054179 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00020hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00020hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 38.81 6.70 Num Hot pixels: 225 Hot pixel threshold: 78.99 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.993851 Iteration 2 Error: 0.079347 Iteration 3 Error: 0.023389 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.14 -0.19 ...... Frame ( 3) shift: -0.28 -0.37 ...... Frame ( 4) shift: -0.42 -0.56 ...... Frame ( 5) shift: -0.56 -0.74 ...... Frame ( 6) shift: -0.67 -0.89 ...... Frame ( 7) shift: -0.74 -1.01 ...... Frame ( 8) shift: -0.82 -1.12 ...... Frame ( 9) shift: -0.84 -1.20 ...... Frame ( 10) shift: -0.80 -1.25 ...... Frame ( 11) shift: -0.76 -1.29 ...... Frame ( 12) shift: -0.72 -1.31 ...... Frame ( 13) shift: -0.68 -1.29 ...... Frame ( 14) shift: -0.63 -1.28 ...... Frame ( 15) shift: -0.60 -1.32 ...... Frame ( 16) shift: -0.59 -1.40 ...... Frame ( 17) shift: -0.57 -1.48 ...... Frame ( 18) shift: -0.54 -1.50 ...... Frame ( 19) shift: -0.52 -1.47 ...... Frame ( 20) shift: -0.49 -1.44 ...... Frame ( 21) shift: -0.44 -1.40 ...... Frame ( 22) shift: -0.37 -1.37 ...... Frame ( 23) shift: -0.31 -1.34 ...... Frame ( 24) shift: -0.26 -1.31 ...... Frame ( 25) shift: -0.22 -1.29 ...... Frame ( 26) shift: -0.19 -1.26 ...... Frame ( 27) shift: -0.14 -1.25 ...... Frame ( 28) shift: -0.09 -1.25 ...... Frame ( 29) shift: -0.03 -1.25 ...... Frame ( 30) shift: -0.01 -1.28 ...... Frame ( 31) shift: -0.04 -1.34 ...... Frame ( 32) shift: -0.06 -1.39 ...... Frame ( 33) shift: -0.06 -1.45 ...... Frame ( 34) shift: -0.03 -1.49 ...... Frame ( 35) shift: -0.01 -1.54 ...... Frame ( 36) shift: 0.04 -1.55 ...... Frame ( 37) shift: 0.10 -1.54 ...... Frame ( 38) shift: 0.16 -1.53 ...... Frame ( 39) shift: 0.22 -1.52 ...... Frame ( 40) shift: 0.28 -1.51 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.665463 Iteration 2 Error: 0.146571 Iteration 3 Error: 0.029250 Align patch 2 23 left Iteration 1 Error: 0.703678 Iteration 2 Error: 0.156921 Iteration 3 Error: 0.034993 Align patch 3 22 left Iteration 1 Error: 0.948341 Iteration 2 Error: 0.148940 Iteration 3 Error: 0.022108 Align patch 4 21 left Iteration 1 Error: 0.835296 Iteration 2 Error: 0.153312 Iteration 3 Error: 0.028798 Align patch 5 20 left Iteration 1 Error: 1.020569 Iteration 2 Error: 0.142409 Iteration 3 Error: 0.025879 Align patch 6 19 left Iteration 1 Error: 0.975348 Iteration 2 Error: 0.252880 Iteration 3 Error: 0.049330 Align patch 7 18 left Iteration 1 Error: 0.649526 Iteration 2 Error: 0.130420 Iteration 3 Error: 0.033918 Align patch 8 17 left Iteration 1 Error: 0.682961 Iteration 2 Error: 0.140657 Iteration 3 Error: 0.057467 Iteration 4 Error: 0.013827 Align patch 9 16 left Iteration 1 Error: 0.846146 Iteration 2 Error: 0.105239 Iteration 3 Error: 0.027602 Align patch 10 15 left Iteration 1 Error: 0.731973 Iteration 2 Error: 0.130790 Iteration 3 Error: 0.022640 Align patch 11 14 left Iteration 1 Error: 0.563824 Iteration 2 Error: 0.105921 Iteration 3 Error: 0.023382 Align patch 12 13 left Iteration 1 Error: 0.541630 Iteration 2 Error: 0.085252 Iteration 3 Error: 0.017976 Align patch 13 12 left Iteration 1 Error: 0.594304 Iteration 2 Error: 0.076311 Iteration 3 Error: 0.019617 Align patch 14 11 left Iteration 1 Error: 0.551043 Iteration 2 Error: 0.132475 Iteration 3 Error: 0.031162 Align patch 15 10 left Iteration 1 Error: 0.759849 Iteration 2 Error: 0.104950 Iteration 3 Error: 0.024745 Align patch 16 9 left Iteration 1 Error: 1.074304 Iteration 2 Error: 0.183795 Iteration 3 Error: 0.050102 Iteration 4 Error: 0.019286 Align patch 17 8 left Iteration 1 Error: 0.906124 Iteration 2 Error: 0.132703 Iteration 3 Error: 0.038570 Align patch 18 7 left Iteration 1 Error: 0.774700 Iteration 2 Error: 0.104828 Iteration 3 Error: 0.021326 Align patch 19 6 left Iteration 1 Error: 0.600302 Iteration 2 Error: 0.192925 Iteration 3 Error: 0.063797 Iteration 4 Error: 0.022418 Align patch 20 5 left Iteration 1 Error: 1.079671 Iteration 2 Error: 0.127157 Iteration 3 Error: 0.031239 Align patch 21 4 left Iteration 1 Error: 0.791209 Iteration 2 Error: 0.082699 Iteration 3 Error: 0.020625 Align patch 22 3 left Iteration 1 Error: 0.734437 Iteration 2 Error: 0.142329 Iteration 3 Error: 0.023282 Align patch 23 2 left Iteration 1 Error: 0.846236 Iteration 2 Error: 0.110010 Iteration 3 Error: 0.031537 Align patch 24 1 left Iteration 1 Error: 0.761756 Iteration 2 Error: 0.140755 Iteration 3 Error: 0.032109 Align patch 25 0 left Iteration 1 Error: 0.745211 Iteration 2 Error: 0.136863 Iteration 3 Error: 0.045470 3D Fitting completed. Patch alignment time: 14.88(sec) Local motion has been corrected. Process thread exits. Computational time: 23.424503 sec Total time: 29.497541 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00020hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00020hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.813360s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00020hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.163112s ........................................ >>>>>>TIME<<<<<< FFT: 1.137817s Defocus_U Defocus_V Angle CCC 14406.28 15160.19 2.26 0.042566 Final Values Defocus_U Defocus_V Angle CCC 14409.41 15207.08 5.44 0.062100 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00012gr_00012sq_v01_00020hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00020hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 38.66 6.75 Num Hot pixels: 218 Hot pixel threshold: 79.14 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.502357 Iteration 2 Error: 0.633268 Iteration 3 Error: 0.358115 Iteration 4 Error: 0.199447 Iteration 5 Error: 0.102999 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.17 -0.06 ...... Frame ( 3) shift: -0.35 -0.11 ...... Frame ( 4) shift: -0.52 -0.17 ...... Frame ( 5) shift: -0.70 -0.22 ...... Frame ( 6) shift: -0.86 -0.15 ...... Frame ( 7) shift: -1.01 0.05 ...... Frame ( 8) shift: -1.17 0.25 ...... Frame ( 9) shift: -1.28 0.47 ...... Frame ( 10) shift: -1.35 0.71 ...... Frame ( 11) shift: -1.42 0.95 ...... Frame ( 12) shift: -1.48 1.18 ...... Frame ( 13) shift: -1.53 1.41 ...... Frame ( 14) shift: -1.57 1.64 ...... Frame ( 15) shift: -1.62 1.87 ...... Frame ( 16) shift: -1.67 2.11 ...... Frame ( 17) shift: -1.71 2.35 ...... Frame ( 18) shift: -1.79 2.53 ...... Frame ( 19) shift: -1.89 2.65 ...... Frame ( 20) shift: -2.00 2.77 ...... Frame ( 21) shift: -2.12 2.93 ...... Frame ( 22) shift: -2.26 3.13 ...... Frame ( 23) shift: -2.40 3.32 ...... Frame ( 24) shift: -2.52 3.50 ...... Frame ( 25) shift: -2.61 3.67 ...... Frame ( 26) shift: -2.70 3.83 ...... Frame ( 27) shift: -2.77 4.01 ...... Frame ( 28) shift: -2.83 4.22 ...... Frame ( 29) shift: -2.89 4.42 ...... Frame ( 30) shift: -3.00 4.59 ...... Frame ( 31) shift: -3.17 4.74 ...... Frame ( 32) shift: -3.34 4.88 ...... Frame ( 33) shift: -3.50 5.02 ...... Frame ( 34) shift: -3.66 5.15 ...... Frame ( 35) shift: -3.81 5.29 ...... Frame ( 36) shift: -3.93 5.41 ...... Frame ( 37) shift: -4.00 5.52 ...... Frame ( 38) shift: -4.08 5.63 ...... Frame ( 39) shift: -4.15 5.75 ...... Frame ( 40) shift: -4.23 5.86 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.454446 Iteration 2 Error: 0.542244 Iteration 3 Error: 0.108280 Iteration 4 Error: 0.053335 Iteration 5 Error: 0.013660 Align patch 2 23 left Iteration 1 Error: 1.403388 Iteration 2 Error: 0.371559 Iteration 3 Error: 0.113460 Iteration 4 Error: 0.061510 Iteration 5 Error: 0.021129 Align patch 3 22 left Iteration 1 Error: 0.915838 Iteration 2 Error: 0.348977 Iteration 3 Error: 0.129279 Iteration 4 Error: 0.071154 Iteration 5 Error: 0.028449 Align patch 4 21 left Iteration 1 Error: 1.124612 Iteration 2 Error: 0.386410 Iteration 3 Error: 0.145372 Iteration 4 Error: 0.081749 Iteration 5 Error: 0.045509 Align patch 5 20 left Iteration 1 Error: 1.200984 Iteration 2 Error: 0.540009 Iteration 3 Error: 0.313562 Iteration 4 Error: 0.189921 Iteration 5 Error: 0.095152 Align patch 5 20 left Iteration 1 Error: 0.892570 Iteration 2 Error: 0.131425 Iteration 3 Error: 0.020057 Align patch 6 19 left Iteration 1 Error: 1.505490 Iteration 2 Error: 0.443687 Iteration 3 Error: 0.080875 Iteration 4 Error: 0.031922 Align patch 7 18 left Iteration 1 Error: 0.796559 Iteration 2 Error: 0.222353 Iteration 3 Error: 0.067654 Iteration 4 Error: 0.027923 Align patch 8 17 left Iteration 1 Error: 0.920467 Iteration 2 Error: 0.260002 Iteration 3 Error: 0.123109 Iteration 4 Error: 0.069809 Iteration 5 Error: 0.026082 Align patch 9 16 left Iteration 1 Error: 1.706504 Iteration 2 Error: 0.531199 Iteration 3 Error: 0.286146 Iteration 4 Error: 0.155027 Iteration 5 Error: 0.096264 Align patch 9 16 left Iteration 1 Error: 1.821508 Iteration 2 Error: 0.359262 Iteration 3 Error: 0.125028 Iteration 4 Error: 0.042595 Align patch 10 15 left Iteration 1 Error: 0.953521 Iteration 2 Error: 0.620560 Iteration 3 Error: 0.172497 Iteration 4 Error: 0.112719 Iteration 5 Error: 0.056001 Align patch 10 15 left Iteration 1 Error: 1.759653 Iteration 2 Error: 0.427865 Iteration 3 Error: 0.151053 Iteration 4 Error: 0.056347 Iteration 5 Error: 0.032197 Align patch 11 14 left Iteration 1 Error: 0.864913 Iteration 2 Error: 0.145217 Iteration 3 Error: 0.044806 Align patch 12 13 left Iteration 1 Error: 0.876525 Iteration 2 Error: 0.195101 Iteration 3 Error: 0.058623 Iteration 4 Error: 0.024586 Align patch 13 12 left Iteration 1 Error: 1.834231 Iteration 2 Error: 0.556129 Iteration 3 Error: 0.198825 Iteration 4 Error: 0.066216 Iteration 5 Error: 0.027142 Align patch 14 11 left Iteration 1 Error: 2.796926 Iteration 2 Error: 0.809404 Iteration 3 Error: 0.319487 Iteration 4 Error: 0.166930 Iteration 5 Error: 0.075652 Align patch 14 11 left Iteration 1 Error: 3.444602 Iteration 2 Error: 0.522459 Iteration 3 Error: 0.121368 Iteration 4 Error: 0.045066 Align patch 15 10 left Iteration 1 Error: 3.367404 Iteration 2 Error: 2.196900 Iteration 3 Error: 0.691476 Iteration 4 Error: 0.378169 Iteration 5 Error: 0.210342 Align patch 15 10 left Iteration 1 Error: 3.790930 Iteration 2 Error: 0.999592 Iteration 3 Error: 0.206310 Iteration 4 Error: 0.073210 Iteration 5 Error: 0.022183 Align patch 16 9 left Iteration 1 Error: 0.918077 Iteration 2 Error: 0.274842 Iteration 3 Error: 0.141213 Iteration 4 Error: 0.065610 Iteration 5 Error: 0.031498 Align patch 17 8 left Iteration 1 Error: 0.571928 Iteration 2 Error: 0.128088 Iteration 3 Error: 0.047119 Align patch 18 7 left Iteration 1 Error: 2.243717 Iteration 2 Error: 0.732141 Iteration 3 Error: 0.271991 Iteration 4 Error: 0.132045 Iteration 5 Error: 0.062220 Align patch 18 7 left Iteration 1 Error: 2.435166 Iteration 2 Error: 0.483210 Iteration 3 Error: 0.076102 Iteration 4 Error: 0.022464 Align patch 19 6 left Iteration 1 Error: 2.597133 Iteration 2 Error: 0.844458 Iteration 3 Error: 0.253191 Iteration 4 Error: 0.086260 Iteration 5 Error: 0.028162 Align patch 20 5 left Iteration 1 Error: 4.727404 Iteration 2 Error: 1.525207 Iteration 3 Error: 0.608256 Iteration 4 Error: 0.225012 Iteration 5 Error: 0.096125 Align patch 20 5 left Iteration 1 Error: 3.745189 Iteration 2 Error: 0.920829 Iteration 3 Error: 0.205093 Iteration 4 Error: 0.055212 Iteration 5 Error: 0.015051 Align patch 21 4 left Iteration 1 Error: 1.570731 Iteration 2 Error: 0.377935 Iteration 3 Error: 0.135801 Iteration 4 Error: 0.044689 Align patch 22 3 left Iteration 1 Error: 1.584409 Iteration 2 Error: 0.274436 Iteration 3 Error: 0.082421 Iteration 4 Error: 0.043400 Align patch 23 2 left Iteration 1 Error: 1.190564 Iteration 2 Error: 0.321162 Iteration 3 Error: 0.113855 Iteration 4 Error: 0.062771 Iteration 5 Error: 0.030895 Align patch 24 1 left Iteration 1 Error: 1.495111 Iteration 2 Error: 0.507994 Iteration 3 Error: 0.307674 Iteration 4 Error: 0.142838 Iteration 5 Error: 0.073998 Align patch 24 1 left Iteration 1 Error: 1.951044 Iteration 2 Error: 0.459926 Iteration 3 Error: 0.144369 Iteration 4 Error: 0.049002 Align patch 25 0 left Iteration 1 Error: 0.943624 Iteration 2 Error: 0.372085 Iteration 3 Error: 0.193470 Iteration 4 Error: 0.119432 Iteration 5 Error: 0.081071 Align patch 25 0 left Iteration 1 Error: 2.054425 Iteration 2 Error: 0.523089 Iteration 3 Error: 0.184615 Iteration 4 Error: 0.067733 Iteration 5 Error: 0.028969 3D Fitting completed. Patch alignment time: 26.88(sec) Local motion has been corrected. Process thread exits. Computational time: 35.907013 sec Total time: 43.280777 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00020hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00020hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.592534s Reading file: gc_18feb27f_CTD_g1_00012gr_00012sq_v01_00020hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.251957s ........................................ >>>>>>TIME<<<<<< FFT: 1.044303s Defocus_U Defocus_V Angle CCC 10958.81 10264.04 82.60 0.055192 Final Values Defocus_U Defocus_V Angle CCC 11008.86 10320.36 83.87 0.096902 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00010sq_v01_00002hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00002hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.993e-02 CC threshold: 0.734 Mean Std: 34.73 6.31 Num Hot pixels: 194 Hot pixel threshold: 72.56 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.101750 Iteration 2 Error: 0.192801 Iteration 3 Error: 0.034093 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.03 -0.23 ...... Frame ( 3) shift: 0.06 -0.45 ...... Frame ( 4) shift: 0.09 -0.68 ...... Frame ( 5) shift: 0.12 -0.90 ...... Frame ( 6) shift: 0.16 -1.01 ...... Frame ( 7) shift: 0.22 -1.00 ...... Frame ( 8) shift: 0.28 -0.98 ...... Frame ( 9) shift: 0.31 -0.95 ...... Frame ( 10) shift: 0.30 -0.89 ...... Frame ( 11) shift: 0.29 -0.83 ...... Frame ( 12) shift: 0.29 -0.78 ...... Frame ( 13) shift: 0.31 -0.74 ...... Frame ( 14) shift: 0.33 -0.70 ...... Frame ( 15) shift: 0.36 -0.64 ...... Frame ( 16) shift: 0.39 -0.56 ...... Frame ( 17) shift: 0.42 -0.48 ...... Frame ( 18) shift: 0.47 -0.44 ...... Frame ( 19) shift: 0.53 -0.42 ...... Frame ( 20) shift: 0.59 -0.41 ...... Frame ( 21) shift: 0.62 -0.36 ...... Frame ( 22) shift: 0.64 -0.27 ...... Frame ( 23) shift: 0.65 -0.18 ...... Frame ( 24) shift: 0.66 -0.10 ...... Frame ( 25) shift: 0.67 -0.02 ...... Frame ( 26) shift: 0.68 0.05 ...... Frame ( 27) shift: 0.68 0.13 ...... Frame ( 28) shift: 0.69 0.19 ...... Frame ( 29) shift: 0.69 0.26 ...... Frame ( 30) shift: 0.70 0.31 ...... Frame ( 31) shift: 0.72 0.35 ...... Frame ( 32) shift: 0.75 0.39 ...... Frame ( 33) shift: 0.76 0.41 ...... Frame ( 34) shift: 0.75 0.41 ...... Frame ( 35) shift: 0.74 0.42 ...... Frame ( 36) shift: 0.78 0.48 ...... Frame ( 37) shift: 0.86 0.61 ...... Frame ( 38) shift: 0.94 0.73 ...... Frame ( 39) shift: 1.01 0.85 ...... Frame ( 40) shift: 1.09 0.98 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.033165 Iteration 2 Error: 0.270261 Iteration 3 Error: 0.076739 Iteration 4 Error: 0.042259 Align patch 2 23 left Iteration 1 Error: 0.777352 Iteration 2 Error: 0.289273 Iteration 3 Error: 0.099456 Iteration 4 Error: 0.038836 Align patch 3 22 left Iteration 1 Error: 1.204092 Iteration 2 Error: 0.228681 Iteration 3 Error: 0.088906 Iteration 4 Error: 0.020213 Align patch 4 21 left Iteration 1 Error: 1.013387 Iteration 2 Error: 0.173428 Iteration 3 Error: 0.055310 Iteration 4 Error: 0.016535 Align patch 5 20 left Iteration 1 Error: 1.344458 Iteration 2 Error: 0.237653 Iteration 3 Error: 0.089898 Iteration 4 Error: 0.034471 Align patch 6 19 left Iteration 1 Error: 0.605356 Iteration 2 Error: 0.166992 Iteration 3 Error: 0.072439 Iteration 4 Error: 0.034008 Align patch 7 18 left Iteration 1 Error: 1.013512 Iteration 2 Error: 0.265494 Iteration 3 Error: 0.057132 Iteration 4 Error: 0.021477 Align patch 8 17 left Iteration 1 Error: 1.211285 Iteration 2 Error: 0.237904 Iteration 3 Error: 0.033041 Align patch 9 16 left Iteration 1 Error: 1.440595 Iteration 2 Error: 0.185658 Iteration 3 Error: 0.053287 Iteration 4 Error: 0.015982 Align patch 10 15 left Iteration 1 Error: 1.170487 Iteration 2 Error: 0.122360 Iteration 3 Error: 0.045326 Align patch 11 14 left Iteration 1 Error: 0.768743 Iteration 2 Error: 0.162767 Iteration 3 Error: 0.077524 Iteration 4 Error: 0.035962 Align patch 12 13 left Iteration 1 Error: 0.927650 Iteration 2 Error: 0.190490 Iteration 3 Error: 0.048522 Align patch 13 12 left Iteration 1 Error: 1.032736 Iteration 2 Error: 0.166627 Iteration 3 Error: 0.098743 Iteration 4 Error: 0.026857 Align patch 14 11 left Iteration 1 Error: 0.912860 Iteration 2 Error: 0.110794 Iteration 3 Error: 0.025803 Align patch 15 10 left Iteration 1 Error: 0.850062 Iteration 2 Error: 0.195494 Iteration 3 Error: 0.039156 Align patch 16 9 left Iteration 1 Error: 0.900091 Iteration 2 Error: 0.104969 Iteration 3 Error: 0.030767 Align patch 17 8 left Iteration 1 Error: 0.733539 Iteration 2 Error: 0.255377 Iteration 3 Error: 0.079631 Iteration 4 Error: 0.033759 Align patch 18 7 left Iteration 1 Error: 0.979678 Iteration 2 Error: 0.205865 Iteration 3 Error: 0.067142 Iteration 4 Error: 0.027089 Align patch 19 6 left Iteration 1 Error: 0.790361 Iteration 2 Error: 0.193800 Iteration 3 Error: 0.038521 Align patch 20 5 left Iteration 1 Error: 0.457890 Iteration 2 Error: 0.083048 Iteration 3 Error: 0.023507 Align patch 21 4 left Iteration 1 Error: 1.092646 Iteration 2 Error: 0.151934 Iteration 3 Error: 0.030723 Align patch 22 3 left Iteration 1 Error: 1.400361 Iteration 2 Error: 0.189358 Iteration 3 Error: 0.060183 Iteration 4 Error: 0.011269 Align patch 23 2 left Iteration 1 Error: 1.084135 Iteration 2 Error: 0.125555 Iteration 3 Error: 0.044397 Align patch 24 1 left Iteration 1 Error: 0.816571 Iteration 2 Error: 0.325914 Iteration 3 Error: 0.083182 Iteration 4 Error: 0.032335 Align patch 25 0 left Iteration 1 Error: 0.548272 Iteration 2 Error: 0.115376 Iteration 3 Error: 0.027249 3D Fitting completed. Patch alignment time: 16.32(sec) Local motion has been corrected. Process thread exits. Computational time: 25.169676 sec Total time: 30.843353 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00002hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00002hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.721759s Reading file: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00002hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.352050s ........................................ >>>>>>TIME<<<<<< FFT: 1.029180s Defocus_U Defocus_V Angle CCC 8031.25 8906.25 17.60 0.004248 Final Values Defocus_U Defocus_V Angle CCC 8151.61 9023.49 14.03 0.008882 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00010sq_v01_00002hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00002hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 38.07 6.63 Num Hot pixels: 205 Hot pixel threshold: 77.84 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.121296 Iteration 2 Error: 0.208025 Iteration 3 Error: 0.047079 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.07 0.07 ...... Frame ( 3) shift: -0.14 0.14 ...... Frame ( 4) shift: -0.21 0.22 ...... Frame ( 5) shift: -0.27 0.29 ...... Frame ( 6) shift: -0.28 0.30 ...... Frame ( 7) shift: -0.23 0.26 ...... Frame ( 8) shift: -0.18 0.22 ...... Frame ( 9) shift: -0.13 0.22 ...... Frame ( 10) shift: -0.08 0.25 ...... Frame ( 11) shift: -0.04 0.28 ...... Frame ( 12) shift: -0.03 0.33 ...... Frame ( 13) shift: -0.05 0.41 ...... Frame ( 14) shift: -0.07 0.49 ...... Frame ( 15) shift: -0.06 0.54 ...... Frame ( 16) shift: -0.03 0.58 ...... Frame ( 17) shift: 0.00 0.62 ...... Frame ( 18) shift: 0.04 0.66 ...... Frame ( 19) shift: 0.10 0.72 ...... Frame ( 20) shift: 0.15 0.78 ...... Frame ( 21) shift: 0.24 0.85 ...... Frame ( 22) shift: 0.34 0.94 ...... Frame ( 23) shift: 0.45 1.03 ...... Frame ( 24) shift: 0.50 1.09 ...... Frame ( 25) shift: 0.48 1.14 ...... Frame ( 26) shift: 0.46 1.19 ...... Frame ( 27) shift: 0.50 1.26 ...... Frame ( 28) shift: 0.59 1.35 ...... Frame ( 29) shift: 0.69 1.45 ...... Frame ( 30) shift: 0.76 1.52 ...... Frame ( 31) shift: 0.83 1.56 ...... Frame ( 32) shift: 0.89 1.61 ...... Frame ( 33) shift: 0.91 1.64 ...... Frame ( 34) shift: 0.89 1.65 ...... Frame ( 35) shift: 0.87 1.66 ...... Frame ( 36) shift: 0.89 1.70 ...... Frame ( 37) shift: 0.94 1.77 ...... Frame ( 38) shift: 1.00 1.85 ...... Frame ( 39) shift: 1.05 1.92 ...... Frame ( 40) shift: 1.11 2.00 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.712168 Iteration 2 Error: 0.089687 Iteration 3 Error: 0.016110 Align patch 2 23 left Iteration 1 Error: 0.556760 Iteration 2 Error: 0.107205 Iteration 3 Error: 0.035429 Align patch 3 22 left Iteration 1 Error: 1.079637 Iteration 2 Error: 0.138536 Iteration 3 Error: 0.042098 Align patch 4 21 left Iteration 1 Error: 0.472490 Iteration 2 Error: 0.069850 Iteration 3 Error: 0.020015 Align patch 5 20 left Iteration 1 Error: 0.672631 Iteration 2 Error: 0.114768 Iteration 3 Error: 0.021007 Align patch 6 19 left Iteration 1 Error: 0.706589 Iteration 2 Error: 0.072976 Iteration 3 Error: 0.018368 Align patch 7 18 left Iteration 1 Error: 0.673417 Iteration 2 Error: 0.168818 Iteration 3 Error: 0.038935 Align patch 8 17 left Iteration 1 Error: 0.817107 Iteration 2 Error: 0.126155 Iteration 3 Error: 0.047345 Align patch 9 16 left Iteration 1 Error: 0.650946 Iteration 2 Error: 0.083996 Iteration 3 Error: 0.020294 Align patch 10 15 left Iteration 1 Error: 0.709314 Iteration 2 Error: 0.110716 Iteration 3 Error: 0.022525 Align patch 11 14 left Iteration 1 Error: 0.859744 Iteration 2 Error: 0.185876 Iteration 3 Error: 0.061051 Iteration 4 Error: 0.013462 Align patch 12 13 left Iteration 1 Error: 0.756745 Iteration 2 Error: 0.090779 Iteration 3 Error: 0.019729 Align patch 13 12 left Iteration 1 Error: 1.165470 Iteration 2 Error: 0.137333 Iteration 3 Error: 0.021113 Align patch 14 11 left Iteration 1 Error: 0.644092 Iteration 2 Error: 0.163295 Iteration 3 Error: 0.022833 Align patch 15 10 left Iteration 1 Error: 0.510516 Iteration 2 Error: 0.122775 Iteration 3 Error: 0.029242 Align patch 16 9 left Iteration 1 Error: 0.434417 Iteration 2 Error: 0.064960 Iteration 3 Error: 0.017681 Align patch 17 8 left Iteration 1 Error: 0.613909 Iteration 2 Error: 0.100524 Iteration 3 Error: 0.019467 Align patch 18 7 left Iteration 1 Error: 0.495022 Iteration 2 Error: 0.092272 Iteration 3 Error: 0.024166 Align patch 19 6 left Iteration 1 Error: 0.955721 Iteration 2 Error: 0.095534 Iteration 3 Error: 0.008258 Align patch 20 5 left Iteration 1 Error: 0.849372 Iteration 2 Error: 0.104104 Iteration 3 Error: 0.019931 Align patch 21 4 left Iteration 1 Error: 0.614539 Iteration 2 Error: 0.099284 Iteration 3 Error: 0.026157 Align patch 22 3 left Iteration 1 Error: 1.026669 Iteration 2 Error: 0.180429 Iteration 3 Error: 0.053641 Iteration 4 Error: 0.014337 Align patch 23 2 left Iteration 1 Error: 1.051055 Iteration 2 Error: 0.112476 Iteration 3 Error: 0.033268 Align patch 24 1 left Iteration 1 Error: 0.612144 Iteration 2 Error: 0.094446 Iteration 3 Error: 0.019825 Align patch 25 0 left Iteration 1 Error: 0.790910 Iteration 2 Error: 0.188354 Iteration 3 Error: 0.059033 Iteration 4 Error: 0.016447 3D Fitting completed. Patch alignment time: 15.66(sec) Local motion has been corrected. Process thread exits. Computational time: 24.415916 sec Total time: 30.204693 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00002hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00002hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.766568s Reading file: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00002hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.234837s ........................................ >>>>>>TIME<<<<<< FFT: 1.085884s Defocus_U Defocus_V Angle CCC 11458.95 12376.99 4.02 0.035458 Final Values Defocus_U Defocus_V Angle CCC 11501.15 12384.82 3.40 0.054180 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00010sq_v01_00002hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00002hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 38.36 6.66 Num Hot pixels: 192 Hot pixel threshold: 78.35 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.616308 Iteration 2 Error: 0.301511 Iteration 3 Error: 0.087298 Iteration 4 Error: 0.020616 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.01 0.08 ...... Frame ( 3) shift: 0.01 0.16 ...... Frame ( 4) shift: 0.02 0.25 ...... Frame ( 5) shift: 0.02 0.33 ...... Frame ( 6) shift: 0.09 0.34 ...... Frame ( 7) shift: 0.24 0.27 ...... Frame ( 8) shift: 0.38 0.20 ...... Frame ( 9) shift: 0.52 0.19 ...... Frame ( 10) shift: 0.66 0.22 ...... Frame ( 11) shift: 0.79 0.26 ...... Frame ( 12) shift: 0.85 0.30 ...... Frame ( 13) shift: 0.83 0.35 ...... Frame ( 14) shift: 0.82 0.39 ...... Frame ( 15) shift: 0.85 0.41 ...... Frame ( 16) shift: 0.94 0.40 ...... Frame ( 17) shift: 1.04 0.38 ...... Frame ( 18) shift: 1.10 0.40 ...... Frame ( 19) shift: 1.15 0.45 ...... Frame ( 20) shift: 1.19 0.50 ...... Frame ( 21) shift: 1.25 0.52 ...... Frame ( 22) shift: 1.33 0.51 ...... Frame ( 23) shift: 1.41 0.50 ...... Frame ( 24) shift: 1.49 0.49 ...... Frame ( 25) shift: 1.58 0.49 ...... Frame ( 26) shift: 1.66 0.48 ...... Frame ( 27) shift: 1.73 0.50 ...... Frame ( 28) shift: 1.77 0.55 ...... Frame ( 29) shift: 1.82 0.59 ...... Frame ( 30) shift: 1.93 0.60 ...... Frame ( 31) shift: 2.12 0.58 ...... Frame ( 32) shift: 2.31 0.56 ...... Frame ( 33) shift: 2.41 0.59 ...... Frame ( 34) shift: 2.40 0.68 ...... Frame ( 35) shift: 2.40 0.76 ...... Frame ( 36) shift: 2.48 0.87 ...... Frame ( 37) shift: 2.65 0.99 ...... Frame ( 38) shift: 2.81 1.12 ...... Frame ( 39) shift: 2.98 1.24 ...... Frame ( 40) shift: 3.14 1.37 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.718814 Iteration 2 Error: 0.086910 Iteration 3 Error: 0.021526 Align patch 2 23 left Iteration 1 Error: 0.903259 Iteration 2 Error: 0.117021 Iteration 3 Error: 0.037671 Align patch 3 22 left Iteration 1 Error: 0.559581 Iteration 2 Error: 0.093963 Iteration 3 Error: 0.022455 Align patch 4 21 left Iteration 1 Error: 0.728391 Iteration 2 Error: 0.131518 Iteration 3 Error: 0.033350 Align patch 5 20 left Iteration 1 Error: 1.072128 Iteration 2 Error: 0.175543 Iteration 3 Error: 0.072013 Iteration 4 Error: 0.033478 Align patch 6 19 left Iteration 1 Error: 0.725664 Iteration 2 Error: 0.186075 Iteration 3 Error: 0.045946 Align patch 7 18 left Iteration 1 Error: 0.600923 Iteration 2 Error: 0.076181 Iteration 3 Error: 0.022834 Align patch 8 17 left Iteration 1 Error: 0.727356 Iteration 2 Error: 0.257392 Iteration 3 Error: 0.078537 Iteration 4 Error: 0.028446 Align patch 9 16 left Iteration 1 Error: 0.755367 Iteration 2 Error: 0.114028 Iteration 3 Error: 0.040853 Align patch 10 15 left Iteration 1 Error: 0.957670 Iteration 2 Error: 0.178492 Iteration 3 Error: 0.049352 Align patch 11 14 left Iteration 1 Error: 0.616751 Iteration 2 Error: 0.179420 Iteration 3 Error: 0.068067 Iteration 4 Error: 0.023316 Align patch 12 13 left Iteration 1 Error: 0.816821 Iteration 2 Error: 0.130999 Iteration 3 Error: 0.027217 Align patch 13 12 left Iteration 1 Error: 0.679885 Iteration 2 Error: 0.126003 Iteration 3 Error: 0.047258 Align patch 14 11 left Iteration 1 Error: 1.595898 Iteration 2 Error: 0.205041 Iteration 3 Error: 0.044234 Align patch 15 10 left Iteration 1 Error: 0.883061 Iteration 2 Error: 0.172679 Iteration 3 Error: 0.044586 Align patch 16 9 left Iteration 1 Error: 0.811004 Iteration 2 Error: 0.183428 Iteration 3 Error: 0.061301 Iteration 4 Error: 0.021388 Align patch 17 8 left Iteration 1 Error: 0.726203 Iteration 2 Error: 0.138399 Iteration 3 Error: 0.048656 Align patch 18 7 left Iteration 1 Error: 0.738905 Iteration 2 Error: 0.212645 Iteration 3 Error: 0.091266 Iteration 4 Error: 0.030709 Align patch 19 6 left Iteration 1 Error: 0.706881 Iteration 2 Error: 0.130116 Iteration 3 Error: 0.037489 Align patch 20 5 left Iteration 1 Error: 1.304699 Iteration 2 Error: 0.304451 Iteration 3 Error: 0.082142 Iteration 4 Error: 0.027892 Align patch 21 4 left Iteration 1 Error: 0.529664 Iteration 2 Error: 0.106637 Iteration 3 Error: 0.049896 Align patch 22 3 left Iteration 1 Error: 0.701906 Iteration 2 Error: 0.173990 Iteration 3 Error: 0.036692 Align patch 23 2 left Iteration 1 Error: 1.152599 Iteration 2 Error: 0.258557 Iteration 3 Error: 0.123915 Iteration 4 Error: 0.061560 Iteration 5 Error: 0.039756 Align patch 24 1 left Iteration 1 Error: 0.769869 Iteration 2 Error: 0.144398 Iteration 3 Error: 0.050139 Iteration 4 Error: 0.023437 Align patch 25 0 left Iteration 1 Error: 0.910237 Iteration 2 Error: 0.135860 Iteration 3 Error: 0.043416 3D Fitting completed. Patch alignment time: 16.05(sec) Local motion has been corrected. Process thread exits. Computational time: 25.166199 sec Total time: 31.464338 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00002hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00002hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.748264s Reading file: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00002hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.268071s ........................................ >>>>>>TIME<<<<<< FFT: 1.027037s Defocus_U Defocus_V Angle CCC 11767.61 11162.08 88.58 0.033541 Final Values Defocus_U Defocus_V Angle CCC 11758.22 11187.12 89.52 0.052463 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00010sq_v01_00004hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00004hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.331e-01 9.908e-02 CC threshold: 0.728 Mean Std: 34.57 6.31 Num Hot pixels: 190 Hot pixel threshold: 72.42 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 4.205824 Iteration 2 Error: 0.562384 Iteration 3 Error: 0.348266 Iteration 4 Error: 0.185672 Iteration 5 Error: 0.095742 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.34 -0.77 ...... Frame ( 3) shift: 0.69 -1.54 ...... Frame ( 4) shift: 1.03 -2.31 ...... Frame ( 5) shift: 1.37 -3.08 ...... Frame ( 6) shift: 1.66 -3.68 ...... Frame ( 7) shift: 1.88 -4.11 ...... Frame ( 8) shift: 2.10 -4.54 ...... Frame ( 9) shift: 2.33 -4.85 ...... Frame ( 10) shift: 2.58 -5.06 ...... Frame ( 11) shift: 2.83 -5.26 ...... Frame ( 12) shift: 2.99 -5.43 ...... Frame ( 13) shift: 3.05 -5.56 ...... Frame ( 14) shift: 3.12 -5.69 ...... Frame ( 15) shift: 3.21 -5.78 ...... Frame ( 16) shift: 3.33 -5.82 ...... Frame ( 17) shift: 3.45 -5.86 ...... Frame ( 18) shift: 3.58 -5.90 ...... Frame ( 19) shift: 3.73 -5.92 ...... Frame ( 20) shift: 3.87 -5.94 ...... Frame ( 21) shift: 3.94 -5.96 ...... Frame ( 22) shift: 3.94 -5.98 ...... Frame ( 23) shift: 3.94 -6.01 ...... Frame ( 24) shift: 3.94 -6.02 ...... Frame ( 25) shift: 3.95 -6.02 ...... Frame ( 26) shift: 3.95 -6.02 ...... Frame ( 27) shift: 3.98 -6.08 ...... Frame ( 28) shift: 4.04 -6.21 ...... Frame ( 29) shift: 4.09 -6.35 ...... Frame ( 30) shift: 4.12 -6.44 ...... Frame ( 31) shift: 4.11 -6.50 ...... Frame ( 32) shift: 4.11 -6.55 ...... Frame ( 33) shift: 4.19 -6.59 ...... Frame ( 34) shift: 4.34 -6.62 ...... Frame ( 35) shift: 4.50 -6.64 ...... Frame ( 36) shift: 4.54 -6.65 ...... Frame ( 37) shift: 4.48 -6.66 ...... Frame ( 38) shift: 4.41 -6.66 ...... Frame ( 39) shift: 4.35 -6.67 ...... Frame ( 40) shift: 4.29 -6.67 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.100231 Iteration 2 Error: 0.472135 Iteration 3 Error: 0.150845 Iteration 4 Error: 0.072939 Iteration 5 Error: 0.035432 Align patch 2 23 left Iteration 1 Error: 1.017022 Iteration 2 Error: 0.603417 Iteration 3 Error: 0.167208 Iteration 4 Error: 0.099701 Iteration 5 Error: 0.032420 Align patch 3 22 left Iteration 1 Error: 1.182865 Iteration 2 Error: 0.230598 Iteration 3 Error: 0.066978 Iteration 4 Error: 0.032591 Align patch 4 21 left Iteration 1 Error: 1.321962 Iteration 2 Error: 0.336840 Iteration 3 Error: 0.132629 Iteration 4 Error: 0.040794 Align patch 5 20 left Iteration 1 Error: 3.300974 Iteration 2 Error: 0.558884 Iteration 3 Error: 0.211592 Iteration 4 Error: 0.062303 Iteration 5 Error: 0.041285 Align patch 6 19 left Iteration 1 Error: 3.758422 Iteration 2 Error: 0.388975 Iteration 3 Error: 0.126523 Iteration 4 Error: 0.060985 Iteration 5 Error: 0.030021 Align patch 7 18 left Iteration 1 Error: 1.673351 Iteration 2 Error: 0.511337 Iteration 3 Error: 0.185911 Iteration 4 Error: 0.087600 Iteration 5 Error: 0.026139 Align patch 8 17 left Iteration 1 Error: 1.223193 Iteration 2 Error: 0.254566 Iteration 3 Error: 0.072152 Iteration 4 Error: 0.027308 Align patch 9 16 left Iteration 1 Error: 1.632147 Iteration 2 Error: 0.378063 Iteration 3 Error: 0.111494 Iteration 4 Error: 0.042172 Align patch 10 15 left Iteration 1 Error: 2.375566 Iteration 2 Error: 0.398828 Iteration 3 Error: 0.105310 Iteration 4 Error: 0.050384 Iteration 5 Error: 0.017851 Align patch 11 14 left Iteration 1 Error: 4.085180 Iteration 2 Error: 0.692521 Iteration 3 Error: 0.200391 Iteration 4 Error: 0.088310 Iteration 5 Error: 0.033093 Align patch 12 13 left Iteration 1 Error: 3.047016 Iteration 2 Error: 0.598511 Iteration 3 Error: 0.127047 Iteration 4 Error: 0.065964 Iteration 5 Error: 0.028363 Align patch 13 12 left Iteration 1 Error: 1.115635 Iteration 2 Error: 0.214619 Iteration 3 Error: 0.043671 Align patch 14 11 left Iteration 1 Error: 1.015375 Iteration 2 Error: 0.231355 Iteration 3 Error: 0.056004 Iteration 4 Error: 0.018507 Align patch 15 10 left Iteration 1 Error: 2.704912 Iteration 2 Error: 0.314691 Iteration 3 Error: 0.093927 Iteration 4 Error: 0.027968 Align patch 16 9 left Iteration 1 Error: 3.248393 Iteration 2 Error: 0.759591 Iteration 3 Error: 0.241226 Iteration 4 Error: 0.092415 Iteration 5 Error: 0.052275 Align patch 16 9 left Iteration 1 Error: 2.524001 Iteration 2 Error: 0.438855 Iteration 3 Error: 0.119558 Iteration 4 Error: 0.037034 Align patch 17 8 left Iteration 1 Error: 1.819627 Iteration 2 Error: 0.303041 Iteration 3 Error: 0.073440 Iteration 4 Error: 0.042081 Align patch 18 7 left Iteration 1 Error: 1.225828 Iteration 2 Error: 0.259677 Iteration 3 Error: 0.113918 Iteration 4 Error: 0.046457 Align patch 19 6 left Iteration 1 Error: 1.648395 Iteration 2 Error: 0.237073 Iteration 3 Error: 0.074648 Iteration 4 Error: 0.036871 Align patch 20 5 left Iteration 1 Error: 3.377035 Iteration 2 Error: 1.991758 Iteration 3 Error: 0.331616 Iteration 4 Error: 0.079357 Iteration 5 Error: 0.038507 Align patch 21 4 left Iteration 1 Error: 1.806300 Iteration 2 Error: 0.402363 Iteration 3 Error: 0.090451 Iteration 4 Error: 0.030054 Align patch 22 3 left Iteration 1 Error: 2.067252 Iteration 2 Error: 0.343614 Iteration 3 Error: 0.082122 Iteration 4 Error: 0.030684 Align patch 23 2 left Iteration 1 Error: 1.142790 Iteration 2 Error: 0.329208 Iteration 3 Error: 0.116279 Iteration 4 Error: 0.055182 Iteration 5 Error: 0.023639 Align patch 24 1 left Iteration 1 Error: 2.130816 Iteration 2 Error: 0.374484 Iteration 3 Error: 0.164917 Iteration 4 Error: 0.062086 Iteration 5 Error: 0.026846 Align patch 25 0 left Iteration 1 Error: 4.314331 Iteration 2 Error: 0.819274 Iteration 3 Error: 0.201585 Iteration 4 Error: 0.099402 Iteration 5 Error: 0.037925 3D Fitting completed. Patch alignment time: 19.32(sec) Local motion has been corrected. Process thread exits. Computational time: 28.338331 sec Total time: 34.791286 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00004hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00004hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.743840s Reading file: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00004hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.858623s ........................................ >>>>>>TIME<<<<<< FFT: 1.076160s Defocus_U Defocus_V Angle CCC 10521.49 10607.43 18.05 -0.008356 Final Values Defocus_U Defocus_V Angle CCC 10469.89 10574.63 42.35 -0.096805 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00010sq_v01_00004hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00004hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 38.49 6.59 Num Hot pixels: 218 Hot pixel threshold: 78.01 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.063766 Iteration 2 Error: 0.135733 Iteration 3 Error: 0.028231 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.05 0.22 ...... Frame ( 3) shift: 0.09 0.44 ...... Frame ( 4) shift: 0.14 0.66 ...... Frame ( 5) shift: 0.19 0.89 ...... Frame ( 6) shift: 0.24 1.02 ...... Frame ( 7) shift: 0.29 1.08 ...... Frame ( 8) shift: 0.35 1.14 ...... Frame ( 9) shift: 0.35 1.20 ...... Frame ( 10) shift: 0.30 1.25 ...... Frame ( 11) shift: 0.25 1.31 ...... Frame ( 12) shift: 0.20 1.32 ...... Frame ( 13) shift: 0.14 1.28 ...... Frame ( 14) shift: 0.09 1.23 ...... Frame ( 15) shift: 0.06 1.24 ...... Frame ( 16) shift: 0.07 1.31 ...... Frame ( 17) shift: 0.07 1.37 ...... Frame ( 18) shift: 0.08 1.40 ...... Frame ( 19) shift: 0.10 1.40 ...... Frame ( 20) shift: 0.11 1.40 ...... Frame ( 21) shift: 0.08 1.39 ...... Frame ( 22) shift: 0.00 1.37 ...... Frame ( 23) shift: -0.08 1.35 ...... Frame ( 24) shift: -0.10 1.38 ...... Frame ( 25) shift: -0.08 1.45 ...... Frame ( 26) shift: -0.06 1.52 ...... Frame ( 27) shift: -0.04 1.60 ...... Frame ( 28) shift: -0.02 1.69 ...... Frame ( 29) shift: 0.00 1.77 ...... Frame ( 30) shift: 0.01 1.82 ...... Frame ( 31) shift: 0.00 1.83 ...... Frame ( 32) shift: -0.01 1.83 ...... Frame ( 33) shift: 0.00 1.87 ...... Frame ( 34) shift: 0.03 1.93 ...... Frame ( 35) shift: 0.06 2.00 ...... Frame ( 36) shift: 0.08 2.04 ...... Frame ( 37) shift: 0.08 2.07 ...... Frame ( 38) shift: 0.08 2.09 ...... Frame ( 39) shift: 0.08 2.12 ...... Frame ( 40) shift: 0.08 2.15 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.711242 Iteration 2 Error: 0.153228 Iteration 3 Error: 0.033818 Align patch 2 23 left Iteration 1 Error: 0.556813 Iteration 2 Error: 0.078298 Iteration 3 Error: 0.025527 Align patch 3 22 left Iteration 1 Error: 0.715925 Iteration 2 Error: 0.169028 Iteration 3 Error: 0.039584 Align patch 4 21 left Iteration 1 Error: 0.876102 Iteration 2 Error: 0.167118 Iteration 3 Error: 0.032185 Align patch 5 20 left Iteration 1 Error: 0.665852 Iteration 2 Error: 0.072176 Iteration 3 Error: 0.049759 Align patch 6 19 left Iteration 1 Error: 0.893398 Iteration 2 Error: 0.183502 Iteration 3 Error: 0.053651 Iteration 4 Error: 0.023053 Align patch 7 18 left Iteration 1 Error: 0.625165 Iteration 2 Error: 0.127009 Iteration 3 Error: 0.034235 Align patch 8 17 left Iteration 1 Error: 0.779023 Iteration 2 Error: 0.095934 Iteration 3 Error: 0.027780 Align patch 9 16 left Iteration 1 Error: 0.641064 Iteration 2 Error: 0.129837 Iteration 3 Error: 0.030969 Align patch 10 15 left Iteration 1 Error: 0.834803 Iteration 2 Error: 0.134759 Iteration 3 Error: 0.034547 Align patch 11 14 left Iteration 1 Error: 1.315142 Iteration 2 Error: 0.268172 Iteration 3 Error: 0.044459 Align patch 12 13 left Iteration 1 Error: 1.185196 Iteration 2 Error: 0.220710 Iteration 3 Error: 0.066733 Iteration 4 Error: 0.019340 Align patch 13 12 left Iteration 1 Error: 0.599520 Iteration 2 Error: 0.105184 Iteration 3 Error: 0.022866 Align patch 14 11 left Iteration 1 Error: 0.544476 Iteration 2 Error: 0.101527 Iteration 3 Error: 0.023858 Align patch 15 10 left Iteration 1 Error: 0.666764 Iteration 2 Error: 0.186381 Iteration 3 Error: 0.073276 Iteration 4 Error: 0.019681 Align patch 16 9 left Iteration 1 Error: 0.688053 Iteration 2 Error: 0.122242 Iteration 3 Error: 0.043005 Align patch 17 8 left Iteration 1 Error: 0.922539 Iteration 2 Error: 0.105023 Iteration 3 Error: 0.028440 Align patch 18 7 left Iteration 1 Error: 0.728726 Iteration 2 Error: 0.086714 Iteration 3 Error: 0.028348 Align patch 19 6 left Iteration 1 Error: 0.881122 Iteration 2 Error: 0.164863 Iteration 3 Error: 0.050504 Iteration 4 Error: 0.016653 Align patch 20 5 left Iteration 1 Error: 1.150665 Iteration 2 Error: 0.217041 Iteration 3 Error: 0.042417 Align patch 21 4 left Iteration 1 Error: 1.466230 Iteration 2 Error: 0.154244 Iteration 3 Error: 0.050652 Iteration 4 Error: 0.022063 Align patch 22 3 left Iteration 1 Error: 0.935489 Iteration 2 Error: 0.131591 Iteration 3 Error: 0.048320 Align patch 23 2 left Iteration 1 Error: 1.540774 Iteration 2 Error: 0.139303 Iteration 3 Error: 0.040907 Align patch 24 1 left Iteration 1 Error: 0.829748 Iteration 2 Error: 0.142437 Iteration 3 Error: 0.029666 Align patch 25 0 left Iteration 1 Error: 0.981472 Iteration 2 Error: 0.144829 Iteration 3 Error: 0.051558 Iteration 4 Error: 0.013024 3D Fitting completed. Patch alignment time: 15.69(sec) Local motion has been corrected. Process thread exits. Computational time: 24.612967 sec Total time: 30.259621 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00004hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00004hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.650993s Reading file: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00004hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.110468s ........................................ >>>>>>TIME<<<<<< FFT: 1.021410s Defocus_U Defocus_V Angle CCC 11310.55 11834.00 4.31 0.027480 Final Values Defocus_U Defocus_V Angle CCC 11330.86 11835.56 3.69 0.045087 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00010sq_v01_00004hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00004hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 9.999e-02 CC threshold: 0.734 Mean Std: 37.28 6.50 Num Hot pixels: 196 Hot pixel threshold: 76.30 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.840031 Iteration 2 Error: 0.137087 Iteration 3 Error: 0.022941 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.21 0.01 ...... Frame ( 3) shift: -0.41 0.01 ...... Frame ( 4) shift: -0.62 0.02 ...... Frame ( 5) shift: -0.82 0.03 ...... Frame ( 6) shift: -0.96 0.04 ...... Frame ( 7) shift: -1.03 0.05 ...... Frame ( 8) shift: -1.10 0.06 ...... Frame ( 9) shift: -1.12 0.08 ...... Frame ( 10) shift: -1.08 0.11 ...... Frame ( 11) shift: -1.04 0.13 ...... Frame ( 12) shift: -1.04 0.18 ...... Frame ( 13) shift: -1.09 0.23 ...... Frame ( 14) shift: -1.13 0.29 ...... Frame ( 15) shift: -1.13 0.34 ...... Frame ( 16) shift: -1.07 0.37 ...... Frame ( 17) shift: -1.01 0.41 ...... Frame ( 18) shift: -1.00 0.45 ...... Frame ( 19) shift: -1.02 0.50 ...... Frame ( 20) shift: -1.05 0.54 ...... Frame ( 21) shift: -1.06 0.57 ...... Frame ( 22) shift: -1.04 0.60 ...... Frame ( 23) shift: -1.02 0.62 ...... Frame ( 24) shift: -1.02 0.65 ...... Frame ( 25) shift: -1.04 0.67 ...... Frame ( 26) shift: -1.05 0.69 ...... Frame ( 27) shift: -1.08 0.74 ...... Frame ( 28) shift: -1.10 0.82 ...... Frame ( 29) shift: -1.13 0.89 ...... Frame ( 30) shift: -1.16 0.91 ...... Frame ( 31) shift: -1.20 0.88 ...... Frame ( 32) shift: -1.24 0.85 ...... Frame ( 33) shift: -1.22 0.89 ...... Frame ( 34) shift: -1.13 1.00 ...... Frame ( 35) shift: -1.05 1.11 ...... Frame ( 36) shift: -0.99 1.19 ...... Frame ( 37) shift: -0.97 1.24 ...... Frame ( 38) shift: -0.94 1.29 ...... Frame ( 39) shift: -0.92 1.34 ...... Frame ( 40) shift: -0.90 1.39 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.934878 Iteration 2 Error: 0.164812 Iteration 3 Error: 0.058352 Iteration 4 Error: 0.019862 Align patch 2 23 left Iteration 1 Error: 0.857616 Iteration 2 Error: 0.185621 Iteration 3 Error: 0.057160 Iteration 4 Error: 0.017750 Align patch 3 22 left Iteration 1 Error: 0.737946 Iteration 2 Error: 0.192401 Iteration 3 Error: 0.062162 Iteration 4 Error: 0.029353 Align patch 4 21 left Iteration 1 Error: 0.737715 Iteration 2 Error: 0.097494 Iteration 3 Error: 0.014392 Align patch 5 20 left Iteration 1 Error: 0.746018 Iteration 2 Error: 0.087859 Iteration 3 Error: 0.018799 Align patch 6 19 left Iteration 1 Error: 0.590162 Iteration 2 Error: 0.126902 Iteration 3 Error: 0.027804 Align patch 7 18 left Iteration 1 Error: 0.576611 Iteration 2 Error: 0.096789 Iteration 3 Error: 0.044018 Align patch 8 17 left Iteration 1 Error: 1.010679 Iteration 2 Error: 0.284559 Iteration 3 Error: 0.087449 Iteration 4 Error: 0.035995 Align patch 9 16 left Iteration 1 Error: 0.991113 Iteration 2 Error: 0.138543 Iteration 3 Error: 0.029021 Align patch 10 15 left Iteration 1 Error: 0.742281 Iteration 2 Error: 0.140931 Iteration 3 Error: 0.038306 Align patch 11 14 left Iteration 1 Error: 0.806039 Iteration 2 Error: 0.129496 Iteration 3 Error: 0.033605 Align patch 12 13 left Iteration 1 Error: 0.822732 Iteration 2 Error: 0.210055 Iteration 3 Error: 0.075991 Iteration 4 Error: 0.019621 Align patch 13 12 left Iteration 1 Error: 1.294205 Iteration 2 Error: 0.135139 Iteration 3 Error: 0.047024 Align patch 14 11 left Iteration 1 Error: 1.224610 Iteration 2 Error: 0.079550 Iteration 3 Error: 0.026337 Align patch 15 10 left Iteration 1 Error: 0.978554 Iteration 2 Error: 0.312316 Iteration 3 Error: 0.080832 Iteration 4 Error: 0.035312 Align patch 16 9 left Iteration 1 Error: 0.700049 Iteration 2 Error: 0.168712 Iteration 3 Error: 0.045253 Align patch 17 8 left Iteration 1 Error: 0.915945 Iteration 2 Error: 0.168811 Iteration 3 Error: 0.025225 Align patch 18 7 left Iteration 1 Error: 1.023059 Iteration 2 Error: 0.265456 Iteration 3 Error: 0.072614 Iteration 4 Error: 0.023684 Align patch 19 6 left Iteration 1 Error: 0.580553 Iteration 2 Error: 0.109429 Iteration 3 Error: 0.029102 Align patch 20 5 left Iteration 1 Error: 0.641574 Iteration 2 Error: 0.134798 Iteration 3 Error: 0.017195 Align patch 21 4 left Iteration 1 Error: 0.686232 Iteration 2 Error: 0.175897 Iteration 3 Error: 0.045866 Align patch 22 3 left Iteration 1 Error: 0.869294 Iteration 2 Error: 0.092760 Iteration 3 Error: 0.022583 Align patch 23 2 left Iteration 1 Error: 0.583031 Iteration 2 Error: 0.139852 Iteration 3 Error: 0.039063 Align patch 24 1 left Iteration 1 Error: 0.672562 Iteration 2 Error: 0.112852 Iteration 3 Error: 0.029836 Align patch 25 0 left Iteration 1 Error: 0.627082 Iteration 2 Error: 0.103539 Iteration 3 Error: 0.024705 3D Fitting completed. Patch alignment time: 15.77(sec) Local motion has been corrected. Process thread exits. Computational time: 24.375278 sec Total time: 30.884790 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00004hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00004hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.756565s Reading file: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00004hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.977094s ........................................ >>>>>>TIME<<<<<< FFT: 1.073486s Defocus_U Defocus_V Angle CCC 14095.70 14931.65 3.90 0.034196 Final Values Defocus_U Defocus_V Angle CCC 14111.33 15000.48 5.85 0.046848 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00010sq_v01_00004hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00004hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 40.42 6.82 Num Hot pixels: 220 Hot pixel threshold: 81.37 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.662037 Iteration 2 Error: 0.248937 Iteration 3 Error: 0.040518 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.06 0.03 ...... Frame ( 3) shift: -0.13 0.07 ...... Frame ( 4) shift: -0.19 0.10 ...... Frame ( 5) shift: -0.26 0.14 ...... Frame ( 6) shift: -0.25 0.15 ...... Frame ( 7) shift: -0.17 0.15 ...... Frame ( 8) shift: -0.09 0.14 ...... Frame ( 9) shift: -0.04 0.17 ...... Frame ( 10) shift: -0.02 0.22 ...... Frame ( 11) shift: -0.01 0.28 ...... Frame ( 12) shift: 0.01 0.30 ...... Frame ( 13) shift: 0.02 0.29 ...... Frame ( 14) shift: 0.04 0.27 ...... Frame ( 15) shift: 0.09 0.27 ...... Frame ( 16) shift: 0.17 0.29 ...... Frame ( 17) shift: 0.26 0.31 ...... Frame ( 18) shift: 0.38 0.34 ...... Frame ( 19) shift: 0.53 0.38 ...... Frame ( 20) shift: 0.69 0.42 ...... Frame ( 21) shift: 0.80 0.46 ...... Frame ( 22) shift: 0.88 0.50 ...... Frame ( 23) shift: 0.96 0.53 ...... Frame ( 24) shift: 1.04 0.54 ...... Frame ( 25) shift: 1.13 0.51 ...... Frame ( 26) shift: 1.22 0.48 ...... Frame ( 27) shift: 1.31 0.47 ...... Frame ( 28) shift: 1.41 0.47 ...... Frame ( 29) shift: 1.51 0.47 ...... Frame ( 30) shift: 1.55 0.48 ...... Frame ( 31) shift: 1.55 0.50 ...... Frame ( 32) shift: 1.54 0.52 ...... Frame ( 33) shift: 1.56 0.54 ...... Frame ( 34) shift: 1.60 0.56 ...... Frame ( 35) shift: 1.63 0.58 ...... Frame ( 36) shift: 1.76 0.59 ...... Frame ( 37) shift: 1.99 0.59 ...... Frame ( 38) shift: 2.22 0.59 ...... Frame ( 39) shift: 2.45 0.60 ...... Frame ( 40) shift: 2.67 0.60 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.809946 Iteration 2 Error: 0.118392 Iteration 3 Error: 0.028603 Align patch 2 23 left Iteration 1 Error: 0.582426 Iteration 2 Error: 0.133963 Iteration 3 Error: 0.038334 Align patch 3 22 left Iteration 1 Error: 0.559957 Iteration 2 Error: 0.100873 Iteration 3 Error: 0.027717 Align patch 4 21 left Iteration 1 Error: 0.631660 Iteration 2 Error: 0.085317 Iteration 3 Error: 0.019166 Align patch 5 20 left Iteration 1 Error: 0.660080 Iteration 2 Error: 0.106169 Iteration 3 Error: 0.025661 Align patch 6 19 left Iteration 1 Error: 0.826414 Iteration 2 Error: 0.139898 Iteration 3 Error: 0.028508 Align patch 7 18 left Iteration 1 Error: 0.635168 Iteration 2 Error: 0.090698 Iteration 3 Error: 0.028960 Align patch 8 17 left Iteration 1 Error: 0.676365 Iteration 2 Error: 0.125603 Iteration 3 Error: 0.042109 Align patch 9 16 left Iteration 1 Error: 0.556893 Iteration 2 Error: 0.062071 Iteration 3 Error: 0.016295 Align patch 10 15 left Iteration 1 Error: 0.474232 Iteration 2 Error: 0.068377 Iteration 3 Error: 0.009969 Align patch 11 14 left Iteration 1 Error: 0.878531 Iteration 2 Error: 0.204397 Iteration 3 Error: 0.080812 Iteration 4 Error: 0.022110 Align patch 12 13 left Iteration 1 Error: 0.538083 Iteration 2 Error: 0.116413 Iteration 3 Error: 0.033042 Align patch 13 12 left Iteration 1 Error: 0.439480 Iteration 2 Error: 0.092074 Iteration 3 Error: 0.026056 Align patch 14 11 left Iteration 1 Error: 0.399312 Iteration 2 Error: 0.052125 Iteration 3 Error: 0.010629 Align patch 15 10 left Iteration 1 Error: 0.509772 Iteration 2 Error: 0.070562 Iteration 3 Error: 0.014463 Align patch 16 9 left Iteration 1 Error: 0.874282 Iteration 2 Error: 0.186381 Iteration 3 Error: 0.043635 Align patch 17 8 left Iteration 1 Error: 0.694559 Iteration 2 Error: 0.148601 Iteration 3 Error: 0.027549 Align patch 18 7 left Iteration 1 Error: 0.592575 Iteration 2 Error: 0.078118 Iteration 3 Error: 0.016090 Align patch 19 6 left Iteration 1 Error: 0.409194 Iteration 2 Error: 0.076745 Iteration 3 Error: 0.014199 Align patch 20 5 left Iteration 1 Error: 0.862924 Iteration 2 Error: 0.210045 Iteration 3 Error: 0.032146 Align patch 21 4 left Iteration 1 Error: 0.590958 Iteration 2 Error: 0.125481 Iteration 3 Error: 0.026431 Align patch 22 3 left Iteration 1 Error: 0.501533 Iteration 2 Error: 0.092012 Iteration 3 Error: 0.022901 Align patch 23 2 left Iteration 1 Error: 0.807515 Iteration 2 Error: 0.110289 Iteration 3 Error: 0.020538 Align patch 24 1 left Iteration 1 Error: 0.777488 Iteration 2 Error: 0.196688 Iteration 3 Error: 0.029028 Align patch 25 0 left Iteration 1 Error: 0.905569 Iteration 2 Error: 0.166421 Iteration 3 Error: 0.035367 3D Fitting completed. Patch alignment time: 15.87(sec) Local motion has been corrected. Process thread exits. Computational time: 24.456371 sec Total time: 30.169130 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00004hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00004hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.742446s Reading file: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00004hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.809980s ........................................ >>>>>>TIME<<<<<< FFT: 1.066597s Defocus_U Defocus_V Angle CCC 14064.50 13369.11 86.21 0.061241 Final Values Defocus_U Defocus_V Angle CCC 14067.63 13372.23 85.90 0.094565 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00010sq_v01_00005hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00005hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.989e-02 CC threshold: 0.734 Mean Std: 35.69 6.33 Num Hot pixels: 210 Hot pixel threshold: 73.69 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.429579 Iteration 2 Error: 0.203504 Iteration 3 Error: 0.072815 Iteration 4 Error: 0.024838 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.27 -0.25 ...... Frame ( 3) shift: 0.54 -0.49 ...... Frame ( 4) shift: 0.81 -0.74 ...... Frame ( 5) shift: 1.08 -0.98 ...... Frame ( 6) shift: 1.23 -1.20 ...... Frame ( 7) shift: 1.26 -1.38 ...... Frame ( 8) shift: 1.29 -1.56 ...... Frame ( 9) shift: 1.37 -1.63 ...... Frame ( 10) shift: 1.50 -1.60 ...... Frame ( 11) shift: 1.63 -1.57 ...... Frame ( 12) shift: 1.71 -1.56 ...... Frame ( 13) shift: 1.73 -1.57 ...... Frame ( 14) shift: 1.76 -1.58 ...... Frame ( 15) shift: 1.80 -1.54 ...... Frame ( 16) shift: 1.85 -1.45 ...... Frame ( 17) shift: 1.90 -1.36 ...... Frame ( 18) shift: 1.93 -1.28 ...... Frame ( 19) shift: 1.93 -1.22 ...... Frame ( 20) shift: 1.93 -1.15 ...... Frame ( 21) shift: 1.93 -1.07 ...... Frame ( 22) shift: 1.93 -0.98 ...... Frame ( 23) shift: 1.92 -0.89 ...... Frame ( 24) shift: 1.92 -0.82 ...... Frame ( 25) shift: 1.93 -0.76 ...... Frame ( 26) shift: 1.93 -0.71 ...... Frame ( 27) shift: 1.95 -0.64 ...... Frame ( 28) shift: 1.99 -0.55 ...... Frame ( 29) shift: 2.03 -0.47 ...... Frame ( 30) shift: 2.02 -0.37 ...... Frame ( 31) shift: 1.98 -0.26 ...... Frame ( 32) shift: 1.94 -0.16 ...... Frame ( 33) shift: 1.97 -0.05 ...... Frame ( 34) shift: 2.07 0.06 ...... Frame ( 35) shift: 2.17 0.16 ...... Frame ( 36) shift: 2.22 0.25 ...... Frame ( 37) shift: 2.21 0.31 ...... Frame ( 38) shift: 2.20 0.37 ...... Frame ( 39) shift: 2.19 0.44 ...... Frame ( 40) shift: 2.17 0.50 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.807805 Iteration 2 Error: 0.153829 Iteration 3 Error: 0.044345 Align patch 2 23 left Iteration 1 Error: 0.947940 Iteration 2 Error: 0.245464 Iteration 3 Error: 0.052784 Iteration 4 Error: 0.015760 Align patch 3 22 left Iteration 1 Error: 2.207461 Iteration 2 Error: 0.897066 Iteration 3 Error: 0.382924 Iteration 4 Error: 0.265788 Iteration 5 Error: 0.177045 Align patch 3 22 left Iteration 1 Error: 2.390442 Iteration 2 Error: 0.523519 Iteration 3 Error: 0.085118 Iteration 4 Error: 0.034835 Align patch 4 21 left Iteration 1 Error: 3.020914 Iteration 2 Error: 1.027610 Iteration 3 Error: 0.471655 Iteration 4 Error: 0.206102 Iteration 5 Error: 0.142388 Align patch 4 21 left Iteration 1 Error: 2.902713 Iteration 2 Error: 0.514554 Iteration 3 Error: 0.137832 Iteration 4 Error: 0.049446 Align patch 5 20 left Iteration 1 Error: 2.095085 Iteration 2 Error: 0.660426 Iteration 3 Error: 0.361568 Iteration 4 Error: 0.142909 Iteration 5 Error: 0.082115 Align patch 5 20 left Iteration 1 Error: 2.358552 Iteration 2 Error: 0.356285 Iteration 3 Error: 0.076023 Iteration 4 Error: 0.027986 Align patch 6 19 left Iteration 1 Error: 0.828747 Iteration 2 Error: 0.187656 Iteration 3 Error: 0.043763 Align patch 7 18 left Iteration 1 Error: 0.862788 Iteration 2 Error: 0.305712 Iteration 3 Error: 0.098195 Iteration 4 Error: 0.038906 Align patch 8 17 left Iteration 1 Error: 1.307662 Iteration 2 Error: 0.325212 Iteration 3 Error: 0.136645 Iteration 4 Error: 0.066384 Iteration 5 Error: 0.026017 Align patch 9 16 left Iteration 1 Error: 1.827254 Iteration 2 Error: 0.490959 Iteration 3 Error: 0.117185 Iteration 4 Error: 0.042833 Align patch 10 15 left Iteration 1 Error: 1.687539 Iteration 2 Error: 0.380941 Iteration 3 Error: 0.096796 Iteration 4 Error: 0.051209 Iteration 5 Error: 0.013562 Align patch 11 14 left Iteration 1 Error: 1.008942 Iteration 2 Error: 0.244196 Iteration 3 Error: 0.050306 Iteration 4 Error: 0.026606 Align patch 12 13 left Iteration 1 Error: 1.126099 Iteration 2 Error: 0.247187 Iteration 3 Error: 0.155727 Iteration 4 Error: 0.047773 Align patch 13 12 left Iteration 1 Error: 1.215164 Iteration 2 Error: 0.360254 Iteration 3 Error: 0.073816 Iteration 4 Error: 0.044519 Align patch 14 11 left Iteration 1 Error: 1.567844 Iteration 2 Error: 0.340168 Iteration 3 Error: 0.149949 Iteration 4 Error: 0.047803 Align patch 15 10 left Iteration 1 Error: 1.322259 Iteration 2 Error: 0.199254 Iteration 3 Error: 0.070791 Iteration 4 Error: 0.017620 Align patch 16 9 left Iteration 1 Error: 4.571537 Iteration 2 Error: 0.764838 Iteration 3 Error: 0.206429 Iteration 4 Error: 0.077066 Iteration 5 Error: 0.022099 Align patch 17 8 left Iteration 1 Error: 1.890293 Iteration 2 Error: 0.479216 Iteration 3 Error: 0.173002 Iteration 4 Error: 0.103916 Iteration 5 Error: 0.041700 Align patch 18 7 left Iteration 1 Error: 1.392680 Iteration 2 Error: 0.446251 Iteration 3 Error: 0.144622 Iteration 4 Error: 0.073762 Iteration 5 Error: 0.025564 Align patch 19 6 left Iteration 1 Error: 1.667783 Iteration 2 Error: 0.372297 Iteration 3 Error: 0.173849 Iteration 4 Error: 0.080623 Iteration 5 Error: 0.040065 Align patch 20 5 left Iteration 1 Error: 1.061298 Iteration 2 Error: 0.211060 Iteration 3 Error: 0.048712 Align patch 21 4 left Iteration 1 Error: 1.204911 Iteration 2 Error: 0.316137 Iteration 3 Error: 0.192755 Iteration 4 Error: 0.100932 Iteration 5 Error: 0.063714 Align patch 21 4 left Iteration 1 Error: 3.514125 Iteration 2 Error: 0.487573 Iteration 3 Error: 0.106022 Iteration 4 Error: 0.030275 Align patch 22 3 left Iteration 1 Error: 2.152796 Iteration 2 Error: 0.374582 Iteration 3 Error: 0.158745 Iteration 4 Error: 0.088735 Iteration 5 Error: 0.043827 Align patch 23 2 left Iteration 1 Error: 1.828405 Iteration 2 Error: 0.617455 Iteration 3 Error: 0.268561 Iteration 4 Error: 0.141170 Iteration 5 Error: 0.067521 Align patch 23 2 left Iteration 1 Error: 1.634422 Iteration 2 Error: 0.230436 Iteration 3 Error: 0.058991 Iteration 4 Error: 0.018997 Align patch 24 1 left Iteration 1 Error: 1.070841 Iteration 2 Error: 0.422715 Iteration 3 Error: 0.130498 Iteration 4 Error: 0.063343 Iteration 5 Error: 0.016141 Align patch 25 0 left Iteration 1 Error: 0.699228 Iteration 2 Error: 0.336016 Iteration 3 Error: 0.073798 Iteration 4 Error: 0.040268 3D Fitting completed. Patch alignment time: 22.62(sec) Local motion has been corrected. Process thread exits. Computational time: 31.580128 sec Total time: 37.331940 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00005hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00005hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.671023s Reading file: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00005hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.669416s ........................................ >>>>>>TIME<<<<<< FFT: 1.014753s Defocus_U Defocus_V Angle CCC 11951.23 12502.06 13.89 0.020936 Final Values Defocus_U Defocus_V Angle CCC 11968.35 12503.73 27.29 0.029046 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00010sq_v01_00005hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00005hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.305e-01 9.742e-02 CC threshold: 0.715 Mean Std: 30.07 6.16 Num Hot pixels: 172 Hot pixel threshold: 67.06 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.295424 Iteration 2 Error: 0.157285 Iteration 3 Error: 0.038533 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.12 -0.11 ...... Frame ( 3) shift: 0.25 -0.21 ...... Frame ( 4) shift: 0.37 -0.32 ...... Frame ( 5) shift: 0.50 -0.42 ...... Frame ( 6) shift: 0.63 -0.50 ...... Frame ( 7) shift: 0.77 -0.55 ...... Frame ( 8) shift: 0.91 -0.60 ...... Frame ( 9) shift: 1.00 -0.64 ...... Frame ( 10) shift: 1.04 -0.66 ...... Frame ( 11) shift: 1.09 -0.68 ...... Frame ( 12) shift: 1.11 -0.72 ...... Frame ( 13) shift: 1.13 -0.78 ...... Frame ( 14) shift: 1.15 -0.85 ...... Frame ( 15) shift: 1.19 -0.86 ...... Frame ( 16) shift: 1.25 -0.82 ...... Frame ( 17) shift: 1.32 -0.78 ...... Frame ( 18) shift: 1.40 -0.80 ...... Frame ( 19) shift: 1.52 -0.88 ...... Frame ( 20) shift: 1.63 -0.96 ...... Frame ( 21) shift: 1.68 -1.03 ...... Frame ( 22) shift: 1.68 -1.07 ...... Frame ( 23) shift: 1.68 -1.11 ...... Frame ( 24) shift: 1.68 -1.15 ...... Frame ( 25) shift: 1.67 -1.20 ...... Frame ( 26) shift: 1.67 -1.25 ...... Frame ( 27) shift: 1.67 -1.27 ...... Frame ( 28) shift: 1.69 -1.25 ...... Frame ( 29) shift: 1.71 -1.24 ...... Frame ( 30) shift: 1.75 -1.21 ...... Frame ( 31) shift: 1.80 -1.17 ...... Frame ( 32) shift: 1.85 -1.13 ...... Frame ( 33) shift: 1.87 -1.11 ...... Frame ( 34) shift: 1.86 -1.10 ...... Frame ( 35) shift: 1.86 -1.09 ...... Frame ( 36) shift: 1.90 -1.10 ...... Frame ( 37) shift: 1.98 -1.10 ...... Frame ( 38) shift: 2.06 -1.11 ...... Frame ( 39) shift: 2.15 -1.12 ...... Frame ( 40) shift: 2.23 -1.13 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.366071 Iteration 2 Error: 0.728210 Iteration 3 Error: 0.474050 Iteration 4 Error: 0.298987 Iteration 5 Error: 0.215939 Align patch 1 24 left Iteration 1 Error: 1.933538 Iteration 2 Error: 0.623568 Iteration 3 Error: 0.205904 Iteration 4 Error: 0.087174 Iteration 5 Error: 0.025563 Align patch 2 23 left Iteration 1 Error: 1.251610 Iteration 2 Error: 0.479724 Iteration 3 Error: 0.253246 Iteration 4 Error: 0.171339 Iteration 5 Error: 0.093098 Align patch 2 23 left Iteration 1 Error: 1.452285 Iteration 2 Error: 0.482882 Iteration 3 Error: 0.162144 Iteration 4 Error: 0.048620 Align patch 3 22 left Iteration 1 Error: 1.292439 Iteration 2 Error: 0.219864 Iteration 3 Error: 0.076629 Iteration 4 Error: 0.026671 Align patch 4 21 left Iteration 1 Error: 0.914964 Iteration 2 Error: 0.219703 Iteration 3 Error: 0.070274 Iteration 4 Error: 0.026506 Align patch 5 20 left Iteration 1 Error: 1.683382 Iteration 2 Error: 0.286436 Iteration 3 Error: 0.068477 Iteration 4 Error: 0.020221 Align patch 6 19 left Iteration 1 Error: 2.836078 Iteration 2 Error: 1.657121 Iteration 3 Error: 0.500561 Iteration 4 Error: 0.170073 Iteration 5 Error: 0.080487 Align patch 6 19 left Iteration 1 Error: 3.070054 Iteration 2 Error: 0.833725 Iteration 3 Error: 0.171954 Iteration 4 Error: 0.042917 Align patch 7 18 left Iteration 1 Error: 1.150456 Iteration 2 Error: 0.577732 Iteration 3 Error: 0.260027 Iteration 4 Error: 0.131022 Iteration 5 Error: 0.061993 Align patch 7 18 left Iteration 1 Error: 1.984562 Iteration 2 Error: 0.641502 Iteration 3 Error: 0.148462 Iteration 4 Error: 0.040177 Align patch 8 17 left Iteration 1 Error: 1.261148 Iteration 2 Error: 0.325680 Iteration 3 Error: 0.121910 Iteration 4 Error: 0.061360 Iteration 5 Error: 0.025547 Align patch 9 16 left Iteration 1 Error: 1.851394 Iteration 2 Error: 0.184811 Iteration 3 Error: 0.046321 Align patch 10 15 left Iteration 1 Error: 1.002036 Iteration 2 Error: 0.258350 Iteration 3 Error: 0.064425 Iteration 4 Error: 0.022040 Align patch 11 14 left Iteration 1 Error: 2.701072 Iteration 2 Error: 0.878353 Iteration 3 Error: 0.446545 Iteration 4 Error: 0.241987 Iteration 5 Error: 0.115322 Align patch 11 14 left Iteration 1 Error: 2.844837 Iteration 2 Error: 0.585822 Iteration 3 Error: 0.095542 Iteration 4 Error: 0.025899 Align patch 12 13 left Iteration 1 Error: 2.540030 Iteration 2 Error: 0.731884 Iteration 3 Error: 0.188904 Iteration 4 Error: 0.059757 Iteration 5 Error: 0.022964 Align patch 13 12 left Iteration 1 Error: 1.213547 Iteration 2 Error: 0.493149 Iteration 3 Error: 0.252023 Iteration 4 Error: 0.144653 Iteration 5 Error: 0.085245 Align patch 13 12 left Iteration 1 Error: 1.400286 Iteration 2 Error: 0.333893 Iteration 3 Error: 0.061089 Iteration 4 Error: 0.019680 Align patch 14 11 left Iteration 1 Error: 1.094097 Iteration 2 Error: 0.293443 Iteration 3 Error: 0.110012 Iteration 4 Error: 0.039571 Align patch 15 10 left Iteration 1 Error: 0.643472 Iteration 2 Error: 0.082763 Iteration 3 Error: 0.044010 Align patch 16 9 left Iteration 1 Error: 1.403292 Iteration 2 Error: 0.435839 Iteration 3 Error: 0.204285 Iteration 4 Error: 0.094979 Iteration 5 Error: 0.048874 Align patch 17 8 left Iteration 1 Error: 2.111321 Iteration 2 Error: 0.455111 Iteration 3 Error: 0.165687 Iteration 4 Error: 0.057975 Iteration 5 Error: 0.025921 Align patch 18 7 left Iteration 1 Error: 0.975331 Iteration 2 Error: 0.240217 Iteration 3 Error: 0.112385 Iteration 4 Error: 0.039257 Align patch 19 6 left Iteration 1 Error: 0.957852 Iteration 2 Error: 0.162394 Iteration 3 Error: 0.066357 Iteration 4 Error: 0.026115 Align patch 20 5 left Iteration 1 Error: 0.656075 Iteration 2 Error: 0.135681 Iteration 3 Error: 0.057290 Iteration 4 Error: 0.012035 Align patch 21 4 left Iteration 1 Error: 1.170108 Iteration 2 Error: 0.480076 Iteration 3 Error: 0.248715 Iteration 4 Error: 0.113329 Iteration 5 Error: 0.062537 Align patch 21 4 left Iteration 1 Error: 1.899269 Iteration 2 Error: 0.360380 Iteration 3 Error: 0.107162 Iteration 4 Error: 0.035349 Align patch 22 3 left Iteration 1 Error: 1.722960 Iteration 2 Error: 0.406875 Iteration 3 Error: 0.146171 Iteration 4 Error: 0.077748 Iteration 5 Error: 0.030628 Align patch 23 2 left Iteration 1 Error: 1.741167 Iteration 2 Error: 0.329248 Iteration 3 Error: 0.080187 Iteration 4 Error: 0.024248 Align patch 24 1 left Iteration 1 Error: 0.670079 Iteration 2 Error: 0.121307 Iteration 3 Error: 0.036009 Align patch 25 0 left Iteration 1 Error: 1.127300 Iteration 2 Error: 0.264398 Iteration 3 Error: 0.078642 Iteration 4 Error: 0.037384 3D Fitting completed. Patch alignment time: 23.36(sec) Local motion has been corrected. Process thread exits. Computational time: 32.074741 sec Total time: 37.790749 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00005hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00005hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.575284s Reading file: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00005hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.735558s ........................................ >>>>>>TIME<<<<<< FFT: 0.947668s Defocus_U Defocus_V Angle CCC 7781.25 8027.37 2.52 -0.077861 Final Values Defocus_U Defocus_V Angle CCC 7785.94 8013.32 0.96 -0.288522 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00010sq_v01_00006hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00006hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.998e-02 CC threshold: 0.734 Mean Std: 35.52 6.36 Num Hot pixels: 197 Hot pixel threshold: 73.70 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.889032 Iteration 2 Error: 0.213731 Iteration 3 Error: 0.067035 Iteration 4 Error: 0.026537 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.09 0.02 ...... Frame ( 3) shift: -0.17 0.05 ...... Frame ( 4) shift: -0.26 0.07 ...... Frame ( 5) shift: -0.35 0.10 ...... Frame ( 6) shift: -0.35 0.13 ...... Frame ( 7) shift: -0.27 0.18 ...... Frame ( 8) shift: -0.18 0.22 ...... Frame ( 9) shift: -0.12 0.26 ...... Frame ( 10) shift: -0.08 0.30 ...... Frame ( 11) shift: -0.04 0.33 ...... Frame ( 12) shift: 0.02 0.38 ...... Frame ( 13) shift: 0.08 0.43 ...... Frame ( 14) shift: 0.15 0.48 ...... Frame ( 15) shift: 0.18 0.53 ...... Frame ( 16) shift: 0.19 0.59 ...... Frame ( 17) shift: 0.19 0.64 ...... Frame ( 18) shift: 0.23 0.67 ...... Frame ( 19) shift: 0.30 0.67 ...... Frame ( 20) shift: 0.38 0.67 ...... Frame ( 21) shift: 0.46 0.67 ...... Frame ( 22) shift: 0.55 0.66 ...... Frame ( 23) shift: 0.65 0.65 ...... Frame ( 24) shift: 0.74 0.66 ...... Frame ( 25) shift: 0.82 0.71 ...... Frame ( 26) shift: 0.90 0.76 ...... Frame ( 27) shift: 0.96 0.80 ...... Frame ( 28) shift: 0.99 0.84 ...... Frame ( 29) shift: 1.02 0.87 ...... Frame ( 30) shift: 1.04 0.93 ...... Frame ( 31) shift: 1.05 1.00 ...... Frame ( 32) shift: 1.05 1.08 ...... Frame ( 33) shift: 1.11 1.11 ...... Frame ( 34) shift: 1.21 1.11 ...... Frame ( 35) shift: 1.32 1.10 ...... Frame ( 36) shift: 1.37 1.15 ...... Frame ( 37) shift: 1.36 1.25 ...... Frame ( 38) shift: 1.35 1.35 ...... Frame ( 39) shift: 1.34 1.45 ...... Frame ( 40) shift: 1.34 1.55 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.886372 Iteration 2 Error: 0.170247 Iteration 3 Error: 0.086864 Iteration 4 Error: 0.021985 Align patch 2 23 left Iteration 1 Error: 0.570560 Iteration 2 Error: 0.119472 Iteration 3 Error: 0.054711 Iteration 4 Error: 0.026168 Align patch 3 22 left Iteration 1 Error: 0.853553 Iteration 2 Error: 0.362141 Iteration 3 Error: 0.151670 Iteration 4 Error: 0.072341 Iteration 5 Error: 0.044114 Align patch 4 21 left Iteration 1 Error: 0.879246 Iteration 2 Error: 0.171161 Iteration 3 Error: 0.025413 Align patch 5 20 left Iteration 1 Error: 1.028866 Iteration 2 Error: 0.221127 Iteration 3 Error: 0.043327 Align patch 6 19 left Iteration 1 Error: 0.704586 Iteration 2 Error: 0.157899 Iteration 3 Error: 0.058754 Iteration 4 Error: 0.009604 Align patch 7 18 left Iteration 1 Error: 0.712912 Iteration 2 Error: 0.148579 Iteration 3 Error: 0.024401 Align patch 8 17 left Iteration 1 Error: 0.688109 Iteration 2 Error: 0.203938 Iteration 3 Error: 0.048772 Align patch 9 16 left Iteration 1 Error: 0.862679 Iteration 2 Error: 0.252812 Iteration 3 Error: 0.073758 Iteration 4 Error: 0.022429 Align patch 10 15 left Iteration 1 Error: 0.848808 Iteration 2 Error: 0.186428 Iteration 3 Error: 0.067270 Iteration 4 Error: 0.028999 Align patch 11 14 left Iteration 1 Error: 0.901330 Iteration 2 Error: 0.109911 Iteration 3 Error: 0.027006 Align patch 12 13 left Iteration 1 Error: 0.885889 Iteration 2 Error: 0.136043 Iteration 3 Error: 0.047598 Align patch 13 12 left Iteration 1 Error: 0.759014 Iteration 2 Error: 0.195169 Iteration 3 Error: 0.086045 Iteration 4 Error: 0.031183 Align patch 14 11 left Iteration 1 Error: 0.768171 Iteration 2 Error: 0.178854 Iteration 3 Error: 0.050055 Iteration 4 Error: 0.015072 Align patch 15 10 left Iteration 1 Error: 0.700274 Iteration 2 Error: 0.186858 Iteration 3 Error: 0.068937 Iteration 4 Error: 0.025653 Align patch 16 9 left Iteration 1 Error: 0.918387 Iteration 2 Error: 0.221950 Iteration 3 Error: 0.079307 Iteration 4 Error: 0.044595 Align patch 17 8 left Iteration 1 Error: 0.933057 Iteration 2 Error: 0.215596 Iteration 3 Error: 0.042666 Align patch 18 7 left Iteration 1 Error: 0.985903 Iteration 2 Error: 0.309227 Iteration 3 Error: 0.104656 Iteration 4 Error: 0.034504 Align patch 19 6 left Iteration 1 Error: 0.753830 Iteration 2 Error: 0.161519 Iteration 3 Error: 0.031885 Align patch 20 5 left Iteration 1 Error: 0.716901 Iteration 2 Error: 0.091076 Iteration 3 Error: 0.027707 Align patch 21 4 left Iteration 1 Error: 1.004836 Iteration 2 Error: 0.261304 Iteration 3 Error: 0.110690 Iteration 4 Error: 0.039978 Align patch 22 3 left Iteration 1 Error: 0.660897 Iteration 2 Error: 0.159548 Iteration 3 Error: 0.046868 Align patch 23 2 left Iteration 1 Error: 0.916152 Iteration 2 Error: 0.160903 Iteration 3 Error: 0.056896 Iteration 4 Error: 0.015161 Align patch 24 1 left Iteration 1 Error: 0.739340 Iteration 2 Error: 0.131522 Iteration 3 Error: 0.038166 Align patch 25 0 left Iteration 1 Error: 0.903503 Iteration 2 Error: 0.178619 Iteration 3 Error: 0.045614 3D Fitting completed. Patch alignment time: 15.76(sec) Local motion has been corrected. Process thread exits. Computational time: 24.567186 sec Total time: 30.071081 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00006hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00006hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.749697s Reading file: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00006hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.668627s ........................................ >>>>>>TIME<<<<<< FFT: 1.048041s Defocus_U Defocus_V Angle CCC 12521.49 13498.07 14.00 0.022688 Final Values Defocus_U Defocus_V Angle CCC 12540.19 13691.94 13.40 0.030646 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00010sq_v01_00006hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00006hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.998e-02 CC threshold: 0.734 Mean Std: 28.33 5.69 Num Hot pixels: 178 Hot pixel threshold: 62.44 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.580395 Iteration 2 Error: 0.141666 Iteration 3 Error: 0.045749 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.01 -0.05 ...... Frame ( 3) shift: 0.02 -0.10 ...... Frame ( 4) shift: 0.02 -0.15 ...... Frame ( 5) shift: 0.03 -0.20 ...... Frame ( 6) shift: -0.00 -0.20 ...... Frame ( 7) shift: -0.07 -0.15 ...... Frame ( 8) shift: -0.14 -0.09 ...... Frame ( 9) shift: -0.18 -0.06 ...... Frame ( 10) shift: -0.18 -0.06 ...... Frame ( 11) shift: -0.18 -0.06 ...... Frame ( 12) shift: -0.18 -0.07 ...... Frame ( 13) shift: -0.19 -0.09 ...... Frame ( 14) shift: -0.20 -0.10 ...... Frame ( 15) shift: -0.19 -0.07 ...... Frame ( 16) shift: -0.15 -0.01 ...... Frame ( 17) shift: -0.11 0.05 ...... Frame ( 18) shift: -0.04 0.07 ...... Frame ( 19) shift: 0.07 0.03 ...... Frame ( 20) shift: 0.18 -0.01 ...... Frame ( 21) shift: 0.24 0.02 ...... Frame ( 22) shift: 0.26 0.11 ...... Frame ( 23) shift: 0.28 0.20 ...... Frame ( 24) shift: 0.34 0.31 ...... Frame ( 25) shift: 0.43 0.43 ...... Frame ( 26) shift: 0.52 0.55 ...... Frame ( 27) shift: 0.57 0.61 ...... Frame ( 28) shift: 0.58 0.59 ...... Frame ( 29) shift: 0.60 0.57 ...... Frame ( 30) shift: 0.60 0.55 ...... Frame ( 31) shift: 0.60 0.51 ...... Frame ( 32) shift: 0.60 0.47 ...... Frame ( 33) shift: 0.65 0.48 ...... Frame ( 34) shift: 0.73 0.54 ...... Frame ( 35) shift: 0.82 0.60 ...... Frame ( 36) shift: 0.85 0.62 ...... Frame ( 37) shift: 0.84 0.61 ...... Frame ( 38) shift: 0.83 0.60 ...... Frame ( 39) shift: 0.81 0.59 ...... Frame ( 40) shift: 0.80 0.58 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.775754 Iteration 2 Error: 0.124395 Iteration 3 Error: 0.027945 Align patch 2 23 left Iteration 1 Error: 0.886268 Iteration 2 Error: 0.140289 Iteration 3 Error: 0.038009 Align patch 3 22 left Iteration 1 Error: 0.889522 Iteration 2 Error: 0.200553 Iteration 3 Error: 0.046092 Align patch 4 21 left Iteration 1 Error: 0.790862 Iteration 2 Error: 0.304751 Iteration 3 Error: 0.116695 Iteration 4 Error: 0.054814 Iteration 5 Error: 0.021437 Align patch 5 20 left Iteration 1 Error: 0.939013 Iteration 2 Error: 0.184685 Iteration 3 Error: 0.050221 Iteration 4 Error: 0.022478 Align patch 6 19 left Iteration 1 Error: 1.337231 Iteration 2 Error: 0.204626 Iteration 3 Error: 0.074743 Iteration 4 Error: 0.041053 Align patch 7 18 left Iteration 1 Error: 1.768785 Iteration 2 Error: 0.353845 Iteration 3 Error: 0.131407 Iteration 4 Error: 0.042047 Align patch 8 17 left Iteration 1 Error: 1.399982 Iteration 2 Error: 0.169015 Iteration 3 Error: 0.040963 Align patch 9 16 left Iteration 1 Error: 0.984261 Iteration 2 Error: 0.174676 Iteration 3 Error: 0.112752 Iteration 4 Error: 0.027832 Align patch 10 15 left Iteration 1 Error: 0.889698 Iteration 2 Error: 0.384881 Iteration 3 Error: 0.150952 Iteration 4 Error: 0.114369 Iteration 5 Error: 0.041897 Align patch 11 14 left Iteration 1 Error: 1.294748 Iteration 2 Error: 0.385855 Iteration 3 Error: 0.070975 Iteration 4 Error: 0.043129 Align patch 12 13 left Iteration 1 Error: 0.984563 Iteration 2 Error: 0.252443 Iteration 3 Error: 0.071434 Iteration 4 Error: 0.022650 Align patch 13 12 left Iteration 1 Error: 1.141768 Iteration 2 Error: 0.227310 Iteration 3 Error: 0.077925 Iteration 4 Error: 0.028453 Align patch 14 11 left Iteration 1 Error: 0.911239 Iteration 2 Error: 0.218600 Iteration 3 Error: 0.076308 Iteration 4 Error: 0.031898 Align patch 15 10 left Iteration 1 Error: 1.192220 Iteration 2 Error: 0.136045 Iteration 3 Error: 0.048384 Align patch 16 9 left Iteration 1 Error: 1.246859 Iteration 2 Error: 0.397993 Iteration 3 Error: 0.075170 Iteration 4 Error: 0.039650 Align patch 17 8 left Iteration 1 Error: 1.404232 Iteration 2 Error: 0.447533 Iteration 3 Error: 0.074365 Iteration 4 Error: 0.052065 Iteration 5 Error: 0.016178 Align patch 18 7 left Iteration 1 Error: 1.110264 Iteration 2 Error: 0.246862 Iteration 3 Error: 0.069536 Iteration 4 Error: 0.018817 Align patch 19 6 left Iteration 1 Error: 0.759876 Iteration 2 Error: 0.285663 Iteration 3 Error: 0.051683 Iteration 4 Error: 0.023986 Align patch 20 5 left Iteration 1 Error: 1.245546 Iteration 2 Error: 0.254500 Iteration 3 Error: 0.089817 Iteration 4 Error: 0.020577 Align patch 21 4 left Iteration 1 Error: 1.297007 Iteration 2 Error: 0.165234 Iteration 3 Error: 0.030191 Align patch 22 3 left Iteration 1 Error: 1.294961 Iteration 2 Error: 0.134969 Iteration 3 Error: 0.024880 Align patch 23 2 left Iteration 1 Error: 1.066422 Iteration 2 Error: 0.222478 Iteration 3 Error: 0.080133 Iteration 4 Error: 0.057482 Iteration 5 Error: 0.018446 Align patch 24 1 left Iteration 1 Error: 1.335367 Iteration 2 Error: 0.179996 Iteration 3 Error: 0.054182 Iteration 4 Error: 0.009814 Align patch 25 0 left Iteration 1 Error: 1.863429 Iteration 2 Error: 0.222753 Iteration 3 Error: 0.093009 Iteration 4 Error: 0.024539 3D Fitting completed. Patch alignment time: 17.15(sec) Local motion has been corrected. Process thread exits. Computational time: 25.369764 sec Total time: 31.035061 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00006hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00006hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.716255s Reading file: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00006hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.271924s ........................................ >>>>>>TIME<<<<<< FFT: 1.040763s Defocus_U Defocus_V Angle CCC 9867.15 9324.34 31.01 0.004327 Final Values Defocus_U Defocus_V Angle CCC 9948.38 9277.51 26.72 0.003858 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00010sq_v01_00006hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00006hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.995e-02 CC threshold: 0.734 Mean Std: 39.95 6.74 Num Hot pixels: 200 Hot pixel threshold: 80.40 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 4.291517 Iteration 2 Error: 1.945719 Iteration 3 Error: 1.273995 Iteration 4 Error: 0.702178 Iteration 5 Error: 0.420558 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.09 -0.14 ...... Frame ( 3) shift: 0.19 -0.28 ...... Frame ( 4) shift: 0.28 -0.43 ...... Frame ( 5) shift: 0.38 -0.57 ...... Frame ( 6) shift: 0.55 -0.75 ...... Frame ( 7) shift: 0.80 -0.98 ...... Frame ( 8) shift: 1.04 -1.20 ...... Frame ( 9) shift: 1.33 -1.33 ...... Frame ( 10) shift: 1.65 -1.35 ...... Frame ( 11) shift: 1.97 -1.37 ...... Frame ( 12) shift: 2.34 -1.42 ...... Frame ( 13) shift: 2.74 -1.50 ...... Frame ( 14) shift: 3.15 -1.58 ...... Frame ( 15) shift: 3.54 -1.66 ...... Frame ( 16) shift: 3.92 -1.75 ...... Frame ( 17) shift: 4.30 -1.83 ...... Frame ( 18) shift: 4.65 -1.97 ...... Frame ( 19) shift: 4.97 -2.17 ...... Frame ( 20) shift: 5.29 -2.37 ...... Frame ( 21) shift: 5.66 -2.50 ...... Frame ( 22) shift: 6.07 -2.56 ...... Frame ( 23) shift: 6.48 -2.63 ...... Frame ( 24) shift: 6.85 -2.67 ...... Frame ( 25) shift: 7.18 -2.70 ...... Frame ( 26) shift: 7.51 -2.73 ...... Frame ( 27) shift: 7.85 -2.84 ...... Frame ( 28) shift: 8.20 -3.02 ...... Frame ( 29) shift: 8.55 -3.21 ...... Frame ( 30) shift: 8.90 -3.35 ...... Frame ( 31) shift: 9.26 -3.44 ...... Frame ( 32) shift: 9.62 -3.54 ...... Frame ( 33) shift: 9.97 -3.65 ...... Frame ( 34) shift: 10.30 -3.77 ...... Frame ( 35) shift: 10.63 -3.90 ...... Frame ( 36) shift: 11.01 -4.04 ...... Frame ( 37) shift: 11.42 -4.19 ...... Frame ( 38) shift: 11.84 -4.34 ...... Frame ( 39) shift: 12.26 -4.49 ...... Frame ( 40) shift: 12.67 -4.65 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 4.690518 Iteration 2 Error: 2.453044 Iteration 3 Error: 0.723632 Iteration 4 Error: 0.409712 Iteration 5 Error: 0.176107 Align patch 1 24 left Iteration 1 Error: 4.200128 Iteration 2 Error: 1.600447 Iteration 3 Error: 0.489958 Iteration 4 Error: 0.237085 Iteration 5 Error: 0.107971 Align patch 2 23 left Iteration 1 Error: 1.802711 Iteration 2 Error: 1.457789 Iteration 3 Error: 0.559181 Iteration 4 Error: 0.431202 Iteration 5 Error: 0.264777 Align patch 2 23 left Iteration 1 Error: 1.980571 Iteration 2 Error: 0.690730 Iteration 3 Error: 0.352309 Iteration 4 Error: 0.167484 Iteration 5 Error: 0.083940 Align patch 3 22 left Iteration 1 Error: 0.955586 Iteration 2 Error: 0.333474 Iteration 3 Error: 0.164615 Iteration 4 Error: 0.110260 Iteration 5 Error: 0.073100 Align patch 3 22 left Iteration 1 Error: 1.094929 Iteration 2 Error: 0.189788 Iteration 3 Error: 0.067934 Iteration 4 Error: 0.021466 Align patch 4 21 left Iteration 1 Error: 1.985573 Iteration 2 Error: 0.464085 Iteration 3 Error: 0.213405 Iteration 4 Error: 0.078949 Iteration 5 Error: 0.034693 Align patch 5 20 left Iteration 1 Error: 3.225589 Iteration 2 Error: 0.783402 Iteration 3 Error: 0.313330 Iteration 4 Error: 0.143202 Iteration 5 Error: 0.081871 Align patch 5 20 left Iteration 1 Error: 2.415184 Iteration 2 Error: 0.362678 Iteration 3 Error: 0.082575 Iteration 4 Error: 0.027418 Align patch 6 19 left Iteration 1 Error: 6.263117 Iteration 2 Error: 2.285080 Iteration 3 Error: 1.094491 Iteration 4 Error: 0.420752 Iteration 5 Error: 0.164150 Align patch 6 19 left Iteration 1 Error: 5.541655 Iteration 2 Error: 1.723869 Iteration 3 Error: 0.457893 Iteration 4 Error: 0.158807 Iteration 5 Error: 0.074677 Align patch 7 18 left Iteration 1 Error: 5.005596 Iteration 2 Error: 1.969427 Iteration 3 Error: 0.482347 Iteration 4 Error: 0.213413 Iteration 5 Error: 0.071366 Align patch 7 18 left Iteration 1 Error: 3.584862 Iteration 2 Error: 1.244271 Iteration 3 Error: 0.391339 Iteration 4 Error: 0.180798 Iteration 5 Error: 0.071682 Align patch 8 17 left Iteration 1 Error: 0.752872 Iteration 2 Error: 0.378538 Iteration 3 Error: 0.128925 Iteration 4 Error: 0.088303 Iteration 5 Error: 0.039191 Align patch 9 16 left Iteration 1 Error: 1.049218 Iteration 2 Error: 0.302117 Iteration 3 Error: 0.085226 Iteration 4 Error: 0.039494 Align patch 10 15 left Iteration 1 Error: 2.846038 Iteration 2 Error: 0.717974 Iteration 3 Error: 0.258950 Iteration 4 Error: 0.136659 Iteration 5 Error: 0.050169 Align patch 10 15 left Iteration 1 Error: 2.586363 Iteration 2 Error: 0.446457 Iteration 3 Error: 0.077865 Iteration 4 Error: 0.025134 Align patch 11 14 left Iteration 1 Error: 5.432076 Iteration 2 Error: 2.938673 Iteration 3 Error: 1.216117 Iteration 4 Error: 0.507292 Iteration 5 Error: 0.230929 Align patch 11 14 left Iteration 1 Error: 5.500383 Iteration 2 Error: 1.599082 Iteration 3 Error: 0.587838 Iteration 4 Error: 0.244577 Iteration 5 Error: 0.116031 Align patch 12 13 left Iteration 1 Error: 5.389093 Iteration 2 Error: 2.232281 Iteration 3 Error: 0.742713 Iteration 4 Error: 0.278234 Iteration 5 Error: 0.149709 Align patch 12 13 left Iteration 1 Error: 4.203571 Iteration 2 Error: 1.184132 Iteration 3 Error: 0.494225 Iteration 4 Error: 0.209801 Iteration 5 Error: 0.092993 Align patch 13 12 left Iteration 1 Error: 1.751713 Iteration 2 Error: 0.543774 Iteration 3 Error: 0.117775 Iteration 4 Error: 0.061204 Iteration 5 Error: 0.016478 Align patch 14 11 left Iteration 1 Error: 1.282600 Iteration 2 Error: 0.372926 Iteration 3 Error: 0.124208 Iteration 4 Error: 0.061176 Iteration 5 Error: 0.022786 Align patch 15 10 left Iteration 1 Error: 2.845009 Iteration 2 Error: 0.623454 Iteration 3 Error: 0.327336 Iteration 4 Error: 0.137503 Iteration 5 Error: 0.071646 Align patch 15 10 left Iteration 1 Error: 2.369600 Iteration 2 Error: 0.488850 Iteration 3 Error: 0.113696 Iteration 4 Error: 0.030921 Align patch 16 9 left Iteration 1 Error: 5.340866 Iteration 2 Error: 2.400826 Iteration 3 Error: 1.057248 Iteration 4 Error: 0.467940 Iteration 5 Error: 0.176894 Align patch 16 9 left Iteration 1 Error: 5.756334 Iteration 2 Error: 1.426714 Iteration 3 Error: 0.567017 Iteration 4 Error: 0.224541 Iteration 5 Error: 0.094104 Align patch 17 8 left Iteration 1 Error: 3.808771 Iteration 2 Error: 1.122514 Iteration 3 Error: 0.504528 Iteration 4 Error: 0.245030 Iteration 5 Error: 0.131118 Align patch 17 8 left Iteration 1 Error: 3.993473 Iteration 2 Error: 1.388164 Iteration 3 Error: 0.425360 Iteration 4 Error: 0.201614 Iteration 5 Error: 0.097153 Align patch 18 7 left Iteration 1 Error: 1.222109 Iteration 2 Error: 0.259346 Iteration 3 Error: 0.080930 Iteration 4 Error: 0.043837 Align patch 19 6 left Iteration 1 Error: 1.451376 Iteration 2 Error: 0.338350 Iteration 3 Error: 0.134906 Iteration 4 Error: 0.071742 Iteration 5 Error: 0.038364 Align patch 20 5 left Iteration 1 Error: 3.303052 Iteration 2 Error: 2.290139 Iteration 3 Error: 0.694740 Iteration 4 Error: 0.301136 Iteration 5 Error: 0.099774 Align patch 20 5 left Iteration 1 Error: 2.047710 Iteration 2 Error: 0.422051 Iteration 3 Error: 0.126623 Iteration 4 Error: 0.037029 Align patch 21 4 left Iteration 1 Error: 4.127187 Iteration 2 Error: 1.816489 Iteration 3 Error: 1.298070 Iteration 4 Error: 0.628647 Iteration 5 Error: 0.327545 Align patch 21 4 left Iteration 1 Error: 5.030408 Iteration 2 Error: 1.470274 Iteration 3 Error: 0.618614 Iteration 4 Error: 0.248249 Iteration 5 Error: 0.128120 Align patch 22 3 left Iteration 1 Error: 5.538034 Iteration 2 Error: 1.391225 Iteration 3 Error: 0.504436 Iteration 4 Error: 0.215526 Iteration 5 Error: 0.119684 Align patch 22 3 left Iteration 1 Error: 3.857299 Iteration 2 Error: 1.157883 Iteration 3 Error: 0.409651 Iteration 4 Error: 0.164301 Iteration 5 Error: 0.074724 Align patch 23 2 left Iteration 1 Error: 0.969130 Iteration 2 Error: 0.416260 Iteration 3 Error: 0.234582 Iteration 4 Error: 0.108448 Iteration 5 Error: 0.064606 Align patch 23 2 left Iteration 1 Error: 1.521131 Iteration 2 Error: 0.268060 Iteration 3 Error: 0.076717 Iteration 4 Error: 0.025257 Align patch 24 1 left Iteration 1 Error: 1.201687 Iteration 2 Error: 0.475261 Iteration 3 Error: 0.159551 Iteration 4 Error: 0.079447 Iteration 5 Error: 0.038684 Align patch 25 0 left Iteration 1 Error: 4.103193 Iteration 2 Error: 1.683919 Iteration 3 Error: 0.524257 Iteration 4 Error: 0.227771 Iteration 5 Error: 0.082439 Align patch 25 0 left Iteration 1 Error: 2.464135 Iteration 2 Error: 0.534100 Iteration 3 Error: 0.146663 Iteration 4 Error: 0.041922 3D Fitting completed. Patch alignment time: 34.93(sec) Local motion has been corrected. Process thread exits. Computational time: 44.353024 sec Total time: 50.877316 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00006hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00006hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.833810s Reading file: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00006hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.805869s ........................................ >>>>>>TIME<<<<<< FFT: 1.043342s Defocus_U Defocus_V Angle CCC 12705.11 13669.95 5.20 0.059831 Final Values Defocus_U Defocus_V Angle CCC 12722.31 13677.78 4.58 0.106397 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00010sq_v01_00006hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00006hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.734 Mean Std: 39.51 6.68 Num Hot pixels: 229 Hot pixel threshold: 79.58 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.707401 Iteration 2 Error: 0.151331 Iteration 3 Error: 0.050039 Iteration 4 Error: 0.013834 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.01 0.04 ...... Frame ( 3) shift: 0.03 0.07 ...... Frame ( 4) shift: 0.04 0.11 ...... Frame ( 5) shift: 0.05 0.15 ...... Frame ( 6) shift: 0.11 0.18 ...... Frame ( 7) shift: 0.20 0.20 ...... Frame ( 8) shift: 0.29 0.22 ...... Frame ( 9) shift: 0.37 0.24 ...... Frame ( 10) shift: 0.44 0.25 ...... Frame ( 11) shift: 0.51 0.27 ...... Frame ( 12) shift: 0.54 0.26 ...... Frame ( 13) shift: 0.51 0.23 ...... Frame ( 14) shift: 0.49 0.19 ...... Frame ( 15) shift: 0.52 0.21 ...... Frame ( 16) shift: 0.61 0.29 ...... Frame ( 17) shift: 0.70 0.37 ...... Frame ( 18) shift: 0.76 0.38 ...... Frame ( 19) shift: 0.81 0.31 ...... Frame ( 20) shift: 0.86 0.25 ...... Frame ( 21) shift: 0.90 0.29 ...... Frame ( 22) shift: 0.93 0.42 ...... Frame ( 23) shift: 0.96 0.56 ...... Frame ( 24) shift: 1.00 0.63 ...... Frame ( 25) shift: 1.04 0.62 ...... Frame ( 26) shift: 1.08 0.61 ...... Frame ( 27) shift: 1.12 0.59 ...... Frame ( 28) shift: 1.16 0.57 ...... Frame ( 29) shift: 1.21 0.55 ...... Frame ( 30) shift: 1.25 0.57 ...... Frame ( 31) shift: 1.30 0.63 ...... Frame ( 32) shift: 1.36 0.69 ...... Frame ( 33) shift: 1.40 0.74 ...... Frame ( 34) shift: 1.44 0.77 ...... Frame ( 35) shift: 1.48 0.80 ...... Frame ( 36) shift: 1.51 0.84 ...... Frame ( 37) shift: 1.52 0.87 ...... Frame ( 38) shift: 1.53 0.91 ...... Frame ( 39) shift: 1.55 0.94 ...... Frame ( 40) shift: 1.56 0.98 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.862041 Iteration 2 Error: 0.194567 Iteration 3 Error: 0.070732 Iteration 4 Error: 0.029862 Align patch 2 23 left Iteration 1 Error: 0.649876 Iteration 2 Error: 0.132339 Iteration 3 Error: 0.033805 Align patch 3 22 left Iteration 1 Error: 0.861051 Iteration 2 Error: 0.191877 Iteration 3 Error: 0.062079 Iteration 4 Error: 0.025325 Align patch 4 21 left Iteration 1 Error: 0.800471 Iteration 2 Error: 0.259172 Iteration 3 Error: 0.066605 Iteration 4 Error: 0.027841 Align patch 5 20 left Iteration 1 Error: 0.790228 Iteration 2 Error: 0.150730 Iteration 3 Error: 0.032149 Align patch 6 19 left Iteration 1 Error: 0.992620 Iteration 2 Error: 0.159655 Iteration 3 Error: 0.027955 Align patch 7 18 left Iteration 1 Error: 0.596101 Iteration 2 Error: 0.137109 Iteration 3 Error: 0.042487 Align patch 8 17 left Iteration 1 Error: 1.010452 Iteration 2 Error: 0.141338 Iteration 3 Error: 0.062678 Iteration 4 Error: 0.022181 Align patch 9 16 left Iteration 1 Error: 0.739119 Iteration 2 Error: 0.140189 Iteration 3 Error: 0.040384 Align patch 10 15 left Iteration 1 Error: 0.762988 Iteration 2 Error: 0.146887 Iteration 3 Error: 0.034251 Align patch 11 14 left Iteration 1 Error: 0.760954 Iteration 2 Error: 0.143061 Iteration 3 Error: 0.034106 Align patch 12 13 left Iteration 1 Error: 0.879633 Iteration 2 Error: 0.130072 Iteration 3 Error: 0.028160 Align patch 13 12 left Iteration 1 Error: 1.082893 Iteration 2 Error: 0.157297 Iteration 3 Error: 0.049099 Align patch 14 11 left Iteration 1 Error: 0.875469 Iteration 2 Error: 0.195777 Iteration 3 Error: 0.049965 Align patch 15 10 left Iteration 1 Error: 1.030779 Iteration 2 Error: 0.325965 Iteration 3 Error: 0.099169 Iteration 4 Error: 0.036727 Align patch 16 9 left Iteration 1 Error: 0.871975 Iteration 2 Error: 0.257839 Iteration 3 Error: 0.047449 Align patch 17 8 left Iteration 1 Error: 0.729391 Iteration 2 Error: 0.094871 Iteration 3 Error: 0.033279 Align patch 18 7 left Iteration 1 Error: 0.700297 Iteration 2 Error: 0.150052 Iteration 3 Error: 0.049934 Align patch 19 6 left Iteration 1 Error: 0.885718 Iteration 2 Error: 0.123388 Iteration 3 Error: 0.042844 Align patch 20 5 left Iteration 1 Error: 0.975323 Iteration 2 Error: 0.129898 Iteration 3 Error: 0.034127 Align patch 21 4 left Iteration 1 Error: 0.685023 Iteration 2 Error: 0.147299 Iteration 3 Error: 0.041245 Align patch 22 3 left Iteration 1 Error: 0.691092 Iteration 2 Error: 0.130336 Iteration 3 Error: 0.029169 Align patch 23 2 left Iteration 1 Error: 1.015739 Iteration 2 Error: 0.199271 Iteration 3 Error: 0.051108 Iteration 4 Error: 0.022011 Align patch 24 1 left Iteration 1 Error: 0.988305 Iteration 2 Error: 0.161379 Iteration 3 Error: 0.040449 Align patch 25 0 left Iteration 1 Error: 0.518923 Iteration 2 Error: 0.104463 Iteration 3 Error: 0.055398 Iteration 4 Error: 0.013460 3D Fitting completed. Patch alignment time: 16.13(sec) Local motion has been corrected. Process thread exits. Computational time: 25.229923 sec Total time: 32.625336 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00006hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00006hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.836465s Reading file: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00006hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.807404s ........................................ >>>>>>TIME<<<<<< FFT: 1.056715s Defocus_U Defocus_V Angle CCC 13027.73 12398.15 84.52 0.036379 Final Values Defocus_U Defocus_V Angle CCC 13063.68 12402.85 85.46 0.059249 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00010sq_v01_00007hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00007hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 38.73 6.76 Num Hot pixels: 195 Hot pixel threshold: 79.27 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.847326 Iteration 2 Error: 0.329295 Iteration 3 Error: 0.083485 Iteration 4 Error: 0.022600 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.16 0.11 ...... Frame ( 3) shift: -0.32 0.22 ...... Frame ( 4) shift: -0.48 0.33 ...... Frame ( 5) shift: -0.64 0.44 ...... Frame ( 6) shift: -0.73 0.52 ...... Frame ( 7) shift: -0.74 0.57 ...... Frame ( 8) shift: -0.74 0.61 ...... Frame ( 9) shift: -0.73 0.64 ...... Frame ( 10) shift: -0.68 0.65 ...... Frame ( 11) shift: -0.64 0.67 ...... Frame ( 12) shift: -0.60 0.71 ...... Frame ( 13) shift: -0.55 0.78 ...... Frame ( 14) shift: -0.50 0.85 ...... Frame ( 15) shift: -0.44 0.94 ...... Frame ( 16) shift: -0.38 1.05 ...... Frame ( 17) shift: -0.31 1.15 ...... Frame ( 18) shift: -0.29 1.25 ...... Frame ( 19) shift: -0.32 1.35 ...... Frame ( 20) shift: -0.36 1.44 ...... Frame ( 21) shift: -0.33 1.56 ...... Frame ( 22) shift: -0.25 1.71 ...... Frame ( 23) shift: -0.16 1.86 ...... Frame ( 24) shift: -0.11 2.00 ...... Frame ( 25) shift: -0.08 2.14 ...... Frame ( 26) shift: -0.06 2.27 ...... Frame ( 27) shift: -0.02 2.37 ...... Frame ( 28) shift: 0.03 2.43 ...... Frame ( 29) shift: 0.08 2.50 ...... Frame ( 30) shift: 0.14 2.58 ...... Frame ( 31) shift: 0.21 2.69 ...... Frame ( 32) shift: 0.28 2.80 ...... Frame ( 33) shift: 0.28 2.90 ...... Frame ( 34) shift: 0.23 2.99 ...... Frame ( 35) shift: 0.17 3.08 ...... Frame ( 36) shift: 0.18 3.19 ...... Frame ( 37) shift: 0.25 3.34 ...... Frame ( 38) shift: 0.32 3.48 ...... Frame ( 39) shift: 0.39 3.62 ...... Frame ( 40) shift: 0.46 3.76 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.511216 Iteration 2 Error: 0.195987 Iteration 3 Error: 0.063836 Iteration 4 Error: 0.025670 Align patch 2 23 left Iteration 1 Error: 0.586379 Iteration 2 Error: 0.088605 Iteration 3 Error: 0.021695 Align patch 3 22 left Iteration 1 Error: 0.802525 Iteration 2 Error: 0.092958 Iteration 3 Error: 0.025144 Align patch 4 21 left Iteration 1 Error: 0.687878 Iteration 2 Error: 0.121587 Iteration 3 Error: 0.029319 Align patch 5 20 left Iteration 1 Error: 0.676754 Iteration 2 Error: 0.090697 Iteration 3 Error: 0.026755 Align patch 6 19 left Iteration 1 Error: 0.485329 Iteration 2 Error: 0.135780 Iteration 3 Error: 0.042767 Align patch 7 18 left Iteration 1 Error: 0.554863 Iteration 2 Error: 0.053244 Iteration 3 Error: 0.010254 Align patch 8 17 left Iteration 1 Error: 0.607696 Iteration 2 Error: 0.091171 Iteration 3 Error: 0.028142 Align patch 9 16 left Iteration 1 Error: 0.535000 Iteration 2 Error: 0.154948 Iteration 3 Error: 0.039504 Align patch 10 15 left Iteration 1 Error: 0.658503 Iteration 2 Error: 0.069439 Iteration 3 Error: 0.018115 Align patch 11 14 left Iteration 1 Error: 0.565368 Iteration 2 Error: 0.124635 Iteration 3 Error: 0.018315 Align patch 12 13 left Iteration 1 Error: 0.699445 Iteration 2 Error: 0.173890 Iteration 3 Error: 0.053290 Iteration 4 Error: 0.018265 Align patch 13 12 left Iteration 1 Error: 0.570633 Iteration 2 Error: 0.089818 Iteration 3 Error: 0.019526 Align patch 14 11 left Iteration 1 Error: 0.529810 Iteration 2 Error: 0.074407 Iteration 3 Error: 0.012347 Align patch 15 10 left Iteration 1 Error: 0.550588 Iteration 2 Error: 0.083870 Iteration 3 Error: 0.024476 Align patch 16 9 left Iteration 1 Error: 0.710989 Iteration 2 Error: 0.074658 Iteration 3 Error: 0.012060 Align patch 17 8 left Iteration 1 Error: 0.606530 Iteration 2 Error: 0.106798 Iteration 3 Error: 0.024353 Align patch 18 7 left Iteration 1 Error: 0.374761 Iteration 2 Error: 0.053978 Iteration 3 Error: 0.016948 Align patch 19 6 left Iteration 1 Error: 0.515559 Iteration 2 Error: 0.065441 Iteration 3 Error: 0.013973 Align patch 20 5 left Iteration 1 Error: 0.807245 Iteration 2 Error: 0.174493 Iteration 3 Error: 0.037062 Align patch 21 4 left Iteration 1 Error: 1.293645 Iteration 2 Error: 0.193042 Iteration 3 Error: 0.064693 Iteration 4 Error: 0.016935 Align patch 22 3 left Iteration 1 Error: 0.853932 Iteration 2 Error: 0.125795 Iteration 3 Error: 0.031296 Align patch 23 2 left Iteration 1 Error: 0.459967 Iteration 2 Error: 0.068889 Iteration 3 Error: 0.016549 Align patch 24 1 left Iteration 1 Error: 0.543102 Iteration 2 Error: 0.074526 Iteration 3 Error: 0.011156 Align patch 25 0 left Iteration 1 Error: 0.723949 Iteration 2 Error: 0.117938 Iteration 3 Error: 0.027532 3D Fitting completed. Patch alignment time: 15.34(sec) Local motion has been corrected. Process thread exits. Computational time: 24.132195 sec Total time: 29.884674 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00007hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00007hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.551268s Reading file: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00007hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.373533s ........................................ >>>>>>TIME<<<<<< FFT: 0.935532s Defocus_U Defocus_V Angle CCC 10353.52 11193.38 12.41 0.052740 Final Values Defocus_U Defocus_V Angle CCC 10356.65 11215.26 11.16 0.086777 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00010sq_v01_00007hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00007hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.002e-01 CC threshold: 0.736 Mean Std: 39.15 6.86 Num Hot pixels: 213 Hot pixel threshold: 80.31 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.841817 Iteration 2 Error: 0.155780 Iteration 3 Error: 0.032838 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.10 -0.08 ...... Frame ( 3) shift: -0.20 -0.16 ...... Frame ( 4) shift: -0.30 -0.25 ...... Frame ( 5) shift: -0.41 -0.33 ...... Frame ( 6) shift: -0.49 -0.35 ...... Frame ( 7) shift: -0.56 -0.31 ...... Frame ( 8) shift: -0.63 -0.27 ...... Frame ( 9) shift: -0.65 -0.24 ...... Frame ( 10) shift: -0.61 -0.21 ...... Frame ( 11) shift: -0.58 -0.17 ...... Frame ( 12) shift: -0.54 -0.14 ...... Frame ( 13) shift: -0.51 -0.11 ...... Frame ( 14) shift: -0.48 -0.09 ...... Frame ( 15) shift: -0.43 -0.04 ...... Frame ( 16) shift: -0.34 0.03 ...... Frame ( 17) shift: -0.26 0.11 ...... Frame ( 18) shift: -0.21 0.17 ...... Frame ( 19) shift: -0.18 0.23 ...... Frame ( 20) shift: -0.15 0.29 ...... Frame ( 21) shift: -0.12 0.33 ...... Frame ( 22) shift: -0.07 0.37 ...... Frame ( 23) shift: -0.03 0.41 ...... Frame ( 24) shift: 0.03 0.42 ...... Frame ( 25) shift: 0.10 0.41 ...... Frame ( 26) shift: 0.16 0.40 ...... Frame ( 27) shift: 0.24 0.46 ...... Frame ( 28) shift: 0.31 0.57 ...... Frame ( 29) shift: 0.39 0.68 ...... Frame ( 30) shift: 0.43 0.75 ...... Frame ( 31) shift: 0.45 0.79 ...... Frame ( 32) shift: 0.47 0.82 ...... Frame ( 33) shift: 0.47 0.88 ...... Frame ( 34) shift: 0.47 0.95 ...... Frame ( 35) shift: 0.47 1.03 ...... Frame ( 36) shift: 0.48 1.06 ...... Frame ( 37) shift: 0.51 1.06 ...... Frame ( 38) shift: 0.55 1.05 ...... Frame ( 39) shift: 0.58 1.04 ...... Frame ( 40) shift: 0.62 1.04 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.655485 Iteration 2 Error: 0.111951 Iteration 3 Error: 0.023025 Align patch 2 23 left Iteration 1 Error: 0.577989 Iteration 2 Error: 0.087925 Iteration 3 Error: 0.027299 Align patch 3 22 left Iteration 1 Error: 0.684905 Iteration 2 Error: 0.068667 Iteration 3 Error: 0.016052 Align patch 4 21 left Iteration 1 Error: 0.499711 Iteration 2 Error: 0.078827 Iteration 3 Error: 0.014472 Align patch 5 20 left Iteration 1 Error: 0.389273 Iteration 2 Error: 0.078245 Iteration 3 Error: 0.010919 Align patch 6 19 left Iteration 1 Error: 0.487759 Iteration 2 Error: 0.094273 Iteration 3 Error: 0.015117 Align patch 7 18 left Iteration 1 Error: 0.704859 Iteration 2 Error: 0.106444 Iteration 3 Error: 0.022138 Align patch 8 17 left Iteration 1 Error: 0.492028 Iteration 2 Error: 0.072487 Iteration 3 Error: 0.017844 Align patch 9 16 left Iteration 1 Error: 0.549085 Iteration 2 Error: 0.114232 Iteration 3 Error: 0.017700 Align patch 10 15 left Iteration 1 Error: 0.591708 Iteration 2 Error: 0.082240 Iteration 3 Error: 0.017473 Align patch 11 14 left Iteration 1 Error: 1.009244 Iteration 2 Error: 0.100639 Iteration 3 Error: 0.028657 Align patch 12 13 left Iteration 1 Error: 0.340870 Iteration 2 Error: 0.040248 Align patch 13 12 left Iteration 1 Error: 0.402924 Iteration 2 Error: 0.059109 Iteration 3 Error: 0.016618 Align patch 14 11 left Iteration 1 Error: 0.606962 Iteration 2 Error: 0.110674 Iteration 3 Error: 0.023285 Align patch 15 10 left Iteration 1 Error: 0.849135 Iteration 2 Error: 0.118211 Iteration 3 Error: 0.025245 Align patch 16 9 left Iteration 1 Error: 1.577354 Iteration 2 Error: 0.132974 Iteration 3 Error: 0.039372 Align patch 17 8 left Iteration 1 Error: 0.893641 Iteration 2 Error: 0.104996 Iteration 3 Error: 0.021240 Align patch 18 7 left Iteration 1 Error: 0.901127 Iteration 2 Error: 0.195058 Iteration 3 Error: 0.037579 Align patch 19 6 left Iteration 1 Error: 0.456105 Iteration 2 Error: 0.067737 Iteration 3 Error: 0.008145 Align patch 20 5 left Iteration 1 Error: 0.880835 Iteration 2 Error: 0.066577 Iteration 3 Error: 0.011651 Align patch 21 4 left Iteration 1 Error: 1.057721 Iteration 2 Error: 0.126323 Iteration 3 Error: 0.033953 Align patch 22 3 left Iteration 1 Error: 0.665323 Iteration 2 Error: 0.079555 Iteration 3 Error: 0.018733 Align patch 23 2 left Iteration 1 Error: 0.709158 Iteration 2 Error: 0.096978 Iteration 3 Error: 0.018811 Align patch 24 1 left Iteration 1 Error: 0.476892 Iteration 2 Error: 0.050746 Iteration 3 Error: 0.007600 Align patch 25 0 left Iteration 1 Error: 0.549296 Iteration 2 Error: 0.074988 Iteration 3 Error: 0.015208 3D Fitting completed. Patch alignment time: 15.48(sec) Local motion has been corrected. Process thread exits. Computational time: 24.040817 sec Total time: 29.913219 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00007hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00007hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.736171s Reading file: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00007hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.074474s ........................................ >>>>>>TIME<<<<<< FFT: 0.948304s Defocus_U Defocus_V Angle CCC 13650.40 14044.93 1.32 0.051539 Final Values Defocus_U Defocus_V Angle CCC 13650.40 14044.93 2.58 0.079624 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00010sq_v01_00007hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00007hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.003e-01 CC threshold: 0.736 Mean Std: 41.98 7.02 Num Hot pixels: 225 Hot pixel threshold: 84.10 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.276115 Iteration 2 Error: 0.212745 Iteration 3 Error: 0.048964 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.02 0.13 ...... Frame ( 3) shift: 0.05 0.27 ...... Frame ( 4) shift: 0.07 0.40 ...... Frame ( 5) shift: 0.09 0.54 ...... Frame ( 6) shift: 0.11 0.62 ...... Frame ( 7) shift: 0.14 0.64 ...... Frame ( 8) shift: 0.16 0.67 ...... Frame ( 9) shift: 0.23 0.72 ...... Frame ( 10) shift: 0.35 0.79 ...... Frame ( 11) shift: 0.47 0.87 ...... Frame ( 12) shift: 0.53 0.94 ...... Frame ( 13) shift: 0.53 1.00 ...... Frame ( 14) shift: 0.53 1.06 ...... Frame ( 15) shift: 0.53 1.15 ...... Frame ( 16) shift: 0.52 1.27 ...... Frame ( 17) shift: 0.50 1.39 ...... Frame ( 18) shift: 0.51 1.47 ...... Frame ( 19) shift: 0.55 1.52 ...... Frame ( 20) shift: 0.58 1.57 ...... Frame ( 21) shift: 0.62 1.65 ...... Frame ( 22) shift: 0.66 1.75 ...... Frame ( 23) shift: 0.69 1.85 ...... Frame ( 24) shift: 0.72 1.94 ...... Frame ( 25) shift: 0.72 2.03 ...... Frame ( 26) shift: 0.73 2.12 ...... Frame ( 27) shift: 0.75 2.17 ...... Frame ( 28) shift: 0.77 2.20 ...... Frame ( 29) shift: 0.79 2.23 ...... Frame ( 30) shift: 0.80 2.25 ...... Frame ( 31) shift: 0.81 2.27 ...... Frame ( 32) shift: 0.82 2.28 ...... Frame ( 33) shift: 0.85 2.32 ...... Frame ( 34) shift: 0.90 2.39 ...... Frame ( 35) shift: 0.95 2.46 ...... Frame ( 36) shift: 0.97 2.52 ...... Frame ( 37) shift: 0.97 2.58 ...... Frame ( 38) shift: 0.96 2.63 ...... Frame ( 39) shift: 0.96 2.69 ...... Frame ( 40) shift: 0.95 2.74 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.123866 Iteration 2 Error: 0.363532 Iteration 3 Error: 0.132570 Iteration 4 Error: 0.047525 Align patch 2 23 left Iteration 1 Error: 1.056138 Iteration 2 Error: 0.194965 Iteration 3 Error: 0.056800 Iteration 4 Error: 0.019713 Align patch 3 22 left Iteration 1 Error: 0.664647 Iteration 2 Error: 0.137469 Iteration 3 Error: 0.036187 Align patch 4 21 left Iteration 1 Error: 0.876869 Iteration 2 Error: 0.091528 Iteration 3 Error: 0.019215 Align patch 5 20 left Iteration 1 Error: 0.575108 Iteration 2 Error: 0.089131 Iteration 3 Error: 0.013874 Align patch 6 19 left Iteration 1 Error: 2.018774 Iteration 2 Error: 0.385321 Iteration 3 Error: 0.093443 Iteration 4 Error: 0.032498 Align patch 7 18 left Iteration 1 Error: 0.881066 Iteration 2 Error: 0.339525 Iteration 3 Error: 0.111678 Iteration 4 Error: 0.043691 Align patch 8 17 left Iteration 1 Error: 0.803883 Iteration 2 Error: 0.101559 Iteration 3 Error: 0.021377 Align patch 9 16 left Iteration 1 Error: 0.500645 Iteration 2 Error: 0.088285 Iteration 3 Error: 0.020975 Align patch 10 15 left Iteration 1 Error: 0.492899 Iteration 2 Error: 0.064186 Iteration 3 Error: 0.009811 Align patch 11 14 left Iteration 1 Error: 1.110956 Iteration 2 Error: 0.245148 Iteration 3 Error: 0.057751 Iteration 4 Error: 0.026652 Align patch 12 13 left Iteration 1 Error: 0.753637 Iteration 2 Error: 0.142061 Iteration 3 Error: 0.044115 Align patch 13 12 left Iteration 1 Error: 0.379699 Iteration 2 Error: 0.052820 Iteration 3 Error: 0.012408 Align patch 14 11 left Iteration 1 Error: 0.560840 Iteration 2 Error: 0.120298 Iteration 3 Error: 0.039512 Align patch 15 10 left Iteration 1 Error: 1.050151 Iteration 2 Error: 0.109590 Iteration 3 Error: 0.035778 Align patch 16 9 left Iteration 1 Error: 0.522068 Iteration 2 Error: 0.116905 Iteration 3 Error: 0.040372 Align patch 17 8 left Iteration 1 Error: 0.418448 Iteration 2 Error: 0.126382 Iteration 3 Error: 0.035011 Align patch 18 7 left Iteration 1 Error: 0.751849 Iteration 2 Error: 0.165477 Iteration 3 Error: 0.032983 Align patch 19 6 left Iteration 1 Error: 0.677018 Iteration 2 Error: 0.107725 Iteration 3 Error: 0.036051 Align patch 20 5 left Iteration 1 Error: 0.580383 Iteration 2 Error: 0.128474 Iteration 3 Error: 0.023052 Align patch 21 4 left Iteration 1 Error: 0.863334 Iteration 2 Error: 0.159948 Iteration 3 Error: 0.045566 Align patch 22 3 left Iteration 1 Error: 0.570784 Iteration 2 Error: 0.079730 Iteration 3 Error: 0.018992 Align patch 23 2 left Iteration 1 Error: 1.929355 Iteration 2 Error: 0.197374 Iteration 3 Error: 0.042059 Align patch 24 1 left Iteration 1 Error: 0.852610 Iteration 2 Error: 0.166553 Iteration 3 Error: 0.034858 Align patch 25 0 left Iteration 1 Error: 0.732887 Iteration 2 Error: 0.114956 Iteration 3 Error: 0.022205 3D Fitting completed. Patch alignment time: 16.00(sec) Local motion has been corrected. Process thread exits. Computational time: 24.713936 sec Total time: 30.503841 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00007hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00007hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.693963s Reading file: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00007hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.300661s ........................................ >>>>>>TIME<<<<<< FFT: 0.927933s Defocus_U Defocus_V Angle CCC 12187.51 12988.29 5.89 0.059716 Final Values Defocus_U Defocus_V Angle CCC 12185.94 12989.85 5.89 0.102408 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00010sq_v01_00007hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00007hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 41.98 7.00 Num Hot pixels: 212 Hot pixel threshold: 83.96 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.046744 Iteration 2 Error: 0.176851 Iteration 3 Error: 0.041814 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.04 0.06 ...... Frame ( 3) shift: -0.08 0.12 ...... Frame ( 4) shift: -0.11 0.17 ...... Frame ( 5) shift: -0.15 0.23 ...... Frame ( 6) shift: -0.14 0.33 ...... Frame ( 7) shift: -0.09 0.47 ...... Frame ( 8) shift: -0.04 0.60 ...... Frame ( 9) shift: 0.02 0.70 ...... Frame ( 10) shift: 0.10 0.76 ...... Frame ( 11) shift: 0.18 0.82 ...... Frame ( 12) shift: 0.23 0.88 ...... Frame ( 13) shift: 0.24 0.94 ...... Frame ( 14) shift: 0.26 1.00 ...... Frame ( 15) shift: 0.29 1.05 ...... Frame ( 16) shift: 0.33 1.09 ...... Frame ( 17) shift: 0.37 1.14 ...... Frame ( 18) shift: 0.42 1.20 ...... Frame ( 19) shift: 0.47 1.27 ...... Frame ( 20) shift: 0.52 1.35 ...... Frame ( 21) shift: 0.54 1.43 ...... Frame ( 22) shift: 0.53 1.53 ...... Frame ( 23) shift: 0.52 1.62 ...... Frame ( 24) shift: 0.50 1.65 ...... Frame ( 25) shift: 0.48 1.62 ...... Frame ( 26) shift: 0.46 1.59 ...... Frame ( 27) shift: 0.44 1.62 ...... Frame ( 28) shift: 0.43 1.70 ...... Frame ( 29) shift: 0.41 1.78 ...... Frame ( 30) shift: 0.42 1.80 ...... Frame ( 31) shift: 0.46 1.78 ...... Frame ( 32) shift: 0.49 1.75 ...... Frame ( 33) shift: 0.49 1.75 ...... Frame ( 34) shift: 0.45 1.78 ...... Frame ( 35) shift: 0.40 1.81 ...... Frame ( 36) shift: 0.38 1.82 ...... Frame ( 37) shift: 0.37 1.84 ...... Frame ( 38) shift: 0.36 1.85 ...... Frame ( 39) shift: 0.35 1.86 ...... Frame ( 40) shift: 0.35 1.87 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.981615 Iteration 2 Error: 0.253734 Iteration 3 Error: 0.096583 Iteration 4 Error: 0.029680 Align patch 2 23 left Iteration 1 Error: 1.209470 Iteration 2 Error: 0.157718 Iteration 3 Error: 0.047733 Align patch 3 22 left Iteration 1 Error: 0.766733 Iteration 2 Error: 0.129082 Iteration 3 Error: 0.028891 Align patch 4 21 left Iteration 1 Error: 0.631746 Iteration 2 Error: 0.180567 Iteration 3 Error: 0.026340 Align patch 5 20 left Iteration 1 Error: 0.834250 Iteration 2 Error: 0.130812 Iteration 3 Error: 0.026135 Align patch 6 19 left Iteration 1 Error: 1.784219 Iteration 2 Error: 0.176917 Iteration 3 Error: 0.039888 Align patch 7 18 left Iteration 1 Error: 0.775548 Iteration 2 Error: 0.081612 Iteration 3 Error: 0.024113 Align patch 8 17 left Iteration 1 Error: 1.092059 Iteration 2 Error: 0.126496 Iteration 3 Error: 0.044692 Align patch 9 16 left Iteration 1 Error: 0.982634 Iteration 2 Error: 0.146235 Iteration 3 Error: 0.028419 Align patch 10 15 left Iteration 1 Error: 0.659119 Iteration 2 Error: 0.115175 Iteration 3 Error: 0.037707 Align patch 11 14 left Iteration 1 Error: 0.582751 Iteration 2 Error: 0.136738 Iteration 3 Error: 0.054143 Iteration 4 Error: 0.020416 Align patch 12 13 left Iteration 1 Error: 0.835009 Iteration 2 Error: 0.207887 Iteration 3 Error: 0.047651 Align patch 13 12 left Iteration 1 Error: 0.572735 Iteration 2 Error: 0.136116 Iteration 3 Error: 0.038385 Align patch 14 11 left Iteration 1 Error: 0.693702 Iteration 2 Error: 0.098910 Iteration 3 Error: 0.027183 Align patch 15 10 left Iteration 1 Error: 0.946364 Iteration 2 Error: 0.129003 Iteration 3 Error: 0.024156 Align patch 16 9 left Iteration 1 Error: 0.629962 Iteration 2 Error: 0.143949 Iteration 3 Error: 0.042281 Align patch 17 8 left Iteration 1 Error: 0.693336 Iteration 2 Error: 0.126249 Iteration 3 Error: 0.023605 Align patch 18 7 left Iteration 1 Error: 0.709276 Iteration 2 Error: 0.132455 Iteration 3 Error: 0.045472 Align patch 19 6 left Iteration 1 Error: 0.487147 Iteration 2 Error: 0.058314 Iteration 3 Error: 0.019153 Align patch 20 5 left Iteration 1 Error: 0.931186 Iteration 2 Error: 0.182484 Iteration 3 Error: 0.048805 Align patch 21 4 left Iteration 1 Error: 0.878461 Iteration 2 Error: 0.160373 Iteration 3 Error: 0.031551 Align patch 22 3 left Iteration 1 Error: 0.840500 Iteration 2 Error: 0.102499 Iteration 3 Error: 0.029658 Align patch 23 2 left Iteration 1 Error: 0.559675 Iteration 2 Error: 0.114536 Iteration 3 Error: 0.035996 Align patch 24 1 left Iteration 1 Error: 0.695577 Iteration 2 Error: 0.270592 Iteration 3 Error: 0.112950 Iteration 4 Error: 0.046161 Align patch 25 0 left Iteration 1 Error: 1.032299 Iteration 2 Error: 0.145126 Iteration 3 Error: 0.038093 3D Fitting completed. Patch alignment time: 15.78(sec) Local motion has been corrected. Process thread exits. Computational time: 24.576897 sec Total time: 30.328222 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00007hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00007hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.558134s Reading file: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00007hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.137811s ........................................ >>>>>>TIME<<<<<< FFT: 0.883916s Defocus_U Defocus_V Angle CCC 12121.15 11464.90 84.89 0.047706 Final Values Defocus_U Defocus_V Angle CCC 12139.92 11489.92 84.89 0.086243 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00010sq_v01_00008hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00008hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.002e-01 CC threshold: 0.736 Mean Std: 40.03 6.80 Num Hot pixels: 220 Hot pixel threshold: 80.84 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.023822 Iteration 2 Error: 0.510768 Iteration 3 Error: 0.163521 Iteration 4 Error: 0.064850 Iteration 5 Error: 0.033691 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.10 -0.04 ...... Frame ( 3) shift: -0.21 -0.07 ...... Frame ( 4) shift: -0.31 -0.11 ...... Frame ( 5) shift: -0.42 -0.15 ...... Frame ( 6) shift: -0.41 -0.15 ...... Frame ( 7) shift: -0.31 -0.11 ...... Frame ( 8) shift: -0.20 -0.08 ...... Frame ( 9) shift: -0.06 -0.06 ...... Frame ( 10) shift: 0.10 -0.05 ...... Frame ( 11) shift: 0.27 -0.04 ...... Frame ( 12) shift: 0.42 0.02 ...... Frame ( 13) shift: 0.57 0.14 ...... Frame ( 14) shift: 0.72 0.26 ...... Frame ( 15) shift: 0.82 0.37 ...... Frame ( 16) shift: 0.86 0.48 ...... Frame ( 17) shift: 0.91 0.59 ...... Frame ( 18) shift: 1.02 0.67 ...... Frame ( 19) shift: 1.19 0.73 ...... Frame ( 20) shift: 1.37 0.79 ...... Frame ( 21) shift: 1.51 0.87 ...... Frame ( 22) shift: 1.62 0.96 ...... Frame ( 23) shift: 1.73 1.05 ...... Frame ( 24) shift: 1.81 1.15 ...... Frame ( 25) shift: 1.86 1.26 ...... Frame ( 26) shift: 1.90 1.37 ...... Frame ( 27) shift: 1.98 1.44 ...... Frame ( 28) shift: 2.09 1.49 ...... Frame ( 29) shift: 2.20 1.54 ...... Frame ( 30) shift: 2.31 1.60 ...... Frame ( 31) shift: 2.42 1.68 ...... Frame ( 32) shift: 2.52 1.76 ...... Frame ( 33) shift: 2.61 1.85 ...... Frame ( 34) shift: 2.66 1.95 ...... Frame ( 35) shift: 2.71 2.04 ...... Frame ( 36) shift: 2.81 2.11 ...... Frame ( 37) shift: 2.96 2.16 ...... Frame ( 38) shift: 3.11 2.21 ...... Frame ( 39) shift: 3.25 2.25 ...... Frame ( 40) shift: 3.40 2.30 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.786085 Iteration 2 Error: 0.380020 Iteration 3 Error: 0.078237 Iteration 4 Error: 0.027509 Align patch 2 23 left Iteration 1 Error: 1.185693 Iteration 2 Error: 0.355470 Iteration 3 Error: 0.102872 Iteration 4 Error: 0.032629 Align patch 3 22 left Iteration 1 Error: 0.883181 Iteration 2 Error: 0.145227 Iteration 3 Error: 0.045028 Align patch 4 21 left Iteration 1 Error: 0.508016 Iteration 2 Error: 0.088839 Iteration 3 Error: 0.022702 Align patch 5 20 left Iteration 1 Error: 1.527906 Iteration 2 Error: 0.527734 Iteration 3 Error: 0.093167 Iteration 4 Error: 0.030611 Align patch 6 19 left Iteration 1 Error: 1.685908 Iteration 2 Error: 0.646913 Iteration 3 Error: 0.200162 Iteration 4 Error: 0.082505 Iteration 5 Error: 0.030839 Align patch 7 18 left Iteration 1 Error: 1.221008 Iteration 2 Error: 0.338572 Iteration 3 Error: 0.121337 Iteration 4 Error: 0.049766 Align patch 8 17 left Iteration 1 Error: 1.044704 Iteration 2 Error: 0.239460 Iteration 3 Error: 0.063900 Iteration 4 Error: 0.030810 Align patch 9 16 left Iteration 1 Error: 0.613458 Iteration 2 Error: 0.079477 Iteration 3 Error: 0.027282 Align patch 10 15 left Iteration 1 Error: 1.417225 Iteration 2 Error: 0.306265 Iteration 3 Error: 0.098872 Iteration 4 Error: 0.027724 Align patch 11 14 left Iteration 1 Error: 2.301440 Iteration 2 Error: 0.628695 Iteration 3 Error: 0.278052 Iteration 4 Error: 0.133601 Iteration 5 Error: 0.053787 Align patch 11 14 left Iteration 1 Error: 1.739791 Iteration 2 Error: 0.227900 Iteration 3 Error: 0.044091 Align patch 12 13 left Iteration 1 Error: 1.624762 Iteration 2 Error: 0.338426 Iteration 3 Error: 0.106643 Iteration 4 Error: 0.039628 Align patch 13 12 left Iteration 1 Error: 0.923322 Iteration 2 Error: 0.238199 Iteration 3 Error: 0.046294 Align patch 14 11 left Iteration 1 Error: 0.988548 Iteration 2 Error: 0.282495 Iteration 3 Error: 0.074109 Iteration 4 Error: 0.025857 Align patch 15 10 left Iteration 1 Error: 0.990541 Iteration 2 Error: 0.256045 Iteration 3 Error: 0.081004 Iteration 4 Error: 0.028636 Align patch 16 9 left Iteration 1 Error: 1.290340 Iteration 2 Error: 0.306897 Iteration 3 Error: 0.145634 Iteration 4 Error: 0.059203 Iteration 5 Error: 0.039387 Align patch 17 8 left Iteration 1 Error: 1.398193 Iteration 2 Error: 0.270789 Iteration 3 Error: 0.084053 Iteration 4 Error: 0.035674 Align patch 18 7 left Iteration 1 Error: 0.654001 Iteration 2 Error: 0.095625 Iteration 3 Error: 0.026149 Align patch 19 6 left Iteration 1 Error: 1.268610 Iteration 2 Error: 0.253188 Iteration 3 Error: 0.095886 Iteration 4 Error: 0.033450 Align patch 20 5 left Iteration 1 Error: 1.771899 Iteration 2 Error: 0.407571 Iteration 3 Error: 0.105330 Iteration 4 Error: 0.040076 Align patch 21 4 left Iteration 1 Error: 0.990914 Iteration 2 Error: 0.145533 Iteration 3 Error: 0.047090 Align patch 22 3 left Iteration 1 Error: 0.844591 Iteration 2 Error: 0.105282 Iteration 3 Error: 0.041266 Align patch 23 2 left Iteration 1 Error: 0.558971 Iteration 2 Error: 0.165351 Iteration 3 Error: 0.045089 Align patch 24 1 left Iteration 1 Error: 1.383448 Iteration 2 Error: 0.652284 Iteration 3 Error: 0.161436 Iteration 4 Error: 0.064458 Iteration 5 Error: 0.018996 Align patch 25 0 left Iteration 1 Error: 1.607036 Iteration 2 Error: 0.266618 Iteration 3 Error: 0.077410 Iteration 4 Error: 0.023690 3D Fitting completed. Patch alignment time: 17.88(sec) Local motion has been corrected. Process thread exits. Computational time: 27.199537 sec Total time: 32.947845 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00008hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00008hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.755637s Reading file: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00008hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.050069s ........................................ >>>>>>TIME<<<<<< FFT: 0.995368s Defocus_U Defocus_V Angle CCC 11751.97 12619.16 10.76 0.056436 Final Values Defocus_U Defocus_V Angle CCC 11762.91 12623.86 10.45 0.091993 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00010sq_v01_00008hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00008hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 40.59 6.91 Num Hot pixels: 228 Hot pixel threshold: 82.03 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.525726 Iteration 2 Error: 0.304529 Iteration 3 Error: 0.092656 Iteration 4 Error: 0.032028 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.04 0.11 ...... Frame ( 3) shift: 0.08 0.23 ...... Frame ( 4) shift: 0.12 0.34 ...... Frame ( 5) shift: 0.16 0.46 ...... Frame ( 6) shift: 0.23 0.56 ...... Frame ( 7) shift: 0.34 0.65 ...... Frame ( 8) shift: 0.44 0.74 ...... Frame ( 9) shift: 0.53 0.85 ...... Frame ( 10) shift: 0.61 0.99 ...... Frame ( 11) shift: 0.69 1.13 ...... Frame ( 12) shift: 0.75 1.23 ...... Frame ( 13) shift: 0.80 1.31 ...... Frame ( 14) shift: 0.84 1.38 ...... Frame ( 15) shift: 0.91 1.46 ...... Frame ( 16) shift: 0.98 1.54 ...... Frame ( 17) shift: 1.06 1.62 ...... Frame ( 18) shift: 1.12 1.66 ...... Frame ( 19) shift: 1.18 1.66 ...... Frame ( 20) shift: 1.24 1.67 ...... Frame ( 21) shift: 1.30 1.69 ...... Frame ( 22) shift: 1.36 1.73 ...... Frame ( 23) shift: 1.42 1.77 ...... Frame ( 24) shift: 1.48 1.81 ...... Frame ( 25) shift: 1.53 1.84 ...... Frame ( 26) shift: 1.59 1.88 ...... Frame ( 27) shift: 1.64 1.93 ...... Frame ( 28) shift: 1.68 2.01 ...... Frame ( 29) shift: 1.72 2.08 ...... Frame ( 30) shift: 1.76 2.14 ...... Frame ( 31) shift: 1.81 2.18 ...... Frame ( 32) shift: 1.86 2.22 ...... Frame ( 33) shift: 1.89 2.29 ...... Frame ( 34) shift: 1.89 2.38 ...... Frame ( 35) shift: 1.89 2.48 ...... Frame ( 36) shift: 1.93 2.57 ...... Frame ( 37) shift: 2.01 2.65 ...... Frame ( 38) shift: 2.09 2.73 ...... Frame ( 39) shift: 2.18 2.81 ...... Frame ( 40) shift: 2.26 2.90 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.107040 Iteration 2 Error: 0.352624 Iteration 3 Error: 0.151714 Iteration 4 Error: 0.065842 Iteration 5 Error: 0.025719 Align patch 2 23 left Iteration 1 Error: 0.840005 Iteration 2 Error: 0.192972 Iteration 3 Error: 0.072365 Iteration 4 Error: 0.027110 Align patch 3 22 left Iteration 1 Error: 0.790188 Iteration 2 Error: 0.115026 Iteration 3 Error: 0.030643 Align patch 4 21 left Iteration 1 Error: 0.691019 Iteration 2 Error: 0.143060 Iteration 3 Error: 0.031709 Align patch 5 20 left Iteration 1 Error: 0.938520 Iteration 2 Error: 0.152476 Iteration 3 Error: 0.031726 Align patch 6 19 left Iteration 1 Error: 2.037636 Iteration 2 Error: 0.363367 Iteration 3 Error: 0.132568 Iteration 4 Error: 0.057240 Iteration 5 Error: 0.030021 Align patch 7 18 left Iteration 1 Error: 1.621399 Iteration 2 Error: 0.351619 Iteration 3 Error: 0.174430 Iteration 4 Error: 0.084951 Iteration 5 Error: 0.031302 Align patch 8 17 left Iteration 1 Error: 1.021342 Iteration 2 Error: 0.233059 Iteration 3 Error: 0.088420 Iteration 4 Error: 0.039974 Align patch 9 16 left Iteration 1 Error: 0.990490 Iteration 2 Error: 0.192768 Iteration 3 Error: 0.036477 Align patch 10 15 left Iteration 1 Error: 1.174268 Iteration 2 Error: 0.200268 Iteration 3 Error: 0.044836 Align patch 11 14 left Iteration 1 Error: 1.838047 Iteration 2 Error: 0.432498 Iteration 3 Error: 0.128931 Iteration 4 Error: 0.061618 Iteration 5 Error: 0.032086 Align patch 12 13 left Iteration 1 Error: 0.939040 Iteration 2 Error: 0.283052 Iteration 3 Error: 0.135960 Iteration 4 Error: 0.072723 Iteration 5 Error: 0.045568 Align patch 13 12 left Iteration 1 Error: 0.634151 Iteration 2 Error: 0.153699 Iteration 3 Error: 0.026925 Align patch 14 11 left Iteration 1 Error: 0.731978 Iteration 2 Error: 0.174429 Iteration 3 Error: 0.064791 Iteration 4 Error: 0.021980 Align patch 15 10 left Iteration 1 Error: 0.983024 Iteration 2 Error: 0.254639 Iteration 3 Error: 0.062646 Iteration 4 Error: 0.021898 Align patch 16 9 left Iteration 1 Error: 0.837412 Iteration 2 Error: 0.242584 Iteration 3 Error: 0.074666 Iteration 4 Error: 0.029632 Align patch 17 8 left Iteration 1 Error: 0.941830 Iteration 2 Error: 0.169741 Iteration 3 Error: 0.055121 Iteration 4 Error: 0.016167 Align patch 18 7 left Iteration 1 Error: 0.816056 Iteration 2 Error: 0.111727 Iteration 3 Error: 0.034321 Align patch 19 6 left Iteration 1 Error: 0.850543 Iteration 2 Error: 0.208516 Iteration 3 Error: 0.057422 Iteration 4 Error: 0.021142 Align patch 20 5 left Iteration 1 Error: 1.240655 Iteration 2 Error: 0.233982 Iteration 3 Error: 0.052341 Iteration 4 Error: 0.014197 Align patch 21 4 left Iteration 1 Error: 0.652804 Iteration 2 Error: 0.113135 Iteration 3 Error: 0.027744 Align patch 22 3 left Iteration 1 Error: 1.046503 Iteration 2 Error: 0.198581 Iteration 3 Error: 0.039847 Align patch 23 2 left Iteration 1 Error: 0.867730 Iteration 2 Error: 0.094999 Iteration 3 Error: 0.033816 Align patch 24 1 left Iteration 1 Error: 0.770615 Iteration 2 Error: 0.171406 Iteration 3 Error: 0.053690 Iteration 4 Error: 0.018463 Align patch 25 0 left Iteration 1 Error: 0.719349 Iteration 2 Error: 0.136192 Iteration 3 Error: 0.037113 3D Fitting completed. Patch alignment time: 17.41(sec) Local motion has been corrected. Process thread exits. Computational time: 26.640720 sec Total time: 32.425663 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00008hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00008hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.539980s Reading file: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00008hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.956171s ........................................ >>>>>>TIME<<<<<< FFT: 0.908492s Defocus_U Defocus_V Angle CCC 8707.03 9222.66 1.96 0.039789 Final Values Defocus_U Defocus_V Angle CCC 8714.85 9224.22 1.34 0.078516 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00010sq_v01_00008hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00008hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 40.53 6.90 Num Hot pixels: 185 Hot pixel threshold: 81.93 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.044503 Iteration 2 Error: 0.648914 Iteration 3 Error: 0.300743 Iteration 4 Error: 0.151400 Iteration 5 Error: 0.081156 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.21 -0.22 ...... Frame ( 3) shift: -0.43 -0.44 ...... Frame ( 4) shift: -0.64 -0.65 ...... Frame ( 5) shift: -0.86 -0.87 ...... Frame ( 6) shift: -0.94 -1.03 ...... Frame ( 7) shift: -0.90 -1.13 ...... Frame ( 8) shift: -0.87 -1.23 ...... Frame ( 9) shift: -0.69 -1.29 ...... Frame ( 10) shift: -0.39 -1.32 ...... Frame ( 11) shift: -0.09 -1.34 ...... Frame ( 12) shift: 0.20 -1.33 ...... Frame ( 13) shift: 0.48 -1.30 ...... Frame ( 14) shift: 0.76 -1.26 ...... Frame ( 15) shift: 1.03 -1.18 ...... Frame ( 16) shift: 1.28 -1.04 ...... Frame ( 17) shift: 1.52 -0.91 ...... Frame ( 18) shift: 1.78 -0.81 ...... Frame ( 19) shift: 2.04 -0.74 ...... Frame ( 20) shift: 2.30 -0.67 ...... Frame ( 21) shift: 2.53 -0.58 ...... Frame ( 22) shift: 2.74 -0.46 ...... Frame ( 23) shift: 2.94 -0.34 ...... Frame ( 24) shift: 3.16 -0.20 ...... Frame ( 25) shift: 3.38 -0.05 ...... Frame ( 26) shift: 3.61 0.10 ...... Frame ( 27) shift: 3.75 0.25 ...... Frame ( 28) shift: 3.82 0.38 ...... Frame ( 29) shift: 3.88 0.52 ...... Frame ( 30) shift: 3.99 0.64 ...... Frame ( 31) shift: 4.13 0.75 ...... Frame ( 32) shift: 4.27 0.87 ...... Frame ( 33) shift: 4.35 0.93 ...... Frame ( 34) shift: 4.35 0.94 ...... Frame ( 35) shift: 4.36 0.95 ...... Frame ( 36) shift: 4.36 0.98 ...... Frame ( 37) shift: 4.36 1.05 ...... Frame ( 38) shift: 4.36 1.11 ...... Frame ( 39) shift: 4.36 1.17 ...... Frame ( 40) shift: 4.36 1.24 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 3.454280 Iteration 2 Error: 0.661678 Iteration 3 Error: 0.173270 Iteration 4 Error: 0.054850 Iteration 5 Error: 0.019364 Align patch 2 23 left Iteration 1 Error: 2.219466 Iteration 2 Error: 0.666021 Iteration 3 Error: 0.198975 Iteration 4 Error: 0.112613 Iteration 5 Error: 0.034237 Align patch 3 22 left Iteration 1 Error: 1.549898 Iteration 2 Error: 0.421237 Iteration 3 Error: 0.257373 Iteration 4 Error: 0.104815 Iteration 5 Error: 0.052241 Align patch 3 22 left Iteration 1 Error: 2.022952 Iteration 2 Error: 0.276063 Iteration 3 Error: 0.064979 Iteration 4 Error: 0.020744 Align patch 4 21 left Iteration 1 Error: 0.758424 Iteration 2 Error: 0.189734 Iteration 3 Error: 0.080552 Iteration 4 Error: 0.036527 Align patch 5 20 left Iteration 1 Error: 1.987069 Iteration 2 Error: 0.487056 Iteration 3 Error: 0.174391 Iteration 4 Error: 0.057252 Iteration 5 Error: 0.022503 Align patch 6 19 left Iteration 1 Error: 2.723336 Iteration 2 Error: 0.476032 Iteration 3 Error: 0.227823 Iteration 4 Error: 0.075826 Iteration 5 Error: 0.034109 Align patch 7 18 left Iteration 1 Error: 1.348623 Iteration 2 Error: 0.379697 Iteration 3 Error: 0.114109 Iteration 4 Error: 0.044334 Align patch 8 17 left Iteration 1 Error: 2.093983 Iteration 2 Error: 0.366804 Iteration 3 Error: 0.142441 Iteration 4 Error: 0.070756 Iteration 5 Error: 0.045539 Align patch 9 16 left Iteration 1 Error: 0.501003 Iteration 2 Error: 0.153721 Iteration 3 Error: 0.033764 Align patch 10 15 left Iteration 1 Error: 1.634159 Iteration 2 Error: 0.585607 Iteration 3 Error: 0.185927 Iteration 4 Error: 0.070349 Iteration 5 Error: 0.022730 Align patch 11 14 left Iteration 1 Error: 2.884354 Iteration 2 Error: 0.437907 Iteration 3 Error: 0.125919 Iteration 4 Error: 0.038633 Align patch 12 13 left Iteration 1 Error: 1.324039 Iteration 2 Error: 0.374922 Iteration 3 Error: 0.130620 Iteration 4 Error: 0.066081 Iteration 5 Error: 0.030395 Align patch 13 12 left Iteration 1 Error: 1.312175 Iteration 2 Error: 0.329223 Iteration 3 Error: 0.156638 Iteration 4 Error: 0.085938 Iteration 5 Error: 0.045122 Align patch 14 11 left Iteration 1 Error: 0.795564 Iteration 2 Error: 0.169994 Iteration 3 Error: 0.063808 Iteration 4 Error: 0.028654 Align patch 15 10 left Iteration 1 Error: 1.630685 Iteration 2 Error: 0.338964 Iteration 3 Error: 0.145028 Iteration 4 Error: 0.059379 Iteration 5 Error: 0.026829 Align patch 16 9 left Iteration 1 Error: 2.150494 Iteration 2 Error: 0.686999 Iteration 3 Error: 0.214117 Iteration 4 Error: 0.098995 Iteration 5 Error: 0.031630 Align patch 17 8 left Iteration 1 Error: 1.587761 Iteration 2 Error: 0.401671 Iteration 3 Error: 0.150778 Iteration 4 Error: 0.087371 Iteration 5 Error: 0.051415 Align patch 17 8 left Iteration 1 Error: 1.184981 Iteration 2 Error: 0.175335 Iteration 3 Error: 0.060078 Iteration 4 Error: 0.020668 Align patch 18 7 left Iteration 1 Error: 0.520945 Iteration 2 Error: 0.151719 Iteration 3 Error: 0.081779 Iteration 4 Error: 0.025347 Align patch 19 6 left Iteration 1 Error: 0.697259 Iteration 2 Error: 0.148656 Iteration 3 Error: 0.051985 Iteration 4 Error: 0.026747 Align patch 20 5 left Iteration 1 Error: 2.057962 Iteration 2 Error: 0.500182 Iteration 3 Error: 0.107357 Iteration 4 Error: 0.049066 Align patch 21 4 left Iteration 1 Error: 0.964290 Iteration 2 Error: 0.196215 Iteration 3 Error: 0.101720 Iteration 4 Error: 0.037523 Align patch 22 3 left Iteration 1 Error: 0.978098 Iteration 2 Error: 0.300021 Iteration 3 Error: 0.120777 Iteration 4 Error: 0.047603 Align patch 23 2 left Iteration 1 Error: 1.502039 Iteration 2 Error: 0.288786 Iteration 3 Error: 0.054161 Iteration 4 Error: 0.028986 Align patch 24 1 left Iteration 1 Error: 1.435451 Iteration 2 Error: 0.311085 Iteration 3 Error: 0.164309 Iteration 4 Error: 0.055754 Iteration 5 Error: 0.023684 Align patch 25 0 left Iteration 1 Error: 1.995319 Iteration 2 Error: 0.626738 Iteration 3 Error: 0.155635 Iteration 4 Error: 0.064628 Iteration 5 Error: 0.026159 3D Fitting completed. Patch alignment time: 19.80(sec) Local motion has been corrected. Process thread exits. Computational time: 29.131483 sec Total time: 35.087128 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00008hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00008hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.534050s Reading file: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00008hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.960212s ........................................ >>>>>>TIME<<<<<< FFT: 0.970582s Defocus_U Defocus_V Angle CCC 13703.13 14601.57 4.39 0.063522 Final Values Defocus_U Defocus_V Angle CCC 13703.13 14620.33 5.02 0.101150 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00010sq_v01_00008hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00008hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.003e-01 CC threshold: 0.736 Mean Std: 41.63 7.02 Num Hot pixels: 212 Hot pixel threshold: 83.74 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.151737 Iteration 2 Error: 0.290045 Iteration 3 Error: 0.092403 Iteration 4 Error: 0.033423 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.01 0.01 ...... Frame ( 3) shift: 0.01 0.02 ...... Frame ( 4) shift: 0.02 0.03 ...... Frame ( 5) shift: 0.03 0.05 ...... Frame ( 6) shift: 0.06 0.06 ...... Frame ( 7) shift: 0.11 0.07 ...... Frame ( 8) shift: 0.17 0.08 ...... Frame ( 9) shift: 0.25 0.13 ...... Frame ( 10) shift: 0.37 0.22 ...... Frame ( 11) shift: 0.48 0.30 ...... Frame ( 12) shift: 0.59 0.36 ...... Frame ( 13) shift: 0.69 0.40 ...... Frame ( 14) shift: 0.79 0.44 ...... Frame ( 15) shift: 0.87 0.52 ...... Frame ( 16) shift: 0.94 0.64 ...... Frame ( 17) shift: 1.00 0.76 ...... Frame ( 18) shift: 1.07 0.86 ...... Frame ( 19) shift: 1.15 0.95 ...... Frame ( 20) shift: 1.22 1.04 ...... Frame ( 21) shift: 1.28 1.11 ...... Frame ( 22) shift: 1.31 1.18 ...... Frame ( 23) shift: 1.34 1.25 ...... Frame ( 24) shift: 1.37 1.31 ...... Frame ( 25) shift: 1.40 1.38 ...... Frame ( 26) shift: 1.43 1.46 ...... Frame ( 27) shift: 1.46 1.51 ...... Frame ( 28) shift: 1.49 1.55 ...... Frame ( 29) shift: 1.53 1.59 ...... Frame ( 30) shift: 1.57 1.61 ...... Frame ( 31) shift: 1.62 1.60 ...... Frame ( 32) shift: 1.68 1.58 ...... Frame ( 33) shift: 1.68 1.60 ...... Frame ( 34) shift: 1.64 1.64 ...... Frame ( 35) shift: 1.60 1.68 ...... Frame ( 36) shift: 1.58 1.77 ...... Frame ( 37) shift: 1.60 1.90 ...... Frame ( 38) shift: 1.61 2.04 ...... Frame ( 39) shift: 1.62 2.17 ...... Frame ( 40) shift: 1.63 2.30 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.823729 Iteration 2 Error: 0.433775 Iteration 3 Error: 0.132770 Iteration 4 Error: 0.050438 Iteration 5 Error: 0.019636 Align patch 2 23 left Iteration 1 Error: 1.394650 Iteration 2 Error: 0.296672 Iteration 3 Error: 0.113021 Iteration 4 Error: 0.071329 Iteration 5 Error: 0.026022 Align patch 3 22 left Iteration 1 Error: 0.818988 Iteration 2 Error: 0.204361 Iteration 3 Error: 0.074108 Iteration 4 Error: 0.034944 Align patch 4 21 left Iteration 1 Error: 0.600857 Iteration 2 Error: 0.081509 Iteration 3 Error: 0.021114 Align patch 5 20 left Iteration 1 Error: 1.081235 Iteration 2 Error: 0.247747 Iteration 3 Error: 0.048937 Align patch 6 19 left Iteration 1 Error: 2.701432 Iteration 2 Error: 0.478772 Iteration 3 Error: 0.214434 Iteration 4 Error: 0.085943 Iteration 5 Error: 0.041666 Align patch 7 18 left Iteration 1 Error: 2.329807 Iteration 2 Error: 0.439574 Iteration 3 Error: 0.219583 Iteration 4 Error: 0.077201 Iteration 5 Error: 0.040937 Align patch 8 17 left Iteration 1 Error: 0.879015 Iteration 2 Error: 0.294453 Iteration 3 Error: 0.100429 Iteration 4 Error: 0.051851 Iteration 5 Error: 0.018766 Align patch 9 16 left Iteration 1 Error: 0.750905 Iteration 2 Error: 0.133306 Iteration 3 Error: 0.045646 Align patch 10 15 left Iteration 1 Error: 1.130987 Iteration 2 Error: 0.232802 Iteration 3 Error: 0.048669 Align patch 11 14 left Iteration 1 Error: 2.435076 Iteration 2 Error: 0.336930 Iteration 3 Error: 0.091843 Iteration 4 Error: 0.035634 Align patch 12 13 left Iteration 1 Error: 2.392499 Iteration 2 Error: 0.540053 Iteration 3 Error: 0.134997 Iteration 4 Error: 0.079877 Iteration 5 Error: 0.029716 Align patch 13 12 left Iteration 1 Error: 0.842336 Iteration 2 Error: 0.240554 Iteration 3 Error: 0.084989 Iteration 4 Error: 0.033867 Align patch 14 11 left Iteration 1 Error: 0.689411 Iteration 2 Error: 0.162142 Iteration 3 Error: 0.059473 Iteration 4 Error: 0.017867 Align patch 15 10 left Iteration 1 Error: 1.251040 Iteration 2 Error: 0.297430 Iteration 3 Error: 0.071609 Iteration 4 Error: 0.018613 Align patch 16 9 left Iteration 1 Error: 1.229315 Iteration 2 Error: 0.321461 Iteration 3 Error: 0.119297 Iteration 4 Error: 0.071736 Iteration 5 Error: 0.021727 Align patch 17 8 left Iteration 1 Error: 0.700356 Iteration 2 Error: 0.118174 Iteration 3 Error: 0.051231 Iteration 4 Error: 0.018069 Align patch 18 7 left Iteration 1 Error: 1.164678 Iteration 2 Error: 0.155500 Iteration 3 Error: 0.033384 Align patch 19 6 left Iteration 1 Error: 0.752400 Iteration 2 Error: 0.205437 Iteration 3 Error: 0.070863 Iteration 4 Error: 0.022597 Align patch 20 5 left Iteration 1 Error: 1.793837 Iteration 2 Error: 0.275636 Iteration 3 Error: 0.080792 Iteration 4 Error: 0.024374 Align patch 21 4 left Iteration 1 Error: 0.449828 Iteration 2 Error: 0.062128 Iteration 3 Error: 0.013639 Align patch 22 3 left Iteration 1 Error: 0.653342 Iteration 2 Error: 0.065758 Iteration 3 Error: 0.019796 Align patch 23 2 left Iteration 1 Error: 0.590544 Iteration 2 Error: 0.160224 Iteration 3 Error: 0.048505 Align patch 24 1 left Iteration 1 Error: 1.235698 Iteration 2 Error: 0.258457 Iteration 3 Error: 0.056174 Iteration 4 Error: 0.016903 Align patch 25 0 left Iteration 1 Error: 1.258268 Iteration 2 Error: 0.196817 Iteration 3 Error: 0.028838 3D Fitting completed. Patch alignment time: 16.84(sec) Local motion has been corrected. Process thread exits. Computational time: 25.263113 sec Total time: 30.972847 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00008hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00008hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.541528s Reading file: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00008hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.724545s ........................................ >>>>>>TIME<<<<<< FFT: 0.952120s Defocus_U Defocus_V Angle CCC 13905.52 13246.84 84.72 0.065671 Final Values Defocus_U Defocus_V Angle CCC 13910.21 13251.54 84.72 0.108728 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00010sq_v01_00009hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00009hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 1.000e-01 CC threshold: 0.734 Mean Std: 34.34 7.41 Num Hot pixels: 121 Hot pixel threshold: 78.80 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.029379 Iteration 2 Error: 0.642492 Iteration 3 Error: 0.301356 Iteration 4 Error: 0.201029 Iteration 5 Error: 0.139172 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.04 -0.18 ...... Frame ( 3) shift: 0.07 -0.37 ...... Frame ( 4) shift: 0.11 -0.55 ...... Frame ( 5) shift: 0.15 -0.74 ...... Frame ( 6) shift: 0.15 -0.85 ...... Frame ( 7) shift: 0.12 -0.89 ...... Frame ( 8) shift: 0.09 -0.93 ...... Frame ( 9) shift: 0.03 -0.99 ...... Frame ( 10) shift: -0.07 -1.08 ...... Frame ( 11) shift: -0.17 -1.17 ...... Frame ( 12) shift: -0.29 -1.21 ...... Frame ( 13) shift: -0.42 -1.22 ...... Frame ( 14) shift: -0.56 -1.22 ...... Frame ( 15) shift: -0.67 -1.27 ...... Frame ( 16) shift: -0.74 -1.38 ...... Frame ( 17) shift: -0.82 -1.49 ...... Frame ( 18) shift: -0.89 -1.57 ...... Frame ( 19) shift: -0.95 -1.61 ...... Frame ( 20) shift: -1.01 -1.66 ...... Frame ( 21) shift: -1.15 -1.72 ...... Frame ( 22) shift: -1.36 -1.81 ...... Frame ( 23) shift: -1.58 -1.89 ...... Frame ( 24) shift: -1.77 -1.97 ...... Frame ( 25) shift: -1.94 -2.05 ...... Frame ( 26) shift: -2.10 -2.12 ...... Frame ( 27) shift: -2.24 -2.15 ...... Frame ( 28) shift: -2.35 -2.13 ...... Frame ( 29) shift: -2.45 -2.11 ...... Frame ( 30) shift: -2.59 -2.17 ...... Frame ( 31) shift: -2.77 -2.30 ...... Frame ( 32) shift: -2.95 -2.43 ...... Frame ( 33) shift: -3.10 -2.56 ...... Frame ( 34) shift: -3.24 -2.69 ...... Frame ( 35) shift: -3.37 -2.82 ...... Frame ( 36) shift: -3.47 -2.94 ...... Frame ( 37) shift: -3.53 -3.05 ...... Frame ( 38) shift: -3.59 -3.17 ...... Frame ( 39) shift: -3.65 -3.28 ...... Frame ( 40) shift: -3.71 -3.40 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 12.731160 Iteration 2 Error: 4.324350 Iteration 3 Error: 3.489935 Iteration 4 Error: 1.200841 Iteration 5 Error: 0.271654 Align patch 1 24 left Iteration 1 Error: 9.826346 Iteration 2 Error: 3.622294 Iteration 3 Error: 0.838010 Iteration 4 Error: 0.304288 Iteration 5 Error: 0.072515 Align patch 2 23 left Iteration 1 Error: 7.840750 Iteration 2 Error: 4.423773 Iteration 3 Error: 1.492462 Iteration 4 Error: 1.202470 Iteration 5 Error: 0.738503 Align patch 2 23 left Iteration 1 Error: 9.213497 Iteration 2 Error: 4.306409 Iteration 3 Error: 1.200144 Iteration 4 Error: 0.358189 Iteration 5 Error: 0.165437 Align patch 3 22 left Iteration 1 Error: 5.849860 Iteration 2 Error: 7.573699 Iteration 3 Error: 4.593666 Iteration 4 Error: 1.851827 Iteration 5 Error: 1.678211 Align patch 3 22 left Iteration 1 Error: 4.180968 Iteration 2 Error: 3.742216 Iteration 3 Error: 1.862072 Iteration 4 Error: 0.769412 Iteration 5 Error: 0.290862 Align patch 4 21 left Iteration 1 Error: 7.293427 Iteration 2 Error: 5.072124 Iteration 3 Error: 0.932702 Iteration 4 Error: 0.427387 Iteration 5 Error: 0.203578 Align patch 4 21 left Iteration 1 Error: 6.221457 Iteration 2 Error: 2.602146 Iteration 3 Error: 0.909823 Iteration 4 Error: 0.355574 Iteration 5 Error: 0.177165 Align patch 5 20 left Iteration 1 Error: 6.021402 Iteration 2 Error: 3.293739 Iteration 3 Error: 1.583193 Iteration 4 Error: 0.787834 Iteration 5 Error: 0.495115 Align patch 5 20 left Iteration 1 Error: 6.193563 Iteration 2 Error: 2.437483 Iteration 3 Error: 0.722085 Iteration 4 Error: 0.350982 Iteration 5 Error: 0.166723 Align patch 6 19 left Iteration 1 Error: 10.663744 Iteration 2 Error: 4.762791 Iteration 3 Error: 2.874635 Iteration 4 Error: 1.172171 Iteration 5 Error: 0.647660 Align patch 6 19 left Iteration 1 Error: 9.791233 Iteration 2 Error: 4.164948 Iteration 3 Error: 0.984378 Iteration 4 Error: 0.345262 Iteration 5 Error: 0.130813 Align patch 7 18 left Iteration 1 Error: 14.836639 Iteration 2 Error: 10.531016 Iteration 3 Error: 1.822457 Iteration 4 Error: 0.597663 Iteration 5 Error: 0.320946 Align patch 7 18 left Iteration 1 Error: 10.057841 Iteration 2 Error: 2.966098 Iteration 3 Error: 0.880468 Iteration 4 Error: 0.267322 Iteration 5 Error: 0.111987 Align patch 8 17 left Iteration 1 Error: 7.349385 Iteration 2 Error: 10.649989 Iteration 3 Error: 4.122003 Iteration 4 Error: 1.227695 Iteration 5 Error: 0.458513 Align patch 8 17 left Iteration 1 Error: 3.955023 Iteration 2 Error: 6.402458 Iteration 3 Error: 3.251191 Iteration 4 Error: 0.878967 Iteration 5 Error: 0.331091 Align patch 9 16 left Iteration 1 Error: 9.307053 Iteration 2 Error: 2.468296 Iteration 3 Error: 1.138213 Iteration 4 Error: 0.469208 Iteration 5 Error: 0.539884 Align patch 9 16 left Iteration 1 Error: 7.000750 Iteration 2 Error: 3.137723 Iteration 3 Error: 1.350982 Iteration 4 Error: 0.672553 Iteration 5 Error: 0.378837 Align patch 10 15 left Iteration 1 Error: 6.637877 Iteration 2 Error: 4.146774 Iteration 3 Error: 1.236663 Iteration 4 Error: 0.880534 Iteration 5 Error: 0.428630 Align patch 10 15 left Iteration 1 Error: 6.497652 Iteration 2 Error: 3.179633 Iteration 3 Error: 1.134874 Iteration 4 Error: 0.601938 Iteration 5 Error: 0.362727 Align patch 11 14 left Iteration 1 Error: 12.659458 Iteration 2 Error: 10.540765 Iteration 3 Error: 2.633677 Iteration 4 Error: 2.764484 Iteration 5 Error: 1.592760 Align patch 11 14 left Iteration 1 Error: 12.332888 Iteration 2 Error: 4.559092 Iteration 3 Error: 1.980625 Iteration 4 Error: 0.760158 Iteration 5 Error: 0.558630 Align patch 12 13 left Iteration 1 Error: 11.727704 Iteration 2 Error: 12.112118 Iteration 3 Error: 6.420726 Iteration 4 Error: 3.077695 Iteration 5 Error: 1.335628 Align patch 12 13 left Iteration 1 Error: 12.115961 Iteration 2 Error: 3.692958 Iteration 3 Error: 1.218490 Iteration 4 Error: 0.668109 Iteration 5 Error: 0.366369 Align patch 13 12 left Iteration 1 Error: 25.682707 Iteration 2 Error: 14.090953 Iteration 3 Error: 6.053794 Iteration 4 Error: 4.204690 Iteration 5 Error: 2.826679 Align patch 13 12 left Iteration 1 Error: 11.337461 Iteration 2 Error: 6.569091 Iteration 3 Error: 2.592200 Iteration 4 Error: 1.159713 Iteration 5 Error: 0.586526 Align patch 14 11 left Iteration 1 Error: 6.945660 Iteration 2 Error: 2.326174 Iteration 3 Error: 1.434612 Iteration 4 Error: 1.013856 Iteration 5 Error: 0.655255 Align patch 14 11 left Iteration 1 Error: 9.867901 Iteration 2 Error: 3.825319 Iteration 3 Error: 1.336317 Iteration 4 Error: 0.916694 Iteration 5 Error: 0.809105 Align patch 15 10 left Iteration 1 Error: 2.526005 Iteration 2 Error: 3.902465 Iteration 3 Error: 3.291500 Iteration 4 Error: 1.159050 Iteration 5 Error: 0.688246 Align patch 15 10 left Iteration 1 Error: 6.744478 Iteration 2 Error: 3.006942 Iteration 3 Error: 1.159316 Iteration 4 Error: 0.744606 Iteration 5 Error: 0.558809 Align patch 16 9 left Iteration 1 Error: 12.753902 Iteration 2 Error: 10.882784 Iteration 3 Error: 2.502453 Iteration 4 Error: 2.369613 Iteration 5 Error: 6.729877 Align patch 16 9 left Iteration 1 Error: 24.703510 Iteration 2 Error: 14.824479 Iteration 3 Error: 28.046028 Iteration 4 Error: 4.451782 Iteration 5 Error: 1.888597 Align patch 17 8 left Iteration 1 Error: 50.170700 Iteration 2 Error: 35.989655 Iteration 3 Error: 27.883259 Iteration 4 Error: 18.073774 Iteration 5 Error: 25.091803 Align patch 17 8 left Iteration 1 Error: 42.396622 Iteration 2 Error: 15.576149 Iteration 3 Error: 14.885279 Iteration 4 Error: 16.562580 Iteration 5 Error: 15.644190 Align patch 18 7 left Iteration 1 Error: 46.279373 Iteration 2 Error: 39.723129 Iteration 3 Error: 27.779013 Iteration 4 Error: 10.002456 Iteration 5 Error: 39.699554 Align patch 18 7 left Iteration 1 Error: 45.031643 Iteration 2 Error: 34.304577 Iteration 3 Error: 10.485021 Iteration 4 Error: 9.677889 Iteration 5 Error: 15.036677 Align patch 19 6 left Iteration 1 Error: 11.809044 Iteration 2 Error: 2.326948 Iteration 3 Error: 1.823251 Iteration 4 Error: 0.945091 Iteration 5 Error: 0.434839 Align patch 19 6 left Iteration 1 Error: 4.358808 Iteration 2 Error: 0.510793 Iteration 3 Error: 0.139614 Iteration 4 Error: 0.042994 Align patch 20 5 left Iteration 1 Error: 1.214404 Iteration 2 Error: 0.317315 Iteration 3 Error: 0.087902 Iteration 4 Error: 0.039776 Align patch 21 4 left Iteration 1 Error: 3.434469 Iteration 2 Error: 0.550534 Iteration 3 Error: 0.370779 Iteration 4 Error: 0.245806 Iteration 5 Error: 0.203171 Align patch 21 4 left Iteration 1 Error: 4.260065 Iteration 2 Error: 0.920681 Iteration 3 Error: 0.574963 Iteration 4 Error: 0.333387 Iteration 5 Error: 0.201693 Align patch 22 3 left Iteration 1 Error: 2.469146 Iteration 2 Error: 0.509786 Iteration 3 Error: 0.163134 Iteration 4 Error: 0.075795 Iteration 5 Error: 0.025479 Align patch 23 2 left Iteration 1 Error: 36.290760 Iteration 2 Error: 35.938293 Iteration 3 Error: 35.937664 Iteration 4 Error: 30.730238 Iteration 5 Error: 26.243103 Align patch 23 2 left Iteration 1 Error: 30.055603 Iteration 2 Error: 24.569675 Iteration 3 Error: 19.229858 Iteration 4 Error: 20.746336 Iteration 5 Error: 20.060228 Align patch 24 1 left Iteration 1 Error: 35.938137 Iteration 2 Error: 31.498690 Iteration 3 Error: 36.532333 Iteration 4 Error: 36.144073 Iteration 5 Error: 35.693420 Align patch 24 1 left Iteration 1 Error: 5.099685 Iteration 2 Error: 1.196738 Iteration 3 Error: 0.509500 Iteration 4 Error: 0.269400 Iteration 5 Error: 0.121298 Align patch 25 0 left Iteration 1 Error: 37.134068 Iteration 2 Error: 22.310965 Iteration 3 Error: 19.974611 Iteration 4 Error: 8.903362 Iteration 5 Error: 4.942225 Align patch 25 0 left Iteration 1 Error: 30.005680 Iteration 2 Error: 18.935709 Iteration 3 Error: 12.963506 Iteration 4 Error: 7.971579 Iteration 5 Error: 6.676350 3D Fitting completed. Patch alignment time: 39.49(sec) Local motion has been corrected. Process thread exits. Computational time: 48.658623 sec Total time: 54.575638 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00009hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00009hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.588562s Reading file: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00009hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.422816s ........................................ >>>>>>TIME<<<<<< FFT: 0.938938s Defocus_U Defocus_V Angle CCC 9795.02 10732.56 17.35 -0.018081 Final Values Defocus_U Defocus_V Angle CCC 9830.99 10731.03 19.24 0.001648 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00010sq_v01_00009hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00009hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.003e-01 CC threshold: 0.737 Mean Std: 38.65 6.68 Num Hot pixels: 209 Hot pixel threshold: 78.74 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.354888 Iteration 2 Error: 0.229239 Iteration 3 Error: 0.055730 Iteration 4 Error: 0.016962 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.38 -0.31 ...... Frame ( 3) shift: -0.76 -0.62 ...... Frame ( 4) shift: -1.14 -0.92 ...... Frame ( 5) shift: -1.52 -1.23 ...... Frame ( 6) shift: -1.73 -1.42 ...... Frame ( 7) shift: -1.78 -1.47 ...... Frame ( 8) shift: -1.83 -1.53 ...... Frame ( 9) shift: -1.83 -1.50 ...... Frame ( 10) shift: -1.78 -1.38 ...... Frame ( 11) shift: -1.73 -1.25 ...... Frame ( 12) shift: -1.65 -1.11 ...... Frame ( 13) shift: -1.54 -0.96 ...... Frame ( 14) shift: -1.43 -0.80 ...... Frame ( 15) shift: -1.35 -0.70 ...... Frame ( 16) shift: -1.29 -0.64 ...... Frame ( 17) shift: -1.24 -0.58 ...... Frame ( 18) shift: -1.19 -0.49 ...... Frame ( 19) shift: -1.13 -0.36 ...... Frame ( 20) shift: -1.07 -0.24 ...... Frame ( 21) shift: -1.03 -0.13 ...... Frame ( 22) shift: -1.00 -0.02 ...... Frame ( 23) shift: -0.97 0.08 ...... Frame ( 24) shift: -0.94 0.16 ...... Frame ( 25) shift: -0.92 0.23 ...... Frame ( 26) shift: -0.89 0.29 ...... Frame ( 27) shift: -0.86 0.31 ...... Frame ( 28) shift: -0.81 0.30 ...... Frame ( 29) shift: -0.76 0.28 ...... Frame ( 30) shift: -0.71 0.32 ...... Frame ( 31) shift: -0.65 0.40 ...... Frame ( 32) shift: -0.60 0.49 ...... Frame ( 33) shift: -0.57 0.56 ...... Frame ( 34) shift: -0.56 0.61 ...... Frame ( 35) shift: -0.56 0.67 ...... Frame ( 36) shift: -0.52 0.73 ...... Frame ( 37) shift: -0.46 0.81 ...... Frame ( 38) shift: -0.40 0.88 ...... Frame ( 39) shift: -0.34 0.95 ...... Frame ( 40) shift: -0.28 1.02 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.871937 Iteration 2 Error: 0.165049 Iteration 3 Error: 0.045353 Align patch 2 23 left Iteration 1 Error: 0.750531 Iteration 2 Error: 0.137366 Iteration 3 Error: 0.035060 Align patch 3 22 left Iteration 1 Error: 1.335979 Iteration 2 Error: 0.215509 Iteration 3 Error: 0.063034 Iteration 4 Error: 0.013271 Align patch 4 21 left Iteration 1 Error: 0.724819 Iteration 2 Error: 0.099125 Iteration 3 Error: 0.031067 Align patch 5 20 left Iteration 1 Error: 0.872370 Iteration 2 Error: 0.073426 Iteration 3 Error: 0.015490 Align patch 6 19 left Iteration 1 Error: 1.107088 Iteration 2 Error: 0.173770 Iteration 3 Error: 0.042537 Align patch 7 18 left Iteration 1 Error: 0.505048 Iteration 2 Error: 0.045641 Align patch 8 17 left Iteration 1 Error: 0.816382 Iteration 2 Error: 0.052904 Iteration 3 Error: 0.017574 Align patch 9 16 left Iteration 1 Error: 0.560256 Iteration 2 Error: 0.080331 Iteration 3 Error: 0.019478 Align patch 10 15 left Iteration 1 Error: 0.540372 Iteration 2 Error: 0.066852 Iteration 3 Error: 0.014757 Align patch 11 14 left Iteration 1 Error: 0.633116 Iteration 2 Error: 0.099310 Iteration 3 Error: 0.026403 Align patch 12 13 left Iteration 1 Error: 1.062844 Iteration 2 Error: 0.176164 Iteration 3 Error: 0.046501 Align patch 13 12 left Iteration 1 Error: 0.699076 Iteration 2 Error: 0.106777 Iteration 3 Error: 0.021481 Align patch 14 11 left Iteration 1 Error: 0.611781 Iteration 2 Error: 0.194606 Iteration 3 Error: 0.048889 Align patch 15 10 left Iteration 1 Error: 0.598096 Iteration 2 Error: 0.127295 Iteration 3 Error: 0.029386 Align patch 16 9 left Iteration 1 Error: 0.770717 Iteration 2 Error: 0.116107 Iteration 3 Error: 0.034315 Align patch 17 8 left Iteration 1 Error: 0.538965 Iteration 2 Error: 0.096605 Iteration 3 Error: 0.024718 Align patch 18 7 left Iteration 1 Error: 0.451939 Iteration 2 Error: 0.067572 Iteration 3 Error: 0.012937 Align patch 19 6 left Iteration 1 Error: 0.576337 Iteration 2 Error: 0.100776 Iteration 3 Error: 0.020001 Align patch 20 5 left Iteration 1 Error: 0.609206 Iteration 2 Error: 0.084643 Iteration 3 Error: 0.026396 Align patch 21 4 left Iteration 1 Error: 0.657623 Iteration 2 Error: 0.116952 Iteration 3 Error: 0.018947 Align patch 22 3 left Iteration 1 Error: 0.239940 Iteration 2 Error: 0.042921 Align patch 23 2 left Iteration 1 Error: 0.526790 Iteration 2 Error: 0.070096 Iteration 3 Error: 0.028676 Align patch 24 1 left Iteration 1 Error: 0.404029 Iteration 2 Error: 0.054198 Iteration 3 Error: 0.009295 Align patch 25 0 left Iteration 1 Error: 0.674139 Iteration 2 Error: 0.117129 Iteration 3 Error: 0.017924 3D Fitting completed. Patch alignment time: 14.72(sec) Local motion has been corrected. Process thread exits. Computational time: 23.857580 sec Total time: 29.649632 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00009hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00009hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.564751s Reading file: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00009hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.463829s ........................................ >>>>>>TIME<<<<<< FFT: 0.939572s Defocus_U Defocus_V Angle CCC 12681.63 13251.96 1.55 0.057788 Final Values Defocus_U Defocus_V Angle CCC 13267.60 12694.14 89.69 0.087482 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00010sq_v01_00009hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00009hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 36.98 6.51 Num Hot pixels: 212 Hot pixel threshold: 76.06 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.905179 Iteration 2 Error: 0.152348 Iteration 3 Error: 0.036462 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.14 -0.14 ...... Frame ( 3) shift: -0.29 -0.29 ...... Frame ( 4) shift: -0.43 -0.43 ...... Frame ( 5) shift: -0.57 -0.57 ...... Frame ( 6) shift: -0.67 -0.67 ...... Frame ( 7) shift: -0.72 -0.71 ...... Frame ( 8) shift: -0.78 -0.74 ...... Frame ( 9) shift: -0.78 -0.76 ...... Frame ( 10) shift: -0.72 -0.76 ...... Frame ( 11) shift: -0.66 -0.76 ...... Frame ( 12) shift: -0.61 -0.74 ...... Frame ( 13) shift: -0.55 -0.71 ...... Frame ( 14) shift: -0.50 -0.67 ...... Frame ( 15) shift: -0.48 -0.63 ...... Frame ( 16) shift: -0.49 -0.59 ...... Frame ( 17) shift: -0.49 -0.54 ...... Frame ( 18) shift: -0.48 -0.48 ...... Frame ( 19) shift: -0.45 -0.40 ...... Frame ( 20) shift: -0.41 -0.32 ...... Frame ( 21) shift: -0.36 -0.26 ...... Frame ( 22) shift: -0.30 -0.22 ...... Frame ( 23) shift: -0.24 -0.18 ...... Frame ( 24) shift: -0.18 -0.16 ...... Frame ( 25) shift: -0.12 -0.16 ...... Frame ( 26) shift: -0.05 -0.16 ...... Frame ( 27) shift: -0.00 -0.14 ...... Frame ( 28) shift: 0.04 -0.09 ...... Frame ( 29) shift: 0.08 -0.05 ...... Frame ( 30) shift: 0.10 -0.02 ...... Frame ( 31) shift: 0.09 -0.01 ...... Frame ( 32) shift: 0.09 0.00 ...... Frame ( 33) shift: 0.11 0.04 ...... Frame ( 34) shift: 0.17 0.10 ...... Frame ( 35) shift: 0.23 0.15 ...... Frame ( 36) shift: 0.28 0.23 ...... Frame ( 37) shift: 0.33 0.32 ...... Frame ( 38) shift: 0.39 0.42 ...... Frame ( 39) shift: 0.44 0.51 ...... Frame ( 40) shift: 0.49 0.60 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.522027 Iteration 2 Error: 0.153004 Iteration 3 Error: 0.025357 Align patch 2 23 left Iteration 1 Error: 0.780529 Iteration 2 Error: 0.111932 Iteration 3 Error: 0.034558 Align patch 3 22 left Iteration 1 Error: 0.787599 Iteration 2 Error: 0.098930 Iteration 3 Error: 0.028433 Align patch 4 21 left Iteration 1 Error: 0.564567 Iteration 2 Error: 0.096038 Iteration 3 Error: 0.027984 Align patch 5 20 left Iteration 1 Error: 0.935435 Iteration 2 Error: 0.161556 Iteration 3 Error: 0.042734 Align patch 6 19 left Iteration 1 Error: 0.876826 Iteration 2 Error: 0.191041 Iteration 3 Error: 0.059742 Iteration 4 Error: 0.013021 Align patch 7 18 left Iteration 1 Error: 0.590098 Iteration 2 Error: 0.103034 Iteration 3 Error: 0.017368 Align patch 8 17 left Iteration 1 Error: 0.737461 Iteration 2 Error: 0.147902 Iteration 3 Error: 0.032467 Align patch 9 16 left Iteration 1 Error: 0.739498 Iteration 2 Error: 0.128221 Iteration 3 Error: 0.030233 Align patch 10 15 left Iteration 1 Error: 1.616265 Iteration 2 Error: 0.245768 Iteration 3 Error: 0.055110 Iteration 4 Error: 0.014620 Align patch 11 14 left Iteration 1 Error: 0.849721 Iteration 2 Error: 0.201258 Iteration 3 Error: 0.068236 Iteration 4 Error: 0.025473 Align patch 12 13 left Iteration 1 Error: 0.819650 Iteration 2 Error: 0.135375 Iteration 3 Error: 0.024481 Align patch 13 12 left Iteration 1 Error: 0.459286 Iteration 2 Error: 0.116323 Iteration 3 Error: 0.030146 Align patch 14 11 left Iteration 1 Error: 0.646082 Iteration 2 Error: 0.138308 Iteration 3 Error: 0.030060 Align patch 15 10 left Iteration 1 Error: 0.750778 Iteration 2 Error: 0.078223 Iteration 3 Error: 0.026608 Align patch 16 9 left Iteration 1 Error: 0.986523 Iteration 2 Error: 0.127818 Iteration 3 Error: 0.037073 Align patch 17 8 left Iteration 1 Error: 0.785724 Iteration 2 Error: 0.093725 Iteration 3 Error: 0.045278 Align patch 18 7 left Iteration 1 Error: 0.664998 Iteration 2 Error: 0.102587 Iteration 3 Error: 0.040914 Align patch 19 6 left Iteration 1 Error: 0.666283 Iteration 2 Error: 0.104757 Iteration 3 Error: 0.029169 Align patch 20 5 left Iteration 1 Error: 0.521896 Iteration 2 Error: 0.134129 Iteration 3 Error: 0.056649 Iteration 4 Error: 0.014646 Align patch 21 4 left Iteration 1 Error: 0.717957 Iteration 2 Error: 0.089111 Iteration 3 Error: 0.021244 Align patch 22 3 left Iteration 1 Error: 0.843891 Iteration 2 Error: 0.206618 Iteration 3 Error: 0.055522 Iteration 4 Error: 0.032215 Align patch 23 2 left Iteration 1 Error: 0.767474 Iteration 2 Error: 0.218292 Iteration 3 Error: 0.057489 Iteration 4 Error: 0.020534 Align patch 24 1 left Iteration 1 Error: 0.932482 Iteration 2 Error: 0.187607 Iteration 3 Error: 0.032964 Align patch 25 0 left Iteration 1 Error: 0.824235 Iteration 2 Error: 0.213343 Iteration 3 Error: 0.083875 Iteration 4 Error: 0.030999 3D Fitting completed. Patch alignment time: 15.04(sec) Local motion has been corrected. Process thread exits. Computational time: 23.590570 sec Total time: 29.238579 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00009hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00009hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.543220s Reading file: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00009hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.500042s ........................................ >>>>>>TIME<<<<<< FFT: 0.944124s Defocus_U Defocus_V Angle CCC 14062.52 13144.52 88.92 0.031315 Final Values Defocus_U Defocus_V Angle CCC 14068.65 13150.81 83.42 0.040775 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00010sq_v01_00009hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00009hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 40.31 6.82 Num Hot pixels: 226 Hot pixel threshold: 81.21 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.968605 Iteration 2 Error: 0.218519 Iteration 3 Error: 0.066963 Iteration 4 Error: 0.029279 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.15 -0.34 ...... Frame ( 3) shift: -0.30 -0.68 ...... Frame ( 4) shift: -0.45 -1.03 ...... Frame ( 5) shift: -0.60 -1.37 ...... Frame ( 6) shift: -0.68 -1.57 ...... Frame ( 7) shift: -0.68 -1.62 ...... Frame ( 8) shift: -0.68 -1.68 ...... Frame ( 9) shift: -0.65 -1.67 ...... Frame ( 10) shift: -0.58 -1.61 ...... Frame ( 11) shift: -0.51 -1.55 ...... Frame ( 12) shift: -0.45 -1.48 ...... Frame ( 13) shift: -0.39 -1.42 ...... Frame ( 14) shift: -0.32 -1.36 ...... Frame ( 15) shift: -0.24 -1.29 ...... Frame ( 16) shift: -0.13 -1.21 ...... Frame ( 17) shift: -0.03 -1.14 ...... Frame ( 18) shift: 0.09 -1.05 ...... Frame ( 19) shift: 0.21 -0.96 ...... Frame ( 20) shift: 0.33 -0.87 ...... Frame ( 21) shift: 0.41 -0.79 ...... Frame ( 22) shift: 0.44 -0.73 ...... Frame ( 23) shift: 0.47 -0.66 ...... Frame ( 24) shift: 0.48 -0.61 ...... Frame ( 25) shift: 0.49 -0.57 ...... Frame ( 26) shift: 0.49 -0.53 ...... Frame ( 27) shift: 0.52 -0.50 ...... Frame ( 28) shift: 0.57 -0.46 ...... Frame ( 29) shift: 0.62 -0.42 ...... Frame ( 30) shift: 0.69 -0.34 ...... Frame ( 31) shift: 0.77 -0.22 ...... Frame ( 32) shift: 0.86 -0.09 ...... Frame ( 33) shift: 0.90 -0.06 ...... Frame ( 34) shift: 0.92 -0.11 ...... Frame ( 35) shift: 0.93 -0.17 ...... Frame ( 36) shift: 0.95 -0.19 ...... Frame ( 37) shift: 1.00 -0.17 ...... Frame ( 38) shift: 1.05 -0.15 ...... Frame ( 39) shift: 1.09 -0.14 ...... Frame ( 40) shift: 1.14 -0.12 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.377126 Iteration 2 Error: 0.329681 Iteration 3 Error: 0.058469 Iteration 4 Error: 0.015969 Align patch 2 23 left Iteration 1 Error: 1.257238 Iteration 2 Error: 0.182354 Iteration 3 Error: 0.063292 Iteration 4 Error: 0.020008 Align patch 3 22 left Iteration 1 Error: 0.528282 Iteration 2 Error: 0.110875 Iteration 3 Error: 0.032453 Align patch 4 21 left Iteration 1 Error: 0.566373 Iteration 2 Error: 0.170907 Iteration 3 Error: 0.054804 Iteration 4 Error: 0.019028 Align patch 5 20 left Iteration 1 Error: 0.545352 Iteration 2 Error: 0.239740 Iteration 3 Error: 0.086617 Iteration 4 Error: 0.039700 Align patch 6 19 left Iteration 1 Error: 1.087799 Iteration 2 Error: 0.201469 Iteration 3 Error: 0.053769 Iteration 4 Error: 0.014921 Align patch 7 18 left Iteration 1 Error: 1.291634 Iteration 2 Error: 0.197791 Iteration 3 Error: 0.053469 Iteration 4 Error: 0.014907 Align patch 8 17 left Iteration 1 Error: 0.774247 Iteration 2 Error: 0.180418 Iteration 3 Error: 0.080011 Iteration 4 Error: 0.033356 Align patch 9 16 left Iteration 1 Error: 0.505071 Iteration 2 Error: 0.090584 Iteration 3 Error: 0.029048 Align patch 10 15 left Iteration 1 Error: 0.845857 Iteration 2 Error: 0.236470 Iteration 3 Error: 0.074835 Iteration 4 Error: 0.029938 Align patch 11 14 left Iteration 1 Error: 1.665579 Iteration 2 Error: 0.166186 Iteration 3 Error: 0.045444 Align patch 12 13 left Iteration 1 Error: 0.697779 Iteration 2 Error: 0.095944 Iteration 3 Error: 0.020345 Align patch 13 12 left Iteration 1 Error: 0.649504 Iteration 2 Error: 0.181008 Iteration 3 Error: 0.068518 Iteration 4 Error: 0.026383 Align patch 14 11 left Iteration 1 Error: 1.083719 Iteration 2 Error: 0.108593 Iteration 3 Error: 0.032283 Align patch 15 10 left Iteration 1 Error: 0.783634 Iteration 2 Error: 0.165523 Iteration 3 Error: 0.057175 Iteration 4 Error: 0.022123 Align patch 16 9 left Iteration 1 Error: 0.660399 Iteration 2 Error: 0.113213 Iteration 3 Error: 0.024879 Align patch 17 8 left Iteration 1 Error: 0.585349 Iteration 2 Error: 0.103453 Iteration 3 Error: 0.025702 Align patch 18 7 left Iteration 1 Error: 0.811050 Iteration 2 Error: 0.115411 Iteration 3 Error: 0.028591 Align patch 19 6 left Iteration 1 Error: 0.459662 Iteration 2 Error: 0.073044 Iteration 3 Error: 0.021469 Align patch 20 5 left Iteration 1 Error: 2.236573 Iteration 2 Error: 0.334475 Iteration 3 Error: 0.133891 Iteration 4 Error: 0.057425 Iteration 5 Error: 0.025145 Align patch 21 4 left Iteration 1 Error: 0.855891 Iteration 2 Error: 0.123221 Iteration 3 Error: 0.032666 Align patch 22 3 left Iteration 1 Error: 0.762054 Iteration 2 Error: 0.098626 Iteration 3 Error: 0.025263 Align patch 23 2 left Iteration 1 Error: 0.668029 Iteration 2 Error: 0.185349 Iteration 3 Error: 0.058007 Iteration 4 Error: 0.014758 Align patch 24 1 left Iteration 1 Error: 0.752476 Iteration 2 Error: 0.116646 Iteration 3 Error: 0.036142 Align patch 25 0 left Iteration 1 Error: 1.746964 Iteration 2 Error: 0.342212 Iteration 3 Error: 0.091314 Iteration 4 Error: 0.033303 3D Fitting completed. Patch alignment time: 15.96(sec) Local motion has been corrected. Process thread exits. Computational time: 24.736189 sec Total time: 30.595728 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00009hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00009hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.786808s Reading file: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00009hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.455399s ........................................ >>>>>>TIME<<<<<< FFT: 1.055791s Defocus_U Defocus_V Angle CCC 12074.28 11449.19 86.18 0.055674 Final Values Defocus_U Defocus_V Angle CCC 12085.22 11460.13 84.93 0.092118 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00010sq_v01_00010hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00010hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.001e-01 CC threshold: 0.735 Mean Std: 39.21 6.65 Num Hot pixels: 227 Hot pixel threshold: 79.14 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.167133 Iteration 2 Error: 0.309057 Iteration 3 Error: 0.110431 Iteration 4 Error: 0.052087 Iteration 5 Error: 0.021754 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.01 -0.13 ...... Frame ( 3) shift: -0.02 -0.26 ...... Frame ( 4) shift: -0.03 -0.39 ...... Frame ( 5) shift: -0.04 -0.52 ...... Frame ( 6) shift: 0.02 -0.58 ...... Frame ( 7) shift: 0.16 -0.57 ...... Frame ( 8) shift: 0.30 -0.56 ...... Frame ( 9) shift: 0.42 -0.49 ...... Frame ( 10) shift: 0.51 -0.37 ...... Frame ( 11) shift: 0.61 -0.24 ...... Frame ( 12) shift: 0.71 -0.15 ...... Frame ( 13) shift: 0.82 -0.10 ...... Frame ( 14) shift: 0.92 -0.04 ...... Frame ( 15) shift: 1.02 0.02 ...... Frame ( 16) shift: 1.11 0.09 ...... Frame ( 17) shift: 1.19 0.16 ...... Frame ( 18) shift: 1.27 0.21 ...... Frame ( 19) shift: 1.34 0.25 ...... Frame ( 20) shift: 1.40 0.29 ...... Frame ( 21) shift: 1.45 0.36 ...... Frame ( 22) shift: 1.47 0.45 ...... Frame ( 23) shift: 1.50 0.55 ...... Frame ( 24) shift: 1.53 0.62 ...... Frame ( 25) shift: 1.59 0.65 ...... Frame ( 26) shift: 1.64 0.69 ...... Frame ( 27) shift: 1.67 0.71 ...... Frame ( 28) shift: 1.68 0.73 ...... Frame ( 29) shift: 1.70 0.75 ...... Frame ( 30) shift: 1.74 0.78 ...... Frame ( 31) shift: 1.80 0.82 ...... Frame ( 32) shift: 1.86 0.86 ...... Frame ( 33) shift: 1.92 0.91 ...... Frame ( 34) shift: 1.97 0.97 ...... Frame ( 35) shift: 2.03 1.02 ...... Frame ( 36) shift: 2.10 1.08 ...... Frame ( 37) shift: 2.20 1.14 ...... Frame ( 38) shift: 2.30 1.21 ...... Frame ( 39) shift: 2.40 1.27 ...... Frame ( 40) shift: 2.50 1.33 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.865853 Iteration 2 Error: 0.309339 Iteration 3 Error: 0.144408 Iteration 4 Error: 0.097635 Iteration 5 Error: 0.049264 Align patch 2 23 left Iteration 1 Error: 0.886530 Iteration 2 Error: 0.383589 Iteration 3 Error: 0.215348 Iteration 4 Error: 0.123310 Iteration 5 Error: 0.070363 Align patch 2 23 left Iteration 1 Error: 1.664707 Iteration 2 Error: 0.279760 Iteration 3 Error: 0.068065 Iteration 4 Error: 0.017703 Align patch 3 22 left Iteration 1 Error: 1.197106 Iteration 2 Error: 0.346778 Iteration 3 Error: 0.196766 Iteration 4 Error: 0.097656 Iteration 5 Error: 0.056098 Align patch 3 22 left Iteration 1 Error: 1.357900 Iteration 2 Error: 0.256461 Iteration 3 Error: 0.057321 Iteration 4 Error: 0.015656 Align patch 4 21 left Iteration 1 Error: 0.828476 Iteration 2 Error: 0.200979 Iteration 3 Error: 0.051138 Iteration 4 Error: 0.021621 Align patch 5 20 left Iteration 1 Error: 0.834294 Iteration 2 Error: 0.190428 Iteration 3 Error: 0.031812 Align patch 6 19 left Iteration 1 Error: 1.291208 Iteration 2 Error: 0.221662 Iteration 3 Error: 0.058190 Iteration 4 Error: 0.019833 Align patch 7 18 left Iteration 1 Error: 1.166581 Iteration 2 Error: 0.257151 Iteration 3 Error: 0.079650 Iteration 4 Error: 0.033657 Align patch 8 17 left Iteration 1 Error: 1.086837 Iteration 2 Error: 0.362284 Iteration 3 Error: 0.137362 Iteration 4 Error: 0.066161 Iteration 5 Error: 0.032048 Align patch 9 16 left Iteration 1 Error: 0.745362 Iteration 2 Error: 0.268641 Iteration 3 Error: 0.060407 Iteration 4 Error: 0.026947 Align patch 10 15 left Iteration 1 Error: 0.677252 Iteration 2 Error: 0.144851 Iteration 3 Error: 0.033874 Align patch 11 14 left Iteration 1 Error: 0.821244 Iteration 2 Error: 0.192232 Iteration 3 Error: 0.107857 Iteration 4 Error: 0.056209 Iteration 5 Error: 0.031181 Align patch 12 13 left Iteration 1 Error: 0.535728 Iteration 2 Error: 0.168246 Iteration 3 Error: 0.057980 Iteration 4 Error: 0.028944 Align patch 13 12 left Iteration 1 Error: 1.145265 Iteration 2 Error: 0.122338 Iteration 3 Error: 0.045589 Align patch 14 11 left Iteration 1 Error: 0.700765 Iteration 2 Error: 0.163052 Iteration 3 Error: 0.092658 Iteration 4 Error: 0.056879 Iteration 5 Error: 0.032608 Align patch 15 10 left Iteration 1 Error: 0.779726 Iteration 2 Error: 0.220388 Iteration 3 Error: 0.047904 Align patch 16 9 left Iteration 1 Error: 0.906451 Iteration 2 Error: 0.165469 Iteration 3 Error: 0.027599 Align patch 17 8 left Iteration 1 Error: 0.682044 Iteration 2 Error: 0.124171 Iteration 3 Error: 0.035774 Align patch 18 7 left Iteration 1 Error: 0.642344 Iteration 2 Error: 0.167333 Iteration 3 Error: 0.082910 Iteration 4 Error: 0.035776 Align patch 19 6 left Iteration 1 Error: 1.007815 Iteration 2 Error: 0.236448 Iteration 3 Error: 0.121830 Iteration 4 Error: 0.056855 Iteration 5 Error: 0.026810 Align patch 20 5 left Iteration 1 Error: 1.183404 Iteration 2 Error: 0.343077 Iteration 3 Error: 0.095748 Iteration 4 Error: 0.032811 Align patch 21 4 left Iteration 1 Error: 1.243127 Iteration 2 Error: 0.242774 Iteration 3 Error: 0.045193 Align patch 22 3 left Iteration 1 Error: 0.562161 Iteration 2 Error: 0.139558 Iteration 3 Error: 0.057338 Iteration 4 Error: 0.022486 Align patch 23 2 left Iteration 1 Error: 0.630320 Iteration 2 Error: 0.181624 Iteration 3 Error: 0.047971 Align patch 24 1 left Iteration 1 Error: 1.042571 Iteration 2 Error: 0.266968 Iteration 3 Error: 0.107713 Iteration 4 Error: 0.039845 Align patch 25 0 left Iteration 1 Error: 0.938749 Iteration 2 Error: 0.147170 Iteration 3 Error: 0.060489 Iteration 4 Error: 0.016987 3D Fitting completed. Patch alignment time: 19.02(sec) Local motion has been corrected. Process thread exits. Computational time: 28.490147 sec Total time: 34.653942 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00010hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00010hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.798324s Reading file: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00010hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.233209s ........................................ >>>>>>TIME<<<<<< FFT: 1.053280s Defocus_U Defocus_V Angle CCC 9089.85 9906.25 15.64 0.027819 Final Values Defocus_U Defocus_V Angle CCC 9074.20 9940.65 15.95 0.051300 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00010sq_v01_00010hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00010hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 37.00 6.48 Num Hot pixels: 199 Hot pixel threshold: 75.89 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.622549 Iteration 2 Error: 0.123754 Iteration 3 Error: 0.033221 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.15 0.01 ...... Frame ( 3) shift: -0.30 0.01 ...... Frame ( 4) shift: -0.45 0.02 ...... Frame ( 5) shift: -0.60 0.03 ...... Frame ( 6) shift: -0.67 0.05 ...... Frame ( 7) shift: -0.67 0.09 ...... Frame ( 8) shift: -0.66 0.13 ...... Frame ( 9) shift: -0.62 0.15 ...... Frame ( 10) shift: -0.56 0.16 ...... Frame ( 11) shift: -0.49 0.18 ...... Frame ( 12) shift: -0.43 0.20 ...... Frame ( 13) shift: -0.38 0.23 ...... Frame ( 14) shift: -0.33 0.27 ...... Frame ( 15) shift: -0.33 0.30 ...... Frame ( 16) shift: -0.38 0.33 ...... Frame ( 17) shift: -0.43 0.36 ...... Frame ( 18) shift: -0.42 0.41 ...... Frame ( 19) shift: -0.37 0.48 ...... Frame ( 20) shift: -0.31 0.55 ...... Frame ( 21) shift: -0.27 0.60 ...... Frame ( 22) shift: -0.25 0.65 ...... Frame ( 23) shift: -0.23 0.69 ...... Frame ( 24) shift: -0.21 0.74 ...... Frame ( 25) shift: -0.19 0.80 ...... Frame ( 26) shift: -0.17 0.86 ...... Frame ( 27) shift: -0.14 0.94 ...... Frame ( 28) shift: -0.10 1.04 ...... Frame ( 29) shift: -0.07 1.15 ...... Frame ( 30) shift: -0.03 1.19 ...... Frame ( 31) shift: 0.02 1.15 ...... Frame ( 32) shift: 0.06 1.12 ...... Frame ( 33) shift: 0.10 1.13 ...... Frame ( 34) shift: 0.12 1.17 ...... Frame ( 35) shift: 0.14 1.21 ...... Frame ( 36) shift: 0.13 1.23 ...... Frame ( 37) shift: 0.08 1.22 ...... Frame ( 38) shift: 0.03 1.21 ...... Frame ( 39) shift: -0.02 1.19 ...... Frame ( 40) shift: -0.07 1.18 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.762333 Iteration 2 Error: 0.145749 Iteration 3 Error: 0.033400 Align patch 2 23 left Iteration 1 Error: 0.678909 Iteration 2 Error: 0.080705 Iteration 3 Error: 0.026535 Align patch 3 22 left Iteration 1 Error: 0.612123 Iteration 2 Error: 0.130317 Iteration 3 Error: 0.045213 Align patch 4 21 left Iteration 1 Error: 0.880978 Iteration 2 Error: 0.149530 Iteration 3 Error: 0.039811 Align patch 5 20 left Iteration 1 Error: 0.684862 Iteration 2 Error: 0.152738 Iteration 3 Error: 0.022460 Align patch 6 19 left Iteration 1 Error: 0.820272 Iteration 2 Error: 0.241821 Iteration 3 Error: 0.053882 Iteration 4 Error: 0.018206 Align patch 7 18 left Iteration 1 Error: 0.768390 Iteration 2 Error: 0.128774 Iteration 3 Error: 0.042894 Align patch 8 17 left Iteration 1 Error: 1.076794 Iteration 2 Error: 0.165205 Iteration 3 Error: 0.033431 Align patch 9 16 left Iteration 1 Error: 0.957450 Iteration 2 Error: 0.169574 Iteration 3 Error: 0.068325 Iteration 4 Error: 0.021757 Align patch 10 15 left Iteration 1 Error: 0.724265 Iteration 2 Error: 0.193476 Iteration 3 Error: 0.058733 Iteration 4 Error: 0.023270 Align patch 11 14 left Iteration 1 Error: 1.398692 Iteration 2 Error: 0.354594 Iteration 3 Error: 0.124381 Iteration 4 Error: 0.082619 Iteration 5 Error: 0.032028 Align patch 12 13 left Iteration 1 Error: 1.846583 Iteration 2 Error: 0.199322 Iteration 3 Error: 0.049991 Align patch 13 12 left Iteration 1 Error: 0.908477 Iteration 2 Error: 0.158226 Iteration 3 Error: 0.046527 Align patch 14 11 left Iteration 1 Error: 0.682999 Iteration 2 Error: 0.215980 Iteration 3 Error: 0.063089 Iteration 4 Error: 0.025079 Align patch 15 10 left Iteration 1 Error: 0.856107 Iteration 2 Error: 0.211712 Iteration 3 Error: 0.038756 Align patch 16 9 left Iteration 1 Error: 1.593863 Iteration 2 Error: 0.288393 Iteration 3 Error: 0.045589 Align patch 17 8 left Iteration 1 Error: 0.894849 Iteration 2 Error: 0.198951 Iteration 3 Error: 0.068658 Iteration 4 Error: 0.018325 Align patch 18 7 left Iteration 1 Error: 1.271550 Iteration 2 Error: 0.144666 Iteration 3 Error: 0.033674 Align patch 19 6 left Iteration 1 Error: 0.801361 Iteration 2 Error: 0.253493 Iteration 3 Error: 0.080838 Iteration 4 Error: 0.039583 Align patch 20 5 left Iteration 1 Error: 0.634067 Iteration 2 Error: 0.075675 Iteration 3 Error: 0.016882 Align patch 21 4 left Iteration 1 Error: 1.311824 Iteration 2 Error: 0.139818 Iteration 3 Error: 0.028816 Align patch 22 3 left Iteration 1 Error: 1.209702 Iteration 2 Error: 0.196272 Iteration 3 Error: 0.058320 Iteration 4 Error: 0.020181 Align patch 23 2 left Iteration 1 Error: 0.961298 Iteration 2 Error: 0.128229 Iteration 3 Error: 0.030384 Align patch 24 1 left Iteration 1 Error: 1.033037 Iteration 2 Error: 0.131162 Iteration 3 Error: 0.037977 Align patch 25 0 left Iteration 1 Error: 1.065741 Iteration 2 Error: 0.195804 Iteration 3 Error: 0.037742 3D Fitting completed. Patch alignment time: 15.90(sec) Local motion has been corrected. Process thread exits. Computational time: 24.427607 sec Total time: 32.042156 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00010hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00010hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.741919s Reading file: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00010hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.362311s ........................................ >>>>>>TIME<<<<<< FFT: 1.046585s Defocus_U Defocus_V Angle CCC 10601.58 10898.47 18.17 0.019402 Final Values Defocus_U Defocus_V Angle CCC 10698.46 10911.03 36.64 0.029949 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00010sq_v01_00010hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00010hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 40.80 6.85 Num Hot pixels: 214 Hot pixel threshold: 81.87 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.200722 Iteration 2 Error: 0.267743 Iteration 3 Error: 0.073051 Iteration 4 Error: 0.028319 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.05 0.05 ...... Frame ( 3) shift: -0.11 0.11 ...... Frame ( 4) shift: -0.16 0.16 ...... Frame ( 5) shift: -0.21 0.21 ...... Frame ( 6) shift: -0.19 0.26 ...... Frame ( 7) shift: -0.08 0.32 ...... Frame ( 8) shift: 0.03 0.37 ...... Frame ( 9) shift: 0.11 0.47 ...... Frame ( 10) shift: 0.17 0.61 ...... Frame ( 11) shift: 0.23 0.76 ...... Frame ( 12) shift: 0.31 0.87 ...... Frame ( 13) shift: 0.41 0.97 ...... Frame ( 14) shift: 0.52 1.06 ...... Frame ( 15) shift: 0.57 1.14 ...... Frame ( 16) shift: 0.57 1.21 ...... Frame ( 17) shift: 0.57 1.27 ...... Frame ( 18) shift: 0.58 1.36 ...... Frame ( 19) shift: 0.62 1.46 ...... Frame ( 20) shift: 0.65 1.56 ...... Frame ( 21) shift: 0.66 1.64 ...... Frame ( 22) shift: 0.65 1.70 ...... Frame ( 23) shift: 0.64 1.75 ...... Frame ( 24) shift: 0.70 1.80 ...... Frame ( 25) shift: 0.85 1.85 ...... Frame ( 26) shift: 1.00 1.89 ...... Frame ( 27) shift: 1.08 1.91 ...... Frame ( 28) shift: 1.10 1.90 ...... Frame ( 29) shift: 1.12 1.89 ...... Frame ( 30) shift: 1.16 1.92 ...... Frame ( 31) shift: 1.22 1.99 ...... Frame ( 32) shift: 1.27 2.05 ...... Frame ( 33) shift: 1.29 2.06 ...... Frame ( 34) shift: 1.26 2.01 ...... Frame ( 35) shift: 1.24 1.97 ...... Frame ( 36) shift: 1.24 2.00 ...... Frame ( 37) shift: 1.27 2.11 ...... Frame ( 38) shift: 1.30 2.21 ...... Frame ( 39) shift: 1.33 2.32 ...... Frame ( 40) shift: 1.36 2.43 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.940828 Iteration 2 Error: 0.306927 Iteration 3 Error: 0.082060 Iteration 4 Error: 0.037245 Align patch 2 23 left Iteration 1 Error: 0.802857 Iteration 2 Error: 0.217792 Iteration 3 Error: 0.069085 Iteration 4 Error: 0.044774 Align patch 3 22 left Iteration 1 Error: 0.946751 Iteration 2 Error: 0.413431 Iteration 3 Error: 0.115068 Iteration 4 Error: 0.057689 Iteration 5 Error: 0.020416 Align patch 4 21 left Iteration 1 Error: 0.707779 Iteration 2 Error: 0.246355 Iteration 3 Error: 0.082350 Iteration 4 Error: 0.040933 Align patch 5 20 left Iteration 1 Error: 0.813188 Iteration 2 Error: 0.169630 Iteration 3 Error: 0.043610 Align patch 6 19 left Iteration 1 Error: 1.689309 Iteration 2 Error: 0.393687 Iteration 3 Error: 0.125054 Iteration 4 Error: 0.059104 Iteration 5 Error: 0.035523 Align patch 7 18 left Iteration 1 Error: 0.683129 Iteration 2 Error: 0.204410 Iteration 3 Error: 0.086316 Iteration 4 Error: 0.032231 Align patch 8 17 left Iteration 1 Error: 0.770142 Iteration 2 Error: 0.169573 Iteration 3 Error: 0.054270 Iteration 4 Error: 0.020886 Align patch 9 16 left Iteration 1 Error: 0.664430 Iteration 2 Error: 0.153066 Iteration 3 Error: 0.051711 Iteration 4 Error: 0.018413 Align patch 10 15 left Iteration 1 Error: 0.693702 Iteration 2 Error: 0.184906 Iteration 3 Error: 0.064891 Iteration 4 Error: 0.018743 Align patch 11 14 left Iteration 1 Error: 0.722777 Iteration 2 Error: 0.106541 Iteration 3 Error: 0.033488 Align patch 12 13 left Iteration 1 Error: 0.787152 Iteration 2 Error: 0.222893 Iteration 3 Error: 0.063635 Iteration 4 Error: 0.031683 Align patch 13 12 left Iteration 1 Error: 0.480189 Iteration 2 Error: 0.176310 Iteration 3 Error: 0.053952 Iteration 4 Error: 0.028304 Align patch 14 11 left Iteration 1 Error: 0.857277 Iteration 2 Error: 0.149433 Iteration 3 Error: 0.030387 Align patch 15 10 left Iteration 1 Error: 0.705207 Iteration 2 Error: 0.137050 Iteration 3 Error: 0.052957 Iteration 4 Error: 0.013709 Align patch 16 9 left Iteration 1 Error: 1.022219 Iteration 2 Error: 0.190914 Iteration 3 Error: 0.074660 Iteration 4 Error: 0.020900 Align patch 17 8 left Iteration 1 Error: 0.631986 Iteration 2 Error: 0.141441 Iteration 3 Error: 0.040328 Align patch 18 7 left Iteration 1 Error: 0.749209 Iteration 2 Error: 0.152691 Iteration 3 Error: 0.052780 Iteration 4 Error: 0.016762 Align patch 19 6 left Iteration 1 Error: 1.139973 Iteration 2 Error: 0.144041 Iteration 3 Error: 0.048893 Align patch 20 5 left Iteration 1 Error: 0.813591 Iteration 2 Error: 0.213070 Iteration 3 Error: 0.069195 Iteration 4 Error: 0.021422 Align patch 21 4 left Iteration 1 Error: 0.738534 Iteration 2 Error: 0.152180 Iteration 3 Error: 0.028492 Align patch 22 3 left Iteration 1 Error: 0.403163 Iteration 2 Error: 0.052340 Iteration 3 Error: 0.016768 Align patch 23 2 left Iteration 1 Error: 0.579404 Iteration 2 Error: 0.108423 Iteration 3 Error: 0.029268 Align patch 24 1 left Iteration 1 Error: 1.202606 Iteration 2 Error: 0.217189 Iteration 3 Error: 0.060865 Iteration 4 Error: 0.017686 Align patch 25 0 left Iteration 1 Error: 0.917545 Iteration 2 Error: 0.195381 Iteration 3 Error: 0.068056 Iteration 4 Error: 0.026711 3D Fitting completed. Patch alignment time: 17.07(sec) Local motion has been corrected. Process thread exits. Computational time: 26.113644 sec Total time: 33.190414 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00010hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00010hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.804986s Reading file: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00010hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.411607s ........................................ >>>>>>TIME<<<<<< FFT: 1.068740s Defocus_U Defocus_V Angle CCC 11064.43 11861.45 6.47 0.040644 Final Values Defocus_U Defocus_V Angle CCC 11089.43 11886.45 5.22 0.072034 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00010sq_v01_00010hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00010hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 1.000e-01 CC threshold: 0.734 Mean Std: 38.28 6.59 Num Hot pixels: 227 Hot pixel threshold: 77.83 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.000889 Iteration 2 Error: 0.190010 Iteration 3 Error: 0.058639 Iteration 4 Error: 0.023697 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.07 -0.19 ...... Frame ( 3) shift: 0.14 -0.38 ...... Frame ( 4) shift: 0.22 -0.57 ...... Frame ( 5) shift: 0.29 -0.76 ...... Frame ( 6) shift: 0.29 -0.86 ...... Frame ( 7) shift: 0.22 -0.86 ...... Frame ( 8) shift: 0.15 -0.86 ...... Frame ( 9) shift: 0.19 -0.83 ...... Frame ( 10) shift: 0.31 -0.78 ...... Frame ( 11) shift: 0.44 -0.72 ...... Frame ( 12) shift: 0.54 -0.71 ...... Frame ( 13) shift: 0.59 -0.74 ...... Frame ( 14) shift: 0.64 -0.77 ...... Frame ( 15) shift: 0.69 -0.75 ...... Frame ( 16) shift: 0.74 -0.68 ...... Frame ( 17) shift: 0.78 -0.62 ...... Frame ( 18) shift: 0.81 -0.57 ...... Frame ( 19) shift: 0.84 -0.54 ...... Frame ( 20) shift: 0.87 -0.51 ...... Frame ( 21) shift: 0.92 -0.45 ...... Frame ( 22) shift: 0.98 -0.38 ...... Frame ( 23) shift: 1.04 -0.31 ...... Frame ( 24) shift: 1.12 -0.26 ...... Frame ( 25) shift: 1.22 -0.22 ...... Frame ( 26) shift: 1.33 -0.19 ...... Frame ( 27) shift: 1.40 -0.15 ...... Frame ( 28) shift: 1.44 -0.10 ...... Frame ( 29) shift: 1.47 -0.06 ...... Frame ( 30) shift: 1.50 -0.03 ...... Frame ( 31) shift: 1.52 -0.03 ...... Frame ( 32) shift: 1.54 -0.02 ...... Frame ( 33) shift: 1.58 0.04 ...... Frame ( 34) shift: 1.62 0.15 ...... Frame ( 35) shift: 1.67 0.27 ...... Frame ( 36) shift: 1.72 0.35 ...... Frame ( 37) shift: 1.77 0.39 ...... Frame ( 38) shift: 1.82 0.42 ...... Frame ( 39) shift: 1.87 0.46 ...... Frame ( 40) shift: 1.92 0.50 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.766429 Iteration 2 Error: 0.150747 Iteration 3 Error: 0.049440 Align patch 2 23 left Iteration 1 Error: 1.090630 Iteration 2 Error: 0.184573 Iteration 3 Error: 0.051850 Iteration 4 Error: 0.021779 Align patch 3 22 left Iteration 1 Error: 1.147273 Iteration 2 Error: 0.319658 Iteration 3 Error: 0.097993 Iteration 4 Error: 0.028425 Align patch 4 21 left Iteration 1 Error: 0.497866 Iteration 2 Error: 0.145842 Iteration 3 Error: 0.048014 Align patch 5 20 left Iteration 1 Error: 1.241910 Iteration 2 Error: 0.367942 Iteration 3 Error: 0.142947 Iteration 4 Error: 0.036082 Align patch 6 19 left Iteration 1 Error: 1.713289 Iteration 2 Error: 0.407907 Iteration 3 Error: 0.145021 Iteration 4 Error: 0.049925 Align patch 7 18 left Iteration 1 Error: 1.287672 Iteration 2 Error: 0.342365 Iteration 3 Error: 0.182611 Iteration 4 Error: 0.090295 Iteration 5 Error: 0.042022 Align patch 8 17 left Iteration 1 Error: 0.872740 Iteration 2 Error: 0.320309 Iteration 3 Error: 0.131132 Iteration 4 Error: 0.083749 Iteration 5 Error: 0.037638 Align patch 9 16 left Iteration 1 Error: 0.766862 Iteration 2 Error: 0.140256 Iteration 3 Error: 0.052087 Iteration 4 Error: 0.014970 Align patch 10 15 left Iteration 1 Error: 1.541523 Iteration 2 Error: 0.316539 Iteration 3 Error: 0.057406 Iteration 4 Error: 0.027527 Align patch 11 14 left Iteration 1 Error: 0.853681 Iteration 2 Error: 0.319418 Iteration 3 Error: 0.108416 Iteration 4 Error: 0.042137 Align patch 12 13 left Iteration 1 Error: 1.410970 Iteration 2 Error: 0.261326 Iteration 3 Error: 0.063367 Iteration 4 Error: 0.025715 Align patch 13 12 left Iteration 1 Error: 1.039013 Iteration 2 Error: 0.209543 Iteration 3 Error: 0.071306 Iteration 4 Error: 0.015789 Align patch 14 11 left Iteration 1 Error: 0.781366 Iteration 2 Error: 0.203818 Iteration 3 Error: 0.046631 Align patch 15 10 left Iteration 1 Error: 0.943367 Iteration 2 Error: 0.220298 Iteration 3 Error: 0.082343 Iteration 4 Error: 0.026516 Align patch 16 9 left Iteration 1 Error: 1.424228 Iteration 2 Error: 0.248592 Iteration 3 Error: 0.098212 Iteration 4 Error: 0.046770 Align patch 17 8 left Iteration 1 Error: 0.783777 Iteration 2 Error: 0.232110 Iteration 3 Error: 0.086421 Iteration 4 Error: 0.027953 Align patch 18 7 left Iteration 1 Error: 0.691663 Iteration 2 Error: 0.143151 Iteration 3 Error: 0.037486 Align patch 19 6 left Iteration 1 Error: 1.015371 Iteration 2 Error: 0.184878 Iteration 3 Error: 0.056560 Iteration 4 Error: 0.028680 Align patch 20 5 left Iteration 1 Error: 1.588228 Iteration 2 Error: 0.276704 Iteration 3 Error: 0.053309 Iteration 4 Error: 0.017794 Align patch 21 4 left Iteration 1 Error: 0.965195 Iteration 2 Error: 0.240161 Iteration 3 Error: 0.044754 Align patch 22 3 left Iteration 1 Error: 0.601042 Iteration 2 Error: 0.119769 Iteration 3 Error: 0.031837 Align patch 23 2 left Iteration 1 Error: 1.168406 Iteration 2 Error: 0.160589 Iteration 3 Error: 0.028244 Align patch 24 1 left Iteration 1 Error: 0.965295 Iteration 2 Error: 0.306824 Iteration 3 Error: 0.091816 Iteration 4 Error: 0.041854 Align patch 25 0 left Iteration 1 Error: 1.208539 Iteration 2 Error: 0.261369 Iteration 3 Error: 0.050324 Iteration 4 Error: 0.019841 3D Fitting completed. Patch alignment time: 17.08(sec) Local motion has been corrected. Process thread exits. Computational time: 25.927259 sec Total time: 31.618097 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00010hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00010hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.691964s Reading file: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00010hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.285761s ........................................ >>>>>>TIME<<<<<< FFT: 1.022450s Defocus_U Defocus_V Angle CCC 15144.54 14492.20 89.39 0.037493 Final Values Defocus_U Defocus_V Angle CCC 14493.76 15142.98 0.02 0.055588 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00010sq_v01_00011hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00011hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 41.88 7.01 Num Hot pixels: 226 Hot pixel threshold: 83.91 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.181414 Iteration 2 Error: 0.196446 Iteration 3 Error: 0.049272 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.07 0.11 ...... Frame ( 3) shift: -0.14 0.22 ...... Frame ( 4) shift: -0.21 0.33 ...... Frame ( 5) shift: -0.28 0.44 ...... Frame ( 6) shift: -0.29 0.53 ...... Frame ( 7) shift: -0.24 0.60 ...... Frame ( 8) shift: -0.18 0.68 ...... Frame ( 9) shift: -0.13 0.73 ...... Frame ( 10) shift: -0.09 0.75 ...... Frame ( 11) shift: -0.04 0.77 ...... Frame ( 12) shift: -0.02 0.84 ...... Frame ( 13) shift: -0.02 0.97 ...... Frame ( 14) shift: -0.02 1.11 ...... Frame ( 15) shift: 0.02 1.22 ...... Frame ( 16) shift: 0.10 1.32 ...... Frame ( 17) shift: 0.18 1.41 ...... Frame ( 18) shift: 0.22 1.51 ...... Frame ( 19) shift: 0.23 1.61 ...... Frame ( 20) shift: 0.24 1.70 ...... Frame ( 21) shift: 0.23 1.79 ...... Frame ( 22) shift: 0.19 1.87 ...... Frame ( 23) shift: 0.16 1.95 ...... Frame ( 24) shift: 0.19 2.00 ...... Frame ( 25) shift: 0.29 2.02 ...... Frame ( 26) shift: 0.39 2.03 ...... Frame ( 27) shift: 0.45 2.06 ...... Frame ( 28) shift: 0.46 2.08 ...... Frame ( 29) shift: 0.47 2.11 ...... Frame ( 30) shift: 0.51 2.12 ...... Frame ( 31) shift: 0.57 2.12 ...... Frame ( 32) shift: 0.64 2.12 ...... Frame ( 33) shift: 0.68 2.14 ...... Frame ( 34) shift: 0.69 2.19 ...... Frame ( 35) shift: 0.71 2.23 ...... Frame ( 36) shift: 0.71 2.27 ...... Frame ( 37) shift: 0.71 2.31 ...... Frame ( 38) shift: 0.71 2.35 ...... Frame ( 39) shift: 0.71 2.39 ...... Frame ( 40) shift: 0.71 2.42 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.101807 Iteration 2 Error: 0.239728 Iteration 3 Error: 0.090931 Iteration 4 Error: 0.035655 Align patch 2 23 left Iteration 1 Error: 1.674438 Iteration 2 Error: 0.228718 Iteration 3 Error: 0.062415 Iteration 4 Error: 0.027789 Align patch 3 22 left Iteration 1 Error: 0.562310 Iteration 2 Error: 0.114878 Iteration 3 Error: 0.040544 Align patch 4 21 left Iteration 1 Error: 0.578029 Iteration 2 Error: 0.123962 Iteration 3 Error: 0.030132 Align patch 5 20 left Iteration 1 Error: 0.866170 Iteration 2 Error: 0.118103 Iteration 3 Error: 0.029044 Align patch 6 19 left Iteration 1 Error: 2.958811 Iteration 2 Error: 0.450496 Iteration 3 Error: 0.150820 Iteration 4 Error: 0.063957 Iteration 5 Error: 0.036487 Align patch 7 18 left Iteration 1 Error: 1.784576 Iteration 2 Error: 0.339251 Iteration 3 Error: 0.098570 Iteration 4 Error: 0.051892 Iteration 5 Error: 0.018335 Align patch 8 17 left Iteration 1 Error: 0.646639 Iteration 2 Error: 0.141004 Iteration 3 Error: 0.050429 Iteration 4 Error: 0.020926 Align patch 9 16 left Iteration 1 Error: 0.532702 Iteration 2 Error: 0.078773 Iteration 3 Error: 0.014035 Align patch 10 15 left Iteration 1 Error: 0.850097 Iteration 2 Error: 0.153481 Iteration 3 Error: 0.027867 Align patch 11 14 left Iteration 1 Error: 0.884801 Iteration 2 Error: 0.243601 Iteration 3 Error: 0.060575 Iteration 4 Error: 0.034418 Align patch 12 13 left Iteration 1 Error: 0.747302 Iteration 2 Error: 0.126653 Iteration 3 Error: 0.054859 Iteration 4 Error: 0.031628 Align patch 13 12 left Iteration 1 Error: 0.771789 Iteration 2 Error: 0.108558 Iteration 3 Error: 0.037602 Align patch 14 11 left Iteration 1 Error: 0.636882 Iteration 2 Error: 0.147003 Iteration 3 Error: 0.038709 Align patch 15 10 left Iteration 1 Error: 0.919679 Iteration 2 Error: 0.118628 Iteration 3 Error: 0.024349 Align patch 16 9 left Iteration 1 Error: 0.881210 Iteration 2 Error: 0.144281 Iteration 3 Error: 0.034264 Align patch 17 8 left Iteration 1 Error: 0.705048 Iteration 2 Error: 0.103652 Iteration 3 Error: 0.029731 Align patch 18 7 left Iteration 1 Error: 0.846163 Iteration 2 Error: 0.116368 Iteration 3 Error: 0.028090 Align patch 19 6 left Iteration 1 Error: 0.631108 Iteration 2 Error: 0.112365 Iteration 3 Error: 0.026825 Align patch 20 5 left Iteration 1 Error: 0.637713 Iteration 2 Error: 0.103087 Iteration 3 Error: 0.018337 Align patch 21 4 left Iteration 1 Error: 0.744376 Iteration 2 Error: 0.130624 Iteration 3 Error: 0.027074 Align patch 22 3 left Iteration 1 Error: 1.351156 Iteration 2 Error: 0.111475 Iteration 3 Error: 0.024303 Align patch 23 2 left Iteration 1 Error: 1.066743 Iteration 2 Error: 0.116512 Iteration 3 Error: 0.026003 Align patch 24 1 left Iteration 1 Error: 0.545941 Iteration 2 Error: 0.120412 Iteration 3 Error: 0.028477 Align patch 25 0 left Iteration 1 Error: 0.511489 Iteration 2 Error: 0.101820 Iteration 3 Error: 0.021523 3D Fitting completed. Patch alignment time: 15.95(sec) Local motion has been corrected. Process thread exits. Computational time: 24.428228 sec Total time: 30.148787 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00011hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00011hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.649631s Reading file: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00011hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.952313s ........................................ >>>>>>TIME<<<<<< FFT: 0.982100s Defocus_U Defocus_V Angle CCC 9783.22 10580.09 13.70 0.056075 Final Values Defocus_U Defocus_V Angle CCC 9787.90 10597.29 14.01 0.102108 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00010sq_v01_00011hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00011hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.003e-01 CC threshold: 0.736 Mean Std: 40.64 6.92 Num Hot pixels: 195 Hot pixel threshold: 82.14 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.018076 Iteration 2 Error: 0.194062 Iteration 3 Error: 0.042403 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.14 0.02 ...... Frame ( 3) shift: -0.27 0.04 ...... Frame ( 4) shift: -0.41 0.07 ...... Frame ( 5) shift: -0.55 0.09 ...... Frame ( 6) shift: -0.62 0.17 ...... Frame ( 7) shift: -0.64 0.31 ...... Frame ( 8) shift: -0.66 0.44 ...... Frame ( 9) shift: -0.66 0.55 ...... Frame ( 10) shift: -0.65 0.62 ...... Frame ( 11) shift: -0.65 0.68 ...... Frame ( 12) shift: -0.63 0.74 ...... Frame ( 13) shift: -0.61 0.79 ...... Frame ( 14) shift: -0.58 0.83 ...... Frame ( 15) shift: -0.57 0.90 ...... Frame ( 16) shift: -0.57 0.99 ...... Frame ( 17) shift: -0.58 1.08 ...... Frame ( 18) shift: -0.57 1.17 ...... Frame ( 19) shift: -0.54 1.25 ...... Frame ( 20) shift: -0.51 1.33 ...... Frame ( 21) shift: -0.48 1.41 ...... Frame ( 22) shift: -0.47 1.48 ...... Frame ( 23) shift: -0.45 1.56 ...... Frame ( 24) shift: -0.48 1.60 ...... Frame ( 25) shift: -0.54 1.59 ...... Frame ( 26) shift: -0.61 1.58 ...... Frame ( 27) shift: -0.62 1.61 ...... Frame ( 28) shift: -0.58 1.66 ...... Frame ( 29) shift: -0.54 1.71 ...... Frame ( 30) shift: -0.49 1.73 ...... Frame ( 31) shift: -0.43 1.71 ...... Frame ( 32) shift: -0.38 1.69 ...... Frame ( 33) shift: -0.34 1.71 ...... Frame ( 34) shift: -0.34 1.77 ...... Frame ( 35) shift: -0.33 1.83 ...... Frame ( 36) shift: -0.34 1.90 ...... Frame ( 37) shift: -0.34 1.99 ...... Frame ( 38) shift: -0.35 2.08 ...... Frame ( 39) shift: -0.35 2.18 ...... Frame ( 40) shift: -0.36 2.27 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.832891 Iteration 2 Error: 0.330225 Iteration 3 Error: 0.094376 Iteration 4 Error: 0.020013 Align patch 2 23 left Iteration 1 Error: 1.239052 Iteration 2 Error: 0.246199 Iteration 3 Error: 0.049678 Align patch 3 22 left Iteration 1 Error: 0.437064 Iteration 2 Error: 0.163163 Iteration 3 Error: 0.047183 Align patch 4 21 left Iteration 1 Error: 0.617161 Iteration 2 Error: 0.083553 Iteration 3 Error: 0.017635 Align patch 5 20 left Iteration 1 Error: 0.749859 Iteration 2 Error: 0.136373 Iteration 3 Error: 0.022207 Align patch 6 19 left Iteration 1 Error: 2.061539 Iteration 2 Error: 0.546067 Iteration 3 Error: 0.137490 Iteration 4 Error: 0.058999 Iteration 5 Error: 0.027203 Align patch 7 18 left Iteration 1 Error: 0.671236 Iteration 2 Error: 0.144762 Iteration 3 Error: 0.068230 Iteration 4 Error: 0.033649 Align patch 8 17 left Iteration 1 Error: 0.694004 Iteration 2 Error: 0.134658 Iteration 3 Error: 0.040450 Align patch 9 16 left Iteration 1 Error: 0.465711 Iteration 2 Error: 0.058884 Iteration 3 Error: 0.012342 Align patch 10 15 left Iteration 1 Error: 0.502559 Iteration 2 Error: 0.066665 Iteration 3 Error: 0.008426 Align patch 11 14 left Iteration 1 Error: 1.179968 Iteration 2 Error: 0.298007 Iteration 3 Error: 0.102272 Iteration 4 Error: 0.047677 Align patch 12 13 left Iteration 1 Error: 0.680108 Iteration 2 Error: 0.174661 Iteration 3 Error: 0.074749 Iteration 4 Error: 0.034303 Align patch 13 12 left Iteration 1 Error: 0.540859 Iteration 2 Error: 0.102945 Iteration 3 Error: 0.029413 Align patch 14 11 left Iteration 1 Error: 0.733508 Iteration 2 Error: 0.123258 Iteration 3 Error: 0.024707 Align patch 15 10 left Iteration 1 Error: 0.554606 Iteration 2 Error: 0.099941 Iteration 3 Error: 0.021460 Align patch 16 9 left Iteration 1 Error: 0.616415 Iteration 2 Error: 0.112592 Iteration 3 Error: 0.035205 Align patch 17 8 left Iteration 1 Error: 0.731804 Iteration 2 Error: 0.085267 Iteration 3 Error: 0.021992 Align patch 18 7 left Iteration 1 Error: 0.540180 Iteration 2 Error: 0.070837 Iteration 3 Error: 0.014900 Align patch 19 6 left Iteration 1 Error: 0.736527 Iteration 2 Error: 0.119767 Iteration 3 Error: 0.035523 Align patch 20 5 left Iteration 1 Error: 0.574813 Iteration 2 Error: 0.120808 Iteration 3 Error: 0.019276 Align patch 21 4 left Iteration 1 Error: 0.593811 Iteration 2 Error: 0.077949 Iteration 3 Error: 0.014630 Align patch 22 3 left Iteration 1 Error: 0.748694 Iteration 2 Error: 0.138886 Iteration 3 Error: 0.029577 Align patch 23 2 left Iteration 1 Error: 1.146932 Iteration 2 Error: 0.182458 Iteration 3 Error: 0.039973 Align patch 24 1 left Iteration 1 Error: 0.761179 Iteration 2 Error: 0.164493 Iteration 3 Error: 0.042523 Align patch 25 0 left Iteration 1 Error: 0.857639 Iteration 2 Error: 0.147689 Iteration 3 Error: 0.031404 3D Fitting completed. Patch alignment time: 15.48(sec) Local motion has been corrected. Process thread exits. Computational time: 24.166107 sec Total time: 29.864332 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00011hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00011hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.671035s Reading file: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00011hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.639116s ........................................ >>>>>>TIME<<<<<< FFT: 1.046150s Defocus_U Defocus_V Angle CCC 10302.74 10802.74 3.96 0.046998 Final Values Defocus_U Defocus_V Angle CCC 10313.67 10826.18 4.92 0.083158 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00010sq_v01_00011hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00011hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 40.93 7.03 Num Hot pixels: 211 Hot pixel threshold: 83.11 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.763621 Iteration 2 Error: 0.123308 Iteration 3 Error: 0.023024 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.17 -0.05 ...... Frame ( 3) shift: -0.33 -0.09 ...... Frame ( 4) shift: -0.50 -0.14 ...... Frame ( 5) shift: -0.67 -0.18 ...... Frame ( 6) shift: -0.76 -0.19 ...... Frame ( 7) shift: -0.78 -0.16 ...... Frame ( 8) shift: -0.80 -0.14 ...... Frame ( 9) shift: -0.79 -0.09 ...... Frame ( 10) shift: -0.74 -0.03 ...... Frame ( 11) shift: -0.70 0.04 ...... Frame ( 12) shift: -0.67 0.11 ...... Frame ( 13) shift: -0.67 0.18 ...... Frame ( 14) shift: -0.67 0.26 ...... Frame ( 15) shift: -0.67 0.31 ...... Frame ( 16) shift: -0.67 0.35 ...... Frame ( 17) shift: -0.67 0.39 ...... Frame ( 18) shift: -0.65 0.44 ...... Frame ( 19) shift: -0.61 0.51 ...... Frame ( 20) shift: -0.58 0.58 ...... Frame ( 21) shift: -0.56 0.63 ...... Frame ( 22) shift: -0.56 0.67 ...... Frame ( 23) shift: -0.56 0.71 ...... Frame ( 24) shift: -0.57 0.74 ...... Frame ( 25) shift: -0.58 0.76 ...... Frame ( 26) shift: -0.59 0.78 ...... Frame ( 27) shift: -0.59 0.82 ...... Frame ( 28) shift: -0.58 0.89 ...... Frame ( 29) shift: -0.56 0.95 ...... Frame ( 30) shift: -0.53 1.00 ...... Frame ( 31) shift: -0.48 1.04 ...... Frame ( 32) shift: -0.43 1.07 ...... Frame ( 33) shift: -0.41 1.11 ...... Frame ( 34) shift: -0.41 1.17 ...... Frame ( 35) shift: -0.41 1.22 ...... Frame ( 36) shift: -0.43 1.26 ...... Frame ( 37) shift: -0.47 1.29 ...... Frame ( 38) shift: -0.51 1.33 ...... Frame ( 39) shift: -0.55 1.36 ...... Frame ( 40) shift: -0.59 1.39 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.537875 Iteration 2 Error: 0.348865 Iteration 3 Error: 0.110290 Iteration 4 Error: 0.036368 Align patch 2 23 left Iteration 1 Error: 0.738423 Iteration 2 Error: 0.157064 Iteration 3 Error: 0.034259 Align patch 3 22 left Iteration 1 Error: 0.496018 Iteration 2 Error: 0.075846 Iteration 3 Error: 0.028735 Align patch 4 21 left Iteration 1 Error: 0.396755 Iteration 2 Error: 0.049070 Align patch 5 20 left Iteration 1 Error: 0.418925 Iteration 2 Error: 0.086934 Iteration 3 Error: 0.017130 Align patch 6 19 left Iteration 1 Error: 1.772374 Iteration 2 Error: 0.472346 Iteration 3 Error: 0.116184 Iteration 4 Error: 0.037946 Align patch 7 18 left Iteration 1 Error: 0.969101 Iteration 2 Error: 0.190221 Iteration 3 Error: 0.077059 Iteration 4 Error: 0.032222 Align patch 8 17 left Iteration 1 Error: 0.523251 Iteration 2 Error: 0.088264 Iteration 3 Error: 0.024670 Align patch 9 16 left Iteration 1 Error: 0.669628 Iteration 2 Error: 0.093214 Iteration 3 Error: 0.022449 Align patch 10 15 left Iteration 1 Error: 0.600634 Iteration 2 Error: 0.081749 Iteration 3 Error: 0.011321 Align patch 11 14 left Iteration 1 Error: 0.868223 Iteration 2 Error: 0.335436 Iteration 3 Error: 0.097532 Iteration 4 Error: 0.053153 Iteration 5 Error: 0.010200 Align patch 12 13 left Iteration 1 Error: 0.721119 Iteration 2 Error: 0.201074 Iteration 3 Error: 0.073027 Iteration 4 Error: 0.026211 Align patch 13 12 left Iteration 1 Error: 0.566528 Iteration 2 Error: 0.089869 Iteration 3 Error: 0.017713 Align patch 14 11 left Iteration 1 Error: 0.495331 Iteration 2 Error: 0.079113 Iteration 3 Error: 0.013632 Align patch 15 10 left Iteration 1 Error: 0.577513 Iteration 2 Error: 0.089584 Iteration 3 Error: 0.013489 Align patch 16 9 left Iteration 1 Error: 0.576699 Iteration 2 Error: 0.073702 Iteration 3 Error: 0.015537 Align patch 17 8 left Iteration 1 Error: 0.460979 Iteration 2 Error: 0.083184 Iteration 3 Error: 0.022576 Align patch 18 7 left Iteration 1 Error: 0.641216 Iteration 2 Error: 0.099174 Iteration 3 Error: 0.028818 Align patch 19 6 left Iteration 1 Error: 0.546933 Iteration 2 Error: 0.061170 Iteration 3 Error: 0.011373 Align patch 20 5 left Iteration 1 Error: 0.490420 Iteration 2 Error: 0.060187 Iteration 3 Error: 0.012584 Align patch 21 4 left Iteration 1 Error: 1.118002 Iteration 2 Error: 0.148817 Iteration 3 Error: 0.036906 Align patch 22 3 left Iteration 1 Error: 0.697354 Iteration 2 Error: 0.120842 Iteration 3 Error: 0.039396 Align patch 23 2 left Iteration 1 Error: 0.575151 Iteration 2 Error: 0.138794 Iteration 3 Error: 0.033289 Align patch 24 1 left Iteration 1 Error: 0.572416 Iteration 2 Error: 0.104505 Iteration 3 Error: 0.021272 Align patch 25 0 left Iteration 1 Error: 0.691552 Iteration 2 Error: 0.092689 Iteration 3 Error: 0.016782 3D Fitting completed. Patch alignment time: 15.72(sec) Local motion has been corrected. Process thread exits. Computational time: 23.747175 sec Total time: 29.822092 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00011hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00011hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.707286s Reading file: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00011hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.124149s ........................................ >>>>>>TIME<<<<<< FFT: 0.934506s Defocus_U Defocus_V Angle CCC 11418.01 12265.67 6.58 0.055437 Final Values Defocus_U Defocus_V Angle CCC 11435.21 12279.74 6.89 0.094752 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00010sq_v01_00011hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00011hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 41.08 6.95 Num Hot pixels: 198 Hot pixel threshold: 82.76 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.757923 Iteration 2 Error: 0.128396 Iteration 3 Error: 0.025415 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.03 0.09 ...... Frame ( 3) shift: -0.05 0.18 ...... Frame ( 4) shift: -0.08 0.27 ...... Frame ( 5) shift: -0.11 0.36 ...... Frame ( 6) shift: -0.12 0.42 ...... Frame ( 7) shift: -0.13 0.47 ...... Frame ( 8) shift: -0.15 0.52 ...... Frame ( 9) shift: -0.15 0.56 ...... Frame ( 10) shift: -0.14 0.59 ...... Frame ( 11) shift: -0.14 0.62 ...... Frame ( 12) shift: -0.08 0.68 ...... Frame ( 13) shift: 0.05 0.77 ...... Frame ( 14) shift: 0.17 0.86 ...... Frame ( 15) shift: 0.25 0.93 ...... Frame ( 16) shift: 0.29 0.99 ...... Frame ( 17) shift: 0.33 1.05 ...... Frame ( 18) shift: 0.34 1.09 ...... Frame ( 19) shift: 0.34 1.10 ...... Frame ( 20) shift: 0.33 1.11 ...... Frame ( 21) shift: 0.33 1.13 ...... Frame ( 22) shift: 0.34 1.16 ...... Frame ( 23) shift: 0.35 1.18 ...... Frame ( 24) shift: 0.38 1.21 ...... Frame ( 25) shift: 0.43 1.24 ...... Frame ( 26) shift: 0.48 1.27 ...... Frame ( 27) shift: 0.50 1.30 ...... Frame ( 28) shift: 0.48 1.34 ...... Frame ( 29) shift: 0.46 1.39 ...... Frame ( 30) shift: 0.45 1.39 ...... Frame ( 31) shift: 0.44 1.37 ...... Frame ( 32) shift: 0.43 1.34 ...... Frame ( 33) shift: 0.44 1.34 ...... Frame ( 34) shift: 0.47 1.35 ...... Frame ( 35) shift: 0.49 1.37 ...... Frame ( 36) shift: 0.52 1.36 ...... Frame ( 37) shift: 0.55 1.32 ...... Frame ( 38) shift: 0.59 1.28 ...... Frame ( 39) shift: 0.62 1.23 ...... Frame ( 40) shift: 0.65 1.19 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.785611 Iteration 2 Error: 0.279420 Iteration 3 Error: 0.112852 Iteration 4 Error: 0.020826 Align patch 2 23 left Iteration 1 Error: 1.288710 Iteration 2 Error: 0.157701 Iteration 3 Error: 0.038640 Align patch 3 22 left Iteration 1 Error: 0.548220 Iteration 2 Error: 0.115846 Iteration 3 Error: 0.035150 Align patch 4 21 left Iteration 1 Error: 0.498338 Iteration 2 Error: 0.079023 Iteration 3 Error: 0.025201 Align patch 5 20 left Iteration 1 Error: 0.591645 Iteration 2 Error: 0.086629 Iteration 3 Error: 0.017986 Align patch 6 19 left Iteration 1 Error: 1.673792 Iteration 2 Error: 0.376115 Iteration 3 Error: 0.075049 Iteration 4 Error: 0.031311 Align patch 7 18 left Iteration 1 Error: 1.443382 Iteration 2 Error: 0.171278 Iteration 3 Error: 0.074293 Iteration 4 Error: 0.018149 Align patch 8 17 left Iteration 1 Error: 0.612631 Iteration 2 Error: 0.103110 Iteration 3 Error: 0.029337 Align patch 9 16 left Iteration 1 Error: 0.550072 Iteration 2 Error: 0.103923 Iteration 3 Error: 0.025639 Align patch 10 15 left Iteration 1 Error: 0.510236 Iteration 2 Error: 0.073458 Iteration 3 Error: 0.019660 Align patch 11 14 left Iteration 1 Error: 0.766510 Iteration 2 Error: 0.134257 Iteration 3 Error: 0.032144 Align patch 12 13 left Iteration 1 Error: 0.607207 Iteration 2 Error: 0.174424 Iteration 3 Error: 0.054074 Iteration 4 Error: 0.024901 Align patch 13 12 left Iteration 1 Error: 0.555079 Iteration 2 Error: 0.096100 Iteration 3 Error: 0.021131 Align patch 14 11 left Iteration 1 Error: 0.462591 Iteration 2 Error: 0.140922 Iteration 3 Error: 0.034364 Align patch 15 10 left Iteration 1 Error: 0.814341 Iteration 2 Error: 0.115500 Iteration 3 Error: 0.028110 Align patch 16 9 left Iteration 1 Error: 0.782464 Iteration 2 Error: 0.138284 Iteration 3 Error: 0.043998 Align patch 17 8 left Iteration 1 Error: 0.572669 Iteration 2 Error: 0.058968 Iteration 3 Error: 0.018505 Align patch 18 7 left Iteration 1 Error: 1.063764 Iteration 2 Error: 0.207844 Iteration 3 Error: 0.041701 Align patch 19 6 left Iteration 1 Error: 0.620579 Iteration 2 Error: 0.062670 Iteration 3 Error: 0.019223 Align patch 20 5 left Iteration 1 Error: 0.798396 Iteration 2 Error: 0.184794 Iteration 3 Error: 0.035466 Align patch 21 4 left Iteration 1 Error: 0.821384 Iteration 2 Error: 0.092666 Iteration 3 Error: 0.021471 Align patch 22 3 left Iteration 1 Error: 0.624609 Iteration 2 Error: 0.127305 Iteration 3 Error: 0.028903 Align patch 23 2 left Iteration 1 Error: 0.847687 Iteration 2 Error: 0.108216 Iteration 3 Error: 0.037738 Align patch 24 1 left Iteration 1 Error: 0.723227 Iteration 2 Error: 0.076675 Iteration 3 Error: 0.016365 Align patch 25 0 left Iteration 1 Error: 0.797516 Iteration 2 Error: 0.120277 Iteration 3 Error: 0.029880 3D Fitting completed. Patch alignment time: 16.03(sec) Local motion has been corrected. Process thread exits. Computational time: 24.687805 sec Total time: 30.674149 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00011hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00011hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.810658s Reading file: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00011hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.989182s ........................................ >>>>>>TIME<<<<<< FFT: 1.052677s Defocus_U Defocus_V Angle CCC 12640.63 12054.70 82.35 0.048516 Final Values Defocus_U Defocus_V Angle CCC 12659.39 12060.95 82.98 0.083913 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00010sq_v01_00012hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00012hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 41.19 7.01 Num Hot pixels: 203 Hot pixel threshold: 83.26 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.477240 Iteration 2 Error: 0.337691 Iteration 3 Error: 0.097931 Iteration 4 Error: 0.030588 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.13 0.01 ...... Frame ( 3) shift: -0.25 0.01 ...... Frame ( 4) shift: -0.38 0.02 ...... Frame ( 5) shift: -0.50 0.03 ...... Frame ( 6) shift: -0.57 0.05 ...... Frame ( 7) shift: -0.58 0.08 ...... Frame ( 8) shift: -0.59 0.12 ...... Frame ( 9) shift: -0.50 0.19 ...... Frame ( 10) shift: -0.31 0.28 ...... Frame ( 11) shift: -0.12 0.38 ...... Frame ( 12) shift: 0.02 0.50 ...... Frame ( 13) shift: 0.11 0.65 ...... Frame ( 14) shift: 0.20 0.80 ...... Frame ( 15) shift: 0.28 0.92 ...... Frame ( 16) shift: 0.33 1.02 ...... Frame ( 17) shift: 0.39 1.11 ...... Frame ( 18) shift: 0.43 1.20 ...... Frame ( 19) shift: 0.44 1.28 ...... Frame ( 20) shift: 0.46 1.36 ...... Frame ( 21) shift: 0.51 1.43 ...... Frame ( 22) shift: 0.59 1.49 ...... Frame ( 23) shift: 0.67 1.56 ...... Frame ( 24) shift: 0.72 1.61 ...... Frame ( 25) shift: 0.74 1.65 ...... Frame ( 26) shift: 0.76 1.69 ...... Frame ( 27) shift: 0.79 1.78 ...... Frame ( 28) shift: 0.85 1.93 ...... Frame ( 29) shift: 0.90 2.08 ...... Frame ( 30) shift: 0.96 2.17 ...... Frame ( 31) shift: 1.04 2.22 ...... Frame ( 32) shift: 1.12 2.27 ...... Frame ( 33) shift: 1.19 2.35 ...... Frame ( 34) shift: 1.24 2.44 ...... Frame ( 35) shift: 1.28 2.54 ...... Frame ( 36) shift: 1.31 2.62 ...... Frame ( 37) shift: 1.32 2.69 ...... Frame ( 38) shift: 1.32 2.76 ...... Frame ( 39) shift: 1.33 2.83 ...... Frame ( 40) shift: 1.33 2.90 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 3.025953 Iteration 2 Error: 0.552401 Iteration 3 Error: 0.164900 Iteration 4 Error: 0.066659 Iteration 5 Error: 0.024666 Align patch 2 23 left Iteration 1 Error: 1.132283 Iteration 2 Error: 0.210746 Iteration 3 Error: 0.088146 Iteration 4 Error: 0.029006 Align patch 3 22 left Iteration 1 Error: 0.633108 Iteration 2 Error: 0.121033 Iteration 3 Error: 0.041790 Align patch 4 21 left Iteration 1 Error: 0.459790 Iteration 2 Error: 0.059798 Iteration 3 Error: 0.010638 Align patch 5 20 left Iteration 1 Error: 0.527201 Iteration 2 Error: 0.102188 Iteration 3 Error: 0.018212 Align patch 6 19 left Iteration 1 Error: 2.393691 Iteration 2 Error: 0.517153 Iteration 3 Error: 0.164406 Iteration 4 Error: 0.061218 Iteration 5 Error: 0.027303 Align patch 7 18 left Iteration 1 Error: 1.181167 Iteration 2 Error: 0.217161 Iteration 3 Error: 0.064767 Iteration 4 Error: 0.022664 Align patch 8 17 left Iteration 1 Error: 0.553720 Iteration 2 Error: 0.078180 Iteration 3 Error: 0.014701 Align patch 9 16 left Iteration 1 Error: 0.340890 Iteration 2 Error: 0.048166 Align patch 10 15 left Iteration 1 Error: 0.664201 Iteration 2 Error: 0.130750 Iteration 3 Error: 0.025624 Align patch 11 14 left Iteration 1 Error: 0.976656 Iteration 2 Error: 0.440926 Iteration 3 Error: 0.229183 Iteration 4 Error: 0.125164 Iteration 5 Error: 0.057357 Align patch 11 14 left Iteration 1 Error: 1.444466 Iteration 2 Error: 0.397955 Iteration 3 Error: 0.110257 Iteration 4 Error: 0.032295 Align patch 12 13 left Iteration 1 Error: 0.718841 Iteration 2 Error: 0.152855 Iteration 3 Error: 0.088680 Iteration 4 Error: 0.050585 Iteration 5 Error: 0.031800 Align patch 13 12 left Iteration 1 Error: 0.549776 Iteration 2 Error: 0.135046 Iteration 3 Error: 0.025032 Align patch 14 11 left Iteration 1 Error: 0.598954 Iteration 2 Error: 0.095892 Iteration 3 Error: 0.020060 Align patch 15 10 left Iteration 1 Error: 0.452362 Iteration 2 Error: 0.076928 Iteration 3 Error: 0.026381 Align patch 16 9 left Iteration 1 Error: 1.226158 Iteration 2 Error: 0.317442 Iteration 3 Error: 0.170710 Iteration 4 Error: 0.095469 Iteration 5 Error: 0.062976 Align patch 16 9 left Iteration 1 Error: 1.024010 Iteration 2 Error: 0.274829 Iteration 3 Error: 0.083049 Iteration 4 Error: 0.024281 Align patch 17 8 left Iteration 1 Error: 0.733030 Iteration 2 Error: 0.191376 Iteration 3 Error: 0.093148 Iteration 4 Error: 0.052033 Iteration 5 Error: 0.028924 Align patch 18 7 left Iteration 1 Error: 0.629936 Iteration 2 Error: 0.108000 Iteration 3 Error: 0.026848 Align patch 19 6 left Iteration 1 Error: 0.604658 Iteration 2 Error: 0.063442 Iteration 3 Error: 0.016673 Align patch 20 5 left Iteration 1 Error: 0.724195 Iteration 2 Error: 0.120158 Iteration 3 Error: 0.032677 Align patch 21 4 left Iteration 1 Error: 1.180792 Iteration 2 Error: 0.212372 Iteration 3 Error: 0.036586 Align patch 22 3 left Iteration 1 Error: 0.721340 Iteration 2 Error: 0.123967 Iteration 3 Error: 0.035963 Align patch 23 2 left Iteration 1 Error: 0.975959 Iteration 2 Error: 0.163261 Iteration 3 Error: 0.030646 Align patch 24 1 left Iteration 1 Error: 1.174279 Iteration 2 Error: 0.324492 Iteration 3 Error: 0.065365 Iteration 4 Error: 0.026368 Align patch 25 0 left Iteration 1 Error: 1.159172 Iteration 2 Error: 0.159480 Iteration 3 Error: 0.037140 3D Fitting completed. Patch alignment time: 17.90(sec) Local motion has been corrected. Process thread exits. Computational time: 26.586187 sec Total time: 32.298855 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00012hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00012hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.737602s Reading file: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00012hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.436614s ........................................ >>>>>>TIME<<<<<< FFT: 1.045944s Defocus_U Defocus_V Angle CCC 9984.38 10812.50 13.04 0.054258 Final Values Defocus_U Defocus_V Angle CCC 9990.63 10837.52 12.73 0.095724 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00010sq_v01_00012hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00012hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.350e-01 1.004e-01 CC threshold: 0.737 Mean Std: 40.98 7.13 Num Hot pixels: 199 Hot pixel threshold: 83.73 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.824734 Iteration 2 Error: 0.190644 Iteration 3 Error: 0.051975 Iteration 4 Error: 0.013649 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.09 -0.04 ...... Frame ( 3) shift: -0.19 -0.08 ...... Frame ( 4) shift: -0.28 -0.12 ...... Frame ( 5) shift: -0.38 -0.16 ...... Frame ( 6) shift: -0.41 -0.13 ...... Frame ( 7) shift: -0.37 -0.05 ...... Frame ( 8) shift: -0.34 0.04 ...... Frame ( 9) shift: -0.29 0.12 ...... Frame ( 10) shift: -0.22 0.19 ...... Frame ( 11) shift: -0.16 0.26 ...... Frame ( 12) shift: -0.11 0.33 ...... Frame ( 13) shift: -0.10 0.41 ...... Frame ( 14) shift: -0.08 0.48 ...... Frame ( 15) shift: -0.05 0.55 ...... Frame ( 16) shift: -0.01 0.62 ...... Frame ( 17) shift: 0.04 0.70 ...... Frame ( 18) shift: 0.08 0.71 ...... Frame ( 19) shift: 0.13 0.66 ...... Frame ( 20) shift: 0.17 0.61 ...... Frame ( 21) shift: 0.22 0.58 ...... Frame ( 22) shift: 0.27 0.57 ...... Frame ( 23) shift: 0.32 0.56 ...... Frame ( 24) shift: 0.39 0.60 ...... Frame ( 25) shift: 0.51 0.69 ...... Frame ( 26) shift: 0.62 0.78 ...... Frame ( 27) shift: 0.68 0.85 ...... Frame ( 28) shift: 0.71 0.89 ...... Frame ( 29) shift: 0.74 0.93 ...... Frame ( 30) shift: 0.76 0.99 ...... Frame ( 31) shift: 0.77 1.08 ...... Frame ( 32) shift: 0.78 1.17 ...... Frame ( 33) shift: 0.79 1.21 ...... Frame ( 34) shift: 0.80 1.21 ...... Frame ( 35) shift: 0.81 1.20 ...... Frame ( 36) shift: 0.83 1.21 ...... Frame ( 37) shift: 0.84 1.24 ...... Frame ( 38) shift: 0.86 1.27 ...... Frame ( 39) shift: 0.88 1.30 ...... Frame ( 40) shift: 0.89 1.33 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.106350 Iteration 2 Error: 0.466603 Iteration 3 Error: 0.228997 Iteration 4 Error: 0.097066 Iteration 5 Error: 0.041815 Align patch 2 23 left Iteration 1 Error: 1.100148 Iteration 2 Error: 0.330274 Iteration 3 Error: 0.152310 Iteration 4 Error: 0.065146 Iteration 5 Error: 0.035982 Align patch 3 22 left Iteration 1 Error: 0.739290 Iteration 2 Error: 0.099371 Iteration 3 Error: 0.047846 Align patch 4 21 left Iteration 1 Error: 0.458060 Iteration 2 Error: 0.046856 Align patch 5 20 left Iteration 1 Error: 0.423071 Iteration 2 Error: 0.084569 Iteration 3 Error: 0.015199 Align patch 6 19 left Iteration 1 Error: 2.868108 Iteration 2 Error: 0.529233 Iteration 3 Error: 0.132842 Iteration 4 Error: 0.054323 Iteration 5 Error: 0.028945 Align patch 7 18 left Iteration 1 Error: 0.390687 Iteration 2 Error: 0.136512 Iteration 3 Error: 0.060447 Iteration 4 Error: 0.025887 Align patch 8 17 left Iteration 1 Error: 0.914959 Iteration 2 Error: 0.129635 Iteration 3 Error: 0.041990 Align patch 9 16 left Iteration 1 Error: 0.678835 Iteration 2 Error: 0.091447 Iteration 3 Error: 0.020699 Align patch 10 15 left Iteration 1 Error: 0.507840 Iteration 2 Error: 0.081224 Iteration 3 Error: 0.011803 Align patch 11 14 left Iteration 1 Error: 1.707076 Iteration 2 Error: 0.407814 Iteration 3 Error: 0.099529 Iteration 4 Error: 0.037379 Align patch 12 13 left Iteration 1 Error: 0.919572 Iteration 2 Error: 0.141933 Iteration 3 Error: 0.023402 Align patch 13 12 left Iteration 1 Error: 0.895612 Iteration 2 Error: 0.218110 Iteration 3 Error: 0.073541 Iteration 4 Error: 0.020630 Align patch 14 11 left Iteration 1 Error: 0.521987 Iteration 2 Error: 0.095387 Iteration 3 Error: 0.019197 Align patch 15 10 left Iteration 1 Error: 0.664718 Iteration 2 Error: 0.106602 Iteration 3 Error: 0.021678 Align patch 16 9 left Iteration 1 Error: 0.855085 Iteration 2 Error: 0.197736 Iteration 3 Error: 0.085585 Iteration 4 Error: 0.033121 Align patch 17 8 left Iteration 1 Error: 0.614532 Iteration 2 Error: 0.154306 Iteration 3 Error: 0.040756 Align patch 18 7 left Iteration 1 Error: 0.500273 Iteration 2 Error: 0.081629 Iteration 3 Error: 0.030498 Align patch 19 6 left Iteration 1 Error: 0.582628 Iteration 2 Error: 0.092196 Iteration 3 Error: 0.023991 Align patch 20 5 left Iteration 1 Error: 0.587521 Iteration 2 Error: 0.101042 Iteration 3 Error: 0.019852 Align patch 21 4 left Iteration 1 Error: 0.494955 Iteration 2 Error: 0.055832 Iteration 3 Error: 0.015278 Align patch 22 3 left Iteration 1 Error: 0.890029 Iteration 2 Error: 0.098049 Iteration 3 Error: 0.032274 Align patch 23 2 left Iteration 1 Error: 0.682459 Iteration 2 Error: 0.112499 Iteration 3 Error: 0.025779 Align patch 24 1 left Iteration 1 Error: 0.550408 Iteration 2 Error: 0.117553 Iteration 3 Error: 0.021269 Align patch 25 0 left Iteration 1 Error: 0.566644 Iteration 2 Error: 0.083754 Iteration 3 Error: 0.012913 3D Fitting completed. Patch alignment time: 15.92(sec) Local motion has been corrected. Process thread exits. Computational time: 25.099731 sec Total time: 30.856524 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00012hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00012hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.564255s Reading file: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00012hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.425276s ........................................ >>>>>>TIME<<<<<< FFT: 0.962443s Defocus_U Defocus_V Angle CCC 11381.82 11891.64 2.55 0.052265 Final Values Defocus_U Defocus_V Angle CCC 11399.01 11915.08 2.27 0.088815 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00010sq_v01_00012hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00012hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.350e-01 1.004e-01 CC threshold: 0.737 Mean Std: 41.61 7.01 Num Hot pixels: 226 Hot pixel threshold: 83.67 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.873187 Iteration 2 Error: 0.134812 Iteration 3 Error: 0.028886 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.22 -0.16 ...... Frame ( 3) shift: -0.44 -0.32 ...... Frame ( 4) shift: -0.66 -0.48 ...... Frame ( 5) shift: -0.88 -0.64 ...... Frame ( 6) shift: -0.95 -0.70 ...... Frame ( 7) shift: -0.86 -0.67 ...... Frame ( 8) shift: -0.77 -0.64 ...... Frame ( 9) shift: -0.74 -0.60 ...... Frame ( 10) shift: -0.77 -0.57 ...... Frame ( 11) shift: -0.80 -0.55 ...... Frame ( 12) shift: -0.77 -0.48 ...... Frame ( 13) shift: -0.69 -0.38 ...... Frame ( 14) shift: -0.60 -0.28 ...... Frame ( 15) shift: -0.54 -0.17 ...... Frame ( 16) shift: -0.51 -0.05 ...... Frame ( 17) shift: -0.49 0.07 ...... Frame ( 18) shift: -0.48 0.17 ...... Frame ( 19) shift: -0.49 0.26 ...... Frame ( 20) shift: -0.50 0.35 ...... Frame ( 21) shift: -0.49 0.43 ...... Frame ( 22) shift: -0.46 0.51 ...... Frame ( 23) shift: -0.42 0.58 ...... Frame ( 24) shift: -0.42 0.63 ...... Frame ( 25) shift: -0.45 0.64 ...... Frame ( 26) shift: -0.48 0.66 ...... Frame ( 27) shift: -0.49 0.66 ...... Frame ( 28) shift: -0.49 0.63 ...... Frame ( 29) shift: -0.48 0.61 ...... Frame ( 30) shift: -0.49 0.63 ...... Frame ( 31) shift: -0.53 0.69 ...... Frame ( 32) shift: -0.56 0.76 ...... Frame ( 33) shift: -0.55 0.78 ...... Frame ( 34) shift: -0.49 0.75 ...... Frame ( 35) shift: -0.44 0.72 ...... Frame ( 36) shift: -0.42 0.74 ...... Frame ( 37) shift: -0.45 0.82 ...... Frame ( 38) shift: -0.47 0.90 ...... Frame ( 39) shift: -0.50 0.97 ...... Frame ( 40) shift: -0.52 1.05 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.075994 Iteration 2 Error: 0.269082 Iteration 3 Error: 0.095434 Iteration 4 Error: 0.039663 Align patch 2 23 left Iteration 1 Error: 1.765893 Iteration 2 Error: 0.212158 Iteration 3 Error: 0.064773 Iteration 4 Error: 0.023543 Align patch 3 22 left Iteration 1 Error: 0.704702 Iteration 2 Error: 0.092257 Iteration 3 Error: 0.026893 Align patch 4 21 left Iteration 1 Error: 0.533562 Iteration 2 Error: 0.046656 Align patch 5 20 left Iteration 1 Error: 0.609941 Iteration 2 Error: 0.093683 Iteration 3 Error: 0.020110 Align patch 6 19 left Iteration 1 Error: 2.092187 Iteration 2 Error: 0.344463 Iteration 3 Error: 0.075409 Iteration 4 Error: 0.044745 Align patch 7 18 left Iteration 1 Error: 1.195733 Iteration 2 Error: 0.169446 Iteration 3 Error: 0.047697 Align patch 8 17 left Iteration 1 Error: 0.551295 Iteration 2 Error: 0.097437 Iteration 3 Error: 0.022932 Align patch 9 16 left Iteration 1 Error: 0.710818 Iteration 2 Error: 0.071560 Iteration 3 Error: 0.015167 Align patch 10 15 left Iteration 1 Error: 0.938725 Iteration 2 Error: 0.139826 Iteration 3 Error: 0.019860 Align patch 11 14 left Iteration 1 Error: 1.115797 Iteration 2 Error: 0.124906 Iteration 3 Error: 0.048914 Align patch 12 13 left Iteration 1 Error: 0.436910 Iteration 2 Error: 0.047173 Align patch 13 12 left Iteration 1 Error: 0.453333 Iteration 2 Error: 0.051673 Iteration 3 Error: 0.009861 Align patch 14 11 left Iteration 1 Error: 1.110829 Iteration 2 Error: 0.100745 Iteration 3 Error: 0.021425 Align patch 15 10 left Iteration 1 Error: 0.583071 Iteration 2 Error: 0.099015 Iteration 3 Error: 0.016705 Align patch 16 9 left Iteration 1 Error: 0.596266 Iteration 2 Error: 0.108172 Iteration 3 Error: 0.019044 Align patch 17 8 left Iteration 1 Error: 0.627972 Iteration 2 Error: 0.077405 Iteration 3 Error: 0.022955 Align patch 18 7 left Iteration 1 Error: 0.592760 Iteration 2 Error: 0.081381 Iteration 3 Error: 0.025283 Align patch 19 6 left Iteration 1 Error: 0.837987 Iteration 2 Error: 0.106937 Iteration 3 Error: 0.025050 Align patch 20 5 left Iteration 1 Error: 0.709539 Iteration 2 Error: 0.113206 Iteration 3 Error: 0.022144 Align patch 21 4 left Iteration 1 Error: 0.572995 Iteration 2 Error: 0.084252 Iteration 3 Error: 0.024949 Align patch 22 3 left Iteration 1 Error: 0.557103 Iteration 2 Error: 0.065709 Iteration 3 Error: 0.021267 Align patch 23 2 left Iteration 1 Error: 0.727386 Iteration 2 Error: 0.066985 Iteration 3 Error: 0.012777 Align patch 24 1 left Iteration 1 Error: 0.534681 Iteration 2 Error: 0.089791 Iteration 3 Error: 0.016026 Align patch 25 0 left Iteration 1 Error: 0.537602 Iteration 2 Error: 0.086805 Iteration 3 Error: 0.018446 3D Fitting completed. Patch alignment time: 15.08(sec) Local motion has been corrected. Process thread exits. Computational time: 23.107485 sec Total time: 28.859154 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00012hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00012hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.672723s Reading file: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00012hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.478968s ........................................ >>>>>>TIME<<<<<< FFT: 0.929676s Defocus_U Defocus_V Angle CCC 12804.70 13609.39 4.79 0.068470 Final Values Defocus_U Defocus_V Angle CCC 12809.39 13607.83 4.79 0.110196 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00010sq_v01_00012hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00012hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.350e-01 1.004e-01 CC threshold: 0.738 Mean Std: 40.64 6.98 Num Hot pixels: 228 Hot pixel threshold: 82.51 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.688454 Iteration 2 Error: 0.099624 Iteration 3 Error: 0.020911 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.11 0.03 ...... Frame ( 3) shift: -0.21 0.07 ...... Frame ( 4) shift: -0.32 0.10 ...... Frame ( 5) shift: -0.42 0.13 ...... Frame ( 6) shift: -0.49 0.16 ...... Frame ( 7) shift: -0.51 0.19 ...... Frame ( 8) shift: -0.54 0.21 ...... Frame ( 9) shift: -0.56 0.25 ...... Frame ( 10) shift: -0.58 0.29 ...... Frame ( 11) shift: -0.60 0.33 ...... Frame ( 12) shift: -0.59 0.39 ...... Frame ( 13) shift: -0.56 0.48 ...... Frame ( 14) shift: -0.52 0.57 ...... Frame ( 15) shift: -0.49 0.64 ...... Frame ( 16) shift: -0.45 0.67 ...... Frame ( 17) shift: -0.40 0.71 ...... Frame ( 18) shift: -0.43 0.73 ...... Frame ( 19) shift: -0.52 0.72 ...... Frame ( 20) shift: -0.61 0.71 ...... Frame ( 21) shift: -0.61 0.72 ...... Frame ( 22) shift: -0.54 0.76 ...... Frame ( 23) shift: -0.46 0.80 ...... Frame ( 24) shift: -0.42 0.83 ...... Frame ( 25) shift: -0.43 0.84 ...... Frame ( 26) shift: -0.44 0.86 ...... Frame ( 27) shift: -0.47 0.89 ...... Frame ( 28) shift: -0.51 0.93 ...... Frame ( 29) shift: -0.54 0.96 ...... Frame ( 30) shift: -0.58 1.02 ...... Frame ( 31) shift: -0.62 1.09 ...... Frame ( 32) shift: -0.65 1.17 ...... Frame ( 33) shift: -0.66 1.21 ...... Frame ( 34) shift: -0.63 1.22 ...... Frame ( 35) shift: -0.60 1.23 ...... Frame ( 36) shift: -0.58 1.24 ...... Frame ( 37) shift: -0.57 1.25 ...... Frame ( 38) shift: -0.56 1.27 ...... Frame ( 39) shift: -0.55 1.28 ...... Frame ( 40) shift: -0.54 1.29 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.765429 Iteration 2 Error: 0.296177 Iteration 3 Error: 0.100251 Iteration 4 Error: 0.042593 Align patch 2 23 left Iteration 1 Error: 0.729124 Iteration 2 Error: 0.112371 Iteration 3 Error: 0.017984 Align patch 3 22 left Iteration 1 Error: 0.836774 Iteration 2 Error: 0.086372 Iteration 3 Error: 0.015294 Align patch 4 21 left Iteration 1 Error: 0.456611 Iteration 2 Error: 0.119035 Iteration 3 Error: 0.027033 Align patch 5 20 left Iteration 1 Error: 0.646407 Iteration 2 Error: 0.064844 Iteration 3 Error: 0.011387 Align patch 6 19 left Iteration 1 Error: 1.252215 Iteration 2 Error: 0.243271 Iteration 3 Error: 0.087055 Iteration 4 Error: 0.037059 Align patch 7 18 left Iteration 1 Error: 0.956716 Iteration 2 Error: 0.132786 Iteration 3 Error: 0.032288 Align patch 8 17 left Iteration 1 Error: 0.422680 Iteration 2 Error: 0.070204 Iteration 3 Error: 0.011647 Align patch 9 16 left Iteration 1 Error: 0.670364 Iteration 2 Error: 0.127821 Iteration 3 Error: 0.020429 Align patch 10 15 left Iteration 1 Error: 0.588307 Iteration 2 Error: 0.060472 Iteration 3 Error: 0.013300 Align patch 11 14 left Iteration 1 Error: 1.014861 Iteration 2 Error: 0.096887 Iteration 3 Error: 0.019963 Align patch 12 13 left Iteration 1 Error: 0.431412 Iteration 2 Error: 0.071658 Iteration 3 Error: 0.018029 Align patch 13 12 left Iteration 1 Error: 0.466100 Iteration 2 Error: 0.121503 Iteration 3 Error: 0.039470 Align patch 14 11 left Iteration 1 Error: 1.049101 Iteration 2 Error: 0.184946 Iteration 3 Error: 0.043031 Align patch 15 10 left Iteration 1 Error: 0.614641 Iteration 2 Error: 0.085101 Iteration 3 Error: 0.013435 Align patch 16 9 left Iteration 1 Error: 0.706643 Iteration 2 Error: 0.136851 Iteration 3 Error: 0.026111 Align patch 17 8 left Iteration 1 Error: 0.584255 Iteration 2 Error: 0.076254 Iteration 3 Error: 0.020968 Align patch 18 7 left Iteration 1 Error: 0.539263 Iteration 2 Error: 0.108265 Iteration 3 Error: 0.025021 Align patch 19 6 left Iteration 1 Error: 0.862204 Iteration 2 Error: 0.109984 Iteration 3 Error: 0.020691 Align patch 20 5 left Iteration 1 Error: 0.463498 Iteration 2 Error: 0.117701 Iteration 3 Error: 0.025842 Align patch 21 4 left Iteration 1 Error: 0.565390 Iteration 2 Error: 0.123123 Iteration 3 Error: 0.032478 Align patch 22 3 left Iteration 1 Error: 0.542825 Iteration 2 Error: 0.089084 Iteration 3 Error: 0.020791 Align patch 23 2 left Iteration 1 Error: 0.465965 Iteration 2 Error: 0.058276 Iteration 3 Error: 0.016774 Align patch 24 1 left Iteration 1 Error: 0.616745 Iteration 2 Error: 0.167968 Iteration 3 Error: 0.032143 Align patch 25 0 left Iteration 1 Error: 0.555146 Iteration 2 Error: 0.067264 Iteration 3 Error: 0.013847 3D Fitting completed. Patch alignment time: 15.42(sec) Local motion has been corrected. Process thread exits. Computational time: 24.042418 sec Total time: 29.790182 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00012hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00012hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.767417s Reading file: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00012hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.892037s ........................................ >>>>>>TIME<<<<<< FFT: 0.942205s Defocus_U Defocus_V Angle CCC 11130.91 10462.90 83.34 0.056877 Final Values Defocus_U Defocus_V Angle CCC 11141.85 10486.34 84.29 0.096666 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00010sq_v01_00013hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00013hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.003e-01 CC threshold: 0.736 Mean Std: 38.64 6.71 Num Hot pixels: 186 Hot pixel threshold: 78.87 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.032247 Iteration 2 Error: 0.237832 Iteration 3 Error: 0.067275 Iteration 4 Error: 0.017195 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.27 -0.20 ...... Frame ( 3) shift: -0.54 -0.41 ...... Frame ( 4) shift: -0.81 -0.61 ...... Frame ( 5) shift: -1.08 -0.81 ...... Frame ( 6) shift: -1.23 -0.90 ...... Frame ( 7) shift: -1.27 -0.87 ...... Frame ( 8) shift: -1.30 -0.83 ...... Frame ( 9) shift: -1.29 -0.76 ...... Frame ( 10) shift: -1.24 -0.66 ...... Frame ( 11) shift: -1.19 -0.55 ...... Frame ( 12) shift: -1.12 -0.44 ...... Frame ( 13) shift: -1.01 -0.32 ...... Frame ( 14) shift: -0.90 -0.21 ...... Frame ( 15) shift: -0.79 -0.12 ...... Frame ( 16) shift: -0.68 -0.05 ...... Frame ( 17) shift: -0.57 0.02 ...... Frame ( 18) shift: -0.52 0.07 ...... Frame ( 19) shift: -0.53 0.10 ...... Frame ( 20) shift: -0.54 0.13 ...... Frame ( 21) shift: -0.52 0.16 ...... Frame ( 22) shift: -0.49 0.19 ...... Frame ( 23) shift: -0.45 0.21 ...... Frame ( 24) shift: -0.37 0.27 ...... Frame ( 25) shift: -0.26 0.34 ...... Frame ( 26) shift: -0.15 0.42 ...... Frame ( 27) shift: -0.04 0.51 ...... Frame ( 28) shift: 0.05 0.60 ...... Frame ( 29) shift: 0.14 0.69 ...... Frame ( 30) shift: 0.16 0.74 ...... Frame ( 31) shift: 0.11 0.76 ...... Frame ( 32) shift: 0.06 0.77 ...... Frame ( 33) shift: 0.05 0.80 ...... Frame ( 34) shift: 0.10 0.84 ...... Frame ( 35) shift: 0.16 0.88 ...... Frame ( 36) shift: 0.17 0.92 ...... Frame ( 37) shift: 0.14 0.94 ...... Frame ( 38) shift: 0.11 0.96 ...... Frame ( 39) shift: 0.09 0.99 ...... Frame ( 40) shift: 0.06 1.01 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.510131 Iteration 2 Error: 0.405150 Iteration 3 Error: 0.149694 Iteration 4 Error: 0.064258 Iteration 5 Error: 0.039281 Align patch 2 23 left Iteration 1 Error: 0.958772 Iteration 2 Error: 0.251094 Iteration 3 Error: 0.080464 Iteration 4 Error: 0.034299 Align patch 3 22 left Iteration 1 Error: 0.607307 Iteration 2 Error: 0.073600 Iteration 3 Error: 0.010074 Align patch 4 21 left Iteration 1 Error: 0.504864 Iteration 2 Error: 0.092706 Iteration 3 Error: 0.023025 Align patch 5 20 left Iteration 1 Error: 1.020586 Iteration 2 Error: 0.165837 Iteration 3 Error: 0.037843 Align patch 6 19 left Iteration 1 Error: 2.015105 Iteration 2 Error: 0.356111 Iteration 3 Error: 0.093353 Iteration 4 Error: 0.043399 Align patch 7 18 left Iteration 1 Error: 1.018777 Iteration 2 Error: 0.254178 Iteration 3 Error: 0.079535 Iteration 4 Error: 0.035272 Align patch 8 17 left Iteration 1 Error: 0.468181 Iteration 2 Error: 0.098463 Iteration 3 Error: 0.039857 Align patch 9 16 left Iteration 1 Error: 0.543011 Iteration 2 Error: 0.067618 Iteration 3 Error: 0.012603 Align patch 10 15 left Iteration 1 Error: 0.784435 Iteration 2 Error: 0.121367 Iteration 3 Error: 0.026302 Align patch 11 14 left Iteration 1 Error: 0.818855 Iteration 2 Error: 0.213116 Iteration 3 Error: 0.086311 Iteration 4 Error: 0.036711 Align patch 12 13 left Iteration 1 Error: 0.941518 Iteration 2 Error: 0.195507 Iteration 3 Error: 0.065763 Iteration 4 Error: 0.027314 Align patch 13 12 left Iteration 1 Error: 0.734197 Iteration 2 Error: 0.138660 Iteration 3 Error: 0.035613 Align patch 14 11 left Iteration 1 Error: 0.380862 Iteration 2 Error: 0.043882 Align patch 15 10 left Iteration 1 Error: 0.738858 Iteration 2 Error: 0.165118 Iteration 3 Error: 0.035537 Align patch 16 9 left Iteration 1 Error: 0.868428 Iteration 2 Error: 0.167589 Iteration 3 Error: 0.062888 Iteration 4 Error: 0.030664 Align patch 17 8 left Iteration 1 Error: 0.585734 Iteration 2 Error: 0.085655 Iteration 3 Error: 0.025481 Align patch 18 7 left Iteration 1 Error: 0.740685 Iteration 2 Error: 0.109788 Iteration 3 Error: 0.023848 Align patch 19 6 left Iteration 1 Error: 0.808159 Iteration 2 Error: 0.096702 Iteration 3 Error: 0.021496 Align patch 20 5 left Iteration 1 Error: 0.648955 Iteration 2 Error: 0.140755 Iteration 3 Error: 0.027118 Align patch 21 4 left Iteration 1 Error: 1.062485 Iteration 2 Error: 0.175514 Iteration 3 Error: 0.035612 Align patch 22 3 left Iteration 1 Error: 0.782610 Iteration 2 Error: 0.138243 Iteration 3 Error: 0.042729 Align patch 23 2 left Iteration 1 Error: 0.642898 Iteration 2 Error: 0.203228 Iteration 3 Error: 0.054550 Iteration 4 Error: 0.019175 Align patch 24 1 left Iteration 1 Error: 0.972710 Iteration 2 Error: 0.125663 Iteration 3 Error: 0.035161 Align patch 25 0 left Iteration 1 Error: 0.709671 Iteration 2 Error: 0.182399 Iteration 3 Error: 0.040113 3D Fitting completed. Patch alignment time: 15.73(sec) Local motion has been corrected. Process thread exits. Computational time: 23.901190 sec Total time: 29.398956 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00013hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00013hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.555111s Reading file: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00013hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.190159s ........................................ >>>>>>TIME<<<<<< FFT: 0.956719s Defocus_U Defocus_V Angle CCC 13474.61 14322.27 10.43 0.054812 Final Values Defocus_U Defocus_V Angle CCC 13476.17 14333.23 10.43 0.082259 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00010sq_v01_00013hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00013hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 40.87 6.95 Num Hot pixels: 203 Hot pixel threshold: 82.54 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.190294 Iteration 2 Error: 0.206170 Iteration 3 Error: 0.051638 Iteration 4 Error: 0.018539 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.15 0.00 ...... Frame ( 3) shift: -0.30 0.00 ...... Frame ( 4) shift: -0.46 0.01 ...... Frame ( 5) shift: -0.61 0.01 ...... Frame ( 6) shift: -0.67 0.05 ...... Frame ( 7) shift: -0.62 0.12 ...... Frame ( 8) shift: -0.58 0.20 ...... Frame ( 9) shift: -0.50 0.28 ...... Frame ( 10) shift: -0.38 0.37 ...... Frame ( 11) shift: -0.26 0.47 ...... Frame ( 12) shift: -0.19 0.58 ...... Frame ( 13) shift: -0.19 0.71 ...... Frame ( 14) shift: -0.18 0.83 ...... Frame ( 15) shift: -0.16 0.95 ...... Frame ( 16) shift: -0.13 1.05 ...... Frame ( 17) shift: -0.10 1.15 ...... Frame ( 18) shift: -0.03 1.24 ...... Frame ( 19) shift: 0.06 1.32 ...... Frame ( 20) shift: 0.15 1.40 ...... Frame ( 21) shift: 0.20 1.48 ...... Frame ( 22) shift: 0.20 1.57 ...... Frame ( 23) shift: 0.20 1.65 ...... Frame ( 24) shift: 0.19 1.70 ...... Frame ( 25) shift: 0.18 1.71 ...... Frame ( 26) shift: 0.18 1.73 ...... Frame ( 27) shift: 0.20 1.79 ...... Frame ( 28) shift: 0.27 1.90 ...... Frame ( 29) shift: 0.33 2.01 ...... Frame ( 30) shift: 0.37 2.07 ...... Frame ( 31) shift: 0.38 2.09 ...... Frame ( 32) shift: 0.40 2.11 ...... Frame ( 33) shift: 0.44 2.11 ...... Frame ( 34) shift: 0.52 2.10 ...... Frame ( 35) shift: 0.59 2.09 ...... Frame ( 36) shift: 0.60 2.13 ...... Frame ( 37) shift: 0.56 2.22 ...... Frame ( 38) shift: 0.51 2.31 ...... Frame ( 39) shift: 0.47 2.40 ...... Frame ( 40) shift: 0.42 2.49 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.110687 Iteration 2 Error: 0.452614 Iteration 3 Error: 0.163254 Iteration 4 Error: 0.060781 Iteration 5 Error: 0.020915 Align patch 2 23 left Iteration 1 Error: 1.488395 Iteration 2 Error: 0.300159 Iteration 3 Error: 0.097475 Iteration 4 Error: 0.036273 Align patch 3 22 left Iteration 1 Error: 0.540916 Iteration 2 Error: 0.093991 Iteration 3 Error: 0.022617 Align patch 4 21 left Iteration 1 Error: 0.693811 Iteration 2 Error: 0.121210 Iteration 3 Error: 0.029699 Align patch 5 20 left Iteration 1 Error: 0.613168 Iteration 2 Error: 0.081006 Iteration 3 Error: 0.017189 Align patch 6 19 left Iteration 1 Error: 1.725816 Iteration 2 Error: 0.351951 Iteration 3 Error: 0.106572 Iteration 4 Error: 0.041259 Align patch 7 18 left Iteration 1 Error: 1.606032 Iteration 2 Error: 0.319522 Iteration 3 Error: 0.086512 Iteration 4 Error: 0.031598 Align patch 8 17 left Iteration 1 Error: 0.616474 Iteration 2 Error: 0.080894 Iteration 3 Error: 0.023735 Align patch 9 16 left Iteration 1 Error: 0.807670 Iteration 2 Error: 0.066023 Iteration 3 Error: 0.016461 Align patch 10 15 left Iteration 1 Error: 0.734789 Iteration 2 Error: 0.062687 Iteration 3 Error: 0.013465 Align patch 11 14 left Iteration 1 Error: 1.693558 Iteration 2 Error: 0.318004 Iteration 3 Error: 0.087290 Iteration 4 Error: 0.027160 Align patch 12 13 left Iteration 1 Error: 1.271279 Iteration 2 Error: 0.281482 Iteration 3 Error: 0.086549 Iteration 4 Error: 0.036392 Align patch 13 12 left Iteration 1 Error: 0.452804 Iteration 2 Error: 0.074026 Iteration 3 Error: 0.020448 Align patch 14 11 left Iteration 1 Error: 0.447239 Iteration 2 Error: 0.081018 Iteration 3 Error: 0.023711 Align patch 15 10 left Iteration 1 Error: 0.652840 Iteration 2 Error: 0.077862 Iteration 3 Error: 0.013689 Align patch 16 9 left Iteration 1 Error: 0.871307 Iteration 2 Error: 0.170969 Iteration 3 Error: 0.047422 Align patch 17 8 left Iteration 1 Error: 0.953907 Iteration 2 Error: 0.089849 Iteration 3 Error: 0.024587 Align patch 18 7 left Iteration 1 Error: 0.668561 Iteration 2 Error: 0.122397 Iteration 3 Error: 0.030129 Align patch 19 6 left Iteration 1 Error: 0.865104 Iteration 2 Error: 0.179157 Iteration 3 Error: 0.035222 Align patch 20 5 left Iteration 1 Error: 0.728900 Iteration 2 Error: 0.123021 Iteration 3 Error: 0.023228 Align patch 21 4 left Iteration 1 Error: 0.844655 Iteration 2 Error: 0.149351 Iteration 3 Error: 0.043896 Align patch 22 3 left Iteration 1 Error: 0.549928 Iteration 2 Error: 0.101117 Iteration 3 Error: 0.021268 Align patch 23 2 left Iteration 1 Error: 0.705850 Iteration 2 Error: 0.092525 Iteration 3 Error: 0.024277 Align patch 24 1 left Iteration 1 Error: 0.888579 Iteration 2 Error: 0.134318 Iteration 3 Error: 0.021654 Align patch 25 0 left Iteration 1 Error: 0.833680 Iteration 2 Error: 0.141466 Iteration 3 Error: 0.029082 3D Fitting completed. Patch alignment time: 15.92(sec) Local motion has been corrected. Process thread exits. Computational time: 24.871880 sec Total time: 30.974989 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00013hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00013hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.759173s Reading file: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00013hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.802598s ........................................ >>>>>>TIME<<<<<< FFT: 0.957175s Defocus_U Defocus_V Angle CCC 12861.35 13369.17 1.09 0.063833 Final Values Defocus_U Defocus_V Angle CCC 12878.53 13367.67 0.46 0.103481 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00010sq_v01_00013hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00013hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 38.10 6.61 Num Hot pixels: 196 Hot pixel threshold: 77.74 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.702361 Iteration 2 Error: 0.151609 Iteration 3 Error: 0.038193 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.17 -0.08 ...... Frame ( 3) shift: -0.34 -0.15 ...... Frame ( 4) shift: -0.51 -0.23 ...... Frame ( 5) shift: -0.68 -0.30 ...... Frame ( 6) shift: -0.77 -0.33 ...... Frame ( 7) shift: -0.78 -0.31 ...... Frame ( 8) shift: -0.79 -0.28 ...... Frame ( 9) shift: -0.81 -0.24 ...... Frame ( 10) shift: -0.84 -0.16 ...... Frame ( 11) shift: -0.88 -0.09 ...... Frame ( 12) shift: -0.87 -0.00 ...... Frame ( 13) shift: -0.82 0.11 ...... Frame ( 14) shift: -0.77 0.22 ...... Frame ( 15) shift: -0.75 0.29 ...... Frame ( 16) shift: -0.76 0.33 ...... Frame ( 17) shift: -0.76 0.36 ...... Frame ( 18) shift: -0.73 0.42 ...... Frame ( 19) shift: -0.65 0.52 ...... Frame ( 20) shift: -0.58 0.62 ...... Frame ( 21) shift: -0.51 0.69 ...... Frame ( 22) shift: -0.44 0.73 ...... Frame ( 23) shift: -0.37 0.77 ...... Frame ( 24) shift: -0.34 0.78 ...... Frame ( 25) shift: -0.36 0.77 ...... Frame ( 26) shift: -0.37 0.76 ...... Frame ( 27) shift: -0.37 0.78 ...... Frame ( 28) shift: -0.35 0.83 ...... Frame ( 29) shift: -0.33 0.88 ...... Frame ( 30) shift: -0.30 0.92 ...... Frame ( 31) shift: -0.27 0.94 ...... Frame ( 32) shift: -0.24 0.96 ...... Frame ( 33) shift: -0.24 1.00 ...... Frame ( 34) shift: -0.28 1.05 ...... Frame ( 35) shift: -0.31 1.10 ...... Frame ( 36) shift: -0.32 1.14 ...... Frame ( 37) shift: -0.30 1.16 ...... Frame ( 38) shift: -0.28 1.19 ...... Frame ( 39) shift: -0.26 1.21 ...... Frame ( 40) shift: -0.24 1.23 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.083291 Iteration 2 Error: 0.185432 Iteration 3 Error: 0.049943 Align patch 2 23 left Iteration 1 Error: 0.829497 Iteration 2 Error: 0.152638 Iteration 3 Error: 0.031029 Align patch 3 22 left Iteration 1 Error: 1.311885 Iteration 2 Error: 0.211766 Iteration 3 Error: 0.066506 Iteration 4 Error: 0.013622 Align patch 4 21 left Iteration 1 Error: 0.579394 Iteration 2 Error: 0.094757 Iteration 3 Error: 0.018398 Align patch 5 20 left Iteration 1 Error: 0.790867 Iteration 2 Error: 0.114647 Iteration 3 Error: 0.019508 Align patch 6 19 left Iteration 1 Error: 1.036815 Iteration 2 Error: 0.170717 Iteration 3 Error: 0.054940 Iteration 4 Error: 0.021075 Align patch 7 18 left Iteration 1 Error: 0.762401 Iteration 2 Error: 0.153739 Iteration 3 Error: 0.040096 Align patch 8 17 left Iteration 1 Error: 0.714229 Iteration 2 Error: 0.133001 Iteration 3 Error: 0.027731 Align patch 9 16 left Iteration 1 Error: 1.388643 Iteration 2 Error: 0.208544 Iteration 3 Error: 0.073000 Iteration 4 Error: 0.017664 Align patch 10 15 left Iteration 1 Error: 1.060015 Iteration 2 Error: 0.146906 Iteration 3 Error: 0.036849 Align patch 11 14 left Iteration 1 Error: 0.904497 Iteration 2 Error: 0.148403 Iteration 3 Error: 0.057310 Iteration 4 Error: 0.023197 Align patch 12 13 left Iteration 1 Error: 0.614290 Iteration 2 Error: 0.128351 Iteration 3 Error: 0.031333 Align patch 13 12 left Iteration 1 Error: 0.599418 Iteration 2 Error: 0.143546 Iteration 3 Error: 0.035457 Align patch 14 11 left Iteration 1 Error: 0.876805 Iteration 2 Error: 0.153975 Iteration 3 Error: 0.044155 Align patch 15 10 left Iteration 1 Error: 1.214445 Iteration 2 Error: 0.103328 Iteration 3 Error: 0.027441 Align patch 16 9 left Iteration 1 Error: 0.815604 Iteration 2 Error: 0.111027 Iteration 3 Error: 0.029738 Align patch 17 8 left Iteration 1 Error: 0.789509 Iteration 2 Error: 0.099060 Iteration 3 Error: 0.023962 Align patch 18 7 left Iteration 1 Error: 0.496254 Iteration 2 Error: 0.089489 Iteration 3 Error: 0.027268 Align patch 19 6 left Iteration 1 Error: 0.706872 Iteration 2 Error: 0.084979 Iteration 3 Error: 0.022186 Align patch 20 5 left Iteration 1 Error: 0.933431 Iteration 2 Error: 0.110259 Iteration 3 Error: 0.021787 Align patch 21 4 left Iteration 1 Error: 0.611782 Iteration 2 Error: 0.121352 Iteration 3 Error: 0.039972 Align patch 22 3 left Iteration 1 Error: 1.018989 Iteration 2 Error: 0.136398 Iteration 3 Error: 0.047389 Align patch 23 2 left Iteration 1 Error: 0.593546 Iteration 2 Error: 0.131551 Iteration 3 Error: 0.031979 Align patch 24 1 left Iteration 1 Error: 0.916966 Iteration 2 Error: 0.185238 Iteration 3 Error: 0.067120 Iteration 4 Error: 0.025979 Align patch 25 0 left Iteration 1 Error: 1.051100 Iteration 2 Error: 0.159930 Iteration 3 Error: 0.039604 3D Fitting completed. Patch alignment time: 15.81(sec) Local motion has been corrected. Process thread exits. Computational time: 24.295567 sec Total time: 30.560232 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00013hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00013hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.767212s Reading file: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00013hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.223212s ........................................ >>>>>>TIME<<<<<< FFT: 1.059132s Defocus_U Defocus_V Angle CCC 12992.19 13886.72 8.27 0.044699 Final Values Defocus_U Defocus_V Angle CCC 12990.64 13944.56 7.04 0.065066 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00010sq_v01_00013hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00013hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 38.43 6.69 Num Hot pixels: 206 Hot pixel threshold: 78.56 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.894160 Iteration 2 Error: 0.149498 Iteration 3 Error: 0.047315 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.31 -0.20 ...... Frame ( 3) shift: -0.62 -0.40 ...... Frame ( 4) shift: -0.92 -0.61 ...... Frame ( 5) shift: -1.23 -0.81 ...... Frame ( 6) shift: -1.39 -0.95 ...... Frame ( 7) shift: -1.40 -1.02 ...... Frame ( 8) shift: -1.41 -1.09 ...... Frame ( 9) shift: -1.38 -1.10 ...... Frame ( 10) shift: -1.32 -1.03 ...... Frame ( 11) shift: -1.27 -0.96 ...... Frame ( 12) shift: -1.22 -0.89 ...... Frame ( 13) shift: -1.17 -0.82 ...... Frame ( 14) shift: -1.13 -0.75 ...... Frame ( 15) shift: -1.07 -0.71 ...... Frame ( 16) shift: -1.01 -0.70 ...... Frame ( 17) shift: -0.94 -0.70 ...... Frame ( 18) shift: -0.88 -0.66 ...... Frame ( 19) shift: -0.80 -0.60 ...... Frame ( 20) shift: -0.73 -0.54 ...... Frame ( 21) shift: -0.65 -0.45 ...... Frame ( 22) shift: -0.56 -0.33 ...... Frame ( 23) shift: -0.46 -0.21 ...... Frame ( 24) shift: -0.43 -0.13 ...... Frame ( 25) shift: -0.47 -0.07 ...... Frame ( 26) shift: -0.51 -0.02 ...... Frame ( 27) shift: -0.51 0.07 ...... Frame ( 28) shift: -0.48 0.19 ...... Frame ( 29) shift: -0.45 0.30 ...... Frame ( 30) shift: -0.43 0.34 ...... Frame ( 31) shift: -0.43 0.30 ...... Frame ( 32) shift: -0.42 0.26 ...... Frame ( 33) shift: -0.41 0.26 ...... Frame ( 34) shift: -0.38 0.29 ...... Frame ( 35) shift: -0.35 0.32 ...... Frame ( 36) shift: -0.35 0.33 ...... Frame ( 37) shift: -0.36 0.33 ...... Frame ( 38) shift: -0.37 0.33 ...... Frame ( 39) shift: -0.38 0.33 ...... Frame ( 40) shift: -0.39 0.33 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.218375 Iteration 2 Error: 0.180677 Iteration 3 Error: 0.058851 Iteration 4 Error: 0.023192 Align patch 2 23 left Iteration 1 Error: 0.879382 Iteration 2 Error: 0.162494 Iteration 3 Error: 0.052764 Iteration 4 Error: 0.015798 Align patch 3 22 left Iteration 1 Error: 0.888659 Iteration 2 Error: 0.172681 Iteration 3 Error: 0.033774 Align patch 4 21 left Iteration 1 Error: 0.767252 Iteration 2 Error: 0.089341 Iteration 3 Error: 0.017873 Align patch 5 20 left Iteration 1 Error: 0.639316 Iteration 2 Error: 0.166919 Iteration 3 Error: 0.037357 Align patch 6 19 left Iteration 1 Error: 0.951650 Iteration 2 Error: 0.253520 Iteration 3 Error: 0.081673 Iteration 4 Error: 0.019118 Align patch 7 18 left Iteration 1 Error: 0.907087 Iteration 2 Error: 0.196398 Iteration 3 Error: 0.047900 Align patch 8 17 left Iteration 1 Error: 0.680106 Iteration 2 Error: 0.124334 Iteration 3 Error: 0.033371 Align patch 9 16 left Iteration 1 Error: 0.458092 Iteration 2 Error: 0.150126 Iteration 3 Error: 0.031543 Align patch 10 15 left Iteration 1 Error: 1.195631 Iteration 2 Error: 0.138633 Iteration 3 Error: 0.028934 Align patch 11 14 left Iteration 1 Error: 1.176150 Iteration 2 Error: 0.233802 Iteration 3 Error: 0.067064 Iteration 4 Error: 0.018966 Align patch 12 13 left Iteration 1 Error: 0.611367 Iteration 2 Error: 0.175811 Iteration 3 Error: 0.041838 Align patch 13 12 left Iteration 1 Error: 0.602442 Iteration 2 Error: 0.092389 Iteration 3 Error: 0.022291 Align patch 14 11 left Iteration 1 Error: 0.478749 Iteration 2 Error: 0.061967 Iteration 3 Error: 0.008400 Align patch 15 10 left Iteration 1 Error: 0.513059 Iteration 2 Error: 0.079245 Iteration 3 Error: 0.015917 Align patch 16 9 left Iteration 1 Error: 1.160800 Iteration 2 Error: 0.304697 Iteration 3 Error: 0.094098 Iteration 4 Error: 0.057322 Iteration 5 Error: 0.018492 Align patch 17 8 left Iteration 1 Error: 1.030886 Iteration 2 Error: 0.132297 Iteration 3 Error: 0.025540 Align patch 18 7 left Iteration 1 Error: 0.896707 Iteration 2 Error: 0.119286 Iteration 3 Error: 0.029953 Align patch 19 6 left Iteration 1 Error: 0.489576 Iteration 2 Error: 0.090318 Iteration 3 Error: 0.015588 Align patch 20 5 left Iteration 1 Error: 0.460149 Iteration 2 Error: 0.065050 Iteration 3 Error: 0.011418 Align patch 21 4 left Iteration 1 Error: 0.869061 Iteration 2 Error: 0.135854 Iteration 3 Error: 0.041835 Align patch 22 3 left Iteration 1 Error: 0.563777 Iteration 2 Error: 0.077307 Iteration 3 Error: 0.019968 Align patch 23 2 left Iteration 1 Error: 0.926998 Iteration 2 Error: 0.226854 Iteration 3 Error: 0.036263 Align patch 24 1 left Iteration 1 Error: 0.636919 Iteration 2 Error: 0.086314 Iteration 3 Error: 0.025597 Align patch 25 0 left Iteration 1 Error: 0.709936 Iteration 2 Error: 0.127933 Iteration 3 Error: 0.027508 3D Fitting completed. Patch alignment time: 16.21(sec) Local motion has been corrected. Process thread exits. Computational time: 25.048260 sec Total time: 30.772490 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00013hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00013hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.673098s Reading file: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00013hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.164836s ........................................ >>>>>>TIME<<<<<< FFT: 0.934193s Defocus_U Defocus_V Angle CCC 10914.08 10304.71 85.13 0.045033 Final Values Defocus_U Defocus_V Angle CCC 10967.23 10323.48 84.20 0.074208 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00010sq_v01_00014hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00014hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 39.64 6.95 Num Hot pixels: 208 Hot pixel threshold: 81.31 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.958279 Iteration 2 Error: 0.147165 Iteration 3 Error: 0.035091 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.11 0.00 ...... Frame ( 3) shift: -0.22 0.00 ...... Frame ( 4) shift: -0.33 0.00 ...... Frame ( 5) shift: -0.44 0.00 ...... Frame ( 6) shift: -0.51 -0.02 ...... Frame ( 7) shift: -0.55 -0.05 ...... Frame ( 8) shift: -0.58 -0.09 ...... Frame ( 9) shift: -0.57 -0.08 ...... Frame ( 10) shift: -0.52 -0.02 ...... Frame ( 11) shift: -0.47 0.03 ...... Frame ( 12) shift: -0.43 0.09 ...... Frame ( 13) shift: -0.41 0.15 ...... Frame ( 14) shift: -0.39 0.21 ...... Frame ( 15) shift: -0.35 0.28 ...... Frame ( 16) shift: -0.27 0.35 ...... Frame ( 17) shift: -0.20 0.41 ...... Frame ( 18) shift: -0.16 0.48 ...... Frame ( 19) shift: -0.14 0.56 ...... Frame ( 20) shift: -0.13 0.63 ...... Frame ( 21) shift: -0.11 0.71 ...... Frame ( 22) shift: -0.09 0.81 ...... Frame ( 23) shift: -0.06 0.91 ...... Frame ( 24) shift: -0.02 0.95 ...... Frame ( 25) shift: 0.04 0.92 ...... Frame ( 26) shift: 0.09 0.90 ...... Frame ( 27) shift: 0.13 0.93 ...... Frame ( 28) shift: 0.16 1.00 ...... Frame ( 29) shift: 0.18 1.08 ...... Frame ( 30) shift: 0.18 1.12 ...... Frame ( 31) shift: 0.17 1.11 ...... Frame ( 32) shift: 0.15 1.10 ...... Frame ( 33) shift: 0.18 1.13 ...... Frame ( 34) shift: 0.24 1.20 ...... Frame ( 35) shift: 0.30 1.28 ...... Frame ( 36) shift: 0.35 1.35 ...... Frame ( 37) shift: 0.38 1.42 ...... Frame ( 38) shift: 0.42 1.48 ...... Frame ( 39) shift: 0.46 1.55 ...... Frame ( 40) shift: 0.50 1.62 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.878409 Iteration 2 Error: 0.144123 Iteration 3 Error: 0.061740 Iteration 4 Error: 0.018903 Align patch 2 23 left Iteration 1 Error: 0.983112 Iteration 2 Error: 0.199304 Iteration 3 Error: 0.042034 Align patch 3 22 left Iteration 1 Error: 0.799071 Iteration 2 Error: 0.176541 Iteration 3 Error: 0.051932 Iteration 4 Error: 0.015873 Align patch 4 21 left Iteration 1 Error: 0.529404 Iteration 2 Error: 0.098855 Iteration 3 Error: 0.019025 Align patch 5 20 left Iteration 1 Error: 0.529846 Iteration 2 Error: 0.075119 Iteration 3 Error: 0.013424 Align patch 6 19 left Iteration 1 Error: 1.141957 Iteration 2 Error: 0.215689 Iteration 3 Error: 0.100155 Iteration 4 Error: 0.041532 Align patch 7 18 left Iteration 1 Error: 0.791199 Iteration 2 Error: 0.260618 Iteration 3 Error: 0.108349 Iteration 4 Error: 0.044063 Align patch 8 17 left Iteration 1 Error: 0.627767 Iteration 2 Error: 0.086310 Iteration 3 Error: 0.022205 Align patch 9 16 left Iteration 1 Error: 1.020936 Iteration 2 Error: 0.084070 Iteration 3 Error: 0.028279 Align patch 10 15 left Iteration 1 Error: 0.457019 Iteration 2 Error: 0.098892 Iteration 3 Error: 0.022661 Align patch 11 14 left Iteration 1 Error: 0.839667 Iteration 2 Error: 0.371790 Iteration 3 Error: 0.119314 Iteration 4 Error: 0.044811 Align patch 12 13 left Iteration 1 Error: 0.640957 Iteration 2 Error: 0.138070 Iteration 3 Error: 0.040763 Align patch 13 12 left Iteration 1 Error: 0.755827 Iteration 2 Error: 0.114220 Iteration 3 Error: 0.030516 Align patch 14 11 left Iteration 1 Error: 0.837243 Iteration 2 Error: 0.103411 Iteration 3 Error: 0.025908 Align patch 15 10 left Iteration 1 Error: 0.629594 Iteration 2 Error: 0.092329 Iteration 3 Error: 0.020540 Align patch 16 9 left Iteration 1 Error: 0.738866 Iteration 2 Error: 0.100649 Iteration 3 Error: 0.025255 Align patch 17 8 left Iteration 1 Error: 0.568985 Iteration 2 Error: 0.093044 Iteration 3 Error: 0.017351 Align patch 18 7 left Iteration 1 Error: 0.715410 Iteration 2 Error: 0.136489 Iteration 3 Error: 0.033796 Align patch 19 6 left Iteration 1 Error: 0.432138 Iteration 2 Error: 0.075557 Iteration 3 Error: 0.015494 Align patch 20 5 left Iteration 1 Error: 0.411241 Iteration 2 Error: 0.082297 Iteration 3 Error: 0.013992 Align patch 21 4 left Iteration 1 Error: 0.710300 Iteration 2 Error: 0.138439 Iteration 3 Error: 0.023933 Align patch 22 3 left Iteration 1 Error: 0.561762 Iteration 2 Error: 0.109299 Iteration 3 Error: 0.030294 Align patch 23 2 left Iteration 1 Error: 0.953983 Iteration 2 Error: 0.118678 Iteration 3 Error: 0.028386 Align patch 24 1 left Iteration 1 Error: 0.852839 Iteration 2 Error: 0.161584 Iteration 3 Error: 0.031027 Align patch 25 0 left Iteration 1 Error: 0.165686 Iteration 2 Error: 0.042844 3D Fitting completed. Patch alignment time: 15.08(sec) Local motion has been corrected. Process thread exits. Computational time: 24.015648 sec Total time: 29.656876 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00014hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00014hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.559071s Reading file: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00014hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.982071s ........................................ >>>>>>TIME<<<<<< FFT: 0.980133s Defocus_U Defocus_V Angle CCC 8517.58 9373.05 13.21 0.034367 Final Values Defocus_U Defocus_V Angle CCC 8520.70 9373.05 13.21 0.066937 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00010sq_v01_00014hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00014hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.002e-01 CC threshold: 0.736 Mean Std: 38.13 6.64 Num Hot pixels: 213 Hot pixel threshold: 77.99 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.894648 Iteration 2 Error: 0.208589 Iteration 3 Error: 0.070415 Iteration 4 Error: 0.018486 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.11 -0.12 ...... Frame ( 3) shift: -0.22 -0.25 ...... Frame ( 4) shift: -0.33 -0.37 ...... Frame ( 5) shift: -0.44 -0.50 ...... Frame ( 6) shift: -0.44 -0.54 ...... Frame ( 7) shift: -0.33 -0.50 ...... Frame ( 8) shift: -0.23 -0.45 ...... Frame ( 9) shift: -0.15 -0.41 ...... Frame ( 10) shift: -0.12 -0.36 ...... Frame ( 11) shift: -0.08 -0.31 ...... Frame ( 12) shift: -0.07 -0.25 ...... Frame ( 13) shift: -0.08 -0.17 ...... Frame ( 14) shift: -0.09 -0.10 ...... Frame ( 15) shift: -0.06 -0.06 ...... Frame ( 16) shift: 0.01 -0.05 ...... Frame ( 17) shift: 0.09 -0.05 ...... Frame ( 18) shift: 0.15 -0.00 ...... Frame ( 19) shift: 0.21 0.09 ...... Frame ( 20) shift: 0.28 0.18 ...... Frame ( 21) shift: 0.36 0.23 ...... Frame ( 22) shift: 0.45 0.25 ...... Frame ( 23) shift: 0.55 0.27 ...... Frame ( 24) shift: 0.62 0.32 ...... Frame ( 25) shift: 0.67 0.39 ...... Frame ( 26) shift: 0.71 0.47 ...... Frame ( 27) shift: 0.75 0.52 ...... Frame ( 28) shift: 0.77 0.56 ...... Frame ( 29) shift: 0.80 0.60 ...... Frame ( 30) shift: 0.87 0.66 ...... Frame ( 31) shift: 0.98 0.73 ...... Frame ( 32) shift: 1.10 0.80 ...... Frame ( 33) shift: 1.18 0.84 ...... Frame ( 34) shift: 1.21 0.85 ...... Frame ( 35) shift: 1.25 0.87 ...... Frame ( 36) shift: 1.23 0.87 ...... Frame ( 37) shift: 1.16 0.86 ...... Frame ( 38) shift: 1.09 0.85 ...... Frame ( 39) shift: 1.02 0.84 ...... Frame ( 40) shift: 0.96 0.83 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.071203 Iteration 2 Error: 0.253687 Iteration 3 Error: 0.111845 Iteration 4 Error: 0.037834 Align patch 2 23 left Iteration 1 Error: 0.762245 Iteration 2 Error: 0.111258 Iteration 3 Error: 0.059810 Iteration 4 Error: 0.021533 Align patch 3 22 left Iteration 1 Error: 0.863115 Iteration 2 Error: 0.152441 Iteration 3 Error: 0.052348 Iteration 4 Error: 0.013390 Align patch 4 21 left Iteration 1 Error: 0.554810 Iteration 2 Error: 0.107023 Iteration 3 Error: 0.034933 Align patch 5 20 left Iteration 1 Error: 0.968755 Iteration 2 Error: 0.185167 Iteration 3 Error: 0.046633 Align patch 6 19 left Iteration 1 Error: 1.455044 Iteration 2 Error: 0.250889 Iteration 3 Error: 0.098471 Iteration 4 Error: 0.046924 Align patch 7 18 left Iteration 1 Error: 2.042517 Iteration 2 Error: 0.346439 Iteration 3 Error: 0.087209 Iteration 4 Error: 0.035140 Align patch 8 17 left Iteration 1 Error: 0.981575 Iteration 2 Error: 0.136803 Iteration 3 Error: 0.056321 Iteration 4 Error: 0.013175 Align patch 9 16 left Iteration 1 Error: 0.602290 Iteration 2 Error: 0.099226 Iteration 3 Error: 0.018891 Align patch 10 15 left Iteration 1 Error: 0.986870 Iteration 2 Error: 0.106072 Iteration 3 Error: 0.019814 Align patch 11 14 left Iteration 1 Error: 0.933214 Iteration 2 Error: 0.321672 Iteration 3 Error: 0.160388 Iteration 4 Error: 0.069238 Iteration 5 Error: 0.039817 Align patch 12 13 left Iteration 1 Error: 0.860222 Iteration 2 Error: 0.120654 Iteration 3 Error: 0.040295 Align patch 13 12 left Iteration 1 Error: 0.445851 Iteration 2 Error: 0.078435 Iteration 3 Error: 0.019229 Align patch 14 11 left Iteration 1 Error: 0.653818 Iteration 2 Error: 0.098937 Iteration 3 Error: 0.034912 Align patch 15 10 left Iteration 1 Error: 0.662557 Iteration 2 Error: 0.107406 Iteration 3 Error: 0.036323 Align patch 16 9 left Iteration 1 Error: 0.954837 Iteration 2 Error: 0.221622 Iteration 3 Error: 0.059862 Iteration 4 Error: 0.026237 Align patch 17 8 left Iteration 1 Error: 0.485458 Iteration 2 Error: 0.104313 Iteration 3 Error: 0.020886 Align patch 18 7 left Iteration 1 Error: 0.685403 Iteration 2 Error: 0.135952 Iteration 3 Error: 0.036246 Align patch 19 6 left Iteration 1 Error: 0.513236 Iteration 2 Error: 0.058461 Iteration 3 Error: 0.016717 Align patch 20 5 left Iteration 1 Error: 0.516187 Iteration 2 Error: 0.108741 Iteration 3 Error: 0.032897 Align patch 21 4 left Iteration 1 Error: 0.807949 Iteration 2 Error: 0.103167 Iteration 3 Error: 0.024027 Align patch 22 3 left Iteration 1 Error: 0.728240 Iteration 2 Error: 0.114226 Iteration 3 Error: 0.031429 Align patch 23 2 left Iteration 1 Error: 0.691882 Iteration 2 Error: 0.132272 Iteration 3 Error: 0.030237 Align patch 24 1 left Iteration 1 Error: 0.798564 Iteration 2 Error: 0.109734 Iteration 3 Error: 0.030430 Align patch 25 0 left Iteration 1 Error: 0.904973 Iteration 2 Error: 0.084321 Iteration 3 Error: 0.030692 3D Fitting completed. Patch alignment time: 16.00(sec) Local motion has been corrected. Process thread exits. Computational time: 24.948656 sec Total time: 31.934097 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00014hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00014hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.745712s Reading file: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00014hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.838889s ........................................ >>>>>>TIME<<<<<< FFT: 1.018074s Defocus_U Defocus_V Angle CCC 10988.30 11589.88 5.82 0.042075 Final Values Defocus_U Defocus_V Angle CCC 11010.18 11614.89 7.09 0.066775 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00010sq_v01_00014hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00014hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.003e-01 CC threshold: 0.737 Mean Std: 39.06 6.71 Num Hot pixels: 243 Hot pixel threshold: 79.33 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.580840 Iteration 2 Error: 0.128419 Iteration 3 Error: 0.031983 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.13 -0.17 ...... Frame ( 3) shift: -0.26 -0.33 ...... Frame ( 4) shift: -0.39 -0.50 ...... Frame ( 5) shift: -0.51 -0.67 ...... Frame ( 6) shift: -0.55 -0.76 ...... Frame ( 7) shift: -0.50 -0.76 ...... Frame ( 8) shift: -0.45 -0.76 ...... Frame ( 9) shift: -0.40 -0.75 ...... Frame ( 10) shift: -0.36 -0.73 ...... Frame ( 11) shift: -0.32 -0.70 ...... Frame ( 12) shift: -0.30 -0.67 ...... Frame ( 13) shift: -0.32 -0.63 ...... Frame ( 14) shift: -0.34 -0.59 ...... Frame ( 15) shift: -0.35 -0.55 ...... Frame ( 16) shift: -0.37 -0.53 ...... Frame ( 17) shift: -0.39 -0.50 ...... Frame ( 18) shift: -0.38 -0.48 ...... Frame ( 19) shift: -0.35 -0.46 ...... Frame ( 20) shift: -0.32 -0.45 ...... Frame ( 21) shift: -0.28 -0.42 ...... Frame ( 22) shift: -0.22 -0.38 ...... Frame ( 23) shift: -0.16 -0.34 ...... Frame ( 24) shift: -0.11 -0.25 ...... Frame ( 25) shift: -0.05 -0.11 ...... Frame ( 26) shift: 0.01 0.03 ...... Frame ( 27) shift: 0.05 0.11 ...... Frame ( 28) shift: 0.08 0.13 ...... Frame ( 29) shift: 0.11 0.14 ...... Frame ( 30) shift: 0.10 0.17 ...... Frame ( 31) shift: 0.05 0.20 ...... Frame ( 32) shift: -0.01 0.22 ...... Frame ( 33) shift: -0.01 0.24 ...... Frame ( 34) shift: 0.04 0.23 ...... Frame ( 35) shift: 0.09 0.23 ...... Frame ( 36) shift: 0.14 0.23 ...... Frame ( 37) shift: 0.19 0.23 ...... Frame ( 38) shift: 0.24 0.23 ...... Frame ( 39) shift: 0.29 0.23 ...... Frame ( 40) shift: 0.34 0.23 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.392831 Iteration 2 Error: 0.291361 Iteration 3 Error: 0.082075 Iteration 4 Error: 0.034188 Align patch 2 23 left Iteration 1 Error: 1.446032 Iteration 2 Error: 0.252752 Iteration 3 Error: 0.074069 Iteration 4 Error: 0.020824 Align patch 3 22 left Iteration 1 Error: 0.612357 Iteration 2 Error: 0.093074 Iteration 3 Error: 0.024607 Align patch 4 21 left Iteration 1 Error: 0.699088 Iteration 2 Error: 0.122169 Iteration 3 Error: 0.025918 Align patch 5 20 left Iteration 1 Error: 0.967384 Iteration 2 Error: 0.139230 Iteration 3 Error: 0.039411 Align patch 6 19 left Iteration 1 Error: 1.446575 Iteration 2 Error: 0.217109 Iteration 3 Error: 0.057627 Iteration 4 Error: 0.012845 Align patch 7 18 left Iteration 1 Error: 1.483232 Iteration 2 Error: 0.185193 Iteration 3 Error: 0.051177 Iteration 4 Error: 0.017128 Align patch 8 17 left Iteration 1 Error: 0.706709 Iteration 2 Error: 0.167341 Iteration 3 Error: 0.027551 Align patch 9 16 left Iteration 1 Error: 1.081080 Iteration 2 Error: 0.124939 Iteration 3 Error: 0.030133 Align patch 10 15 left Iteration 1 Error: 0.646710 Iteration 2 Error: 0.113857 Iteration 3 Error: 0.018152 Align patch 11 14 left Iteration 1 Error: 1.045979 Iteration 2 Error: 0.185388 Iteration 3 Error: 0.043832 Align patch 12 13 left Iteration 1 Error: 0.782464 Iteration 2 Error: 0.140536 Iteration 3 Error: 0.021585 Align patch 13 12 left Iteration 1 Error: 0.496142 Iteration 2 Error: 0.049900 Align patch 14 11 left Iteration 1 Error: 0.562454 Iteration 2 Error: 0.127073 Iteration 3 Error: 0.029128 Align patch 15 10 left Iteration 1 Error: 0.493885 Iteration 2 Error: 0.154325 Iteration 3 Error: 0.034653 Align patch 16 9 left Iteration 1 Error: 0.788444 Iteration 2 Error: 0.080529 Iteration 3 Error: 0.016944 Align patch 17 8 left Iteration 1 Error: 0.657017 Iteration 2 Error: 0.121827 Iteration 3 Error: 0.035217 Align patch 18 7 left Iteration 1 Error: 0.598140 Iteration 2 Error: 0.107958 Iteration 3 Error: 0.027047 Align patch 19 6 left Iteration 1 Error: 0.522960 Iteration 2 Error: 0.111001 Iteration 3 Error: 0.039073 Align patch 20 5 left Iteration 1 Error: 0.541982 Iteration 2 Error: 0.066919 Iteration 3 Error: 0.016277 Align patch 21 4 left Iteration 1 Error: 0.445636 Iteration 2 Error: 0.082375 Iteration 3 Error: 0.012632 Align patch 22 3 left Iteration 1 Error: 0.706358 Iteration 2 Error: 0.117190 Iteration 3 Error: 0.028338 Align patch 23 2 left Iteration 1 Error: 0.764924 Iteration 2 Error: 0.093559 Iteration 3 Error: 0.014230 Align patch 24 1 left Iteration 1 Error: 0.873944 Iteration 2 Error: 0.101214 Iteration 3 Error: 0.020810 Align patch 25 0 left Iteration 1 Error: 0.712611 Iteration 2 Error: 0.125301 Iteration 3 Error: 0.024794 3D Fitting completed. Patch alignment time: 15.99(sec) Local motion has been corrected. Process thread exits. Computational time: 24.730179 sec Total time: 30.610054 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00014hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00014hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.772149s Reading file: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00014hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.622309s ........................................ >>>>>>TIME<<<<<< FFT: 1.042565s Defocus_U Defocus_V Angle CCC 11779.30 12654.30 4.94 0.046988 Final Values Defocus_U Defocus_V Angle CCC 11798.05 12673.05 4.00 0.073253 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00010sq_v01_00014hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00014hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 36.68 6.53 Num Hot pixels: 222 Hot pixel threshold: 75.84 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.851130 Iteration 2 Error: 0.167896 Iteration 3 Error: 0.035957 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.08 -0.20 ...... Frame ( 3) shift: -0.17 -0.40 ...... Frame ( 4) shift: -0.25 -0.61 ...... Frame ( 5) shift: -0.34 -0.81 ...... Frame ( 6) shift: -0.36 -0.97 ...... Frame ( 7) shift: -0.32 -1.08 ...... Frame ( 8) shift: -0.27 -1.20 ...... Frame ( 9) shift: -0.21 -1.24 ...... Frame ( 10) shift: -0.12 -1.21 ...... Frame ( 11) shift: -0.03 -1.18 ...... Frame ( 12) shift: 0.05 -1.17 ...... Frame ( 13) shift: 0.11 -1.17 ...... Frame ( 14) shift: 0.18 -1.17 ...... Frame ( 15) shift: 0.24 -1.17 ...... Frame ( 16) shift: 0.29 -1.17 ...... Frame ( 17) shift: 0.34 -1.18 ...... Frame ( 18) shift: 0.41 -1.14 ...... Frame ( 19) shift: 0.50 -1.08 ...... Frame ( 20) shift: 0.58 -1.01 ...... Frame ( 21) shift: 0.67 -0.95 ...... Frame ( 22) shift: 0.78 -0.89 ...... Frame ( 23) shift: 0.88 -0.83 ...... Frame ( 24) shift: 0.93 -0.80 ...... Frame ( 25) shift: 0.93 -0.80 ...... Frame ( 26) shift: 0.93 -0.80 ...... Frame ( 27) shift: 0.97 -0.79 ...... Frame ( 28) shift: 1.06 -0.77 ...... Frame ( 29) shift: 1.15 -0.75 ...... Frame ( 30) shift: 1.19 -0.73 ...... Frame ( 31) shift: 1.20 -0.72 ...... Frame ( 32) shift: 1.20 -0.70 ...... Frame ( 33) shift: 1.23 -0.70 ...... Frame ( 34) shift: 1.29 -0.73 ...... Frame ( 35) shift: 1.34 -0.75 ...... Frame ( 36) shift: 1.39 -0.76 ...... Frame ( 37) shift: 1.42 -0.77 ...... Frame ( 38) shift: 1.46 -0.78 ...... Frame ( 39) shift: 1.50 -0.79 ...... Frame ( 40) shift: 1.53 -0.80 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.557222 Iteration 2 Error: 0.528296 Iteration 3 Error: 0.194759 Iteration 4 Error: 0.109761 Iteration 5 Error: 0.053741 Align patch 1 24 left Iteration 1 Error: 1.826692 Iteration 2 Error: 0.346799 Iteration 3 Error: 0.107654 Iteration 4 Error: 0.035183 Align patch 2 23 left Iteration 1 Error: 1.773549 Iteration 2 Error: 0.280448 Iteration 3 Error: 0.111174 Iteration 4 Error: 0.040813 Align patch 3 22 left Iteration 1 Error: 1.534223 Iteration 2 Error: 0.335236 Iteration 3 Error: 0.093006 Iteration 4 Error: 0.030832 Align patch 4 21 left Iteration 1 Error: 1.251902 Iteration 2 Error: 0.160811 Iteration 3 Error: 0.021194 Align patch 5 20 left Iteration 1 Error: 0.707917 Iteration 2 Error: 0.033939 Align patch 6 19 left Iteration 1 Error: 1.614317 Iteration 2 Error: 0.387880 Iteration 3 Error: 0.198013 Iteration 4 Error: 0.118321 Iteration 5 Error: 0.068574 Align patch 6 19 left Iteration 1 Error: 1.643593 Iteration 2 Error: 0.325084 Iteration 3 Error: 0.104888 Iteration 4 Error: 0.052499 Iteration 5 Error: 0.015968 Align patch 7 18 left Iteration 1 Error: 1.355536 Iteration 2 Error: 0.300351 Iteration 3 Error: 0.084621 Iteration 4 Error: 0.041925 Align patch 8 17 left Iteration 1 Error: 0.942017 Iteration 2 Error: 0.203356 Iteration 3 Error: 0.069625 Iteration 4 Error: 0.015430 Align patch 9 16 left Iteration 1 Error: 0.737601 Iteration 2 Error: 0.121708 Iteration 3 Error: 0.032147 Align patch 10 15 left Iteration 1 Error: 1.539808 Iteration 2 Error: 0.232288 Iteration 3 Error: 0.045278 Align patch 11 14 left Iteration 1 Error: 0.994856 Iteration 2 Error: 0.291010 Iteration 3 Error: 0.132077 Iteration 4 Error: 0.072392 Iteration 5 Error: 0.051579 Align patch 11 14 left Iteration 1 Error: 1.217711 Iteration 2 Error: 0.346987 Iteration 3 Error: 0.118902 Iteration 4 Error: 0.049423 Align patch 12 13 left Iteration 1 Error: 0.965544 Iteration 2 Error: 0.472271 Iteration 3 Error: 0.224650 Iteration 4 Error: 0.156068 Iteration 5 Error: 0.086563 Align patch 12 13 left Iteration 1 Error: 1.101896 Iteration 2 Error: 0.262084 Iteration 3 Error: 0.096094 Iteration 4 Error: 0.038485 Align patch 13 12 left Iteration 1 Error: 0.757628 Iteration 2 Error: 0.172966 Iteration 3 Error: 0.034543 Align patch 14 11 left Iteration 1 Error: 1.017861 Iteration 2 Error: 0.229590 Iteration 3 Error: 0.052997 Iteration 4 Error: 0.015076 Align patch 15 10 left Iteration 1 Error: 1.026822 Iteration 2 Error: 0.233529 Iteration 3 Error: 0.048084 Align patch 16 9 left Iteration 1 Error: 1.218166 Iteration 2 Error: 0.388381 Iteration 3 Error: 0.114818 Iteration 4 Error: 0.086838 Iteration 5 Error: 0.051572 Align patch 16 9 left Iteration 1 Error: 1.095644 Iteration 2 Error: 0.273706 Iteration 3 Error: 0.102909 Iteration 4 Error: 0.049826 Align patch 17 8 left Iteration 1 Error: 1.580089 Iteration 2 Error: 0.693207 Iteration 3 Error: 0.120164 Iteration 4 Error: 0.084423 Iteration 5 Error: 0.019344 Align patch 18 7 left Iteration 1 Error: 0.722867 Iteration 2 Error: 0.202548 Iteration 3 Error: 0.104282 Iteration 4 Error: 0.052663 Iteration 5 Error: 0.037343 Align patch 19 6 left Iteration 1 Error: 0.933690 Iteration 2 Error: 0.233553 Iteration 3 Error: 0.037045 Align patch 20 5 left Iteration 1 Error: 0.820112 Iteration 2 Error: 0.250575 Iteration 3 Error: 0.090704 Iteration 4 Error: 0.033618 Align patch 21 4 left Iteration 1 Error: 0.832098 Iteration 2 Error: 0.171551 Iteration 3 Error: 0.055966 Iteration 4 Error: 0.020432 Align patch 22 3 left Iteration 1 Error: 0.881154 Iteration 2 Error: 0.172130 Iteration 3 Error: 0.050415 Iteration 4 Error: 0.014665 Align patch 23 2 left Iteration 1 Error: 1.046327 Iteration 2 Error: 0.270506 Iteration 3 Error: 0.106632 Iteration 4 Error: 0.033734 Align patch 24 1 left Iteration 1 Error: 0.877706 Iteration 2 Error: 0.119982 Iteration 3 Error: 0.047495 Align patch 25 0 left Iteration 1 Error: 0.933112 Iteration 2 Error: 0.161799 Iteration 3 Error: 0.060188 Iteration 4 Error: 0.027962 3D Fitting completed. Patch alignment time: 21.75(sec) Local motion has been corrected. Process thread exits. Computational time: 30.677212 sec Total time: 36.485260 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00014hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00014hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.566006s Reading file: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00014hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.417418s ........................................ >>>>>>TIME<<<<<< FFT: 0.949128s Defocus_U Defocus_V Angle CCC 10617.29 10214.76 72.21 0.022732 Final Values Defocus_U Defocus_V Angle CCC 10559.45 10153.85 63.11 0.033072 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00010sq_v01_00015hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00015hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.366e-01 1.015e-01 CC threshold: 0.746 Mean Std: 33.63 6.43 Num Hot pixels: 192 Hot pixel threshold: 72.19 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.692908 Iteration 2 Error: 0.347801 Iteration 3 Error: 0.069412 Iteration 4 Error: 0.016713 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.08 0.04 ...... Frame ( 3) shift: 0.16 0.07 ...... Frame ( 4) shift: 0.24 0.11 ...... Frame ( 5) shift: 0.32 0.15 ...... Frame ( 6) shift: 0.40 0.17 ...... Frame ( 7) shift: 0.50 0.17 ...... Frame ( 8) shift: 0.60 0.16 ...... Frame ( 9) shift: 0.72 0.19 ...... Frame ( 10) shift: 0.85 0.24 ...... Frame ( 11) shift: 0.99 0.29 ...... Frame ( 12) shift: 1.14 0.34 ...... Frame ( 13) shift: 1.29 0.39 ...... Frame ( 14) shift: 1.45 0.43 ...... Frame ( 15) shift: 1.58 0.46 ...... Frame ( 16) shift: 1.69 0.47 ...... Frame ( 17) shift: 1.79 0.47 ...... Frame ( 18) shift: 1.92 0.48 ...... Frame ( 19) shift: 2.06 0.47 ...... Frame ( 20) shift: 2.19 0.47 ...... Frame ( 21) shift: 2.34 0.45 ...... Frame ( 22) shift: 2.49 0.42 ...... Frame ( 23) shift: 2.65 0.39 ...... Frame ( 24) shift: 2.81 0.40 ...... Frame ( 25) shift: 2.98 0.45 ...... Frame ( 26) shift: 3.15 0.50 ...... Frame ( 27) shift: 3.34 0.53 ...... Frame ( 28) shift: 3.53 0.56 ...... Frame ( 29) shift: 3.72 0.58 ...... Frame ( 30) shift: 3.89 0.62 ...... Frame ( 31) shift: 4.04 0.67 ...... Frame ( 32) shift: 4.19 0.72 ...... Frame ( 33) shift: 4.38 0.74 ...... Frame ( 34) shift: 4.62 0.72 ...... Frame ( 35) shift: 4.86 0.70 ...... Frame ( 36) shift: 5.02 0.71 ...... Frame ( 37) shift: 5.11 0.74 ...... Frame ( 38) shift: 5.20 0.77 ...... Frame ( 39) shift: 5.30 0.80 ...... Frame ( 40) shift: 5.39 0.83 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.438824 Iteration 2 Error: 0.222970 Iteration 3 Error: 0.027523 Align patch 2 23 left Iteration 1 Error: 1.108615 Iteration 2 Error: 0.177382 Iteration 3 Error: 0.021493 Align patch 3 22 left Iteration 1 Error: 1.167665 Iteration 2 Error: 0.182014 Iteration 3 Error: 0.034842 Align patch 4 21 left Iteration 1 Error: 1.328236 Iteration 2 Error: 0.253901 Iteration 3 Error: 0.035136 Align patch 5 20 left Iteration 1 Error: 1.511461 Iteration 2 Error: 0.147097 Iteration 3 Error: 0.028664 Align patch 6 19 left Iteration 1 Error: 1.099476 Iteration 2 Error: 0.199553 Iteration 3 Error: 0.036433 Align patch 7 18 left Iteration 1 Error: 0.713305 Iteration 2 Error: 0.134484 Iteration 3 Error: 0.019481 Align patch 8 17 left Iteration 1 Error: 0.504909 Iteration 2 Error: 0.060519 Iteration 3 Error: 0.008698 Align patch 9 16 left Iteration 1 Error: 0.979439 Iteration 2 Error: 0.139181 Iteration 3 Error: 0.016698 Align patch 10 15 left Iteration 1 Error: 1.388269 Iteration 2 Error: 0.180409 Iteration 3 Error: 0.022178 Align patch 11 14 left Iteration 1 Error: 1.566521 Iteration 2 Error: 0.276189 Iteration 3 Error: 0.040401 Align patch 12 13 left Iteration 1 Error: 1.226938 Iteration 2 Error: 0.273517 Iteration 3 Error: 0.045324 Align patch 13 12 left Iteration 1 Error: 0.821703 Iteration 2 Error: 0.115290 Iteration 3 Error: 0.022880 Align patch 14 11 left Iteration 1 Error: 0.541341 Iteration 2 Error: 0.052213 Iteration 3 Error: 0.008390 Align patch 15 10 left Iteration 1 Error: 0.963151 Iteration 2 Error: 0.123872 Iteration 3 Error: 0.017175 Align patch 16 9 left Iteration 1 Error: 1.462735 Iteration 2 Error: 0.198238 Iteration 3 Error: 0.042023 Align patch 17 8 left Iteration 1 Error: 1.017532 Iteration 2 Error: 0.198201 Iteration 3 Error: 0.050918 Iteration 4 Error: 0.012217 Align patch 18 7 left Iteration 1 Error: 0.446567 Iteration 2 Error: 0.068560 Iteration 3 Error: 0.015392 Align patch 19 6 left Iteration 1 Error: 0.310194 Iteration 2 Error: 0.038428 Align patch 20 5 left Iteration 1 Error: 1.166542 Iteration 2 Error: 0.147468 Iteration 3 Error: 0.021520 Align patch 21 4 left Iteration 1 Error: 1.526789 Iteration 2 Error: 0.284961 Iteration 3 Error: 0.081083 Iteration 4 Error: 0.024243 Align patch 22 3 left Iteration 1 Error: 0.915919 Iteration 2 Error: 0.217422 Iteration 3 Error: 0.058149 Iteration 4 Error: 0.017575 Align patch 23 2 left Iteration 1 Error: 0.479805 Iteration 2 Error: 0.063505 Iteration 3 Error: 0.013543 Align patch 24 1 left Iteration 1 Error: 0.600626 Iteration 2 Error: 0.096714 Iteration 3 Error: 0.018104 Align patch 25 0 left Iteration 1 Error: 0.871581 Iteration 2 Error: 0.123093 Iteration 3 Error: 0.019325 3D Fitting completed. Patch alignment time: 15.36(sec) Local motion has been corrected. Process thread exits. Computational time: 24.499636 sec Total time: 30.442270 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00015hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00015hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.731302s Reading file: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00015hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.494537s ........................................ >>>>>>TIME<<<<<< FFT: 0.817764s Defocus_U Defocus_V Angle CCC 13050.78 13925.78 12.46 0.139843 Final Values Defocus_U Defocus_V Angle CCC 13047.70 13947.70 13.71 0.194650 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00010sq_v01_00015hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00015hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.352e-01 1.006e-01 CC threshold: 0.739 Mean Std: 39.02 6.94 Num Hot pixels: 180 Hot pixel threshold: 80.65 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.809855 Iteration 2 Error: 0.174394 Iteration 3 Error: 0.036649 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.13 0.01 ...... Frame ( 3) shift: -0.26 0.02 ...... Frame ( 4) shift: -0.38 0.03 ...... Frame ( 5) shift: -0.51 0.04 ...... Frame ( 6) shift: -0.56 0.04 ...... Frame ( 7) shift: -0.54 0.03 ...... Frame ( 8) shift: -0.51 0.02 ...... Frame ( 9) shift: -0.48 0.06 ...... Frame ( 10) shift: -0.45 0.14 ...... Frame ( 11) shift: -0.41 0.22 ...... Frame ( 12) shift: -0.37 0.30 ...... Frame ( 13) shift: -0.30 0.39 ...... Frame ( 14) shift: -0.24 0.49 ...... Frame ( 15) shift: -0.21 0.57 ...... Frame ( 16) shift: -0.20 0.64 ...... Frame ( 17) shift: -0.20 0.71 ...... Frame ( 18) shift: -0.19 0.76 ...... Frame ( 19) shift: -0.19 0.80 ...... Frame ( 20) shift: -0.19 0.83 ...... Frame ( 21) shift: -0.17 0.84 ...... Frame ( 22) shift: -0.14 0.85 ...... Frame ( 23) shift: -0.11 0.85 ...... Frame ( 24) shift: -0.05 0.90 ...... Frame ( 25) shift: 0.05 0.99 ...... Frame ( 26) shift: 0.14 1.09 ...... Frame ( 27) shift: 0.22 1.14 ...... Frame ( 28) shift: 0.30 1.15 ...... Frame ( 29) shift: 0.37 1.15 ...... Frame ( 30) shift: 0.45 1.16 ...... Frame ( 31) shift: 0.54 1.17 ...... Frame ( 32) shift: 0.62 1.17 ...... Frame ( 33) shift: 0.68 1.17 ...... Frame ( 34) shift: 0.72 1.16 ...... Frame ( 35) shift: 0.76 1.15 ...... Frame ( 36) shift: 0.79 1.16 ...... Frame ( 37) shift: 0.81 1.17 ...... Frame ( 38) shift: 0.83 1.19 ...... Frame ( 39) shift: 0.85 1.20 ...... Frame ( 40) shift: 0.87 1.22 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.865112 Iteration 2 Error: 0.124172 Iteration 3 Error: 0.027702 Align patch 2 23 left Iteration 1 Error: 0.926857 Iteration 2 Error: 0.145945 Iteration 3 Error: 0.052606 Iteration 4 Error: 0.018924 Align patch 3 22 left Iteration 1 Error: 0.453095 Iteration 2 Error: 0.074874 Iteration 3 Error: 0.020730 Align patch 4 21 left Iteration 1 Error: 0.510470 Iteration 2 Error: 0.058817 Iteration 3 Error: 0.007857 Align patch 5 20 left Iteration 1 Error: 0.320393 Iteration 2 Error: 0.124977 Iteration 3 Error: 0.057842 Iteration 4 Error: 0.027590 Align patch 6 19 left Iteration 1 Error: 0.838485 Iteration 2 Error: 0.247927 Iteration 3 Error: 0.079060 Iteration 4 Error: 0.028500 Align patch 7 18 left Iteration 1 Error: 0.710772 Iteration 2 Error: 0.116244 Iteration 3 Error: 0.039480 Align patch 8 17 left Iteration 1 Error: 0.744452 Iteration 2 Error: 0.044903 Align patch 9 16 left Iteration 1 Error: 0.620788 Iteration 2 Error: 0.093729 Iteration 3 Error: 0.015186 Align patch 10 15 left Iteration 1 Error: 0.399460 Iteration 2 Error: 0.070193 Iteration 3 Error: 0.010795 Align patch 11 14 left Iteration 1 Error: 0.772514 Iteration 2 Error: 0.169247 Iteration 3 Error: 0.034961 Align patch 12 13 left Iteration 1 Error: 0.802640 Iteration 2 Error: 0.140970 Iteration 3 Error: 0.022153 Align patch 13 12 left Iteration 1 Error: 0.486674 Iteration 2 Error: 0.069141 Iteration 3 Error: 0.016889 Align patch 14 11 left Iteration 1 Error: 0.556979 Iteration 2 Error: 0.104280 Iteration 3 Error: 0.017717 Align patch 15 10 left Iteration 1 Error: 0.476682 Iteration 2 Error: 0.063700 Iteration 3 Error: 0.007982 Align patch 16 9 left Iteration 1 Error: 0.758960 Iteration 2 Error: 0.150368 Iteration 3 Error: 0.058068 Iteration 4 Error: 0.024521 Align patch 17 8 left Iteration 1 Error: 0.788621 Iteration 2 Error: 0.120510 Iteration 3 Error: 0.029100 Align patch 18 7 left Iteration 1 Error: 0.453767 Iteration 2 Error: 0.127739 Iteration 3 Error: 0.015442 Align patch 19 6 left Iteration 1 Error: 0.563269 Iteration 2 Error: 0.079998 Iteration 3 Error: 0.016886 Align patch 20 5 left Iteration 1 Error: 0.451400 Iteration 2 Error: 0.109166 Iteration 3 Error: 0.020460 Align patch 21 4 left Iteration 1 Error: 0.707922 Iteration 2 Error: 0.180967 Iteration 3 Error: 0.071407 Iteration 4 Error: 0.022676 Align patch 22 3 left Iteration 1 Error: 0.961813 Iteration 2 Error: 0.171469 Iteration 3 Error: 0.061773 Iteration 4 Error: 0.025050 Align patch 23 2 left Iteration 1 Error: 0.605061 Iteration 2 Error: 0.064555 Iteration 3 Error: 0.014083 Align patch 24 1 left Iteration 1 Error: 0.525536 Iteration 2 Error: 0.064835 Iteration 3 Error: 0.013256 Align patch 25 0 left Iteration 1 Error: 0.593518 Iteration 2 Error: 0.089712 Iteration 3 Error: 0.017143 3D Fitting completed. Patch alignment time: 15.82(sec) Local motion has been corrected. Process thread exits. Computational time: 24.822563 sec Total time: 30.576256 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00015hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00015hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.979364s Reading file: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00015hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.650293s ........................................ >>>>>>TIME<<<<<< FFT: 1.048890s Defocus_U Defocus_V Angle CCC 10003.92 10417.99 4.05 0.052271 Final Values Defocus_U Defocus_V Angle CCC 10000.76 10436.83 3.73 0.085736 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00010sq_v01_00015hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00015hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.356e-01 1.008e-01 CC threshold: 0.740 Mean Std: 38.12 6.68 Num Hot pixels: 195 Hot pixel threshold: 78.22 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.643977 Iteration 2 Error: 0.069581 Iteration 3 Error: 0.009436 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.08 -0.08 ...... Frame ( 3) shift: -0.16 -0.16 ...... Frame ( 4) shift: -0.24 -0.24 ...... Frame ( 5) shift: -0.32 -0.32 ...... Frame ( 6) shift: -0.38 -0.40 ...... Frame ( 7) shift: -0.40 -0.46 ...... Frame ( 8) shift: -0.42 -0.53 ...... Frame ( 9) shift: -0.43 -0.55 ...... Frame ( 10) shift: -0.42 -0.54 ...... Frame ( 11) shift: -0.41 -0.52 ...... Frame ( 12) shift: -0.40 -0.48 ...... Frame ( 13) shift: -0.39 -0.41 ...... Frame ( 14) shift: -0.38 -0.35 ...... Frame ( 15) shift: -0.34 -0.32 ...... Frame ( 16) shift: -0.27 -0.31 ...... Frame ( 17) shift: -0.19 -0.30 ...... Frame ( 18) shift: -0.15 -0.30 ...... Frame ( 19) shift: -0.15 -0.30 ...... Frame ( 20) shift: -0.14 -0.30 ...... Frame ( 21) shift: -0.15 -0.30 ...... Frame ( 22) shift: -0.18 -0.28 ...... Frame ( 23) shift: -0.21 -0.26 ...... Frame ( 24) shift: -0.22 -0.22 ...... Frame ( 25) shift: -0.20 -0.15 ...... Frame ( 26) shift: -0.18 -0.09 ...... Frame ( 27) shift: -0.19 -0.02 ...... Frame ( 28) shift: -0.24 0.03 ...... Frame ( 29) shift: -0.28 0.09 ...... Frame ( 30) shift: -0.30 0.14 ...... Frame ( 31) shift: -0.27 0.18 ...... Frame ( 32) shift: -0.25 0.22 ...... Frame ( 33) shift: -0.25 0.26 ...... Frame ( 34) shift: -0.28 0.30 ...... Frame ( 35) shift: -0.30 0.34 ...... Frame ( 36) shift: -0.31 0.38 ...... Frame ( 37) shift: -0.30 0.43 ...... Frame ( 38) shift: -0.28 0.49 ...... Frame ( 39) shift: -0.27 0.54 ...... Frame ( 40) shift: -0.26 0.59 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.045154 Iteration 2 Error: 0.103860 Iteration 3 Error: 0.016130 Align patch 2 23 left Iteration 1 Error: 0.995386 Iteration 2 Error: 0.109207 Iteration 3 Error: 0.022474 Align patch 3 22 left Iteration 1 Error: 0.745685 Iteration 2 Error: 0.062384 Iteration 3 Error: 0.020340 Align patch 4 21 left Iteration 1 Error: 0.438792 Iteration 2 Error: 0.067872 Iteration 3 Error: 0.014128 Align patch 5 20 left Iteration 1 Error: 0.542982 Iteration 2 Error: 0.040678 Align patch 6 19 left Iteration 1 Error: 0.802816 Iteration 2 Error: 0.125800 Iteration 3 Error: 0.027915 Align patch 7 18 left Iteration 1 Error: 0.359196 Iteration 2 Error: 0.045297 Align patch 8 17 left Iteration 1 Error: 0.491406 Iteration 2 Error: 0.061361 Iteration 3 Error: 0.010312 Align patch 9 16 left Iteration 1 Error: 0.467992 Iteration 2 Error: 0.091172 Iteration 3 Error: 0.016410 Align patch 10 15 left Iteration 1 Error: 0.476564 Iteration 2 Error: 0.089785 Iteration 3 Error: 0.029992 Align patch 11 14 left Iteration 1 Error: 0.373197 Iteration 2 Error: 0.070801 Iteration 3 Error: 0.014578 Align patch 12 13 left Iteration 1 Error: 0.332926 Iteration 2 Error: 0.050701 Iteration 3 Error: 0.010611 Align patch 13 12 left Iteration 1 Error: 0.420223 Iteration 2 Error: 0.045818 Align patch 14 11 left Iteration 1 Error: 0.619342 Iteration 2 Error: 0.073977 Iteration 3 Error: 0.010781 Align patch 15 10 left Iteration 1 Error: 0.611728 Iteration 2 Error: 0.052799 Iteration 3 Error: 0.009815 Align patch 16 9 left Iteration 1 Error: 0.492918 Iteration 2 Error: 0.070975 Iteration 3 Error: 0.009728 Align patch 17 8 left Iteration 1 Error: 0.617863 Iteration 2 Error: 0.083053 Iteration 3 Error: 0.019028 Align patch 18 7 left Iteration 1 Error: 0.571951 Iteration 2 Error: 0.070952 Iteration 3 Error: 0.008803 Align patch 19 6 left Iteration 1 Error: 0.531272 Iteration 2 Error: 0.053832 Iteration 3 Error: 0.010111 Align patch 20 5 left Iteration 1 Error: 0.550525 Iteration 2 Error: 0.058551 Iteration 3 Error: 0.009725 Align patch 21 4 left Iteration 1 Error: 0.387610 Iteration 2 Error: 0.071836 Iteration 3 Error: 0.008464 Align patch 22 3 left Iteration 1 Error: 0.488821 Iteration 2 Error: 0.074155 Iteration 3 Error: 0.013072 Align patch 23 2 left Iteration 1 Error: 0.384475 Iteration 2 Error: 0.033932 Align patch 24 1 left Iteration 1 Error: 0.500037 Iteration 2 Error: 0.049694 Align patch 25 0 left Iteration 1 Error: 0.734875 Iteration 2 Error: 0.086927 Iteration 3 Error: 0.013770 3D Fitting completed. Patch alignment time: 14.14(sec) Local motion has been corrected. Process thread exits. Computational time: 23.298988 sec Total time: 29.346682 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00015hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00015hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.788653s Reading file: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00015hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.486360s ........................................ >>>>>>TIME<<<<<< FFT: 1.057761s Defocus_U Defocus_V Angle CCC 13886.72 14734.38 4.13 0.084593 Final Values Defocus_U Defocus_V Angle CCC 13899.23 14734.38 4.13 0.124771 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00010sq_v01_00015hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00015hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 37.98 6.61 Num Hot pixels: 217 Hot pixel threshold: 77.63 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.526460 Iteration 2 Error: 0.059239 Iteration 3 Error: 0.013172 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.12 0.06 ...... Frame ( 3) shift: -0.24 0.11 ...... Frame ( 4) shift: -0.35 0.17 ...... Frame ( 5) shift: -0.47 0.23 ...... Frame ( 6) shift: -0.54 0.29 ...... Frame ( 7) shift: -0.57 0.37 ...... Frame ( 8) shift: -0.60 0.44 ...... Frame ( 9) shift: -0.63 0.44 ...... Frame ( 10) shift: -0.66 0.37 ...... Frame ( 11) shift: -0.70 0.30 ...... Frame ( 12) shift: -0.69 0.25 ...... Frame ( 13) shift: -0.65 0.20 ...... Frame ( 14) shift: -0.62 0.16 ...... Frame ( 15) shift: -0.62 0.14 ...... Frame ( 16) shift: -0.66 0.16 ...... Frame ( 17) shift: -0.70 0.17 ...... Frame ( 18) shift: -0.73 0.20 ...... Frame ( 19) shift: -0.74 0.23 ...... Frame ( 20) shift: -0.75 0.27 ...... Frame ( 21) shift: -0.75 0.32 ...... Frame ( 22) shift: -0.73 0.37 ...... Frame ( 23) shift: -0.71 0.42 ...... Frame ( 24) shift: -0.71 0.47 ...... Frame ( 25) shift: -0.72 0.52 ...... Frame ( 26) shift: -0.73 0.56 ...... Frame ( 27) shift: -0.72 0.60 ...... Frame ( 28) shift: -0.68 0.63 ...... Frame ( 29) shift: -0.63 0.65 ...... Frame ( 30) shift: -0.57 0.66 ...... Frame ( 31) shift: -0.49 0.65 ...... Frame ( 32) shift: -0.41 0.63 ...... Frame ( 33) shift: -0.37 0.65 ...... Frame ( 34) shift: -0.38 0.69 ...... Frame ( 35) shift: -0.38 0.73 ...... Frame ( 36) shift: -0.37 0.76 ...... Frame ( 37) shift: -0.36 0.79 ...... Frame ( 38) shift: -0.35 0.82 ...... Frame ( 39) shift: -0.34 0.86 ...... Frame ( 40) shift: -0.33 0.89 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.983781 Iteration 2 Error: 0.145456 Iteration 3 Error: 0.054254 Iteration 4 Error: 0.015729 Align patch 2 23 left Iteration 1 Error: 0.919309 Iteration 2 Error: 0.127596 Iteration 3 Error: 0.035532 Align patch 3 22 left Iteration 1 Error: 0.565051 Iteration 2 Error: 0.079606 Iteration 3 Error: 0.023079 Align patch 4 21 left Iteration 1 Error: 0.725965 Iteration 2 Error: 0.121045 Iteration 3 Error: 0.027867 Align patch 5 20 left Iteration 1 Error: 0.638845 Iteration 2 Error: 0.078322 Iteration 3 Error: 0.013663 Align patch 6 19 left Iteration 1 Error: 1.173573 Iteration 2 Error: 0.122022 Iteration 3 Error: 0.022088 Align patch 7 18 left Iteration 1 Error: 0.859703 Iteration 2 Error: 0.090919 Iteration 3 Error: 0.015507 Align patch 8 17 left Iteration 1 Error: 0.767337 Iteration 2 Error: 0.095826 Iteration 3 Error: 0.014220 Align patch 9 16 left Iteration 1 Error: 0.616334 Iteration 2 Error: 0.166157 Iteration 3 Error: 0.044364 Align patch 10 15 left Iteration 1 Error: 0.739570 Iteration 2 Error: 0.149938 Iteration 3 Error: 0.032957 Align patch 11 14 left Iteration 1 Error: 0.660694 Iteration 2 Error: 0.108409 Iteration 3 Error: 0.035724 Align patch 12 13 left Iteration 1 Error: 0.739766 Iteration 2 Error: 0.118471 Iteration 3 Error: 0.032733 Align patch 13 12 left Iteration 1 Error: 0.606517 Iteration 2 Error: 0.061530 Iteration 3 Error: 0.015543 Align patch 14 11 left Iteration 1 Error: 0.409729 Iteration 2 Error: 0.061006 Iteration 3 Error: 0.013028 Align patch 15 10 left Iteration 1 Error: 0.750331 Iteration 2 Error: 0.111775 Iteration 3 Error: 0.020833 Align patch 16 9 left Iteration 1 Error: 0.633680 Iteration 2 Error: 0.072114 Iteration 3 Error: 0.016123 Align patch 17 8 left Iteration 1 Error: 0.662658 Iteration 2 Error: 0.139945 Iteration 3 Error: 0.031428 Align patch 18 7 left Iteration 1 Error: 0.688983 Iteration 2 Error: 0.100013 Iteration 3 Error: 0.019713 Align patch 19 6 left Iteration 1 Error: 0.687596 Iteration 2 Error: 0.103587 Iteration 3 Error: 0.023425 Align patch 20 5 left Iteration 1 Error: 0.532076 Iteration 2 Error: 0.095748 Iteration 3 Error: 0.018519 Align patch 21 4 left Iteration 1 Error: 0.665694 Iteration 2 Error: 0.151228 Iteration 3 Error: 0.023310 Align patch 22 3 left Iteration 1 Error: 0.857052 Iteration 2 Error: 0.117349 Iteration 3 Error: 0.028845 Align patch 23 2 left Iteration 1 Error: 0.517137 Iteration 2 Error: 0.105017 Iteration 3 Error: 0.020442 Align patch 24 1 left Iteration 1 Error: 0.427872 Iteration 2 Error: 0.081235 Iteration 3 Error: 0.013775 Align patch 25 0 left Iteration 1 Error: 0.662935 Iteration 2 Error: 0.089357 Iteration 3 Error: 0.015221 3D Fitting completed. Patch alignment time: 14.58(sec) Local motion has been corrected. Process thread exits. Computational time: 22.398207 sec Total time: 27.854441 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00015hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00015hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.749844s Reading file: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00015hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.366054s ........................................ >>>>>>TIME<<<<<< FFT: 1.063896s Defocus_U Defocus_V Angle CCC 10887.89 10182.72 81.86 0.037189 Final Values Defocus_U Defocus_V Angle CCC 10923.83 10193.66 82.17 0.060898 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00010sq_v01_00016hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00016hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.999e-02 CC threshold: 0.734 Mean Std: 38.36 6.57 Num Hot pixels: 230 Hot pixel threshold: 77.76 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.332877 Iteration 2 Error: 0.376045 Iteration 3 Error: 0.118599 Iteration 4 Error: 0.052357 Iteration 5 Error: 0.022740 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.11 -0.07 ...... Frame ( 3) shift: -0.23 -0.15 ...... Frame ( 4) shift: -0.34 -0.22 ...... Frame ( 5) shift: -0.45 -0.30 ...... Frame ( 6) shift: -0.52 -0.29 ...... Frame ( 7) shift: -0.54 -0.21 ...... Frame ( 8) shift: -0.56 -0.13 ...... Frame ( 9) shift: -0.55 -0.07 ...... Frame ( 10) shift: -0.50 -0.04 ...... Frame ( 11) shift: -0.45 -0.00 ...... Frame ( 12) shift: -0.44 0.05 ...... Frame ( 13) shift: -0.45 0.12 ...... Frame ( 14) shift: -0.47 0.19 ...... Frame ( 15) shift: -0.44 0.27 ...... Frame ( 16) shift: -0.35 0.37 ...... Frame ( 17) shift: -0.26 0.47 ...... Frame ( 18) shift: -0.22 0.56 ...... Frame ( 19) shift: -0.23 0.64 ...... Frame ( 20) shift: -0.24 0.72 ...... Frame ( 21) shift: -0.19 0.82 ...... Frame ( 22) shift: -0.07 0.93 ...... Frame ( 23) shift: 0.05 1.05 ...... Frame ( 24) shift: 0.16 1.15 ...... Frame ( 25) shift: 0.26 1.25 ...... Frame ( 26) shift: 0.37 1.34 ...... Frame ( 27) shift: 0.41 1.45 ...... Frame ( 28) shift: 0.39 1.57 ...... Frame ( 29) shift: 0.36 1.69 ...... Frame ( 30) shift: 0.37 1.81 ...... Frame ( 31) shift: 0.39 1.91 ...... Frame ( 32) shift: 0.41 2.02 ...... Frame ( 33) shift: 0.45 2.09 ...... Frame ( 34) shift: 0.50 2.12 ...... Frame ( 35) shift: 0.56 2.16 ...... Frame ( 36) shift: 0.60 2.20 ...... Frame ( 37) shift: 0.63 2.24 ...... Frame ( 38) shift: 0.67 2.28 ...... Frame ( 39) shift: 0.70 2.32 ...... Frame ( 40) shift: 0.74 2.35 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.062081 Iteration 2 Error: 0.295539 Iteration 3 Error: 0.152310 Iteration 4 Error: 0.071532 Iteration 5 Error: 0.039635 Align patch 2 23 left Iteration 1 Error: 0.683998 Iteration 2 Error: 0.109154 Iteration 3 Error: 0.050438 Iteration 4 Error: 0.029519 Align patch 3 22 left Iteration 1 Error: 0.792227 Iteration 2 Error: 0.166282 Iteration 3 Error: 0.071727 Iteration 4 Error: 0.030885 Align patch 4 21 left Iteration 1 Error: 1.056704 Iteration 2 Error: 0.151876 Iteration 3 Error: 0.035512 Align patch 5 20 left Iteration 1 Error: 0.990560 Iteration 2 Error: 0.138534 Iteration 3 Error: 0.036958 Align patch 6 19 left Iteration 1 Error: 1.439723 Iteration 2 Error: 0.322975 Iteration 3 Error: 0.185112 Iteration 4 Error: 0.075087 Iteration 5 Error: 0.053472 Align patch 6 19 left Iteration 1 Error: 1.345298 Iteration 2 Error: 0.289973 Iteration 3 Error: 0.076105 Iteration 4 Error: 0.032442 Align patch 7 18 left Iteration 1 Error: 1.657614 Iteration 2 Error: 0.388025 Iteration 3 Error: 0.162778 Iteration 4 Error: 0.083179 Iteration 5 Error: 0.038354 Align patch 8 17 left Iteration 1 Error: 0.707673 Iteration 2 Error: 0.264402 Iteration 3 Error: 0.057097 Iteration 4 Error: 0.033480 Align patch 9 16 left Iteration 1 Error: 1.057006 Iteration 2 Error: 0.185280 Iteration 3 Error: 0.098466 Iteration 4 Error: 0.030985 Align patch 10 15 left Iteration 1 Error: 1.082390 Iteration 2 Error: 0.199643 Iteration 3 Error: 0.051444 Iteration 4 Error: 0.019887 Align patch 11 14 left Iteration 1 Error: 1.023814 Iteration 2 Error: 0.508989 Iteration 3 Error: 0.254657 Iteration 4 Error: 0.128993 Iteration 5 Error: 0.087787 Align patch 11 14 left Iteration 1 Error: 1.230724 Iteration 2 Error: 0.295121 Iteration 3 Error: 0.086713 Iteration 4 Error: 0.021262 Align patch 12 13 left Iteration 1 Error: 0.916591 Iteration 2 Error: 0.158092 Iteration 3 Error: 0.040243 Align patch 13 12 left Iteration 1 Error: 0.626740 Iteration 2 Error: 0.095902 Iteration 3 Error: 0.021289 Align patch 14 11 left Iteration 1 Error: 0.728095 Iteration 2 Error: 0.123123 Iteration 3 Error: 0.051478 Iteration 4 Error: 0.021178 Align patch 15 10 left Iteration 1 Error: 1.338450 Iteration 2 Error: 0.253898 Iteration 3 Error: 0.091737 Iteration 4 Error: 0.024108 Align patch 16 9 left Iteration 1 Error: 0.742112 Iteration 2 Error: 0.146157 Iteration 3 Error: 0.054386 Iteration 4 Error: 0.025416 Align patch 17 8 left Iteration 1 Error: 0.705918 Iteration 2 Error: 0.371133 Iteration 3 Error: 0.131046 Iteration 4 Error: 0.079174 Iteration 5 Error: 0.036866 Align patch 18 7 left Iteration 1 Error: 0.858544 Iteration 2 Error: 0.209558 Iteration 3 Error: 0.103885 Iteration 4 Error: 0.025780 Align patch 19 6 left Iteration 1 Error: 0.873864 Iteration 2 Error: 0.137408 Iteration 3 Error: 0.024320 Align patch 20 5 left Iteration 1 Error: 0.679841 Iteration 2 Error: 0.188122 Iteration 3 Error: 0.062681 Iteration 4 Error: 0.019467 Align patch 21 4 left Iteration 1 Error: 1.102821 Iteration 2 Error: 0.231484 Iteration 3 Error: 0.058249 Iteration 4 Error: 0.019990 Align patch 22 3 left Iteration 1 Error: 1.009145 Iteration 2 Error: 0.353562 Iteration 3 Error: 0.126263 Iteration 4 Error: 0.042311 Align patch 23 2 left Iteration 1 Error: 1.170699 Iteration 2 Error: 0.157022 Iteration 3 Error: 0.040662 Align patch 24 1 left Iteration 1 Error: 0.747604 Iteration 2 Error: 0.123022 Iteration 3 Error: 0.035732 Align patch 25 0 left Iteration 1 Error: 0.921259 Iteration 2 Error: 0.198786 Iteration 3 Error: 0.043856 3D Fitting completed. Patch alignment time: 19.14(sec) Local motion has been corrected. Process thread exits. Computational time: 28.806772 sec Total time: 34.466400 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00016hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00016hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.548635s Reading file: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00016hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.491271s ........................................ >>>>>>TIME<<<<<< FFT: 0.950687s Defocus_U Defocus_V Angle CCC 12427.73 13166.02 8.98 0.031830 Final Values Defocus_U Defocus_V Angle CCC 12432.41 13155.11 7.42 0.048714 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00010sq_v01_00016hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00016hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.002e-01 CC threshold: 0.736 Mean Std: 37.33 6.54 Num Hot pixels: 235 Hot pixel threshold: 76.57 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.479049 Iteration 2 Error: 0.093655 Iteration 3 Error: 0.017507 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.25 -0.13 ...... Frame ( 3) shift: -0.51 -0.27 ...... Frame ( 4) shift: -0.76 -0.40 ...... Frame ( 5) shift: -1.01 -0.53 ...... Frame ( 6) shift: -1.14 -0.61 ...... Frame ( 7) shift: -1.14 -0.62 ...... Frame ( 8) shift: -1.14 -0.64 ...... Frame ( 9) shift: -1.12 -0.64 ...... Frame ( 10) shift: -1.09 -0.63 ...... Frame ( 11) shift: -1.06 -0.62 ...... Frame ( 12) shift: -1.02 -0.60 ...... Frame ( 13) shift: -0.96 -0.58 ...... Frame ( 14) shift: -0.90 -0.57 ...... Frame ( 15) shift: -0.86 -0.54 ...... Frame ( 16) shift: -0.85 -0.50 ...... Frame ( 17) shift: -0.84 -0.45 ...... Frame ( 18) shift: -0.82 -0.41 ...... Frame ( 19) shift: -0.80 -0.36 ...... Frame ( 20) shift: -0.78 -0.32 ...... Frame ( 21) shift: -0.77 -0.27 ...... Frame ( 22) shift: -0.77 -0.22 ...... Frame ( 23) shift: -0.78 -0.17 ...... Frame ( 24) shift: -0.79 -0.15 ...... Frame ( 25) shift: -0.80 -0.15 ...... Frame ( 26) shift: -0.82 -0.16 ...... Frame ( 27) shift: -0.78 -0.11 ...... Frame ( 28) shift: -0.68 -0.02 ...... Frame ( 29) shift: -0.58 0.07 ...... Frame ( 30) shift: -0.53 0.12 ...... Frame ( 31) shift: -0.54 0.13 ...... Frame ( 32) shift: -0.55 0.14 ...... Frame ( 33) shift: -0.53 0.13 ...... Frame ( 34) shift: -0.48 0.10 ...... Frame ( 35) shift: -0.44 0.08 ...... Frame ( 36) shift: -0.42 0.08 ...... Frame ( 37) shift: -0.42 0.11 ...... Frame ( 38) shift: -0.43 0.15 ...... Frame ( 39) shift: -0.44 0.18 ...... Frame ( 40) shift: -0.44 0.22 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.679876 Iteration 2 Error: 0.095205 Iteration 3 Error: 0.029283 Align patch 2 23 left Iteration 1 Error: 1.144087 Iteration 2 Error: 0.099636 Iteration 3 Error: 0.017246 Align patch 3 22 left Iteration 1 Error: 0.643096 Iteration 2 Error: 0.088774 Iteration 3 Error: 0.018912 Align patch 4 21 left Iteration 1 Error: 0.642381 Iteration 2 Error: 0.150934 Iteration 3 Error: 0.052933 Iteration 4 Error: 0.015493 Align patch 5 20 left Iteration 1 Error: 0.739278 Iteration 2 Error: 0.065837 Iteration 3 Error: 0.008538 Align patch 6 19 left Iteration 1 Error: 1.292202 Iteration 2 Error: 0.242308 Iteration 3 Error: 0.050474 Iteration 4 Error: 0.018102 Align patch 7 18 left Iteration 1 Error: 0.719834 Iteration 2 Error: 0.115305 Iteration 3 Error: 0.033112 Align patch 8 17 left Iteration 1 Error: 0.645140 Iteration 2 Error: 0.073409 Iteration 3 Error: 0.032880 Align patch 9 16 left Iteration 1 Error: 0.789875 Iteration 2 Error: 0.170715 Iteration 3 Error: 0.034908 Align patch 10 15 left Iteration 1 Error: 0.857737 Iteration 2 Error: 0.070319 Iteration 3 Error: 0.014598 Align patch 11 14 left Iteration 1 Error: 0.673051 Iteration 2 Error: 0.130755 Iteration 3 Error: 0.057074 Iteration 4 Error: 0.020125 Align patch 12 13 left Iteration 1 Error: 0.614426 Iteration 2 Error: 0.134686 Iteration 3 Error: 0.028639 Align patch 13 12 left Iteration 1 Error: 0.719775 Iteration 2 Error: 0.081795 Iteration 3 Error: 0.021146 Align patch 14 11 left Iteration 1 Error: 0.589371 Iteration 2 Error: 0.111826 Iteration 3 Error: 0.030159 Align patch 15 10 left Iteration 1 Error: 0.531305 Iteration 2 Error: 0.097095 Iteration 3 Error: 0.016636 Align patch 16 9 left Iteration 1 Error: 0.553547 Iteration 2 Error: 0.086289 Iteration 3 Error: 0.019794 Align patch 17 8 left Iteration 1 Error: 0.890291 Iteration 2 Error: 0.166182 Iteration 3 Error: 0.048395 Align patch 18 7 left Iteration 1 Error: 0.799485 Iteration 2 Error: 0.222293 Iteration 3 Error: 0.093145 Iteration 4 Error: 0.035128 Align patch 19 6 left Iteration 1 Error: 0.659070 Iteration 2 Error: 0.093897 Iteration 3 Error: 0.021831 Align patch 20 5 left Iteration 1 Error: 0.768533 Iteration 2 Error: 0.080552 Iteration 3 Error: 0.024876 Align patch 21 4 left Iteration 1 Error: 0.498027 Iteration 2 Error: 0.078532 Iteration 3 Error: 0.019914 Align patch 22 3 left Iteration 1 Error: 0.953183 Iteration 2 Error: 0.079961 Iteration 3 Error: 0.015477 Align patch 23 2 left Iteration 1 Error: 0.631993 Iteration 2 Error: 0.096503 Iteration 3 Error: 0.026795 Align patch 24 1 left Iteration 1 Error: 0.568356 Iteration 2 Error: 0.098938 Iteration 3 Error: 0.019791 Align patch 25 0 left Iteration 1 Error: 0.617059 Iteration 2 Error: 0.086841 Iteration 3 Error: 0.023341 3D Fitting completed. Patch alignment time: 15.67(sec) Local motion has been corrected. Process thread exits. Computational time: 24.548948 sec Total time: 30.034531 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00016hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00016hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.783612s Reading file: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00016hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.434701s ........................................ >>>>>>TIME<<<<<< FFT: 0.949363s Defocus_U Defocus_V Angle CCC 8603.52 8021.48 84.58 0.017383 Final Values Defocus_U Defocus_V Angle CCC 8592.57 8038.69 84.89 0.034815 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00010sq_v01_00016hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00016hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 29.62 5.79 Num Hot pixels: 206 Hot pixel threshold: 64.37 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.468026 Iteration 2 Error: 0.274711 Iteration 3 Error: 0.072587 Iteration 4 Error: 0.024112 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.09 0.26 ...... Frame ( 3) shift: 0.19 0.52 ...... Frame ( 4) shift: 0.28 0.77 ...... Frame ( 5) shift: 0.37 1.03 ...... Frame ( 6) shift: 0.43 1.17 ...... Frame ( 7) shift: 0.45 1.19 ...... Frame ( 8) shift: 0.46 1.22 ...... Frame ( 9) shift: 0.42 1.26 ...... Frame ( 10) shift: 0.32 1.33 ...... Frame ( 11) shift: 0.22 1.39 ...... Frame ( 12) shift: 0.15 1.47 ...... Frame ( 13) shift: 0.10 1.57 ...... Frame ( 14) shift: 0.06 1.67 ...... Frame ( 15) shift: 0.00 1.80 ...... Frame ( 16) shift: -0.06 1.98 ...... Frame ( 17) shift: -0.12 2.15 ...... Frame ( 18) shift: -0.23 2.25 ...... Frame ( 19) shift: -0.38 2.27 ...... Frame ( 20) shift: -0.53 2.29 ...... Frame ( 21) shift: -0.62 2.34 ...... Frame ( 22) shift: -0.64 2.42 ...... Frame ( 23) shift: -0.65 2.50 ...... Frame ( 24) shift: -0.66 2.55 ...... Frame ( 25) shift: -0.66 2.57 ...... Frame ( 26) shift: -0.66 2.59 ...... Frame ( 27) shift: -0.67 2.61 ...... Frame ( 28) shift: -0.68 2.65 ...... Frame ( 29) shift: -0.69 2.68 ...... Frame ( 30) shift: -0.71 2.70 ...... Frame ( 31) shift: -0.74 2.70 ...... Frame ( 32) shift: -0.77 2.71 ...... Frame ( 33) shift: -0.73 2.69 ...... Frame ( 34) shift: -0.63 2.65 ...... Frame ( 35) shift: -0.53 2.61 ...... Frame ( 36) shift: -0.43 2.58 ...... Frame ( 37) shift: -0.35 2.56 ...... Frame ( 38) shift: -0.26 2.54 ...... Frame ( 39) shift: -0.18 2.52 ...... Frame ( 40) shift: -0.09 2.50 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.532870 Iteration 2 Error: 0.551229 Iteration 3 Error: 0.183110 Iteration 4 Error: 0.110219 Iteration 5 Error: 0.036489 Align patch 2 23 left Iteration 1 Error: 1.028967 Iteration 2 Error: 0.324287 Iteration 3 Error: 0.096469 Iteration 4 Error: 0.051908 Iteration 5 Error: 0.018795 Align patch 3 22 left Iteration 1 Error: 1.403617 Iteration 2 Error: 0.341205 Iteration 3 Error: 0.112119 Iteration 4 Error: 0.046599 Align patch 4 21 left Iteration 1 Error: 2.425361 Iteration 2 Error: 0.750184 Iteration 3 Error: 0.395146 Iteration 4 Error: 0.173463 Iteration 5 Error: 0.075335 Align patch 4 21 left Iteration 1 Error: 2.396239 Iteration 2 Error: 0.663978 Iteration 3 Error: 0.129107 Iteration 4 Error: 0.036465 Align patch 5 20 left Iteration 1 Error: 2.326823 Iteration 2 Error: 0.843419 Iteration 3 Error: 0.552718 Iteration 4 Error: 0.528695 Iteration 5 Error: 0.346728 Align patch 5 20 left Iteration 1 Error: 2.891582 Iteration 2 Error: 0.742704 Iteration 3 Error: 0.213417 Iteration 4 Error: 0.095013 Iteration 5 Error: 0.039907 Align patch 6 19 left Iteration 1 Error: 1.174779 Iteration 2 Error: 0.620580 Iteration 3 Error: 0.244549 Iteration 4 Error: 0.133936 Iteration 5 Error: 0.103371 Align patch 6 19 left Iteration 1 Error: 1.290978 Iteration 2 Error: 0.115808 Iteration 3 Error: 0.016959 Align patch 7 18 left Iteration 1 Error: 1.087763 Iteration 2 Error: 0.131867 Iteration 3 Error: 0.035972 Align patch 8 17 left Iteration 1 Error: 1.138540 Iteration 2 Error: 0.287734 Iteration 3 Error: 0.099208 Iteration 4 Error: 0.039741 Align patch 9 16 left Iteration 1 Error: 2.827350 Iteration 2 Error: 1.266150 Iteration 3 Error: 0.513766 Iteration 4 Error: 0.263990 Iteration 5 Error: 0.137583 Align patch 9 16 left Iteration 1 Error: 2.313623 Iteration 2 Error: 0.862272 Iteration 3 Error: 0.143265 Iteration 4 Error: 0.067847 Iteration 5 Error: 0.012495 Align patch 10 15 left Iteration 1 Error: 2.051643 Iteration 2 Error: 1.208782 Iteration 3 Error: 0.562145 Iteration 4 Error: 0.452532 Iteration 5 Error: 0.398596 Align patch 10 15 left Iteration 1 Error: 2.489345 Iteration 2 Error: 0.839240 Iteration 3 Error: 0.266137 Iteration 4 Error: 0.090163 Iteration 5 Error: 0.038226 Align patch 11 14 left Iteration 1 Error: 1.145667 Iteration 2 Error: 0.192777 Iteration 3 Error: 0.084981 Iteration 4 Error: 0.017356 Align patch 12 13 left Iteration 1 Error: 1.868878 Iteration 2 Error: 0.540942 Iteration 3 Error: 0.119456 Iteration 4 Error: 0.037438 Align patch 13 12 left Iteration 1 Error: 1.194904 Iteration 2 Error: 0.385602 Iteration 3 Error: 0.096181 Iteration 4 Error: 0.031679 Align patch 14 11 left Iteration 1 Error: 1.087171 Iteration 2 Error: 0.320993 Iteration 3 Error: 0.179448 Iteration 4 Error: 0.077972 Iteration 5 Error: 0.048857 Align patch 15 10 left Iteration 1 Error: 1.162379 Iteration 2 Error: 0.374941 Iteration 3 Error: 0.158519 Iteration 4 Error: 0.091752 Iteration 5 Error: 0.058251 Align patch 15 10 left Iteration 1 Error: 1.345864 Iteration 2 Error: 0.259546 Iteration 3 Error: 0.079179 Iteration 4 Error: 0.019246 Align patch 16 9 left Iteration 1 Error: 1.379929 Iteration 2 Error: 0.330004 Iteration 3 Error: 0.096115 Iteration 4 Error: 0.037411 Align patch 17 8 left Iteration 1 Error: 1.018368 Iteration 2 Error: 0.213602 Iteration 3 Error: 0.082386 Iteration 4 Error: 0.031327 Align patch 18 7 left Iteration 1 Error: 0.758919 Iteration 2 Error: 0.193976 Iteration 3 Error: 0.089459 Iteration 4 Error: 0.031991 Align patch 19 6 left Iteration 1 Error: 0.743713 Iteration 2 Error: 0.145907 Iteration 3 Error: 0.040232 Align patch 20 5 left Iteration 1 Error: 0.815274 Iteration 2 Error: 0.205888 Iteration 3 Error: 0.072391 Iteration 4 Error: 0.036974 Align patch 21 4 left Iteration 1 Error: 1.387323 Iteration 2 Error: 0.347584 Iteration 3 Error: 0.091849 Iteration 4 Error: 0.031551 Align patch 22 3 left Iteration 1 Error: 1.430938 Iteration 2 Error: 0.496333 Iteration 3 Error: 0.222455 Iteration 4 Error: 0.111100 Iteration 5 Error: 0.052243 Align patch 22 3 left Iteration 1 Error: 1.472221 Iteration 2 Error: 0.260967 Iteration 3 Error: 0.076036 Iteration 4 Error: 0.027495 Align patch 23 2 left Iteration 1 Error: 0.810979 Iteration 2 Error: 0.265627 Iteration 3 Error: 0.056451 Iteration 4 Error: 0.031250 Align patch 24 1 left Iteration 1 Error: 0.769471 Iteration 2 Error: 0.188459 Iteration 3 Error: 0.062228 Iteration 4 Error: 0.023915 Align patch 25 0 left Iteration 1 Error: 1.228142 Iteration 2 Error: 0.199803 Iteration 3 Error: 0.063064 Iteration 4 Error: 0.020170 3D Fitting completed. Patch alignment time: 23.37(sec) Local motion has been corrected. Process thread exits. Computational time: 32.606884 sec Total time: 38.443462 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00016hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00016hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.610933s Reading file: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00016hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.732097s ........................................ >>>>>>TIME<<<<<< FFT: 0.994787s Defocus_U Defocus_V Angle CCC 12511.71 13468.78 1.53 0.018682 Final Values Defocus_U Defocus_V Angle CCC 12533.59 13303.22 0.01 0.025392 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00010sq_v01_00016hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00016hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 34.64 6.23 Num Hot pixels: 195 Hot pixel threshold: 72.02 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.888390 Iteration 2 Error: 0.172488 Iteration 3 Error: 0.046292 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.15 0.07 ...... Frame ( 3) shift: 0.31 0.14 ...... Frame ( 4) shift: 0.46 0.22 ...... Frame ( 5) shift: 0.61 0.29 ...... Frame ( 6) shift: 0.72 0.30 ...... Frame ( 7) shift: 0.80 0.24 ...... Frame ( 8) shift: 0.87 0.19 ...... Frame ( 9) shift: 0.91 0.18 ...... Frame ( 10) shift: 0.92 0.22 ...... Frame ( 11) shift: 0.92 0.26 ...... Frame ( 12) shift: 0.92 0.30 ...... Frame ( 13) shift: 0.92 0.36 ...... Frame ( 14) shift: 0.91 0.41 ...... Frame ( 15) shift: 0.94 0.47 ...... Frame ( 16) shift: 0.98 0.54 ...... Frame ( 17) shift: 1.03 0.61 ...... Frame ( 18) shift: 1.07 0.69 ...... Frame ( 19) shift: 1.10 0.77 ...... Frame ( 20) shift: 1.14 0.86 ...... Frame ( 21) shift: 1.17 0.93 ...... Frame ( 22) shift: 1.22 1.00 ...... Frame ( 23) shift: 1.26 1.07 ...... Frame ( 24) shift: 1.28 1.12 ...... Frame ( 25) shift: 1.28 1.15 ...... Frame ( 26) shift: 1.27 1.18 ...... Frame ( 27) shift: 1.28 1.20 ...... Frame ( 28) shift: 1.32 1.23 ...... Frame ( 29) shift: 1.35 1.26 ...... Frame ( 30) shift: 1.38 1.25 ...... Frame ( 31) shift: 1.41 1.21 ...... Frame ( 32) shift: 1.43 1.17 ...... Frame ( 33) shift: 1.47 1.15 ...... Frame ( 34) shift: 1.52 1.15 ...... Frame ( 35) shift: 1.57 1.14 ...... Frame ( 36) shift: 1.62 1.17 ...... Frame ( 37) shift: 1.66 1.22 ...... Frame ( 38) shift: 1.71 1.27 ...... Frame ( 39) shift: 1.76 1.32 ...... Frame ( 40) shift: 1.81 1.37 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.923154 Iteration 2 Error: 0.315053 Iteration 3 Error: 0.078545 Iteration 4 Error: 0.035030 Align patch 2 23 left Iteration 1 Error: 1.066554 Iteration 2 Error: 0.218289 Iteration 3 Error: 0.058725 Iteration 4 Error: 0.020327 Align patch 3 22 left Iteration 1 Error: 0.721284 Iteration 2 Error: 0.140720 Iteration 3 Error: 0.035853 Align patch 4 21 left Iteration 1 Error: 1.337595 Iteration 2 Error: 0.344843 Iteration 3 Error: 0.102551 Iteration 4 Error: 0.039465 Align patch 5 20 left Iteration 1 Error: 1.166835 Iteration 2 Error: 0.173364 Iteration 3 Error: 0.043609 Align patch 6 19 left Iteration 1 Error: 1.202925 Iteration 2 Error: 0.317942 Iteration 3 Error: 0.117375 Iteration 4 Error: 0.061282 Iteration 5 Error: 0.029270 Align patch 7 18 left Iteration 1 Error: 1.052588 Iteration 2 Error: 0.243745 Iteration 3 Error: 0.086422 Iteration 4 Error: 0.023604 Align patch 8 17 left Iteration 1 Error: 0.620693 Iteration 2 Error: 0.231631 Iteration 3 Error: 0.071492 Iteration 4 Error: 0.030483 Align patch 9 16 left Iteration 1 Error: 1.488382 Iteration 2 Error: 0.178302 Iteration 3 Error: 0.031146 Align patch 10 15 left Iteration 1 Error: 1.457731 Iteration 2 Error: 0.230747 Iteration 3 Error: 0.054214 Iteration 4 Error: 0.020900 Align patch 11 14 left Iteration 1 Error: 0.772735 Iteration 2 Error: 0.184419 Iteration 3 Error: 0.062869 Iteration 4 Error: 0.025320 Align patch 12 13 left Iteration 1 Error: 0.873794 Iteration 2 Error: 0.201998 Iteration 3 Error: 0.117624 Iteration 4 Error: 0.044260 Align patch 13 12 left Iteration 1 Error: 0.973431 Iteration 2 Error: 0.160415 Iteration 3 Error: 0.032943 Align patch 14 11 left Iteration 1 Error: 0.771320 Iteration 2 Error: 0.127419 Iteration 3 Error: 0.031720 Align patch 15 10 left Iteration 1 Error: 0.809120 Iteration 2 Error: 0.172738 Iteration 3 Error: 0.052831 Iteration 4 Error: 0.020410 Align patch 16 9 left Iteration 1 Error: 0.928073 Iteration 2 Error: 0.258470 Iteration 3 Error: 0.093091 Iteration 4 Error: 0.050461 Iteration 5 Error: 0.031026 Align patch 17 8 left Iteration 1 Error: 0.979233 Iteration 2 Error: 0.144691 Iteration 3 Error: 0.036622 Align patch 18 7 left Iteration 1 Error: 1.277641 Iteration 2 Error: 0.348632 Iteration 3 Error: 0.140324 Iteration 4 Error: 0.038471 Align patch 19 6 left Iteration 1 Error: 1.058805 Iteration 2 Error: 0.215336 Iteration 3 Error: 0.085566 Iteration 4 Error: 0.027767 Align patch 20 5 left Iteration 1 Error: 0.955656 Iteration 2 Error: 0.146707 Iteration 3 Error: 0.049708 Align patch 21 4 left Iteration 1 Error: 0.920303 Iteration 2 Error: 0.179925 Iteration 3 Error: 0.071863 Iteration 4 Error: 0.032990 Align patch 22 3 left Iteration 1 Error: 0.650132 Iteration 2 Error: 0.196013 Iteration 3 Error: 0.057893 Iteration 4 Error: 0.022835 Align patch 23 2 left Iteration 1 Error: 0.694966 Iteration 2 Error: 0.225130 Iteration 3 Error: 0.055374 Iteration 4 Error: 0.020019 Align patch 24 1 left Iteration 1 Error: 1.400583 Iteration 2 Error: 0.207258 Iteration 3 Error: 0.060990 Iteration 4 Error: 0.023219 Align patch 25 0 left Iteration 1 Error: 1.292856 Iteration 2 Error: 0.160740 Iteration 3 Error: 0.044493 3D Fitting completed. Patch alignment time: 16.27(sec) Local motion has been corrected. Process thread exits. Computational time: 24.861303 sec Total time: 30.915485 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00016hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00016hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.794319s Reading file: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00016hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.464653s ........................................ >>>>>>TIME<<<<<< FFT: 0.928462s Defocus_U Defocus_V Angle CCC 10988.24 10394.76 81.71 0.018377 Final Values Defocus_U Defocus_V Angle CCC 10952.31 10315.07 82.02 0.025453 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00010sq_v01_00017hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00017hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.996e-02 CC threshold: 0.734 Mean Std: 34.08 6.21 Num Hot pixels: 211 Hot pixel threshold: 71.32 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.590041 Iteration 2 Error: 0.151323 Iteration 3 Error: 0.046337 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.07 0.04 ...... Frame ( 3) shift: -0.13 0.08 ...... Frame ( 4) shift: -0.20 0.12 ...... Frame ( 5) shift: -0.26 0.16 ...... Frame ( 6) shift: -0.31 0.15 ...... Frame ( 7) shift: -0.35 0.07 ...... Frame ( 8) shift: -0.38 -0.00 ...... Frame ( 9) shift: -0.39 -0.00 ...... Frame ( 10) shift: -0.37 0.07 ...... Frame ( 11) shift: -0.34 0.14 ...... Frame ( 12) shift: -0.34 0.18 ...... Frame ( 13) shift: -0.35 0.17 ...... Frame ( 14) shift: -0.36 0.17 ...... Frame ( 15) shift: -0.36 0.23 ...... Frame ( 16) shift: -0.34 0.37 ...... Frame ( 17) shift: -0.32 0.50 ...... Frame ( 18) shift: -0.29 0.61 ...... Frame ( 19) shift: -0.23 0.70 ...... Frame ( 20) shift: -0.18 0.79 ...... Frame ( 21) shift: -0.13 0.86 ...... Frame ( 22) shift: -0.07 0.92 ...... Frame ( 23) shift: -0.02 0.98 ...... Frame ( 24) shift: 0.02 1.02 ...... Frame ( 25) shift: 0.05 1.06 ...... Frame ( 26) shift: 0.07 1.10 ...... Frame ( 27) shift: 0.08 1.12 ...... Frame ( 28) shift: 0.07 1.12 ...... Frame ( 29) shift: 0.06 1.12 ...... Frame ( 30) shift: 0.05 1.13 ...... Frame ( 31) shift: 0.04 1.15 ...... Frame ( 32) shift: 0.04 1.16 ...... Frame ( 33) shift: 0.01 1.18 ...... Frame ( 34) shift: -0.03 1.20 ...... Frame ( 35) shift: -0.07 1.22 ...... Frame ( 36) shift: -0.07 1.22 ...... Frame ( 37) shift: -0.01 1.19 ...... Frame ( 38) shift: 0.04 1.17 ...... Frame ( 39) shift: 0.10 1.14 ...... Frame ( 40) shift: 0.15 1.12 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.027326 Iteration 2 Error: 0.275781 Iteration 3 Error: 0.059120 Iteration 4 Error: 0.026933 Align patch 2 23 left Iteration 1 Error: 1.178744 Iteration 2 Error: 0.201425 Iteration 3 Error: 0.110379 Iteration 4 Error: 0.023234 Align patch 3 22 left Iteration 1 Error: 0.702837 Iteration 2 Error: 0.154049 Iteration 3 Error: 0.027598 Align patch 4 21 left Iteration 1 Error: 0.905721 Iteration 2 Error: 0.156727 Iteration 3 Error: 0.039031 Align patch 5 20 left Iteration 1 Error: 0.856149 Iteration 2 Error: 0.226703 Iteration 3 Error: 0.059764 Iteration 4 Error: 0.024377 Align patch 6 19 left Iteration 1 Error: 0.799719 Iteration 2 Error: 0.158683 Iteration 3 Error: 0.054616 Iteration 4 Error: 0.024266 Align patch 7 18 left Iteration 1 Error: 1.037126 Iteration 2 Error: 0.156497 Iteration 3 Error: 0.066250 Iteration 4 Error: 0.023453 Align patch 8 17 left Iteration 1 Error: 1.339168 Iteration 2 Error: 0.115571 Iteration 3 Error: 0.040273 Align patch 9 16 left Iteration 1 Error: 1.067652 Iteration 2 Error: 0.161404 Iteration 3 Error: 0.055227 Iteration 4 Error: 0.018810 Align patch 10 15 left Iteration 1 Error: 0.718552 Iteration 2 Error: 0.161561 Iteration 3 Error: 0.039735 Align patch 11 14 left Iteration 1 Error: 1.208628 Iteration 2 Error: 0.235226 Iteration 3 Error: 0.076823 Iteration 4 Error: 0.037826 Align patch 12 13 left Iteration 1 Error: 0.992974 Iteration 2 Error: 0.169657 Iteration 3 Error: 0.026899 Align patch 13 12 left Iteration 1 Error: 0.934856 Iteration 2 Error: 0.215808 Iteration 3 Error: 0.057343 Iteration 4 Error: 0.029007 Align patch 14 11 left Iteration 1 Error: 1.119210 Iteration 2 Error: 0.353339 Iteration 3 Error: 0.083852 Iteration 4 Error: 0.035110 Align patch 15 10 left Iteration 1 Error: 0.969753 Iteration 2 Error: 0.204654 Iteration 3 Error: 0.086891 Iteration 4 Error: 0.030152 Align patch 16 9 left Iteration 1 Error: 0.891006 Iteration 2 Error: 0.190431 Iteration 3 Error: 0.093217 Iteration 4 Error: 0.029497 Align patch 17 8 left Iteration 1 Error: 0.970549 Iteration 2 Error: 0.178718 Iteration 3 Error: 0.045013 Align patch 18 7 left Iteration 1 Error: 0.990572 Iteration 2 Error: 0.207498 Iteration 3 Error: 0.078765 Iteration 4 Error: 0.025309 Align patch 19 6 left Iteration 1 Error: 1.383797 Iteration 2 Error: 0.294781 Iteration 3 Error: 0.136186 Iteration 4 Error: 0.063246 Iteration 5 Error: 0.027102 Align patch 20 5 left Iteration 1 Error: 1.196893 Iteration 2 Error: 0.347512 Iteration 3 Error: 0.091964 Iteration 4 Error: 0.029801 Align patch 21 4 left Iteration 1 Error: 0.897394 Iteration 2 Error: 0.191925 Iteration 3 Error: 0.103545 Iteration 4 Error: 0.024076 Align patch 22 3 left Iteration 1 Error: 1.377971 Iteration 2 Error: 0.300198 Iteration 3 Error: 0.067908 Iteration 4 Error: 0.024152 Align patch 23 2 left Iteration 1 Error: 0.777351 Iteration 2 Error: 0.196714 Iteration 3 Error: 0.039369 Align patch 24 1 left Iteration 1 Error: 1.161716 Iteration 2 Error: 0.202414 Iteration 3 Error: 0.060033 Iteration 4 Error: 0.016176 Align patch 25 0 left Iteration 1 Error: 1.121594 Iteration 2 Error: 0.112733 Iteration 3 Error: 0.050664 Iteration 4 Error: 0.021102 3D Fitting completed. Patch alignment time: 16.65(sec) Local motion has been corrected. Process thread exits. Computational time: 25.737572 sec Total time: 31.541664 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00017hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00017hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.579924s Reading file: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00017hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.153476s ........................................ >>>>>>TIME<<<<<< FFT: 1.048522s Defocus_U Defocus_V Angle CCC 11408.20 12404.30 30.32 0.019647 Final Values Defocus_U Defocus_V Angle CCC 11315.91 12712.34 31.01 0.027464 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00010sq_v01_00018hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00018hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.993e-02 CC threshold: 0.734 Mean Std: 36.98 6.45 Num Hot pixels: 242 Hot pixel threshold: 75.68 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.027681 Iteration 2 Error: 0.244136 Iteration 3 Error: 0.063047 Iteration 4 Error: 0.022084 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.04 -0.01 ...... Frame ( 3) shift: -0.07 -0.02 ...... Frame ( 4) shift: -0.11 -0.03 ...... Frame ( 5) shift: -0.15 -0.04 ...... Frame ( 6) shift: -0.12 -0.05 ...... Frame ( 7) shift: -0.02 -0.06 ...... Frame ( 8) shift: 0.07 -0.07 ...... Frame ( 9) shift: 0.16 -0.06 ...... Frame ( 10) shift: 0.24 -0.02 ...... Frame ( 11) shift: 0.32 0.03 ...... Frame ( 12) shift: 0.39 0.10 ...... Frame ( 13) shift: 0.47 0.20 ...... Frame ( 14) shift: 0.55 0.30 ...... Frame ( 15) shift: 0.62 0.37 ...... Frame ( 16) shift: 0.67 0.40 ...... Frame ( 17) shift: 0.72 0.44 ...... Frame ( 18) shift: 0.74 0.50 ...... Frame ( 19) shift: 0.73 0.57 ...... Frame ( 20) shift: 0.71 0.65 ...... Frame ( 21) shift: 0.78 0.70 ...... Frame ( 22) shift: 0.94 0.73 ...... Frame ( 23) shift: 1.09 0.77 ...... Frame ( 24) shift: 1.21 0.78 ...... Frame ( 25) shift: 1.30 0.77 ...... Frame ( 26) shift: 1.40 0.77 ...... Frame ( 27) shift: 1.49 0.78 ...... Frame ( 28) shift: 1.58 0.81 ...... Frame ( 29) shift: 1.67 0.84 ...... Frame ( 30) shift: 1.72 0.84 ...... Frame ( 31) shift: 1.72 0.82 ...... Frame ( 32) shift: 1.73 0.80 ...... Frame ( 33) shift: 1.72 0.82 ...... Frame ( 34) shift: 1.70 0.88 ...... Frame ( 35) shift: 1.68 0.93 ...... Frame ( 36) shift: 1.72 0.98 ...... Frame ( 37) shift: 1.83 1.02 ...... Frame ( 38) shift: 1.93 1.06 ...... Frame ( 39) shift: 2.04 1.09 ...... Frame ( 40) shift: 2.15 1.13 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.081386 Iteration 2 Error: 0.328360 Iteration 3 Error: 0.075153 Iteration 4 Error: 0.035000 Align patch 2 23 left Iteration 1 Error: 0.742824 Iteration 2 Error: 0.184649 Iteration 3 Error: 0.071582 Iteration 4 Error: 0.032874 Align patch 3 22 left Iteration 1 Error: 1.441231 Iteration 2 Error: 0.323874 Iteration 3 Error: 0.129359 Iteration 4 Error: 0.041956 Align patch 4 21 left Iteration 1 Error: 0.951116 Iteration 2 Error: 0.162012 Iteration 3 Error: 0.093548 Iteration 4 Error: 0.018248 Align patch 5 20 left Iteration 1 Error: 1.087127 Iteration 2 Error: 0.356303 Iteration 3 Error: 0.091008 Iteration 4 Error: 0.041241 Align patch 6 19 left Iteration 1 Error: 1.014970 Iteration 2 Error: 0.270315 Iteration 3 Error: 0.081498 Iteration 4 Error: 0.031210 Align patch 7 18 left Iteration 1 Error: 0.767702 Iteration 2 Error: 0.181269 Iteration 3 Error: 0.043047 Align patch 8 17 left Iteration 1 Error: 0.785080 Iteration 2 Error: 0.193738 Iteration 3 Error: 0.057169 Iteration 4 Error: 0.023717 Align patch 9 16 left Iteration 1 Error: 0.840116 Iteration 2 Error: 0.191704 Iteration 3 Error: 0.045358 Align patch 10 15 left Iteration 1 Error: 0.781747 Iteration 2 Error: 0.168032 Iteration 3 Error: 0.057955 Iteration 4 Error: 0.017270 Align patch 11 14 left Iteration 1 Error: 1.076757 Iteration 2 Error: 0.145406 Iteration 3 Error: 0.028064 Align patch 12 13 left Iteration 1 Error: 0.811319 Iteration 2 Error: 0.200783 Iteration 3 Error: 0.072040 Iteration 4 Error: 0.022168 Align patch 13 12 left Iteration 1 Error: 0.879880 Iteration 2 Error: 0.136763 Iteration 3 Error: 0.063781 Iteration 4 Error: 0.023216 Align patch 14 11 left Iteration 1 Error: 0.484294 Iteration 2 Error: 0.090334 Iteration 3 Error: 0.021497 Align patch 15 10 left Iteration 1 Error: 0.553275 Iteration 2 Error: 0.067470 Iteration 3 Error: 0.018394 Align patch 16 9 left Iteration 1 Error: 0.900903 Iteration 2 Error: 0.271323 Iteration 3 Error: 0.073215 Iteration 4 Error: 0.024630 Align patch 17 8 left Iteration 1 Error: 1.242512 Iteration 2 Error: 0.193487 Iteration 3 Error: 0.075562 Iteration 4 Error: 0.047766 Align patch 18 7 left Iteration 1 Error: 1.015229 Iteration 2 Error: 0.177321 Iteration 3 Error: 0.050390 Iteration 4 Error: 0.019554 Align patch 19 6 left Iteration 1 Error: 0.684902 Iteration 2 Error: 0.114523 Iteration 3 Error: 0.026108 Align patch 20 5 left Iteration 1 Error: 0.910581 Iteration 2 Error: 0.098981 Iteration 3 Error: 0.021077 Align patch 21 4 left Iteration 1 Error: 1.268283 Iteration 2 Error: 0.333068 Iteration 3 Error: 0.076426 Iteration 4 Error: 0.030317 Align patch 22 3 left Iteration 1 Error: 0.767490 Iteration 2 Error: 0.252390 Iteration 3 Error: 0.047831 Align patch 23 2 left Iteration 1 Error: 0.693249 Iteration 2 Error: 0.156312 Iteration 3 Error: 0.047082 Align patch 24 1 left Iteration 1 Error: 1.292682 Iteration 2 Error: 0.319767 Iteration 3 Error: 0.099542 Iteration 4 Error: 0.037318 Align patch 25 0 left Iteration 1 Error: 0.899312 Iteration 2 Error: 0.201044 Iteration 3 Error: 0.034604 3D Fitting completed. Patch alignment time: 16.72(sec) Local motion has been corrected. Process thread exits. Computational time: 26.604988 sec Total time: 33.113468 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00018hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00018hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.587193s Reading file: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00018hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.387099s ........................................ >>>>>>TIME<<<<<< FFT: 1.057078s Defocus_U Defocus_V Angle CCC 10429.70 11296.94 13.57 0.025214 Final Values Defocus_U Defocus_V Angle CCC 10481.25 11392.35 13.90 0.038417 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00010sq_v01_00018hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00018hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.001e-01 CC threshold: 0.735 Mean Std: 34.58 6.21 Num Hot pixels: 223 Hot pixel threshold: 71.81 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.752708 Iteration 2 Error: 0.408916 Iteration 3 Error: 0.217305 Iteration 4 Error: 0.073621 Iteration 5 Error: 0.058842 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.06 -0.40 ...... Frame ( 3) shift: 0.12 -0.80 ...... Frame ( 4) shift: 0.17 -1.19 ...... Frame ( 5) shift: 0.23 -1.59 ...... Frame ( 6) shift: 0.22 -1.90 ...... Frame ( 7) shift: 0.13 -2.13 ...... Frame ( 8) shift: 0.04 -2.35 ...... Frame ( 9) shift: 0.06 -2.57 ...... Frame ( 10) shift: 0.19 -2.78 ...... Frame ( 11) shift: 0.32 -3.00 ...... Frame ( 12) shift: 0.40 -3.16 ...... Frame ( 13) shift: 0.43 -3.26 ...... Frame ( 14) shift: 0.45 -3.37 ...... Frame ( 15) shift: 0.46 -3.25 ...... Frame ( 16) shift: 0.46 -2.91 ...... Frame ( 17) shift: 0.46 -2.56 ...... Frame ( 18) shift: 0.48 -2.37 ...... Frame ( 19) shift: 0.54 -2.32 ...... Frame ( 20) shift: 0.59 -2.27 ...... Frame ( 21) shift: 0.56 -2.35 ...... Frame ( 22) shift: 0.45 -2.57 ...... Frame ( 23) shift: 0.35 -2.79 ...... Frame ( 24) shift: 0.32 -2.93 ...... Frame ( 25) shift: 0.39 -3.01 ...... Frame ( 26) shift: 0.45 -3.09 ...... Frame ( 27) shift: 0.47 -3.04 ...... Frame ( 28) shift: 0.43 -2.86 ...... Frame ( 29) shift: 0.39 -2.67 ...... Frame ( 30) shift: 0.41 -2.65 ...... Frame ( 31) shift: 0.50 -2.79 ...... Frame ( 32) shift: 0.59 -2.93 ...... Frame ( 33) shift: 0.59 -3.05 ...... Frame ( 34) shift: 0.51 -3.14 ...... Frame ( 35) shift: 0.43 -3.23 ...... Frame ( 36) shift: 0.41 -3.42 ...... Frame ( 37) shift: 0.46 -3.70 ...... Frame ( 38) shift: 0.50 -3.97 ...... Frame ( 39) shift: 0.55 -4.25 ...... Frame ( 40) shift: 0.59 -4.53 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 35.944962 Iteration 2 Error: 34.414856 Iteration 3 Error: 34.600010 Iteration 4 Error: 34.615303 Iteration 5 Error: 34.456944 Align patch 1 24 left Iteration 1 Error: 20.237925 Iteration 2 Error: 1.541945 Iteration 3 Error: 0.668279 Iteration 4 Error: 0.422483 Iteration 5 Error: 0.325138 Align patch 2 23 left Iteration 1 Error: 32.162132 Iteration 2 Error: 24.533669 Iteration 3 Error: 22.852072 Iteration 4 Error: 22.411900 Iteration 5 Error: 22.212084 Align patch 2 23 left Iteration 1 Error: 2.962584 Iteration 2 Error: 1.161074 Iteration 3 Error: 0.780686 Iteration 4 Error: 0.856139 Iteration 5 Error: 0.650631 Align patch 3 22 left Iteration 1 Error: 27.870361 Iteration 2 Error: 26.528624 Iteration 3 Error: 26.862309 Iteration 4 Error: 26.861156 Iteration 5 Error: 27.420147 Align patch 3 22 left Iteration 1 Error: 6.513364 Iteration 2 Error: 1.731404 Iteration 3 Error: 2.008774 Iteration 4 Error: 1.981273 Iteration 5 Error: 0.711827 Align patch 4 21 left Iteration 1 Error: 36.960880 Iteration 2 Error: 33.999996 Iteration 3 Error: 38.523727 Iteration 4 Error: 36.697754 Iteration 5 Error: 33.872093 Align patch 4 21 left Iteration 1 Error: 23.862665 Iteration 2 Error: 3.528911 Iteration 3 Error: 25.329941 Iteration 4 Error: 4.852808 Iteration 5 Error: 19.674795 Align patch 5 20 left Iteration 1 Error: 9.585888 Iteration 2 Error: 8.287730 Iteration 3 Error: 8.666253 Iteration 4 Error: 8.495536 Iteration 5 Error: 8.572365 Align patch 5 20 left Iteration 1 Error: 7.215254 Iteration 2 Error: 2.371002 Iteration 3 Error: 2.723789 Iteration 4 Error: 1.678302 Iteration 5 Error: 0.934438 Align patch 6 19 left Iteration 1 Error: 28.408497 Iteration 2 Error: 29.201523 Iteration 3 Error: 33.842907 Iteration 4 Error: 33.181992 Iteration 5 Error: 33.329281 Align patch 6 19 left Iteration 1 Error: 5.734738 Iteration 2 Error: 1.974318 Iteration 3 Error: 1.293025 Iteration 4 Error: 0.815825 Iteration 5 Error: 0.639260 Align patch 7 18 left Iteration 1 Error: 21.412109 Iteration 2 Error: 4.110719 Iteration 3 Error: 1.784887 Iteration 4 Error: 1.024983 Iteration 5 Error: 0.575045 Align patch 7 18 left Iteration 1 Error: 19.302147 Iteration 2 Error: 4.387856 Iteration 3 Error: 1.330595 Iteration 4 Error: 0.827113 Iteration 5 Error: 0.720244 Align patch 8 17 left Iteration 1 Error: 26.131702 Iteration 2 Error: 32.142204 Iteration 3 Error: 31.278158 Iteration 4 Error: 31.087358 Iteration 5 Error: 30.697414 Align patch 8 17 left Iteration 1 Error: 25.986946 Iteration 2 Error: 28.202641 Iteration 3 Error: 26.579561 Iteration 4 Error: 19.366095 Iteration 5 Error: 7.097826 Align patch 9 16 left Iteration 1 Error: 36.879059 Iteration 2 Error: 36.959629 Iteration 3 Error: 28.278919 Iteration 4 Error: 28.066175 Iteration 5 Error: 28.264175 Align patch 9 16 left Iteration 1 Error: 23.287266 Iteration 2 Error: 25.276077 Iteration 3 Error: 17.914597 Iteration 4 Error: 32.727341 Iteration 5 Error: 35.100620 Align patch 10 15 left Iteration 1 Error: 4.232445 Iteration 2 Error: 12.036190 Iteration 3 Error: 11.311324 Iteration 4 Error: 11.756599 Iteration 5 Error: 12.098823 Align patch 10 15 left Iteration 1 Error: 21.192575 Iteration 2 Error: 4.695043 Iteration 3 Error: 25.228540 Iteration 4 Error: 29.369257 Iteration 5 Error: 27.551472 Align patch 11 14 left Iteration 1 Error: 19.348083 Iteration 2 Error: 37.977993 Iteration 3 Error: 35.271053 Iteration 4 Error: 36.571854 Iteration 5 Error: 26.333200 Align patch 11 14 left Iteration 1 Error: 25.927418 Iteration 2 Error: 22.900904 Iteration 3 Error: 19.142878 Iteration 4 Error: 17.675409 Iteration 5 Error: 13.656636 Align patch 12 13 left Iteration 1 Error: 35.959538 Iteration 2 Error: 31.760605 Iteration 3 Error: 32.088291 Iteration 4 Error: 14.876188 Iteration 5 Error: 14.681982 Align patch 12 13 left Iteration 1 Error: 12.181083 Iteration 2 Error: 20.833019 Iteration 3 Error: 22.957260 Iteration 4 Error: 20.866508 Iteration 5 Error: 29.185068 Align patch 13 12 left Iteration 1 Error: 34.402061 Iteration 2 Error: 51.304699 Iteration 3 Error: 51.957436 Iteration 4 Error: 51.473328 Iteration 5 Error: 52.107559 Align patch 13 12 left Iteration 1 Error: 33.525700 Iteration 2 Error: 33.768559 Iteration 3 Error: 32.763111 Iteration 4 Error: 29.271854 Iteration 5 Error: 29.936611 Align patch 14 11 left Iteration 1 Error: 30.925869 Iteration 2 Error: 33.071182 Iteration 3 Error: 32.933109 Iteration 4 Error: 30.652203 Iteration 5 Error: 45.027584 Align patch 14 11 left Iteration 1 Error: 36.596306 Iteration 2 Error: 34.464275 Iteration 3 Error: 54.889454 Iteration 4 Error: 28.848129 Iteration 5 Error: 29.522070 Align patch 15 10 left Iteration 1 Error: 2.387421 Iteration 2 Error: 1.638665 Iteration 3 Error: 1.068663 Iteration 4 Error: 0.953222 Iteration 5 Error: 0.610510 Align patch 15 10 left Iteration 1 Error: 3.284733 Iteration 2 Error: 2.148670 Iteration 3 Error: 2.709847 Iteration 4 Error: 1.341750 Iteration 5 Error: 1.441748 Align patch 16 9 left Iteration 1 Error: 26.000965 Iteration 2 Error: 22.689766 Iteration 3 Error: 9.148124 Iteration 4 Error: 7.802520 Iteration 5 Error: 5.393418 Align patch 16 9 left Iteration 1 Error: 31.214632 Iteration 2 Error: 23.670162 Iteration 3 Error: 1.903662 Iteration 4 Error: 6.378326 Iteration 5 Error: 14.220879 Align patch 17 8 left Iteration 1 Error: 30.787994 Iteration 2 Error: 28.168148 Iteration 3 Error: 40.737373 Iteration 4 Error: 40.783031 Iteration 5 Error: 45.000282 Align patch 17 8 left Iteration 1 Error: 14.585872 Iteration 2 Error: 3.297759 Iteration 3 Error: 2.628968 Iteration 4 Error: 0.825117 Iteration 5 Error: 0.970470 Align patch 18 7 left Iteration 1 Error: 20.698397 Iteration 2 Error: 20.541355 Iteration 3 Error: 21.770779 Iteration 4 Error: 51.871342 Iteration 5 Error: 51.820946 Align patch 18 7 left Iteration 1 Error: 22.378160 Iteration 2 Error: 41.179131 Iteration 3 Error: 39.802406 Iteration 4 Error: 37.564854 Iteration 5 Error: 39.214336 Align patch 19 6 left Iteration 1 Error: 47.092548 Iteration 2 Error: 46.361225 Iteration 3 Error: 44.980549 Iteration 4 Error: 43.885540 Iteration 5 Error: 43.924522 Align patch 19 6 left Iteration 1 Error: 7.658144 Iteration 2 Error: 9.111360 Iteration 3 Error: 2.137257 Iteration 4 Error: 32.911755 Iteration 5 Error: 1.623604 Align patch 20 5 left Iteration 1 Error: 8.067612 Iteration 2 Error: 22.482681 Iteration 3 Error: 20.509809 Iteration 4 Error: 20.486479 Iteration 5 Error: 18.728254 Align patch 20 5 left Iteration 1 Error: 3.413509 Iteration 2 Error: 1.981078 Iteration 3 Error: 2.382169 Iteration 4 Error: 1.776855 Iteration 5 Error: 1.212057 Align patch 21 4 left Iteration 1 Error: 16.496092 Iteration 2 Error: 12.432037 Iteration 3 Error: 1.146290 Iteration 4 Error: 0.788418 Iteration 5 Error: 0.372216 Align patch 21 4 left Iteration 1 Error: 24.605238 Iteration 2 Error: 20.810286 Iteration 3 Error: 4.743793 Iteration 4 Error: 1.290663 Iteration 5 Error: 1.251181 Align patch 22 3 left Iteration 1 Error: 27.343199 Iteration 2 Error: 29.537401 Iteration 3 Error: 29.173565 Iteration 4 Error: 29.040176 Iteration 5 Error: 28.958649 Align patch 22 3 left Iteration 1 Error: 15.349519 Iteration 2 Error: 22.463358 Iteration 3 Error: 19.689247 Iteration 4 Error: 20.106464 Iteration 5 Error: 21.758224 Align patch 23 2 left Iteration 1 Error: 9.467484 Iteration 2 Error: 29.761774 Iteration 3 Error: 30.109634 Iteration 4 Error: 30.640059 Iteration 5 Error: 30.669270 Align patch 23 2 left Iteration 1 Error: 19.262192 Iteration 2 Error: 18.405411 Iteration 3 Error: 11.609233 Iteration 4 Error: 23.009716 Iteration 5 Error: 26.296997 Align patch 24 1 left Iteration 1 Error: 3.902191 Iteration 2 Error: 3.383234 Iteration 3 Error: 6.702562 Iteration 4 Error: 2.110844 Iteration 5 Error: 1.549789 Align patch 24 1 left Iteration 1 Error: 5.434459 Iteration 2 Error: 2.417783 Iteration 3 Error: 4.368554 Iteration 4 Error: 3.062618 Iteration 5 Error: 4.785101 Align patch 25 0 left Iteration 1 Error: 32.474541 Iteration 2 Error: 2.270119 Iteration 3 Error: 39.196632 Iteration 4 Error: 0.810879 Iteration 5 Error: 1.620319 Align patch 25 0 left Iteration 1 Error: 4.038680 Iteration 2 Error: 2.890350 Iteration 3 Error: 1.359638 Iteration 4 Error: 1.341879 Iteration 5 Error: 1.048812 3D Fitting completed. Patch alignment time: 40.61(sec) Local motion has been corrected. Process thread exits. Computational time: 49.791466 sec Total time: 55.956440 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00018hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00018hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.556099s Reading file: gc_18feb27f_CTD_g1_00017gr_00010sq_v01_00018hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.500868s ........................................ >>>>>>TIME<<<<<< FFT: 0.947157s Defocus_U Defocus_V Angle CCC 9410.23 7964.79 79.04 0.036787 Final Values Defocus_U Defocus_V Angle CCC 9407.17 7977.35 77.79 0.074561 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00002hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00002hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.997e-02 CC threshold: 0.734 Mean Std: 41.82 7.01 Num Hot pixels: 234 Hot pixel threshold: 83.86 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.774823 Iteration 2 Error: 0.389586 Iteration 3 Error: 0.153306 Iteration 4 Error: 0.063174 Iteration 5 Error: 0.019061 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.16 -0.00 ...... Frame ( 3) shift: -0.31 -0.01 ...... Frame ( 4) shift: -0.47 -0.01 ...... Frame ( 5) shift: -0.62 -0.01 ...... Frame ( 6) shift: -0.66 0.04 ...... Frame ( 7) shift: -0.57 0.16 ...... Frame ( 8) shift: -0.48 0.27 ...... Frame ( 9) shift: -0.41 0.39 ...... Frame ( 10) shift: -0.36 0.52 ...... Frame ( 11) shift: -0.30 0.65 ...... Frame ( 12) shift: -0.24 0.82 ...... Frame ( 13) shift: -0.16 1.02 ...... Frame ( 14) shift: -0.08 1.21 ...... Frame ( 15) shift: -0.02 1.36 ...... Frame ( 16) shift: 0.02 1.45 ...... Frame ( 17) shift: 0.06 1.54 ...... Frame ( 18) shift: 0.09 1.66 ...... Frame ( 19) shift: 0.11 1.78 ...... Frame ( 20) shift: 0.14 1.91 ...... Frame ( 21) shift: 0.17 2.01 ...... Frame ( 22) shift: 0.20 2.06 ...... Frame ( 23) shift: 0.23 2.12 ...... Frame ( 24) shift: 0.28 2.22 ...... Frame ( 25) shift: 0.34 2.35 ...... Frame ( 26) shift: 0.40 2.49 ...... Frame ( 27) shift: 0.42 2.62 ...... Frame ( 28) shift: 0.41 2.74 ...... Frame ( 29) shift: 0.39 2.86 ...... Frame ( 30) shift: 0.40 2.97 ...... Frame ( 31) shift: 0.43 3.05 ...... Frame ( 32) shift: 0.46 3.14 ...... Frame ( 33) shift: 0.52 3.23 ...... Frame ( 34) shift: 0.61 3.34 ...... Frame ( 35) shift: 0.70 3.44 ...... Frame ( 36) shift: 0.79 3.55 ...... Frame ( 37) shift: 0.89 3.67 ...... Frame ( 38) shift: 0.98 3.79 ...... Frame ( 39) shift: 1.08 3.91 ...... Frame ( 40) shift: 1.18 4.02 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.975081 Iteration 2 Error: 0.230024 Iteration 3 Error: 0.090824 Iteration 4 Error: 0.027459 Align patch 2 23 left Iteration 1 Error: 0.829465 Iteration 2 Error: 0.199001 Iteration 3 Error: 0.069665 Iteration 4 Error: 0.019831 Align patch 3 22 left Iteration 1 Error: 0.788833 Iteration 2 Error: 0.143304 Iteration 3 Error: 0.030768 Align patch 4 21 left Iteration 1 Error: 1.011650 Iteration 2 Error: 0.174985 Iteration 3 Error: 0.072944 Iteration 4 Error: 0.043107 Align patch 5 20 left Iteration 1 Error: 0.684732 Iteration 2 Error: 0.117392 Iteration 3 Error: 0.026344 Align patch 6 19 left Iteration 1 Error: 0.879474 Iteration 2 Error: 0.207181 Iteration 3 Error: 0.065881 Iteration 4 Error: 0.020188 Align patch 7 18 left Iteration 1 Error: 0.790633 Iteration 2 Error: 0.137191 Iteration 3 Error: 0.028768 Align patch 8 17 left Iteration 1 Error: 1.143470 Iteration 2 Error: 0.218190 Iteration 3 Error: 0.046693 Align patch 9 16 left Iteration 1 Error: 1.239053 Iteration 2 Error: 0.230292 Iteration 3 Error: 0.166470 Iteration 4 Error: 0.064645 Iteration 5 Error: 0.045379 Align patch 10 15 left Iteration 1 Error: 1.024997 Iteration 2 Error: 0.262761 Iteration 3 Error: 0.155445 Iteration 4 Error: 0.083430 Iteration 5 Error: 0.053671 Align patch 10 15 left Iteration 1 Error: 1.127397 Iteration 2 Error: 0.159193 Iteration 3 Error: 0.058943 Iteration 4 Error: 0.015423 Align patch 11 14 left Iteration 1 Error: 0.969116 Iteration 2 Error: 0.191181 Iteration 3 Error: 0.048097 Align patch 12 13 left Iteration 1 Error: 0.990284 Iteration 2 Error: 0.161362 Iteration 3 Error: 0.043904 Align patch 13 12 left Iteration 1 Error: 0.558005 Iteration 2 Error: 0.202828 Iteration 3 Error: 0.037039 Align patch 14 11 left Iteration 1 Error: 1.608492 Iteration 2 Error: 0.232405 Iteration 3 Error: 0.109604 Iteration 4 Error: 0.033929 Align patch 15 10 left Iteration 1 Error: 0.687756 Iteration 2 Error: 0.331939 Iteration 3 Error: 0.150273 Iteration 4 Error: 0.066506 Iteration 5 Error: 0.037835 Align patch 16 9 left Iteration 1 Error: 1.602296 Iteration 2 Error: 0.319886 Iteration 3 Error: 0.162926 Iteration 4 Error: 0.049882 Align patch 17 8 left Iteration 1 Error: 0.958831 Iteration 2 Error: 0.293471 Iteration 3 Error: 0.069481 Iteration 4 Error: 0.027802 Align patch 18 7 left Iteration 1 Error: 0.623363 Iteration 2 Error: 0.109533 Iteration 3 Error: 0.039519 Align patch 19 6 left Iteration 1 Error: 0.743112 Iteration 2 Error: 0.171918 Iteration 3 Error: 0.077109 Iteration 4 Error: 0.035382 Align patch 20 5 left Iteration 1 Error: 0.537559 Iteration 2 Error: 0.176796 Iteration 3 Error: 0.089284 Iteration 4 Error: 0.045788 Align patch 21 4 left Iteration 1 Error: 1.294049 Iteration 2 Error: 0.190417 Iteration 3 Error: 0.049395 Align patch 22 3 left Iteration 1 Error: 1.108808 Iteration 2 Error: 0.207613 Iteration 3 Error: 0.039274 Align patch 23 2 left Iteration 1 Error: 0.900153 Iteration 2 Error: 0.217272 Iteration 3 Error: 0.046857 Align patch 24 1 left Iteration 1 Error: 0.759292 Iteration 2 Error: 0.160061 Iteration 3 Error: 0.062916 Iteration 4 Error: 0.024429 Align patch 25 0 left Iteration 1 Error: 0.941458 Iteration 2 Error: 0.258708 Iteration 3 Error: 0.047602 3D Fitting completed. Patch alignment time: 16.93(sec) Local motion has been corrected. Process thread exits. Computational time: 26.151497 sec Total time: 33.480240 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00002hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00002hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.536555s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00002hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.098255s ........................................ >>>>>>TIME<<<<<< FFT: 0.980537s Defocus_U Defocus_V Angle CCC 9490.23 10298.83 12.42 0.041715 Final Values Defocus_U Defocus_V Angle CCC 9483.99 10314.48 11.80 0.077771 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00002hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00002hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.001e-01 CC threshold: 0.735 Mean Std: 41.63 6.96 Num Hot pixels: 230 Hot pixel threshold: 83.40 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.523711 Iteration 2 Error: 0.269033 Iteration 3 Error: 0.072406 Iteration 4 Error: 0.023920 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.10 -0.03 ...... Frame ( 3) shift: -0.19 -0.07 ...... Frame ( 4) shift: -0.29 -0.10 ...... Frame ( 5) shift: -0.38 -0.14 ...... Frame ( 6) shift: -0.41 -0.13 ...... Frame ( 7) shift: -0.35 -0.08 ...... Frame ( 8) shift: -0.30 -0.04 ...... Frame ( 9) shift: -0.23 0.06 ...... Frame ( 10) shift: -0.16 0.21 ...... Frame ( 11) shift: -0.09 0.36 ...... Frame ( 12) shift: -0.05 0.46 ...... Frame ( 13) shift: -0.03 0.52 ...... Frame ( 14) shift: -0.02 0.59 ...... Frame ( 15) shift: 0.00 0.63 ...... Frame ( 16) shift: 0.03 0.64 ...... Frame ( 17) shift: 0.05 0.66 ...... Frame ( 18) shift: 0.08 0.73 ...... Frame ( 19) shift: 0.12 0.84 ...... Frame ( 20) shift: 0.15 0.95 ...... Frame ( 21) shift: 0.21 1.03 ...... Frame ( 22) shift: 0.28 1.07 ...... Frame ( 23) shift: 0.34 1.10 ...... Frame ( 24) shift: 0.41 1.18 ...... Frame ( 25) shift: 0.48 1.31 ...... Frame ( 26) shift: 0.55 1.43 ...... Frame ( 27) shift: 0.60 1.52 ...... Frame ( 28) shift: 0.64 1.57 ...... Frame ( 29) shift: 0.68 1.62 ...... Frame ( 30) shift: 0.71 1.70 ...... Frame ( 31) shift: 0.72 1.81 ...... Frame ( 32) shift: 0.73 1.92 ...... Frame ( 33) shift: 0.76 2.05 ...... Frame ( 34) shift: 0.83 2.20 ...... Frame ( 35) shift: 0.89 2.35 ...... Frame ( 36) shift: 0.95 2.44 ...... Frame ( 37) shift: 1.01 2.48 ...... Frame ( 38) shift: 1.07 2.52 ...... Frame ( 39) shift: 1.13 2.56 ...... Frame ( 40) shift: 1.19 2.60 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.962023 Iteration 2 Error: 0.251681 Iteration 3 Error: 0.074198 Iteration 4 Error: 0.033838 Align patch 2 23 left Iteration 1 Error: 0.578053 Iteration 2 Error: 0.083371 Iteration 3 Error: 0.016930 Align patch 3 22 left Iteration 1 Error: 0.859255 Iteration 2 Error: 0.153566 Iteration 3 Error: 0.038055 Align patch 4 21 left Iteration 1 Error: 0.615832 Iteration 2 Error: 0.057775 Iteration 3 Error: 0.016448 Align patch 5 20 left Iteration 1 Error: 0.724236 Iteration 2 Error: 0.095809 Iteration 3 Error: 0.012721 Align patch 6 19 left Iteration 1 Error: 1.038101 Iteration 2 Error: 0.266682 Iteration 3 Error: 0.058226 Iteration 4 Error: 0.026129 Align patch 7 18 left Iteration 1 Error: 0.802930 Iteration 2 Error: 0.171877 Iteration 3 Error: 0.062462 Iteration 4 Error: 0.024294 Align patch 8 17 left Iteration 1 Error: 0.356485 Iteration 2 Error: 0.087948 Iteration 3 Error: 0.030635 Align patch 9 16 left Iteration 1 Error: 0.580728 Iteration 2 Error: 0.173439 Iteration 3 Error: 0.047753 Align patch 10 15 left Iteration 1 Error: 0.659102 Iteration 2 Error: 0.124939 Iteration 3 Error: 0.025910 Align patch 11 14 left Iteration 1 Error: 0.599817 Iteration 2 Error: 0.107019 Iteration 3 Error: 0.032326 Align patch 12 13 left Iteration 1 Error: 0.588102 Iteration 2 Error: 0.071395 Iteration 3 Error: 0.026030 Align patch 13 12 left Iteration 1 Error: 0.644607 Iteration 2 Error: 0.141375 Iteration 3 Error: 0.033280 Align patch 14 11 left Iteration 1 Error: 0.617530 Iteration 2 Error: 0.070074 Iteration 3 Error: 0.023031 Align patch 15 10 left Iteration 1 Error: 1.436128 Iteration 2 Error: 0.122005 Iteration 3 Error: 0.029256 Align patch 16 9 left Iteration 1 Error: 0.866618 Iteration 2 Error: 0.096695 Iteration 3 Error: 0.037878 Align patch 17 8 left Iteration 1 Error: 0.868388 Iteration 2 Error: 0.106577 Iteration 3 Error: 0.020275 Align patch 18 7 left Iteration 1 Error: 0.889080 Iteration 2 Error: 0.163198 Iteration 3 Error: 0.041457 Align patch 19 6 left Iteration 1 Error: 0.592431 Iteration 2 Error: 0.091401 Iteration 3 Error: 0.014200 Align patch 20 5 left Iteration 1 Error: 0.850581 Iteration 2 Error: 0.159686 Iteration 3 Error: 0.041566 Align patch 21 4 left Iteration 1 Error: 0.831189 Iteration 2 Error: 0.170492 Iteration 3 Error: 0.068938 Iteration 4 Error: 0.020410 Align patch 22 3 left Iteration 1 Error: 1.124747 Iteration 2 Error: 0.305447 Iteration 3 Error: 0.039817 Align patch 23 2 left Iteration 1 Error: 0.545730 Iteration 2 Error: 0.129380 Iteration 3 Error: 0.035751 Align patch 24 1 left Iteration 1 Error: 0.556493 Iteration 2 Error: 0.069980 Iteration 3 Error: 0.025599 Align patch 25 0 left Iteration 1 Error: 0.841967 Iteration 2 Error: 0.125649 Iteration 3 Error: 0.034997 3D Fitting completed. Patch alignment time: 15.08(sec) Local motion has been corrected. Process thread exits. Computational time: 23.656507 sec Total time: 29.184645 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00002hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00002hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.570107s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00002hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.863820s ........................................ >>>>>>TIME<<<<<< FFT: 0.991084s Defocus_U Defocus_V Angle CCC 13351.28 13785.47 0.04 0.051796 Final Values Defocus_U Defocus_V Angle CCC 13371.61 13808.92 0.36 0.086014 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00002hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00002hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 43.84 7.24 Num Hot pixels: 219 Hot pixel threshold: 87.28 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.793388 Iteration 2 Error: 0.106811 Iteration 3 Error: 0.025164 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.28 -0.13 ...... Frame ( 3) shift: -0.56 -0.27 ...... Frame ( 4) shift: -0.85 -0.40 ...... Frame ( 5) shift: -1.13 -0.53 ...... Frame ( 6) shift: -1.27 -0.54 ...... Frame ( 7) shift: -1.26 -0.43 ...... Frame ( 8) shift: -1.25 -0.32 ...... Frame ( 9) shift: -1.26 -0.26 ...... Frame ( 10) shift: -1.28 -0.23 ...... Frame ( 11) shift: -1.29 -0.21 ...... Frame ( 12) shift: -1.28 -0.16 ...... Frame ( 13) shift: -1.25 -0.08 ...... Frame ( 14) shift: -1.21 -0.00 ...... Frame ( 15) shift: -1.21 0.08 ...... Frame ( 16) shift: -1.25 0.18 ...... Frame ( 17) shift: -1.28 0.28 ...... Frame ( 18) shift: -1.29 0.33 ...... Frame ( 19) shift: -1.27 0.31 ...... Frame ( 20) shift: -1.24 0.30 ...... Frame ( 21) shift: -1.23 0.32 ...... Frame ( 22) shift: -1.22 0.38 ...... Frame ( 23) shift: -1.20 0.45 ...... Frame ( 24) shift: -1.18 0.48 ...... Frame ( 25) shift: -1.15 0.50 ...... Frame ( 26) shift: -1.12 0.51 ...... Frame ( 27) shift: -1.10 0.54 ...... Frame ( 28) shift: -1.07 0.57 ...... Frame ( 29) shift: -1.05 0.61 ...... Frame ( 30) shift: -1.04 0.65 ...... Frame ( 31) shift: -1.05 0.68 ...... Frame ( 32) shift: -1.05 0.71 ...... Frame ( 33) shift: -1.04 0.75 ...... Frame ( 34) shift: -1.01 0.80 ...... Frame ( 35) shift: -0.98 0.85 ...... Frame ( 36) shift: -0.93 0.86 ...... Frame ( 37) shift: -0.87 0.82 ...... Frame ( 38) shift: -0.80 0.78 ...... Frame ( 39) shift: -0.74 0.74 ...... Frame ( 40) shift: -0.68 0.70 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.618940 Iteration 2 Error: 0.084146 Iteration 3 Error: 0.026872 Align patch 2 23 left Iteration 1 Error: 0.917311 Iteration 2 Error: 0.129640 Iteration 3 Error: 0.034273 Align patch 3 22 left Iteration 1 Error: 0.928836 Iteration 2 Error: 0.081656 Iteration 3 Error: 0.014175 Align patch 4 21 left Iteration 1 Error: 1.190920 Iteration 2 Error: 0.120716 Iteration 3 Error: 0.030327 Align patch 5 20 left Iteration 1 Error: 1.058003 Iteration 2 Error: 0.153701 Iteration 3 Error: 0.040551 Align patch 6 19 left Iteration 1 Error: 0.662991 Iteration 2 Error: 0.130833 Iteration 3 Error: 0.033541 Align patch 7 18 left Iteration 1 Error: 0.872846 Iteration 2 Error: 0.116281 Iteration 3 Error: 0.035776 Align patch 8 17 left Iteration 1 Error: 0.588433 Iteration 2 Error: 0.103922 Iteration 3 Error: 0.040067 Align patch 9 16 left Iteration 1 Error: 0.845865 Iteration 2 Error: 0.118051 Iteration 3 Error: 0.036669 Align patch 10 15 left Iteration 1 Error: 0.966289 Iteration 2 Error: 0.099157 Iteration 3 Error: 0.020821 Align patch 11 14 left Iteration 1 Error: 0.642539 Iteration 2 Error: 0.105109 Iteration 3 Error: 0.040372 Align patch 12 13 left Iteration 1 Error: 0.965373 Iteration 2 Error: 0.148606 Iteration 3 Error: 0.031057 Align patch 13 12 left Iteration 1 Error: 0.570394 Iteration 2 Error: 0.066391 Iteration 3 Error: 0.022546 Align patch 14 11 left Iteration 1 Error: 0.626486 Iteration 2 Error: 0.085682 Iteration 3 Error: 0.012757 Align patch 15 10 left Iteration 1 Error: 0.609796 Iteration 2 Error: 0.066265 Iteration 3 Error: 0.015953 Align patch 16 9 left Iteration 1 Error: 1.251184 Iteration 2 Error: 0.152752 Iteration 3 Error: 0.033289 Align patch 17 8 left Iteration 1 Error: 1.563715 Iteration 2 Error: 0.312882 Iteration 3 Error: 0.097464 Iteration 4 Error: 0.036631 Align patch 18 7 left Iteration 1 Error: 0.790124 Iteration 2 Error: 0.124923 Iteration 3 Error: 0.027948 Align patch 19 6 left Iteration 1 Error: 0.488245 Iteration 2 Error: 0.100542 Iteration 3 Error: 0.029931 Align patch 20 5 left Iteration 1 Error: 1.083908 Iteration 2 Error: 0.098378 Iteration 3 Error: 0.029443 Align patch 21 4 left Iteration 1 Error: 1.405421 Iteration 2 Error: 0.210159 Iteration 3 Error: 0.026181 Align patch 22 3 left Iteration 1 Error: 1.645775 Iteration 2 Error: 0.182913 Iteration 3 Error: 0.036000 Align patch 23 2 left Iteration 1 Error: 1.158872 Iteration 2 Error: 0.133278 Iteration 3 Error: 0.026690 Align patch 24 1 left Iteration 1 Error: 0.574613 Iteration 2 Error: 0.098881 Iteration 3 Error: 0.022416 Align patch 25 0 left Iteration 1 Error: 1.284916 Iteration 2 Error: 0.163285 Iteration 3 Error: 0.040937 3D Fitting completed. Patch alignment time: 15.54(sec) Local motion has been corrected. Process thread exits. Computational time: 24.381554 sec Total time: 30.527884 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00002hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00002hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.815968s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00002hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.794041s ........................................ >>>>>>TIME<<<<<< FFT: 0.979462s Defocus_U Defocus_V Angle CCC 11066.41 11937.50 5.62 0.047807 Final Values Defocus_U Defocus_V Angle CCC 11083.60 11942.19 6.25 0.088703 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00002hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00002hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.001e-01 CC threshold: 0.735 Mean Std: 43.72 7.24 Num Hot pixels: 234 Hot pixel threshold: 87.14 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.958632 Iteration 2 Error: 0.199935 Iteration 3 Error: 0.045777 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.24 0.02 ...... Frame ( 3) shift: -0.48 0.04 ...... Frame ( 4) shift: -0.72 0.06 ...... Frame ( 5) shift: -0.96 0.07 ...... Frame ( 6) shift: -1.08 0.10 ...... Frame ( 7) shift: -1.07 0.15 ...... Frame ( 8) shift: -1.07 0.19 ...... Frame ( 9) shift: -1.07 0.25 ...... Frame ( 10) shift: -1.07 0.34 ...... Frame ( 11) shift: -1.08 0.43 ...... Frame ( 12) shift: -1.07 0.49 ...... Frame ( 13) shift: -1.06 0.53 ...... Frame ( 14) shift: -1.05 0.57 ...... Frame ( 15) shift: -1.04 0.64 ...... Frame ( 16) shift: -1.02 0.74 ...... Frame ( 17) shift: -1.01 0.83 ...... Frame ( 18) shift: -0.98 0.91 ...... Frame ( 19) shift: -0.93 0.97 ...... Frame ( 20) shift: -0.89 1.03 ...... Frame ( 21) shift: -0.83 1.09 ...... Frame ( 22) shift: -0.78 1.14 ...... Frame ( 23) shift: -0.72 1.19 ...... Frame ( 24) shift: -0.68 1.27 ...... Frame ( 25) shift: -0.66 1.37 ...... Frame ( 26) shift: -0.64 1.48 ...... Frame ( 27) shift: -0.65 1.54 ...... Frame ( 28) shift: -0.69 1.56 ...... Frame ( 29) shift: -0.73 1.58 ...... Frame ( 30) shift: -0.73 1.61 ...... Frame ( 31) shift: -0.72 1.67 ...... Frame ( 32) shift: -0.70 1.74 ...... Frame ( 33) shift: -0.66 1.79 ...... Frame ( 34) shift: -0.60 1.84 ...... Frame ( 35) shift: -0.55 1.88 ...... Frame ( 36) shift: -0.51 1.90 ...... Frame ( 37) shift: -0.48 1.88 ...... Frame ( 38) shift: -0.45 1.86 ...... Frame ( 39) shift: -0.42 1.84 ...... Frame ( 40) shift: -0.39 1.82 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.913467 Iteration 2 Error: 0.088809 Iteration 3 Error: 0.014888 Align patch 2 23 left Iteration 1 Error: 0.869084 Iteration 2 Error: 0.242345 Iteration 3 Error: 0.071603 Iteration 4 Error: 0.030721 Align patch 3 22 left Iteration 1 Error: 0.712542 Iteration 2 Error: 0.113290 Iteration 3 Error: 0.033124 Align patch 4 21 left Iteration 1 Error: 0.547050 Iteration 2 Error: 0.138812 Iteration 3 Error: 0.029546 Align patch 5 20 left Iteration 1 Error: 0.718080 Iteration 2 Error: 0.159783 Iteration 3 Error: 0.038036 Align patch 6 19 left Iteration 1 Error: 0.640889 Iteration 2 Error: 0.132656 Iteration 3 Error: 0.030942 Align patch 7 18 left Iteration 1 Error: 0.597848 Iteration 2 Error: 0.123910 Iteration 3 Error: 0.028123 Align patch 8 17 left Iteration 1 Error: 0.793303 Iteration 2 Error: 0.161115 Iteration 3 Error: 0.040032 Align patch 9 16 left Iteration 1 Error: 0.643208 Iteration 2 Error: 0.101626 Iteration 3 Error: 0.024764 Align patch 10 15 left Iteration 1 Error: 0.596932 Iteration 2 Error: 0.145394 Iteration 3 Error: 0.029337 Align patch 11 14 left Iteration 1 Error: 0.608581 Iteration 2 Error: 0.089822 Iteration 3 Error: 0.024009 Align patch 12 13 left Iteration 1 Error: 0.984542 Iteration 2 Error: 0.213521 Iteration 3 Error: 0.052550 Iteration 4 Error: 0.017652 Align patch 13 12 left Iteration 1 Error: 0.653767 Iteration 2 Error: 0.158268 Iteration 3 Error: 0.032213 Align patch 14 11 left Iteration 1 Error: 0.539546 Iteration 2 Error: 0.106405 Iteration 3 Error: 0.044719 Align patch 15 10 left Iteration 1 Error: 0.514414 Iteration 2 Error: 0.116351 Iteration 3 Error: 0.035067 Align patch 16 9 left Iteration 1 Error: 0.764130 Iteration 2 Error: 0.114531 Iteration 3 Error: 0.026690 Align patch 17 8 left Iteration 1 Error: 0.728254 Iteration 2 Error: 0.102691 Iteration 3 Error: 0.027947 Align patch 18 7 left Iteration 1 Error: 0.635422 Iteration 2 Error: 0.223476 Iteration 3 Error: 0.098999 Iteration 4 Error: 0.040468 Align patch 19 6 left Iteration 1 Error: 0.621598 Iteration 2 Error: 0.145177 Iteration 3 Error: 0.049967 Align patch 20 5 left Iteration 1 Error: 0.551433 Iteration 2 Error: 0.089909 Iteration 3 Error: 0.019487 Align patch 21 4 left Iteration 1 Error: 0.835823 Iteration 2 Error: 0.149388 Iteration 3 Error: 0.026750 Align patch 22 3 left Iteration 1 Error: 0.511933 Iteration 2 Error: 0.055521 Iteration 3 Error: 0.015000 Align patch 23 2 left Iteration 1 Error: 0.780949 Iteration 2 Error: 0.100632 Iteration 3 Error: 0.032281 Align patch 24 1 left Iteration 1 Error: 0.846312 Iteration 2 Error: 0.140796 Iteration 3 Error: 0.030956 Align patch 25 0 left Iteration 1 Error: 0.688509 Iteration 2 Error: 0.159237 Iteration 3 Error: 0.046344 3D Fitting completed. Patch alignment time: 15.74(sec) Local motion has been corrected. Process thread exits. Computational time: 25.092575 sec Total time: 31.878075 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00002hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00002hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.774068s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00002hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.422125s ........................................ >>>>>>TIME<<<<<< FFT: 1.059370s Defocus_U Defocus_V Angle CCC 9773.45 9171.87 87.81 0.041580 Final Values Defocus_U Defocus_V Angle CCC 9776.54 9171.90 87.81 0.087511 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00003hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00003hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.994e-02 CC threshold: 0.734 Mean Std: 39.56 6.74 Num Hot pixels: 236 Hot pixel threshold: 80.02 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.081746 Iteration 2 Error: 0.500256 Iteration 3 Error: 0.184305 Iteration 4 Error: 0.078375 Iteration 5 Error: 0.032742 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.01 0.08 ...... Frame ( 3) shift: 0.02 0.16 ...... Frame ( 4) shift: 0.03 0.23 ...... Frame ( 5) shift: 0.04 0.31 ...... Frame ( 6) shift: 0.08 0.37 ...... Frame ( 7) shift: 0.15 0.40 ...... Frame ( 8) shift: 0.22 0.44 ...... Frame ( 9) shift: 0.29 0.50 ...... Frame ( 10) shift: 0.34 0.57 ...... Frame ( 11) shift: 0.40 0.65 ...... Frame ( 12) shift: 0.48 0.71 ...... Frame ( 13) shift: 0.60 0.77 ...... Frame ( 14) shift: 0.71 0.83 ...... Frame ( 15) shift: 0.81 0.90 ...... Frame ( 16) shift: 0.88 0.99 ...... Frame ( 17) shift: 0.96 1.08 ...... Frame ( 18) shift: 1.05 1.18 ...... Frame ( 19) shift: 1.15 1.27 ...... Frame ( 20) shift: 1.26 1.36 ...... Frame ( 21) shift: 1.38 1.46 ...... Frame ( 22) shift: 1.51 1.55 ...... Frame ( 23) shift: 1.64 1.64 ...... Frame ( 24) shift: 1.77 1.72 ...... Frame ( 25) shift: 1.89 1.80 ...... Frame ( 26) shift: 2.02 1.88 ...... Frame ( 27) shift: 2.15 2.00 ...... Frame ( 28) shift: 2.28 2.16 ...... Frame ( 29) shift: 2.42 2.33 ...... Frame ( 30) shift: 2.52 2.44 ...... Frame ( 31) shift: 2.57 2.50 ...... Frame ( 32) shift: 2.62 2.56 ...... Frame ( 33) shift: 2.68 2.69 ...... Frame ( 34) shift: 2.76 2.87 ...... Frame ( 35) shift: 2.83 3.06 ...... Frame ( 36) shift: 2.89 3.19 ...... Frame ( 37) shift: 2.95 3.25 ...... Frame ( 38) shift: 3.01 3.31 ...... Frame ( 39) shift: 3.07 3.37 ...... Frame ( 40) shift: 3.13 3.43 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.910457 Iteration 2 Error: 0.204378 Iteration 3 Error: 0.072686 Iteration 4 Error: 0.034415 Align patch 2 23 left Iteration 1 Error: 0.691657 Iteration 2 Error: 0.128384 Iteration 3 Error: 0.061356 Iteration 4 Error: 0.033035 Align patch 3 22 left Iteration 1 Error: 1.531498 Iteration 2 Error: 0.305335 Iteration 3 Error: 0.062737 Iteration 4 Error: 0.021957 Align patch 4 21 left Iteration 1 Error: 1.094514 Iteration 2 Error: 0.265543 Iteration 3 Error: 0.097024 Iteration 4 Error: 0.038424 Align patch 5 20 left Iteration 1 Error: 1.070970 Iteration 2 Error: 0.138962 Iteration 3 Error: 0.055359 Iteration 4 Error: 0.018040 Align patch 6 19 left Iteration 1 Error: 0.882088 Iteration 2 Error: 0.226628 Iteration 3 Error: 0.063143 Iteration 4 Error: 0.023331 Align patch 7 18 left Iteration 1 Error: 0.790503 Iteration 2 Error: 0.424152 Iteration 3 Error: 0.199226 Iteration 4 Error: 0.118968 Iteration 5 Error: 0.054517 Align patch 7 18 left Iteration 1 Error: 0.888297 Iteration 2 Error: 0.141273 Iteration 3 Error: 0.055821 Iteration 4 Error: 0.023297 Align patch 8 17 left Iteration 1 Error: 1.092301 Iteration 2 Error: 0.269293 Iteration 3 Error: 0.088699 Iteration 4 Error: 0.049518 Align patch 9 16 left Iteration 1 Error: 0.904603 Iteration 2 Error: 0.177777 Iteration 3 Error: 0.051296 Iteration 4 Error: 0.016965 Align patch 10 15 left Iteration 1 Error: 0.744044 Iteration 2 Error: 0.101802 Iteration 3 Error: 0.040116 Align patch 11 14 left Iteration 1 Error: 0.816804 Iteration 2 Error: 0.278005 Iteration 3 Error: 0.043740 Align patch 12 13 left Iteration 1 Error: 1.127193 Iteration 2 Error: 0.176774 Iteration 3 Error: 0.079457 Iteration 4 Error: 0.025713 Align patch 13 12 left Iteration 1 Error: 0.803370 Iteration 2 Error: 0.093859 Iteration 3 Error: 0.021680 Align patch 14 11 left Iteration 1 Error: 0.646718 Iteration 2 Error: 0.296798 Iteration 3 Error: 0.135334 Iteration 4 Error: 0.053060 Iteration 5 Error: 0.025272 Align patch 15 10 left Iteration 1 Error: 0.909979 Iteration 2 Error: 0.299098 Iteration 3 Error: 0.127335 Iteration 4 Error: 0.063720 Iteration 5 Error: 0.023441 Align patch 16 9 left Iteration 1 Error: 0.930409 Iteration 2 Error: 0.315297 Iteration 3 Error: 0.088361 Iteration 4 Error: 0.030412 Align patch 17 8 left Iteration 1 Error: 0.932732 Iteration 2 Error: 0.348923 Iteration 3 Error: 0.149355 Iteration 4 Error: 0.096100 Iteration 5 Error: 0.045609 Align patch 18 7 left Iteration 1 Error: 0.914881 Iteration 2 Error: 0.212930 Iteration 3 Error: 0.074529 Iteration 4 Error: 0.032292 Align patch 19 6 left Iteration 1 Error: 0.779988 Iteration 2 Error: 0.213726 Iteration 3 Error: 0.118210 Iteration 4 Error: 0.033912 Align patch 20 5 left Iteration 1 Error: 0.503704 Iteration 2 Error: 0.190532 Iteration 3 Error: 0.063518 Iteration 4 Error: 0.021028 Align patch 21 4 left Iteration 1 Error: 0.830847 Iteration 2 Error: 0.222254 Iteration 3 Error: 0.078112 Iteration 4 Error: 0.020270 Align patch 22 3 left Iteration 1 Error: 1.358187 Iteration 2 Error: 0.264987 Iteration 3 Error: 0.058984 Iteration 4 Error: 0.028204 Align patch 23 2 left Iteration 1 Error: 1.124311 Iteration 2 Error: 0.256737 Iteration 3 Error: 0.073967 Iteration 4 Error: 0.029347 Align patch 24 1 left Iteration 1 Error: 0.868779 Iteration 2 Error: 0.205522 Iteration 3 Error: 0.059169 Iteration 4 Error: 0.026677 Align patch 25 0 left Iteration 1 Error: 1.223051 Iteration 2 Error: 0.227544 Iteration 3 Error: 0.087230 Iteration 4 Error: 0.033263 3D Fitting completed. Patch alignment time: 18.26(sec) Local motion has been corrected. Process thread exits. Computational time: 27.803289 sec Total time: 33.597332 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00003hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00003hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.820471s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00003hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.324205s ........................................ >>>>>>TIME<<<<<< FFT: 1.061705s Defocus_U Defocus_V Angle CCC 12626.95 13373.05 4.16 0.034947 Final Values Defocus_U Defocus_V Angle CCC 12631.76 13415.34 4.16 0.054538 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00003hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00003hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.997e-02 CC threshold: 0.734 Mean Std: 37.45 6.52 Num Hot pixels: 210 Hot pixel threshold: 76.57 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.667814 Iteration 2 Error: 0.438984 Iteration 3 Error: 0.157118 Iteration 4 Error: 0.071097 Iteration 5 Error: 0.025969 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.04 -0.08 ...... Frame ( 3) shift: 0.08 -0.16 ...... Frame ( 4) shift: 0.12 -0.23 ...... Frame ( 5) shift: 0.16 -0.31 ...... Frame ( 6) shift: 0.23 -0.31 ...... Frame ( 7) shift: 0.33 -0.22 ...... Frame ( 8) shift: 0.42 -0.14 ...... Frame ( 9) shift: 0.53 -0.08 ...... Frame ( 10) shift: 0.66 -0.04 ...... Frame ( 11) shift: 0.78 0.00 ...... Frame ( 12) shift: 0.88 0.08 ...... Frame ( 13) shift: 0.97 0.20 ...... Frame ( 14) shift: 1.06 0.32 ...... Frame ( 15) shift: 1.16 0.40 ...... Frame ( 16) shift: 1.27 0.44 ...... Frame ( 17) shift: 1.38 0.48 ...... Frame ( 18) shift: 1.53 0.61 ...... Frame ( 19) shift: 1.71 0.83 ...... Frame ( 20) shift: 1.89 1.04 ...... Frame ( 21) shift: 2.01 1.22 ...... Frame ( 22) shift: 2.06 1.35 ...... Frame ( 23) shift: 2.11 1.48 ...... Frame ( 24) shift: 2.16 1.59 ...... Frame ( 25) shift: 2.19 1.69 ...... Frame ( 26) shift: 2.22 1.80 ...... Frame ( 27) shift: 2.30 1.86 ...... Frame ( 28) shift: 2.43 1.88 ...... Frame ( 29) shift: 2.56 1.91 ...... Frame ( 30) shift: 2.63 1.96 ...... Frame ( 31) shift: 2.66 2.03 ...... Frame ( 32) shift: 2.69 2.10 ...... Frame ( 33) shift: 2.76 2.11 ...... Frame ( 34) shift: 2.87 2.05 ...... Frame ( 35) shift: 2.98 1.98 ...... Frame ( 36) shift: 3.08 1.98 ...... Frame ( 37) shift: 3.17 2.04 ...... Frame ( 38) shift: 3.25 2.10 ...... Frame ( 39) shift: 3.34 2.16 ...... Frame ( 40) shift: 3.42 2.21 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.941920 Iteration 2 Error: 0.333043 Iteration 3 Error: 0.063640 Iteration 4 Error: 0.027666 Align patch 2 23 left Iteration 1 Error: 1.140880 Iteration 2 Error: 0.227062 Iteration 3 Error: 0.079351 Iteration 4 Error: 0.046421 Align patch 3 22 left Iteration 1 Error: 1.305163 Iteration 2 Error: 0.226242 Iteration 3 Error: 0.066539 Iteration 4 Error: 0.020347 Align patch 4 21 left Iteration 1 Error: 0.971666 Iteration 2 Error: 0.230876 Iteration 3 Error: 0.093511 Iteration 4 Error: 0.044244 Align patch 5 20 left Iteration 1 Error: 1.435871 Iteration 2 Error: 0.299302 Iteration 3 Error: 0.110087 Iteration 4 Error: 0.055915 Iteration 5 Error: 0.020586 Align patch 6 19 left Iteration 1 Error: 1.146029 Iteration 2 Error: 0.299782 Iteration 3 Error: 0.094823 Iteration 4 Error: 0.031553 Align patch 7 18 left Iteration 1 Error: 1.208667 Iteration 2 Error: 0.250207 Iteration 3 Error: 0.098776 Iteration 4 Error: 0.043956 Align patch 8 17 left Iteration 1 Error: 0.839949 Iteration 2 Error: 0.210919 Iteration 3 Error: 0.060352 Iteration 4 Error: 0.043921 Align patch 9 16 left Iteration 1 Error: 1.669786 Iteration 2 Error: 0.371242 Iteration 3 Error: 0.142428 Iteration 4 Error: 0.060243 Iteration 5 Error: 0.030452 Align patch 10 15 left Iteration 1 Error: 1.979848 Iteration 2 Error: 0.393447 Iteration 3 Error: 0.103083 Iteration 4 Error: 0.036842 Align patch 11 14 left Iteration 1 Error: 1.506035 Iteration 2 Error: 0.319331 Iteration 3 Error: 0.082968 Iteration 4 Error: 0.030780 Align patch 12 13 left Iteration 1 Error: 0.793906 Iteration 2 Error: 0.212573 Iteration 3 Error: 0.059094 Iteration 4 Error: 0.028526 Align patch 13 12 left Iteration 1 Error: 0.958724 Iteration 2 Error: 0.148713 Iteration 3 Error: 0.042888 Align patch 14 11 left Iteration 1 Error: 0.841652 Iteration 2 Error: 0.255844 Iteration 3 Error: 0.122264 Iteration 4 Error: 0.055811 Iteration 5 Error: 0.021448 Align patch 15 10 left Iteration 1 Error: 1.818933 Iteration 2 Error: 0.382154 Iteration 3 Error: 0.174034 Iteration 4 Error: 0.075369 Iteration 5 Error: 0.042343 Align patch 16 9 left Iteration 1 Error: 1.296350 Iteration 2 Error: 0.304195 Iteration 3 Error: 0.153010 Iteration 4 Error: 0.088231 Iteration 5 Error: 0.047790 Align patch 17 8 left Iteration 1 Error: 1.270573 Iteration 2 Error: 0.299889 Iteration 3 Error: 0.201572 Iteration 4 Error: 0.089995 Iteration 5 Error: 0.059270 Align patch 17 8 left Iteration 1 Error: 0.951687 Iteration 2 Error: 0.151359 Iteration 3 Error: 0.047878 Align patch 18 7 left Iteration 1 Error: 0.904642 Iteration 2 Error: 0.383933 Iteration 3 Error: 0.184380 Iteration 4 Error: 0.114852 Iteration 5 Error: 0.064007 Align patch 18 7 left Iteration 1 Error: 0.768502 Iteration 2 Error: 0.076007 Iteration 3 Error: 0.021150 Align patch 19 6 left Iteration 1 Error: 0.937523 Iteration 2 Error: 0.207980 Iteration 3 Error: 0.056101 Iteration 4 Error: 0.021752 Align patch 20 5 left Iteration 1 Error: 0.735419 Iteration 2 Error: 0.111370 Iteration 3 Error: 0.036144 Align patch 21 4 left Iteration 1 Error: 1.285390 Iteration 2 Error: 0.586385 Iteration 3 Error: 0.262916 Iteration 4 Error: 0.186389 Iteration 5 Error: 0.088344 Align patch 21 4 left Iteration 1 Error: 0.779001 Iteration 2 Error: 0.151732 Iteration 3 Error: 0.045977 Align patch 22 3 left Iteration 1 Error: 2.056662 Iteration 2 Error: 0.457088 Iteration 3 Error: 0.116188 Iteration 4 Error: 0.044346 Align patch 23 2 left Iteration 1 Error: 0.945794 Iteration 2 Error: 0.184611 Iteration 3 Error: 0.056349 Iteration 4 Error: 0.023750 Align patch 24 1 left Iteration 1 Error: 0.548267 Iteration 2 Error: 0.184719 Iteration 3 Error: 0.086775 Iteration 4 Error: 0.040873 Align patch 25 0 left Iteration 1 Error: 0.874879 Iteration 2 Error: 0.332297 Iteration 3 Error: 0.081067 Iteration 4 Error: 0.053352 Iteration 5 Error: 0.019622 3D Fitting completed. Patch alignment time: 20.38(sec) Local motion has been corrected. Process thread exits. Computational time: 30.187677 sec Total time: 35.740414 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00003hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00003hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.765592s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00003hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.503521s ........................................ >>>>>>TIME<<<<<< FFT: 0.952763s Defocus_U Defocus_V Angle CCC 10268.21 9814.23 86.63 0.027484 Final Values Defocus_U Defocus_V Angle CCC 10194.75 9809.66 81.06 0.044414 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00004hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00004hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.319e-01 9.831e-02 CC threshold: 0.722 Mean Std: 39.92 6.89 Num Hot pixels: 202 Hot pixel threshold: 81.23 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.690354 Iteration 2 Error: 0.342435 Iteration 3 Error: 0.102700 Iteration 4 Error: 0.037906 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.18 0.01 ...... Frame ( 3) shift: 0.36 0.02 ...... Frame ( 4) shift: 0.55 0.04 ...... Frame ( 5) shift: 0.73 0.05 ...... Frame ( 6) shift: 0.88 0.08 ...... Frame ( 7) shift: 0.99 0.12 ...... Frame ( 8) shift: 1.10 0.16 ...... Frame ( 9) shift: 1.21 0.21 ...... Frame ( 10) shift: 1.33 0.27 ...... Frame ( 11) shift: 1.45 0.33 ...... Frame ( 12) shift: 1.53 0.39 ...... Frame ( 13) shift: 1.57 0.44 ...... Frame ( 14) shift: 1.62 0.50 ...... Frame ( 15) shift: 1.67 0.56 ...... Frame ( 16) shift: 1.74 0.61 ...... Frame ( 17) shift: 1.80 0.66 ...... Frame ( 18) shift: 1.91 0.70 ...... Frame ( 19) shift: 2.06 0.73 ...... Frame ( 20) shift: 2.21 0.75 ...... Frame ( 21) shift: 2.34 0.80 ...... Frame ( 22) shift: 2.43 0.89 ...... Frame ( 23) shift: 2.53 0.98 ...... Frame ( 24) shift: 2.62 1.01 ...... Frame ( 25) shift: 2.71 0.99 ...... Frame ( 26) shift: 2.80 0.97 ...... Frame ( 27) shift: 2.89 0.98 ...... Frame ( 28) shift: 3.00 1.01 ...... Frame ( 29) shift: 3.11 1.04 ...... Frame ( 30) shift: 3.18 1.04 ...... Frame ( 31) shift: 3.23 1.01 ...... Frame ( 32) shift: 3.28 0.98 ...... Frame ( 33) shift: 3.37 1.00 ...... Frame ( 34) shift: 3.51 1.09 ...... Frame ( 35) shift: 3.64 1.18 ...... Frame ( 36) shift: 3.72 1.25 ...... Frame ( 37) shift: 3.76 1.30 ...... Frame ( 38) shift: 3.80 1.35 ...... Frame ( 39) shift: 3.84 1.40 ...... Frame ( 40) shift: 3.88 1.45 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.222530 Iteration 2 Error: 0.380755 Iteration 3 Error: 0.205768 Iteration 4 Error: 0.101933 Iteration 5 Error: 0.056808 Align patch 1 24 left Iteration 1 Error: 0.882717 Iteration 2 Error: 0.195066 Iteration 3 Error: 0.054148 Iteration 4 Error: 0.022514 Align patch 2 23 left Iteration 1 Error: 0.775517 Iteration 2 Error: 0.220156 Iteration 3 Error: 0.064206 Iteration 4 Error: 0.025876 Align patch 3 22 left Iteration 1 Error: 0.835331 Iteration 2 Error: 0.215838 Iteration 3 Error: 0.066313 Iteration 4 Error: 0.033631 Align patch 4 21 left Iteration 1 Error: 0.787078 Iteration 2 Error: 0.150757 Iteration 3 Error: 0.022236 Align patch 5 20 left Iteration 1 Error: 1.768677 Iteration 2 Error: 0.269343 Iteration 3 Error: 0.052814 Iteration 4 Error: 0.015896 Align patch 6 19 left Iteration 1 Error: 0.933005 Iteration 2 Error: 0.706474 Iteration 3 Error: 0.331261 Iteration 4 Error: 0.231605 Iteration 5 Error: 0.107360 Align patch 6 19 left Iteration 1 Error: 0.987264 Iteration 2 Error: 0.159884 Iteration 3 Error: 0.037856 Align patch 7 18 left Iteration 1 Error: 0.812502 Iteration 2 Error: 0.198424 Iteration 3 Error: 0.050550 Iteration 4 Error: 0.017391 Align patch 8 17 left Iteration 1 Error: 0.751456 Iteration 2 Error: 0.209027 Iteration 3 Error: 0.057312 Iteration 4 Error: 0.034688 Align patch 9 16 left Iteration 1 Error: 0.809643 Iteration 2 Error: 0.152256 Iteration 3 Error: 0.038915 Align patch 10 15 left Iteration 1 Error: 0.948134 Iteration 2 Error: 0.133327 Iteration 3 Error: 0.040278 Align patch 11 14 left Iteration 1 Error: 0.837167 Iteration 2 Error: 0.186098 Iteration 3 Error: 0.038284 Align patch 12 13 left Iteration 1 Error: 1.961082 Iteration 2 Error: 0.336405 Iteration 3 Error: 0.084199 Iteration 4 Error: 0.021439 Align patch 13 12 left Iteration 1 Error: 0.573656 Iteration 2 Error: 0.127704 Iteration 3 Error: 0.032652 Align patch 14 11 left Iteration 1 Error: 0.817193 Iteration 2 Error: 0.146917 Iteration 3 Error: 0.032044 Align patch 15 10 left Iteration 1 Error: 0.752194 Iteration 2 Error: 0.174267 Iteration 3 Error: 0.046221 Align patch 16 9 left Iteration 1 Error: 1.381223 Iteration 2 Error: 0.251533 Iteration 3 Error: 0.078824 Iteration 4 Error: 0.034705 Align patch 17 8 left Iteration 1 Error: 1.291804 Iteration 2 Error: 0.295743 Iteration 3 Error: 0.090231 Iteration 4 Error: 0.024211 Align patch 18 7 left Iteration 1 Error: 0.687350 Iteration 2 Error: 0.191578 Iteration 3 Error: 0.061422 Iteration 4 Error: 0.025715 Align patch 19 6 left Iteration 1 Error: 1.082210 Iteration 2 Error: 0.260615 Iteration 3 Error: 0.067025 Iteration 4 Error: 0.031407 Align patch 20 5 left Iteration 1 Error: 0.774717 Iteration 2 Error: 0.245757 Iteration 3 Error: 0.070255 Iteration 4 Error: 0.021796 Align patch 21 4 left Iteration 1 Error: 0.633413 Iteration 2 Error: 0.163813 Iteration 3 Error: 0.052496 Iteration 4 Error: 0.020887 Align patch 22 3 left Iteration 1 Error: 1.143369 Iteration 2 Error: 0.209711 Iteration 3 Error: 0.050630 Iteration 4 Error: 0.018576 Align patch 23 2 left Iteration 1 Error: 0.711773 Iteration 2 Error: 0.148735 Iteration 3 Error: 0.054188 Iteration 4 Error: 0.019536 Align patch 24 1 left Iteration 1 Error: 1.040668 Iteration 2 Error: 0.157825 Iteration 3 Error: 0.065019 Iteration 4 Error: 0.022594 Align patch 25 0 left Iteration 1 Error: 0.597937 Iteration 2 Error: 0.093591 Iteration 3 Error: 0.040495 3D Fitting completed. Patch alignment time: 17.73(sec) Local motion has been corrected. Process thread exits. Computational time: 25.801104 sec Total time: 31.710920 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00004hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00004hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.556274s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00004hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.501120s ........................................ >>>>>>TIME<<<<<< FFT: 0.913417s Defocus_U Defocus_V Angle CCC 9511.98 9027.46 89.76 -0.044735 Final Values Defocus_U Defocus_V Angle CCC 9530.74 9033.72 89.44 -0.228424 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00004hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00004hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.292e-01 9.651e-02 CC threshold: 0.708 Mean Std: 34.32 6.61 Num Hot pixels: 184 Hot pixel threshold: 74.00 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.338084 Iteration 2 Error: 0.189476 Iteration 3 Error: 0.049311 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.19 0.09 ...... Frame ( 3) shift: 0.38 0.17 ...... Frame ( 4) shift: 0.57 0.26 ...... Frame ( 5) shift: 0.75 0.34 ...... Frame ( 6) shift: 0.90 0.39 ...... Frame ( 7) shift: 0.99 0.38 ...... Frame ( 8) shift: 1.09 0.38 ...... Frame ( 9) shift: 1.14 0.39 ...... Frame ( 10) shift: 1.14 0.40 ...... Frame ( 11) shift: 1.14 0.42 ...... Frame ( 12) shift: 1.17 0.46 ...... Frame ( 13) shift: 1.21 0.52 ...... Frame ( 14) shift: 1.26 0.57 ...... Frame ( 15) shift: 1.31 0.60 ...... Frame ( 16) shift: 1.36 0.59 ...... Frame ( 17) shift: 1.40 0.58 ...... Frame ( 18) shift: 1.43 0.56 ...... Frame ( 19) shift: 1.43 0.54 ...... Frame ( 20) shift: 1.44 0.51 ...... Frame ( 21) shift: 1.48 0.53 ...... Frame ( 22) shift: 1.57 0.58 ...... Frame ( 23) shift: 1.66 0.64 ...... Frame ( 24) shift: 1.76 0.66 ...... Frame ( 25) shift: 1.87 0.66 ...... Frame ( 26) shift: 1.99 0.66 ...... Frame ( 27) shift: 2.09 0.64 ...... Frame ( 28) shift: 2.18 0.61 ...... Frame ( 29) shift: 2.28 0.58 ...... Frame ( 30) shift: 2.38 0.59 ...... Frame ( 31) shift: 2.49 0.64 ...... Frame ( 32) shift: 2.59 0.69 ...... Frame ( 33) shift: 2.69 0.69 ...... Frame ( 34) shift: 2.78 0.62 ...... Frame ( 35) shift: 2.86 0.56 ...... Frame ( 36) shift: 2.94 0.52 ...... Frame ( 37) shift: 3.02 0.51 ...... Frame ( 38) shift: 3.09 0.50 ...... Frame ( 39) shift: 3.17 0.49 ...... Frame ( 40) shift: 3.25 0.47 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.898014 Iteration 2 Error: 0.164317 Iteration 3 Error: 0.030725 Align patch 2 23 left Iteration 1 Error: 0.723859 Iteration 2 Error: 0.137657 Iteration 3 Error: 0.030301 Align patch 3 22 left Iteration 1 Error: 0.621306 Iteration 2 Error: 0.105889 Iteration 3 Error: 0.031756 Align patch 4 21 left Iteration 1 Error: 0.853091 Iteration 2 Error: 0.162728 Iteration 3 Error: 0.027005 Align patch 5 20 left Iteration 1 Error: 1.185882 Iteration 2 Error: 0.235427 Iteration 3 Error: 0.040074 Align patch 6 19 left Iteration 1 Error: 1.006337 Iteration 2 Error: 0.185678 Iteration 3 Error: 0.059831 Iteration 4 Error: 0.016638 Align patch 7 18 left Iteration 1 Error: 0.543619 Iteration 2 Error: 0.121873 Iteration 3 Error: 0.045641 Align patch 8 17 left Iteration 1 Error: 0.722969 Iteration 2 Error: 0.212614 Iteration 3 Error: 0.046194 Align patch 9 16 left Iteration 1 Error: 0.943052 Iteration 2 Error: 0.166576 Iteration 3 Error: 0.037268 Align patch 10 15 left Iteration 1 Error: 0.877239 Iteration 2 Error: 0.181240 Iteration 3 Error: 0.059345 Iteration 4 Error: 0.017751 Align patch 11 14 left Iteration 1 Error: 0.631300 Iteration 2 Error: 0.138630 Iteration 3 Error: 0.053378 Iteration 4 Error: 0.014585 Align patch 12 13 left Iteration 1 Error: 0.880654 Iteration 2 Error: 0.149093 Iteration 3 Error: 0.034559 Align patch 13 12 left Iteration 1 Error: 0.594327 Iteration 2 Error: 0.099052 Iteration 3 Error: 0.018151 Align patch 14 11 left Iteration 1 Error: 0.597426 Iteration 2 Error: 0.069780 Iteration 3 Error: 0.014910 Align patch 15 10 left Iteration 1 Error: 1.095863 Iteration 2 Error: 0.108197 Iteration 3 Error: 0.036805 Align patch 16 9 left Iteration 1 Error: 0.661453 Iteration 2 Error: 0.160556 Iteration 3 Error: 0.031571 Align patch 17 8 left Iteration 1 Error: 0.763353 Iteration 2 Error: 0.100976 Iteration 3 Error: 0.034509 Align patch 18 7 left Iteration 1 Error: 0.784817 Iteration 2 Error: 0.154516 Iteration 3 Error: 0.030844 Align patch 19 6 left Iteration 1 Error: 0.448557 Iteration 2 Error: 0.106866 Iteration 3 Error: 0.022559 Align patch 20 5 left Iteration 1 Error: 0.834440 Iteration 2 Error: 0.130344 Iteration 3 Error: 0.023938 Align patch 21 4 left Iteration 1 Error: 0.577146 Iteration 2 Error: 0.118571 Iteration 3 Error: 0.024408 Align patch 22 3 left Iteration 1 Error: 0.762779 Iteration 2 Error: 0.101074 Iteration 3 Error: 0.024289 Align patch 23 2 left Iteration 1 Error: 0.725004 Iteration 2 Error: 0.110419 Iteration 3 Error: 0.028408 Align patch 24 1 left Iteration 1 Error: 0.781413 Iteration 2 Error: 0.109600 Iteration 3 Error: 0.028600 Align patch 25 0 left Iteration 1 Error: 0.787968 Iteration 2 Error: 0.123048 Iteration 3 Error: 0.036414 3D Fitting completed. Patch alignment time: 14.94(sec) Local motion has been corrected. Process thread exits. Computational time: 23.420403 sec Total time: 30.203279 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00004hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00004hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.823346s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00004hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.494524s ........................................ >>>>>>TIME<<<<<< FFT: 0.945502s Defocus_U Defocus_V Angle CCC 11433.90 12992.72 2.39 -0.065413 Final Values Defocus_U Defocus_V Angle CCC 11299.91 13108.94 3.96 -0.295101 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00004hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00004hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.341e-01 9.975e-02 CC threshold: 0.733 Mean Std: 40.06 6.77 Num Hot pixels: 217 Hot pixel threshold: 80.68 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 7.619588 Iteration 2 Error: 2.142457 Iteration 3 Error: 0.564756 Iteration 4 Error: 0.214053 Iteration 5 Error: 0.105429 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.51 -0.96 ...... Frame ( 3) shift: 1.02 -1.92 ...... Frame ( 4) shift: 1.53 -2.88 ...... Frame ( 5) shift: 2.04 -3.84 ...... Frame ( 6) shift: 2.52 -4.66 ...... Frame ( 7) shift: 2.96 -5.36 ...... Frame ( 8) shift: 3.41 -6.06 ...... Frame ( 9) shift: 3.82 -6.59 ...... Frame ( 10) shift: 4.19 -6.95 ...... Frame ( 11) shift: 4.56 -7.31 ...... Frame ( 12) shift: 4.88 -7.67 ...... Frame ( 13) shift: 5.13 -8.03 ...... Frame ( 14) shift: 5.38 -8.39 ...... Frame ( 15) shift: 5.53 -8.65 ...... Frame ( 16) shift: 5.58 -8.80 ...... Frame ( 17) shift: 5.63 -8.96 ...... Frame ( 18) shift: 5.74 -9.12 ...... Frame ( 19) shift: 5.92 -9.29 ...... Frame ( 20) shift: 6.10 -9.46 ...... Frame ( 21) shift: 6.25 -9.61 ...... Frame ( 22) shift: 6.36 -9.74 ...... Frame ( 23) shift: 6.47 -9.86 ...... Frame ( 24) shift: 6.60 -9.95 ...... Frame ( 25) shift: 6.76 -10.01 ...... Frame ( 26) shift: 6.91 -10.07 ...... Frame ( 27) shift: 7.05 -10.12 ...... Frame ( 28) shift: 7.18 -10.17 ...... Frame ( 29) shift: 7.30 -10.21 ...... Frame ( 30) shift: 7.44 -10.27 ...... Frame ( 31) shift: 7.59 -10.32 ...... Frame ( 32) shift: 7.74 -10.38 ...... Frame ( 33) shift: 7.85 -10.43 ...... Frame ( 34) shift: 7.91 -10.49 ...... Frame ( 35) shift: 7.98 -10.54 ...... Frame ( 36) shift: 8.06 -10.56 ...... Frame ( 37) shift: 8.17 -10.57 ...... Frame ( 38) shift: 8.28 -10.57 ...... Frame ( 39) shift: 8.39 -10.57 ...... Frame ( 40) shift: 8.50 -10.57 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.416656 Iteration 2 Error: 0.301070 Iteration 3 Error: 0.085657 Iteration 4 Error: 0.052697 Iteration 5 Error: 0.024003 Align patch 2 23 left Iteration 1 Error: 1.787154 Iteration 2 Error: 0.334691 Iteration 3 Error: 0.096327 Iteration 4 Error: 0.026733 Align patch 3 22 left Iteration 1 Error: 2.704109 Iteration 2 Error: 0.467047 Iteration 3 Error: 0.113076 Iteration 4 Error: 0.058066 Iteration 5 Error: 0.021677 Align patch 4 21 left Iteration 1 Error: 5.132859 Iteration 2 Error: 1.034762 Iteration 3 Error: 0.416297 Iteration 4 Error: 0.173238 Iteration 5 Error: 0.083739 Align patch 4 21 left Iteration 1 Error: 3.536557 Iteration 2 Error: 0.380556 Iteration 3 Error: 0.061915 Iteration 4 Error: 0.019658 Align patch 5 20 left Iteration 1 Error: 6.321910 Iteration 2 Error: 0.935373 Iteration 3 Error: 0.266331 Iteration 4 Error: 0.083068 Iteration 5 Error: 0.024586 Align patch 6 19 left Iteration 1 Error: 2.266832 Iteration 2 Error: 0.554367 Iteration 3 Error: 0.135960 Iteration 4 Error: 0.070991 Iteration 5 Error: 0.032683 Align patch 7 18 left Iteration 1 Error: 0.914025 Iteration 2 Error: 0.242017 Iteration 3 Error: 0.135389 Iteration 4 Error: 0.067393 Iteration 5 Error: 0.034326 Align patch 8 17 left Iteration 1 Error: 1.565123 Iteration 2 Error: 0.217147 Iteration 3 Error: 0.049852 Align patch 9 16 left Iteration 1 Error: 2.651062 Iteration 2 Error: 0.429098 Iteration 3 Error: 0.159529 Iteration 4 Error: 0.043355 Align patch 10 15 left Iteration 1 Error: 5.019351 Iteration 2 Error: 0.709712 Iteration 3 Error: 0.271539 Iteration 4 Error: 0.110405 Iteration 5 Error: 0.050263 Align patch 10 15 left Iteration 1 Error: 4.141878 Iteration 2 Error: 0.333779 Iteration 3 Error: 0.066629 Iteration 4 Error: 0.023614 Align patch 11 14 left Iteration 1 Error: 3.733321 Iteration 2 Error: 0.822251 Iteration 3 Error: 0.397985 Iteration 4 Error: 0.157337 Iteration 5 Error: 0.080417 Align patch 11 14 left Iteration 1 Error: 3.082762 Iteration 2 Error: 0.449075 Iteration 3 Error: 0.105225 Iteration 4 Error: 0.028112 Align patch 12 13 left Iteration 1 Error: 2.759210 Iteration 2 Error: 0.463583 Iteration 3 Error: 0.149362 Iteration 4 Error: 0.079242 Iteration 5 Error: 0.036615 Align patch 13 12 left Iteration 1 Error: 1.228086 Iteration 2 Error: 0.427717 Iteration 3 Error: 0.111624 Iteration 4 Error: 0.179604 Iteration 5 Error: 0.061315 Align patch 13 12 left Iteration 1 Error: 1.083702 Iteration 2 Error: 0.109325 Iteration 3 Error: 0.026336 Align patch 14 11 left Iteration 1 Error: 1.882092 Iteration 2 Error: 0.408893 Iteration 3 Error: 0.203585 Iteration 4 Error: 0.118049 Iteration 5 Error: 0.097087 Align patch 14 11 left Iteration 1 Error: 1.425695 Iteration 2 Error: 0.195660 Iteration 3 Error: 0.053380 Iteration 4 Error: 0.014595 Align patch 15 10 left Iteration 1 Error: 3.719162 Iteration 2 Error: 0.685669 Iteration 3 Error: 0.293391 Iteration 4 Error: 0.092201 Iteration 5 Error: 0.033724 Align patch 16 9 left Iteration 1 Error: 3.086467 Iteration 2 Error: 0.837464 Iteration 3 Error: 0.451148 Iteration 4 Error: 0.256484 Iteration 5 Error: 0.129802 Align patch 16 9 left Iteration 1 Error: 3.019204 Iteration 2 Error: 0.441162 Iteration 3 Error: 0.103821 Iteration 4 Error: 0.028536 Align patch 17 8 left Iteration 1 Error: 2.075495 Iteration 2 Error: 0.555403 Iteration 3 Error: 0.127650 Iteration 4 Error: 0.046902 Align patch 18 7 left Iteration 1 Error: 1.232458 Iteration 2 Error: 0.309502 Iteration 3 Error: 0.098375 Iteration 4 Error: 0.035166 Align patch 19 6 left Iteration 1 Error: 0.877526 Iteration 2 Error: 0.232363 Iteration 3 Error: 0.100382 Iteration 4 Error: 0.047811 Align patch 20 5 left Iteration 1 Error: 2.639735 Iteration 2 Error: 0.666764 Iteration 3 Error: 0.208861 Iteration 4 Error: 0.081443 Iteration 5 Error: 0.027665 Align patch 21 4 left Iteration 1 Error: 2.401290 Iteration 2 Error: 0.458270 Iteration 3 Error: 0.111117 Iteration 4 Error: 0.038204 Align patch 22 3 left Iteration 1 Error: 1.854384 Iteration 2 Error: 0.361110 Iteration 3 Error: 0.113100 Iteration 4 Error: 0.027000 Align patch 23 2 left Iteration 1 Error: 1.331834 Iteration 2 Error: 0.329895 Iteration 3 Error: 0.140046 Iteration 4 Error: 0.061922 Iteration 5 Error: 0.029145 Align patch 24 1 left Iteration 1 Error: 0.797077 Iteration 2 Error: 0.237923 Iteration 3 Error: 0.057986 Iteration 4 Error: 0.026732 Align patch 25 0 left Iteration 1 Error: 2.600514 Iteration 2 Error: 0.463112 Iteration 3 Error: 0.153627 Iteration 4 Error: 0.053670 Iteration 5 Error: 0.032574 3D Fitting completed. Patch alignment time: 22.65(sec) Local motion has been corrected. Process thread exits. Computational time: 31.373888 sec Total time: 38.521217 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00004hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00004hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.565448s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00004hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.253825s ........................................ >>>>>>TIME<<<<<< FFT: 0.925915s Defocus_U Defocus_V Angle CCC 14402.35 13726.57 83.42 0.041099 Final Values Defocus_U Defocus_V Angle CCC 14414.86 13723.45 83.73 0.030468 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00005hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00005hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.001e-01 CC threshold: 0.735 Mean Std: 39.00 6.66 Num Hot pixels: 201 Hot pixel threshold: 78.97 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.139337 Iteration 2 Error: 0.280667 Iteration 3 Error: 0.087700 Iteration 4 Error: 0.034018 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.06 0.12 ...... Frame ( 3) shift: 0.12 0.24 ...... Frame ( 4) shift: 0.19 0.37 ...... Frame ( 5) shift: 0.25 0.49 ...... Frame ( 6) shift: 0.36 0.59 ...... Frame ( 7) shift: 0.53 0.68 ...... Frame ( 8) shift: 0.69 0.76 ...... Frame ( 9) shift: 0.75 0.81 ...... Frame ( 10) shift: 0.69 0.80 ...... Frame ( 11) shift: 0.63 0.80 ...... Frame ( 12) shift: 0.63 0.84 ...... Frame ( 13) shift: 0.69 0.92 ...... Frame ( 14) shift: 0.75 1.01 ...... Frame ( 15) shift: 0.80 1.07 ...... Frame ( 16) shift: 0.86 1.12 ...... Frame ( 17) shift: 0.91 1.17 ...... Frame ( 18) shift: 0.95 1.19 ...... Frame ( 19) shift: 0.97 1.18 ...... Frame ( 20) shift: 1.00 1.17 ...... Frame ( 21) shift: 1.08 1.17 ...... Frame ( 22) shift: 1.20 1.18 ...... Frame ( 23) shift: 1.33 1.19 ...... Frame ( 24) shift: 1.44 1.24 ...... Frame ( 25) shift: 1.53 1.32 ...... Frame ( 26) shift: 1.62 1.41 ...... Frame ( 27) shift: 1.67 1.46 ...... Frame ( 28) shift: 1.66 1.48 ...... Frame ( 29) shift: 1.65 1.49 ...... Frame ( 30) shift: 1.66 1.55 ...... Frame ( 31) shift: 1.69 1.65 ...... Frame ( 32) shift: 1.71 1.75 ...... Frame ( 33) shift: 1.78 1.82 ...... Frame ( 34) shift: 1.90 1.87 ...... Frame ( 35) shift: 2.02 1.92 ...... Frame ( 36) shift: 2.10 1.97 ...... Frame ( 37) shift: 2.14 2.02 ...... Frame ( 38) shift: 2.18 2.06 ...... Frame ( 39) shift: 2.21 2.11 ...... Frame ( 40) shift: 2.25 2.16 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.824211 Iteration 2 Error: 0.205171 Iteration 3 Error: 0.030699 Align patch 2 23 left Iteration 1 Error: 0.622539 Iteration 2 Error: 0.215041 Iteration 3 Error: 0.044197 Align patch 3 22 left Iteration 1 Error: 0.913968 Iteration 2 Error: 0.208545 Iteration 3 Error: 0.083626 Iteration 4 Error: 0.039391 Align patch 4 21 left Iteration 1 Error: 0.805235 Iteration 2 Error: 0.194299 Iteration 3 Error: 0.047955 Align patch 5 20 left Iteration 1 Error: 0.951574 Iteration 2 Error: 0.219686 Iteration 3 Error: 0.053644 Iteration 4 Error: 0.019024 Align patch 6 19 left Iteration 1 Error: 0.901080 Iteration 2 Error: 0.281828 Iteration 3 Error: 0.094825 Iteration 4 Error: 0.058465 Iteration 5 Error: 0.030361 Align patch 7 18 left Iteration 1 Error: 0.861065 Iteration 2 Error: 0.303043 Iteration 3 Error: 0.135728 Iteration 4 Error: 0.049336 Align patch 8 17 left Iteration 1 Error: 0.832477 Iteration 2 Error: 0.162280 Iteration 3 Error: 0.033235 Align patch 9 16 left Iteration 1 Error: 0.663913 Iteration 2 Error: 0.122545 Iteration 3 Error: 0.039226 Align patch 10 15 left Iteration 1 Error: 0.862461 Iteration 2 Error: 0.191465 Iteration 3 Error: 0.042706 Align patch 11 14 left Iteration 1 Error: 0.944916 Iteration 2 Error: 0.409327 Iteration 3 Error: 0.184981 Iteration 4 Error: 0.107398 Iteration 5 Error: 0.083597 Align patch 11 14 left Iteration 1 Error: 0.892831 Iteration 2 Error: 0.186564 Iteration 3 Error: 0.078590 Iteration 4 Error: 0.034065 Align patch 12 13 left Iteration 1 Error: 0.947436 Iteration 2 Error: 0.257250 Iteration 3 Error: 0.075875 Iteration 4 Error: 0.039751 Align patch 13 12 left Iteration 1 Error: 0.835786 Iteration 2 Error: 0.169831 Iteration 3 Error: 0.050705 Iteration 4 Error: 0.016777 Align patch 14 11 left Iteration 1 Error: 0.839956 Iteration 2 Error: 0.129854 Iteration 3 Error: 0.047619 Align patch 15 10 left Iteration 1 Error: 0.892907 Iteration 2 Error: 0.119901 Iteration 3 Error: 0.058326 Iteration 4 Error: 0.015306 Align patch 16 9 left Iteration 1 Error: 1.053608 Iteration 2 Error: 0.362465 Iteration 3 Error: 0.157963 Iteration 4 Error: 0.061108 Iteration 5 Error: 0.029724 Align patch 17 8 left Iteration 1 Error: 0.851157 Iteration 2 Error: 0.206871 Iteration 3 Error: 0.058004 Iteration 4 Error: 0.037698 Align patch 18 7 left Iteration 1 Error: 1.225093 Iteration 2 Error: 0.186807 Iteration 3 Error: 0.038415 Align patch 19 6 left Iteration 1 Error: 0.566162 Iteration 2 Error: 0.192658 Iteration 3 Error: 0.064348 Iteration 4 Error: 0.022874 Align patch 20 5 left Iteration 1 Error: 0.582250 Iteration 2 Error: 0.120910 Iteration 3 Error: 0.029807 Align patch 21 4 left Iteration 1 Error: 0.976541 Iteration 2 Error: 0.636875 Iteration 3 Error: 0.270933 Iteration 4 Error: 0.154009 Iteration 5 Error: 0.068811 Align patch 21 4 left Iteration 1 Error: 0.878979 Iteration 2 Error: 0.253259 Iteration 3 Error: 0.091400 Iteration 4 Error: 0.024128 Align patch 22 3 left Iteration 1 Error: 0.894094 Iteration 2 Error: 0.262605 Iteration 3 Error: 0.055376 Iteration 4 Error: 0.020553 Align patch 23 2 left Iteration 1 Error: 1.163973 Iteration 2 Error: 0.488966 Iteration 3 Error: 0.174879 Iteration 4 Error: 0.113833 Iteration 5 Error: 0.052299 Align patch 23 2 left Iteration 1 Error: 0.774531 Iteration 2 Error: 0.134671 Iteration 3 Error: 0.049925 Align patch 24 1 left Iteration 1 Error: 0.802059 Iteration 2 Error: 0.201243 Iteration 3 Error: 0.055255 Iteration 4 Error: 0.019096 Align patch 25 0 left Iteration 1 Error: 0.702674 Iteration 2 Error: 0.139479 Iteration 3 Error: 0.041698 3D Fitting completed. Patch alignment time: 18.65(sec) Local motion has been corrected. Process thread exits. Computational time: 28.163015 sec Total time: 34.084412 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00005hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00005hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.760596s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00005hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.188068s ........................................ >>>>>>TIME<<<<<< FFT: 1.063055s Defocus_U Defocus_V Angle CCC 8859.40 9628.97 15.50 0.025028 Final Values Defocus_U Defocus_V Angle CCC 8871.88 9685.24 15.50 0.048158 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00005hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00005hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.001e-01 CC threshold: 0.736 Mean Std: 41.92 6.99 Num Hot pixels: 215 Hot pixel threshold: 83.87 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.432482 Iteration 2 Error: 0.070643 Iteration 3 Error: 0.019514 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.06 -0.00 ...... Frame ( 3) shift: -0.12 -0.01 ...... Frame ( 4) shift: -0.19 -0.01 ...... Frame ( 5) shift: -0.25 -0.01 ...... Frame ( 6) shift: -0.26 0.01 ...... Frame ( 7) shift: -0.23 0.04 ...... Frame ( 8) shift: -0.20 0.08 ...... Frame ( 9) shift: -0.19 0.12 ...... Frame ( 10) shift: -0.21 0.14 ...... Frame ( 11) shift: -0.23 0.17 ...... Frame ( 12) shift: -0.24 0.19 ...... Frame ( 13) shift: -0.24 0.20 ...... Frame ( 14) shift: -0.24 0.21 ...... Frame ( 15) shift: -0.21 0.23 ...... Frame ( 16) shift: -0.15 0.28 ...... Frame ( 17) shift: -0.09 0.32 ...... Frame ( 18) shift: -0.04 0.38 ...... Frame ( 19) shift: 0.01 0.44 ...... Frame ( 20) shift: 0.06 0.51 ...... Frame ( 21) shift: 0.07 0.55 ...... Frame ( 22) shift: 0.06 0.56 ...... Frame ( 23) shift: 0.05 0.57 ...... Frame ( 24) shift: 0.06 0.61 ...... Frame ( 25) shift: 0.09 0.66 ...... Frame ( 26) shift: 0.12 0.72 ...... Frame ( 27) shift: 0.12 0.76 ...... Frame ( 28) shift: 0.10 0.77 ...... Frame ( 29) shift: 0.07 0.78 ...... Frame ( 30) shift: 0.06 0.77 ...... Frame ( 31) shift: 0.06 0.72 ...... Frame ( 32) shift: 0.07 0.67 ...... Frame ( 33) shift: 0.10 0.65 ...... Frame ( 34) shift: 0.16 0.66 ...... Frame ( 35) shift: 0.22 0.66 ...... Frame ( 36) shift: 0.24 0.69 ...... Frame ( 37) shift: 0.22 0.73 ...... Frame ( 38) shift: 0.21 0.77 ...... Frame ( 39) shift: 0.19 0.81 ...... Frame ( 40) shift: 0.17 0.85 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.797544 Iteration 2 Error: 0.145118 Iteration 3 Error: 0.032448 Align patch 2 23 left Iteration 1 Error: 0.439182 Iteration 2 Error: 0.063796 Iteration 3 Error: 0.017072 Align patch 3 22 left Iteration 1 Error: 0.744213 Iteration 2 Error: 0.150075 Iteration 3 Error: 0.023896 Align patch 4 21 left Iteration 1 Error: 0.705966 Iteration 2 Error: 0.119206 Iteration 3 Error: 0.019803 Align patch 5 20 left Iteration 1 Error: 0.570386 Iteration 2 Error: 0.051831 Iteration 3 Error: 0.009557 Align patch 6 19 left Iteration 1 Error: 0.932103 Iteration 2 Error: 0.150597 Iteration 3 Error: 0.025952 Align patch 7 18 left Iteration 1 Error: 0.435232 Iteration 2 Error: 0.058014 Iteration 3 Error: 0.012889 Align patch 8 17 left Iteration 1 Error: 0.558832 Iteration 2 Error: 0.109620 Iteration 3 Error: 0.033614 Align patch 9 16 left Iteration 1 Error: 0.622665 Iteration 2 Error: 0.086228 Iteration 3 Error: 0.017233 Align patch 10 15 left Iteration 1 Error: 0.752458 Iteration 2 Error: 0.071581 Iteration 3 Error: 0.013985 Align patch 11 14 left Iteration 1 Error: 0.695595 Iteration 2 Error: 0.132589 Iteration 3 Error: 0.034637 Align patch 12 13 left Iteration 1 Error: 0.765302 Iteration 2 Error: 0.147534 Iteration 3 Error: 0.026362 Align patch 13 12 left Iteration 1 Error: 0.995957 Iteration 2 Error: 0.142444 Iteration 3 Error: 0.050472 Iteration 4 Error: 0.014732 Align patch 14 11 left Iteration 1 Error: 0.603673 Iteration 2 Error: 0.081020 Iteration 3 Error: 0.023787 Align patch 15 10 left Iteration 1 Error: 0.746334 Iteration 2 Error: 0.095317 Iteration 3 Error: 0.015157 Align patch 16 9 left Iteration 1 Error: 0.636819 Iteration 2 Error: 0.131432 Iteration 3 Error: 0.026232 Align patch 17 8 left Iteration 1 Error: 0.741324 Iteration 2 Error: 0.100638 Iteration 3 Error: 0.019614 Align patch 18 7 left Iteration 1 Error: 0.736455 Iteration 2 Error: 0.092935 Iteration 3 Error: 0.027063 Align patch 19 6 left Iteration 1 Error: 0.601401 Iteration 2 Error: 0.077926 Iteration 3 Error: 0.019803 Align patch 20 5 left Iteration 1 Error: 0.690321 Iteration 2 Error: 0.136005 Iteration 3 Error: 0.033618 Align patch 21 4 left Iteration 1 Error: 0.622324 Iteration 2 Error: 0.106608 Iteration 3 Error: 0.029376 Align patch 22 3 left Iteration 1 Error: 0.804323 Iteration 2 Error: 0.139242 Iteration 3 Error: 0.057243 Iteration 4 Error: 0.014083 Align patch 23 2 left Iteration 1 Error: 0.665671 Iteration 2 Error: 0.129537 Iteration 3 Error: 0.028935 Align patch 24 1 left Iteration 1 Error: 0.766943 Iteration 2 Error: 0.115777 Iteration 3 Error: 0.026879 Align patch 25 0 left Iteration 1 Error: 0.615376 Iteration 2 Error: 0.113671 Iteration 3 Error: 0.035624 3D Fitting completed. Patch alignment time: 15.49(sec) Local motion has been corrected. Process thread exits. Computational time: 23.745403 sec Total time: 29.402893 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00005hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00005hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.546294s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00005hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.491191s ........................................ >>>>>>TIME<<<<<< FFT: 0.930338s Defocus_U Defocus_V Angle CCC 12388.70 11861.35 89.24 0.041406 Final Values Defocus_U Defocus_V Angle CCC 11870.73 12379.32 0.18 0.073124 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00005hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00005hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 39.95 6.90 Num Hot pixels: 194 Hot pixel threshold: 81.33 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.679543 Iteration 2 Error: 0.067526 Iteration 3 Error: 0.010820 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.15 0.06 ...... Frame ( 3) shift: -0.31 0.12 ...... Frame ( 4) shift: -0.46 0.17 ...... Frame ( 5) shift: -0.62 0.23 ...... Frame ( 6) shift: -0.71 0.28 ...... Frame ( 7) shift: -0.75 0.31 ...... Frame ( 8) shift: -0.79 0.34 ...... Frame ( 9) shift: -0.80 0.36 ...... Frame ( 10) shift: -0.78 0.35 ...... Frame ( 11) shift: -0.76 0.35 ...... Frame ( 12) shift: -0.75 0.36 ...... Frame ( 13) shift: -0.75 0.39 ...... Frame ( 14) shift: -0.74 0.42 ...... Frame ( 15) shift: -0.77 0.46 ...... Frame ( 16) shift: -0.81 0.52 ...... Frame ( 17) shift: -0.85 0.58 ...... Frame ( 18) shift: -0.88 0.61 ...... Frame ( 19) shift: -0.89 0.62 ...... Frame ( 20) shift: -0.90 0.63 ...... Frame ( 21) shift: -0.88 0.67 ...... Frame ( 22) shift: -0.85 0.73 ...... Frame ( 23) shift: -0.82 0.80 ...... Frame ( 24) shift: -0.77 0.83 ...... Frame ( 25) shift: -0.69 0.82 ...... Frame ( 26) shift: -0.62 0.80 ...... Frame ( 27) shift: -0.62 0.76 ...... Frame ( 28) shift: -0.71 0.68 ...... Frame ( 29) shift: -0.80 0.61 ...... Frame ( 30) shift: -0.83 0.61 ...... Frame ( 31) shift: -0.78 0.69 ...... Frame ( 32) shift: -0.73 0.77 ...... Frame ( 33) shift: -0.73 0.83 ...... Frame ( 34) shift: -0.77 0.85 ...... Frame ( 35) shift: -0.82 0.88 ...... Frame ( 36) shift: -0.83 0.88 ...... Frame ( 37) shift: -0.81 0.88 ...... Frame ( 38) shift: -0.79 0.87 ...... Frame ( 39) shift: -0.76 0.86 ...... Frame ( 40) shift: -0.74 0.85 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.667536 Iteration 2 Error: 0.072783 Iteration 3 Error: 0.019394 Align patch 2 23 left Iteration 1 Error: 0.538902 Iteration 2 Error: 0.134271 Iteration 3 Error: 0.019256 Align patch 3 22 left Iteration 1 Error: 0.583169 Iteration 2 Error: 0.073294 Iteration 3 Error: 0.019306 Align patch 4 21 left Iteration 1 Error: 0.799954 Iteration 2 Error: 0.100633 Iteration 3 Error: 0.021586 Align patch 5 20 left Iteration 1 Error: 0.833015 Iteration 2 Error: 0.099051 Iteration 3 Error: 0.013562 Align patch 6 19 left Iteration 1 Error: 0.404456 Iteration 2 Error: 0.034739 Align patch 7 18 left Iteration 1 Error: 0.476407 Iteration 2 Error: 0.071083 Iteration 3 Error: 0.019083 Align patch 8 17 left Iteration 1 Error: 0.485051 Iteration 2 Error: 0.106562 Iteration 3 Error: 0.030012 Align patch 9 16 left Iteration 1 Error: 0.654962 Iteration 2 Error: 0.108887 Iteration 3 Error: 0.012283 Align patch 10 15 left Iteration 1 Error: 0.739811 Iteration 2 Error: 0.133238 Iteration 3 Error: 0.026605 Align patch 11 14 left Iteration 1 Error: 0.701053 Iteration 2 Error: 0.111232 Iteration 3 Error: 0.020378 Align patch 12 13 left Iteration 1 Error: 0.673229 Iteration 2 Error: 0.081623 Iteration 3 Error: 0.014162 Align patch 13 12 left Iteration 1 Error: 0.728423 Iteration 2 Error: 0.109547 Iteration 3 Error: 0.024663 Align patch 14 11 left Iteration 1 Error: 0.614865 Iteration 2 Error: 0.081127 Iteration 3 Error: 0.016580 Align patch 15 10 left Iteration 1 Error: 0.523289 Iteration 2 Error: 0.064485 Iteration 3 Error: 0.016097 Align patch 16 9 left Iteration 1 Error: 0.946877 Iteration 2 Error: 0.143067 Iteration 3 Error: 0.026725 Align patch 17 8 left Iteration 1 Error: 0.694326 Iteration 2 Error: 0.149113 Iteration 3 Error: 0.041475 Align patch 18 7 left Iteration 1 Error: 0.597425 Iteration 2 Error: 0.108594 Iteration 3 Error: 0.023785 Align patch 19 6 left Iteration 1 Error: 0.538657 Iteration 2 Error: 0.106907 Iteration 3 Error: 0.031371 Align patch 20 5 left Iteration 1 Error: 0.661410 Iteration 2 Error: 0.102344 Iteration 3 Error: 0.015268 Align patch 21 4 left Iteration 1 Error: 0.933285 Iteration 2 Error: 0.095256 Iteration 3 Error: 0.010256 Align patch 22 3 left Iteration 1 Error: 0.679233 Iteration 2 Error: 0.092243 Iteration 3 Error: 0.018364 Align patch 23 2 left Iteration 1 Error: 0.577158 Iteration 2 Error: 0.060783 Iteration 3 Error: 0.016471 Align patch 24 1 left Iteration 1 Error: 0.654546 Iteration 2 Error: 0.132113 Iteration 3 Error: 0.020931 Align patch 25 0 left Iteration 1 Error: 0.745141 Iteration 2 Error: 0.176644 Iteration 3 Error: 0.046771 3D Fitting completed. Patch alignment time: 14.67(sec) Local motion has been corrected. Process thread exits. Computational time: 22.936640 sec Total time: 28.810972 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00005hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00005hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.684279s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00005hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.411678s ........................................ >>>>>>TIME<<<<<< FFT: 1.035596s Defocus_U Defocus_V Angle CCC 9691.44 10531.28 6.40 0.040462 Final Values Defocus_U Defocus_V Angle CCC 9686.74 10554.75 6.40 0.071658 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00005hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00005hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 42.92 7.19 Num Hot pixels: 230 Hot pixel threshold: 86.04 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.408529 Iteration 2 Error: 0.074079 Iteration 3 Error: 0.011958 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.21 -0.02 ...... Frame ( 3) shift: -0.43 -0.03 ...... Frame ( 4) shift: -0.64 -0.05 ...... Frame ( 5) shift: -0.85 -0.07 ...... Frame ( 6) shift: -0.96 -0.09 ...... Frame ( 7) shift: -0.95 -0.12 ...... Frame ( 8) shift: -0.94 -0.14 ...... Frame ( 9) shift: -0.94 -0.14 ...... Frame ( 10) shift: -0.95 -0.11 ...... Frame ( 11) shift: -0.96 -0.08 ...... Frame ( 12) shift: -0.94 -0.05 ...... Frame ( 13) shift: -0.87 0.00 ...... Frame ( 14) shift: -0.80 0.05 ...... Frame ( 15) shift: -0.76 0.08 ...... Frame ( 16) shift: -0.74 0.08 ...... Frame ( 17) shift: -0.73 0.09 ...... Frame ( 18) shift: -0.68 0.12 ...... Frame ( 19) shift: -0.61 0.18 ...... Frame ( 20) shift: -0.53 0.24 ...... Frame ( 21) shift: -0.49 0.24 ...... Frame ( 22) shift: -0.48 0.18 ...... Frame ( 23) shift: -0.48 0.13 ...... Frame ( 24) shift: -0.46 0.11 ...... Frame ( 25) shift: -0.45 0.14 ...... Frame ( 26) shift: -0.43 0.16 ...... Frame ( 27) shift: -0.40 0.17 ...... Frame ( 28) shift: -0.36 0.17 ...... Frame ( 29) shift: -0.32 0.16 ...... Frame ( 30) shift: -0.29 0.16 ...... Frame ( 31) shift: -0.26 0.16 ...... Frame ( 32) shift: -0.24 0.16 ...... Frame ( 33) shift: -0.20 0.16 ...... Frame ( 34) shift: -0.15 0.14 ...... Frame ( 35) shift: -0.10 0.13 ...... Frame ( 36) shift: -0.09 0.12 ...... Frame ( 37) shift: -0.12 0.12 ...... Frame ( 38) shift: -0.14 0.12 ...... Frame ( 39) shift: -0.17 0.12 ...... Frame ( 40) shift: -0.20 0.11 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.898956 Iteration 2 Error: 0.202253 Iteration 3 Error: 0.037618 Align patch 2 23 left Iteration 1 Error: 0.586928 Iteration 2 Error: 0.050220 Iteration 3 Error: 0.011845 Align patch 3 22 left Iteration 1 Error: 0.660884 Iteration 2 Error: 0.078406 Iteration 3 Error: 0.015750 Align patch 4 21 left Iteration 1 Error: 0.798253 Iteration 2 Error: 0.122070 Iteration 3 Error: 0.035424 Align patch 5 20 left Iteration 1 Error: 0.949118 Iteration 2 Error: 0.146782 Iteration 3 Error: 0.030976 Align patch 6 19 left Iteration 1 Error: 1.230540 Iteration 2 Error: 0.192275 Iteration 3 Error: 0.052294 Iteration 4 Error: 0.013401 Align patch 7 18 left Iteration 1 Error: 0.949669 Iteration 2 Error: 0.087474 Iteration 3 Error: 0.017269 Align patch 8 17 left Iteration 1 Error: 1.187432 Iteration 2 Error: 0.134097 Iteration 3 Error: 0.032049 Align patch 9 16 left Iteration 1 Error: 0.689595 Iteration 2 Error: 0.158358 Iteration 3 Error: 0.036530 Align patch 10 15 left Iteration 1 Error: 0.697456 Iteration 2 Error: 0.107724 Iteration 3 Error: 0.050078 Iteration 4 Error: 0.010422 Align patch 11 14 left Iteration 1 Error: 1.147654 Iteration 2 Error: 0.155394 Iteration 3 Error: 0.044702 Align patch 12 13 left Iteration 1 Error: 0.933530 Iteration 2 Error: 0.103077 Iteration 3 Error: 0.027957 Align patch 13 12 left Iteration 1 Error: 0.588199 Iteration 2 Error: 0.065892 Iteration 3 Error: 0.014852 Align patch 14 11 left Iteration 1 Error: 0.780121 Iteration 2 Error: 0.123156 Iteration 3 Error: 0.024887 Align patch 15 10 left Iteration 1 Error: 0.624698 Iteration 2 Error: 0.105136 Iteration 3 Error: 0.028231 Align patch 16 9 left Iteration 1 Error: 0.539007 Iteration 2 Error: 0.110821 Iteration 3 Error: 0.032152 Align patch 17 8 left Iteration 1 Error: 0.617421 Iteration 2 Error: 0.171692 Iteration 3 Error: 0.046303 Align patch 18 7 left Iteration 1 Error: 0.808612 Iteration 2 Error: 0.089956 Iteration 3 Error: 0.016071 Align patch 19 6 left Iteration 1 Error: 0.803799 Iteration 2 Error: 0.100276 Iteration 3 Error: 0.023482 Align patch 20 5 left Iteration 1 Error: 0.596621 Iteration 2 Error: 0.063756 Iteration 3 Error: 0.014114 Align patch 21 4 left Iteration 1 Error: 0.952399 Iteration 2 Error: 0.112220 Iteration 3 Error: 0.024035 Align patch 22 3 left Iteration 1 Error: 0.699558 Iteration 2 Error: 0.087720 Iteration 3 Error: 0.020760 Align patch 23 2 left Iteration 1 Error: 0.483044 Iteration 2 Error: 0.072561 Iteration 3 Error: 0.017528 Align patch 24 1 left Iteration 1 Error: 0.684997 Iteration 2 Error: 0.100296 Iteration 3 Error: 0.019772 Align patch 25 0 left Iteration 1 Error: 0.788915 Iteration 2 Error: 0.103441 Iteration 3 Error: 0.020950 3D Fitting completed. Patch alignment time: 15.20(sec) Local motion has been corrected. Process thread exits. Computational time: 23.469761 sec Total time: 29.002731 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00005hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00005hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.772365s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00005hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.369524s ........................................ >>>>>>TIME<<<<<< FFT: 1.065812s Defocus_U Defocus_V Angle CCC 9993.43 9377.71 83.98 0.039872 Final Values Defocus_U Defocus_V Angle CCC 9980.93 9352.71 84.93 0.079044 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00006hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00006hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.317e-01 9.813e-02 CC threshold: 0.720 Mean Std: 37.99 6.74 Num Hot pixels: 213 Hot pixel threshold: 78.45 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.752594 Iteration 2 Error: 0.328897 Iteration 3 Error: 0.076534 Iteration 4 Error: 0.024863 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.18 0.02 ...... Frame ( 3) shift: 0.37 0.05 ...... Frame ( 4) shift: 0.55 0.07 ...... Frame ( 5) shift: 0.74 0.10 ...... Frame ( 6) shift: 0.91 0.11 ...... Frame ( 7) shift: 1.09 0.11 ...... Frame ( 8) shift: 1.26 0.12 ...... Frame ( 9) shift: 1.39 0.14 ...... Frame ( 10) shift: 1.47 0.18 ...... Frame ( 11) shift: 1.54 0.21 ...... Frame ( 12) shift: 1.62 0.22 ...... Frame ( 13) shift: 1.70 0.20 ...... Frame ( 14) shift: 1.78 0.19 ...... Frame ( 15) shift: 1.85 0.20 ...... Frame ( 16) shift: 1.91 0.24 ...... Frame ( 17) shift: 1.98 0.28 ...... Frame ( 18) shift: 2.05 0.27 ...... Frame ( 19) shift: 2.12 0.21 ...... Frame ( 20) shift: 2.20 0.15 ...... Frame ( 21) shift: 2.29 0.17 ...... Frame ( 22) shift: 2.40 0.27 ...... Frame ( 23) shift: 2.51 0.36 ...... Frame ( 24) shift: 2.62 0.44 ...... Frame ( 25) shift: 2.73 0.49 ...... Frame ( 26) shift: 2.84 0.54 ...... Frame ( 27) shift: 2.94 0.59 ...... Frame ( 28) shift: 3.04 0.65 ...... Frame ( 29) shift: 3.13 0.72 ...... Frame ( 30) shift: 3.25 0.75 ...... Frame ( 31) shift: 3.39 0.77 ...... Frame ( 32) shift: 3.53 0.78 ...... Frame ( 33) shift: 3.62 0.81 ...... Frame ( 34) shift: 3.65 0.84 ...... Frame ( 35) shift: 3.69 0.88 ...... Frame ( 36) shift: 3.73 0.89 ...... Frame ( 37) shift: 3.77 0.87 ...... Frame ( 38) shift: 3.82 0.85 ...... Frame ( 39) shift: 3.86 0.83 ...... Frame ( 40) shift: 3.91 0.81 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.943547 Iteration 2 Error: 0.302832 Iteration 3 Error: 0.098027 Iteration 4 Error: 0.036357 Align patch 2 23 left Iteration 1 Error: 0.866065 Iteration 2 Error: 0.232107 Iteration 3 Error: 0.070443 Iteration 4 Error: 0.026272 Align patch 3 22 left Iteration 1 Error: 0.807027 Iteration 2 Error: 0.133789 Iteration 3 Error: 0.038395 Align patch 4 21 left Iteration 1 Error: 0.774483 Iteration 2 Error: 0.116626 Iteration 3 Error: 0.025337 Align patch 5 20 left Iteration 1 Error: 0.742203 Iteration 2 Error: 0.171646 Iteration 3 Error: 0.038299 Align patch 6 19 left Iteration 1 Error: 0.804011 Iteration 2 Error: 0.175700 Iteration 3 Error: 0.039888 Align patch 7 18 left Iteration 1 Error: 0.915047 Iteration 2 Error: 0.256402 Iteration 3 Error: 0.100706 Iteration 4 Error: 0.024708 Align patch 8 17 left Iteration 1 Error: 0.762553 Iteration 2 Error: 0.206881 Iteration 3 Error: 0.055852 Iteration 4 Error: 0.014469 Align patch 9 16 left Iteration 1 Error: 0.877234 Iteration 2 Error: 0.127864 Iteration 3 Error: 0.020078 Align patch 10 15 left Iteration 1 Error: 0.868416 Iteration 2 Error: 0.181768 Iteration 3 Error: 0.052435 Iteration 4 Error: 0.014699 Align patch 11 14 left Iteration 1 Error: 0.572160 Iteration 2 Error: 0.192845 Iteration 3 Error: 0.060289 Iteration 4 Error: 0.033340 Align patch 12 13 left Iteration 1 Error: 0.867487 Iteration 2 Error: 0.202360 Iteration 3 Error: 0.064789 Iteration 4 Error: 0.024983 Align patch 13 12 left Iteration 1 Error: 0.621230 Iteration 2 Error: 0.102261 Iteration 3 Error: 0.028133 Align patch 14 11 left Iteration 1 Error: 0.567058 Iteration 2 Error: 0.098654 Iteration 3 Error: 0.022990 Align patch 15 10 left Iteration 1 Error: 0.594766 Iteration 2 Error: 0.100954 Iteration 3 Error: 0.026028 Align patch 16 9 left Iteration 1 Error: 0.793255 Iteration 2 Error: 0.199336 Iteration 3 Error: 0.065368 Iteration 4 Error: 0.021659 Align patch 17 8 left Iteration 1 Error: 1.042621 Iteration 2 Error: 0.307042 Iteration 3 Error: 0.090908 Iteration 4 Error: 0.032831 Align patch 18 7 left Iteration 1 Error: 0.640840 Iteration 2 Error: 0.091587 Iteration 3 Error: 0.027688 Align patch 19 6 left Iteration 1 Error: 1.076116 Iteration 2 Error: 0.300392 Iteration 3 Error: 0.046096 Align patch 20 5 left Iteration 1 Error: 1.040275 Iteration 2 Error: 0.224297 Iteration 3 Error: 0.066340 Iteration 4 Error: 0.018488 Align patch 21 4 left Iteration 1 Error: 1.235556 Iteration 2 Error: 0.202265 Iteration 3 Error: 0.092351 Iteration 4 Error: 0.029271 Align patch 22 3 left Iteration 1 Error: 0.678149 Iteration 2 Error: 0.206448 Iteration 3 Error: 0.073344 Iteration 4 Error: 0.021556 Align patch 23 2 left Iteration 1 Error: 0.872665 Iteration 2 Error: 0.150165 Iteration 3 Error: 0.043275 Align patch 24 1 left Iteration 1 Error: 0.976190 Iteration 2 Error: 0.191806 Iteration 3 Error: 0.037338 Align patch 25 0 left Iteration 1 Error: 1.351762 Iteration 2 Error: 0.160026 Iteration 3 Error: 0.049250 3D Fitting completed. Patch alignment time: 16.84(sec) Local motion has been corrected. Process thread exits. Computational time: 25.049408 sec Total time: 30.567003 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00006hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00006hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.594666s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00006hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.378430s ........................................ >>>>>>TIME<<<<<< FFT: 1.009226s Defocus_U Defocus_V Angle CCC 12900.40 13775.40 11.46 -0.036182 Final Values Defocus_U Defocus_V Angle CCC 12941.01 13794.23 11.15 -0.222804 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00006hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00006hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.382e-01 1.026e-01 CC threshold: 0.754 Mean Std: 33.16 6.90 Num Hot pixels: 176 Hot pixel threshold: 74.55 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 3.053345 Iteration 2 Error: 0.120121 Iteration 3 Error: 0.017416 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.56 0.59 ...... Frame ( 3) shift: 1.11 1.17 ...... Frame ( 4) shift: 1.67 1.76 ...... Frame ( 5) shift: 2.22 2.35 ...... Frame ( 6) shift: 2.61 2.71 ...... Frame ( 7) shift: 2.83 2.87 ...... Frame ( 8) shift: 3.04 3.02 ...... Frame ( 9) shift: 3.16 3.12 ...... Frame ( 10) shift: 3.18 3.16 ...... Frame ( 11) shift: 3.20 3.21 ...... Frame ( 12) shift: 3.21 3.24 ...... Frame ( 13) shift: 3.23 3.25 ...... Frame ( 14) shift: 3.24 3.27 ...... Frame ( 15) shift: 3.24 3.25 ...... Frame ( 16) shift: 3.25 3.20 ...... Frame ( 17) shift: 3.25 3.16 ...... Frame ( 18) shift: 3.23 3.13 ...... Frame ( 19) shift: 3.19 3.11 ...... Frame ( 20) shift: 3.15 3.10 ...... Frame ( 21) shift: 3.12 3.07 ...... Frame ( 22) shift: 3.08 3.03 ...... Frame ( 23) shift: 3.05 3.00 ...... Frame ( 24) shift: 3.03 2.98 ...... Frame ( 25) shift: 3.03 3.00 ...... Frame ( 26) shift: 3.04 3.01 ...... Frame ( 27) shift: 3.06 3.00 ...... Frame ( 28) shift: 3.10 2.97 ...... Frame ( 29) shift: 3.13 2.95 ...... Frame ( 30) shift: 3.15 2.94 ...... Frame ( 31) shift: 3.14 2.97 ...... Frame ( 32) shift: 3.13 3.00 ...... Frame ( 33) shift: 3.15 2.99 ...... Frame ( 34) shift: 3.21 2.95 ...... Frame ( 35) shift: 3.26 2.90 ...... Frame ( 36) shift: 3.30 2.87 ...... Frame ( 37) shift: 3.32 2.84 ...... Frame ( 38) shift: 3.34 2.82 ...... Frame ( 39) shift: 3.37 2.80 ...... Frame ( 40) shift: 3.39 2.78 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 3.663609 Iteration 2 Error: 0.433552 Iteration 3 Error: 0.075243 Iteration 4 Error: 0.017900 Align patch 2 23 left Iteration 1 Error: 1.564229 Iteration 2 Error: 0.095469 Iteration 3 Error: 0.012492 Align patch 3 22 left Iteration 1 Error: 3.272600 Iteration 2 Error: 0.169765 Iteration 3 Error: 0.027296 Align patch 4 21 left Iteration 1 Error: 4.532400 Iteration 2 Error: 0.225308 Iteration 3 Error: 0.068612 Iteration 4 Error: 0.015596 Align patch 5 20 left Iteration 1 Error: 3.378617 Iteration 2 Error: 0.163005 Iteration 3 Error: 0.034679 Align patch 6 19 left Iteration 1 Error: 2.772639 Iteration 2 Error: 0.207476 Iteration 3 Error: 0.028904 Align patch 7 18 left Iteration 1 Error: 1.487068 Iteration 2 Error: 0.120046 Iteration 3 Error: 0.020179 Align patch 8 17 left Iteration 1 Error: 2.780429 Iteration 2 Error: 0.125929 Iteration 3 Error: 0.015766 Align patch 9 16 left Iteration 1 Error: 2.010007 Iteration 2 Error: 0.107962 Iteration 3 Error: 0.013587 Align patch 10 15 left Iteration 1 Error: 2.768870 Iteration 2 Error: 0.349703 Iteration 3 Error: 0.065371 Iteration 4 Error: 0.011337 Align patch 11 14 left Iteration 1 Error: 1.434306 Iteration 2 Error: 0.134003 Iteration 3 Error: 0.027437 Align patch 12 13 left Iteration 1 Error: 0.780464 Iteration 2 Error: 0.035304 Align patch 13 12 left Iteration 1 Error: 1.097949 Iteration 2 Error: 0.054075 Iteration 3 Error: 0.005965 Align patch 14 11 left Iteration 1 Error: 1.913641 Iteration 2 Error: 0.179659 Iteration 3 Error: 0.025516 Align patch 15 10 left Iteration 1 Error: 3.346391 Iteration 2 Error: 0.309700 Iteration 3 Error: 0.038064 Align patch 16 9 left Iteration 1 Error: 1.711176 Iteration 2 Error: 0.143505 Iteration 3 Error: 0.012796 Align patch 17 8 left Iteration 1 Error: 1.725796 Iteration 2 Error: 0.083023 Iteration 3 Error: 0.004819 Align patch 18 7 left Iteration 1 Error: 1.242076 Iteration 2 Error: 0.099076 Iteration 3 Error: 0.012978 Align patch 19 6 left Iteration 1 Error: 2.338018 Iteration 2 Error: 0.250379 Iteration 3 Error: 0.039256 Align patch 20 5 left Iteration 1 Error: 3.354553 Iteration 2 Error: 0.380134 Iteration 3 Error: 0.062436 Iteration 4 Error: 0.010965 Align patch 21 4 left Iteration 1 Error: 2.359734 Iteration 2 Error: 0.145286 Iteration 3 Error: 0.011393 Align patch 22 3 left Iteration 1 Error: 2.623546 Iteration 2 Error: 0.197454 Iteration 3 Error: 0.010672 Align patch 23 2 left Iteration 1 Error: 2.363309 Iteration 2 Error: 0.146671 Iteration 3 Error: 0.009145 Align patch 24 1 left Iteration 1 Error: 1.893292 Iteration 2 Error: 0.153577 Iteration 3 Error: 0.032965 Align patch 25 0 left Iteration 1 Error: 3.406992 Iteration 2 Error: 0.559729 Iteration 3 Error: 0.122932 Iteration 4 Error: 0.032762 3D Fitting completed. Patch alignment time: 14.49(sec) Local motion has been corrected. Process thread exits. Computational time: 22.783268 sec Total time: 28.657112 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00006hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00006hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.672321s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00006hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.180305s ........................................ >>>>>>TIME<<<<<< FFT: 0.937252s Defocus_U Defocus_V Angle CCC 9742.19 9308.60 89.38 0.151533 Final Values Defocus_U Defocus_V Angle CCC 9751.57 9321.10 89.70 0.262063 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00006hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00006hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.333e-01 9.927e-02 CC threshold: 0.729 Mean Std: 38.67 6.69 Num Hot pixels: 200 Hot pixel threshold: 78.82 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 8.017453 Iteration 2 Error: 1.864895 Iteration 3 Error: 0.454462 Iteration 4 Error: 0.175935 Iteration 5 Error: 0.074267 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.38 -0.60 ...... Frame ( 3) shift: 0.76 -1.21 ...... Frame ( 4) shift: 1.13 -1.81 ...... Frame ( 5) shift: 1.51 -2.42 ...... Frame ( 6) shift: 1.93 -2.95 ...... Frame ( 7) shift: 2.40 -3.42 ...... Frame ( 8) shift: 2.87 -3.89 ...... Frame ( 9) shift: 3.31 -4.35 ...... Frame ( 10) shift: 3.74 -4.79 ...... Frame ( 11) shift: 4.16 -5.24 ...... Frame ( 12) shift: 4.54 -5.64 ...... Frame ( 13) shift: 4.89 -5.99 ...... Frame ( 14) shift: 5.23 -6.33 ...... Frame ( 15) shift: 5.56 -6.66 ...... Frame ( 16) shift: 5.88 -6.96 ...... Frame ( 17) shift: 6.19 -7.27 ...... Frame ( 18) shift: 6.44 -7.58 ...... Frame ( 19) shift: 6.62 -7.90 ...... Frame ( 20) shift: 6.81 -8.22 ...... Frame ( 21) shift: 6.95 -8.48 ...... Frame ( 22) shift: 7.05 -8.68 ...... Frame ( 23) shift: 7.14 -8.87 ...... Frame ( 24) shift: 7.29 -9.02 ...... Frame ( 25) shift: 7.48 -9.11 ...... Frame ( 26) shift: 7.67 -9.20 ...... Frame ( 27) shift: 7.83 -9.29 ...... Frame ( 28) shift: 7.96 -9.38 ...... Frame ( 29) shift: 8.08 -9.47 ...... Frame ( 30) shift: 8.26 -9.59 ...... Frame ( 31) shift: 8.49 -9.73 ...... Frame ( 32) shift: 8.73 -9.88 ...... Frame ( 33) shift: 8.93 -10.01 ...... Frame ( 34) shift: 9.12 -10.14 ...... Frame ( 35) shift: 9.30 -10.26 ...... Frame ( 36) shift: 9.43 -10.35 ...... Frame ( 37) shift: 9.50 -10.39 ...... Frame ( 38) shift: 9.58 -10.44 ...... Frame ( 39) shift: 9.65 -10.48 ...... Frame ( 40) shift: 9.73 -10.52 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 3.871845 Iteration 2 Error: 0.972849 Iteration 3 Error: 0.260940 Iteration 4 Error: 0.105566 Iteration 5 Error: 0.038851 Align patch 2 23 left Iteration 1 Error: 3.194544 Iteration 2 Error: 0.865741 Iteration 3 Error: 0.318908 Iteration 4 Error: 0.120041 Iteration 5 Error: 0.061922 Align patch 2 23 left Iteration 1 Error: 3.142591 Iteration 2 Error: 0.440150 Iteration 3 Error: 0.093981 Iteration 4 Error: 0.027288 Align patch 3 22 left Iteration 1 Error: 3.426335 Iteration 2 Error: 0.589046 Iteration 3 Error: 0.215720 Iteration 4 Error: 0.095832 Iteration 5 Error: 0.034951 Align patch 4 21 left Iteration 1 Error: 1.448177 Iteration 2 Error: 0.305445 Iteration 3 Error: 0.074833 Iteration 4 Error: 0.040670 Align patch 5 20 left Iteration 1 Error: 1.330796 Iteration 2 Error: 0.311501 Iteration 3 Error: 0.118766 Iteration 4 Error: 0.047811 Align patch 6 19 left Iteration 1 Error: 2.275107 Iteration 2 Error: 0.478813 Iteration 3 Error: 0.132969 Iteration 4 Error: 0.050801 Iteration 5 Error: 0.021421 Align patch 7 18 left Iteration 1 Error: 2.212270 Iteration 2 Error: 0.581846 Iteration 3 Error: 0.164323 Iteration 4 Error: 0.052691 Iteration 5 Error: 0.017496 Align patch 8 17 left Iteration 1 Error: 2.896504 Iteration 2 Error: 0.526839 Iteration 3 Error: 0.164015 Iteration 4 Error: 0.055973 Iteration 5 Error: 0.020041 Align patch 9 16 left Iteration 1 Error: 1.573532 Iteration 2 Error: 0.401774 Iteration 3 Error: 0.090782 Iteration 4 Error: 0.043757 Align patch 10 15 left Iteration 1 Error: 1.419695 Iteration 2 Error: 0.361562 Iteration 3 Error: 0.064846 Iteration 4 Error: 0.037338 Align patch 11 14 left Iteration 1 Error: 1.347651 Iteration 2 Error: 0.365055 Iteration 3 Error: 0.093770 Iteration 4 Error: 0.031162 Align patch 12 13 left Iteration 1 Error: 1.480944 Iteration 2 Error: 0.476600 Iteration 3 Error: 0.108416 Iteration 4 Error: 0.057869 Iteration 5 Error: 0.023066 Align patch 13 12 left Iteration 1 Error: 1.299538 Iteration 2 Error: 0.188015 Iteration 3 Error: 0.067470 Iteration 4 Error: 0.022934 Align patch 14 11 left Iteration 1 Error: 0.732950 Iteration 2 Error: 0.137294 Iteration 3 Error: 0.052220 Iteration 4 Error: 0.015683 Align patch 15 10 left Iteration 1 Error: 1.124569 Iteration 2 Error: 0.214433 Iteration 3 Error: 0.048954 Align patch 16 9 left Iteration 1 Error: 0.984471 Iteration 2 Error: 0.236431 Iteration 3 Error: 0.085722 Iteration 4 Error: 0.026855 Align patch 17 8 left Iteration 1 Error: 0.584813 Iteration 2 Error: 0.067850 Iteration 3 Error: 0.028445 Align patch 18 7 left Iteration 1 Error: 1.013441 Iteration 2 Error: 0.163357 Iteration 3 Error: 0.052044 Iteration 4 Error: 0.019487 Align patch 19 6 left Iteration 1 Error: 1.636298 Iteration 2 Error: 0.497902 Iteration 3 Error: 0.095634 Iteration 4 Error: 0.040305 Align patch 20 5 left Iteration 1 Error: 2.047030 Iteration 2 Error: 0.488686 Iteration 3 Error: 0.126321 Iteration 4 Error: 0.047967 Align patch 21 4 left Iteration 1 Error: 1.376758 Iteration 2 Error: 0.283817 Iteration 3 Error: 0.060752 Iteration 4 Error: 0.017178 Align patch 22 3 left Iteration 1 Error: 1.846016 Iteration 2 Error: 0.360092 Iteration 3 Error: 0.079257 Iteration 4 Error: 0.028648 Align patch 23 2 left Iteration 1 Error: 2.118332 Iteration 2 Error: 0.400958 Iteration 3 Error: 0.099892 Iteration 4 Error: 0.027585 Align patch 24 1 left Iteration 1 Error: 2.604727 Iteration 2 Error: 0.387267 Iteration 3 Error: 0.079459 Iteration 4 Error: 0.018955 Align patch 25 0 left Iteration 1 Error: 3.775417 Iteration 2 Error: 0.761808 Iteration 3 Error: 0.255805 Iteration 4 Error: 0.097345 Iteration 5 Error: 0.036676 3D Fitting completed. Patch alignment time: 18.69(sec) Local motion has been corrected. Process thread exits. Computational time: 27.731117 sec Total time: 33.114063 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00006hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00006hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.773215s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00006hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.044602s ........................................ >>>>>>TIME<<<<<< FFT: 0.991040s Defocus_U Defocus_V Angle CCC 14535.16 15554.69 5.13 -0.010932 Final Values Defocus_U Defocus_V Angle CCC 14533.59 15565.63 5.76 -0.164688 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00006hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00006hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.363e-01 1.013e-01 CC threshold: 0.744 Mean Std: 39.62 7.12 Num Hot pixels: 182 Hot pixel threshold: 82.32 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.903039 Iteration 2 Error: 0.369011 Iteration 3 Error: 0.092034 Iteration 4 Error: 0.026585 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.17 -0.03 ...... Frame ( 3) shift: 0.34 -0.05 ...... Frame ( 4) shift: 0.51 -0.08 ...... Frame ( 5) shift: 0.68 -0.11 ...... Frame ( 6) shift: 0.80 -0.00 ...... Frame ( 7) shift: 0.88 0.23 ...... Frame ( 8) shift: 0.95 0.46 ...... Frame ( 9) shift: 0.97 0.67 ...... Frame ( 10) shift: 0.93 0.84 ...... Frame ( 11) shift: 0.88 1.01 ...... Frame ( 12) shift: 0.84 1.17 ...... Frame ( 13) shift: 0.78 1.30 ...... Frame ( 14) shift: 0.73 1.43 ...... Frame ( 15) shift: 0.69 1.59 ...... Frame ( 16) shift: 0.65 1.79 ...... Frame ( 17) shift: 0.62 1.98 ...... Frame ( 18) shift: 0.61 2.14 ...... Frame ( 19) shift: 0.62 2.26 ...... Frame ( 20) shift: 0.63 2.39 ...... Frame ( 21) shift: 0.63 2.49 ...... Frame ( 22) shift: 0.62 2.55 ...... Frame ( 23) shift: 0.60 2.62 ...... Frame ( 24) shift: 0.59 2.68 ...... Frame ( 25) shift: 0.58 2.73 ...... Frame ( 26) shift: 0.56 2.79 ...... Frame ( 27) shift: 0.56 2.83 ...... Frame ( 28) shift: 0.56 2.85 ...... Frame ( 29) shift: 0.57 2.88 ...... Frame ( 30) shift: 0.57 2.89 ...... Frame ( 31) shift: 0.58 2.89 ...... Frame ( 32) shift: 0.58 2.89 ...... Frame ( 33) shift: 0.61 2.90 ...... Frame ( 34) shift: 0.67 2.91 ...... Frame ( 35) shift: 0.72 2.92 ...... Frame ( 36) shift: 0.75 2.95 ...... Frame ( 37) shift: 0.74 2.99 ...... Frame ( 38) shift: 0.74 3.04 ...... Frame ( 39) shift: 0.73 3.09 ...... Frame ( 40) shift: 0.73 3.14 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 8.718944 Iteration 2 Error: 0.379387 Iteration 3 Error: 0.031287 Align patch 2 23 left Iteration 1 Error: 7.391079 Iteration 2 Error: 0.649381 Iteration 3 Error: 0.085324 Iteration 4 Error: 0.020597 Align patch 3 22 left Iteration 1 Error: 3.785433 Iteration 2 Error: 0.363118 Iteration 3 Error: 0.049918 Align patch 4 21 left Iteration 1 Error: 2.594187 Iteration 2 Error: 0.319259 Iteration 3 Error: 0.052451 Iteration 4 Error: 0.010764 Align patch 5 20 left Iteration 1 Error: 1.094653 Iteration 2 Error: 0.143564 Iteration 3 Error: 0.024665 Align patch 6 19 left Iteration 1 Error: 9.235070 Iteration 2 Error: 0.396175 Iteration 3 Error: 0.029571 Align patch 7 18 left Iteration 1 Error: 6.584569 Iteration 2 Error: 0.815029 Iteration 3 Error: 0.147095 Iteration 4 Error: 0.069098 Iteration 5 Error: 0.017615 Align patch 8 17 left Iteration 1 Error: 2.288368 Iteration 2 Error: 0.101778 Iteration 3 Error: 0.015919 Align patch 9 16 left Iteration 1 Error: 1.536798 Iteration 2 Error: 0.063000 Iteration 3 Error: 0.006861 Align patch 10 15 left Iteration 1 Error: 1.991060 Iteration 2 Error: 0.152979 Iteration 3 Error: 0.013482 Align patch 11 14 left Iteration 1 Error: 9.186584 Iteration 2 Error: 0.676497 Iteration 3 Error: 0.178255 Iteration 4 Error: 0.045264 Align patch 12 13 left Iteration 1 Error: 5.335287 Iteration 2 Error: 0.728735 Iteration 3 Error: 0.138547 Iteration 4 Error: 0.032407 Align patch 13 12 left Iteration 1 Error: 0.688570 Iteration 2 Error: 0.032789 Align patch 14 11 left Iteration 1 Error: 3.308523 Iteration 2 Error: 0.370993 Iteration 3 Error: 0.089158 Iteration 4 Error: 0.019910 Align patch 15 10 left Iteration 1 Error: 4.282821 Iteration 2 Error: 0.218631 Iteration 3 Error: 0.050396 Iteration 4 Error: 0.013331 Align patch 16 9 left Iteration 1 Error: 2.595449 Iteration 2 Error: 0.402755 Iteration 3 Error: 0.141505 Iteration 4 Error: 0.031920 Align patch 17 8 left Iteration 1 Error: 2.267568 Iteration 2 Error: 0.392595 Iteration 3 Error: 0.067275 Iteration 4 Error: 0.022312 Align patch 18 7 left Iteration 1 Error: 1.047158 Iteration 2 Error: 0.224045 Iteration 3 Error: 0.048821 Align patch 19 6 left Iteration 1 Error: 5.181573 Iteration 2 Error: 0.438396 Iteration 3 Error: 0.040346 Align patch 20 5 left Iteration 1 Error: 5.204107 Iteration 2 Error: 0.418850 Iteration 3 Error: 0.036549 Align patch 21 4 left Iteration 1 Error: 3.421041 Iteration 2 Error: 0.368564 Iteration 3 Error: 0.066551 Iteration 4 Error: 0.019741 Align patch 22 3 left Iteration 1 Error: 1.706543 Iteration 2 Error: 0.495544 Iteration 3 Error: 0.098533 Iteration 4 Error: 0.039032 Align patch 23 2 left Iteration 1 Error: 3.255500 Iteration 2 Error: 0.291984 Iteration 3 Error: 0.048952 Align patch 24 1 left Iteration 1 Error: 4.972802 Iteration 2 Error: 0.264835 Iteration 3 Error: 0.025818 Align patch 25 0 left Iteration 1 Error: 4.227365 Iteration 2 Error: 0.202626 Iteration 3 Error: 0.026450 3D Fitting completed. Patch alignment time: 16.41(sec) Local motion has been corrected. Process thread exits. Computational time: 25.070221 sec Total time: 31.287645 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00006hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00006hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.563072s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00006hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.036938s ........................................ >>>>>>TIME<<<<<< FFT: 0.993238s Defocus_U Defocus_V Angle CCC 14011.73 13417.98 80.59 0.153809 Final Values Defocus_U Defocus_V Angle CCC 13994.54 13428.92 80.28 0.228224 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00007hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00007hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 41.38 6.94 Num Hot pixels: 219 Hot pixel threshold: 83.02 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.369107 Iteration 2 Error: 0.278996 Iteration 3 Error: 0.079350 Iteration 4 Error: 0.020768 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.11 -0.04 ...... Frame ( 3) shift: -0.22 -0.09 ...... Frame ( 4) shift: -0.33 -0.13 ...... Frame ( 5) shift: -0.44 -0.17 ...... Frame ( 6) shift: -0.46 -0.18 ...... Frame ( 7) shift: -0.38 -0.15 ...... Frame ( 8) shift: -0.30 -0.13 ...... Frame ( 9) shift: -0.23 -0.11 ...... Frame ( 10) shift: -0.17 -0.11 ...... Frame ( 11) shift: -0.11 -0.10 ...... Frame ( 12) shift: -0.03 -0.08 ...... Frame ( 13) shift: 0.05 -0.03 ...... Frame ( 14) shift: 0.14 0.01 ...... Frame ( 15) shift: 0.19 0.07 ...... Frame ( 16) shift: 0.21 0.14 ...... Frame ( 17) shift: 0.22 0.22 ...... Frame ( 18) shift: 0.28 0.28 ...... Frame ( 19) shift: 0.38 0.32 ...... Frame ( 20) shift: 0.49 0.36 ...... Frame ( 21) shift: 0.61 0.44 ...... Frame ( 22) shift: 0.75 0.56 ...... Frame ( 23) shift: 0.89 0.68 ...... Frame ( 24) shift: 1.00 0.76 ...... Frame ( 25) shift: 1.07 0.78 ...... Frame ( 26) shift: 1.14 0.81 ...... Frame ( 27) shift: 1.21 0.83 ...... Frame ( 28) shift: 1.26 0.85 ...... Frame ( 29) shift: 1.32 0.86 ...... Frame ( 30) shift: 1.38 0.92 ...... Frame ( 31) shift: 1.44 1.02 ...... Frame ( 32) shift: 1.50 1.12 ...... Frame ( 33) shift: 1.58 1.17 ...... Frame ( 34) shift: 1.68 1.17 ...... Frame ( 35) shift: 1.77 1.17 ...... Frame ( 36) shift: 1.85 1.19 ...... Frame ( 37) shift: 1.90 1.21 ...... Frame ( 38) shift: 1.95 1.24 ...... Frame ( 39) shift: 2.01 1.26 ...... Frame ( 40) shift: 2.06 1.29 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.770810 Iteration 2 Error: 0.124037 Iteration 3 Error: 0.036139 Align patch 2 23 left Iteration 1 Error: 1.006846 Iteration 2 Error: 0.178631 Iteration 3 Error: 0.053986 Iteration 4 Error: 0.027855 Align patch 3 22 left Iteration 1 Error: 0.672123 Iteration 2 Error: 0.181468 Iteration 3 Error: 0.040991 Align patch 4 21 left Iteration 1 Error: 0.719988 Iteration 2 Error: 0.087270 Iteration 3 Error: 0.026217 Align patch 5 20 left Iteration 1 Error: 0.823984 Iteration 2 Error: 0.119892 Iteration 3 Error: 0.022114 Align patch 6 19 left Iteration 1 Error: 0.738075 Iteration 2 Error: 0.142346 Iteration 3 Error: 0.035259 Align patch 7 18 left Iteration 1 Error: 0.739632 Iteration 2 Error: 0.207460 Iteration 3 Error: 0.058194 Iteration 4 Error: 0.026048 Align patch 8 17 left Iteration 1 Error: 0.740990 Iteration 2 Error: 0.112548 Iteration 3 Error: 0.037494 Align patch 9 16 left Iteration 1 Error: 1.020193 Iteration 2 Error: 0.145465 Iteration 3 Error: 0.039516 Align patch 10 15 left Iteration 1 Error: 0.828191 Iteration 2 Error: 0.176151 Iteration 3 Error: 0.057000 Iteration 4 Error: 0.021815 Align patch 11 14 left Iteration 1 Error: 1.172776 Iteration 2 Error: 0.254781 Iteration 3 Error: 0.056117 Iteration 4 Error: 0.026091 Align patch 12 13 left Iteration 1 Error: 0.605010 Iteration 2 Error: 0.198625 Iteration 3 Error: 0.066140 Iteration 4 Error: 0.037600 Align patch 13 12 left Iteration 1 Error: 0.880047 Iteration 2 Error: 0.191551 Iteration 3 Error: 0.051875 Iteration 4 Error: 0.019569 Align patch 14 11 left Iteration 1 Error: 1.080197 Iteration 2 Error: 0.182847 Iteration 3 Error: 0.056207 Iteration 4 Error: 0.015220 Align patch 15 10 left Iteration 1 Error: 0.874962 Iteration 2 Error: 0.120938 Iteration 3 Error: 0.039150 Align patch 16 9 left Iteration 1 Error: 1.085776 Iteration 2 Error: 0.142154 Iteration 3 Error: 0.034878 Align patch 17 8 left Iteration 1 Error: 0.608848 Iteration 2 Error: 0.166474 Iteration 3 Error: 0.053707 Iteration 4 Error: 0.018578 Align patch 18 7 left Iteration 1 Error: 0.819886 Iteration 2 Error: 0.116145 Iteration 3 Error: 0.046373 Align patch 19 6 left Iteration 1 Error: 0.593972 Iteration 2 Error: 0.083368 Iteration 3 Error: 0.018884 Align patch 20 5 left Iteration 1 Error: 0.498168 Iteration 2 Error: 0.105547 Iteration 3 Error: 0.022677 Align patch 21 4 left Iteration 1 Error: 0.758323 Iteration 2 Error: 0.179771 Iteration 3 Error: 0.058666 Iteration 4 Error: 0.021363 Align patch 22 3 left Iteration 1 Error: 1.206556 Iteration 2 Error: 0.144592 Iteration 3 Error: 0.036658 Align patch 23 2 left Iteration 1 Error: 0.661851 Iteration 2 Error: 0.146687 Iteration 3 Error: 0.055644 Iteration 4 Error: 0.029867 Align patch 24 1 left Iteration 1 Error: 0.760020 Iteration 2 Error: 0.187542 Iteration 3 Error: 0.055627 Iteration 4 Error: 0.020502 Align patch 25 0 left Iteration 1 Error: 0.630935 Iteration 2 Error: 0.116276 Iteration 3 Error: 0.034775 3D Fitting completed. Patch alignment time: 16.19(sec) Local motion has been corrected. Process thread exits. Computational time: 25.389702 sec Total time: 32.097507 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00007hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00007hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.684723s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00007hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.868201s ........................................ >>>>>>TIME<<<<<< FFT: 1.044090s Defocus_U Defocus_V Angle CCC 11421.92 12210.99 12.85 0.042479 Final Values Defocus_U Defocus_V Angle CCC 11431.30 12226.62 13.17 0.073060 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00007hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00007hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 38.78 6.65 Num Hot pixels: 193 Hot pixel threshold: 78.68 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.795294 Iteration 2 Error: 0.153411 Iteration 3 Error: 0.037829 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.01 0.00 ...... Frame ( 3) shift: 0.03 0.01 ...... Frame ( 4) shift: 0.04 0.01 ...... Frame ( 5) shift: 0.06 0.01 ...... Frame ( 6) shift: 0.09 0.05 ...... Frame ( 7) shift: 0.15 0.14 ...... Frame ( 8) shift: 0.20 0.22 ...... Frame ( 9) shift: 0.25 0.25 ...... Frame ( 10) shift: 0.28 0.22 ...... Frame ( 11) shift: 0.32 0.19 ...... Frame ( 12) shift: 0.37 0.18 ...... Frame ( 13) shift: 0.44 0.20 ...... Frame ( 14) shift: 0.51 0.23 ...... Frame ( 15) shift: 0.54 0.25 ...... Frame ( 16) shift: 0.53 0.29 ...... Frame ( 17) shift: 0.52 0.32 ...... Frame ( 18) shift: 0.52 0.37 ...... Frame ( 19) shift: 0.54 0.43 ...... Frame ( 20) shift: 0.55 0.49 ...... Frame ( 21) shift: 0.56 0.54 ...... Frame ( 22) shift: 0.55 0.57 ...... Frame ( 23) shift: 0.55 0.60 ...... Frame ( 24) shift: 0.59 0.63 ...... Frame ( 25) shift: 0.67 0.68 ...... Frame ( 26) shift: 0.75 0.72 ...... Frame ( 27) shift: 0.78 0.77 ...... Frame ( 28) shift: 0.76 0.84 ...... Frame ( 29) shift: 0.74 0.91 ...... Frame ( 30) shift: 0.75 0.96 ...... Frame ( 31) shift: 0.77 0.99 ...... Frame ( 32) shift: 0.79 1.02 ...... Frame ( 33) shift: 0.80 1.03 ...... Frame ( 34) shift: 0.81 1.00 ...... Frame ( 35) shift: 0.81 0.98 ...... Frame ( 36) shift: 0.84 1.01 ...... Frame ( 37) shift: 0.91 1.11 ...... Frame ( 38) shift: 0.97 1.21 ...... Frame ( 39) shift: 1.04 1.31 ...... Frame ( 40) shift: 1.10 1.41 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.708989 Iteration 2 Error: 0.134271 Iteration 3 Error: 0.029151 Align patch 2 23 left Iteration 1 Error: 0.720221 Iteration 2 Error: 0.126736 Iteration 3 Error: 0.035130 Align patch 3 22 left Iteration 1 Error: 0.658692 Iteration 2 Error: 0.104128 Iteration 3 Error: 0.024402 Align patch 4 21 left Iteration 1 Error: 0.786318 Iteration 2 Error: 0.114134 Iteration 3 Error: 0.035489 Align patch 5 20 left Iteration 1 Error: 0.697381 Iteration 2 Error: 0.099820 Iteration 3 Error: 0.020003 Align patch 6 19 left Iteration 1 Error: 0.897598 Iteration 2 Error: 0.178925 Iteration 3 Error: 0.050670 Iteration 4 Error: 0.016314 Align patch 7 18 left Iteration 1 Error: 0.786610 Iteration 2 Error: 0.123243 Iteration 3 Error: 0.024919 Align patch 8 17 left Iteration 1 Error: 0.748473 Iteration 2 Error: 0.097979 Iteration 3 Error: 0.031795 Align patch 9 16 left Iteration 1 Error: 0.829984 Iteration 2 Error: 0.108724 Iteration 3 Error: 0.030832 Align patch 10 15 left Iteration 1 Error: 0.453132 Iteration 2 Error: 0.073166 Iteration 3 Error: 0.014202 Align patch 11 14 left Iteration 1 Error: 0.764510 Iteration 2 Error: 0.173435 Iteration 3 Error: 0.044283 Align patch 12 13 left Iteration 1 Error: 0.984742 Iteration 2 Error: 0.112343 Iteration 3 Error: 0.037854 Align patch 13 12 left Iteration 1 Error: 0.608361 Iteration 2 Error: 0.089288 Iteration 3 Error: 0.019894 Align patch 14 11 left Iteration 1 Error: 0.618427 Iteration 2 Error: 0.175639 Iteration 3 Error: 0.083706 Iteration 4 Error: 0.038940 Align patch 15 10 left Iteration 1 Error: 0.761473 Iteration 2 Error: 0.147618 Iteration 3 Error: 0.025132 Align patch 16 9 left Iteration 1 Error: 0.810082 Iteration 2 Error: 0.140562 Iteration 3 Error: 0.024068 Align patch 17 8 left Iteration 1 Error: 0.760003 Iteration 2 Error: 0.146450 Iteration 3 Error: 0.041668 Align patch 18 7 left Iteration 1 Error: 0.644924 Iteration 2 Error: 0.083580 Iteration 3 Error: 0.012118 Align patch 19 6 left Iteration 1 Error: 1.005701 Iteration 2 Error: 0.147357 Iteration 3 Error: 0.039652 Align patch 20 5 left Iteration 1 Error: 0.822519 Iteration 2 Error: 0.093522 Iteration 3 Error: 0.022358 Align patch 21 4 left Iteration 1 Error: 1.099154 Iteration 2 Error: 0.186384 Iteration 3 Error: 0.025383 Align patch 22 3 left Iteration 1 Error: 0.635922 Iteration 2 Error: 0.148899 Iteration 3 Error: 0.041186 Align patch 23 2 left Iteration 1 Error: 1.174185 Iteration 2 Error: 0.181786 Iteration 3 Error: 0.065381 Iteration 4 Error: 0.017334 Align patch 24 1 left Iteration 1 Error: 0.768372 Iteration 2 Error: 0.198751 Iteration 3 Error: 0.035774 Align patch 25 0 left Iteration 1 Error: 0.573213 Iteration 2 Error: 0.162520 Iteration 3 Error: 0.042995 3D Fitting completed. Patch alignment time: 15.27(sec) Local motion has been corrected. Process thread exits. Computational time: 24.253250 sec Total time: 29.732727 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00007hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00007hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.747232s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00007hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.634883s ........................................ >>>>>>TIME<<<<<< FFT: 1.042988s Defocus_U Defocus_V Angle CCC 9335.94 9730.47 10.34 0.024799 Final Values Defocus_U Defocus_V Angle CCC 9354.70 9739.86 10.66 0.043050 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00007hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00007hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.001e-01 CC threshold: 0.736 Mean Std: 43.48 7.24 Num Hot pixels: 210 Hot pixel threshold: 86.89 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.786412 Iteration 2 Error: 0.114138 Iteration 3 Error: 0.023764 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.23 -0.04 ...... Frame ( 3) shift: -0.46 -0.08 ...... Frame ( 4) shift: -0.69 -0.11 ...... Frame ( 5) shift: -0.92 -0.15 ...... Frame ( 6) shift: -1.02 -0.16 ...... Frame ( 7) shift: -1.01 -0.13 ...... Frame ( 8) shift: -1.00 -0.10 ...... Frame ( 9) shift: -0.95 -0.06 ...... Frame ( 10) shift: -0.88 -0.02 ...... Frame ( 11) shift: -0.80 0.02 ...... Frame ( 12) shift: -0.75 0.06 ...... Frame ( 13) shift: -0.73 0.10 ...... Frame ( 14) shift: -0.70 0.15 ...... Frame ( 15) shift: -0.67 0.19 ...... Frame ( 16) shift: -0.63 0.23 ...... Frame ( 17) shift: -0.59 0.27 ...... Frame ( 18) shift: -0.54 0.33 ...... Frame ( 19) shift: -0.49 0.41 ...... Frame ( 20) shift: -0.44 0.50 ...... Frame ( 21) shift: -0.39 0.60 ...... Frame ( 22) shift: -0.36 0.74 ...... Frame ( 23) shift: -0.32 0.88 ...... Frame ( 24) shift: -0.28 0.95 ...... Frame ( 25) shift: -0.23 0.95 ...... Frame ( 26) shift: -0.19 0.95 ...... Frame ( 27) shift: -0.16 0.93 ...... Frame ( 28) shift: -0.16 0.88 ...... Frame ( 29) shift: -0.15 0.82 ...... Frame ( 30) shift: -0.13 0.81 ...... Frame ( 31) shift: -0.11 0.83 ...... Frame ( 32) shift: -0.09 0.85 ...... Frame ( 33) shift: -0.07 0.89 ...... Frame ( 34) shift: -0.05 0.94 ...... Frame ( 35) shift: -0.04 0.98 ...... Frame ( 36) shift: -0.02 1.02 ...... Frame ( 37) shift: 0.00 1.05 ...... Frame ( 38) shift: 0.03 1.08 ...... Frame ( 39) shift: 0.05 1.11 ...... Frame ( 40) shift: 0.08 1.14 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.103713 Iteration 2 Error: 0.129714 Iteration 3 Error: 0.039672 Align patch 2 23 left Iteration 1 Error: 0.800472 Iteration 2 Error: 0.147039 Iteration 3 Error: 0.040650 Align patch 3 22 left Iteration 1 Error: 0.637633 Iteration 2 Error: 0.128828 Iteration 3 Error: 0.041537 Align patch 4 21 left Iteration 1 Error: 0.646065 Iteration 2 Error: 0.115181 Iteration 3 Error: 0.026149 Align patch 5 20 left Iteration 1 Error: 0.823605 Iteration 2 Error: 0.230807 Iteration 3 Error: 0.050390 Iteration 4 Error: 0.015527 Align patch 6 19 left Iteration 1 Error: 0.852172 Iteration 2 Error: 0.136685 Iteration 3 Error: 0.040118 Align patch 7 18 left Iteration 1 Error: 0.690350 Iteration 2 Error: 0.184612 Iteration 3 Error: 0.040090 Align patch 8 17 left Iteration 1 Error: 0.906540 Iteration 2 Error: 0.097056 Iteration 3 Error: 0.023838 Align patch 9 16 left Iteration 1 Error: 0.459409 Iteration 2 Error: 0.143512 Iteration 3 Error: 0.027959 Align patch 10 15 left Iteration 1 Error: 0.589270 Iteration 2 Error: 0.093770 Iteration 3 Error: 0.022955 Align patch 11 14 left Iteration 1 Error: 0.797070 Iteration 2 Error: 0.170965 Iteration 3 Error: 0.032931 Align patch 12 13 left Iteration 1 Error: 0.828470 Iteration 2 Error: 0.152963 Iteration 3 Error: 0.063474 Iteration 4 Error: 0.019693 Align patch 13 12 left Iteration 1 Error: 0.530539 Iteration 2 Error: 0.067193 Iteration 3 Error: 0.015217 Align patch 14 11 left Iteration 1 Error: 0.593973 Iteration 2 Error: 0.094178 Iteration 3 Error: 0.017537 Align patch 15 10 left Iteration 1 Error: 0.934816 Iteration 2 Error: 0.118681 Iteration 3 Error: 0.021195 Align patch 16 9 left Iteration 1 Error: 1.326359 Iteration 2 Error: 0.134729 Iteration 3 Error: 0.029376 Align patch 17 8 left Iteration 1 Error: 0.813537 Iteration 2 Error: 0.237577 Iteration 3 Error: 0.035082 Align patch 18 7 left Iteration 1 Error: 0.502898 Iteration 2 Error: 0.135408 Iteration 3 Error: 0.038869 Align patch 19 6 left Iteration 1 Error: 0.423856 Iteration 2 Error: 0.083879 Iteration 3 Error: 0.028516 Align patch 20 5 left Iteration 1 Error: 0.892811 Iteration 2 Error: 0.086466 Iteration 3 Error: 0.014680 Align patch 21 4 left Iteration 1 Error: 0.971745 Iteration 2 Error: 0.114611 Iteration 3 Error: 0.031987 Align patch 22 3 left Iteration 1 Error: 1.087802 Iteration 2 Error: 0.197315 Iteration 3 Error: 0.051488 Iteration 4 Error: 0.014722 Align patch 23 2 left Iteration 1 Error: 0.714350 Iteration 2 Error: 0.147040 Iteration 3 Error: 0.038500 Align patch 24 1 left Iteration 1 Error: 0.555434 Iteration 2 Error: 0.063886 Iteration 3 Error: 0.014477 Align patch 25 0 left Iteration 1 Error: 0.411066 Iteration 2 Error: 0.036790 3D Fitting completed. Patch alignment time: 15.85(sec) Local motion has been corrected. Process thread exits. Computational time: 24.961649 sec Total time: 31.149811 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00007hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00007hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.812408s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00007hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.891228s ........................................ >>>>>>TIME<<<<<< FFT: 1.040929s Defocus_U Defocus_V Angle CCC 9433.59 10292.97 6.35 0.042549 Final Values Defocus_U Defocus_V Angle CCC 9433.59 10305.48 6.04 0.086451 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00007hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00007hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.001e-01 CC threshold: 0.735 Mean Std: 40.38 7.01 Num Hot pixels: 227 Hot pixel threshold: 82.43 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.549129 Iteration 2 Error: 0.100322 Iteration 3 Error: 0.030243 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.27 -0.13 ...... Frame ( 3) shift: -0.54 -0.26 ...... Frame ( 4) shift: -0.80 -0.39 ...... Frame ( 5) shift: -1.07 -0.52 ...... Frame ( 6) shift: -1.21 -0.59 ...... Frame ( 7) shift: -1.21 -0.61 ...... Frame ( 8) shift: -1.21 -0.62 ...... Frame ( 9) shift: -1.20 -0.60 ...... Frame ( 10) shift: -1.16 -0.53 ...... Frame ( 11) shift: -1.11 -0.47 ...... Frame ( 12) shift: -1.10 -0.44 ...... Frame ( 13) shift: -1.12 -0.43 ...... Frame ( 14) shift: -1.14 -0.43 ...... Frame ( 15) shift: -1.13 -0.44 ...... Frame ( 16) shift: -1.10 -0.46 ...... Frame ( 17) shift: -1.08 -0.48 ...... Frame ( 18) shift: -1.02 -0.48 ...... Frame ( 19) shift: -0.93 -0.46 ...... Frame ( 20) shift: -0.84 -0.43 ...... Frame ( 21) shift: -0.76 -0.37 ...... Frame ( 22) shift: -0.70 -0.28 ...... Frame ( 23) shift: -0.64 -0.19 ...... Frame ( 24) shift: -0.59 -0.13 ...... Frame ( 25) shift: -0.56 -0.10 ...... Frame ( 26) shift: -0.52 -0.07 ...... Frame ( 27) shift: -0.51 -0.05 ...... Frame ( 28) shift: -0.52 -0.03 ...... Frame ( 29) shift: -0.52 -0.01 ...... Frame ( 30) shift: -0.51 -0.02 ...... Frame ( 31) shift: -0.48 -0.05 ...... Frame ( 32) shift: -0.44 -0.07 ...... Frame ( 33) shift: -0.41 -0.07 ...... Frame ( 34) shift: -0.37 -0.02 ...... Frame ( 35) shift: -0.33 0.02 ...... Frame ( 36) shift: -0.29 0.05 ...... Frame ( 37) shift: -0.24 0.04 ...... Frame ( 38) shift: -0.20 0.04 ...... Frame ( 39) shift: -0.16 0.03 ...... Frame ( 40) shift: -0.11 0.03 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.758917 Iteration 2 Error: 0.099317 Iteration 3 Error: 0.021149 Align patch 2 23 left Iteration 1 Error: 0.577842 Iteration 2 Error: 0.122333 Iteration 3 Error: 0.043277 Align patch 3 22 left Iteration 1 Error: 0.868097 Iteration 2 Error: 0.119156 Iteration 3 Error: 0.041313 Align patch 4 21 left Iteration 1 Error: 0.484352 Iteration 2 Error: 0.063379 Iteration 3 Error: 0.016058 Align patch 5 20 left Iteration 1 Error: 0.770022 Iteration 2 Error: 0.109432 Iteration 3 Error: 0.026757 Align patch 6 19 left Iteration 1 Error: 0.629334 Iteration 2 Error: 0.118727 Iteration 3 Error: 0.040957 Align patch 7 18 left Iteration 1 Error: 0.666116 Iteration 2 Error: 0.087549 Iteration 3 Error: 0.020277 Align patch 8 17 left Iteration 1 Error: 0.780106 Iteration 2 Error: 0.121385 Iteration 3 Error: 0.026425 Align patch 9 16 left Iteration 1 Error: 0.540629 Iteration 2 Error: 0.091923 Iteration 3 Error: 0.025427 Align patch 10 15 left Iteration 1 Error: 0.598950 Iteration 2 Error: 0.098163 Iteration 3 Error: 0.020357 Align patch 11 14 left Iteration 1 Error: 0.616010 Iteration 2 Error: 0.085121 Iteration 3 Error: 0.027745 Align patch 12 13 left Iteration 1 Error: 0.835886 Iteration 2 Error: 0.100676 Iteration 3 Error: 0.016063 Align patch 13 12 left Iteration 1 Error: 0.496956 Iteration 2 Error: 0.085237 Iteration 3 Error: 0.016778 Align patch 14 11 left Iteration 1 Error: 0.773872 Iteration 2 Error: 0.084127 Iteration 3 Error: 0.013442 Align patch 15 10 left Iteration 1 Error: 0.617010 Iteration 2 Error: 0.076379 Iteration 3 Error: 0.015438 Align patch 16 9 left Iteration 1 Error: 0.669716 Iteration 2 Error: 0.125583 Iteration 3 Error: 0.026873 Align patch 17 8 left Iteration 1 Error: 0.844409 Iteration 2 Error: 0.108518 Iteration 3 Error: 0.033082 Align patch 18 7 left Iteration 1 Error: 0.816762 Iteration 2 Error: 0.097480 Iteration 3 Error: 0.021282 Align patch 19 6 left Iteration 1 Error: 0.538211 Iteration 2 Error: 0.176166 Iteration 3 Error: 0.058585 Iteration 4 Error: 0.019002 Align patch 20 5 left Iteration 1 Error: 0.676126 Iteration 2 Error: 0.104906 Iteration 3 Error: 0.028703 Align patch 21 4 left Iteration 1 Error: 0.564967 Iteration 2 Error: 0.094627 Iteration 3 Error: 0.042620 Align patch 22 3 left Iteration 1 Error: 0.680341 Iteration 2 Error: 0.113980 Iteration 3 Error: 0.025225 Align patch 23 2 left Iteration 1 Error: 0.721876 Iteration 2 Error: 0.090174 Iteration 3 Error: 0.021718 Align patch 24 1 left Iteration 1 Error: 0.937760 Iteration 2 Error: 0.188520 Iteration 3 Error: 0.052730 Iteration 4 Error: 0.021350 Align patch 25 0 left Iteration 1 Error: 1.320838 Iteration 2 Error: 0.175833 Iteration 3 Error: 0.031823 3D Fitting completed. Patch alignment time: 15.33(sec) Local motion has been corrected. Process thread exits. Computational time: 24.340366 sec Total time: 29.953381 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00007hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00007hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.797862s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00007hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.720875s ........................................ >>>>>>TIME<<<<<< FFT: 0.942840s Defocus_U Defocus_V Angle CCC 11609.67 10925.51 82.97 0.041991 Final Values Defocus_U Defocus_V Angle CCC 11654.94 11017.78 83.92 0.071494 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00008hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00008hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.352e-01 1.005e-01 CC threshold: 0.739 Mean Std: 37.44 6.62 Num Hot pixels: 207 Hot pixel threshold: 77.18 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.408298 Iteration 2 Error: 0.270996 Iteration 3 Error: 0.052744 Iteration 4 Error: 0.011828 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.08 0.18 ...... Frame ( 3) shift: 0.16 0.37 ...... Frame ( 4) shift: 0.24 0.55 ...... Frame ( 5) shift: 0.31 0.74 ...... Frame ( 6) shift: 0.40 0.93 ...... Frame ( 7) shift: 0.48 1.13 ...... Frame ( 8) shift: 0.57 1.34 ...... Frame ( 9) shift: 0.63 1.51 ...... Frame ( 10) shift: 0.65 1.65 ...... Frame ( 11) shift: 0.67 1.79 ...... Frame ( 12) shift: 0.72 1.90 ...... Frame ( 13) shift: 0.78 1.99 ...... Frame ( 14) shift: 0.84 2.08 ...... Frame ( 15) shift: 0.90 2.16 ...... Frame ( 16) shift: 0.96 2.22 ...... Frame ( 17) shift: 1.01 2.28 ...... Frame ( 18) shift: 1.11 2.38 ...... Frame ( 19) shift: 1.23 2.52 ...... Frame ( 20) shift: 1.36 2.66 ...... Frame ( 21) shift: 1.43 2.73 ...... Frame ( 22) shift: 1.46 2.74 ...... Frame ( 23) shift: 1.48 2.74 ...... Frame ( 24) shift: 1.51 2.80 ...... Frame ( 25) shift: 1.55 2.92 ...... Frame ( 26) shift: 1.59 3.03 ...... Frame ( 27) shift: 1.64 3.15 ...... Frame ( 28) shift: 1.70 3.26 ...... Frame ( 29) shift: 1.76 3.37 ...... Frame ( 30) shift: 1.81 3.47 ...... Frame ( 31) shift: 1.84 3.57 ...... Frame ( 32) shift: 1.88 3.66 ...... Frame ( 33) shift: 1.93 3.74 ...... Frame ( 34) shift: 1.99 3.80 ...... Frame ( 35) shift: 2.06 3.86 ...... Frame ( 36) shift: 2.12 3.92 ...... Frame ( 37) shift: 2.16 3.98 ...... Frame ( 38) shift: 2.21 4.04 ...... Frame ( 39) shift: 2.26 4.11 ...... Frame ( 40) shift: 2.30 4.17 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.641946 Iteration 2 Error: 0.195385 Iteration 3 Error: 0.055483 Iteration 4 Error: 0.023298 Align patch 2 23 left Iteration 1 Error: 1.227415 Iteration 2 Error: 0.138683 Iteration 3 Error: 0.031823 Align patch 3 22 left Iteration 1 Error: 1.113181 Iteration 2 Error: 0.084034 Iteration 3 Error: 0.014784 Align patch 4 21 left Iteration 1 Error: 1.602488 Iteration 2 Error: 0.159868 Iteration 3 Error: 0.035117 Align patch 5 20 left Iteration 1 Error: 2.287371 Iteration 2 Error: 0.148204 Iteration 3 Error: 0.024572 Align patch 6 19 left Iteration 1 Error: 1.452577 Iteration 2 Error: 0.171415 Iteration 3 Error: 0.030757 Align patch 7 18 left Iteration 1 Error: 0.962892 Iteration 2 Error: 0.124807 Iteration 3 Error: 0.031076 Align patch 8 17 left Iteration 1 Error: 0.795897 Iteration 2 Error: 0.098189 Iteration 3 Error: 0.026069 Align patch 9 16 left Iteration 1 Error: 1.062587 Iteration 2 Error: 0.098634 Iteration 3 Error: 0.013525 Align patch 10 15 left Iteration 1 Error: 1.346319 Iteration 2 Error: 0.081982 Iteration 3 Error: 0.006977 Align patch 11 14 left Iteration 1 Error: 1.955747 Iteration 2 Error: 0.256883 Iteration 3 Error: 0.065163 Iteration 4 Error: 0.021326 Align patch 12 13 left Iteration 1 Error: 0.640542 Iteration 2 Error: 0.064578 Iteration 3 Error: 0.013148 Align patch 13 12 left Iteration 1 Error: 0.980413 Iteration 2 Error: 0.111645 Iteration 3 Error: 0.035520 Align patch 14 11 left Iteration 1 Error: 0.500163 Iteration 2 Error: 0.054606 Iteration 3 Error: 0.007348 Align patch 15 10 left Iteration 1 Error: 0.604773 Iteration 2 Error: 0.027190 Align patch 16 9 left Iteration 1 Error: 1.136954 Iteration 2 Error: 0.260064 Iteration 3 Error: 0.072696 Iteration 4 Error: 0.032008 Align patch 17 8 left Iteration 1 Error: 0.747611 Iteration 2 Error: 0.174188 Iteration 3 Error: 0.036574 Align patch 18 7 left Iteration 1 Error: 0.801707 Iteration 2 Error: 0.197961 Iteration 3 Error: 0.033607 Align patch 19 6 left Iteration 1 Error: 1.099724 Iteration 2 Error: 0.166284 Iteration 3 Error: 0.019835 Align patch 20 5 left Iteration 1 Error: 1.136717 Iteration 2 Error: 0.047639 Align patch 21 4 left Iteration 1 Error: 0.827049 Iteration 2 Error: 0.131944 Iteration 3 Error: 0.024344 Align patch 22 3 left Iteration 1 Error: 0.795259 Iteration 2 Error: 0.142717 Iteration 3 Error: 0.049571 Align patch 23 2 left Iteration 1 Error: 0.536208 Iteration 2 Error: 0.112497 Iteration 3 Error: 0.039479 Align patch 24 1 left Iteration 1 Error: 0.982215 Iteration 2 Error: 0.127287 Iteration 3 Error: 0.028720 Align patch 25 0 left Iteration 1 Error: 1.561568 Iteration 2 Error: 0.073874 Iteration 3 Error: 0.004552 3D Fitting completed. Patch alignment time: 15.50(sec) Local motion has been corrected. Process thread exits. Computational time: 24.648451 sec Total time: 30.429346 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00008hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00008hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.557505s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00008hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.761610s ........................................ >>>>>>TIME<<<<<< FFT: 0.830035s Defocus_U Defocus_V Angle CCC 9697.27 10564.46 13.73 0.085061 Final Values Defocus_U Defocus_V Angle CCC 9708.20 10591.03 13.73 0.148133 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00008hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00008hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 41.42 7.03 Num Hot pixels: 189 Hot pixel threshold: 83.60 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.429100 Iteration 2 Error: 0.146426 Iteration 3 Error: 0.034788 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.11 0.19 ...... Frame ( 3) shift: -0.22 0.37 ...... Frame ( 4) shift: -0.32 0.56 ...... Frame ( 5) shift: -0.43 0.75 ...... Frame ( 6) shift: -0.49 0.88 ...... Frame ( 7) shift: -0.51 0.96 ...... Frame ( 8) shift: -0.53 1.05 ...... Frame ( 9) shift: -0.50 1.15 ...... Frame ( 10) shift: -0.41 1.27 ...... Frame ( 11) shift: -0.33 1.39 ...... Frame ( 12) shift: -0.26 1.49 ...... Frame ( 13) shift: -0.22 1.58 ...... Frame ( 14) shift: -0.18 1.67 ...... Frame ( 15) shift: -0.15 1.74 ...... Frame ( 16) shift: -0.15 1.80 ...... Frame ( 17) shift: -0.14 1.85 ...... Frame ( 18) shift: -0.10 1.88 ...... Frame ( 19) shift: -0.02 1.88 ...... Frame ( 20) shift: 0.06 1.89 ...... Frame ( 21) shift: 0.11 1.91 ...... Frame ( 22) shift: 0.13 1.94 ...... Frame ( 23) shift: 0.16 1.98 ...... Frame ( 24) shift: 0.18 2.00 ...... Frame ( 25) shift: 0.21 2.00 ...... Frame ( 26) shift: 0.25 2.01 ...... Frame ( 27) shift: 0.25 2.05 ...... Frame ( 28) shift: 0.23 2.13 ...... Frame ( 29) shift: 0.21 2.21 ...... Frame ( 30) shift: 0.21 2.27 ...... Frame ( 31) shift: 0.23 2.32 ...... Frame ( 32) shift: 0.25 2.36 ...... Frame ( 33) shift: 0.28 2.36 ...... Frame ( 34) shift: 0.33 2.33 ...... Frame ( 35) shift: 0.38 2.29 ...... Frame ( 36) shift: 0.43 2.28 ...... Frame ( 37) shift: 0.48 2.29 ...... Frame ( 38) shift: 0.53 2.30 ...... Frame ( 39) shift: 0.58 2.32 ...... Frame ( 40) shift: 0.64 2.33 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.408966 Iteration 2 Error: 0.084416 Iteration 3 Error: 0.016115 Align patch 2 23 left Iteration 1 Error: 0.797617 Iteration 2 Error: 0.084041 Iteration 3 Error: 0.030893 Align patch 3 22 left Iteration 1 Error: 1.039566 Iteration 2 Error: 0.077266 Iteration 3 Error: 0.010523 Align patch 4 21 left Iteration 1 Error: 0.811385 Iteration 2 Error: 0.100863 Iteration 3 Error: 0.024594 Align patch 5 20 left Iteration 1 Error: 0.751431 Iteration 2 Error: 0.063344 Iteration 3 Error: 0.017081 Align patch 6 19 left Iteration 1 Error: 0.668590 Iteration 2 Error: 0.088898 Iteration 3 Error: 0.017195 Align patch 7 18 left Iteration 1 Error: 0.591738 Iteration 2 Error: 0.089175 Iteration 3 Error: 0.016109 Align patch 8 17 left Iteration 1 Error: 0.889448 Iteration 2 Error: 0.109946 Iteration 3 Error: 0.035385 Align patch 9 16 left Iteration 1 Error: 0.732642 Iteration 2 Error: 0.169438 Iteration 3 Error: 0.033066 Align patch 10 15 left Iteration 1 Error: 0.571572 Iteration 2 Error: 0.153266 Iteration 3 Error: 0.037372 Align patch 11 14 left Iteration 1 Error: 0.873559 Iteration 2 Error: 0.104777 Iteration 3 Error: 0.021567 Align patch 12 13 left Iteration 1 Error: 0.462018 Iteration 2 Error: 0.086914 Iteration 3 Error: 0.016929 Align patch 13 12 left Iteration 1 Error: 0.637603 Iteration 2 Error: 0.081874 Iteration 3 Error: 0.019860 Align patch 14 11 left Iteration 1 Error: 0.419626 Iteration 2 Error: 0.061261 Iteration 3 Error: 0.014324 Align patch 15 10 left Iteration 1 Error: 0.485838 Iteration 2 Error: 0.073967 Iteration 3 Error: 0.017903 Align patch 16 9 left Iteration 1 Error: 0.798840 Iteration 2 Error: 0.153366 Iteration 3 Error: 0.034446 Align patch 17 8 left Iteration 1 Error: 0.520287 Iteration 2 Error: 0.114798 Iteration 3 Error: 0.017243 Align patch 18 7 left Iteration 1 Error: 0.662879 Iteration 2 Error: 0.136274 Iteration 3 Error: 0.043940 Align patch 19 6 left Iteration 1 Error: 0.865539 Iteration 2 Error: 0.101434 Iteration 3 Error: 0.017368 Align patch 20 5 left Iteration 1 Error: 0.726231 Iteration 2 Error: 0.124709 Iteration 3 Error: 0.024469 Align patch 21 4 left Iteration 1 Error: 0.915229 Iteration 2 Error: 0.106837 Iteration 3 Error: 0.019196 Align patch 22 3 left Iteration 1 Error: 0.663735 Iteration 2 Error: 0.092619 Iteration 3 Error: 0.021532 Align patch 23 2 left Iteration 1 Error: 0.643331 Iteration 2 Error: 0.131120 Iteration 3 Error: 0.039112 Align patch 24 1 left Iteration 1 Error: 0.508804 Iteration 2 Error: 0.066128 Iteration 3 Error: 0.011090 Align patch 25 0 left Iteration 1 Error: 0.737786 Iteration 2 Error: 0.085893 Iteration 3 Error: 0.019354 3D Fitting completed. Patch alignment time: 14.86(sec) Local motion has been corrected. Process thread exits. Computational time: 23.574032 sec Total time: 29.346186 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00008hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00008hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.540831s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00008hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.750501s ........................................ >>>>>>TIME<<<<<< FFT: 0.954511s Defocus_U Defocus_V Angle CCC 8054.64 8507.86 1.92 0.036541 Final Values Defocus_U Defocus_V Angle CCC 8064.01 8514.12 2.24 0.076689 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00008hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00008hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 42.38 7.03 Num Hot pixels: 242 Hot pixel threshold: 84.54 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.097838 Iteration 2 Error: 0.205736 Iteration 3 Error: 0.052279 Iteration 4 Error: 0.016273 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.18 -0.11 ...... Frame ( 3) shift: -0.36 -0.22 ...... Frame ( 4) shift: -0.54 -0.33 ...... Frame ( 5) shift: -0.72 -0.44 ...... Frame ( 6) shift: -0.77 -0.46 ...... Frame ( 7) shift: -0.69 -0.39 ...... Frame ( 8) shift: -0.61 -0.32 ...... Frame ( 9) shift: -0.52 -0.28 ...... Frame ( 10) shift: -0.42 -0.27 ...... Frame ( 11) shift: -0.32 -0.26 ...... Frame ( 12) shift: -0.22 -0.23 ...... Frame ( 13) shift: -0.14 -0.20 ...... Frame ( 14) shift: -0.06 -0.16 ...... Frame ( 15) shift: -0.01 -0.10 ...... Frame ( 16) shift: 0.01 0.01 ...... Frame ( 17) shift: 0.04 0.11 ...... Frame ( 18) shift: 0.09 0.20 ...... Frame ( 19) shift: 0.18 0.29 ...... Frame ( 20) shift: 0.26 0.37 ...... Frame ( 21) shift: 0.35 0.43 ...... Frame ( 22) shift: 0.45 0.46 ...... Frame ( 23) shift: 0.54 0.49 ...... Frame ( 24) shift: 0.57 0.53 ...... Frame ( 25) shift: 0.54 0.59 ...... Frame ( 26) shift: 0.50 0.65 ...... Frame ( 27) shift: 0.49 0.73 ...... Frame ( 28) shift: 0.52 0.82 ...... Frame ( 29) shift: 0.54 0.92 ...... Frame ( 30) shift: 0.57 1.01 ...... Frame ( 31) shift: 0.60 1.10 ...... Frame ( 32) shift: 0.63 1.18 ...... Frame ( 33) shift: 0.65 1.26 ...... Frame ( 34) shift: 0.67 1.34 ...... Frame ( 35) shift: 0.69 1.41 ...... Frame ( 36) shift: 0.71 1.45 ...... Frame ( 37) shift: 0.74 1.44 ...... Frame ( 38) shift: 0.77 1.44 ...... Frame ( 39) shift: 0.79 1.44 ...... Frame ( 40) shift: 0.82 1.43 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.796086 Iteration 2 Error: 0.085240 Iteration 3 Error: 0.022258 Align patch 2 23 left Iteration 1 Error: 0.493078 Iteration 2 Error: 0.111158 Iteration 3 Error: 0.029237 Align patch 3 22 left Iteration 1 Error: 0.489075 Iteration 2 Error: 0.103294 Iteration 3 Error: 0.016649 Align patch 4 21 left Iteration 1 Error: 0.558456 Iteration 2 Error: 0.077320 Iteration 3 Error: 0.026046 Align patch 5 20 left Iteration 1 Error: 0.557802 Iteration 2 Error: 0.080198 Iteration 3 Error: 0.017241 Align patch 6 19 left Iteration 1 Error: 0.564010 Iteration 2 Error: 0.100290 Iteration 3 Error: 0.015345 Align patch 7 18 left Iteration 1 Error: 0.942420 Iteration 2 Error: 0.114748 Iteration 3 Error: 0.029844 Align patch 8 17 left Iteration 1 Error: 0.736061 Iteration 2 Error: 0.132422 Iteration 3 Error: 0.033027 Align patch 9 16 left Iteration 1 Error: 0.866720 Iteration 2 Error: 0.112331 Iteration 3 Error: 0.029296 Align patch 10 15 left Iteration 1 Error: 0.568900 Iteration 2 Error: 0.073261 Iteration 3 Error: 0.017389 Align patch 11 14 left Iteration 1 Error: 0.681667 Iteration 2 Error: 0.106285 Iteration 3 Error: 0.023805 Align patch 12 13 left Iteration 1 Error: 0.972112 Iteration 2 Error: 0.123753 Iteration 3 Error: 0.028333 Align patch 13 12 left Iteration 1 Error: 0.666206 Iteration 2 Error: 0.205793 Iteration 3 Error: 0.070988 Iteration 4 Error: 0.016568 Align patch 14 11 left Iteration 1 Error: 0.600119 Iteration 2 Error: 0.115305 Iteration 3 Error: 0.032905 Align patch 15 10 left Iteration 1 Error: 0.704094 Iteration 2 Error: 0.090669 Iteration 3 Error: 0.017563 Align patch 16 9 left Iteration 1 Error: 0.671463 Iteration 2 Error: 0.118910 Iteration 3 Error: 0.020251 Align patch 17 8 left Iteration 1 Error: 0.678345 Iteration 2 Error: 0.134789 Iteration 3 Error: 0.031589 Align patch 18 7 left Iteration 1 Error: 0.683778 Iteration 2 Error: 0.110040 Iteration 3 Error: 0.023182 Align patch 19 6 left Iteration 1 Error: 0.781536 Iteration 2 Error: 0.140862 Iteration 3 Error: 0.038859 Align patch 20 5 left Iteration 1 Error: 0.560244 Iteration 2 Error: 0.167270 Iteration 3 Error: 0.042982 Align patch 21 4 left Iteration 1 Error: 0.709538 Iteration 2 Error: 0.121456 Iteration 3 Error: 0.032893 Align patch 22 3 left Iteration 1 Error: 0.603951 Iteration 2 Error: 0.120982 Iteration 3 Error: 0.021639 Align patch 23 2 left Iteration 1 Error: 0.662209 Iteration 2 Error: 0.109471 Iteration 3 Error: 0.020842 Align patch 24 1 left Iteration 1 Error: 0.886084 Iteration 2 Error: 0.122182 Iteration 3 Error: 0.027178 Align patch 25 0 left Iteration 1 Error: 0.952053 Iteration 2 Error: 0.146810 Iteration 3 Error: 0.044796 3D Fitting completed. Patch alignment time: 14.79(sec) Local motion has been corrected. Process thread exits. Computational time: 23.797203 sec Total time: 29.553045 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00008hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00008hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.760317s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00008hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.468287s ........................................ >>>>>>TIME<<<<<< FFT: 0.940612s Defocus_U Defocus_V Angle CCC 14048.83 14830.08 6.06 0.058237 Final Values Defocus_U Defocus_V Angle CCC 14053.52 14831.64 6.06 0.093605 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00008hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00008hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 44.01 7.30 Num Hot pixels: 198 Hot pixel threshold: 87.84 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.529665 Iteration 2 Error: 0.057312 Iteration 3 Error: 0.012943 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.19 0.03 ...... Frame ( 3) shift: -0.37 0.07 ...... Frame ( 4) shift: -0.56 0.10 ...... Frame ( 5) shift: -0.74 0.13 ...... Frame ( 6) shift: -0.83 0.17 ...... Frame ( 7) shift: -0.83 0.20 ...... Frame ( 8) shift: -0.82 0.23 ...... Frame ( 9) shift: -0.80 0.26 ...... Frame ( 10) shift: -0.76 0.29 ...... Frame ( 11) shift: -0.72 0.32 ...... Frame ( 12) shift: -0.68 0.36 ...... Frame ( 13) shift: -0.65 0.41 ...... Frame ( 14) shift: -0.62 0.46 ...... Frame ( 15) shift: -0.59 0.50 ...... Frame ( 16) shift: -0.54 0.54 ...... Frame ( 17) shift: -0.50 0.58 ...... Frame ( 18) shift: -0.48 0.62 ...... Frame ( 19) shift: -0.49 0.66 ...... Frame ( 20) shift: -0.50 0.70 ...... Frame ( 21) shift: -0.50 0.71 ...... Frame ( 22) shift: -0.49 0.68 ...... Frame ( 23) shift: -0.48 0.66 ...... Frame ( 24) shift: -0.47 0.66 ...... Frame ( 25) shift: -0.44 0.67 ...... Frame ( 26) shift: -0.41 0.69 ...... Frame ( 27) shift: -0.41 0.72 ...... Frame ( 28) shift: -0.42 0.74 ...... Frame ( 29) shift: -0.44 0.77 ...... Frame ( 30) shift: -0.44 0.78 ...... Frame ( 31) shift: -0.41 0.77 ...... Frame ( 32) shift: -0.38 0.76 ...... Frame ( 33) shift: -0.35 0.76 ...... Frame ( 34) shift: -0.34 0.74 ...... Frame ( 35) shift: -0.32 0.73 ...... Frame ( 36) shift: -0.30 0.76 ...... Frame ( 37) shift: -0.27 0.82 ...... Frame ( 38) shift: -0.25 0.89 ...... Frame ( 39) shift: -0.22 0.96 ...... Frame ( 40) shift: -0.20 1.03 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.123820 Iteration 2 Error: 0.170399 Iteration 3 Error: 0.045592 Align patch 2 23 left Iteration 1 Error: 0.588618 Iteration 2 Error: 0.058535 Iteration 3 Error: 0.013614 Align patch 3 22 left Iteration 1 Error: 0.701901 Iteration 2 Error: 0.093742 Iteration 3 Error: 0.028825 Align patch 4 21 left Iteration 1 Error: 0.655712 Iteration 2 Error: 0.108694 Iteration 3 Error: 0.029082 Align patch 5 20 left Iteration 1 Error: 0.700882 Iteration 2 Error: 0.119595 Iteration 3 Error: 0.018009 Align patch 6 19 left Iteration 1 Error: 1.188205 Iteration 2 Error: 0.134343 Iteration 3 Error: 0.028974 Align patch 7 18 left Iteration 1 Error: 0.621447 Iteration 2 Error: 0.078653 Iteration 3 Error: 0.020884 Align patch 8 17 left Iteration 1 Error: 0.514502 Iteration 2 Error: 0.049497 Align patch 9 16 left Iteration 1 Error: 0.490296 Iteration 2 Error: 0.059917 Iteration 3 Error: 0.018825 Align patch 10 15 left Iteration 1 Error: 0.452074 Iteration 2 Error: 0.079754 Iteration 3 Error: 0.013770 Align patch 11 14 left Iteration 1 Error: 0.585598 Iteration 2 Error: 0.081616 Iteration 3 Error: 0.018921 Align patch 12 13 left Iteration 1 Error: 0.673369 Iteration 2 Error: 0.072550 Iteration 3 Error: 0.015364 Align patch 13 12 left Iteration 1 Error: 0.758874 Iteration 2 Error: 0.115101 Iteration 3 Error: 0.024128 Align patch 14 11 left Iteration 1 Error: 0.608959 Iteration 2 Error: 0.061468 Iteration 3 Error: 0.015793 Align patch 15 10 left Iteration 1 Error: 0.755225 Iteration 2 Error: 0.094861 Iteration 3 Error: 0.018344 Align patch 16 9 left Iteration 1 Error: 0.506200 Iteration 2 Error: 0.081203 Iteration 3 Error: 0.016924 Align patch 17 8 left Iteration 1 Error: 0.637887 Iteration 2 Error: 0.103801 Iteration 3 Error: 0.018638 Align patch 18 7 left Iteration 1 Error: 0.712493 Iteration 2 Error: 0.098562 Iteration 3 Error: 0.021940 Align patch 19 6 left Iteration 1 Error: 0.807063 Iteration 2 Error: 0.073813 Iteration 3 Error: 0.017350 Align patch 20 5 left Iteration 1 Error: 0.784908 Iteration 2 Error: 0.168794 Iteration 3 Error: 0.046948 Align patch 21 4 left Iteration 1 Error: 0.872829 Iteration 2 Error: 0.181475 Iteration 3 Error: 0.029254 Align patch 22 3 left Iteration 1 Error: 0.842142 Iteration 2 Error: 0.106435 Iteration 3 Error: 0.022617 Align patch 23 2 left Iteration 1 Error: 1.025569 Iteration 2 Error: 0.121803 Iteration 3 Error: 0.016838 Align patch 24 1 left Iteration 1 Error: 0.480114 Iteration 2 Error: 0.065662 Iteration 3 Error: 0.014592 Align patch 25 0 left Iteration 1 Error: 0.645726 Iteration 2 Error: 0.094927 Iteration 3 Error: 0.020012 3D Fitting completed. Patch alignment time: 14.14(sec) Local motion has been corrected. Process thread exits. Computational time: 22.715277 sec Total time: 28.662197 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00008hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00008hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.563317s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00008hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.386757s ........................................ >>>>>>TIME<<<<<< FFT: 0.923934s Defocus_U Defocus_V Angle CCC 11421.93 10781.23 85.32 0.060141 Final Values Defocus_U Defocus_V Angle CCC 11443.81 10787.49 85.01 0.107119 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00009hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00009hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.367e-01 1.016e-01 CC threshold: 0.746 Mean Std: 24.85 17.74 Num Hot pixels: 12 Hot pixel threshold: 131.27 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.947624 Iteration 2 Error: 0.238678 Iteration 3 Error: 0.069607 Iteration 4 Error: 0.018615 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.00 0.04 ...... Frame ( 3) shift: -0.00 0.07 ...... Frame ( 4) shift: -0.00 0.11 ...... Frame ( 5) shift: -0.00 0.15 ...... Frame ( 6) shift: 0.00 0.19 ...... Frame ( 7) shift: 0.01 0.23 ...... Frame ( 8) shift: 0.03 0.27 ...... Frame ( 9) shift: 0.05 0.30 ...... Frame ( 10) shift: 0.09 0.33 ...... Frame ( 11) shift: 0.13 0.36 ...... Frame ( 12) shift: 0.16 0.40 ...... Frame ( 13) shift: 0.18 0.43 ...... Frame ( 14) shift: 0.20 0.46 ...... Frame ( 15) shift: 0.23 0.50 ...... Frame ( 16) shift: 0.28 0.54 ...... Frame ( 17) shift: 0.33 0.59 ...... Frame ( 18) shift: 0.35 0.61 ...... Frame ( 19) shift: 0.36 0.62 ...... Frame ( 20) shift: 0.36 0.63 ...... Frame ( 21) shift: 0.35 0.63 ...... Frame ( 22) shift: 0.32 0.63 ...... Frame ( 23) shift: 0.29 0.62 ...... Frame ( 24) shift: 0.28 0.64 ...... Frame ( 25) shift: 0.29 0.69 ...... Frame ( 26) shift: 0.30 0.74 ...... Frame ( 27) shift: 0.32 0.79 ...... Frame ( 28) shift: 0.35 0.86 ...... Frame ( 29) shift: 0.38 0.93 ...... Frame ( 30) shift: 0.41 0.99 ...... Frame ( 31) shift: 0.44 1.03 ...... Frame ( 32) shift: 0.47 1.08 ...... Frame ( 33) shift: 0.49 1.12 ...... Frame ( 34) shift: 0.50 1.16 ...... Frame ( 35) shift: 0.52 1.20 ...... Frame ( 36) shift: 0.54 1.24 ...... Frame ( 37) shift: 0.56 1.29 ...... Frame ( 38) shift: 0.57 1.34 ...... Frame ( 39) shift: 0.59 1.39 ...... Frame ( 40) shift: 0.61 1.44 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.588312 Iteration 2 Error: 0.085663 Iteration 3 Error: 0.015943 Align patch 2 23 left Iteration 1 Error: 0.609270 Iteration 2 Error: 0.114316 Iteration 3 Error: 0.018759 Align patch 3 22 left Iteration 1 Error: 0.598934 Iteration 2 Error: 0.041639 Align patch 4 21 left Iteration 1 Error: 0.307440 Iteration 2 Error: 0.075498 Iteration 3 Error: 0.009873 Align patch 5 20 left Iteration 1 Error: 0.498269 Iteration 2 Error: 0.036746 Align patch 6 19 left Iteration 1 Error: 1.169604 Iteration 2 Error: 0.093017 Iteration 3 Error: 0.026627 Align patch 7 18 left Iteration 1 Error: 0.680487 Iteration 2 Error: 0.077609 Iteration 3 Error: 0.017576 Align patch 8 17 left Iteration 1 Error: 0.383668 Iteration 2 Error: 0.052135 Iteration 3 Error: 0.017128 Align patch 9 16 left Iteration 1 Error: 0.485275 Iteration 2 Error: 0.093752 Iteration 3 Error: 0.025099 Align patch 10 15 left Iteration 1 Error: 0.544603 Iteration 2 Error: 0.020879 Align patch 11 14 left Iteration 1 Error: 1.488811 Iteration 2 Error: 0.217393 Iteration 3 Error: 0.029908 Align patch 12 13 left Iteration 1 Error: 0.761310 Iteration 2 Error: 0.050192 Iteration 3 Error: 0.007757 Align patch 13 12 left Iteration 1 Error: 0.422244 Iteration 2 Error: 0.081784 Iteration 3 Error: 0.022423 Align patch 14 11 left Iteration 1 Error: 0.481609 Iteration 2 Error: 0.073515 Iteration 3 Error: 0.016594 Align patch 15 10 left Iteration 1 Error: 0.452463 Iteration 2 Error: 0.073544 Iteration 3 Error: 0.012872 Align patch 16 9 left Iteration 1 Error: 0.606359 Iteration 2 Error: 0.126329 Iteration 3 Error: 0.026951 Align patch 17 8 left Iteration 1 Error: 0.281343 Iteration 2 Error: 0.078179 Iteration 3 Error: 0.018571 Align patch 18 7 left Iteration 1 Error: 0.447691 Iteration 2 Error: 0.200218 Iteration 3 Error: 0.089598 Iteration 4 Error: 0.040131 Align patch 19 6 left Iteration 1 Error: 0.661390 Iteration 2 Error: 0.075499 Iteration 3 Error: 0.009443 Align patch 20 5 left Iteration 1 Error: 0.660328 Iteration 2 Error: 0.055232 Iteration 3 Error: 0.005314 Align patch 21 4 left Iteration 1 Error: 0.632863 Iteration 2 Error: 0.096513 Iteration 3 Error: 0.015478 Align patch 22 3 left Iteration 1 Error: 0.256242 Iteration 2 Error: 0.131923 Iteration 3 Error: 0.059697 Iteration 4 Error: 0.030466 Align patch 23 2 left Iteration 1 Error: 0.287131 Iteration 2 Error: 0.112109 Iteration 3 Error: 0.039087 Align patch 24 1 left Iteration 1 Error: 0.907687 Iteration 2 Error: 0.120689 Iteration 3 Error: 0.016871 Align patch 25 0 left Iteration 1 Error: 0.615359 Iteration 2 Error: 0.034946 3D Fitting completed. Patch alignment time: 14.62(sec) Local motion has been corrected. Process thread exits. Computational time: 23.952372 sec Total time: 30.026690 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00009hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00009hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.665763s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00009hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.058547s ........................................ >>>>>>TIME<<<<<< FFT: 0.952305s Defocus_U Defocus_V Angle CCC 13255.89 14017.61 12.02 0.013739 Final Values Defocus_U Defocus_V Angle CCC 13265.27 14026.99 11.08 0.031689 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00009hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00009hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.371e-01 1.019e-01 CC threshold: 0.748 Mean Std: 26.14 17.92 Num Hot pixels: 14 Hot pixel threshold: 133.66 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.826286 Iteration 2 Error: 0.085536 Iteration 3 Error: 0.021155 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.00 0.07 ...... Frame ( 3) shift: 0.01 0.14 ...... Frame ( 4) shift: 0.01 0.20 ...... Frame ( 5) shift: 0.02 0.27 ...... Frame ( 6) shift: 0.02 0.34 ...... Frame ( 7) shift: 0.01 0.40 ...... Frame ( 8) shift: 0.01 0.46 ...... Frame ( 9) shift: 0.00 0.52 ...... Frame ( 10) shift: -0.02 0.58 ...... Frame ( 11) shift: -0.03 0.64 ...... Frame ( 12) shift: -0.04 0.68 ...... Frame ( 13) shift: -0.02 0.69 ...... Frame ( 14) shift: -0.01 0.70 ...... Frame ( 15) shift: 0.00 0.71 ...... Frame ( 16) shift: 0.01 0.74 ...... Frame ( 17) shift: 0.03 0.76 ...... Frame ( 18) shift: 0.05 0.81 ...... Frame ( 19) shift: 0.09 0.87 ...... Frame ( 20) shift: 0.12 0.94 ...... Frame ( 21) shift: 0.13 0.98 ...... Frame ( 22) shift: 0.11 1.00 ...... Frame ( 23) shift: 0.09 1.02 ...... Frame ( 24) shift: 0.07 1.05 ...... Frame ( 25) shift: 0.06 1.08 ...... Frame ( 26) shift: 0.04 1.11 ...... Frame ( 27) shift: 0.04 1.15 ...... Frame ( 28) shift: 0.05 1.20 ...... Frame ( 29) shift: 0.06 1.25 ...... Frame ( 30) shift: 0.08 1.29 ...... Frame ( 31) shift: 0.09 1.31 ...... Frame ( 32) shift: 0.11 1.33 ...... Frame ( 33) shift: 0.11 1.34 ...... Frame ( 34) shift: 0.09 1.33 ...... Frame ( 35) shift: 0.07 1.33 ...... Frame ( 36) shift: 0.06 1.35 ...... Frame ( 37) shift: 0.06 1.38 ...... Frame ( 38) shift: 0.06 1.42 ...... Frame ( 39) shift: 0.06 1.46 ...... Frame ( 40) shift: 0.05 1.49 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.145383 Iteration 2 Error: 0.084715 Iteration 3 Error: 0.021258 Align patch 2 23 left Iteration 1 Error: 0.835312 Iteration 2 Error: 0.093989 Iteration 3 Error: 0.025495 Align patch 3 22 left Iteration 1 Error: 0.281454 Iteration 2 Error: 0.034740 Align patch 4 21 left Iteration 1 Error: 0.481449 Iteration 2 Error: 0.039010 Align patch 5 20 left Iteration 1 Error: 0.942918 Iteration 2 Error: 0.051806 Iteration 3 Error: 0.006675 Align patch 6 19 left Iteration 1 Error: 1.882593 Iteration 2 Error: 0.213964 Iteration 3 Error: 0.072422 Iteration 4 Error: 0.025484 Align patch 7 18 left Iteration 1 Error: 1.182273 Iteration 2 Error: 0.147957 Iteration 3 Error: 0.027270 Align patch 8 17 left Iteration 1 Error: 0.618974 Iteration 2 Error: 0.056016 Iteration 3 Error: 0.010237 Align patch 9 16 left Iteration 1 Error: 0.206871 Iteration 2 Error: 0.048095 Align patch 10 15 left Iteration 1 Error: 0.695666 Iteration 2 Error: 0.045755 Align patch 11 14 left Iteration 1 Error: 1.781354 Iteration 2 Error: 0.241223 Iteration 3 Error: 0.054847 Iteration 4 Error: 0.014638 Align patch 12 13 left Iteration 1 Error: 1.171204 Iteration 2 Error: 0.105375 Iteration 3 Error: 0.015710 Align patch 13 12 left Iteration 1 Error: 0.457089 Iteration 2 Error: 0.162944 Iteration 3 Error: 0.061367 Iteration 4 Error: 0.022114 Align patch 14 11 left Iteration 1 Error: 0.508043 Iteration 2 Error: 0.160611 Iteration 3 Error: 0.056501 Iteration 4 Error: 0.018196 Align patch 15 10 left Iteration 1 Error: 0.568446 Iteration 2 Error: 0.058338 Iteration 3 Error: 0.006158 Align patch 16 9 left Iteration 1 Error: 0.788816 Iteration 2 Error: 0.104243 Iteration 3 Error: 0.028408 Align patch 17 8 left Iteration 1 Error: 0.716802 Iteration 2 Error: 0.065242 Iteration 3 Error: 0.016211 Align patch 18 7 left Iteration 1 Error: 0.158102 Iteration 2 Error: 0.049538 Align patch 19 6 left Iteration 1 Error: 0.408257 Iteration 2 Error: 0.076665 Iteration 3 Error: 0.015847 Align patch 20 5 left Iteration 1 Error: 0.366155 Iteration 2 Error: 0.024632 Align patch 21 4 left Iteration 1 Error: 0.608330 Iteration 2 Error: 0.125778 Iteration 3 Error: 0.027594 Align patch 22 3 left Iteration 1 Error: 0.186567 Iteration 2 Error: 0.058490 Iteration 3 Error: 0.014755 Align patch 23 2 left Iteration 1 Error: 0.193853 Iteration 2 Error: 0.075848 Iteration 3 Error: 0.026943 Align patch 24 1 left Iteration 1 Error: 0.423301 Iteration 2 Error: 0.081230 Iteration 3 Error: 0.016705 Align patch 25 0 left Iteration 1 Error: 0.325822 Iteration 2 Error: 0.050037 Iteration 3 Error: 0.009447 3D Fitting completed. Patch alignment time: 15.00(sec) Local motion has been corrected. Process thread exits. Computational time: 23.739582 sec Total time: 29.498903 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00009hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00009hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.672297s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00009hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.280667s ........................................ >>>>>>TIME<<<<<< FFT: 0.888850s Defocus_U Defocus_V Angle CCC 9798.82 10244.21 0.46 0.015254 Final Values Defocus_U Defocus_V Angle CCC 10250.47 9817.57 89.52 0.041058 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00009hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00009hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.368e-01 1.017e-01 CC threshold: 0.747 Mean Std: 28.59 17.28 Num Hot pixels: 11 Hot pixel threshold: 132.26 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.664989 Iteration 2 Error: 0.064449 Iteration 3 Error: 0.012655 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.01 0.06 ...... Frame ( 3) shift: -0.03 0.13 ...... Frame ( 4) shift: -0.04 0.19 ...... Frame ( 5) shift: -0.05 0.26 ...... Frame ( 6) shift: -0.06 0.32 ...... Frame ( 7) shift: -0.07 0.37 ...... Frame ( 8) shift: -0.08 0.43 ...... Frame ( 9) shift: -0.08 0.47 ...... Frame ( 10) shift: -0.07 0.51 ...... Frame ( 11) shift: -0.07 0.55 ...... Frame ( 12) shift: -0.07 0.57 ...... Frame ( 13) shift: -0.07 0.59 ...... Frame ( 14) shift: -0.07 0.60 ...... Frame ( 15) shift: -0.07 0.64 ...... Frame ( 16) shift: -0.08 0.70 ...... Frame ( 17) shift: -0.10 0.76 ...... Frame ( 18) shift: -0.09 0.81 ...... Frame ( 19) shift: -0.06 0.84 ...... Frame ( 20) shift: -0.03 0.87 ...... Frame ( 21) shift: -0.01 0.89 ...... Frame ( 22) shift: -0.01 0.90 ...... Frame ( 23) shift: -0.01 0.91 ...... Frame ( 24) shift: -0.01 0.92 ...... Frame ( 25) shift: -0.01 0.92 ...... Frame ( 26) shift: -0.02 0.92 ...... Frame ( 27) shift: -0.04 0.91 ...... Frame ( 28) shift: -0.05 0.90 ...... Frame ( 29) shift: -0.07 0.88 ...... Frame ( 30) shift: -0.08 0.87 ...... Frame ( 31) shift: -0.09 0.87 ...... Frame ( 32) shift: -0.11 0.88 ...... Frame ( 33) shift: -0.09 0.91 ...... Frame ( 34) shift: -0.06 0.97 ...... Frame ( 35) shift: -0.02 1.03 ...... Frame ( 36) shift: -0.01 1.08 ...... Frame ( 37) shift: -0.03 1.13 ...... Frame ( 38) shift: -0.06 1.18 ...... Frame ( 39) shift: -0.08 1.23 ...... Frame ( 40) shift: -0.10 1.28 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.406704 Iteration 2 Error: 0.091882 Iteration 3 Error: 0.020998 Align patch 2 23 left Iteration 1 Error: 1.032487 Iteration 2 Error: 0.118107 Iteration 3 Error: 0.020795 Align patch 3 22 left Iteration 1 Error: 0.480523 Iteration 2 Error: 0.058764 Iteration 3 Error: 0.007445 Align patch 4 21 left Iteration 1 Error: 0.171063 Iteration 2 Error: 0.023130 Align patch 5 20 left Iteration 1 Error: 0.218078 Iteration 2 Error: 0.026721 Align patch 6 19 left Iteration 1 Error: 1.803338 Iteration 2 Error: 0.193400 Iteration 3 Error: 0.043356 Align patch 7 18 left Iteration 1 Error: 1.200693 Iteration 2 Error: 0.123799 Iteration 3 Error: 0.023330 Align patch 8 17 left Iteration 1 Error: 0.962674 Iteration 2 Error: 0.121261 Iteration 3 Error: 0.022960 Align patch 9 16 left Iteration 1 Error: 0.301448 Iteration 2 Error: 0.058022 Iteration 3 Error: 0.018168 Align patch 10 15 left Iteration 1 Error: 0.316064 Iteration 2 Error: 0.040333 Align patch 11 14 left Iteration 1 Error: 1.127890 Iteration 2 Error: 0.076450 Iteration 3 Error: 0.017560 Align patch 12 13 left Iteration 1 Error: 1.076380 Iteration 2 Error: 0.086170 Iteration 3 Error: 0.011707 Align patch 13 12 left Iteration 1 Error: 0.580111 Iteration 2 Error: 0.028013 Align patch 14 11 left Iteration 1 Error: 0.558120 Iteration 2 Error: 0.073669 Iteration 3 Error: 0.014641 Align patch 15 10 left Iteration 1 Error: 0.640752 Iteration 2 Error: 0.049255 Align patch 16 9 left Iteration 1 Error: 0.543348 Iteration 2 Error: 0.099333 Iteration 3 Error: 0.016303 Align patch 17 8 left Iteration 1 Error: 0.658769 Iteration 2 Error: 0.075550 Iteration 3 Error: 0.019609 Align patch 18 7 left Iteration 1 Error: 0.421064 Iteration 2 Error: 0.104236 Iteration 3 Error: 0.027803 Align patch 19 6 left Iteration 1 Error: 0.374634 Iteration 2 Error: 0.046227 Align patch 20 5 left Iteration 1 Error: 0.428560 Iteration 2 Error: 0.018069 Align patch 21 4 left Iteration 1 Error: 0.440023 Iteration 2 Error: 0.051393 Iteration 3 Error: 0.007470 Align patch 22 3 left Iteration 1 Error: 0.137849 Iteration 2 Error: 0.038071 Align patch 23 2 left Iteration 1 Error: 0.141239 Iteration 2 Error: 0.033627 Align patch 24 1 left Iteration 1 Error: 0.568432 Iteration 2 Error: 0.058495 Iteration 3 Error: 0.008152 Align patch 25 0 left Iteration 1 Error: 0.465036 Iteration 2 Error: 0.077059 Iteration 3 Error: 0.013878 3D Fitting completed. Patch alignment time: 14.07(sec) Local motion has been corrected. Process thread exits. Computational time: 22.460205 sec Total time: 28.295038 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00009hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00009hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.586192s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00009hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.997031s ........................................ >>>>>>TIME<<<<<< FFT: 0.973659s Defocus_U Defocus_V Angle CCC 12388.71 13197.31 4.84 0.040017 Final Values Defocus_U Defocus_V Angle CCC 12415.30 13220.76 4.22 0.072395 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00009hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00009hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.363e-01 1.014e-01 CC threshold: 0.744 Mean Std: 29.89 17.12 Num Hot pixels: 17 Hot pixel threshold: 132.59 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.573022 Iteration 2 Error: 0.105773 Iteration 3 Error: 0.028233 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.01 0.02 ...... Frame ( 3) shift: -0.01 0.05 ...... Frame ( 4) shift: -0.02 0.07 ...... Frame ( 5) shift: -0.02 0.10 ...... Frame ( 6) shift: -0.02 0.13 ...... Frame ( 7) shift: -0.03 0.17 ...... Frame ( 8) shift: -0.03 0.22 ...... Frame ( 9) shift: -0.03 0.25 ...... Frame ( 10) shift: -0.04 0.26 ...... Frame ( 11) shift: -0.05 0.28 ...... Frame ( 12) shift: -0.04 0.32 ...... Frame ( 13) shift: -0.02 0.38 ...... Frame ( 14) shift: 0.00 0.44 ...... Frame ( 15) shift: -0.01 0.48 ...... Frame ( 16) shift: -0.06 0.50 ...... Frame ( 17) shift: -0.10 0.52 ...... Frame ( 18) shift: -0.13 0.54 ...... Frame ( 19) shift: -0.16 0.57 ...... Frame ( 20) shift: -0.18 0.59 ...... Frame ( 21) shift: -0.17 0.62 ...... Frame ( 22) shift: -0.13 0.66 ...... Frame ( 23) shift: -0.09 0.70 ...... Frame ( 24) shift: -0.07 0.72 ...... Frame ( 25) shift: -0.06 0.73 ...... Frame ( 26) shift: -0.05 0.74 ...... Frame ( 27) shift: -0.04 0.76 ...... Frame ( 28) shift: -0.04 0.78 ...... Frame ( 29) shift: -0.03 0.81 ...... Frame ( 30) shift: -0.02 0.83 ...... Frame ( 31) shift: 0.01 0.86 ...... Frame ( 32) shift: 0.03 0.88 ...... Frame ( 33) shift: 0.05 0.90 ...... Frame ( 34) shift: 0.07 0.91 ...... Frame ( 35) shift: 0.09 0.93 ...... Frame ( 36) shift: 0.10 0.95 ...... Frame ( 37) shift: 0.10 0.99 ...... Frame ( 38) shift: 0.10 1.04 ...... Frame ( 39) shift: 0.10 1.08 ...... Frame ( 40) shift: 0.11 1.12 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.858766 Iteration 2 Error: 0.314558 Iteration 3 Error: 0.094582 Iteration 4 Error: 0.046246 Align patch 2 23 left Iteration 1 Error: 0.617358 Iteration 2 Error: 0.165229 Iteration 3 Error: 0.054816 Iteration 4 Error: 0.024906 Align patch 3 22 left Iteration 1 Error: 0.655360 Iteration 2 Error: 0.113964 Iteration 3 Error: 0.028271 Align patch 4 21 left Iteration 1 Error: 0.337918 Iteration 2 Error: 0.022695 Align patch 5 20 left Iteration 1 Error: 0.347171 Iteration 2 Error: 0.018142 Align patch 6 19 left Iteration 1 Error: 0.681397 Iteration 2 Error: 0.131403 Iteration 3 Error: 0.029728 Align patch 7 18 left Iteration 1 Error: 0.701628 Iteration 2 Error: 0.092628 Iteration 3 Error: 0.025053 Align patch 8 17 left Iteration 1 Error: 0.502663 Iteration 2 Error: 0.059620 Iteration 3 Error: 0.014215 Align patch 9 16 left Iteration 1 Error: 0.237666 Iteration 2 Error: 0.026405 Align patch 10 15 left Iteration 1 Error: 0.271087 Iteration 2 Error: 0.024500 Align patch 11 14 left Iteration 1 Error: 0.886424 Iteration 2 Error: 0.111095 Iteration 3 Error: 0.023558 Align patch 12 13 left Iteration 1 Error: 0.409015 Iteration 2 Error: 0.066239 Iteration 3 Error: 0.024210 Align patch 13 12 left Iteration 1 Error: 0.746137 Iteration 2 Error: 0.100251 Iteration 3 Error: 0.019355 Align patch 14 11 left Iteration 1 Error: 0.241379 Iteration 2 Error: 0.047261 Align patch 15 10 left Iteration 1 Error: 0.672933 Iteration 2 Error: 0.260448 Iteration 3 Error: 0.099806 Iteration 4 Error: 0.037971 Align patch 16 9 left Iteration 1 Error: 1.057355 Iteration 2 Error: 0.095623 Iteration 3 Error: 0.032243 Align patch 17 8 left Iteration 1 Error: 0.700667 Iteration 2 Error: 0.067474 Iteration 3 Error: 0.014507 Align patch 18 7 left Iteration 1 Error: 0.330325 Iteration 2 Error: 0.139588 Iteration 3 Error: 0.057003 Iteration 4 Error: 0.026574 Align patch 19 6 left Iteration 1 Error: 0.269492 Iteration 2 Error: 0.052465 Iteration 3 Error: 0.019917 Align patch 20 5 left Iteration 1 Error: 0.386197 Iteration 2 Error: 0.017992 Align patch 21 4 left Iteration 1 Error: 1.395847 Iteration 2 Error: 0.101371 Iteration 3 Error: 0.020986 Align patch 22 3 left Iteration 1 Error: 0.447648 Iteration 2 Error: 0.060827 Iteration 3 Error: 0.013951 Align patch 23 2 left Iteration 1 Error: 0.247514 Iteration 2 Error: 0.129009 Iteration 3 Error: 0.060486 Iteration 4 Error: 0.030738 Align patch 24 1 left Iteration 1 Error: 0.481390 Iteration 2 Error: 0.037224 Align patch 25 0 left Iteration 1 Error: 0.481091 Iteration 2 Error: 0.037081 3D Fitting completed. Patch alignment time: 15.38(sec) Local motion has been corrected. Process thread exits. Computational time: 23.833509 sec Total time: 30.241179 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00009hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00009hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.792283s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00009hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.276933s ........................................ >>>>>>TIME<<<<<< FFT: 1.024197s Defocus_U Defocus_V Angle CCC 11898.54 11281.26 82.15 0.004577 Final Values Defocus_U Defocus_V Angle CCC 11931.39 11342.24 82.46 0.021126 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00010hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00010hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.362e-01 1.012e-01 CC threshold: 0.743 Mean Std: 38.93 6.94 Num Hot pixels: 191 Hot pixel threshold: 80.56 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 3.519227 Iteration 2 Error: 0.154905 Iteration 3 Error: 0.022651 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.38 -0.50 ...... Frame ( 3) shift: 0.75 -1.01 ...... Frame ( 4) shift: 1.13 -1.51 ...... Frame ( 5) shift: 1.51 -2.01 ...... Frame ( 6) shift: 1.82 -2.37 ...... Frame ( 7) shift: 2.06 -2.59 ...... Frame ( 8) shift: 2.31 -2.81 ...... Frame ( 9) shift: 2.51 -2.96 ...... Frame ( 10) shift: 2.66 -3.04 ...... Frame ( 11) shift: 2.81 -3.13 ...... Frame ( 12) shift: 2.92 -3.17 ...... Frame ( 13) shift: 2.98 -3.16 ...... Frame ( 14) shift: 3.04 -3.16 ...... Frame ( 15) shift: 3.10 -3.16 ...... Frame ( 16) shift: 3.15 -3.18 ...... Frame ( 17) shift: 3.20 -3.19 ...... Frame ( 18) shift: 3.29 -3.17 ...... Frame ( 19) shift: 3.42 -3.12 ...... Frame ( 20) shift: 3.56 -3.06 ...... Frame ( 21) shift: 3.67 -3.02 ...... Frame ( 22) shift: 3.75 -3.00 ...... Frame ( 23) shift: 3.84 -2.98 ...... Frame ( 24) shift: 3.94 -2.97 ...... Frame ( 25) shift: 4.05 -2.95 ...... Frame ( 26) shift: 4.16 -2.93 ...... Frame ( 27) shift: 4.23 -2.89 ...... Frame ( 28) shift: 4.28 -2.82 ...... Frame ( 29) shift: 4.32 -2.76 ...... Frame ( 30) shift: 4.39 -2.70 ...... Frame ( 31) shift: 4.47 -2.65 ...... Frame ( 32) shift: 4.56 -2.60 ...... Frame ( 33) shift: 4.65 -2.53 ...... Frame ( 34) shift: 4.75 -2.43 ...... Frame ( 35) shift: 4.86 -2.34 ...... Frame ( 36) shift: 4.95 -2.25 ...... Frame ( 37) shift: 5.04 -2.16 ...... Frame ( 38) shift: 5.13 -2.07 ...... Frame ( 39) shift: 5.22 -1.98 ...... Frame ( 40) shift: 5.31 -1.90 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.588038 Iteration 2 Error: 0.052528 Iteration 3 Error: 0.004459 Align patch 2 23 left Iteration 1 Error: 2.219943 Iteration 2 Error: 0.136557 Iteration 3 Error: 0.011648 Align patch 3 22 left Iteration 1 Error: 1.268869 Iteration 2 Error: 0.138335 Iteration 3 Error: 0.022563 Align patch 4 21 left Iteration 1 Error: 2.966097 Iteration 2 Error: 0.152718 Iteration 3 Error: 0.024357 Align patch 5 20 left Iteration 1 Error: 3.767201 Iteration 2 Error: 0.368180 Iteration 3 Error: 0.058221 Iteration 4 Error: 0.016083 Align patch 6 19 left Iteration 1 Error: 1.381513 Iteration 2 Error: 0.068478 Iteration 3 Error: 0.007406 Align patch 7 18 left Iteration 1 Error: 1.199547 Iteration 2 Error: 0.074572 Iteration 3 Error: 0.008807 Align patch 8 17 left Iteration 1 Error: 1.079860 Iteration 2 Error: 0.056180 Iteration 3 Error: 0.005322 Align patch 9 16 left Iteration 1 Error: 1.858867 Iteration 2 Error: 0.151188 Iteration 3 Error: 0.024865 Align patch 10 15 left Iteration 1 Error: 2.955641 Iteration 2 Error: 0.187421 Iteration 3 Error: 0.034186 Align patch 11 14 left Iteration 1 Error: 1.026320 Iteration 2 Error: 0.067120 Iteration 3 Error: 0.011915 Align patch 12 13 left Iteration 1 Error: 1.062620 Iteration 2 Error: 0.070107 Iteration 3 Error: 0.005673 Align patch 13 12 left Iteration 1 Error: 0.789595 Iteration 2 Error: 0.086891 Iteration 3 Error: 0.010673 Align patch 14 11 left Iteration 1 Error: 0.439925 Iteration 2 Error: 0.023956 Align patch 15 10 left Iteration 1 Error: 1.770642 Iteration 2 Error: 0.112209 Iteration 3 Error: 0.009248 Align patch 16 9 left Iteration 1 Error: 0.922532 Iteration 2 Error: 0.140360 Iteration 3 Error: 0.030339 Align patch 17 8 left Iteration 1 Error: 0.776253 Iteration 2 Error: 0.183064 Iteration 3 Error: 0.034342 Align patch 18 7 left Iteration 1 Error: 1.294911 Iteration 2 Error: 0.125802 Iteration 3 Error: 0.016085 Align patch 19 6 left Iteration 1 Error: 1.282564 Iteration 2 Error: 0.154056 Iteration 3 Error: 0.013127 Align patch 20 5 left Iteration 1 Error: 1.457121 Iteration 2 Error: 0.095124 Iteration 3 Error: 0.008479 Align patch 21 4 left Iteration 1 Error: 1.818585 Iteration 2 Error: 0.243189 Iteration 3 Error: 0.077409 Iteration 4 Error: 0.021135 Align patch 22 3 left Iteration 1 Error: 0.590225 Iteration 2 Error: 0.182414 Iteration 3 Error: 0.050325 Iteration 4 Error: 0.015609 Align patch 23 2 left Iteration 1 Error: 1.157596 Iteration 2 Error: 0.208081 Iteration 3 Error: 0.040670 Align patch 24 1 left Iteration 1 Error: 0.791128 Iteration 2 Error: 0.119292 Iteration 3 Error: 0.032357 Align patch 25 0 left Iteration 1 Error: 1.623441 Iteration 2 Error: 0.136804 Iteration 3 Error: 0.020863 3D Fitting completed. Patch alignment time: 14.60(sec) Local motion has been corrected. Process thread exits. Computational time: 22.721617 sec Total time: 28.482874 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00010hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00010hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.577433s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00010hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.878047s ........................................ >>>>>>TIME<<<<<< FFT: 0.939846s Defocus_U Defocus_V Angle CCC 12583.98 13384.77 10.48 0.153790 Final Values Defocus_U Defocus_V Angle CCC 12604.30 13383.21 10.17 0.237214 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00010hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00010hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 41.09 6.93 Num Hot pixels: 232 Hot pixel threshold: 82.69 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.792527 Iteration 2 Error: 0.142354 Iteration 3 Error: 0.034094 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.16 -0.21 ...... Frame ( 3) shift: -0.32 -0.42 ...... Frame ( 4) shift: -0.49 -0.63 ...... Frame ( 5) shift: -0.65 -0.83 ...... Frame ( 6) shift: -0.70 -0.94 ...... Frame ( 7) shift: -0.63 -0.95 ...... Frame ( 8) shift: -0.57 -0.96 ...... Frame ( 9) shift: -0.53 -0.93 ...... Frame ( 10) shift: -0.52 -0.86 ...... Frame ( 11) shift: -0.51 -0.80 ...... Frame ( 12) shift: -0.50 -0.72 ...... Frame ( 13) shift: -0.49 -0.62 ...... Frame ( 14) shift: -0.48 -0.52 ...... Frame ( 15) shift: -0.45 -0.43 ...... Frame ( 16) shift: -0.40 -0.34 ...... Frame ( 17) shift: -0.35 -0.25 ...... Frame ( 18) shift: -0.32 -0.18 ...... Frame ( 19) shift: -0.30 -0.15 ...... Frame ( 20) shift: -0.27 -0.12 ...... Frame ( 21) shift: -0.23 -0.11 ...... Frame ( 22) shift: -0.18 -0.13 ...... Frame ( 23) shift: -0.13 -0.14 ...... Frame ( 24) shift: -0.10 -0.08 ...... Frame ( 25) shift: -0.09 0.03 ...... Frame ( 26) shift: -0.08 0.15 ...... Frame ( 27) shift: -0.02 0.20 ...... Frame ( 28) shift: 0.07 0.18 ...... Frame ( 29) shift: 0.16 0.17 ...... Frame ( 30) shift: 0.22 0.15 ...... Frame ( 31) shift: 0.24 0.13 ...... Frame ( 32) shift: 0.26 0.11 ...... Frame ( 33) shift: 0.28 0.12 ...... Frame ( 34) shift: 0.30 0.16 ...... Frame ( 35) shift: 0.31 0.20 ...... Frame ( 36) shift: 0.31 0.25 ...... Frame ( 37) shift: 0.29 0.32 ...... Frame ( 38) shift: 0.27 0.38 ...... Frame ( 39) shift: 0.26 0.44 ...... Frame ( 40) shift: 0.24 0.50 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.729936 Iteration 2 Error: 0.097632 Iteration 3 Error: 0.018023 Align patch 2 23 left Iteration 1 Error: 1.117754 Iteration 2 Error: 0.117853 Iteration 3 Error: 0.031420 Align patch 3 22 left Iteration 1 Error: 0.805548 Iteration 2 Error: 0.133363 Iteration 3 Error: 0.026884 Align patch 4 21 left Iteration 1 Error: 0.600633 Iteration 2 Error: 0.082625 Iteration 3 Error: 0.021385 Align patch 5 20 left Iteration 1 Error: 0.553868 Iteration 2 Error: 0.075188 Iteration 3 Error: 0.016981 Align patch 6 19 left Iteration 1 Error: 0.622319 Iteration 2 Error: 0.163341 Iteration 3 Error: 0.035282 Align patch 7 18 left Iteration 1 Error: 0.724916 Iteration 2 Error: 0.094395 Iteration 3 Error: 0.018706 Align patch 8 17 left Iteration 1 Error: 0.468402 Iteration 2 Error: 0.111409 Iteration 3 Error: 0.016220 Align patch 9 16 left Iteration 1 Error: 0.638317 Iteration 2 Error: 0.085161 Iteration 3 Error: 0.026105 Align patch 10 15 left Iteration 1 Error: 0.690283 Iteration 2 Error: 0.116510 Iteration 3 Error: 0.024573 Align patch 11 14 left Iteration 1 Error: 0.534414 Iteration 2 Error: 0.128620 Iteration 3 Error: 0.044151 Align patch 12 13 left Iteration 1 Error: 0.532858 Iteration 2 Error: 0.073890 Iteration 3 Error: 0.028903 Align patch 13 12 left Iteration 1 Error: 0.452679 Iteration 2 Error: 0.108724 Iteration 3 Error: 0.023152 Align patch 14 11 left Iteration 1 Error: 0.468381 Iteration 2 Error: 0.125785 Iteration 3 Error: 0.034342 Align patch 15 10 left Iteration 1 Error: 0.717479 Iteration 2 Error: 0.149771 Iteration 3 Error: 0.051486 Iteration 4 Error: 0.015379 Align patch 16 9 left Iteration 1 Error: 0.623817 Iteration 2 Error: 0.091084 Iteration 3 Error: 0.021942 Align patch 17 8 left Iteration 1 Error: 0.851134 Iteration 2 Error: 0.147011 Iteration 3 Error: 0.050956 Iteration 4 Error: 0.016159 Align patch 18 7 left Iteration 1 Error: 0.504035 Iteration 2 Error: 0.079337 Iteration 3 Error: 0.022443 Align patch 19 6 left Iteration 1 Error: 0.585039 Iteration 2 Error: 0.091393 Iteration 3 Error: 0.020095 Align patch 20 5 left Iteration 1 Error: 0.583461 Iteration 2 Error: 0.091583 Iteration 3 Error: 0.026778 Align patch 21 4 left Iteration 1 Error: 0.612440 Iteration 2 Error: 0.084918 Iteration 3 Error: 0.020323 Align patch 22 3 left Iteration 1 Error: 1.280180 Iteration 2 Error: 0.113858 Iteration 3 Error: 0.024867 Align patch 23 2 left Iteration 1 Error: 0.620274 Iteration 2 Error: 0.094228 Iteration 3 Error: 0.015240 Align patch 24 1 left Iteration 1 Error: 0.468174 Iteration 2 Error: 0.090968 Iteration 3 Error: 0.015996 Align patch 25 0 left Iteration 1 Error: 0.527603 Iteration 2 Error: 0.078194 Iteration 3 Error: 0.020849 3D Fitting completed. Patch alignment time: 15.36(sec) Local motion has been corrected. Process thread exits. Computational time: 23.938236 sec Total time: 29.631908 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00010hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00010hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.576868s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00010hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.316236s ........................................ >>>>>>TIME<<<<<< FFT: 0.966038s Defocus_U Defocus_V Angle CCC 9363.30 8847.65 88.90 0.035939 Final Values Defocus_U Defocus_V Angle CCC 9375.79 8847.66 88.59 0.072559 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00010hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00010hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.359e-01 1.010e-01 CC threshold: 0.742 Mean Std: 36.90 6.60 Num Hot pixels: 187 Hot pixel threshold: 76.48 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.048524 Iteration 2 Error: 0.091162 Iteration 3 Error: 0.011254 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.26 -0.10 ...... Frame ( 3) shift: 0.51 -0.19 ...... Frame ( 4) shift: 0.77 -0.29 ...... Frame ( 5) shift: 1.03 -0.39 ...... Frame ( 6) shift: 1.16 -0.49 ...... Frame ( 7) shift: 1.16 -0.58 ...... Frame ( 8) shift: 1.17 -0.68 ...... Frame ( 9) shift: 1.16 -0.75 ...... Frame ( 10) shift: 1.13 -0.78 ...... Frame ( 11) shift: 1.10 -0.81 ...... Frame ( 12) shift: 1.07 -0.87 ...... Frame ( 13) shift: 1.04 -0.94 ...... Frame ( 14) shift: 1.01 -1.01 ...... Frame ( 15) shift: 0.98 -1.06 ...... Frame ( 16) shift: 0.95 -1.10 ...... Frame ( 17) shift: 0.93 -1.13 ...... Frame ( 18) shift: 0.90 -1.17 ...... Frame ( 19) shift: 0.87 -1.21 ...... Frame ( 20) shift: 0.83 -1.25 ...... Frame ( 21) shift: 0.79 -1.30 ...... Frame ( 22) shift: 0.75 -1.34 ...... Frame ( 23) shift: 0.70 -1.39 ...... Frame ( 24) shift: 0.66 -1.43 ...... Frame ( 25) shift: 0.62 -1.47 ...... Frame ( 26) shift: 0.58 -1.51 ...... Frame ( 27) shift: 0.56 -1.52 ...... Frame ( 28) shift: 0.56 -1.49 ...... Frame ( 29) shift: 0.56 -1.46 ...... Frame ( 30) shift: 0.50 -1.45 ...... Frame ( 31) shift: 0.40 -1.47 ...... Frame ( 32) shift: 0.29 -1.48 ...... Frame ( 33) shift: 0.23 -1.50 ...... Frame ( 34) shift: 0.21 -1.52 ...... Frame ( 35) shift: 0.19 -1.55 ...... Frame ( 36) shift: 0.15 -1.57 ...... Frame ( 37) shift: 0.10 -1.59 ...... Frame ( 38) shift: 0.04 -1.61 ...... Frame ( 39) shift: -0.02 -1.62 ...... Frame ( 40) shift: -0.08 -1.64 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.967869 Iteration 2 Error: 0.281203 Iteration 3 Error: 0.074337 Iteration 4 Error: 0.027628 Align patch 2 23 left Iteration 1 Error: 1.320994 Iteration 2 Error: 0.263745 Iteration 3 Error: 0.054756 Iteration 4 Error: 0.020206 Align patch 3 22 left Iteration 1 Error: 1.339182 Iteration 2 Error: 0.210302 Iteration 3 Error: 0.041451 Align patch 4 21 left Iteration 1 Error: 1.352076 Iteration 2 Error: 0.222923 Iteration 3 Error: 0.038005 Align patch 5 20 left Iteration 1 Error: 1.340035 Iteration 2 Error: 0.232452 Iteration 3 Error: 0.053081 Iteration 4 Error: 0.014851 Align patch 6 19 left Iteration 1 Error: 1.897077 Iteration 2 Error: 0.261214 Iteration 3 Error: 0.044421 Align patch 7 18 left Iteration 1 Error: 1.558004 Iteration 2 Error: 0.216581 Iteration 3 Error: 0.050203 Iteration 4 Error: 0.014349 Align patch 8 17 left Iteration 1 Error: 1.066180 Iteration 2 Error: 0.194980 Iteration 3 Error: 0.046145 Align patch 9 16 left Iteration 1 Error: 1.261761 Iteration 2 Error: 0.251231 Iteration 3 Error: 0.065822 Iteration 4 Error: 0.017931 Align patch 10 15 left Iteration 1 Error: 1.231612 Iteration 2 Error: 0.257916 Iteration 3 Error: 0.068131 Iteration 4 Error: 0.016421 Align patch 11 14 left Iteration 1 Error: 1.320017 Iteration 2 Error: 0.072210 Iteration 3 Error: 0.004755 Align patch 12 13 left Iteration 1 Error: 0.388805 Iteration 2 Error: 0.032104 Align patch 13 12 left Iteration 1 Error: 0.718246 Iteration 2 Error: 0.192437 Iteration 3 Error: 0.037659 Align patch 14 11 left Iteration 1 Error: 1.190875 Iteration 2 Error: 0.183046 Iteration 3 Error: 0.050140 Iteration 4 Error: 0.014066 Align patch 15 10 left Iteration 1 Error: 1.244599 Iteration 2 Error: 0.205497 Iteration 3 Error: 0.048869 Align patch 16 9 left Iteration 1 Error: 1.100462 Iteration 2 Error: 0.048445 Align patch 17 8 left Iteration 1 Error: 0.337641 Iteration 2 Error: 0.018593 Align patch 18 7 left Iteration 1 Error: 0.814211 Iteration 2 Error: 0.082580 Iteration 3 Error: 0.014620 Align patch 19 6 left Iteration 1 Error: 1.067401 Iteration 2 Error: 0.087432 Iteration 3 Error: 0.013476 Align patch 20 5 left Iteration 1 Error: 1.008183 Iteration 2 Error: 0.146454 Iteration 3 Error: 0.039821 Align patch 21 4 left Iteration 1 Error: 1.206663 Iteration 2 Error: 0.063465 Iteration 3 Error: 0.005821 Align patch 22 3 left Iteration 1 Error: 0.612417 Iteration 2 Error: 0.077053 Iteration 3 Error: 0.013641 Align patch 23 2 left Iteration 1 Error: 1.109212 Iteration 2 Error: 0.101445 Iteration 3 Error: 0.006203 Align patch 24 1 left Iteration 1 Error: 2.006981 Iteration 2 Error: 0.116626 Iteration 3 Error: 0.012276 Align patch 25 0 left Iteration 1 Error: 2.158941 Iteration 2 Error: 0.162497 Iteration 3 Error: 0.026329 3D Fitting completed. Patch alignment time: 15.16(sec) Local motion has been corrected. Process thread exits. Computational time: 23.326515 sec Total time: 29.904209 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00010hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00010hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.539131s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00010hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.076210s ........................................ >>>>>>TIME<<<<<< FFT: 0.930160s Defocus_U Defocus_V Angle CCC 12853.52 13623.05 6.49 0.103444 Final Values Defocus_U Defocus_V Angle CCC 12856.64 13616.80 6.49 0.160761 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00010hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00010hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 41.99 7.02 Num Hot pixels: 224 Hot pixel threshold: 84.09 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.966153 Iteration 2 Error: 0.177117 Iteration 3 Error: 0.041013 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.24 -0.19 ...... Frame ( 3) shift: -0.48 -0.37 ...... Frame ( 4) shift: -0.72 -0.56 ...... Frame ( 5) shift: -0.97 -0.75 ...... Frame ( 6) shift: -1.08 -0.85 ...... Frame ( 7) shift: -1.07 -0.88 ...... Frame ( 8) shift: -1.06 -0.90 ...... Frame ( 9) shift: -1.01 -0.88 ...... Frame ( 10) shift: -0.94 -0.81 ...... Frame ( 11) shift: -0.87 -0.75 ...... Frame ( 12) shift: -0.83 -0.70 ...... Frame ( 13) shift: -0.81 -0.67 ...... Frame ( 14) shift: -0.80 -0.64 ...... Frame ( 15) shift: -0.76 -0.59 ...... Frame ( 16) shift: -0.69 -0.53 ...... Frame ( 17) shift: -0.63 -0.47 ...... Frame ( 18) shift: -0.58 -0.41 ...... Frame ( 19) shift: -0.56 -0.35 ...... Frame ( 20) shift: -0.53 -0.29 ...... Frame ( 21) shift: -0.49 -0.26 ...... Frame ( 22) shift: -0.44 -0.24 ...... Frame ( 23) shift: -0.38 -0.22 ...... Frame ( 24) shift: -0.35 -0.17 ...... Frame ( 25) shift: -0.35 -0.10 ...... Frame ( 26) shift: -0.35 -0.03 ...... Frame ( 27) shift: -0.35 0.03 ...... Frame ( 28) shift: -0.34 0.06 ...... Frame ( 29) shift: -0.34 0.10 ...... Frame ( 30) shift: -0.32 0.17 ...... Frame ( 31) shift: -0.29 0.29 ...... Frame ( 32) shift: -0.25 0.41 ...... Frame ( 33) shift: -0.19 0.54 ...... Frame ( 34) shift: -0.10 0.67 ...... Frame ( 35) shift: -0.01 0.79 ...... Frame ( 36) shift: 0.03 0.85 ...... Frame ( 37) shift: -0.00 0.85 ...... Frame ( 38) shift: -0.03 0.84 ...... Frame ( 39) shift: -0.06 0.83 ...... Frame ( 40) shift: -0.09 0.82 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.434778 Iteration 2 Error: 0.261775 Iteration 3 Error: 0.077765 Iteration 4 Error: 0.017035 Align patch 2 23 left Iteration 1 Error: 0.907089 Iteration 2 Error: 0.179052 Iteration 3 Error: 0.058414 Iteration 4 Error: 0.013709 Align patch 3 22 left Iteration 1 Error: 0.608239 Iteration 2 Error: 0.183354 Iteration 3 Error: 0.041198 Align patch 4 21 left Iteration 1 Error: 0.576960 Iteration 2 Error: 0.093273 Iteration 3 Error: 0.024630 Align patch 5 20 left Iteration 1 Error: 0.539632 Iteration 2 Error: 0.073518 Iteration 3 Error: 0.010998 Align patch 6 19 left Iteration 1 Error: 1.073206 Iteration 2 Error: 0.144000 Iteration 3 Error: 0.042929 Align patch 7 18 left Iteration 1 Error: 0.922960 Iteration 2 Error: 0.169780 Iteration 3 Error: 0.042143 Align patch 8 17 left Iteration 1 Error: 0.400674 Iteration 2 Error: 0.046560 Align patch 9 16 left Iteration 1 Error: 0.628279 Iteration 2 Error: 0.088838 Iteration 3 Error: 0.023785 Align patch 10 15 left Iteration 1 Error: 0.809904 Iteration 2 Error: 0.122348 Iteration 3 Error: 0.029422 Align patch 11 14 left Iteration 1 Error: 0.936598 Iteration 2 Error: 0.193462 Iteration 3 Error: 0.043241 Align patch 12 13 left Iteration 1 Error: 0.641882 Iteration 2 Error: 0.073197 Iteration 3 Error: 0.017109 Align patch 13 12 left Iteration 1 Error: 0.773359 Iteration 2 Error: 0.100117 Iteration 3 Error: 0.032117 Align patch 14 11 left Iteration 1 Error: 0.631672 Iteration 2 Error: 0.118159 Iteration 3 Error: 0.039948 Align patch 15 10 left Iteration 1 Error: 0.725837 Iteration 2 Error: 0.086880 Iteration 3 Error: 0.025109 Align patch 16 9 left Iteration 1 Error: 0.695290 Iteration 2 Error: 0.088079 Iteration 3 Error: 0.019149 Align patch 17 8 left Iteration 1 Error: 0.672375 Iteration 2 Error: 0.095006 Iteration 3 Error: 0.026897 Align patch 18 7 left Iteration 1 Error: 0.728958 Iteration 2 Error: 0.113161 Iteration 3 Error: 0.024289 Align patch 19 6 left Iteration 1 Error: 0.905246 Iteration 2 Error: 0.185269 Iteration 3 Error: 0.056031 Iteration 4 Error: 0.018318 Align patch 20 5 left Iteration 1 Error: 0.746726 Iteration 2 Error: 0.158356 Iteration 3 Error: 0.025585 Align patch 21 4 left Iteration 1 Error: 0.834810 Iteration 2 Error: 0.123158 Iteration 3 Error: 0.029899 Align patch 22 3 left Iteration 1 Error: 0.611727 Iteration 2 Error: 0.138924 Iteration 3 Error: 0.034797 Align patch 23 2 left Iteration 1 Error: 0.452857 Iteration 2 Error: 0.093844 Iteration 3 Error: 0.023140 Align patch 24 1 left Iteration 1 Error: 0.754423 Iteration 2 Error: 0.083793 Iteration 3 Error: 0.029514 Align patch 25 0 left Iteration 1 Error: 1.021845 Iteration 2 Error: 0.158828 Iteration 3 Error: 0.042771 3D Fitting completed. Patch alignment time: 15.36(sec) Local motion has been corrected. Process thread exits. Computational time: 24.366007 sec Total time: 30.579948 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00010hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00010hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.566678s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00010hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.999693s ........................................ >>>>>>TIME<<<<<< FFT: 0.927562s Defocus_U Defocus_V Angle CCC 11101.63 10496.11 83.01 0.054813 Final Values Defocus_U Defocus_V Angle CCC 11114.14 10514.87 83.33 0.096697 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00011hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00011hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 44.04 7.43 Num Hot pixels: 196 Hot pixel threshold: 88.62 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.779990 Iteration 2 Error: 0.103761 Iteration 3 Error: 0.024096 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.31 -0.09 ...... Frame ( 3) shift: -0.62 -0.17 ...... Frame ( 4) shift: -0.93 -0.26 ...... Frame ( 5) shift: -1.24 -0.34 ...... Frame ( 6) shift: -1.38 -0.36 ...... Frame ( 7) shift: -1.35 -0.30 ...... Frame ( 8) shift: -1.33 -0.23 ...... Frame ( 9) shift: -1.32 -0.19 ...... Frame ( 10) shift: -1.34 -0.16 ...... Frame ( 11) shift: -1.36 -0.13 ...... Frame ( 12) shift: -1.36 -0.06 ...... Frame ( 13) shift: -1.33 0.04 ...... Frame ( 14) shift: -1.30 0.14 ...... Frame ( 15) shift: -1.29 0.21 ...... Frame ( 16) shift: -1.30 0.23 ...... Frame ( 17) shift: -1.31 0.25 ...... Frame ( 18) shift: -1.31 0.29 ...... Frame ( 19) shift: -1.32 0.35 ...... Frame ( 20) shift: -1.32 0.41 ...... Frame ( 21) shift: -1.30 0.44 ...... Frame ( 22) shift: -1.24 0.46 ...... Frame ( 23) shift: -1.19 0.47 ...... Frame ( 24) shift: -1.13 0.51 ...... Frame ( 25) shift: -1.08 0.59 ...... Frame ( 26) shift: -1.02 0.66 ...... Frame ( 27) shift: -0.98 0.70 ...... Frame ( 28) shift: -0.93 0.70 ...... Frame ( 29) shift: -0.89 0.71 ...... Frame ( 30) shift: -0.85 0.69 ...... Frame ( 31) shift: -0.82 0.63 ...... Frame ( 32) shift: -0.79 0.58 ...... Frame ( 33) shift: -0.78 0.59 ...... Frame ( 34) shift: -0.81 0.66 ...... Frame ( 35) shift: -0.84 0.74 ...... Frame ( 36) shift: -0.86 0.78 ...... Frame ( 37) shift: -0.87 0.78 ...... Frame ( 38) shift: -0.88 0.78 ...... Frame ( 39) shift: -0.89 0.79 ...... Frame ( 40) shift: -0.90 0.79 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.989589 Iteration 2 Error: 0.155148 Iteration 3 Error: 0.045852 Align patch 2 23 left Iteration 1 Error: 1.011006 Iteration 2 Error: 0.170415 Iteration 3 Error: 0.063784 Iteration 4 Error: 0.026008 Align patch 3 22 left Iteration 1 Error: 0.775607 Iteration 2 Error: 0.167500 Iteration 3 Error: 0.064961 Iteration 4 Error: 0.013833 Align patch 4 21 left Iteration 1 Error: 0.632264 Iteration 2 Error: 0.098057 Iteration 3 Error: 0.025130 Align patch 5 20 left Iteration 1 Error: 0.512804 Iteration 2 Error: 0.080268 Iteration 3 Error: 0.014610 Align patch 6 19 left Iteration 1 Error: 1.503450 Iteration 2 Error: 0.182219 Iteration 3 Error: 0.054743 Iteration 4 Error: 0.020893 Align patch 7 18 left Iteration 1 Error: 1.189403 Iteration 2 Error: 0.136739 Iteration 3 Error: 0.040821 Align patch 8 17 left Iteration 1 Error: 0.961967 Iteration 2 Error: 0.083870 Iteration 3 Error: 0.025838 Align patch 9 16 left Iteration 1 Error: 0.647333 Iteration 2 Error: 0.113978 Iteration 3 Error: 0.025001 Align patch 10 15 left Iteration 1 Error: 0.431227 Iteration 2 Error: 0.059704 Iteration 3 Error: 0.014007 Align patch 11 14 left Iteration 1 Error: 0.704733 Iteration 2 Error: 0.177198 Iteration 3 Error: 0.077262 Iteration 4 Error: 0.025827 Align patch 12 13 left Iteration 1 Error: 0.491534 Iteration 2 Error: 0.096828 Iteration 3 Error: 0.021810 Align patch 13 12 left Iteration 1 Error: 0.778214 Iteration 2 Error: 0.137564 Iteration 3 Error: 0.034039 Align patch 14 11 left Iteration 1 Error: 1.033226 Iteration 2 Error: 0.116500 Iteration 3 Error: 0.045681 Align patch 15 10 left Iteration 1 Error: 0.586455 Iteration 2 Error: 0.142197 Iteration 3 Error: 0.018365 Align patch 16 9 left Iteration 1 Error: 1.150148 Iteration 2 Error: 0.151101 Iteration 3 Error: 0.040220 Align patch 17 8 left Iteration 1 Error: 0.955032 Iteration 2 Error: 0.154956 Iteration 3 Error: 0.037793 Align patch 18 7 left Iteration 1 Error: 0.778309 Iteration 2 Error: 0.132718 Iteration 3 Error: 0.024512 Align patch 19 6 left Iteration 1 Error: 0.765359 Iteration 2 Error: 0.080672 Iteration 3 Error: 0.018930 Align patch 20 5 left Iteration 1 Error: 0.513348 Iteration 2 Error: 0.075167 Iteration 3 Error: 0.010180 Align patch 21 4 left Iteration 1 Error: 0.792509 Iteration 2 Error: 0.187396 Iteration 3 Error: 0.052275 Iteration 4 Error: 0.028579 Align patch 22 3 left Iteration 1 Error: 1.054999 Iteration 2 Error: 0.178598 Iteration 3 Error: 0.032330 Align patch 23 2 left Iteration 1 Error: 0.929329 Iteration 2 Error: 0.194849 Iteration 3 Error: 0.029966 Align patch 24 1 left Iteration 1 Error: 0.606685 Iteration 2 Error: 0.097073 Iteration 3 Error: 0.018089 Align patch 25 0 left Iteration 1 Error: 1.048751 Iteration 2 Error: 0.174982 Iteration 3 Error: 0.035791 3D Fitting completed. Patch alignment time: 15.06(sec) Local motion has been corrected. Process thread exits. Computational time: 24.296181 sec Total time: 30.044378 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00011hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00011hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.553930s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00011hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.565330s ........................................ >>>>>>TIME<<<<<< FFT: 0.944726s Defocus_U Defocus_V Angle CCC 8863.28 9781.25 14.29 0.042885 Final Values Defocus_U Defocus_V Angle CCC 8869.54 9784.38 14.61 0.089434 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00011hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00011hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.002e-01 CC threshold: 0.736 Mean Std: 43.17 7.36 Num Hot pixels: 201 Hot pixel threshold: 87.34 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.655110 Iteration 2 Error: 0.115667 Iteration 3 Error: 0.022209 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.23 -0.02 ...... Frame ( 3) shift: -0.45 -0.04 ...... Frame ( 4) shift: -0.68 -0.07 ...... Frame ( 5) shift: -0.90 -0.09 ...... Frame ( 6) shift: -1.01 -0.08 ...... Frame ( 7) shift: -0.99 -0.04 ...... Frame ( 8) shift: -0.98 -0.01 ...... Frame ( 9) shift: -0.95 0.01 ...... Frame ( 10) shift: -0.91 0.02 ...... Frame ( 11) shift: -0.88 0.03 ...... Frame ( 12) shift: -0.83 0.04 ...... Frame ( 13) shift: -0.77 0.07 ...... Frame ( 14) shift: -0.71 0.10 ...... Frame ( 15) shift: -0.64 0.11 ...... Frame ( 16) shift: -0.56 0.11 ...... Frame ( 17) shift: -0.49 0.12 ...... Frame ( 18) shift: -0.44 0.16 ...... Frame ( 19) shift: -0.42 0.25 ...... Frame ( 20) shift: -0.41 0.33 ...... Frame ( 21) shift: -0.38 0.37 ...... Frame ( 22) shift: -0.35 0.36 ...... Frame ( 23) shift: -0.32 0.34 ...... Frame ( 24) shift: -0.30 0.38 ...... Frame ( 25) shift: -0.29 0.46 ...... Frame ( 26) shift: -0.29 0.54 ...... Frame ( 27) shift: -0.26 0.56 ...... Frame ( 28) shift: -0.19 0.53 ...... Frame ( 29) shift: -0.13 0.50 ...... Frame ( 30) shift: -0.10 0.50 ...... Frame ( 31) shift: -0.09 0.51 ...... Frame ( 32) shift: -0.08 0.52 ...... Frame ( 33) shift: -0.05 0.54 ...... Frame ( 34) shift: -0.01 0.58 ...... Frame ( 35) shift: 0.04 0.61 ...... Frame ( 36) shift: 0.07 0.66 ...... Frame ( 37) shift: 0.10 0.71 ...... Frame ( 38) shift: 0.12 0.76 ...... Frame ( 39) shift: 0.14 0.81 ...... Frame ( 40) shift: 0.17 0.86 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.089076 Iteration 2 Error: 0.157289 Iteration 3 Error: 0.043919 Align patch 2 23 left Iteration 1 Error: 1.269030 Iteration 2 Error: 0.136954 Iteration 3 Error: 0.043287 Align patch 3 22 left Iteration 1 Error: 0.738408 Iteration 2 Error: 0.152619 Iteration 3 Error: 0.037733 Align patch 4 21 left Iteration 1 Error: 0.537984 Iteration 2 Error: 0.087854 Iteration 3 Error: 0.020181 Align patch 5 20 left Iteration 1 Error: 0.662219 Iteration 2 Error: 0.055191 Iteration 3 Error: 0.009240 Align patch 6 19 left Iteration 1 Error: 1.562721 Iteration 2 Error: 0.127791 Iteration 3 Error: 0.041133 Align patch 7 18 left Iteration 1 Error: 0.770528 Iteration 2 Error: 0.192121 Iteration 3 Error: 0.052442 Iteration 4 Error: 0.015053 Align patch 8 17 left Iteration 1 Error: 0.644818 Iteration 2 Error: 0.081565 Iteration 3 Error: 0.013402 Align patch 9 16 left Iteration 1 Error: 0.792075 Iteration 2 Error: 0.105614 Iteration 3 Error: 0.025208 Align patch 10 15 left Iteration 1 Error: 0.523712 Iteration 2 Error: 0.049841 Align patch 11 14 left Iteration 1 Error: 0.847973 Iteration 2 Error: 0.145985 Iteration 3 Error: 0.029986 Align patch 12 13 left Iteration 1 Error: 0.865094 Iteration 2 Error: 0.111073 Iteration 3 Error: 0.036949 Align patch 13 12 left Iteration 1 Error: 0.763569 Iteration 2 Error: 0.146369 Iteration 3 Error: 0.047395 Align patch 14 11 left Iteration 1 Error: 0.464864 Iteration 2 Error: 0.048347 Align patch 15 10 left Iteration 1 Error: 0.600625 Iteration 2 Error: 0.053715 Iteration 3 Error: 0.008531 Align patch 16 9 left Iteration 1 Error: 0.860793 Iteration 2 Error: 0.150044 Iteration 3 Error: 0.034642 Align patch 17 8 left Iteration 1 Error: 0.713181 Iteration 2 Error: 0.121556 Iteration 3 Error: 0.020129 Align patch 18 7 left Iteration 1 Error: 0.665762 Iteration 2 Error: 0.101377 Iteration 3 Error: 0.034078 Align patch 19 6 left Iteration 1 Error: 0.787352 Iteration 2 Error: 0.094419 Iteration 3 Error: 0.014915 Align patch 20 5 left Iteration 1 Error: 0.416868 Iteration 2 Error: 0.094029 Iteration 3 Error: 0.017842 Align patch 21 4 left Iteration 1 Error: 1.098340 Iteration 2 Error: 0.172902 Iteration 3 Error: 0.042195 Align patch 22 3 left Iteration 1 Error: 0.823556 Iteration 2 Error: 0.104639 Iteration 3 Error: 0.024923 Align patch 23 2 left Iteration 1 Error: 0.917679 Iteration 2 Error: 0.090775 Iteration 3 Error: 0.027767 Align patch 24 1 left Iteration 1 Error: 0.497375 Iteration 2 Error: 0.135224 Iteration 3 Error: 0.021845 Align patch 25 0 left Iteration 1 Error: 0.811090 Iteration 2 Error: 0.155760 Iteration 3 Error: 0.023026 3D Fitting completed. Patch alignment time: 15.06(sec) Local motion has been corrected. Process thread exits. Computational time: 23.989889 sec Total time: 29.683338 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00011hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00011hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.537480s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00011hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.846155s ........................................ >>>>>>TIME<<<<<< FFT: 0.951127s Defocus_U Defocus_V Angle CCC 9750.01 9285.15 89.08 0.043718 Final Values Defocus_U Defocus_V Angle CCC 9756.27 9294.53 89.40 0.087522 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00011hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00011hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.003e-01 CC threshold: 0.736 Mean Std: 45.06 7.48 Num Hot pixels: 210 Hot pixel threshold: 89.94 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.973720 Iteration 2 Error: 0.100490 Iteration 3 Error: 0.017436 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.29 -0.06 ...... Frame ( 3) shift: -0.59 -0.12 ...... Frame ( 4) shift: -0.88 -0.19 ...... Frame ( 5) shift: -1.18 -0.25 ...... Frame ( 6) shift: -1.32 -0.23 ...... Frame ( 7) shift: -1.30 -0.14 ...... Frame ( 8) shift: -1.28 -0.04 ...... Frame ( 9) shift: -1.28 0.01 ...... Frame ( 10) shift: -1.29 0.01 ...... Frame ( 11) shift: -1.30 0.02 ...... Frame ( 12) shift: -1.30 0.04 ...... Frame ( 13) shift: -1.28 0.09 ...... Frame ( 14) shift: -1.26 0.13 ...... Frame ( 15) shift: -1.25 0.20 ...... Frame ( 16) shift: -1.27 0.29 ...... Frame ( 17) shift: -1.29 0.39 ...... Frame ( 18) shift: -1.32 0.46 ...... Frame ( 19) shift: -1.37 0.50 ...... Frame ( 20) shift: -1.42 0.54 ...... Frame ( 21) shift: -1.43 0.60 ...... Frame ( 22) shift: -1.38 0.68 ...... Frame ( 23) shift: -1.33 0.77 ...... Frame ( 24) shift: -1.33 0.81 ...... Frame ( 25) shift: -1.38 0.80 ...... Frame ( 26) shift: -1.42 0.80 ...... Frame ( 27) shift: -1.45 0.79 ...... Frame ( 28) shift: -1.47 0.77 ...... Frame ( 29) shift: -1.49 0.74 ...... Frame ( 30) shift: -1.50 0.75 ...... Frame ( 31) shift: -1.50 0.80 ...... Frame ( 32) shift: -1.50 0.84 ...... Frame ( 33) shift: -1.50 0.88 ...... Frame ( 34) shift: -1.50 0.92 ...... Frame ( 35) shift: -1.50 0.95 ...... Frame ( 36) shift: -1.49 0.98 ...... Frame ( 37) shift: -1.46 1.01 ...... Frame ( 38) shift: -1.43 1.04 ...... Frame ( 39) shift: -1.39 1.07 ...... Frame ( 40) shift: -1.36 1.10 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.250819 Iteration 2 Error: 0.209383 Iteration 3 Error: 0.071851 Iteration 4 Error: 0.023967 Align patch 2 23 left Iteration 1 Error: 1.982005 Iteration 2 Error: 0.192873 Iteration 3 Error: 0.063593 Iteration 4 Error: 0.020767 Align patch 3 22 left Iteration 1 Error: 0.877172 Iteration 2 Error: 0.185499 Iteration 3 Error: 0.057456 Iteration 4 Error: 0.021514 Align patch 4 21 left Iteration 1 Error: 0.652729 Iteration 2 Error: 0.095072 Iteration 3 Error: 0.013364 Align patch 5 20 left Iteration 1 Error: 0.826324 Iteration 2 Error: 0.134327 Iteration 3 Error: 0.030802 Align patch 6 19 left Iteration 1 Error: 1.574687 Iteration 2 Error: 0.132237 Iteration 3 Error: 0.058843 Iteration 4 Error: 0.021042 Align patch 7 18 left Iteration 1 Error: 0.987178 Iteration 2 Error: 0.188128 Iteration 3 Error: 0.057349 Iteration 4 Error: 0.021604 Align patch 8 17 left Iteration 1 Error: 0.797000 Iteration 2 Error: 0.173026 Iteration 3 Error: 0.058474 Iteration 4 Error: 0.015148 Align patch 9 16 left Iteration 1 Error: 0.473172 Iteration 2 Error: 0.076352 Iteration 3 Error: 0.015120 Align patch 10 15 left Iteration 1 Error: 0.884108 Iteration 2 Error: 0.159467 Iteration 3 Error: 0.049747 Align patch 11 14 left Iteration 1 Error: 0.892723 Iteration 2 Error: 0.156692 Iteration 3 Error: 0.032016 Align patch 12 13 left Iteration 1 Error: 0.882399 Iteration 2 Error: 0.249744 Iteration 3 Error: 0.085455 Iteration 4 Error: 0.040366 Align patch 13 12 left Iteration 1 Error: 0.662756 Iteration 2 Error: 0.134805 Iteration 3 Error: 0.028769 Align patch 14 11 left Iteration 1 Error: 0.467628 Iteration 2 Error: 0.107106 Iteration 3 Error: 0.014018 Align patch 15 10 left Iteration 1 Error: 0.479895 Iteration 2 Error: 0.065514 Iteration 3 Error: 0.020187 Align patch 16 9 left Iteration 1 Error: 0.616215 Iteration 2 Error: 0.123933 Iteration 3 Error: 0.028265 Align patch 17 8 left Iteration 1 Error: 0.741297 Iteration 2 Error: 0.092352 Iteration 3 Error: 0.033947 Align patch 18 7 left Iteration 1 Error: 0.517971 Iteration 2 Error: 0.120440 Iteration 3 Error: 0.027005 Align patch 19 6 left Iteration 1 Error: 0.858826 Iteration 2 Error: 0.130194 Iteration 3 Error: 0.028988 Align patch 20 5 left Iteration 1 Error: 0.669996 Iteration 2 Error: 0.084677 Iteration 3 Error: 0.017817 Align patch 21 4 left Iteration 1 Error: 1.320466 Iteration 2 Error: 0.220562 Iteration 3 Error: 0.044131 Align patch 22 3 left Iteration 1 Error: 1.737983 Iteration 2 Error: 0.167177 Iteration 3 Error: 0.016186 Align patch 23 2 left Iteration 1 Error: 0.899605 Iteration 2 Error: 0.164655 Iteration 3 Error: 0.059282 Iteration 4 Error: 0.022645 Align patch 24 1 left Iteration 1 Error: 0.935413 Iteration 2 Error: 0.098551 Iteration 3 Error: 0.013082 Align patch 25 0 left Iteration 1 Error: 0.716691 Iteration 2 Error: 0.090417 Iteration 3 Error: 0.013983 3D Fitting completed. Patch alignment time: 15.69(sec) Local motion has been corrected. Process thread exits. Computational time: 24.256863 sec Total time: 29.983553 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00011hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00011hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.556315s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00011hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.695705s ........................................ >>>>>>TIME<<<<<< FFT: 0.899885s Defocus_U Defocus_V Angle CCC 10517.58 11388.67 5.16 0.055389 Final Values Defocus_U Defocus_V Angle CCC 10537.90 11405.87 5.16 0.103050 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00011hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00011hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.002e-01 CC threshold: 0.736 Mean Std: 45.17 7.49 Num Hot pixels: 221 Hot pixel threshold: 90.09 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.688311 Iteration 2 Error: 0.077638 Iteration 3 Error: 0.015740 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.24 -0.01 ...... Frame ( 3) shift: -0.49 -0.02 ...... Frame ( 4) shift: -0.73 -0.03 ...... Frame ( 5) shift: -0.98 -0.04 ...... Frame ( 6) shift: -1.13 -0.02 ...... Frame ( 7) shift: -1.19 0.03 ...... Frame ( 8) shift: -1.24 0.07 ...... Frame ( 9) shift: -1.24 0.10 ...... Frame ( 10) shift: -1.17 0.11 ...... Frame ( 11) shift: -1.10 0.12 ...... Frame ( 12) shift: -1.06 0.14 ...... Frame ( 13) shift: -1.07 0.16 ...... Frame ( 14) shift: -1.07 0.19 ...... Frame ( 15) shift: -1.08 0.21 ...... Frame ( 16) shift: -1.08 0.24 ...... Frame ( 17) shift: -1.08 0.27 ...... Frame ( 18) shift: -1.06 0.31 ...... Frame ( 19) shift: -1.01 0.36 ...... Frame ( 20) shift: -0.97 0.40 ...... Frame ( 21) shift: -0.94 0.42 ...... Frame ( 22) shift: -0.93 0.41 ...... Frame ( 23) shift: -0.92 0.40 ...... Frame ( 24) shift: -0.88 0.41 ...... Frame ( 25) shift: -0.83 0.45 ...... Frame ( 26) shift: -0.77 0.48 ...... Frame ( 27) shift: -0.75 0.50 ...... Frame ( 28) shift: -0.75 0.51 ...... Frame ( 29) shift: -0.76 0.52 ...... Frame ( 30) shift: -0.79 0.54 ...... Frame ( 31) shift: -0.84 0.57 ...... Frame ( 32) shift: -0.90 0.60 ...... Frame ( 33) shift: -0.93 0.64 ...... Frame ( 34) shift: -0.92 0.68 ...... Frame ( 35) shift: -0.91 0.71 ...... Frame ( 36) shift: -0.91 0.76 ...... Frame ( 37) shift: -0.91 0.82 ...... Frame ( 38) shift: -0.91 0.88 ...... Frame ( 39) shift: -0.91 0.94 ...... Frame ( 40) shift: -0.91 1.00 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.042176 Iteration 2 Error: 0.156642 Iteration 3 Error: 0.047708 Align patch 2 23 left Iteration 1 Error: 1.539007 Iteration 2 Error: 0.215376 Iteration 3 Error: 0.045185 Align patch 3 22 left Iteration 1 Error: 0.673914 Iteration 2 Error: 0.091976 Iteration 3 Error: 0.023478 Align patch 4 21 left Iteration 1 Error: 0.624722 Iteration 2 Error: 0.126344 Iteration 3 Error: 0.016686 Align patch 5 20 left Iteration 1 Error: 0.706047 Iteration 2 Error: 0.121813 Iteration 3 Error: 0.025931 Align patch 6 19 left Iteration 1 Error: 1.342660 Iteration 2 Error: 0.083580 Iteration 3 Error: 0.023724 Align patch 7 18 left Iteration 1 Error: 1.549668 Iteration 2 Error: 0.202424 Iteration 3 Error: 0.060012 Iteration 4 Error: 0.012497 Align patch 8 17 left Iteration 1 Error: 1.000660 Iteration 2 Error: 0.106696 Iteration 3 Error: 0.020884 Align patch 9 16 left Iteration 1 Error: 0.525118 Iteration 2 Error: 0.074517 Iteration 3 Error: 0.021173 Align patch 10 15 left Iteration 1 Error: 0.556861 Iteration 2 Error: 0.067791 Iteration 3 Error: 0.011683 Align patch 11 14 left Iteration 1 Error: 1.150176 Iteration 2 Error: 0.190979 Iteration 3 Error: 0.058246 Iteration 4 Error: 0.030073 Align patch 12 13 left Iteration 1 Error: 0.744695 Iteration 2 Error: 0.159515 Iteration 3 Error: 0.047744 Align patch 13 12 left Iteration 1 Error: 0.963452 Iteration 2 Error: 0.097113 Iteration 3 Error: 0.031424 Align patch 14 11 left Iteration 1 Error: 0.596496 Iteration 2 Error: 0.100412 Iteration 3 Error: 0.022242 Align patch 15 10 left Iteration 1 Error: 0.664842 Iteration 2 Error: 0.070913 Iteration 3 Error: 0.010123 Align patch 16 9 left Iteration 1 Error: 0.749079 Iteration 2 Error: 0.105232 Iteration 3 Error: 0.012959 Align patch 17 8 left Iteration 1 Error: 0.534966 Iteration 2 Error: 0.097590 Iteration 3 Error: 0.021437 Align patch 18 7 left Iteration 1 Error: 0.643535 Iteration 2 Error: 0.071127 Iteration 3 Error: 0.013158 Align patch 19 6 left Iteration 1 Error: 0.508552 Iteration 2 Error: 0.085412 Iteration 3 Error: 0.025145 Align patch 20 5 left Iteration 1 Error: 0.710401 Iteration 2 Error: 0.103746 Iteration 3 Error: 0.019015 Align patch 21 4 left Iteration 1 Error: 0.758390 Iteration 2 Error: 0.108628 Iteration 3 Error: 0.027749 Align patch 22 3 left Iteration 1 Error: 0.768337 Iteration 2 Error: 0.080437 Iteration 3 Error: 0.023856 Align patch 23 2 left Iteration 1 Error: 0.623043 Iteration 2 Error: 0.122143 Iteration 3 Error: 0.027471 Align patch 24 1 left Iteration 1 Error: 0.932271 Iteration 2 Error: 0.121765 Iteration 3 Error: 0.024614 Align patch 25 0 left Iteration 1 Error: 0.757780 Iteration 2 Error: 0.127323 Iteration 3 Error: 0.024832 3D Fitting completed. Patch alignment time: 15.66(sec) Local motion has been corrected. Process thread exits. Computational time: 25.190403 sec Total time: 30.913771 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00011hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00011hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.685753s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00011hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.210802s ........................................ >>>>>>TIME<<<<<< FFT: 0.954450s Defocus_U Defocus_V Angle CCC 14523.47 13878.92 84.40 0.066474 Final Values Defocus_U Defocus_V Angle CCC 14512.53 13877.36 84.72 0.109691 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00012hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00012hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 43.15 7.19 Num Hot pixels: 219 Hot pixel threshold: 86.31 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.582877 Iteration 2 Error: 0.281474 Iteration 3 Error: 0.076044 Iteration 4 Error: 0.024744 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.17 -0.12 ...... Frame ( 3) shift: -0.33 -0.23 ...... Frame ( 4) shift: -0.50 -0.35 ...... Frame ( 5) shift: -0.67 -0.47 ...... Frame ( 6) shift: -0.68 -0.48 ...... Frame ( 7) shift: -0.54 -0.38 ...... Frame ( 8) shift: -0.39 -0.29 ...... Frame ( 9) shift: -0.29 -0.20 ...... Frame ( 10) shift: -0.23 -0.13 ...... Frame ( 11) shift: -0.17 -0.06 ...... Frame ( 12) shift: -0.08 0.03 ...... Frame ( 13) shift: 0.03 0.13 ...... Frame ( 14) shift: 0.14 0.24 ...... Frame ( 15) shift: 0.23 0.34 ...... Frame ( 16) shift: 0.30 0.44 ...... Frame ( 17) shift: 0.37 0.54 ...... Frame ( 18) shift: 0.46 0.64 ...... Frame ( 19) shift: 0.55 0.73 ...... Frame ( 20) shift: 0.64 0.83 ...... Frame ( 21) shift: 0.69 0.92 ...... Frame ( 22) shift: 0.69 1.00 ...... Frame ( 23) shift: 0.70 1.08 ...... Frame ( 24) shift: 0.74 1.16 ...... Frame ( 25) shift: 0.83 1.23 ...... Frame ( 26) shift: 0.91 1.30 ...... Frame ( 27) shift: 0.97 1.34 ...... Frame ( 28) shift: 1.02 1.35 ...... Frame ( 29) shift: 1.06 1.36 ...... Frame ( 30) shift: 1.08 1.41 ...... Frame ( 31) shift: 1.08 1.50 ...... Frame ( 32) shift: 1.07 1.59 ...... Frame ( 33) shift: 1.12 1.66 ...... Frame ( 34) shift: 1.23 1.72 ...... Frame ( 35) shift: 1.34 1.78 ...... Frame ( 36) shift: 1.38 1.83 ...... Frame ( 37) shift: 1.37 1.89 ...... Frame ( 38) shift: 1.35 1.94 ...... Frame ( 39) shift: 1.34 2.00 ...... Frame ( 40) shift: 1.32 2.05 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.391160 Iteration 2 Error: 0.279079 Iteration 3 Error: 0.129296 Iteration 4 Error: 0.066726 Iteration 5 Error: 0.029294 Align patch 2 23 left Iteration 1 Error: 1.168946 Iteration 2 Error: 0.281896 Iteration 3 Error: 0.114594 Iteration 4 Error: 0.050864 Iteration 5 Error: 0.023575 Align patch 3 22 left Iteration 1 Error: 1.290722 Iteration 2 Error: 0.357661 Iteration 3 Error: 0.111074 Iteration 4 Error: 0.052228 Iteration 5 Error: 0.027313 Align patch 4 21 left Iteration 1 Error: 0.801153 Iteration 2 Error: 0.159105 Iteration 3 Error: 0.035722 Align patch 5 20 left Iteration 1 Error: 0.529360 Iteration 2 Error: 0.072362 Iteration 3 Error: 0.019815 Align patch 6 19 left Iteration 1 Error: 0.678319 Iteration 2 Error: 0.259599 Iteration 3 Error: 0.097223 Iteration 4 Error: 0.051001 Iteration 5 Error: 0.029546 Align patch 7 18 left Iteration 1 Error: 0.780438 Iteration 2 Error: 0.219898 Iteration 3 Error: 0.075027 Iteration 4 Error: 0.034938 Align patch 8 17 left Iteration 1 Error: 0.784631 Iteration 2 Error: 0.199661 Iteration 3 Error: 0.055803 Iteration 4 Error: 0.019631 Align patch 9 16 left Iteration 1 Error: 0.695667 Iteration 2 Error: 0.142911 Iteration 3 Error: 0.049942 Align patch 10 15 left Iteration 1 Error: 0.444396 Iteration 2 Error: 0.054582 Iteration 3 Error: 0.010916 Align patch 11 14 left Iteration 1 Error: 0.701060 Iteration 2 Error: 0.142173 Iteration 3 Error: 0.036576 Align patch 12 13 left Iteration 1 Error: 0.767750 Iteration 2 Error: 0.155187 Iteration 3 Error: 0.038593 Align patch 13 12 left Iteration 1 Error: 0.490903 Iteration 2 Error: 0.075892 Iteration 3 Error: 0.021695 Align patch 14 11 left Iteration 1 Error: 0.569977 Iteration 2 Error: 0.100325 Iteration 3 Error: 0.021989 Align patch 15 10 left Iteration 1 Error: 0.647049 Iteration 2 Error: 0.054852 Iteration 3 Error: 0.020536 Align patch 16 9 left Iteration 1 Error: 0.930238 Iteration 2 Error: 0.169017 Iteration 3 Error: 0.038028 Align patch 17 8 left Iteration 1 Error: 1.050125 Iteration 2 Error: 0.098044 Iteration 3 Error: 0.023060 Align patch 18 7 left Iteration 1 Error: 0.702560 Iteration 2 Error: 0.089827 Iteration 3 Error: 0.017089 Align patch 19 6 left Iteration 1 Error: 0.709112 Iteration 2 Error: 0.072000 Iteration 3 Error: 0.013846 Align patch 20 5 left Iteration 1 Error: 0.904820 Iteration 2 Error: 0.130320 Iteration 3 Error: 0.047899 Align patch 21 4 left Iteration 1 Error: 1.009094 Iteration 2 Error: 0.167876 Iteration 3 Error: 0.051446 Iteration 4 Error: 0.014015 Align patch 22 3 left Iteration 1 Error: 0.574677 Iteration 2 Error: 0.180661 Iteration 3 Error: 0.068291 Iteration 4 Error: 0.026566 Align patch 23 2 left Iteration 1 Error: 0.708066 Iteration 2 Error: 0.119636 Iteration 3 Error: 0.025268 Align patch 24 1 left Iteration 1 Error: 0.720727 Iteration 2 Error: 0.213571 Iteration 3 Error: 0.073567 Iteration 4 Error: 0.025225 Align patch 25 0 left Iteration 1 Error: 0.808514 Iteration 2 Error: 0.206686 Iteration 3 Error: 0.071529 Iteration 4 Error: 0.023800 3D Fitting completed. Patch alignment time: 15.82(sec) Local motion has been corrected. Process thread exits. Computational time: 24.339952 sec Total time: 30.588818 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00012hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00012hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.577577s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00012hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.164561s ........................................ >>>>>>TIME<<<<<< FFT: 0.899041s Defocus_U Defocus_V Angle CCC 11158.21 11962.89 13.24 0.058711 Final Values Defocus_U Defocus_V Angle CCC 11186.33 11962.89 12.93 0.104458 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00012hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00012hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.350e-01 1.004e-01 CC threshold: 0.737 Mean Std: 44.20 7.43 Num Hot pixels: 208 Hot pixel threshold: 88.78 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.901807 Iteration 2 Error: 0.112949 Iteration 3 Error: 0.021072 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.20 -0.03 ...... Frame ( 3) shift: -0.41 -0.07 ...... Frame ( 4) shift: -0.61 -0.10 ...... Frame ( 5) shift: -0.82 -0.13 ...... Frame ( 6) shift: -0.88 -0.09 ...... Frame ( 7) shift: -0.79 0.02 ...... Frame ( 8) shift: -0.70 0.14 ...... Frame ( 9) shift: -0.63 0.23 ...... Frame ( 10) shift: -0.57 0.28 ...... Frame ( 11) shift: -0.51 0.34 ...... Frame ( 12) shift: -0.47 0.41 ...... Frame ( 13) shift: -0.43 0.49 ...... Frame ( 14) shift: -0.39 0.57 ...... Frame ( 15) shift: -0.37 0.61 ...... Frame ( 16) shift: -0.36 0.63 ...... Frame ( 17) shift: -0.35 0.66 ...... Frame ( 18) shift: -0.34 0.71 ...... Frame ( 19) shift: -0.32 0.80 ...... Frame ( 20) shift: -0.31 0.90 ...... Frame ( 21) shift: -0.28 0.96 ...... Frame ( 22) shift: -0.24 1.00 ...... Frame ( 23) shift: -0.21 1.04 ...... Frame ( 24) shift: -0.19 1.07 ...... Frame ( 25) shift: -0.18 1.11 ...... Frame ( 26) shift: -0.18 1.14 ...... Frame ( 27) shift: -0.21 1.16 ...... Frame ( 28) shift: -0.27 1.15 ...... Frame ( 29) shift: -0.32 1.14 ...... Frame ( 30) shift: -0.36 1.14 ...... Frame ( 31) shift: -0.38 1.15 ...... Frame ( 32) shift: -0.39 1.16 ...... Frame ( 33) shift: -0.42 1.17 ...... Frame ( 34) shift: -0.47 1.19 ...... Frame ( 35) shift: -0.51 1.21 ...... Frame ( 36) shift: -0.53 1.25 ...... Frame ( 37) shift: -0.54 1.30 ...... Frame ( 38) shift: -0.55 1.34 ...... Frame ( 39) shift: -0.56 1.39 ...... Frame ( 40) shift: -0.57 1.44 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.890149 Iteration 2 Error: 0.178469 Iteration 3 Error: 0.060148 Iteration 4 Error: 0.024970 Align patch 2 23 left Iteration 1 Error: 0.680815 Iteration 2 Error: 0.193527 Iteration 3 Error: 0.062425 Iteration 4 Error: 0.027999 Align patch 3 22 left Iteration 1 Error: 0.742135 Iteration 2 Error: 0.138438 Iteration 3 Error: 0.032573 Align patch 4 21 left Iteration 1 Error: 0.582633 Iteration 2 Error: 0.092903 Iteration 3 Error: 0.017493 Align patch 5 20 left Iteration 1 Error: 0.574839 Iteration 2 Error: 0.052424 Iteration 3 Error: 0.009913 Align patch 6 19 left Iteration 1 Error: 1.120826 Iteration 2 Error: 0.206735 Iteration 3 Error: 0.077259 Iteration 4 Error: 0.023378 Align patch 7 18 left Iteration 1 Error: 1.019056 Iteration 2 Error: 0.232712 Iteration 3 Error: 0.060155 Iteration 4 Error: 0.019977 Align patch 8 17 left Iteration 1 Error: 0.506081 Iteration 2 Error: 0.072658 Iteration 3 Error: 0.020070 Align patch 9 16 left Iteration 1 Error: 0.586054 Iteration 2 Error: 0.060916 Iteration 3 Error: 0.016004 Align patch 10 15 left Iteration 1 Error: 0.683371 Iteration 2 Error: 0.061902 Iteration 3 Error: 0.010172 Align patch 11 14 left Iteration 1 Error: 1.510566 Iteration 2 Error: 0.133397 Iteration 3 Error: 0.037182 Align patch 12 13 left Iteration 1 Error: 0.553973 Iteration 2 Error: 0.084220 Iteration 3 Error: 0.025915 Align patch 13 12 left Iteration 1 Error: 0.569241 Iteration 2 Error: 0.061525 Iteration 3 Error: 0.013956 Align patch 14 11 left Iteration 1 Error: 0.478787 Iteration 2 Error: 0.079996 Iteration 3 Error: 0.014506 Align patch 15 10 left Iteration 1 Error: 0.326065 Iteration 2 Error: 0.040968 Align patch 16 9 left Iteration 1 Error: 0.681918 Iteration 2 Error: 0.091780 Iteration 3 Error: 0.025115 Align patch 17 8 left Iteration 1 Error: 0.647270 Iteration 2 Error: 0.109651 Iteration 3 Error: 0.022855 Align patch 18 7 left Iteration 1 Error: 0.565805 Iteration 2 Error: 0.112981 Iteration 3 Error: 0.018155 Align patch 19 6 left Iteration 1 Error: 0.470281 Iteration 2 Error: 0.079673 Iteration 3 Error: 0.022105 Align patch 20 5 left Iteration 1 Error: 0.640819 Iteration 2 Error: 0.082957 Iteration 3 Error: 0.012280 Align patch 21 4 left Iteration 1 Error: 1.028658 Iteration 2 Error: 0.138407 Iteration 3 Error: 0.036325 Align patch 22 3 left Iteration 1 Error: 0.778252 Iteration 2 Error: 0.147593 Iteration 3 Error: 0.041365 Align patch 23 2 left Iteration 1 Error: 0.533418 Iteration 2 Error: 0.119070 Iteration 3 Error: 0.018118 Align patch 24 1 left Iteration 1 Error: 0.736679 Iteration 2 Error: 0.147235 Iteration 3 Error: 0.040776 Align patch 25 0 left Iteration 1 Error: 0.684167 Iteration 2 Error: 0.102769 Iteration 3 Error: 0.025809 3D Fitting completed. Patch alignment time: 15.50(sec) Local motion has been corrected. Process thread exits. Computational time: 24.499874 sec Total time: 30.243004 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00012hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00012hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.634437s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00012hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.146460s ........................................ >>>>>>TIME<<<<<< FFT: 1.002958s Defocus_U Defocus_V Angle CCC 12431.68 11923.85 87.94 0.059181 Final Values Defocus_U Defocus_V Angle CCC 12436.37 11950.44 87.63 0.105182 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00012hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00012hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.350e-01 1.004e-01 CC threshold: 0.737 Mean Std: 42.52 7.33 Num Hot pixels: 215 Hot pixel threshold: 86.48 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.191489 Iteration 2 Error: 0.158659 Iteration 3 Error: 0.032940 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.22 -0.08 ...... Frame ( 3) shift: -0.45 -0.17 ...... Frame ( 4) shift: -0.67 -0.25 ...... Frame ( 5) shift: -0.90 -0.34 ...... Frame ( 6) shift: -0.97 -0.33 ...... Frame ( 7) shift: -0.90 -0.23 ...... Frame ( 8) shift: -0.82 -0.12 ...... Frame ( 9) shift: -0.74 -0.05 ...... Frame ( 10) shift: -0.65 0.01 ...... Frame ( 11) shift: -0.57 0.06 ...... Frame ( 12) shift: -0.47 0.12 ...... Frame ( 13) shift: -0.36 0.19 ...... Frame ( 14) shift: -0.25 0.25 ...... Frame ( 15) shift: -0.19 0.27 ...... Frame ( 16) shift: -0.16 0.26 ...... Frame ( 17) shift: -0.14 0.25 ...... Frame ( 18) shift: -0.07 0.27 ...... Frame ( 19) shift: 0.04 0.32 ...... Frame ( 20) shift: 0.15 0.37 ...... Frame ( 21) shift: 0.21 0.40 ...... Frame ( 22) shift: 0.23 0.42 ...... Frame ( 23) shift: 0.25 0.43 ...... Frame ( 24) shift: 0.28 0.45 ...... Frame ( 25) shift: 0.32 0.45 ...... Frame ( 26) shift: 0.36 0.46 ...... Frame ( 27) shift: 0.40 0.50 ...... Frame ( 28) shift: 0.44 0.58 ...... Frame ( 29) shift: 0.47 0.66 ...... Frame ( 30) shift: 0.51 0.74 ...... Frame ( 31) shift: 0.54 0.84 ...... Frame ( 32) shift: 0.58 0.93 ...... Frame ( 33) shift: 0.63 1.01 ...... Frame ( 34) shift: 0.69 1.08 ...... Frame ( 35) shift: 0.76 1.14 ...... Frame ( 36) shift: 0.81 1.20 ...... Frame ( 37) shift: 0.83 1.24 ...... Frame ( 38) shift: 0.86 1.28 ...... Frame ( 39) shift: 0.89 1.33 ...... Frame ( 40) shift: 0.92 1.37 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.809470 Iteration 2 Error: 0.258030 Iteration 3 Error: 0.104885 Iteration 4 Error: 0.016358 Align patch 2 23 left Iteration 1 Error: 1.820776 Iteration 2 Error: 0.203473 Iteration 3 Error: 0.046845 Align patch 3 22 left Iteration 1 Error: 0.808266 Iteration 2 Error: 0.125759 Iteration 3 Error: 0.042156 Align patch 4 21 left Iteration 1 Error: 0.541657 Iteration 2 Error: 0.117781 Iteration 3 Error: 0.029835 Align patch 5 20 left Iteration 1 Error: 1.004616 Iteration 2 Error: 0.086140 Iteration 3 Error: 0.011452 Align patch 6 19 left Iteration 1 Error: 2.375589 Iteration 2 Error: 0.391492 Iteration 3 Error: 0.095756 Iteration 4 Error: 0.029950 Align patch 7 18 left Iteration 1 Error: 1.311460 Iteration 2 Error: 0.192400 Iteration 3 Error: 0.058436 Iteration 4 Error: 0.019343 Align patch 8 17 left Iteration 1 Error: 0.609826 Iteration 2 Error: 0.187997 Iteration 3 Error: 0.062366 Iteration 4 Error: 0.031617 Align patch 9 16 left Iteration 1 Error: 0.788209 Iteration 2 Error: 0.110737 Iteration 3 Error: 0.016111 Align patch 10 15 left Iteration 1 Error: 0.931118 Iteration 2 Error: 0.091597 Iteration 3 Error: 0.032003 Align patch 11 14 left Iteration 1 Error: 0.863552 Iteration 2 Error: 0.198869 Iteration 3 Error: 0.068172 Iteration 4 Error: 0.032060 Align patch 12 13 left Iteration 1 Error: 0.843372 Iteration 2 Error: 0.271315 Iteration 3 Error: 0.074437 Iteration 4 Error: 0.026769 Align patch 13 12 left Iteration 1 Error: 0.346025 Iteration 2 Error: 0.039861 Align patch 14 11 left Iteration 1 Error: 0.868546 Iteration 2 Error: 0.138443 Iteration 3 Error: 0.028559 Align patch 15 10 left Iteration 1 Error: 0.662078 Iteration 2 Error: 0.119307 Iteration 3 Error: 0.022405 Align patch 16 9 left Iteration 1 Error: 0.755727 Iteration 2 Error: 0.126348 Iteration 3 Error: 0.025874 Align patch 17 8 left Iteration 1 Error: 0.667438 Iteration 2 Error: 0.130672 Iteration 3 Error: 0.039761 Align patch 18 7 left Iteration 1 Error: 0.512148 Iteration 2 Error: 0.099105 Iteration 3 Error: 0.023035 Align patch 19 6 left Iteration 1 Error: 0.704788 Iteration 2 Error: 0.092579 Iteration 3 Error: 0.020206 Align patch 20 5 left Iteration 1 Error: 0.785802 Iteration 2 Error: 0.112299 Iteration 3 Error: 0.040597 Align patch 21 4 left Iteration 1 Error: 0.559636 Iteration 2 Error: 0.095287 Iteration 3 Error: 0.019284 Align patch 22 3 left Iteration 1 Error: 0.897926 Iteration 2 Error: 0.097432 Iteration 3 Error: 0.033403 Align patch 23 2 left Iteration 1 Error: 0.936926 Iteration 2 Error: 0.103190 Iteration 3 Error: 0.021735 Align patch 24 1 left Iteration 1 Error: 0.651450 Iteration 2 Error: 0.120719 Iteration 3 Error: 0.021517 Align patch 25 0 left Iteration 1 Error: 0.817016 Iteration 2 Error: 0.124556 Iteration 3 Error: 0.027308 3D Fitting completed. Patch alignment time: 15.05(sec) Local motion has been corrected. Process thread exits. Computational time: 23.807089 sec Total time: 30.276602 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00012hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00012hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.549930s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00012hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.483568s ........................................ >>>>>>TIME<<<<<< FFT: 0.943346s Defocus_U Defocus_V Angle CCC 14158.22 15033.22 3.62 0.070847 Final Values Defocus_U Defocus_V Angle CCC 14176.98 15033.23 3.62 0.113476 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00012hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00012hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.350e-01 1.004e-01 CC threshold: 0.737 Mean Std: 44.49 7.33 Num Hot pixels: 207 Hot pixel threshold: 88.47 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.613797 Iteration 2 Error: 0.080010 Iteration 3 Error: 0.019253 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.16 -0.05 ...... Frame ( 3) shift: -0.33 -0.10 ...... Frame ( 4) shift: -0.49 -0.15 ...... Frame ( 5) shift: -0.66 -0.20 ...... Frame ( 6) shift: -0.74 -0.19 ...... Frame ( 7) shift: -0.74 -0.13 ...... Frame ( 8) shift: -0.75 -0.07 ...... Frame ( 9) shift: -0.71 -0.02 ...... Frame ( 10) shift: -0.62 0.02 ...... Frame ( 11) shift: -0.54 0.06 ...... Frame ( 12) shift: -0.48 0.13 ...... Frame ( 13) shift: -0.44 0.25 ...... Frame ( 14) shift: -0.41 0.37 ...... Frame ( 15) shift: -0.39 0.44 ...... Frame ( 16) shift: -0.39 0.46 ...... Frame ( 17) shift: -0.38 0.48 ...... Frame ( 18) shift: -0.37 0.52 ...... Frame ( 19) shift: -0.35 0.56 ...... Frame ( 20) shift: -0.33 0.60 ...... Frame ( 21) shift: -0.32 0.62 ...... Frame ( 22) shift: -0.30 0.62 ...... Frame ( 23) shift: -0.29 0.61 ...... Frame ( 24) shift: -0.26 0.61 ...... Frame ( 25) shift: -0.24 0.60 ...... Frame ( 26) shift: -0.21 0.60 ...... Frame ( 27) shift: -0.21 0.62 ...... Frame ( 28) shift: -0.23 0.68 ...... Frame ( 29) shift: -0.24 0.74 ...... Frame ( 30) shift: -0.28 0.77 ...... Frame ( 31) shift: -0.34 0.77 ...... Frame ( 32) shift: -0.40 0.76 ...... Frame ( 33) shift: -0.45 0.76 ...... Frame ( 34) shift: -0.48 0.76 ...... Frame ( 35) shift: -0.51 0.76 ...... Frame ( 36) shift: -0.55 0.76 ...... Frame ( 37) shift: -0.61 0.76 ...... Frame ( 38) shift: -0.66 0.76 ...... Frame ( 39) shift: -0.72 0.76 ...... Frame ( 40) shift: -0.77 0.75 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 3.287889 Iteration 2 Error: 0.440098 Iteration 3 Error: 0.136360 Iteration 4 Error: 0.046866 Align patch 2 23 left Iteration 1 Error: 1.952760 Iteration 2 Error: 0.284126 Iteration 3 Error: 0.115358 Iteration 4 Error: 0.035949 Align patch 3 22 left Iteration 1 Error: 1.450278 Iteration 2 Error: 0.282665 Iteration 3 Error: 0.061833 Iteration 4 Error: 0.031024 Align patch 4 21 left Iteration 1 Error: 0.712797 Iteration 2 Error: 0.139025 Iteration 3 Error: 0.027168 Align patch 5 20 left Iteration 1 Error: 0.699479 Iteration 2 Error: 0.068107 Iteration 3 Error: 0.010277 Align patch 6 19 left Iteration 1 Error: 1.904465 Iteration 2 Error: 0.218744 Iteration 3 Error: 0.068377 Iteration 4 Error: 0.021259 Align patch 7 18 left Iteration 1 Error: 1.877378 Iteration 2 Error: 0.272961 Iteration 3 Error: 0.094914 Iteration 4 Error: 0.032325 Align patch 8 17 left Iteration 1 Error: 0.827012 Iteration 2 Error: 0.224056 Iteration 3 Error: 0.077840 Iteration 4 Error: 0.021455 Align patch 9 16 left Iteration 1 Error: 0.613373 Iteration 2 Error: 0.086233 Iteration 3 Error: 0.015569 Align patch 10 15 left Iteration 1 Error: 0.813295 Iteration 2 Error: 0.072414 Iteration 3 Error: 0.008350 Align patch 11 14 left Iteration 1 Error: 1.286586 Iteration 2 Error: 0.237805 Iteration 3 Error: 0.048211 Align patch 12 13 left Iteration 1 Error: 1.301189 Iteration 2 Error: 0.204687 Iteration 3 Error: 0.045372 Align patch 13 12 left Iteration 1 Error: 0.678153 Iteration 2 Error: 0.109486 Iteration 3 Error: 0.027046 Align patch 14 11 left Iteration 1 Error: 0.578320 Iteration 2 Error: 0.071521 Iteration 3 Error: 0.016039 Align patch 15 10 left Iteration 1 Error: 0.565111 Iteration 2 Error: 0.097171 Iteration 3 Error: 0.034239 Align patch 16 9 left Iteration 1 Error: 0.696472 Iteration 2 Error: 0.117215 Iteration 3 Error: 0.029709 Align patch 17 8 left Iteration 1 Error: 0.518831 Iteration 2 Error: 0.123412 Iteration 3 Error: 0.032832 Align patch 18 7 left Iteration 1 Error: 0.871859 Iteration 2 Error: 0.113594 Iteration 3 Error: 0.021705 Align patch 19 6 left Iteration 1 Error: 0.753865 Iteration 2 Error: 0.114155 Iteration 3 Error: 0.030569 Align patch 20 5 left Iteration 1 Error: 0.711031 Iteration 2 Error: 0.174578 Iteration 3 Error: 0.049021 Align patch 21 4 left Iteration 1 Error: 1.067305 Iteration 2 Error: 0.274565 Iteration 3 Error: 0.053936 Iteration 4 Error: 0.013536 Align patch 22 3 left Iteration 1 Error: 1.493492 Iteration 2 Error: 0.190142 Iteration 3 Error: 0.043068 Align patch 23 2 left Iteration 1 Error: 1.446556 Iteration 2 Error: 0.294171 Iteration 3 Error: 0.082177 Iteration 4 Error: 0.028698 Align patch 24 1 left Iteration 1 Error: 0.768367 Iteration 2 Error: 0.116963 Iteration 3 Error: 0.022026 Align patch 25 0 left Iteration 1 Error: 0.699286 Iteration 2 Error: 0.127176 Iteration 3 Error: 0.017575 3D Fitting completed. Patch alignment time: 16.10(sec) Local motion has been corrected. Process thread exits. Computational time: 24.943960 sec Total time: 32.826641 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00012hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00012hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.752375s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00012hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.447414s ........................................ >>>>>>TIME<<<<<< FFT: 1.315316s Defocus_U Defocus_V Angle CCC 10306.67 9701.14 82.55 0.054778 Final Values Defocus_U Defocus_V Angle CCC 10319.17 9698.02 82.87 0.103937 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00013hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00013hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 44.71 7.51 Num Hot pixels: 203 Hot pixel threshold: 89.76 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.799993 Iteration 2 Error: 0.095440 Iteration 3 Error: 0.023381 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.24 -0.05 ...... Frame ( 3) shift: -0.48 -0.10 ...... Frame ( 4) shift: -0.72 -0.15 ...... Frame ( 5) shift: -0.96 -0.20 ...... Frame ( 6) shift: -1.08 -0.19 ...... Frame ( 7) shift: -1.06 -0.12 ...... Frame ( 8) shift: -1.04 -0.06 ...... Frame ( 9) shift: -1.02 0.00 ...... Frame ( 10) shift: -0.98 0.06 ...... Frame ( 11) shift: -0.95 0.11 ...... Frame ( 12) shift: -0.94 0.18 ...... Frame ( 13) shift: -0.96 0.26 ...... Frame ( 14) shift: -0.98 0.34 ...... Frame ( 15) shift: -0.98 0.42 ...... Frame ( 16) shift: -0.96 0.51 ...... Frame ( 17) shift: -0.94 0.60 ...... Frame ( 18) shift: -0.93 0.66 ...... Frame ( 19) shift: -0.94 0.70 ...... Frame ( 20) shift: -0.94 0.75 ...... Frame ( 21) shift: -0.93 0.78 ...... Frame ( 22) shift: -0.90 0.80 ...... Frame ( 23) shift: -0.88 0.82 ...... Frame ( 24) shift: -0.87 0.84 ...... Frame ( 25) shift: -0.87 0.87 ...... Frame ( 26) shift: -0.88 0.89 ...... Frame ( 27) shift: -0.90 0.93 ...... Frame ( 28) shift: -0.94 0.97 ...... Frame ( 29) shift: -0.97 1.01 ...... Frame ( 30) shift: -0.98 1.00 ...... Frame ( 31) shift: -0.94 0.94 ...... Frame ( 32) shift: -0.91 0.89 ...... Frame ( 33) shift: -0.90 0.88 ...... Frame ( 34) shift: -0.92 0.93 ...... Frame ( 35) shift: -0.94 0.97 ...... Frame ( 36) shift: -0.95 1.01 ...... Frame ( 37) shift: -0.96 1.04 ...... Frame ( 38) shift: -0.97 1.07 ...... Frame ( 39) shift: -0.97 1.10 ...... Frame ( 40) shift: -0.98 1.12 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.707192 Iteration 2 Error: 0.134680 Iteration 3 Error: 0.024412 Align patch 2 23 left Iteration 1 Error: 1.274656 Iteration 2 Error: 0.207657 Iteration 3 Error: 0.026435 Align patch 3 22 left Iteration 1 Error: 0.576308 Iteration 2 Error: 0.117662 Iteration 3 Error: 0.025197 Align patch 4 21 left Iteration 1 Error: 0.836777 Iteration 2 Error: 0.071540 Iteration 3 Error: 0.013534 Align patch 5 20 left Iteration 1 Error: 0.712016 Iteration 2 Error: 0.104919 Iteration 3 Error: 0.015560 Align patch 6 19 left Iteration 1 Error: 1.038999 Iteration 2 Error: 0.115278 Iteration 3 Error: 0.027802 Align patch 7 18 left Iteration 1 Error: 0.763254 Iteration 2 Error: 0.088142 Iteration 3 Error: 0.026439 Align patch 8 17 left Iteration 1 Error: 1.252343 Iteration 2 Error: 0.244749 Iteration 3 Error: 0.053976 Iteration 4 Error: 0.016838 Align patch 9 16 left Iteration 1 Error: 1.005350 Iteration 2 Error: 0.110801 Iteration 3 Error: 0.030434 Align patch 10 15 left Iteration 1 Error: 0.868189 Iteration 2 Error: 0.133259 Iteration 3 Error: 0.055641 Iteration 4 Error: 0.009244 Align patch 11 14 left Iteration 1 Error: 1.000567 Iteration 2 Error: 0.192433 Iteration 3 Error: 0.045285 Align patch 12 13 left Iteration 1 Error: 1.148242 Iteration 2 Error: 0.154271 Iteration 3 Error: 0.036781 Align patch 13 12 left Iteration 1 Error: 0.913034 Iteration 2 Error: 0.082680 Iteration 3 Error: 0.018600 Align patch 14 11 left Iteration 1 Error: 0.573259 Iteration 2 Error: 0.063109 Iteration 3 Error: 0.015767 Align patch 15 10 left Iteration 1 Error: 0.659759 Iteration 2 Error: 0.096260 Iteration 3 Error: 0.030883 Align patch 16 9 left Iteration 1 Error: 1.610358 Iteration 2 Error: 0.235981 Iteration 3 Error: 0.088156 Iteration 4 Error: 0.021113 Align patch 17 8 left Iteration 1 Error: 1.201095 Iteration 2 Error: 0.172574 Iteration 3 Error: 0.034480 Align patch 18 7 left Iteration 1 Error: 0.699733 Iteration 2 Error: 0.106170 Iteration 3 Error: 0.039748 Align patch 19 6 left Iteration 1 Error: 0.651716 Iteration 2 Error: 0.084861 Iteration 3 Error: 0.033541 Align patch 20 5 left Iteration 1 Error: 0.548212 Iteration 2 Error: 0.072284 Iteration 3 Error: 0.013721 Align patch 21 4 left Iteration 1 Error: 1.525826 Iteration 2 Error: 0.317462 Iteration 3 Error: 0.043287 Align patch 22 3 left Iteration 1 Error: 0.881584 Iteration 2 Error: 0.183310 Iteration 3 Error: 0.050703 Iteration 4 Error: 0.014538 Align patch 23 2 left Iteration 1 Error: 0.644602 Iteration 2 Error: 0.081759 Iteration 3 Error: 0.026055 Align patch 24 1 left Iteration 1 Error: 0.573217 Iteration 2 Error: 0.076857 Iteration 3 Error: 0.019039 Align patch 25 0 left Iteration 1 Error: 0.500006 Iteration 2 Error: 0.092801 Iteration 3 Error: 0.026584 3D Fitting completed. Patch alignment time: 15.59(sec) Local motion has been corrected. Process thread exits. Computational time: 24.595749 sec Total time: 30.484062 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00013hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00013hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.923422s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00013hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.029628s ........................................ >>>>>>TIME<<<<<< FFT: 0.790377s Defocus_U Defocus_V Angle CCC 13585.96 14425.80 11.21 0.052285 Final Values Defocus_U Defocus_V Angle CCC 13593.77 14417.99 10.90 0.087516 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00013hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00013hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 36.05 6.80 Num Hot pixels: 162 Hot pixel threshold: 76.84 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.146293 Iteration 2 Error: 0.120542 Iteration 3 Error: 0.025492 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.00 -0.39 ...... Frame ( 3) shift: 0.00 -0.79 ...... Frame ( 4) shift: 0.00 -1.18 ...... Frame ( 5) shift: 0.00 -1.58 ...... Frame ( 6) shift: 0.01 -1.78 ...... Frame ( 7) shift: 0.04 -1.79 ...... Frame ( 8) shift: 0.07 -1.79 ...... Frame ( 9) shift: 0.11 -1.82 ...... Frame ( 10) shift: 0.18 -1.86 ...... Frame ( 11) shift: 0.24 -1.90 ...... Frame ( 12) shift: 0.27 -1.92 ...... Frame ( 13) shift: 0.26 -1.92 ...... Frame ( 14) shift: 0.26 -1.92 ...... Frame ( 15) shift: 0.26 -1.89 ...... Frame ( 16) shift: 0.27 -1.81 ...... Frame ( 17) shift: 0.28 -1.74 ...... Frame ( 18) shift: 0.27 -1.71 ...... Frame ( 19) shift: 0.24 -1.72 ...... Frame ( 20) shift: 0.21 -1.73 ...... Frame ( 21) shift: 0.22 -1.73 ...... Frame ( 22) shift: 0.28 -1.73 ...... Frame ( 23) shift: 0.34 -1.72 ...... Frame ( 24) shift: 0.42 -1.72 ...... Frame ( 25) shift: 0.51 -1.71 ...... Frame ( 26) shift: 0.61 -1.71 ...... Frame ( 27) shift: 0.67 -1.68 ...... Frame ( 28) shift: 0.70 -1.63 ...... Frame ( 29) shift: 0.73 -1.57 ...... Frame ( 30) shift: 0.75 -1.53 ...... Frame ( 31) shift: 0.77 -1.51 ...... Frame ( 32) shift: 0.79 -1.49 ...... Frame ( 33) shift: 0.80 -1.45 ...... Frame ( 34) shift: 0.80 -1.39 ...... Frame ( 35) shift: 0.81 -1.34 ...... Frame ( 36) shift: 0.84 -1.31 ...... Frame ( 37) shift: 0.90 -1.33 ...... Frame ( 38) shift: 0.95 -1.35 ...... Frame ( 39) shift: 1.01 -1.36 ...... Frame ( 40) shift: 1.06 -1.38 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.804028 Iteration 2 Error: 0.191084 Iteration 3 Error: 0.055783 Iteration 4 Error: 0.014317 Align patch 2 23 left Iteration 1 Error: 0.963731 Iteration 2 Error: 0.262902 Iteration 3 Error: 0.053287 Iteration 4 Error: 0.023077 Align patch 3 22 left Iteration 1 Error: 0.939418 Iteration 2 Error: 0.139821 Iteration 3 Error: 0.030458 Align patch 4 21 left Iteration 1 Error: 1.306746 Iteration 2 Error: 0.106199 Iteration 3 Error: 0.019286 Align patch 5 20 left Iteration 1 Error: 2.293634 Iteration 2 Error: 0.542629 Iteration 3 Error: 0.186167 Iteration 4 Error: 0.089877 Iteration 5 Error: 0.047076 Align patch 6 19 left Iteration 1 Error: 1.798250 Iteration 2 Error: 0.199540 Iteration 3 Error: 0.059004 Iteration 4 Error: 0.013750 Align patch 7 18 left Iteration 1 Error: 0.779333 Iteration 2 Error: 0.125805 Iteration 3 Error: 0.030617 Align patch 8 17 left Iteration 1 Error: 0.436517 Iteration 2 Error: 0.081758 Iteration 3 Error: 0.024813 Align patch 9 16 left Iteration 1 Error: 0.612016 Iteration 2 Error: 0.108372 Iteration 3 Error: 0.021137 Align patch 10 15 left Iteration 1 Error: 0.796408 Iteration 2 Error: 0.107322 Iteration 3 Error: 0.034292 Align patch 11 14 left Iteration 1 Error: 1.056888 Iteration 2 Error: 0.202917 Iteration 3 Error: 0.045729 Align patch 12 13 left Iteration 1 Error: 1.330404 Iteration 2 Error: 0.112496 Iteration 3 Error: 0.023188 Align patch 13 12 left Iteration 1 Error: 0.734252 Iteration 2 Error: 0.144745 Iteration 3 Error: 0.031505 Align patch 14 11 left Iteration 1 Error: 0.587306 Iteration 2 Error: 0.097897 Iteration 3 Error: 0.025225 Align patch 15 10 left Iteration 1 Error: 1.209232 Iteration 2 Error: 0.137745 Iteration 3 Error: 0.022974 Align patch 16 9 left Iteration 1 Error: 2.751763 Iteration 2 Error: 0.185973 Iteration 3 Error: 0.033560 Align patch 17 8 left Iteration 1 Error: 1.448101 Iteration 2 Error: 0.107551 Iteration 3 Error: 0.022344 Align patch 18 7 left Iteration 1 Error: 0.733525 Iteration 2 Error: 0.100724 Iteration 3 Error: 0.016110 Align patch 19 6 left Iteration 1 Error: 0.656886 Iteration 2 Error: 0.147013 Iteration 3 Error: 0.039393 Align patch 20 5 left Iteration 1 Error: 0.629227 Iteration 2 Error: 0.113411 Iteration 3 Error: 0.023902 Align patch 21 4 left Iteration 1 Error: 2.785251 Iteration 2 Error: 0.249647 Iteration 3 Error: 0.058434 Iteration 4 Error: 0.011576 Align patch 22 3 left Iteration 1 Error: 1.927284 Iteration 2 Error: 0.127668 Iteration 3 Error: 0.048397 Align patch 23 2 left Iteration 1 Error: 0.711273 Iteration 2 Error: 0.109134 Iteration 3 Error: 0.032399 Align patch 24 1 left Iteration 1 Error: 0.752297 Iteration 2 Error: 0.105270 Iteration 3 Error: 0.014322 Align patch 25 0 left Iteration 1 Error: 0.685611 Iteration 2 Error: 0.075093 Iteration 3 Error: 0.015519 3D Fitting completed. Patch alignment time: 15.84(sec) Local motion has been corrected. Process thread exits. Computational time: 24.532055 sec Total time: 31.463654 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00013hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00013hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.562542s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00013hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.314996s ........................................ >>>>>>TIME<<<<<< FFT: 1.025959s Defocus_U Defocus_V Angle CCC 12591.80 12177.74 87.23 0.032368 Final Values Defocus_U Defocus_V Angle CCC 12832.42 12224.87 89.99 0.046167 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00013hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00013hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.350e-01 1.004e-01 CC threshold: 0.737 Mean Std: 44.80 7.54 Num Hot pixels: 217 Hot pixel threshold: 90.07 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.875161 Iteration 2 Error: 0.076680 Iteration 3 Error: 0.011541 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.20 0.04 ...... Frame ( 3) shift: -0.40 0.09 ...... Frame ( 4) shift: -0.60 0.13 ...... Frame ( 5) shift: -0.81 0.18 ...... Frame ( 6) shift: -0.84 0.27 ...... Frame ( 7) shift: -0.70 0.42 ...... Frame ( 8) shift: -0.56 0.56 ...... Frame ( 9) shift: -0.52 0.64 ...... Frame ( 10) shift: -0.59 0.63 ...... Frame ( 11) shift: -0.65 0.63 ...... Frame ( 12) shift: -0.70 0.65 ...... Frame ( 13) shift: -0.73 0.70 ...... Frame ( 14) shift: -0.76 0.75 ...... Frame ( 15) shift: -0.81 0.76 ...... Frame ( 16) shift: -0.86 0.74 ...... Frame ( 17) shift: -0.92 0.72 ...... Frame ( 18) shift: -0.94 0.73 ...... Frame ( 19) shift: -0.93 0.78 ...... Frame ( 20) shift: -0.93 0.82 ...... Frame ( 21) shift: -0.90 0.84 ...... Frame ( 22) shift: -0.87 0.83 ...... Frame ( 23) shift: -0.83 0.83 ...... Frame ( 24) shift: -0.82 0.83 ...... Frame ( 25) shift: -0.85 0.85 ...... Frame ( 26) shift: -0.88 0.86 ...... Frame ( 27) shift: -0.93 0.88 ...... Frame ( 28) shift: -0.99 0.90 ...... Frame ( 29) shift: -1.05 0.92 ...... Frame ( 30) shift: -1.09 0.94 ...... Frame ( 31) shift: -1.13 0.96 ...... Frame ( 32) shift: -1.16 0.98 ...... Frame ( 33) shift: -1.23 1.00 ...... Frame ( 34) shift: -1.32 1.01 ...... Frame ( 35) shift: -1.41 1.03 ...... Frame ( 36) shift: -1.45 1.05 ...... Frame ( 37) shift: -1.42 1.07 ...... Frame ( 38) shift: -1.40 1.08 ...... Frame ( 39) shift: -1.37 1.10 ...... Frame ( 40) shift: -1.35 1.12 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.656195 Iteration 2 Error: 0.390415 Iteration 3 Error: 0.105123 Iteration 4 Error: 0.024849 Align patch 2 23 left Iteration 1 Error: 1.690648 Iteration 2 Error: 0.172809 Iteration 3 Error: 0.035468 Align patch 3 22 left Iteration 1 Error: 1.206482 Iteration 2 Error: 0.212977 Iteration 3 Error: 0.042992 Align patch 4 21 left Iteration 1 Error: 0.857998 Iteration 2 Error: 0.074243 Iteration 3 Error: 0.008610 Align patch 5 20 left Iteration 1 Error: 0.828782 Iteration 2 Error: 0.082351 Iteration 3 Error: 0.017483 Align patch 6 19 left Iteration 1 Error: 1.250807 Iteration 2 Error: 0.145214 Iteration 3 Error: 0.047339 Align patch 7 18 left Iteration 1 Error: 0.892430 Iteration 2 Error: 0.149664 Iteration 3 Error: 0.038029 Align patch 8 17 left Iteration 1 Error: 1.019409 Iteration 2 Error: 0.112800 Iteration 3 Error: 0.035283 Align patch 9 16 left Iteration 1 Error: 0.487113 Iteration 2 Error: 0.054659 Iteration 3 Error: 0.013018 Align patch 10 15 left Iteration 1 Error: 0.696213 Iteration 2 Error: 0.082060 Iteration 3 Error: 0.009638 Align patch 11 14 left Iteration 1 Error: 0.762538 Iteration 2 Error: 0.144015 Iteration 3 Error: 0.034716 Align patch 12 13 left Iteration 1 Error: 0.796721 Iteration 2 Error: 0.116292 Iteration 3 Error: 0.023443 Align patch 13 12 left Iteration 1 Error: 0.457450 Iteration 2 Error: 0.044659 Align patch 14 11 left Iteration 1 Error: 0.539834 Iteration 2 Error: 0.070613 Iteration 3 Error: 0.016163 Align patch 15 10 left Iteration 1 Error: 0.565580 Iteration 2 Error: 0.043669 Align patch 16 9 left Iteration 1 Error: 1.102198 Iteration 2 Error: 0.188001 Iteration 3 Error: 0.039669 Align patch 17 8 left Iteration 1 Error: 0.571274 Iteration 2 Error: 0.090366 Iteration 3 Error: 0.012252 Align patch 18 7 left Iteration 1 Error: 0.832759 Iteration 2 Error: 0.112921 Iteration 3 Error: 0.024926 Align patch 19 6 left Iteration 1 Error: 0.515296 Iteration 2 Error: 0.073322 Iteration 3 Error: 0.018019 Align patch 20 5 left Iteration 1 Error: 0.667014 Iteration 2 Error: 0.051782 Iteration 3 Error: 0.010666 Align patch 21 4 left Iteration 1 Error: 1.448107 Iteration 2 Error: 0.106332 Iteration 3 Error: 0.015875 Align patch 22 3 left Iteration 1 Error: 1.312140 Iteration 2 Error: 0.155487 Iteration 3 Error: 0.023693 Align patch 23 2 left Iteration 1 Error: 1.049149 Iteration 2 Error: 0.119904 Iteration 3 Error: 0.016517 Align patch 24 1 left Iteration 1 Error: 0.991790 Iteration 2 Error: 0.080249 Iteration 3 Error: 0.014780 Align patch 25 0 left Iteration 1 Error: 0.465282 Iteration 2 Error: 0.039835 3D Fitting completed. Patch alignment time: 14.18(sec) Local motion has been corrected. Process thread exits. Computational time: 23.373543 sec Total time: 29.064861 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00013hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00013hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.803117s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00013hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.365761s ........................................ >>>>>>TIME<<<<<< FFT: 0.933153s Defocus_U Defocus_V Angle CCC 10855.51 11675.82 8.64 0.063291 Final Values Defocus_U Defocus_V Angle CCC 10868.01 11691.45 8.33 0.112077 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00013hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00013hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 45.75 7.55 Num Hot pixels: 209 Hot pixel threshold: 91.03 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.282658 Iteration 2 Error: 0.086465 Iteration 3 Error: 0.021509 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.28 0.04 ...... Frame ( 3) shift: -0.57 0.09 ...... Frame ( 4) shift: -0.85 0.13 ...... Frame ( 5) shift: -1.13 0.17 ...... Frame ( 6) shift: -1.29 0.23 ...... Frame ( 7) shift: -1.30 0.29 ...... Frame ( 8) shift: -1.32 0.35 ...... Frame ( 9) shift: -1.34 0.40 ...... Frame ( 10) shift: -1.37 0.44 ...... Frame ( 11) shift: -1.39 0.49 ...... Frame ( 12) shift: -1.43 0.51 ...... Frame ( 13) shift: -1.49 0.50 ...... Frame ( 14) shift: -1.55 0.50 ...... Frame ( 15) shift: -1.56 0.51 ...... Frame ( 16) shift: -1.52 0.53 ...... Frame ( 17) shift: -1.48 0.55 ...... Frame ( 18) shift: -1.49 0.58 ...... Frame ( 19) shift: -1.53 0.62 ...... Frame ( 20) shift: -1.57 0.65 ...... Frame ( 21) shift: -1.61 0.71 ...... Frame ( 22) shift: -1.65 0.80 ...... Frame ( 23) shift: -1.69 0.89 ...... Frame ( 24) shift: -1.70 0.94 ...... Frame ( 25) shift: -1.67 0.97 ...... Frame ( 26) shift: -1.65 1.00 ...... Frame ( 27) shift: -1.65 1.01 ...... Frame ( 28) shift: -1.69 1.00 ...... Frame ( 29) shift: -1.73 1.00 ...... Frame ( 30) shift: -1.77 1.00 ...... Frame ( 31) shift: -1.83 1.01 ...... Frame ( 32) shift: -1.89 1.02 ...... Frame ( 33) shift: -1.93 0.99 ...... Frame ( 34) shift: -1.95 0.94 ...... Frame ( 35) shift: -1.98 0.88 ...... Frame ( 36) shift: -2.01 0.87 ...... Frame ( 37) shift: -2.04 0.90 ...... Frame ( 38) shift: -2.08 0.93 ...... Frame ( 39) shift: -2.12 0.96 ...... Frame ( 40) shift: -2.15 0.99 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.498107 Iteration 2 Error: 0.248453 Iteration 3 Error: 0.190438 Iteration 4 Error: 0.052142 Iteration 5 Error: 0.052191 Align patch 1 24 left Iteration 1 Error: 2.465989 Iteration 2 Error: 0.213750 Iteration 3 Error: 0.056942 Iteration 4 Error: 0.017785 Align patch 2 23 left Iteration 1 Error: 1.852515 Iteration 2 Error: 0.224863 Iteration 3 Error: 0.053509 Iteration 4 Error: 0.030927 Align patch 3 22 left Iteration 1 Error: 1.344209 Iteration 2 Error: 0.225967 Iteration 3 Error: 0.043232 Align patch 4 21 left Iteration 1 Error: 0.691970 Iteration 2 Error: 0.094247 Iteration 3 Error: 0.019313 Align patch 5 20 left Iteration 1 Error: 0.734868 Iteration 2 Error: 0.084031 Iteration 3 Error: 0.018652 Align patch 6 19 left Iteration 1 Error: 1.946804 Iteration 2 Error: 0.304057 Iteration 3 Error: 0.116555 Iteration 4 Error: 0.024951 Align patch 7 18 left Iteration 1 Error: 1.104171 Iteration 2 Error: 0.229669 Iteration 3 Error: 0.096473 Iteration 4 Error: 0.043393 Align patch 8 17 left Iteration 1 Error: 0.822065 Iteration 2 Error: 0.122188 Iteration 3 Error: 0.035138 Align patch 9 16 left Iteration 1 Error: 0.459975 Iteration 2 Error: 0.038888 Align patch 10 15 left Iteration 1 Error: 0.621762 Iteration 2 Error: 0.049170 Align patch 11 14 left Iteration 1 Error: 0.581703 Iteration 2 Error: 0.102756 Iteration 3 Error: 0.026652 Align patch 12 13 left Iteration 1 Error: 0.795713 Iteration 2 Error: 0.091193 Iteration 3 Error: 0.020133 Align patch 13 12 left Iteration 1 Error: 0.723188 Iteration 2 Error: 0.113511 Iteration 3 Error: 0.021643 Align patch 14 11 left Iteration 1 Error: 0.409780 Iteration 2 Error: 0.055558 Iteration 3 Error: 0.015129 Align patch 15 10 left Iteration 1 Error: 0.398386 Iteration 2 Error: 0.037844 Align patch 16 9 left Iteration 1 Error: 0.745981 Iteration 2 Error: 0.115364 Iteration 3 Error: 0.022390 Align patch 17 8 left Iteration 1 Error: 0.771671 Iteration 2 Error: 0.106965 Iteration 3 Error: 0.020183 Align patch 18 7 left Iteration 1 Error: 1.074929 Iteration 2 Error: 0.116094 Iteration 3 Error: 0.018599 Align patch 19 6 left Iteration 1 Error: 0.748873 Iteration 2 Error: 0.102722 Iteration 3 Error: 0.018067 Align patch 20 5 left Iteration 1 Error: 0.529667 Iteration 2 Error: 0.049774 Align patch 21 4 left Iteration 1 Error: 1.070501 Iteration 2 Error: 0.136090 Iteration 3 Error: 0.022628 Align patch 22 3 left Iteration 1 Error: 1.007721 Iteration 2 Error: 0.094956 Iteration 3 Error: 0.013375 Align patch 23 2 left Iteration 1 Error: 1.761835 Iteration 2 Error: 0.144398 Iteration 3 Error: 0.021695 Align patch 24 1 left Iteration 1 Error: 1.334734 Iteration 2 Error: 0.135476 Iteration 3 Error: 0.030511 Align patch 25 0 left Iteration 1 Error: 0.602148 Iteration 2 Error: 0.075760 Iteration 3 Error: 0.011867 3D Fitting completed. Patch alignment time: 15.38(sec) Local motion has been corrected. Process thread exits. Computational time: 23.869652 sec Total time: 30.844076 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00013hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00013hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.569548s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00013hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.317016s ........................................ >>>>>>TIME<<<<<< FFT: 0.997501s Defocus_U Defocus_V Angle CCC 13355.58 12730.35 82.63 0.067422 Final Values Defocus_U Defocus_V Angle CCC 13369.65 12735.04 82.32 0.115074 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00014hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00014hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 38.45 6.59 Num Hot pixels: 221 Hot pixel threshold: 78.01 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.801453 Iteration 2 Error: 0.296762 Iteration 3 Error: 0.081319 Iteration 4 Error: 0.021944 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.28 -0.02 ...... Frame ( 3) shift: 0.55 -0.03 ...... Frame ( 4) shift: 0.83 -0.05 ...... Frame ( 5) shift: 1.10 -0.06 ...... Frame ( 6) shift: 1.32 -0.04 ...... Frame ( 7) shift: 1.47 0.02 ...... Frame ( 8) shift: 1.62 0.08 ...... Frame ( 9) shift: 1.73 0.11 ...... Frame ( 10) shift: 1.80 0.13 ...... Frame ( 11) shift: 1.86 0.15 ...... Frame ( 12) shift: 1.91 0.14 ...... Frame ( 13) shift: 1.94 0.11 ...... Frame ( 14) shift: 1.97 0.08 ...... Frame ( 15) shift: 2.04 0.10 ...... Frame ( 16) shift: 2.15 0.19 ...... Frame ( 17) shift: 2.27 0.28 ...... Frame ( 18) shift: 2.35 0.36 ...... Frame ( 19) shift: 2.38 0.43 ...... Frame ( 20) shift: 2.42 0.49 ...... Frame ( 21) shift: 2.45 0.56 ...... Frame ( 22) shift: 2.49 0.61 ...... Frame ( 23) shift: 2.53 0.67 ...... Frame ( 24) shift: 2.61 0.71 ...... Frame ( 25) shift: 2.73 0.73 ...... Frame ( 26) shift: 2.84 0.75 ...... Frame ( 27) shift: 2.90 0.82 ...... Frame ( 28) shift: 2.90 0.94 ...... Frame ( 29) shift: 2.90 1.06 ...... Frame ( 30) shift: 2.96 1.15 ...... Frame ( 31) shift: 3.07 1.21 ...... Frame ( 32) shift: 3.18 1.27 ...... Frame ( 33) shift: 3.28 1.29 ...... Frame ( 34) shift: 3.36 1.26 ...... Frame ( 35) shift: 3.45 1.24 ...... Frame ( 36) shift: 3.51 1.25 ...... Frame ( 37) shift: 3.54 1.32 ...... Frame ( 38) shift: 3.58 1.38 ...... Frame ( 39) shift: 3.61 1.45 ...... Frame ( 40) shift: 3.65 1.51 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.903312 Iteration 2 Error: 0.153342 Iteration 3 Error: 0.054798 Iteration 4 Error: 0.023110 Align patch 2 23 left Iteration 1 Error: 0.696934 Iteration 2 Error: 0.122706 Iteration 3 Error: 0.024521 Align patch 3 22 left Iteration 1 Error: 0.602740 Iteration 2 Error: 0.071321 Iteration 3 Error: 0.021227 Align patch 4 21 left Iteration 1 Error: 0.667870 Iteration 2 Error: 0.121636 Iteration 3 Error: 0.031921 Align patch 5 20 left Iteration 1 Error: 0.696485 Iteration 2 Error: 0.100273 Iteration 3 Error: 0.039320 Align patch 6 19 left Iteration 1 Error: 1.012859 Iteration 2 Error: 0.161701 Iteration 3 Error: 0.037752 Align patch 7 18 left Iteration 1 Error: 0.633061 Iteration 2 Error: 0.215718 Iteration 3 Error: 0.065180 Iteration 4 Error: 0.032642 Align patch 8 17 left Iteration 1 Error: 0.662131 Iteration 2 Error: 0.135019 Iteration 3 Error: 0.048346 Align patch 9 16 left Iteration 1 Error: 0.977535 Iteration 2 Error: 0.119456 Iteration 3 Error: 0.030022 Align patch 10 15 left Iteration 1 Error: 0.602828 Iteration 2 Error: 0.118031 Iteration 3 Error: 0.035306 Align patch 11 14 left Iteration 1 Error: 0.722615 Iteration 2 Error: 0.110868 Iteration 3 Error: 0.031443 Align patch 12 13 left Iteration 1 Error: 0.703497 Iteration 2 Error: 0.090383 Iteration 3 Error: 0.033301 Align patch 13 12 left Iteration 1 Error: 0.525159 Iteration 2 Error: 0.120342 Iteration 3 Error: 0.049636 Align patch 14 11 left Iteration 1 Error: 1.141724 Iteration 2 Error: 0.221750 Iteration 3 Error: 0.053697 Iteration 4 Error: 0.019767 Align patch 15 10 left Iteration 1 Error: 0.882997 Iteration 2 Error: 0.197788 Iteration 3 Error: 0.039234 Align patch 16 9 left Iteration 1 Error: 0.708312 Iteration 2 Error: 0.174276 Iteration 3 Error: 0.047288 Align patch 17 8 left Iteration 1 Error: 0.879917 Iteration 2 Error: 0.213287 Iteration 3 Error: 0.047792 Align patch 18 7 left Iteration 1 Error: 0.684033 Iteration 2 Error: 0.177485 Iteration 3 Error: 0.043246 Align patch 19 6 left Iteration 1 Error: 0.758968 Iteration 2 Error: 0.078882 Iteration 3 Error: 0.021609 Align patch 20 5 left Iteration 1 Error: 0.819794 Iteration 2 Error: 0.153519 Iteration 3 Error: 0.038452 Align patch 21 4 left Iteration 1 Error: 0.715125 Iteration 2 Error: 0.112844 Iteration 3 Error: 0.041509 Align patch 22 3 left Iteration 1 Error: 0.653127 Iteration 2 Error: 0.106684 Iteration 3 Error: 0.037113 Align patch 23 2 left Iteration 1 Error: 0.754081 Iteration 2 Error: 0.146186 Iteration 3 Error: 0.024044 Align patch 24 1 left Iteration 1 Error: 1.202630 Iteration 2 Error: 0.279244 Iteration 3 Error: 0.081601 Iteration 4 Error: 0.032079 Align patch 25 0 left Iteration 1 Error: 0.819605 Iteration 2 Error: 0.157264 Iteration 3 Error: 0.046328 3D Fitting completed. Patch alignment time: 14.88(sec) Local motion has been corrected. Process thread exits. Computational time: 24.042315 sec Total time: 29.968063 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00014hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00014hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.577929s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00014hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.669430s ........................................ >>>>>>TIME<<<<<< FFT: 0.942737s Defocus_U Defocus_V Angle CCC 9060.55 9814.45 15.42 0.030499 Final Values Defocus_U Defocus_V Angle CCC 9063.68 9839.47 15.11 0.053586 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00014hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00014hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.003e-01 CC threshold: 0.736 Mean Std: 42.01 7.10 Num Hot pixels: 224 Hot pixel threshold: 84.61 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.957611 Iteration 2 Error: 0.211014 Iteration 3 Error: 0.046753 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.19 -0.00 ...... Frame ( 3) shift: -0.38 -0.00 ...... Frame ( 4) shift: -0.57 -0.00 ...... Frame ( 5) shift: -0.76 -0.00 ...... Frame ( 6) shift: -0.83 0.01 ...... Frame ( 7) shift: -0.76 0.04 ...... Frame ( 8) shift: -0.70 0.07 ...... Frame ( 9) shift: -0.65 0.12 ...... Frame ( 10) shift: -0.63 0.20 ...... Frame ( 11) shift: -0.60 0.29 ...... Frame ( 12) shift: -0.55 0.39 ...... Frame ( 13) shift: -0.45 0.52 ...... Frame ( 14) shift: -0.36 0.65 ...... Frame ( 15) shift: -0.27 0.71 ...... Frame ( 16) shift: -0.21 0.71 ...... Frame ( 17) shift: -0.14 0.71 ...... Frame ( 18) shift: -0.09 0.73 ...... Frame ( 19) shift: -0.06 0.78 ...... Frame ( 20) shift: -0.03 0.84 ...... Frame ( 21) shift: -0.04 0.88 ...... Frame ( 22) shift: -0.08 0.92 ...... Frame ( 23) shift: -0.11 0.96 ...... Frame ( 24) shift: -0.12 1.00 ...... Frame ( 25) shift: -0.11 1.04 ...... Frame ( 26) shift: -0.09 1.09 ...... Frame ( 27) shift: -0.04 1.18 ...... Frame ( 28) shift: 0.03 1.34 ...... Frame ( 29) shift: 0.11 1.49 ...... Frame ( 30) shift: 0.21 1.61 ...... Frame ( 31) shift: 0.32 1.69 ...... Frame ( 32) shift: 0.44 1.77 ...... Frame ( 33) shift: 0.49 1.81 ...... Frame ( 34) shift: 0.48 1.81 ...... Frame ( 35) shift: 0.47 1.81 ...... Frame ( 36) shift: 0.44 1.81 ...... Frame ( 37) shift: 0.39 1.82 ...... Frame ( 38) shift: 0.35 1.82 ...... Frame ( 39) shift: 0.30 1.82 ...... Frame ( 40) shift: 0.25 1.83 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.342559 Iteration 2 Error: 0.274913 Iteration 3 Error: 0.082891 Iteration 4 Error: 0.045847 Align patch 2 23 left Iteration 1 Error: 1.105212 Iteration 2 Error: 0.252475 Iteration 3 Error: 0.088571 Iteration 4 Error: 0.042419 Align patch 3 22 left Iteration 1 Error: 0.754372 Iteration 2 Error: 0.125416 Iteration 3 Error: 0.040765 Align patch 4 21 left Iteration 1 Error: 0.521566 Iteration 2 Error: 0.075797 Iteration 3 Error: 0.015525 Align patch 5 20 left Iteration 1 Error: 0.572697 Iteration 2 Error: 0.057214 Iteration 3 Error: 0.012102 Align patch 6 19 left Iteration 1 Error: 0.876477 Iteration 2 Error: 0.212169 Iteration 3 Error: 0.068774 Iteration 4 Error: 0.025504 Align patch 7 18 left Iteration 1 Error: 0.916512 Iteration 2 Error: 0.151066 Iteration 3 Error: 0.048827 Align patch 8 17 left Iteration 1 Error: 1.012085 Iteration 2 Error: 0.102921 Iteration 3 Error: 0.031494 Align patch 9 16 left Iteration 1 Error: 0.849920 Iteration 2 Error: 0.099043 Iteration 3 Error: 0.025857 Align patch 10 15 left Iteration 1 Error: 0.408857 Iteration 2 Error: 0.033456 Align patch 11 14 left Iteration 1 Error: 0.672410 Iteration 2 Error: 0.108168 Iteration 3 Error: 0.027052 Align patch 12 13 left Iteration 1 Error: 0.523665 Iteration 2 Error: 0.098231 Iteration 3 Error: 0.020609 Align patch 13 12 left Iteration 1 Error: 0.923729 Iteration 2 Error: 0.153470 Iteration 3 Error: 0.025470 Align patch 14 11 left Iteration 1 Error: 0.695096 Iteration 2 Error: 0.058832 Iteration 3 Error: 0.014229 Align patch 15 10 left Iteration 1 Error: 0.589462 Iteration 2 Error: 0.084827 Iteration 3 Error: 0.017268 Align patch 16 9 left Iteration 1 Error: 0.593484 Iteration 2 Error: 0.087842 Iteration 3 Error: 0.030818 Align patch 17 8 left Iteration 1 Error: 0.501755 Iteration 2 Error: 0.045979 Align patch 18 7 left Iteration 1 Error: 0.514738 Iteration 2 Error: 0.080039 Iteration 3 Error: 0.023232 Align patch 19 6 left Iteration 1 Error: 0.675158 Iteration 2 Error: 0.155626 Iteration 3 Error: 0.054106 Iteration 4 Error: 0.015284 Align patch 20 5 left Iteration 1 Error: 0.820623 Iteration 2 Error: 0.140803 Iteration 3 Error: 0.032839 Align patch 21 4 left Iteration 1 Error: 0.665393 Iteration 2 Error: 0.128369 Iteration 3 Error: 0.021384 Align patch 22 3 left Iteration 1 Error: 0.714150 Iteration 2 Error: 0.103516 Iteration 3 Error: 0.028637 Align patch 23 2 left Iteration 1 Error: 1.149179 Iteration 2 Error: 0.174411 Iteration 3 Error: 0.031023 Align patch 24 1 left Iteration 1 Error: 0.838792 Iteration 2 Error: 0.174263 Iteration 3 Error: 0.058628 Iteration 4 Error: 0.016054 Align patch 25 0 left Iteration 1 Error: 0.688587 Iteration 2 Error: 0.094441 Iteration 3 Error: 0.024251 3D Fitting completed. Patch alignment time: 15.41(sec) Local motion has been corrected. Process thread exits. Computational time: 24.529119 sec Total time: 31.728987 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00014hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00014hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.781477s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00014hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.751570s ........................................ >>>>>>TIME<<<<<< FFT: 0.948638s Defocus_U Defocus_V Angle CCC 13773.46 13281.23 88.52 0.064602 Final Values Defocus_U Defocus_V Angle CCC 13782.84 13278.11 89.15 0.104738 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00014hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00014hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.001e-01 CC threshold: 0.736 Mean Std: 38.68 6.65 Num Hot pixels: 203 Hot pixel threshold: 78.61 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.891760 Iteration 2 Error: 0.205955 Iteration 3 Error: 0.043622 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.02 0.06 ...... Frame ( 3) shift: 0.05 0.12 ...... Frame ( 4) shift: 0.07 0.18 ...... Frame ( 5) shift: 0.09 0.24 ...... Frame ( 6) shift: 0.09 0.28 ...... Frame ( 7) shift: 0.08 0.30 ...... Frame ( 8) shift: 0.06 0.32 ...... Frame ( 9) shift: 0.06 0.37 ...... Frame ( 10) shift: 0.09 0.46 ...... Frame ( 11) shift: 0.13 0.55 ...... Frame ( 12) shift: 0.16 0.63 ...... Frame ( 13) shift: 0.21 0.71 ...... Frame ( 14) shift: 0.25 0.78 ...... Frame ( 15) shift: 0.28 0.85 ...... Frame ( 16) shift: 0.29 0.91 ...... Frame ( 17) shift: 0.30 0.98 ...... Frame ( 18) shift: 0.35 1.04 ...... Frame ( 19) shift: 0.45 1.09 ...... Frame ( 20) shift: 0.54 1.15 ...... Frame ( 21) shift: 0.58 1.17 ...... Frame ( 22) shift: 0.56 1.15 ...... Frame ( 23) shift: 0.55 1.14 ...... Frame ( 24) shift: 0.55 1.19 ...... Frame ( 25) shift: 0.59 1.31 ...... Frame ( 26) shift: 0.62 1.43 ...... Frame ( 27) shift: 0.64 1.50 ...... Frame ( 28) shift: 0.66 1.50 ...... Frame ( 29) shift: 0.68 1.51 ...... Frame ( 30) shift: 0.73 1.55 ...... Frame ( 31) shift: 0.81 1.62 ...... Frame ( 32) shift: 0.89 1.70 ...... Frame ( 33) shift: 0.97 1.73 ...... Frame ( 34) shift: 1.04 1.73 ...... Frame ( 35) shift: 1.11 1.73 ...... Frame ( 36) shift: 1.15 1.72 ...... Frame ( 37) shift: 1.17 1.70 ...... Frame ( 38) shift: 1.19 1.68 ...... Frame ( 39) shift: 1.20 1.65 ...... Frame ( 40) shift: 1.22 1.63 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.689722 Iteration 2 Error: 0.260110 Iteration 3 Error: 0.070225 Iteration 4 Error: 0.030127 Align patch 2 23 left Iteration 1 Error: 0.673317 Iteration 2 Error: 0.092070 Iteration 3 Error: 0.033418 Align patch 3 22 left Iteration 1 Error: 0.871154 Iteration 2 Error: 0.096027 Iteration 3 Error: 0.021289 Align patch 4 21 left Iteration 1 Error: 0.787257 Iteration 2 Error: 0.168294 Iteration 3 Error: 0.041788 Align patch 5 20 left Iteration 1 Error: 1.261701 Iteration 2 Error: 0.133292 Iteration 3 Error: 0.035167 Align patch 6 19 left Iteration 1 Error: 0.741601 Iteration 2 Error: 0.096536 Iteration 3 Error: 0.029228 Align patch 7 18 left Iteration 1 Error: 0.673986 Iteration 2 Error: 0.092039 Iteration 3 Error: 0.021870 Align patch 8 17 left Iteration 1 Error: 0.895436 Iteration 2 Error: 0.244677 Iteration 3 Error: 0.038157 Align patch 9 16 left Iteration 1 Error: 0.651637 Iteration 2 Error: 0.115886 Iteration 3 Error: 0.020686 Align patch 10 15 left Iteration 1 Error: 0.893034 Iteration 2 Error: 0.205075 Iteration 3 Error: 0.041511 Align patch 11 14 left Iteration 1 Error: 0.665982 Iteration 2 Error: 0.092023 Iteration 3 Error: 0.015191 Align patch 12 13 left Iteration 1 Error: 0.719693 Iteration 2 Error: 0.100416 Iteration 3 Error: 0.023452 Align patch 13 12 left Iteration 1 Error: 0.560358 Iteration 2 Error: 0.124221 Iteration 3 Error: 0.016777 Align patch 14 11 left Iteration 1 Error: 0.676737 Iteration 2 Error: 0.148002 Iteration 3 Error: 0.026179 Align patch 15 10 left Iteration 1 Error: 0.590121 Iteration 2 Error: 0.070670 Iteration 3 Error: 0.020604 Align patch 16 9 left Iteration 1 Error: 0.695651 Iteration 2 Error: 0.160043 Iteration 3 Error: 0.043859 Align patch 17 8 left Iteration 1 Error: 0.522310 Iteration 2 Error: 0.047549 Align patch 18 7 left Iteration 1 Error: 0.682486 Iteration 2 Error: 0.135007 Iteration 3 Error: 0.026865 Align patch 19 6 left Iteration 1 Error: 0.571441 Iteration 2 Error: 0.109230 Iteration 3 Error: 0.028698 Align patch 20 5 left Iteration 1 Error: 0.547303 Iteration 2 Error: 0.140087 Iteration 3 Error: 0.034426 Align patch 21 4 left Iteration 1 Error: 0.906584 Iteration 2 Error: 0.172439 Iteration 3 Error: 0.027358 Align patch 22 3 left Iteration 1 Error: 0.992612 Iteration 2 Error: 0.128457 Iteration 3 Error: 0.030884 Align patch 23 2 left Iteration 1 Error: 0.744230 Iteration 2 Error: 0.107385 Iteration 3 Error: 0.033132 Align patch 24 1 left Iteration 1 Error: 1.394631 Iteration 2 Error: 0.162232 Iteration 3 Error: 0.040062 Align patch 25 0 left Iteration 1 Error: 0.529474 Iteration 2 Error: 0.085903 Iteration 3 Error: 0.024543 3D Fitting completed. Patch alignment time: 15.62(sec) Local motion has been corrected. Process thread exits. Computational time: 24.542917 sec Total time: 30.729595 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00014hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00014hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.770239s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00014hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.427480s ........................................ >>>>>>TIME<<<<<< FFT: 1.156642s Defocus_U Defocus_V Angle CCC 11498.05 12427.73 5.68 0.040376 Final Values Defocus_U Defocus_V Angle CCC 11490.24 12457.44 5.06 0.062326 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00014hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00014hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.002e-01 CC threshold: 0.736 Mean Std: 40.82 6.95 Num Hot pixels: 234 Hot pixel threshold: 82.54 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.661841 Iteration 2 Error: 0.082831 Iteration 3 Error: 0.017865 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.22 -0.22 ...... Frame ( 3) shift: -0.45 -0.43 ...... Frame ( 4) shift: -0.67 -0.65 ...... Frame ( 5) shift: -0.89 -0.87 ...... Frame ( 6) shift: -0.99 -0.96 ...... Frame ( 7) shift: -0.97 -0.93 ...... Frame ( 8) shift: -0.95 -0.90 ...... Frame ( 9) shift: -0.92 -0.86 ...... Frame ( 10) shift: -0.86 -0.80 ...... Frame ( 11) shift: -0.81 -0.74 ...... Frame ( 12) shift: -0.75 -0.67 ...... Frame ( 13) shift: -0.69 -0.59 ...... Frame ( 14) shift: -0.64 -0.52 ...... Frame ( 15) shift: -0.59 -0.47 ...... Frame ( 16) shift: -0.54 -0.45 ...... Frame ( 17) shift: -0.49 -0.43 ...... Frame ( 18) shift: -0.45 -0.42 ...... Frame ( 19) shift: -0.42 -0.42 ...... Frame ( 20) shift: -0.39 -0.42 ...... Frame ( 21) shift: -0.36 -0.46 ...... Frame ( 22) shift: -0.33 -0.52 ...... Frame ( 23) shift: -0.31 -0.59 ...... Frame ( 24) shift: -0.28 -0.62 ...... Frame ( 25) shift: -0.23 -0.60 ...... Frame ( 26) shift: -0.19 -0.58 ...... Frame ( 27) shift: -0.15 -0.60 ...... Frame ( 28) shift: -0.11 -0.65 ...... Frame ( 29) shift: -0.08 -0.71 ...... Frame ( 30) shift: -0.06 -0.70 ...... Frame ( 31) shift: -0.04 -0.63 ...... Frame ( 32) shift: -0.03 -0.57 ...... Frame ( 33) shift: -0.04 -0.54 ...... Frame ( 34) shift: -0.08 -0.54 ...... Frame ( 35) shift: -0.12 -0.54 ...... Frame ( 36) shift: -0.10 -0.54 ...... Frame ( 37) shift: -0.01 -0.53 ...... Frame ( 38) shift: 0.07 -0.52 ...... Frame ( 39) shift: 0.15 -0.51 ...... Frame ( 40) shift: 0.23 -0.49 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.688332 Iteration 2 Error: 0.204752 Iteration 3 Error: 0.056277 Iteration 4 Error: 0.016309 Align patch 2 23 left Iteration 1 Error: 1.219490 Iteration 2 Error: 0.155710 Iteration 3 Error: 0.036150 Align patch 3 22 left Iteration 1 Error: 0.601190 Iteration 2 Error: 0.104185 Iteration 3 Error: 0.036054 Align patch 4 21 left Iteration 1 Error: 0.704618 Iteration 2 Error: 0.087047 Iteration 3 Error: 0.016171 Align patch 5 20 left Iteration 1 Error: 0.455874 Iteration 2 Error: 0.064738 Iteration 3 Error: 0.010966 Align patch 6 19 left Iteration 1 Error: 0.762098 Iteration 2 Error: 0.138672 Iteration 3 Error: 0.038586 Align patch 7 18 left Iteration 1 Error: 0.649384 Iteration 2 Error: 0.103583 Iteration 3 Error: 0.022077 Align patch 8 17 left Iteration 1 Error: 0.611537 Iteration 2 Error: 0.091114 Iteration 3 Error: 0.018075 Align patch 9 16 left Iteration 1 Error: 0.511210 Iteration 2 Error: 0.055302 Iteration 3 Error: 0.011863 Align patch 10 15 left Iteration 1 Error: 0.854404 Iteration 2 Error: 0.085922 Iteration 3 Error: 0.014953 Align patch 11 14 left Iteration 1 Error: 0.948381 Iteration 2 Error: 0.253075 Iteration 3 Error: 0.056778 Iteration 4 Error: 0.024114 Align patch 12 13 left Iteration 1 Error: 0.663441 Iteration 2 Error: 0.158095 Iteration 3 Error: 0.045969 Align patch 13 12 left Iteration 1 Error: 0.422192 Iteration 2 Error: 0.066005 Iteration 3 Error: 0.014158 Align patch 14 11 left Iteration 1 Error: 0.624719 Iteration 2 Error: 0.087363 Iteration 3 Error: 0.017086 Align patch 15 10 left Iteration 1 Error: 0.730315 Iteration 2 Error: 0.141894 Iteration 3 Error: 0.033547 Align patch 16 9 left Iteration 1 Error: 0.752721 Iteration 2 Error: 0.104217 Iteration 3 Error: 0.022439 Align patch 17 8 left Iteration 1 Error: 0.702367 Iteration 2 Error: 0.114769 Iteration 3 Error: 0.022899 Align patch 18 7 left Iteration 1 Error: 0.680080 Iteration 2 Error: 0.145508 Iteration 3 Error: 0.027994 Align patch 19 6 left Iteration 1 Error: 1.127392 Iteration 2 Error: 0.217161 Iteration 3 Error: 0.046281 Align patch 20 5 left Iteration 1 Error: 0.880186 Iteration 2 Error: 0.147567 Iteration 3 Error: 0.039643 Align patch 21 4 left Iteration 1 Error: 0.960924 Iteration 2 Error: 0.115389 Iteration 3 Error: 0.028038 Align patch 22 3 left Iteration 1 Error: 0.452204 Iteration 2 Error: 0.087259 Iteration 3 Error: 0.015716 Align patch 23 2 left Iteration 1 Error: 0.731838 Iteration 2 Error: 0.118349 Iteration 3 Error: 0.029484 Align patch 24 1 left Iteration 1 Error: 1.318447 Iteration 2 Error: 0.226949 Iteration 3 Error: 0.058424 Iteration 4 Error: 0.018300 Align patch 25 0 left Iteration 1 Error: 1.086298 Iteration 2 Error: 0.203635 Iteration 3 Error: 0.041162 3D Fitting completed. Patch alignment time: 15.59(sec) Local motion has been corrected. Process thread exits. Computational time: 24.122311 sec Total time: 29.742838 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00014hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00014hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.546922s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00014hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.766710s ........................................ >>>>>>TIME<<<<<< FFT: 0.927097s Defocus_U Defocus_V Angle CCC 15626.95 14974.61 85.12 0.058230 Final Values Defocus_U Defocus_V Angle CCC 15620.70 14993.36 85.12 0.092157 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00015hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00015hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 43.76 7.57 Num Hot pixels: 187 Hot pixel threshold: 89.16 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.473159 Iteration 2 Error: 0.142896 Iteration 3 Error: 0.024208 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.35 0.03 ...... Frame ( 3) shift: -0.69 0.05 ...... Frame ( 4) shift: -1.04 0.08 ...... Frame ( 5) shift: -1.38 0.10 ...... Frame ( 6) shift: -1.54 0.14 ...... Frame ( 7) shift: -1.53 0.19 ...... Frame ( 8) shift: -1.51 0.23 ...... Frame ( 9) shift: -1.50 0.32 ...... Frame ( 10) shift: -1.49 0.43 ...... Frame ( 11) shift: -1.48 0.55 ...... Frame ( 12) shift: -1.50 0.65 ...... Frame ( 13) shift: -1.54 0.72 ...... Frame ( 14) shift: -1.58 0.80 ...... Frame ( 15) shift: -1.59 0.86 ...... Frame ( 16) shift: -1.58 0.91 ...... Frame ( 17) shift: -1.57 0.95 ...... Frame ( 18) shift: -1.53 1.01 ...... Frame ( 19) shift: -1.47 1.07 ...... Frame ( 20) shift: -1.40 1.13 ...... Frame ( 21) shift: -1.39 1.20 ...... Frame ( 22) shift: -1.43 1.28 ...... Frame ( 23) shift: -1.47 1.36 ...... Frame ( 24) shift: -1.51 1.43 ...... Frame ( 25) shift: -1.54 1.49 ...... Frame ( 26) shift: -1.56 1.55 ...... Frame ( 27) shift: -1.60 1.60 ...... Frame ( 28) shift: -1.65 1.63 ...... Frame ( 29) shift: -1.70 1.67 ...... Frame ( 30) shift: -1.73 1.68 ...... Frame ( 31) shift: -1.74 1.68 ...... Frame ( 32) shift: -1.75 1.68 ...... Frame ( 33) shift: -1.77 1.70 ...... Frame ( 34) shift: -1.79 1.75 ...... Frame ( 35) shift: -1.81 1.80 ...... Frame ( 36) shift: -1.83 1.86 ...... Frame ( 37) shift: -1.85 1.93 ...... Frame ( 38) shift: -1.88 2.00 ...... Frame ( 39) shift: -1.90 2.07 ...... Frame ( 40) shift: -1.93 2.14 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.876409 Iteration 2 Error: 0.402744 Iteration 3 Error: 0.174464 Iteration 4 Error: 0.120418 Iteration 5 Error: 0.063093 Align patch 1 24 left Iteration 1 Error: 2.372694 Iteration 2 Error: 0.267204 Iteration 3 Error: 0.047474 Align patch 2 23 left Iteration 1 Error: 1.866929 Iteration 2 Error: 0.340363 Iteration 3 Error: 0.098833 Iteration 4 Error: 0.039232 Align patch 3 22 left Iteration 1 Error: 0.515840 Iteration 2 Error: 0.064008 Iteration 3 Error: 0.017652 Align patch 4 21 left Iteration 1 Error: 0.888401 Iteration 2 Error: 0.130514 Iteration 3 Error: 0.017396 Align patch 5 20 left Iteration 1 Error: 0.761599 Iteration 2 Error: 0.100109 Iteration 3 Error: 0.020440 Align patch 6 19 left Iteration 1 Error: 1.706375 Iteration 2 Error: 0.313953 Iteration 3 Error: 0.075817 Iteration 4 Error: 0.021460 Align patch 7 18 left Iteration 1 Error: 1.546900 Iteration 2 Error: 0.309854 Iteration 3 Error: 0.094155 Iteration 4 Error: 0.049947 Align patch 8 17 left Iteration 1 Error: 0.726980 Iteration 2 Error: 0.091821 Iteration 3 Error: 0.030873 Align patch 9 16 left Iteration 1 Error: 0.424945 Iteration 2 Error: 0.053548 Iteration 3 Error: 0.009438 Align patch 10 15 left Iteration 1 Error: 0.703706 Iteration 2 Error: 0.080960 Iteration 3 Error: 0.021560 Align patch 11 14 left Iteration 1 Error: 0.910932 Iteration 2 Error: 0.122334 Iteration 3 Error: 0.025772 Align patch 12 13 left Iteration 1 Error: 0.576916 Iteration 2 Error: 0.184873 Iteration 3 Error: 0.049938 Align patch 13 12 left Iteration 1 Error: 0.694196 Iteration 2 Error: 0.080373 Iteration 3 Error: 0.012375 Align patch 14 11 left Iteration 1 Error: 0.587341 Iteration 2 Error: 0.048455 Align patch 15 10 left Iteration 1 Error: 0.416324 Iteration 2 Error: 0.063956 Iteration 3 Error: 0.013583 Align patch 16 9 left Iteration 1 Error: 1.269463 Iteration 2 Error: 0.175335 Iteration 3 Error: 0.032168 Align patch 17 8 left Iteration 1 Error: 0.655313 Iteration 2 Error: 0.156651 Iteration 3 Error: 0.036043 Align patch 18 7 left Iteration 1 Error: 0.678286 Iteration 2 Error: 0.066382 Iteration 3 Error: 0.010496 Align patch 19 6 left Iteration 1 Error: 0.355934 Iteration 2 Error: 0.067718 Iteration 3 Error: 0.015801 Align patch 20 5 left Iteration 1 Error: 0.607601 Iteration 2 Error: 0.124404 Iteration 3 Error: 0.020885 Align patch 21 4 left Iteration 1 Error: 0.979976 Iteration 2 Error: 0.178487 Iteration 3 Error: 0.027408 Align patch 22 3 left Iteration 1 Error: 0.663779 Iteration 2 Error: 0.111857 Iteration 3 Error: 0.025578 Align patch 23 2 left Iteration 1 Error: 0.992006 Iteration 2 Error: 0.114521 Iteration 3 Error: 0.021688 Align patch 24 1 left Iteration 1 Error: 0.460334 Iteration 2 Error: 0.065686 Iteration 3 Error: 0.011384 Align patch 25 0 left Iteration 1 Error: 0.613640 Iteration 2 Error: 0.102645 Iteration 3 Error: 0.014757 3D Fitting completed. Patch alignment time: 15.56(sec) Local motion has been corrected. Process thread exits. Computational time: 24.972237 sec Total time: 31.560093 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00015hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00015hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.517730s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00015hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.377214s ........................................ >>>>>>TIME<<<<<< FFT: 0.935112s Defocus_U Defocus_V Angle CCC 12826.21 13654.34 13.94 0.070057 Final Values Defocus_U Defocus_V Angle CCC 12844.97 13657.47 13.31 0.116411 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00015hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00015hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 42.83 7.46 Num Hot pixels: 178 Hot pixel threshold: 87.60 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.168321 Iteration 2 Error: 0.114181 Iteration 3 Error: 0.018809 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.30 -0.03 ...... Frame ( 3) shift: -0.60 -0.05 ...... Frame ( 4) shift: -0.89 -0.08 ...... Frame ( 5) shift: -1.19 -0.11 ...... Frame ( 6) shift: -1.35 -0.08 ...... Frame ( 7) shift: -1.37 -0.00 ...... Frame ( 8) shift: -1.39 0.08 ...... Frame ( 9) shift: -1.40 0.15 ...... Frame ( 10) shift: -1.39 0.21 ...... Frame ( 11) shift: -1.38 0.27 ...... Frame ( 12) shift: -1.39 0.33 ...... Frame ( 13) shift: -1.40 0.37 ...... Frame ( 14) shift: -1.42 0.41 ...... Frame ( 15) shift: -1.44 0.45 ...... Frame ( 16) shift: -1.45 0.48 ...... Frame ( 17) shift: -1.47 0.51 ...... Frame ( 18) shift: -1.46 0.55 ...... Frame ( 19) shift: -1.41 0.62 ...... Frame ( 20) shift: -1.37 0.69 ...... Frame ( 21) shift: -1.36 0.74 ...... Frame ( 22) shift: -1.40 0.76 ...... Frame ( 23) shift: -1.44 0.79 ...... Frame ( 24) shift: -1.46 0.83 ...... Frame ( 25) shift: -1.46 0.89 ...... Frame ( 26) shift: -1.46 0.94 ...... Frame ( 27) shift: -1.49 1.00 ...... Frame ( 28) shift: -1.54 1.06 ...... Frame ( 29) shift: -1.59 1.12 ...... Frame ( 30) shift: -1.63 1.17 ...... Frame ( 31) shift: -1.64 1.22 ...... Frame ( 32) shift: -1.65 1.27 ...... Frame ( 33) shift: -1.65 1.30 ...... Frame ( 34) shift: -1.64 1.34 ...... Frame ( 35) shift: -1.64 1.37 ...... Frame ( 36) shift: -1.63 1.39 ...... Frame ( 37) shift: -1.61 1.39 ...... Frame ( 38) shift: -1.59 1.39 ...... Frame ( 39) shift: -1.57 1.40 ...... Frame ( 40) shift: -1.55 1.40 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.018828 Iteration 2 Error: 0.276756 Iteration 3 Error: 0.065507 Iteration 4 Error: 0.024597 Align patch 2 23 left Iteration 1 Error: 1.047352 Iteration 2 Error: 0.165932 Iteration 3 Error: 0.017567 Align patch 3 22 left Iteration 1 Error: 0.672887 Iteration 2 Error: 0.071203 Iteration 3 Error: 0.014329 Align patch 4 21 left Iteration 1 Error: 0.565888 Iteration 2 Error: 0.132990 Iteration 3 Error: 0.033503 Align patch 5 20 left Iteration 1 Error: 0.789971 Iteration 2 Error: 0.089782 Iteration 3 Error: 0.017582 Align patch 6 19 left Iteration 1 Error: 0.790293 Iteration 2 Error: 0.184989 Iteration 3 Error: 0.080976 Iteration 4 Error: 0.035451 Align patch 7 18 left Iteration 1 Error: 0.645118 Iteration 2 Error: 0.137360 Iteration 3 Error: 0.031230 Align patch 8 17 left Iteration 1 Error: 0.598082 Iteration 2 Error: 0.104517 Iteration 3 Error: 0.031976 Align patch 9 16 left Iteration 1 Error: 0.307315 Iteration 2 Error: 0.039858 Align patch 10 15 left Iteration 1 Error: 0.392212 Iteration 2 Error: 0.031634 Align patch 11 14 left Iteration 1 Error: 0.799567 Iteration 2 Error: 0.109577 Iteration 3 Error: 0.039873 Align patch 12 13 left Iteration 1 Error: 0.952894 Iteration 2 Error: 0.356251 Iteration 3 Error: 0.100443 Iteration 4 Error: 0.047969 Align patch 13 12 left Iteration 1 Error: 0.920746 Iteration 2 Error: 0.130906 Iteration 3 Error: 0.030800 Align patch 14 11 left Iteration 1 Error: 0.659364 Iteration 2 Error: 0.072076 Iteration 3 Error: 0.017289 Align patch 15 10 left Iteration 1 Error: 0.609731 Iteration 2 Error: 0.078969 Iteration 3 Error: 0.011948 Align patch 16 9 left Iteration 1 Error: 0.801140 Iteration 2 Error: 0.138802 Iteration 3 Error: 0.036141 Align patch 17 8 left Iteration 1 Error: 0.590109 Iteration 2 Error: 0.090124 Iteration 3 Error: 0.020609 Align patch 18 7 left Iteration 1 Error: 0.598825 Iteration 2 Error: 0.108552 Iteration 3 Error: 0.022526 Align patch 19 6 left Iteration 1 Error: 0.819200 Iteration 2 Error: 0.081745 Iteration 3 Error: 0.014618 Align patch 20 5 left Iteration 1 Error: 0.870630 Iteration 2 Error: 0.064332 Iteration 3 Error: 0.015373 Align patch 21 4 left Iteration 1 Error: 0.981607 Iteration 2 Error: 0.205479 Iteration 3 Error: 0.039836 Align patch 22 3 left Iteration 1 Error: 0.819937 Iteration 2 Error: 0.095373 Iteration 3 Error: 0.022165 Align patch 23 2 left Iteration 1 Error: 0.896267 Iteration 2 Error: 0.152533 Iteration 3 Error: 0.036709 Align patch 24 1 left Iteration 1 Error: 0.946793 Iteration 2 Error: 0.093747 Iteration 3 Error: 0.014848 Align patch 25 0 left Iteration 1 Error: 0.698672 Iteration 2 Error: 0.065731 Iteration 3 Error: 0.013698 3D Fitting completed. Patch alignment time: 15.39(sec) Local motion has been corrected. Process thread exits. Computational time: 23.731113 sec Total time: 29.604584 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00015hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00015hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.762289s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00015hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.536973s ........................................ >>>>>>TIME<<<<<< FFT: 0.931576s Defocus_U Defocus_V Angle CCC 11462.92 11959.02 1.88 0.058320 Final Values Defocus_U Defocus_V Angle CCC 11480.11 11973.10 0.01 0.103109 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00015hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00015hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.002e-01 CC threshold: 0.736 Mean Std: 45.52 7.53 Num Hot pixels: 223 Hot pixel threshold: 90.70 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.017566 Iteration 2 Error: 0.174938 Iteration 3 Error: 0.036336 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.40 0.09 ...... Frame ( 3) shift: -0.80 0.18 ...... Frame ( 4) shift: -1.21 0.27 ...... Frame ( 5) shift: -1.61 0.36 ...... Frame ( 6) shift: -1.82 0.45 ...... Frame ( 7) shift: -1.83 0.56 ...... Frame ( 8) shift: -1.84 0.67 ...... Frame ( 9) shift: -1.88 0.74 ...... Frame ( 10) shift: -1.93 0.78 ...... Frame ( 11) shift: -1.99 0.82 ...... Frame ( 12) shift: -2.03 0.87 ...... Frame ( 13) shift: -2.06 0.95 ...... Frame ( 14) shift: -2.08 1.03 ...... Frame ( 15) shift: -2.13 1.10 ...... Frame ( 16) shift: -2.21 1.14 ...... Frame ( 17) shift: -2.29 1.19 ...... Frame ( 18) shift: -2.34 1.24 ...... Frame ( 19) shift: -2.35 1.29 ...... Frame ( 20) shift: -2.37 1.34 ...... Frame ( 21) shift: -2.38 1.41 ...... Frame ( 22) shift: -2.38 1.49 ...... Frame ( 23) shift: -2.37 1.57 ...... Frame ( 24) shift: -2.42 1.62 ...... Frame ( 25) shift: -2.52 1.65 ...... Frame ( 26) shift: -2.63 1.67 ...... Frame ( 27) shift: -2.68 1.67 ...... Frame ( 28) shift: -2.70 1.66 ...... Frame ( 29) shift: -2.71 1.64 ...... Frame ( 30) shift: -2.70 1.65 ...... Frame ( 31) shift: -2.67 1.66 ...... Frame ( 32) shift: -2.64 1.68 ...... Frame ( 33) shift: -2.68 1.71 ...... Frame ( 34) shift: -2.78 1.75 ...... Frame ( 35) shift: -2.89 1.78 ...... Frame ( 36) shift: -2.93 1.82 ...... Frame ( 37) shift: -2.91 1.85 ...... Frame ( 38) shift: -2.90 1.89 ...... Frame ( 39) shift: -2.88 1.92 ...... Frame ( 40) shift: -2.87 1.95 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.391271 Iteration 2 Error: 0.261676 Iteration 3 Error: 0.106723 Iteration 4 Error: 0.029237 Align patch 2 23 left Iteration 1 Error: 1.841535 Iteration 2 Error: 0.183817 Iteration 3 Error: 0.072306 Iteration 4 Error: 0.016550 Align patch 3 22 left Iteration 1 Error: 1.761622 Iteration 2 Error: 0.307322 Iteration 3 Error: 0.108713 Iteration 4 Error: 0.039954 Align patch 4 21 left Iteration 1 Error: 1.288329 Iteration 2 Error: 0.227564 Iteration 3 Error: 0.053525 Iteration 4 Error: 0.021363 Align patch 5 20 left Iteration 1 Error: 0.595507 Iteration 2 Error: 0.157861 Iteration 3 Error: 0.018365 Align patch 6 19 left Iteration 1 Error: 0.752635 Iteration 2 Error: 0.337720 Iteration 3 Error: 0.283911 Iteration 4 Error: 0.243990 Iteration 5 Error: 0.180617 Align patch 6 19 left Iteration 1 Error: 1.889304 Iteration 2 Error: 0.226666 Iteration 3 Error: 0.083497 Iteration 4 Error: 0.023771 Align patch 7 18 left Iteration 1 Error: 1.343966 Iteration 2 Error: 0.195028 Iteration 3 Error: 0.087832 Iteration 4 Error: 0.015903 Align patch 8 17 left Iteration 1 Error: 1.602703 Iteration 2 Error: 0.210417 Iteration 3 Error: 0.040998 Align patch 9 16 left Iteration 1 Error: 0.833990 Iteration 2 Error: 0.213291 Iteration 3 Error: 0.047522 Align patch 10 15 left Iteration 1 Error: 0.517016 Iteration 2 Error: 0.073396 Iteration 3 Error: 0.015843 Align patch 11 14 left Iteration 1 Error: 1.188671 Iteration 2 Error: 0.151165 Iteration 3 Error: 0.048623 Align patch 12 13 left Iteration 1 Error: 0.608757 Iteration 2 Error: 0.133487 Iteration 3 Error: 0.034108 Align patch 13 12 left Iteration 1 Error: 0.422006 Iteration 2 Error: 0.112311 Iteration 3 Error: 0.016421 Align patch 14 11 left Iteration 1 Error: 0.415405 Iteration 2 Error: 0.079995 Iteration 3 Error: 0.013035 Align patch 15 10 left Iteration 1 Error: 0.469585 Iteration 2 Error: 0.053377 Iteration 3 Error: 0.009178 Align patch 16 9 left Iteration 1 Error: 0.945680 Iteration 2 Error: 0.216988 Iteration 3 Error: 0.046627 Align patch 17 8 left Iteration 1 Error: 1.104213 Iteration 2 Error: 0.129176 Iteration 3 Error: 0.038989 Align patch 18 7 left Iteration 1 Error: 0.790869 Iteration 2 Error: 0.083839 Iteration 3 Error: 0.016068 Align patch 19 6 left Iteration 1 Error: 0.841681 Iteration 2 Error: 0.128874 Iteration 3 Error: 0.025674 Align patch 20 5 left Iteration 1 Error: 0.624898 Iteration 2 Error: 0.073437 Iteration 3 Error: 0.015025 Align patch 21 4 left Iteration 1 Error: 1.825339 Iteration 2 Error: 0.372515 Iteration 3 Error: 0.063796 Iteration 4 Error: 0.033065 Align patch 22 3 left Iteration 1 Error: 1.865057 Iteration 2 Error: 0.255468 Iteration 3 Error: 0.050909 Iteration 4 Error: 0.015746 Align patch 23 2 left Iteration 1 Error: 1.084731 Iteration 2 Error: 0.161974 Iteration 3 Error: 0.034508 Align patch 24 1 left Iteration 1 Error: 0.951382 Iteration 2 Error: 0.139262 Iteration 3 Error: 0.030325 Align patch 25 0 left Iteration 1 Error: 0.918532 Iteration 2 Error: 0.187978 Iteration 3 Error: 0.020201 3D Fitting completed. Patch alignment time: 16.38(sec) Local motion has been corrected. Process thread exits. Computational time: 24.607487 sec Total time: 30.243835 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00015hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00015hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.636280s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00015hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 3.356263s ........................................ >>>>>>TIME<<<<<< FFT: 0.957689s Defocus_U Defocus_V Angle CCC 12535.16 13390.62 4.68 0.065779 Final Values Defocus_U Defocus_V Angle CCC 12535.15 13393.75 4.99 0.115303 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00015hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00015hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 44.77 7.51 Num Hot pixels: 213 Hot pixel threshold: 89.82 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.596374 Iteration 2 Error: 0.122203 Iteration 3 Error: 0.024156 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.24 0.14 ...... Frame ( 3) shift: -0.49 0.29 ...... Frame ( 4) shift: -0.73 0.43 ...... Frame ( 5) shift: -0.98 0.58 ...... Frame ( 6) shift: -1.11 0.72 ...... Frame ( 7) shift: -1.14 0.85 ...... Frame ( 8) shift: -1.16 0.99 ...... Frame ( 9) shift: -1.16 1.12 ...... Frame ( 10) shift: -1.11 1.25 ...... Frame ( 11) shift: -1.07 1.38 ...... Frame ( 12) shift: -1.06 1.47 ...... Frame ( 13) shift: -1.09 1.53 ...... Frame ( 14) shift: -1.11 1.59 ...... Frame ( 15) shift: -1.11 1.65 ...... Frame ( 16) shift: -1.10 1.71 ...... Frame ( 17) shift: -1.08 1.78 ...... Frame ( 18) shift: -1.08 1.82 ...... Frame ( 19) shift: -1.11 1.83 ...... Frame ( 20) shift: -1.13 1.85 ...... Frame ( 21) shift: -1.18 1.87 ...... Frame ( 22) shift: -1.25 1.90 ...... Frame ( 23) shift: -1.32 1.93 ...... Frame ( 24) shift: -1.36 1.97 ...... Frame ( 25) shift: -1.37 2.00 ...... Frame ( 26) shift: -1.37 2.03 ...... Frame ( 27) shift: -1.40 2.06 ...... Frame ( 28) shift: -1.44 2.07 ...... Frame ( 29) shift: -1.48 2.08 ...... Frame ( 30) shift: -1.49 2.13 ...... Frame ( 31) shift: -1.48 2.20 ...... Frame ( 32) shift: -1.47 2.28 ...... Frame ( 33) shift: -1.48 2.31 ...... Frame ( 34) shift: -1.50 2.30 ...... Frame ( 35) shift: -1.53 2.29 ...... Frame ( 36) shift: -1.55 2.28 ...... Frame ( 37) shift: -1.57 2.26 ...... Frame ( 38) shift: -1.58 2.24 ...... Frame ( 39) shift: -1.59 2.22 ...... Frame ( 40) shift: -1.61 2.20 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.920555 Iteration 2 Error: 0.280977 Iteration 3 Error: 0.061190 Iteration 4 Error: 0.026996 Align patch 2 23 left Iteration 1 Error: 3.781864 Iteration 2 Error: 0.326564 Iteration 3 Error: 0.085978 Iteration 4 Error: 0.020116 Align patch 3 22 left Iteration 1 Error: 0.814688 Iteration 2 Error: 0.145371 Iteration 3 Error: 0.036657 Align patch 4 21 left Iteration 1 Error: 0.413670 Iteration 2 Error: 0.080052 Iteration 3 Error: 0.019381 Align patch 5 20 left Iteration 1 Error: 0.438957 Iteration 2 Error: 0.048185 Align patch 6 19 left Iteration 1 Error: 2.474451 Iteration 2 Error: 0.405077 Iteration 3 Error: 0.337172 Iteration 4 Error: 0.171975 Iteration 5 Error: 0.093140 Align patch 6 19 left Iteration 1 Error: 3.220429 Iteration 2 Error: 0.190930 Iteration 3 Error: 0.047454 Align patch 7 18 left Iteration 1 Error: 2.496623 Iteration 2 Error: 0.363081 Iteration 3 Error: 0.119814 Iteration 4 Error: 0.034382 Align patch 8 17 left Iteration 1 Error: 0.997334 Iteration 2 Error: 0.293096 Iteration 3 Error: 0.113428 Iteration 4 Error: 0.034702 Align patch 9 16 left Iteration 1 Error: 0.475998 Iteration 2 Error: 0.090379 Iteration 3 Error: 0.022291 Align patch 10 15 left Iteration 1 Error: 0.715568 Iteration 2 Error: 0.061721 Iteration 3 Error: 0.009994 Align patch 11 14 left Iteration 1 Error: 1.841792 Iteration 2 Error: 0.238666 Iteration 3 Error: 0.088917 Iteration 4 Error: 0.023463 Align patch 12 13 left Iteration 1 Error: 1.612014 Iteration 2 Error: 0.328704 Iteration 3 Error: 0.084984 Iteration 4 Error: 0.038459 Align patch 13 12 left Iteration 1 Error: 0.662195 Iteration 2 Error: 0.122625 Iteration 3 Error: 0.043677 Align patch 14 11 left Iteration 1 Error: 0.464546 Iteration 2 Error: 0.061569 Iteration 3 Error: 0.023381 Align patch 15 10 left Iteration 1 Error: 0.784087 Iteration 2 Error: 0.102756 Iteration 3 Error: 0.015578 Align patch 16 9 left Iteration 1 Error: 0.977004 Iteration 2 Error: 0.139542 Iteration 3 Error: 0.029313 Align patch 17 8 left Iteration 1 Error: 0.707602 Iteration 2 Error: 0.114465 Iteration 3 Error: 0.034367 Align patch 18 7 left Iteration 1 Error: 0.767051 Iteration 2 Error: 0.103589 Iteration 3 Error: 0.021385 Align patch 19 6 left Iteration 1 Error: 0.811801 Iteration 2 Error: 0.090994 Iteration 3 Error: 0.021171 Align patch 20 5 left Iteration 1 Error: 1.097243 Iteration 2 Error: 0.163106 Iteration 3 Error: 0.018449 Align patch 21 4 left Iteration 1 Error: 0.927483 Iteration 2 Error: 0.140470 Iteration 3 Error: 0.031214 Align patch 22 3 left Iteration 1 Error: 0.445418 Iteration 2 Error: 0.098802 Iteration 3 Error: 0.028217 Align patch 23 2 left Iteration 1 Error: 0.878622 Iteration 2 Error: 0.083588 Iteration 3 Error: 0.023187 Align patch 24 1 left Iteration 1 Error: 1.421973 Iteration 2 Error: 0.151863 Iteration 3 Error: 0.030297 Align patch 25 0 left Iteration 1 Error: 0.981351 Iteration 2 Error: 0.139794 Iteration 3 Error: 0.029135 3D Fitting completed. Patch alignment time: 15.92(sec) Local motion has been corrected. Process thread exits. Computational time: 23.805656 sec Total time: 30.492931 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00015hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00015hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.668115s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00015hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.273183s ........................................ >>>>>>TIME<<<<<< FFT: 0.958496s Defocus_U Defocus_V Angle CCC 12599.64 12001.96 84.04 0.062570 Final Values Defocus_U Defocus_V Angle CCC 12618.40 12008.21 84.04 0.111698 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00016hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00016hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 42.88 7.27 Num Hot pixels: 228 Hot pixel threshold: 86.49 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.502937 Iteration 2 Error: 0.350252 Iteration 3 Error: 0.087002 Iteration 4 Error: 0.032643 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.27 0.02 ...... Frame ( 3) shift: -0.54 0.04 ...... Frame ( 4) shift: -0.81 0.06 ...... Frame ( 5) shift: -1.08 0.08 ...... Frame ( 6) shift: -1.17 0.14 ...... Frame ( 7) shift: -1.07 0.25 ...... Frame ( 8) shift: -0.98 0.36 ...... Frame ( 9) shift: -0.89 0.47 ...... Frame ( 10) shift: -0.82 0.57 ...... Frame ( 11) shift: -0.74 0.67 ...... Frame ( 12) shift: -0.68 0.76 ...... Frame ( 13) shift: -0.64 0.86 ...... Frame ( 14) shift: -0.59 0.96 ...... Frame ( 15) shift: -0.56 1.07 ...... Frame ( 16) shift: -0.54 1.20 ...... Frame ( 17) shift: -0.51 1.33 ...... Frame ( 18) shift: -0.47 1.43 ...... Frame ( 19) shift: -0.40 1.50 ...... Frame ( 20) shift: -0.34 1.57 ...... Frame ( 21) shift: -0.28 1.66 ...... Frame ( 22) shift: -0.24 1.76 ...... Frame ( 23) shift: -0.20 1.87 ...... Frame ( 24) shift: -0.14 1.97 ...... Frame ( 25) shift: -0.08 2.06 ...... Frame ( 26) shift: -0.01 2.16 ...... Frame ( 27) shift: 0.05 2.28 ...... Frame ( 28) shift: 0.09 2.43 ...... Frame ( 29) shift: 0.14 2.58 ...... Frame ( 30) shift: 0.19 2.70 ...... Frame ( 31) shift: 0.23 2.78 ...... Frame ( 32) shift: 0.28 2.86 ...... Frame ( 33) shift: 0.29 2.94 ...... Frame ( 34) shift: 0.26 2.99 ...... Frame ( 35) shift: 0.24 3.05 ...... Frame ( 36) shift: 0.25 3.11 ...... Frame ( 37) shift: 0.30 3.16 ...... Frame ( 38) shift: 0.35 3.22 ...... Frame ( 39) shift: 0.39 3.27 ...... Frame ( 40) shift: 0.44 3.33 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.138772 Iteration 2 Error: 0.265888 Iteration 3 Error: 0.042766 Align patch 2 23 left Iteration 1 Error: 2.007234 Iteration 2 Error: 0.377547 Iteration 3 Error: 0.113131 Iteration 4 Error: 0.045178 Align patch 3 22 left Iteration 1 Error: 0.917245 Iteration 2 Error: 0.196407 Iteration 3 Error: 0.079383 Iteration 4 Error: 0.032206 Align patch 4 21 left Iteration 1 Error: 0.446008 Iteration 2 Error: 0.068064 Iteration 3 Error: 0.024181 Align patch 5 20 left Iteration 1 Error: 0.461267 Iteration 2 Error: 0.110485 Iteration 3 Error: 0.025766 Align patch 6 19 left Iteration 1 Error: 1.810969 Iteration 2 Error: 0.257516 Iteration 3 Error: 0.082873 Iteration 4 Error: 0.021957 Align patch 7 18 left Iteration 1 Error: 1.113190 Iteration 2 Error: 0.263076 Iteration 3 Error: 0.121535 Iteration 4 Error: 0.056586 Iteration 5 Error: 0.019105 Align patch 8 17 left Iteration 1 Error: 0.815890 Iteration 2 Error: 0.263046 Iteration 3 Error: 0.100108 Iteration 4 Error: 0.034032 Align patch 9 16 left Iteration 1 Error: 0.455385 Iteration 2 Error: 0.094148 Iteration 3 Error: 0.021154 Align patch 10 15 left Iteration 1 Error: 0.910710 Iteration 2 Error: 0.228435 Iteration 3 Error: 0.051086 Iteration 4 Error: 0.010871 Align patch 11 14 left Iteration 1 Error: 1.253178 Iteration 2 Error: 0.259055 Iteration 3 Error: 0.117474 Iteration 4 Error: 0.059798 Iteration 5 Error: 0.029204 Align patch 12 13 left Iteration 1 Error: 1.516272 Iteration 2 Error: 0.180634 Iteration 3 Error: 0.044076 Align patch 13 12 left Iteration 1 Error: 0.505781 Iteration 2 Error: 0.069703 Iteration 3 Error: 0.024318 Align patch 14 11 left Iteration 1 Error: 0.397201 Iteration 2 Error: 0.089620 Iteration 3 Error: 0.042140 Align patch 15 10 left Iteration 1 Error: 0.896482 Iteration 2 Error: 0.187358 Iteration 3 Error: 0.046863 Align patch 16 9 left Iteration 1 Error: 0.586505 Iteration 2 Error: 0.140895 Iteration 3 Error: 0.043765 Align patch 17 8 left Iteration 1 Error: 0.521324 Iteration 2 Error: 0.089315 Iteration 3 Error: 0.026014 Align patch 18 7 left Iteration 1 Error: 0.753332 Iteration 2 Error: 0.110230 Iteration 3 Error: 0.052013 Iteration 4 Error: 0.017131 Align patch 19 6 left Iteration 1 Error: 0.668782 Iteration 2 Error: 0.080776 Iteration 3 Error: 0.019292 Align patch 20 5 left Iteration 1 Error: 0.752731 Iteration 2 Error: 0.103768 Iteration 3 Error: 0.014685 Align patch 21 4 left Iteration 1 Error: 1.608887 Iteration 2 Error: 0.201943 Iteration 3 Error: 0.043282 Align patch 22 3 left Iteration 1 Error: 0.851267 Iteration 2 Error: 0.103354 Iteration 3 Error: 0.047653 Align patch 23 2 left Iteration 1 Error: 0.840445 Iteration 2 Error: 0.140698 Iteration 3 Error: 0.049687 Align patch 24 1 left Iteration 1 Error: 0.898145 Iteration 2 Error: 0.111472 Iteration 3 Error: 0.021275 Align patch 25 0 left Iteration 1 Error: 0.882131 Iteration 2 Error: 0.164923 Iteration 3 Error: 0.033887 3D Fitting completed. Patch alignment time: 15.57(sec) Local motion has been corrected. Process thread exits. Computational time: 24.722994 sec Total time: 30.486498 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00016hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00016hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.763858s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00016hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.351781s ........................................ >>>>>>TIME<<<<<< FFT: 1.013783s Defocus_U Defocus_V Angle CCC 10541.02 11298.83 13.72 0.058937 Final Values Defocus_U Defocus_V Angle CCC 10545.71 11319.15 13.41 0.104226 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00016hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00016hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.350e-01 1.004e-01 CC threshold: 0.737 Mean Std: 44.23 7.45 Num Hot pixels: 203 Hot pixel threshold: 88.96 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.861921 Iteration 2 Error: 0.144124 Iteration 3 Error: 0.020545 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.22 0.03 ...... Frame ( 3) shift: -0.44 0.06 ...... Frame ( 4) shift: -0.66 0.09 ...... Frame ( 5) shift: -0.88 0.12 ...... Frame ( 6) shift: -0.97 0.15 ...... Frame ( 7) shift: -0.94 0.18 ...... Frame ( 8) shift: -0.92 0.21 ...... Frame ( 9) shift: -0.88 0.23 ...... Frame ( 10) shift: -0.83 0.24 ...... Frame ( 11) shift: -0.78 0.25 ...... Frame ( 12) shift: -0.75 0.31 ...... Frame ( 13) shift: -0.74 0.42 ...... Frame ( 14) shift: -0.73 0.54 ...... Frame ( 15) shift: -0.72 0.59 ...... Frame ( 16) shift: -0.71 0.59 ...... Frame ( 17) shift: -0.70 0.58 ...... Frame ( 18) shift: -0.67 0.59 ...... Frame ( 19) shift: -0.63 0.62 ...... Frame ( 20) shift: -0.59 0.65 ...... Frame ( 21) shift: -0.60 0.69 ...... Frame ( 22) shift: -0.64 0.72 ...... Frame ( 23) shift: -0.69 0.75 ...... Frame ( 24) shift: -0.72 0.81 ...... Frame ( 25) shift: -0.73 0.89 ...... Frame ( 26) shift: -0.74 0.96 ...... Frame ( 27) shift: -0.73 1.04 ...... Frame ( 28) shift: -0.71 1.10 ...... Frame ( 29) shift: -0.68 1.17 ...... Frame ( 30) shift: -0.69 1.24 ...... Frame ( 31) shift: -0.74 1.30 ...... Frame ( 32) shift: -0.79 1.36 ...... Frame ( 33) shift: -0.79 1.39 ...... Frame ( 34) shift: -0.75 1.40 ...... Frame ( 35) shift: -0.71 1.41 ...... Frame ( 36) shift: -0.67 1.45 ...... Frame ( 37) shift: -0.62 1.52 ...... Frame ( 38) shift: -0.58 1.59 ...... Frame ( 39) shift: -0.54 1.66 ...... Frame ( 40) shift: -0.50 1.72 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.826957 Iteration 2 Error: 0.343226 Iteration 3 Error: 0.133610 Iteration 4 Error: 0.058481 Iteration 5 Error: 0.025142 Align patch 2 23 left Iteration 1 Error: 1.263636 Iteration 2 Error: 0.309450 Iteration 3 Error: 0.103526 Iteration 4 Error: 0.039542 Align patch 3 22 left Iteration 1 Error: 0.768025 Iteration 2 Error: 0.148161 Iteration 3 Error: 0.041943 Align patch 4 21 left Iteration 1 Error: 0.742698 Iteration 2 Error: 0.077793 Iteration 3 Error: 0.013404 Align patch 5 20 left Iteration 1 Error: 0.570509 Iteration 2 Error: 0.049222 Align patch 6 19 left Iteration 1 Error: 1.782159 Iteration 2 Error: 0.183652 Iteration 3 Error: 0.038233 Align patch 7 18 left Iteration 1 Error: 1.684269 Iteration 2 Error: 0.228345 Iteration 3 Error: 0.085821 Iteration 4 Error: 0.023257 Align patch 8 17 left Iteration 1 Error: 0.693776 Iteration 2 Error: 0.125559 Iteration 3 Error: 0.039803 Align patch 9 16 left Iteration 1 Error: 0.413847 Iteration 2 Error: 0.044106 Align patch 10 15 left Iteration 1 Error: 0.383104 Iteration 2 Error: 0.048889 Align patch 11 14 left Iteration 1 Error: 1.234831 Iteration 2 Error: 0.204022 Iteration 3 Error: 0.050293 Iteration 4 Error: 0.020092 Align patch 12 13 left Iteration 1 Error: 0.714659 Iteration 2 Error: 0.121177 Iteration 3 Error: 0.021477 Align patch 13 12 left Iteration 1 Error: 0.580549 Iteration 2 Error: 0.174698 Iteration 3 Error: 0.046148 Align patch 14 11 left Iteration 1 Error: 0.470673 Iteration 2 Error: 0.082360 Iteration 3 Error: 0.019873 Align patch 15 10 left Iteration 1 Error: 0.709416 Iteration 2 Error: 0.112079 Iteration 3 Error: 0.021873 Align patch 16 9 left Iteration 1 Error: 0.707708 Iteration 2 Error: 0.091560 Iteration 3 Error: 0.015821 Align patch 17 8 left Iteration 1 Error: 0.603644 Iteration 2 Error: 0.091501 Iteration 3 Error: 0.025098 Align patch 18 7 left Iteration 1 Error: 0.918034 Iteration 2 Error: 0.103446 Iteration 3 Error: 0.027221 Align patch 19 6 left Iteration 1 Error: 0.544516 Iteration 2 Error: 0.102006 Iteration 3 Error: 0.024904 Align patch 20 5 left Iteration 1 Error: 0.755248 Iteration 2 Error: 0.098319 Iteration 3 Error: 0.016002 Align patch 21 4 left Iteration 1 Error: 0.783964 Iteration 2 Error: 0.096015 Iteration 3 Error: 0.022486 Align patch 22 3 left Iteration 1 Error: 0.901121 Iteration 2 Error: 0.127954 Iteration 3 Error: 0.030519 Align patch 23 2 left Iteration 1 Error: 0.652595 Iteration 2 Error: 0.157772 Iteration 3 Error: 0.034920 Align patch 24 1 left Iteration 1 Error: 0.929146 Iteration 2 Error: 0.137871 Iteration 3 Error: 0.033984 Align patch 25 0 left Iteration 1 Error: 0.605958 Iteration 2 Error: 0.085404 Iteration 3 Error: 0.017227 3D Fitting completed. Patch alignment time: 15.82(sec) Local motion has been corrected. Process thread exits. Computational time: 24.237347 sec Total time: 29.902422 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00016hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00016hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.563102s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00016hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.430054s ........................................ >>>>>>TIME<<<<<< FFT: 0.910096s Defocus_U Defocus_V Angle CCC 10189.45 10642.58 0.74 0.061619 Final Values Defocus_U Defocus_V Angle CCC 10194.15 10659.78 0.74 0.109592 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00016hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00016hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 41.68 7.33 Num Hot pixels: 215 Hot pixel threshold: 85.63 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.172442 Iteration 2 Error: 0.222099 Iteration 3 Error: 0.054927 Iteration 4 Error: 0.020893 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.31 -0.08 ...... Frame ( 3) shift: -0.63 -0.15 ...... Frame ( 4) shift: -0.94 -0.23 ...... Frame ( 5) shift: -1.25 -0.31 ...... Frame ( 6) shift: -1.42 -0.33 ...... Frame ( 7) shift: -1.45 -0.30 ...... Frame ( 8) shift: -1.47 -0.27 ...... Frame ( 9) shift: -1.47 -0.23 ...... Frame ( 10) shift: -1.43 -0.19 ...... Frame ( 11) shift: -1.40 -0.15 ...... Frame ( 12) shift: -1.36 -0.05 ...... Frame ( 13) shift: -1.31 0.11 ...... Frame ( 14) shift: -1.26 0.28 ...... Frame ( 15) shift: -1.27 0.40 ...... Frame ( 16) shift: -1.32 0.47 ...... Frame ( 17) shift: -1.37 0.55 ...... Frame ( 18) shift: -1.39 0.64 ...... Frame ( 19) shift: -1.37 0.76 ...... Frame ( 20) shift: -1.35 0.87 ...... Frame ( 21) shift: -1.37 0.94 ...... Frame ( 22) shift: -1.42 0.97 ...... Frame ( 23) shift: -1.47 1.00 ...... Frame ( 24) shift: -1.51 1.06 ...... Frame ( 25) shift: -1.52 1.15 ...... Frame ( 26) shift: -1.54 1.24 ...... Frame ( 27) shift: -1.52 1.32 ...... Frame ( 28) shift: -1.47 1.39 ...... Frame ( 29) shift: -1.42 1.45 ...... Frame ( 30) shift: -1.36 1.56 ...... Frame ( 31) shift: -1.29 1.71 ...... Frame ( 32) shift: -1.22 1.86 ...... Frame ( 33) shift: -1.16 1.94 ...... Frame ( 34) shift: -1.10 1.96 ...... Frame ( 35) shift: -1.05 1.98 ...... Frame ( 36) shift: -1.02 2.02 ...... Frame ( 37) shift: -1.01 2.07 ...... Frame ( 38) shift: -1.01 2.12 ...... Frame ( 39) shift: -1.01 2.17 ...... Frame ( 40) shift: -1.00 2.23 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.451887 Iteration 2 Error: 0.544199 Iteration 3 Error: 0.180082 Iteration 4 Error: 0.069296 Iteration 5 Error: 0.032195 Align patch 2 23 left Iteration 1 Error: 1.905798 Iteration 2 Error: 0.535156 Iteration 3 Error: 0.272580 Iteration 4 Error: 0.102779 Iteration 5 Error: 0.045680 Align patch 3 22 left Iteration 1 Error: 1.188552 Iteration 2 Error: 0.243939 Iteration 3 Error: 0.053906 Iteration 4 Error: 0.020403 Align patch 4 21 left Iteration 1 Error: 0.726502 Iteration 2 Error: 0.112415 Iteration 3 Error: 0.038003 Align patch 5 20 left Iteration 1 Error: 0.583778 Iteration 2 Error: 0.125295 Iteration 3 Error: 0.026239 Align patch 6 19 left Iteration 1 Error: 1.997234 Iteration 2 Error: 0.291944 Iteration 3 Error: 0.081383 Iteration 4 Error: 0.025286 Align patch 7 18 left Iteration 1 Error: 1.573281 Iteration 2 Error: 0.317217 Iteration 3 Error: 0.096299 Iteration 4 Error: 0.037561 Align patch 8 17 left Iteration 1 Error: 0.951974 Iteration 2 Error: 0.184730 Iteration 3 Error: 0.054965 Iteration 4 Error: 0.020694 Align patch 9 16 left Iteration 1 Error: 0.958032 Iteration 2 Error: 0.173299 Iteration 3 Error: 0.056086 Iteration 4 Error: 0.017288 Align patch 10 15 left Iteration 1 Error: 0.711882 Iteration 2 Error: 0.116560 Iteration 3 Error: 0.036590 Align patch 11 14 left Iteration 1 Error: 1.255872 Iteration 2 Error: 0.249554 Iteration 3 Error: 0.070540 Iteration 4 Error: 0.027247 Align patch 12 13 left Iteration 1 Error: 0.756561 Iteration 2 Error: 0.262968 Iteration 3 Error: 0.095574 Iteration 4 Error: 0.042033 Align patch 13 12 left Iteration 1 Error: 1.034204 Iteration 2 Error: 0.310540 Iteration 3 Error: 0.072039 Iteration 4 Error: 0.028225 Align patch 14 11 left Iteration 1 Error: 0.682743 Iteration 2 Error: 0.073739 Iteration 3 Error: 0.018329 Align patch 15 10 left Iteration 1 Error: 0.768093 Iteration 2 Error: 0.136714 Iteration 3 Error: 0.031586 Align patch 16 9 left Iteration 1 Error: 1.262723 Iteration 2 Error: 0.317282 Iteration 3 Error: 0.098676 Iteration 4 Error: 0.049452 Align patch 17 8 left Iteration 1 Error: 0.929046 Iteration 2 Error: 0.135401 Iteration 3 Error: 0.047682 Align patch 18 7 left Iteration 1 Error: 2.538826 Iteration 2 Error: 1.167750 Iteration 3 Error: 0.580691 Iteration 4 Error: 0.297820 Iteration 5 Error: 0.212121 Align patch 18 7 left Iteration 1 Error: 2.199536 Iteration 2 Error: 0.526750 Iteration 3 Error: 0.192049 Iteration 4 Error: 0.063853 Iteration 5 Error: 0.032175 Align patch 19 6 left Iteration 1 Error: 0.729795 Iteration 2 Error: 0.091958 Iteration 3 Error: 0.014038 Align patch 20 5 left Iteration 1 Error: 0.404087 Iteration 2 Error: 0.055792 Iteration 3 Error: 0.019434 Align patch 21 4 left Iteration 1 Error: 0.702573 Iteration 2 Error: 0.163056 Iteration 3 Error: 0.045240 Align patch 22 3 left Iteration 1 Error: 0.826283 Iteration 2 Error: 0.151313 Iteration 3 Error: 0.026286 Align patch 23 2 left Iteration 1 Error: 1.780745 Iteration 2 Error: 0.546720 Iteration 3 Error: 0.353249 Iteration 4 Error: 0.220361 Iteration 5 Error: 0.126201 Align patch 23 2 left Iteration 1 Error: 2.297028 Iteration 2 Error: 0.538849 Iteration 3 Error: 0.201983 Iteration 4 Error: 0.075348 Iteration 5 Error: 0.025610 Align patch 24 1 left Iteration 1 Error: 0.990146 Iteration 2 Error: 0.173129 Iteration 3 Error: 0.042427 Align patch 25 0 left Iteration 1 Error: 1.155672 Iteration 2 Error: 0.107814 Iteration 3 Error: 0.022498 3D Fitting completed. Patch alignment time: 18.33(sec) Local motion has been corrected. Process thread exits. Computational time: 27.056358 sec Total time: 33.357262 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00016hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00016hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.763591s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00016hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.573888s ........................................ >>>>>>TIME<<<<<< FFT: 0.932932s Defocus_U Defocus_V Angle CCC 10187.49 11011.75 6.35 0.048760 Final Values Defocus_U Defocus_V Angle CCC 10204.68 11019.57 6.35 0.086537 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00016hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00016hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.351e-01 1.005e-01 CC threshold: 0.738 Mean Std: 41.59 7.42 Num Hot pixels: 186 Hot pixel threshold: 86.13 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.290733 Iteration 2 Error: 0.084650 Iteration 3 Error: 0.018416 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.29 0.10 ...... Frame ( 3) shift: -0.58 0.21 ...... Frame ( 4) shift: -0.86 0.31 ...... Frame ( 5) shift: -1.15 0.41 ...... Frame ( 6) shift: -1.26 0.53 ...... Frame ( 7) shift: -1.20 0.65 ...... Frame ( 8) shift: -1.13 0.77 ...... Frame ( 9) shift: -1.09 0.89 ...... Frame ( 10) shift: -1.09 1.01 ...... Frame ( 11) shift: -1.08 1.13 ...... Frame ( 12) shift: -1.07 1.20 ...... Frame ( 13) shift: -1.06 1.22 ...... Frame ( 14) shift: -1.05 1.24 ...... Frame ( 15) shift: -1.05 1.27 ...... Frame ( 16) shift: -1.06 1.31 ...... Frame ( 17) shift: -1.07 1.35 ...... Frame ( 18) shift: -1.06 1.38 ...... Frame ( 19) shift: -1.03 1.40 ...... Frame ( 20) shift: -1.01 1.42 ...... Frame ( 21) shift: -0.98 1.45 ...... Frame ( 22) shift: -0.95 1.49 ...... Frame ( 23) shift: -0.91 1.53 ...... Frame ( 24) shift: -0.91 1.56 ...... Frame ( 25) shift: -0.92 1.60 ...... Frame ( 26) shift: -0.94 1.64 ...... Frame ( 27) shift: -0.95 1.68 ...... Frame ( 28) shift: -0.95 1.72 ...... Frame ( 29) shift: -0.96 1.75 ...... Frame ( 30) shift: -0.95 1.78 ...... Frame ( 31) shift: -0.93 1.79 ...... Frame ( 32) shift: -0.91 1.81 ...... Frame ( 33) shift: -0.93 1.84 ...... Frame ( 34) shift: -0.99 1.88 ...... Frame ( 35) shift: -1.05 1.92 ...... Frame ( 36) shift: -1.08 1.93 ...... Frame ( 37) shift: -1.09 1.90 ...... Frame ( 38) shift: -1.10 1.87 ...... Frame ( 39) shift: -1.11 1.84 ...... Frame ( 40) shift: -1.12 1.81 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.225966 Iteration 2 Error: 0.231622 Iteration 3 Error: 0.059501 Iteration 4 Error: 0.013438 Align patch 2 23 left Iteration 1 Error: 1.267712 Iteration 2 Error: 0.164023 Iteration 3 Error: 0.030822 Align patch 3 22 left Iteration 1 Error: 0.566710 Iteration 2 Error: 0.067531 Iteration 3 Error: 0.015524 Align patch 4 21 left Iteration 1 Error: 0.490952 Iteration 2 Error: 0.071885 Iteration 3 Error: 0.010579 Align patch 5 20 left Iteration 1 Error: 0.405454 Iteration 2 Error: 0.036296 Align patch 6 19 left Iteration 1 Error: 2.200807 Iteration 2 Error: 0.215150 Iteration 3 Error: 0.068754 Iteration 4 Error: 0.017657 Align patch 7 18 left Iteration 1 Error: 0.513934 Iteration 2 Error: 0.099149 Iteration 3 Error: 0.037524 Align patch 8 17 left Iteration 1 Error: 0.562716 Iteration 2 Error: 0.050719 Iteration 3 Error: 0.010933 Align patch 9 16 left Iteration 1 Error: 0.545198 Iteration 2 Error: 0.056393 Iteration 3 Error: 0.015133 Align patch 10 15 left Iteration 1 Error: 0.716987 Iteration 2 Error: 0.116226 Iteration 3 Error: 0.013820 Align patch 11 14 left Iteration 1 Error: 1.048477 Iteration 2 Error: 0.111901 Iteration 3 Error: 0.020859 Align patch 12 13 left Iteration 1 Error: 0.647138 Iteration 2 Error: 0.082804 Iteration 3 Error: 0.025581 Align patch 13 12 left Iteration 1 Error: 0.506619 Iteration 2 Error: 0.074713 Iteration 3 Error: 0.015280 Align patch 14 11 left Iteration 1 Error: 0.555540 Iteration 2 Error: 0.094920 Iteration 3 Error: 0.018942 Align patch 15 10 left Iteration 1 Error: 0.573818 Iteration 2 Error: 0.092835 Iteration 3 Error: 0.012092 Align patch 16 9 left Iteration 1 Error: 0.718018 Iteration 2 Error: 0.088337 Iteration 3 Error: 0.018727 Align patch 17 8 left Iteration 1 Error: 0.709770 Iteration 2 Error: 0.107436 Iteration 3 Error: 0.020477 Align patch 18 7 left Iteration 1 Error: 0.762386 Iteration 2 Error: 0.108970 Iteration 3 Error: 0.017454 Align patch 19 6 left Iteration 1 Error: 0.752710 Iteration 2 Error: 0.078177 Iteration 3 Error: 0.015011 Align patch 20 5 left Iteration 1 Error: 0.493367 Iteration 2 Error: 0.068643 Iteration 3 Error: 0.011402 Align patch 21 4 left Iteration 1 Error: 0.674943 Iteration 2 Error: 0.150376 Iteration 3 Error: 0.035931 Align patch 22 3 left Iteration 1 Error: 1.416201 Iteration 2 Error: 0.183209 Iteration 3 Error: 0.017280 Align patch 23 2 left Iteration 1 Error: 0.792789 Iteration 2 Error: 0.222437 Iteration 3 Error: 0.047457 Align patch 24 1 left Iteration 1 Error: 0.881092 Iteration 2 Error: 0.094731 Iteration 3 Error: 0.016818 Align patch 25 0 left Iteration 1 Error: 0.450010 Iteration 2 Error: 0.040470 3D Fitting completed. Patch alignment time: 14.66(sec) Local motion has been corrected. Process thread exits. Computational time: 22.972620 sec Total time: 28.657192 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00016hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00016hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.546783s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00016hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.227236s ........................................ >>>>>>TIME<<<<<< FFT: 0.789506s Defocus_U Defocus_V Angle CCC 12351.57 11695.32 84.26 0.069523 Final Values Defocus_U Defocus_V Angle CCC 12370.32 11701.58 83.95 0.117462 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00017hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00017hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.002e-01 CC threshold: 0.736 Mean Std: 43.43 7.33 Num Hot pixels: 237 Hot pixel threshold: 87.41 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.025062 Iteration 2 Error: 0.189844 Iteration 3 Error: 0.036677 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.24 -0.02 ...... Frame ( 3) shift: -0.49 -0.04 ...... Frame ( 4) shift: -0.73 -0.06 ...... Frame ( 5) shift: -0.97 -0.08 ...... Frame ( 6) shift: -1.08 -0.05 ...... Frame ( 7) shift: -1.04 0.05 ...... Frame ( 8) shift: -1.00 0.14 ...... Frame ( 9) shift: -0.95 0.24 ...... Frame ( 10) shift: -0.90 0.34 ...... Frame ( 11) shift: -0.85 0.44 ...... Frame ( 12) shift: -0.80 0.53 ...... Frame ( 13) shift: -0.76 0.60 ...... Frame ( 14) shift: -0.71 0.66 ...... Frame ( 15) shift: -0.66 0.72 ...... Frame ( 16) shift: -0.61 0.77 ...... Frame ( 17) shift: -0.56 0.81 ...... Frame ( 18) shift: -0.53 0.84 ...... Frame ( 19) shift: -0.51 0.85 ...... Frame ( 20) shift: -0.50 0.86 ...... Frame ( 21) shift: -0.44 0.89 ...... Frame ( 22) shift: -0.35 0.94 ...... Frame ( 23) shift: -0.25 0.98 ...... Frame ( 24) shift: -0.23 1.03 ...... Frame ( 25) shift: -0.27 1.08 ...... Frame ( 26) shift: -0.31 1.13 ...... Frame ( 27) shift: -0.32 1.17 ...... Frame ( 28) shift: -0.28 1.19 ...... Frame ( 29) shift: -0.24 1.21 ...... Frame ( 30) shift: -0.25 1.30 ...... Frame ( 31) shift: -0.29 1.45 ...... Frame ( 32) shift: -0.33 1.61 ...... Frame ( 33) shift: -0.32 1.70 ...... Frame ( 34) shift: -0.26 1.72 ...... Frame ( 35) shift: -0.20 1.75 ...... Frame ( 36) shift: -0.17 1.79 ...... Frame ( 37) shift: -0.17 1.84 ...... Frame ( 38) shift: -0.17 1.90 ...... Frame ( 39) shift: -0.17 1.95 ...... Frame ( 40) shift: -0.16 2.00 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.739880 Iteration 2 Error: 0.600439 Iteration 3 Error: 0.236659 Iteration 4 Error: 0.083680 Iteration 5 Error: 0.045041 Align patch 2 23 left Iteration 1 Error: 2.157546 Iteration 2 Error: 0.297499 Iteration 3 Error: 0.081460 Iteration 4 Error: 0.030982 Align patch 3 22 left Iteration 1 Error: 1.312860 Iteration 2 Error: 0.225609 Iteration 3 Error: 0.098092 Iteration 4 Error: 0.027623 Align patch 4 21 left Iteration 1 Error: 0.693964 Iteration 2 Error: 0.176525 Iteration 3 Error: 0.031606 Align patch 5 20 left Iteration 1 Error: 0.515749 Iteration 2 Error: 0.081515 Iteration 3 Error: 0.016398 Align patch 6 19 left Iteration 1 Error: 2.322492 Iteration 2 Error: 0.338227 Iteration 3 Error: 0.128257 Iteration 4 Error: 0.048641 Align patch 7 18 left Iteration 1 Error: 1.520780 Iteration 2 Error: 0.302727 Iteration 3 Error: 0.051299 Iteration 4 Error: 0.024661 Align patch 8 17 left Iteration 1 Error: 1.003536 Iteration 2 Error: 0.131046 Iteration 3 Error: 0.043440 Align patch 9 16 left Iteration 1 Error: 0.504722 Iteration 2 Error: 0.078992 Iteration 3 Error: 0.019949 Align patch 10 15 left Iteration 1 Error: 0.554102 Iteration 2 Error: 0.138832 Iteration 3 Error: 0.025387 Align patch 11 14 left Iteration 1 Error: 0.592747 Iteration 2 Error: 0.115008 Iteration 3 Error: 0.031961 Align patch 12 13 left Iteration 1 Error: 0.684042 Iteration 2 Error: 0.109300 Iteration 3 Error: 0.024021 Align patch 13 12 left Iteration 1 Error: 0.378383 Iteration 2 Error: 0.046820 Align patch 14 11 left Iteration 1 Error: 0.504001 Iteration 2 Error: 0.072893 Iteration 3 Error: 0.016816 Align patch 15 10 left Iteration 1 Error: 0.695736 Iteration 2 Error: 0.083176 Iteration 3 Error: 0.020168 Align patch 16 9 left Iteration 1 Error: 0.546686 Iteration 2 Error: 0.058228 Iteration 3 Error: 0.014991 Align patch 17 8 left Iteration 1 Error: 0.623897 Iteration 2 Error: 0.067494 Iteration 3 Error: 0.025921 Align patch 18 7 left Iteration 1 Error: 0.448958 Iteration 2 Error: 0.081171 Iteration 3 Error: 0.015826 Align patch 19 6 left Iteration 1 Error: 0.860466 Iteration 2 Error: 0.068614 Iteration 3 Error: 0.014585 Align patch 20 5 left Iteration 1 Error: 0.486099 Iteration 2 Error: 0.101631 Iteration 3 Error: 0.012889 Align patch 21 4 left Iteration 1 Error: 0.676508 Iteration 2 Error: 0.154454 Iteration 3 Error: 0.026627 Align patch 22 3 left Iteration 1 Error: 0.832623 Iteration 2 Error: 0.142707 Iteration 3 Error: 0.047717 Align patch 23 2 left Iteration 1 Error: 1.306104 Iteration 2 Error: 0.164791 Iteration 3 Error: 0.040928 Align patch 24 1 left Iteration 1 Error: 0.917128 Iteration 2 Error: 0.099501 Iteration 3 Error: 0.016902 Align patch 25 0 left Iteration 1 Error: 0.696070 Iteration 2 Error: 0.093705 Iteration 3 Error: 0.014950 3D Fitting completed. Patch alignment time: 15.38(sec) Local motion has been corrected. Process thread exits. Computational time: 24.502617 sec Total time: 30.472902 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00017hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00017hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.670679s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00017hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.525238s ........................................ >>>>>>TIME<<<<<< FFT: 0.940158s Defocus_U Defocus_V Angle CCC 12542.97 13390.63 12.66 0.058014 Final Values Defocus_U Defocus_V Angle CCC 12555.47 13393.77 12.66 0.100429 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00017hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00017hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 41.70 7.06 Num Hot pixels: 209 Hot pixel threshold: 84.03 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.135304 Iteration 2 Error: 0.204205 Iteration 3 Error: 0.054022 Iteration 4 Error: 0.018267 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.26 -0.01 ...... Frame ( 3) shift: -0.52 -0.03 ...... Frame ( 4) shift: -0.78 -0.04 ...... Frame ( 5) shift: -1.04 -0.05 ...... Frame ( 6) shift: -1.18 -0.01 ...... Frame ( 7) shift: -1.21 0.08 ...... Frame ( 8) shift: -1.24 0.18 ...... Frame ( 9) shift: -1.20 0.28 ...... Frame ( 10) shift: -1.11 0.37 ...... Frame ( 11) shift: -1.01 0.47 ...... Frame ( 12) shift: -0.95 0.57 ...... Frame ( 13) shift: -0.93 0.67 ...... Frame ( 14) shift: -0.90 0.78 ...... Frame ( 15) shift: -0.87 0.87 ...... Frame ( 16) shift: -0.81 0.97 ...... Frame ( 17) shift: -0.76 1.06 ...... Frame ( 18) shift: -0.70 1.14 ...... Frame ( 19) shift: -0.65 1.20 ...... Frame ( 20) shift: -0.59 1.26 ...... Frame ( 21) shift: -0.55 1.32 ...... Frame ( 22) shift: -0.54 1.39 ...... Frame ( 23) shift: -0.52 1.45 ...... Frame ( 24) shift: -0.48 1.52 ...... Frame ( 25) shift: -0.42 1.58 ...... Frame ( 26) shift: -0.36 1.64 ...... Frame ( 27) shift: -0.34 1.70 ...... Frame ( 28) shift: -0.38 1.76 ...... Frame ( 29) shift: -0.42 1.82 ...... Frame ( 30) shift: -0.45 1.89 ...... Frame ( 31) shift: -0.47 1.97 ...... Frame ( 32) shift: -0.50 2.05 ...... Frame ( 33) shift: -0.49 2.11 ...... Frame ( 34) shift: -0.43 2.16 ...... Frame ( 35) shift: -0.37 2.20 ...... Frame ( 36) shift: -0.33 2.21 ...... Frame ( 37) shift: -0.30 2.19 ...... Frame ( 38) shift: -0.27 2.16 ...... Frame ( 39) shift: -0.24 2.14 ...... Frame ( 40) shift: -0.21 2.12 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.189991 Iteration 2 Error: 0.347435 Iteration 3 Error: 0.121097 Iteration 4 Error: 0.057621 Iteration 5 Error: 0.020830 Align patch 2 23 left Iteration 1 Error: 1.365963 Iteration 2 Error: 0.224161 Iteration 3 Error: 0.106636 Iteration 4 Error: 0.035621 Align patch 3 22 left Iteration 1 Error: 0.672691 Iteration 2 Error: 0.124044 Iteration 3 Error: 0.026982 Align patch 4 21 left Iteration 1 Error: 0.509280 Iteration 2 Error: 0.067413 Iteration 3 Error: 0.023989 Align patch 5 20 left Iteration 1 Error: 0.556981 Iteration 2 Error: 0.092807 Iteration 3 Error: 0.009336 Align patch 6 19 left Iteration 1 Error: 1.234108 Iteration 2 Error: 0.318668 Iteration 3 Error: 0.099529 Iteration 4 Error: 0.036933 Align patch 7 18 left Iteration 1 Error: 1.998593 Iteration 2 Error: 0.379506 Iteration 3 Error: 0.159906 Iteration 4 Error: 0.052584 Iteration 5 Error: 0.032809 Align patch 8 17 left Iteration 1 Error: 0.925776 Iteration 2 Error: 0.114697 Iteration 3 Error: 0.041879 Align patch 9 16 left Iteration 1 Error: 0.535124 Iteration 2 Error: 0.070841 Iteration 3 Error: 0.020351 Align patch 10 15 left Iteration 1 Error: 0.701499 Iteration 2 Error: 0.118886 Iteration 3 Error: 0.021460 Align patch 11 14 left Iteration 1 Error: 0.864724 Iteration 2 Error: 0.186596 Iteration 3 Error: 0.062423 Iteration 4 Error: 0.022888 Align patch 12 13 left Iteration 1 Error: 0.724412 Iteration 2 Error: 0.155204 Iteration 3 Error: 0.055347 Iteration 4 Error: 0.020565 Align patch 13 12 left Iteration 1 Error: 0.703882 Iteration 2 Error: 0.160990 Iteration 3 Error: 0.044591 Align patch 14 11 left Iteration 1 Error: 0.597701 Iteration 2 Error: 0.108915 Iteration 3 Error: 0.031823 Align patch 15 10 left Iteration 1 Error: 1.033353 Iteration 2 Error: 0.154875 Iteration 3 Error: 0.024191 Align patch 16 9 left Iteration 1 Error: 1.048893 Iteration 2 Error: 0.152004 Iteration 3 Error: 0.026351 Align patch 17 8 left Iteration 1 Error: 0.666585 Iteration 2 Error: 0.082947 Iteration 3 Error: 0.028030 Align patch 18 7 left Iteration 1 Error: 0.578660 Iteration 2 Error: 0.149549 Iteration 3 Error: 0.033704 Align patch 19 6 left Iteration 1 Error: 0.559646 Iteration 2 Error: 0.102900 Iteration 3 Error: 0.017445 Align patch 20 5 left Iteration 1 Error: 0.774176 Iteration 2 Error: 0.172852 Iteration 3 Error: 0.040657 Align patch 21 4 left Iteration 1 Error: 1.043782 Iteration 2 Error: 0.112558 Iteration 3 Error: 0.025242 Align patch 22 3 left Iteration 1 Error: 1.173074 Iteration 2 Error: 0.104037 Iteration 3 Error: 0.021205 Align patch 23 2 left Iteration 1 Error: 0.999117 Iteration 2 Error: 0.234482 Iteration 3 Error: 0.077779 Iteration 4 Error: 0.026055 Align patch 24 1 left Iteration 1 Error: 0.882959 Iteration 2 Error: 0.140102 Iteration 3 Error: 0.027567 Align patch 25 0 left Iteration 1 Error: 0.779191 Iteration 2 Error: 0.185952 Iteration 3 Error: 0.037421 3D Fitting completed. Patch alignment time: 15.17(sec) Local motion has been corrected. Process thread exits. Computational time: 24.382099 sec Total time: 31.352194 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00017hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00017hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.526645s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00017hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.478593s ........................................ >>>>>>TIME<<<<<< FFT: 1.033440s Defocus_U Defocus_V Angle CCC 11278.23 11811.70 3.19 0.046139 Final Values Defocus_U Defocus_V Angle CCC 11323.54 11816.40 1.96 0.085121 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00017hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00017hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.002e-01 CC threshold: 0.736 Mean Std: 44.16 7.33 Num Hot pixels: 226 Hot pixel threshold: 88.12 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.821887 Iteration 2 Error: 0.092558 Iteration 3 Error: 0.016302 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.24 0.03 ...... Frame ( 3) shift: -0.48 0.06 ...... Frame ( 4) shift: -0.71 0.09 ...... Frame ( 5) shift: -0.95 0.12 ...... Frame ( 6) shift: -1.06 0.14 ...... Frame ( 7) shift: -1.02 0.16 ...... Frame ( 8) shift: -0.99 0.18 ...... Frame ( 9) shift: -0.98 0.21 ...... Frame ( 10) shift: -0.99 0.27 ...... Frame ( 11) shift: -1.00 0.32 ...... Frame ( 12) shift: -1.01 0.40 ...... Frame ( 13) shift: -1.03 0.50 ...... Frame ( 14) shift: -1.05 0.60 ...... Frame ( 15) shift: -1.08 0.63 ...... Frame ( 16) shift: -1.13 0.59 ...... Frame ( 17) shift: -1.18 0.55 ...... Frame ( 18) shift: -1.17 0.53 ...... Frame ( 19) shift: -1.09 0.54 ...... Frame ( 20) shift: -1.02 0.54 ...... Frame ( 21) shift: -0.98 0.58 ...... Frame ( 22) shift: -1.00 0.66 ...... Frame ( 23) shift: -1.01 0.74 ...... Frame ( 24) shift: -1.04 0.82 ...... Frame ( 25) shift: -1.08 0.88 ...... Frame ( 26) shift: -1.12 0.95 ...... Frame ( 27) shift: -1.12 0.99 ...... Frame ( 28) shift: -1.09 1.01 ...... Frame ( 29) shift: -1.06 1.03 ...... Frame ( 30) shift: -1.02 1.05 ...... Frame ( 31) shift: -0.98 1.06 ...... Frame ( 32) shift: -0.95 1.08 ...... Frame ( 33) shift: -0.91 1.09 ...... Frame ( 34) shift: -0.87 1.08 ...... Frame ( 35) shift: -0.84 1.08 ...... Frame ( 36) shift: -0.79 1.08 ...... Frame ( 37) shift: -0.74 1.08 ...... Frame ( 38) shift: -0.69 1.09 ...... Frame ( 39) shift: -0.64 1.09 ...... Frame ( 40) shift: -0.59 1.09 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.480668 Iteration 2 Error: 0.290664 Iteration 3 Error: 0.048963 Align patch 2 23 left Iteration 1 Error: 1.703981 Iteration 2 Error: 0.149420 Iteration 3 Error: 0.067190 Iteration 4 Error: 0.023089 Align patch 3 22 left Iteration 1 Error: 0.600064 Iteration 2 Error: 0.076660 Iteration 3 Error: 0.017801 Align patch 4 21 left Iteration 1 Error: 0.811950 Iteration 2 Error: 0.121396 Iteration 3 Error: 0.029833 Align patch 5 20 left Iteration 1 Error: 0.616052 Iteration 2 Error: 0.077262 Iteration 3 Error: 0.021487 Align patch 6 19 left Iteration 1 Error: 1.478486 Iteration 2 Error: 0.201817 Iteration 3 Error: 0.038347 Align patch 7 18 left Iteration 1 Error: 0.907814 Iteration 2 Error: 0.092632 Iteration 3 Error: 0.025062 Align patch 8 17 left Iteration 1 Error: 0.775224 Iteration 2 Error: 0.190935 Iteration 3 Error: 0.031528 Align patch 9 16 left Iteration 1 Error: 0.650414 Iteration 2 Error: 0.136082 Iteration 3 Error: 0.012940 Align patch 10 15 left Iteration 1 Error: 0.475756 Iteration 2 Error: 0.081048 Iteration 3 Error: 0.019823 Align patch 11 14 left Iteration 1 Error: 0.998153 Iteration 2 Error: 0.109102 Iteration 3 Error: 0.021165 Align patch 12 13 left Iteration 1 Error: 1.076997 Iteration 2 Error: 0.197471 Iteration 3 Error: 0.053770 Iteration 4 Error: 0.020374 Align patch 13 12 left Iteration 1 Error: 0.910681 Iteration 2 Error: 0.117643 Iteration 3 Error: 0.028989 Align patch 14 11 left Iteration 1 Error: 0.473637 Iteration 2 Error: 0.071581 Iteration 3 Error: 0.015701 Align patch 15 10 left Iteration 1 Error: 0.734941 Iteration 2 Error: 0.119305 Iteration 3 Error: 0.033501 Align patch 16 9 left Iteration 1 Error: 0.761457 Iteration 2 Error: 0.089446 Iteration 3 Error: 0.029318 Align patch 17 8 left Iteration 1 Error: 0.576079 Iteration 2 Error: 0.063173 Iteration 3 Error: 0.015220 Align patch 18 7 left Iteration 1 Error: 0.714776 Iteration 2 Error: 0.072475 Iteration 3 Error: 0.015957 Align patch 19 6 left Iteration 1 Error: 0.758012 Iteration 2 Error: 0.086327 Iteration 3 Error: 0.014291 Align patch 20 5 left Iteration 1 Error: 1.384989 Iteration 2 Error: 0.098404 Iteration 3 Error: 0.028978 Align patch 21 4 left Iteration 1 Error: 0.857729 Iteration 2 Error: 0.126570 Iteration 3 Error: 0.031091 Align patch 22 3 left Iteration 1 Error: 0.765432 Iteration 2 Error: 0.099558 Iteration 3 Error: 0.026022 Align patch 23 2 left Iteration 1 Error: 0.510568 Iteration 2 Error: 0.123281 Iteration 3 Error: 0.018891 Align patch 24 1 left Iteration 1 Error: 0.886159 Iteration 2 Error: 0.072057 Iteration 3 Error: 0.013539 Align patch 25 0 left Iteration 1 Error: 1.387531 Iteration 2 Error: 0.102930 Iteration 3 Error: 0.012753 3D Fitting completed. Patch alignment time: 15.44(sec) Local motion has been corrected. Process thread exits. Computational time: 24.494673 sec Total time: 32.543629 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00017hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00017hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.715731s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00017hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.520308s ........................................ >>>>>>TIME<<<<<< FFT: 1.022789s Defocus_U Defocus_V Angle CCC 11156.27 12031.27 5.49 0.052048 Final Values Defocus_U Defocus_V Angle CCC 11173.47 12042.21 5.17 0.094937 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00017hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00017hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 41.89 7.13 Num Hot pixels: 187 Hot pixel threshold: 84.70 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.381427 Iteration 2 Error: 0.292061 Iteration 3 Error: 0.066207 Iteration 4 Error: 0.020177 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.12 0.08 ...... Frame ( 3) shift: -0.24 0.17 ...... Frame ( 4) shift: -0.36 0.25 ...... Frame ( 5) shift: -0.48 0.33 ...... Frame ( 6) shift: -0.49 0.41 ...... Frame ( 7) shift: -0.40 0.48 ...... Frame ( 8) shift: -0.30 0.54 ...... Frame ( 9) shift: -0.20 0.64 ...... Frame ( 10) shift: -0.09 0.77 ...... Frame ( 11) shift: 0.02 0.90 ...... Frame ( 12) shift: 0.14 1.00 ...... Frame ( 13) shift: 0.28 1.06 ...... Frame ( 14) shift: 0.42 1.11 ...... Frame ( 15) shift: 0.49 1.15 ...... Frame ( 16) shift: 0.51 1.18 ...... Frame ( 17) shift: 0.52 1.20 ...... Frame ( 18) shift: 0.56 1.24 ...... Frame ( 19) shift: 0.64 1.31 ...... Frame ( 20) shift: 0.71 1.37 ...... Frame ( 21) shift: 0.79 1.43 ...... Frame ( 22) shift: 0.86 1.47 ...... Frame ( 23) shift: 0.94 1.51 ...... Frame ( 24) shift: 1.03 1.58 ...... Frame ( 25) shift: 1.14 1.70 ...... Frame ( 26) shift: 1.25 1.81 ...... Frame ( 27) shift: 1.30 1.89 ...... Frame ( 28) shift: 1.30 1.95 ...... Frame ( 29) shift: 1.29 2.00 ...... Frame ( 30) shift: 1.33 2.05 ...... Frame ( 31) shift: 1.42 2.10 ...... Frame ( 32) shift: 1.50 2.14 ...... Frame ( 33) shift: 1.56 2.18 ...... Frame ( 34) shift: 1.60 2.20 ...... Frame ( 35) shift: 1.63 2.22 ...... Frame ( 36) shift: 1.68 2.24 ...... Frame ( 37) shift: 1.75 2.26 ...... Frame ( 38) shift: 1.81 2.28 ...... Frame ( 39) shift: 1.87 2.29 ...... Frame ( 40) shift: 1.93 2.31 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.575784 Iteration 2 Error: 0.154119 Iteration 3 Error: 0.062316 Iteration 4 Error: 0.024014 Align patch 2 23 left Iteration 1 Error: 1.500471 Iteration 2 Error: 0.157003 Iteration 3 Error: 0.038003 Align patch 3 22 left Iteration 1 Error: 0.935422 Iteration 2 Error: 0.174171 Iteration 3 Error: 0.041462 Align patch 4 21 left Iteration 1 Error: 1.062514 Iteration 2 Error: 0.159984 Iteration 3 Error: 0.049002 Align patch 5 20 left Iteration 1 Error: 0.737529 Iteration 2 Error: 0.145126 Iteration 3 Error: 0.064447 Iteration 4 Error: 0.025902 Align patch 6 19 left Iteration 1 Error: 1.916686 Iteration 2 Error: 0.261471 Iteration 3 Error: 0.119633 Iteration 4 Error: 0.048843 Align patch 7 18 left Iteration 1 Error: 2.298908 Iteration 2 Error: 0.350910 Iteration 3 Error: 0.134298 Iteration 4 Error: 0.044375 Align patch 8 17 left Iteration 1 Error: 0.970221 Iteration 2 Error: 0.190807 Iteration 3 Error: 0.053297 Iteration 4 Error: 0.025897 Align patch 9 16 left Iteration 1 Error: 0.934883 Iteration 2 Error: 0.215204 Iteration 3 Error: 0.045468 Align patch 10 15 left Iteration 1 Error: 0.985600 Iteration 2 Error: 0.107078 Iteration 3 Error: 0.019235 Align patch 11 14 left Iteration 1 Error: 1.536787 Iteration 2 Error: 0.251142 Iteration 3 Error: 0.064198 Iteration 4 Error: 0.025950 Align patch 12 13 left Iteration 1 Error: 1.277134 Iteration 2 Error: 0.173660 Iteration 3 Error: 0.029964 Align patch 13 12 left Iteration 1 Error: 0.696536 Iteration 2 Error: 0.127648 Iteration 3 Error: 0.027214 Align patch 14 11 left Iteration 1 Error: 1.027991 Iteration 2 Error: 0.182147 Iteration 3 Error: 0.045559 Align patch 15 10 left Iteration 1 Error: 1.627951 Iteration 2 Error: 0.141400 Iteration 3 Error: 0.020753 Align patch 16 9 left Iteration 1 Error: 0.420170 Iteration 2 Error: 0.094429 Iteration 3 Error: 0.027811 Align patch 17 8 left Iteration 1 Error: 0.703181 Iteration 2 Error: 0.116018 Iteration 3 Error: 0.025883 Align patch 18 7 left Iteration 1 Error: 0.847595 Iteration 2 Error: 0.143171 Iteration 3 Error: 0.041639 Align patch 19 6 left Iteration 1 Error: 0.842154 Iteration 2 Error: 0.204804 Iteration 3 Error: 0.058539 Iteration 4 Error: 0.016052 Align patch 20 5 left Iteration 1 Error: 1.152463 Iteration 2 Error: 0.256925 Iteration 3 Error: 0.061983 Iteration 4 Error: 0.018846 Align patch 21 4 left Iteration 1 Error: 0.711990 Iteration 2 Error: 0.117548 Iteration 3 Error: 0.030179 Align patch 22 3 left Iteration 1 Error: 1.006328 Iteration 2 Error: 0.124757 Iteration 3 Error: 0.025041 Align patch 23 2 left Iteration 1 Error: 0.699977 Iteration 2 Error: 0.173798 Iteration 3 Error: 0.068765 Iteration 4 Error: 0.026213 Align patch 24 1 left Iteration 1 Error: 1.027015 Iteration 2 Error: 0.145805 Iteration 3 Error: 0.047752 Align patch 25 0 left Iteration 1 Error: 1.786256 Iteration 2 Error: 0.290203 Iteration 3 Error: 0.056212 Iteration 4 Error: 0.021471 3D Fitting completed. Patch alignment time: 16.19(sec) Local motion has been corrected. Process thread exits. Computational time: 26.192701 sec Total time: 31.925158 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00017hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00017hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.550550s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00017hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.427019s ........................................ >>>>>>TIME<<<<<< FFT: 0.931740s Defocus_U Defocus_V Angle CCC 12665.68 12010.10 84.19 0.064541 Final Values Defocus_U Defocus_V Angle CCC 12670.37 12024.18 84.19 0.110374 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00018hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00018hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.350e-01 1.004e-01 CC threshold: 0.738 Mean Std: 44.56 7.61 Num Hot pixels: 204 Hot pixel threshold: 90.21 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.071364 Iteration 2 Error: 0.104768 Iteration 3 Error: 0.015620 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.21 0.01 ...... Frame ( 3) shift: -0.41 0.01 ...... Frame ( 4) shift: -0.62 0.02 ...... Frame ( 5) shift: -0.82 0.02 ...... Frame ( 6) shift: -0.91 0.06 ...... Frame ( 7) shift: -0.86 0.13 ...... Frame ( 8) shift: -0.82 0.20 ...... Frame ( 9) shift: -0.77 0.30 ...... Frame ( 10) shift: -0.71 0.45 ...... Frame ( 11) shift: -0.66 0.59 ...... Frame ( 12) shift: -0.59 0.73 ...... Frame ( 13) shift: -0.51 0.86 ...... Frame ( 14) shift: -0.43 0.99 ...... Frame ( 15) shift: -0.36 1.08 ...... Frame ( 16) shift: -0.30 1.15 ...... Frame ( 17) shift: -0.23 1.21 ...... Frame ( 18) shift: -0.20 1.27 ...... Frame ( 19) shift: -0.19 1.32 ...... Frame ( 20) shift: -0.19 1.37 ...... Frame ( 21) shift: -0.19 1.41 ...... Frame ( 22) shift: -0.19 1.44 ...... Frame ( 23) shift: -0.20 1.48 ...... Frame ( 24) shift: -0.22 1.48 ...... Frame ( 25) shift: -0.25 1.46 ...... Frame ( 26) shift: -0.29 1.44 ...... Frame ( 27) shift: -0.34 1.46 ...... Frame ( 28) shift: -0.39 1.52 ...... Frame ( 29) shift: -0.44 1.57 ...... Frame ( 30) shift: -0.46 1.57 ...... Frame ( 31) shift: -0.44 1.51 ...... Frame ( 32) shift: -0.42 1.45 ...... Frame ( 33) shift: -0.43 1.44 ...... Frame ( 34) shift: -0.47 1.47 ...... Frame ( 35) shift: -0.51 1.50 ...... Frame ( 36) shift: -0.56 1.56 ...... Frame ( 37) shift: -0.62 1.65 ...... Frame ( 38) shift: -0.67 1.74 ...... Frame ( 39) shift: -0.73 1.83 ...... Frame ( 40) shift: -0.79 1.91 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.141094 Iteration 2 Error: 0.219378 Iteration 3 Error: 0.161634 Iteration 4 Error: 0.057660 Iteration 5 Error: 0.040501 Align patch 2 23 left Iteration 1 Error: 1.418837 Iteration 2 Error: 0.132012 Iteration 3 Error: 0.051127 Iteration 4 Error: 0.022167 Align patch 3 22 left Iteration 1 Error: 0.843963 Iteration 2 Error: 0.126741 Iteration 3 Error: 0.032347 Align patch 4 21 left Iteration 1 Error: 0.394595 Iteration 2 Error: 0.027213 Align patch 5 20 left Iteration 1 Error: 0.455504 Iteration 2 Error: 0.073191 Iteration 3 Error: 0.007869 Align patch 6 19 left Iteration 1 Error: 0.827571 Iteration 2 Error: 0.183740 Iteration 3 Error: 0.042974 Align patch 7 18 left Iteration 1 Error: 0.805923 Iteration 2 Error: 0.200276 Iteration 3 Error: 0.045652 Align patch 8 17 left Iteration 1 Error: 0.805531 Iteration 2 Error: 0.123139 Iteration 3 Error: 0.036374 Align patch 9 16 left Iteration 1 Error: 0.580953 Iteration 2 Error: 0.074776 Iteration 3 Error: 0.011332 Align patch 10 15 left Iteration 1 Error: 0.677351 Iteration 2 Error: 0.058748 Iteration 3 Error: 0.008993 Align patch 11 14 left Iteration 1 Error: 1.154022 Iteration 2 Error: 0.160279 Iteration 3 Error: 0.046890 Align patch 12 13 left Iteration 1 Error: 0.571530 Iteration 2 Error: 0.103873 Iteration 3 Error: 0.017092 Align patch 13 12 left Iteration 1 Error: 0.540415 Iteration 2 Error: 0.071639 Iteration 3 Error: 0.012738 Align patch 14 11 left Iteration 1 Error: 0.351064 Iteration 2 Error: 0.039473 Align patch 15 10 left Iteration 1 Error: 0.514520 Iteration 2 Error: 0.034102 Align patch 16 9 left Iteration 1 Error: 0.609255 Iteration 2 Error: 0.103195 Iteration 3 Error: 0.018394 Align patch 17 8 left Iteration 1 Error: 0.931015 Iteration 2 Error: 0.092016 Iteration 3 Error: 0.016506 Align patch 18 7 left Iteration 1 Error: 0.618889 Iteration 2 Error: 0.054649 Iteration 3 Error: 0.012314 Align patch 19 6 left Iteration 1 Error: 0.579020 Iteration 2 Error: 0.062321 Iteration 3 Error: 0.012798 Align patch 20 5 left Iteration 1 Error: 0.325019 Iteration 2 Error: 0.041644 Align patch 21 4 left Iteration 1 Error: 1.125818 Iteration 2 Error: 0.191376 Iteration 3 Error: 0.061100 Iteration 4 Error: 0.021899 Align patch 22 3 left Iteration 1 Error: 1.216554 Iteration 2 Error: 0.196639 Iteration 3 Error: 0.031736 Align patch 23 2 left Iteration 1 Error: 0.539806 Iteration 2 Error: 0.058188 Iteration 3 Error: 0.011187 Align patch 24 1 left Iteration 1 Error: 0.774322 Iteration 2 Error: 0.124888 Iteration 3 Error: 0.025825 Align patch 25 0 left Iteration 1 Error: 1.020284 Iteration 2 Error: 0.093983 Iteration 3 Error: 0.015148 3D Fitting completed. Patch alignment time: 15.31(sec) Local motion has been corrected. Process thread exits. Computational time: 24.299482 sec Total time: 30.158159 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00018hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00018hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.761165s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00018hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.510047s ........................................ >>>>>>TIME<<<<<< FFT: 0.956422s Defocus_U Defocus_V Angle CCC 10806.66 11572.29 13.83 0.065791 Final Values Defocus_U Defocus_V Angle CCC 10819.17 11584.80 13.52 0.116991 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00018hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00018hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.353e-01 1.006e-01 CC threshold: 0.739 Mean Std: 42.77 7.49 Num Hot pixels: 191 Hot pixel threshold: 87.69 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.141627 Iteration 2 Error: 0.128436 Iteration 3 Error: 0.024793 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.30 0.15 ...... Frame ( 3) shift: -0.60 0.29 ...... Frame ( 4) shift: -0.90 0.44 ...... Frame ( 5) shift: -1.20 0.58 ...... Frame ( 6) shift: -1.35 0.66 ...... Frame ( 7) shift: -1.34 0.66 ...... Frame ( 8) shift: -1.34 0.67 ...... Frame ( 9) shift: -1.34 0.66 ...... Frame ( 10) shift: -1.35 0.65 ...... Frame ( 11) shift: -1.36 0.64 ...... Frame ( 12) shift: -1.37 0.65 ...... Frame ( 13) shift: -1.37 0.68 ...... Frame ( 14) shift: -1.36 0.71 ...... Frame ( 15) shift: -1.38 0.77 ...... Frame ( 16) shift: -1.41 0.84 ...... Frame ( 17) shift: -1.44 0.92 ...... Frame ( 18) shift: -1.43 0.99 ...... Frame ( 19) shift: -1.38 1.06 ...... Frame ( 20) shift: -1.33 1.13 ...... Frame ( 21) shift: -1.30 1.17 ...... Frame ( 22) shift: -1.29 1.19 ...... Frame ( 23) shift: -1.27 1.22 ...... Frame ( 24) shift: -1.27 1.24 ...... Frame ( 25) shift: -1.28 1.28 ...... Frame ( 26) shift: -1.29 1.31 ...... Frame ( 27) shift: -1.30 1.36 ...... Frame ( 28) shift: -1.31 1.43 ...... Frame ( 29) shift: -1.32 1.50 ...... Frame ( 30) shift: -1.34 1.56 ...... Frame ( 31) shift: -1.36 1.61 ...... Frame ( 32) shift: -1.38 1.66 ...... Frame ( 33) shift: -1.37 1.70 ...... Frame ( 34) shift: -1.35 1.73 ...... Frame ( 35) shift: -1.32 1.76 ...... Frame ( 36) shift: -1.33 1.78 ...... Frame ( 37) shift: -1.37 1.81 ...... Frame ( 38) shift: -1.40 1.84 ...... Frame ( 39) shift: -1.44 1.86 ...... Frame ( 40) shift: -1.48 1.89 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.502039 Iteration 2 Error: 0.182965 Iteration 3 Error: 0.033438 Align patch 2 23 left Iteration 1 Error: 1.204654 Iteration 2 Error: 0.195243 Iteration 3 Error: 0.043162 Align patch 3 22 left Iteration 1 Error: 0.372373 Iteration 2 Error: 0.052646 Iteration 3 Error: 0.014495 Align patch 4 21 left Iteration 1 Error: 0.305996 Iteration 2 Error: 0.039714 Align patch 5 20 left Iteration 1 Error: 0.984947 Iteration 2 Error: 0.181018 Iteration 3 Error: 0.031791 Align patch 6 19 left Iteration 1 Error: 0.660301 Iteration 2 Error: 0.062823 Iteration 3 Error: 0.014335 Align patch 7 18 left Iteration 1 Error: 0.836703 Iteration 2 Error: 0.133142 Iteration 3 Error: 0.034696 Align patch 8 17 left Iteration 1 Error: 0.515076 Iteration 2 Error: 0.099861 Iteration 3 Error: 0.019066 Align patch 9 16 left Iteration 1 Error: 0.295893 Iteration 2 Error: 0.032597 Align patch 10 15 left Iteration 1 Error: 0.656454 Iteration 2 Error: 0.077290 Iteration 3 Error: 0.011534 Align patch 11 14 left Iteration 1 Error: 1.605918 Iteration 2 Error: 0.141210 Iteration 3 Error: 0.052894 Iteration 4 Error: 0.015291 Align patch 12 13 left Iteration 1 Error: 1.166951 Iteration 2 Error: 0.173430 Iteration 3 Error: 0.032301 Align patch 13 12 left Iteration 1 Error: 0.737034 Iteration 2 Error: 0.093657 Iteration 3 Error: 0.021775 Align patch 14 11 left Iteration 1 Error: 0.572508 Iteration 2 Error: 0.091293 Iteration 3 Error: 0.022211 Align patch 15 10 left Iteration 1 Error: 0.521725 Iteration 2 Error: 0.077940 Iteration 3 Error: 0.018093 Align patch 16 9 left Iteration 1 Error: 0.886690 Iteration 2 Error: 0.124969 Iteration 3 Error: 0.023926 Align patch 17 8 left Iteration 1 Error: 0.736235 Iteration 2 Error: 0.101665 Iteration 3 Error: 0.022856 Align patch 18 7 left Iteration 1 Error: 0.886773 Iteration 2 Error: 0.100298 Iteration 3 Error: 0.019521 Align patch 19 6 left Iteration 1 Error: 0.622341 Iteration 2 Error: 0.137316 Iteration 3 Error: 0.024669 Align patch 20 5 left Iteration 1 Error: 0.516673 Iteration 2 Error: 0.048551 Align patch 21 4 left Iteration 1 Error: 0.721704 Iteration 2 Error: 0.059295 Iteration 3 Error: 0.031052 Align patch 22 3 left Iteration 1 Error: 0.761262 Iteration 2 Error: 0.109893 Iteration 3 Error: 0.023022 Align patch 23 2 left Iteration 1 Error: 0.993951 Iteration 2 Error: 0.204161 Iteration 3 Error: 0.058468 Iteration 4 Error: 0.015377 Align patch 24 1 left Iteration 1 Error: 0.924446 Iteration 2 Error: 0.103442 Iteration 3 Error: 0.019654 Align patch 25 0 left Iteration 1 Error: 0.839441 Iteration 2 Error: 0.088886 Iteration 3 Error: 0.011774 3D Fitting completed. Patch alignment time: 15.29(sec) Local motion has been corrected. Process thread exits. Computational time: 23.654966 sec Total time: 29.400957 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00018hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00018hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.733387s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00018hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.622088s ........................................ >>>>>>TIME<<<<<< FFT: 1.259983s Defocus_U Defocus_V Angle CCC 7687.51 8132.82 0.36 0.045606 Final Values Defocus_U Defocus_V Angle CCC 7690.63 8139.07 0.04 0.097097 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00018hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00018hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.003e-01 CC threshold: 0.736 Mean Std: 45.42 7.61 Num Hot pixels: 220 Hot pixel threshold: 91.07 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.387978 Iteration 2 Error: 0.116804 Iteration 3 Error: 0.018990 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.36 0.03 ...... Frame ( 3) shift: -0.73 0.06 ...... Frame ( 4) shift: -1.09 0.08 ...... Frame ( 5) shift: -1.46 0.11 ...... Frame ( 6) shift: -1.64 0.15 ...... Frame ( 7) shift: -1.65 0.19 ...... Frame ( 8) shift: -1.66 0.24 ...... Frame ( 9) shift: -1.64 0.33 ...... Frame ( 10) shift: -1.59 0.48 ...... Frame ( 11) shift: -1.55 0.63 ...... Frame ( 12) shift: -1.53 0.72 ...... Frame ( 13) shift: -1.54 0.77 ...... Frame ( 14) shift: -1.56 0.81 ...... Frame ( 15) shift: -1.58 0.87 ...... Frame ( 16) shift: -1.61 0.94 ...... Frame ( 17) shift: -1.63 1.01 ...... Frame ( 18) shift: -1.62 1.09 ...... Frame ( 19) shift: -1.57 1.16 ...... Frame ( 20) shift: -1.52 1.24 ...... Frame ( 21) shift: -1.49 1.30 ...... Frame ( 22) shift: -1.49 1.33 ...... Frame ( 23) shift: -1.49 1.37 ...... Frame ( 24) shift: -1.50 1.40 ...... Frame ( 25) shift: -1.52 1.41 ...... Frame ( 26) shift: -1.54 1.42 ...... Frame ( 27) shift: -1.57 1.41 ...... Frame ( 28) shift: -1.59 1.38 ...... Frame ( 29) shift: -1.62 1.35 ...... Frame ( 30) shift: -1.64 1.37 ...... Frame ( 31) shift: -1.65 1.44 ...... Frame ( 32) shift: -1.66 1.50 ...... Frame ( 33) shift: -1.69 1.58 ...... Frame ( 34) shift: -1.74 1.66 ...... Frame ( 35) shift: -1.79 1.74 ...... Frame ( 36) shift: -1.82 1.75 ...... Frame ( 37) shift: -1.84 1.71 ...... Frame ( 38) shift: -1.86 1.66 ...... Frame ( 39) shift: -1.87 1.61 ...... Frame ( 40) shift: -1.89 1.56 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 3.099274 Iteration 2 Error: 0.320769 Iteration 3 Error: 0.165541 Iteration 4 Error: 0.036294 Align patch 2 23 left Iteration 1 Error: 3.094062 Iteration 2 Error: 0.138223 Iteration 3 Error: 0.027442 Align patch 3 22 left Iteration 1 Error: 1.818713 Iteration 2 Error: 0.160669 Iteration 3 Error: 0.015978 Align patch 4 21 left Iteration 1 Error: 0.749591 Iteration 2 Error: 0.087313 Iteration 3 Error: 0.019983 Align patch 5 20 left Iteration 1 Error: 0.854268 Iteration 2 Error: 0.214496 Iteration 3 Error: 0.058874 Iteration 4 Error: 0.014724 Align patch 6 19 left Iteration 1 Error: 1.386557 Iteration 2 Error: 0.136202 Iteration 3 Error: 0.039848 Align patch 7 18 left Iteration 1 Error: 1.950673 Iteration 2 Error: 0.219688 Iteration 3 Error: 0.047885 Align patch 8 17 left Iteration 1 Error: 3.000611 Iteration 2 Error: 0.252225 Iteration 3 Error: 0.055431 Iteration 4 Error: 0.013047 Align patch 9 16 left Iteration 1 Error: 0.455784 Iteration 2 Error: 0.068555 Iteration 3 Error: 0.014280 Align patch 10 15 left Iteration 1 Error: 0.425169 Iteration 2 Error: 0.082903 Iteration 3 Error: 0.014969 Align patch 11 14 left Iteration 1 Error: 1.780662 Iteration 2 Error: 0.241197 Iteration 3 Error: 0.031058 Align patch 12 13 left Iteration 1 Error: 0.533183 Iteration 2 Error: 0.094092 Iteration 3 Error: 0.022983 Align patch 13 12 left Iteration 1 Error: 0.718784 Iteration 2 Error: 0.081173 Iteration 3 Error: 0.015916 Align patch 14 11 left Iteration 1 Error: 0.520006 Iteration 2 Error: 0.058597 Iteration 3 Error: 0.009704 Align patch 15 10 left Iteration 1 Error: 0.643993 Iteration 2 Error: 0.073477 Iteration 3 Error: 0.019860 Align patch 16 9 left Iteration 1 Error: 0.754887 Iteration 2 Error: 0.150157 Iteration 3 Error: 0.035174 Align patch 17 8 left Iteration 1 Error: 0.718193 Iteration 2 Error: 0.094457 Iteration 3 Error: 0.019267 Align patch 18 7 left Iteration 1 Error: 0.813990 Iteration 2 Error: 0.088789 Iteration 3 Error: 0.016473 Align patch 19 6 left Iteration 1 Error: 0.576734 Iteration 2 Error: 0.093736 Iteration 3 Error: 0.019129 Align patch 20 5 left Iteration 1 Error: 0.592698 Iteration 2 Error: 0.088444 Iteration 3 Error: 0.015470 Align patch 21 4 left Iteration 1 Error: 1.001944 Iteration 2 Error: 0.151900 Iteration 3 Error: 0.044439 Align patch 22 3 left Iteration 1 Error: 0.914519 Iteration 2 Error: 0.123586 Iteration 3 Error: 0.030025 Align patch 23 2 left Iteration 1 Error: 1.140519 Iteration 2 Error: 0.177222 Iteration 3 Error: 0.024491 Align patch 24 1 left Iteration 1 Error: 0.799130 Iteration 2 Error: 0.088656 Iteration 3 Error: 0.019096 Align patch 25 0 left Iteration 1 Error: 1.044725 Iteration 2 Error: 0.094305 Iteration 3 Error: 0.016518 3D Fitting completed. Patch alignment time: 15.78(sec) Local motion has been corrected. Process thread exits. Computational time: 24.197315 sec Total time: 31.051912 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00018hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00018hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.568855s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00018hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.405606s ........................................ >>>>>>TIME<<<<<< FFT: 0.963183s Defocus_U Defocus_V Angle CCC 11544.92 12357.42 6.47 0.057509 Final Values Defocus_U Defocus_V Angle CCC 11563.70 12366.83 7.10 0.101431 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00018hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00018hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.350e-01 1.004e-01 CC threshold: 0.737 Mean Std: 45.41 7.55 Num Hot pixels: 211 Hot pixel threshold: 90.70 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.186766 Iteration 2 Error: 0.095875 Iteration 3 Error: 0.016700 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.32 -0.00 ...... Frame ( 3) shift: -0.64 -0.01 ...... Frame ( 4) shift: -0.97 -0.01 ...... Frame ( 5) shift: -1.29 -0.01 ...... Frame ( 6) shift: -1.45 -0.01 ...... Frame ( 7) shift: -1.44 0.00 ...... Frame ( 8) shift: -1.43 0.02 ...... Frame ( 9) shift: -1.42 0.04 ...... Frame ( 10) shift: -1.39 0.08 ...... Frame ( 11) shift: -1.37 0.11 ...... Frame ( 12) shift: -1.37 0.14 ...... Frame ( 13) shift: -1.42 0.16 ...... Frame ( 14) shift: -1.46 0.18 ...... Frame ( 15) shift: -1.53 0.20 ...... Frame ( 16) shift: -1.63 0.21 ...... Frame ( 17) shift: -1.72 0.23 ...... Frame ( 18) shift: -1.76 0.23 ...... Frame ( 19) shift: -1.74 0.22 ...... Frame ( 20) shift: -1.71 0.21 ...... Frame ( 21) shift: -1.71 0.23 ...... Frame ( 22) shift: -1.72 0.28 ...... Frame ( 23) shift: -1.73 0.33 ...... Frame ( 24) shift: -1.74 0.39 ...... Frame ( 25) shift: -1.77 0.45 ...... Frame ( 26) shift: -1.79 0.52 ...... Frame ( 27) shift: -1.80 0.55 ...... Frame ( 28) shift: -1.79 0.54 ...... Frame ( 29) shift: -1.79 0.54 ...... Frame ( 30) shift: -1.81 0.55 ...... Frame ( 31) shift: -1.85 0.57 ...... Frame ( 32) shift: -1.90 0.58 ...... Frame ( 33) shift: -1.93 0.62 ...... Frame ( 34) shift: -1.96 0.67 ...... Frame ( 35) shift: -1.99 0.72 ...... Frame ( 36) shift: -2.01 0.76 ...... Frame ( 37) shift: -2.01 0.78 ...... Frame ( 38) shift: -2.01 0.79 ...... Frame ( 39) shift: -2.02 0.81 ...... Frame ( 40) shift: -2.02 0.83 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 3.744998 Iteration 2 Error: 0.422606 Iteration 3 Error: 0.128092 Iteration 4 Error: 0.022874 Align patch 2 23 left Iteration 1 Error: 1.666897 Iteration 2 Error: 0.194880 Iteration 3 Error: 0.081404 Iteration 4 Error: 0.022483 Align patch 3 22 left Iteration 1 Error: 0.934817 Iteration 2 Error: 0.117500 Iteration 3 Error: 0.024742 Align patch 4 21 left Iteration 1 Error: 0.592392 Iteration 2 Error: 0.045282 Align patch 5 20 left Iteration 1 Error: 0.866868 Iteration 2 Error: 0.099640 Iteration 3 Error: 0.018148 Align patch 6 19 left Iteration 1 Error: 2.048984 Iteration 2 Error: 0.250673 Iteration 3 Error: 0.109558 Iteration 4 Error: 0.020512 Align patch 7 18 left Iteration 1 Error: 1.405091 Iteration 2 Error: 0.177467 Iteration 3 Error: 0.039745 Align patch 8 17 left Iteration 1 Error: 0.592673 Iteration 2 Error: 0.079653 Iteration 3 Error: 0.024115 Align patch 9 16 left Iteration 1 Error: 0.666621 Iteration 2 Error: 0.090609 Iteration 3 Error: 0.011182 Align patch 10 15 left Iteration 1 Error: 0.682196 Iteration 2 Error: 0.060403 Iteration 3 Error: 0.009653 Align patch 11 14 left Iteration 1 Error: 0.982924 Iteration 2 Error: 0.303967 Iteration 3 Error: 0.080851 Iteration 4 Error: 0.030797 Align patch 12 13 left Iteration 1 Error: 0.849322 Iteration 2 Error: 0.162033 Iteration 3 Error: 0.040756 Align patch 13 12 left Iteration 1 Error: 0.478001 Iteration 2 Error: 0.097839 Iteration 3 Error: 0.031628 Align patch 14 11 left Iteration 1 Error: 0.350888 Iteration 2 Error: 0.041487 Align patch 15 10 left Iteration 1 Error: 0.519816 Iteration 2 Error: 0.053986 Iteration 3 Error: 0.017034 Align patch 16 9 left Iteration 1 Error: 0.655768 Iteration 2 Error: 0.087050 Iteration 3 Error: 0.022687 Align patch 17 8 left Iteration 1 Error: 0.616184 Iteration 2 Error: 0.064212 Iteration 3 Error: 0.020058 Align patch 18 7 left Iteration 1 Error: 1.209210 Iteration 2 Error: 0.104305 Iteration 3 Error: 0.018016 Align patch 19 6 left Iteration 1 Error: 0.882920 Iteration 2 Error: 0.157355 Iteration 3 Error: 0.026152 Align patch 20 5 left Iteration 1 Error: 0.812369 Iteration 2 Error: 0.082048 Iteration 3 Error: 0.016794 Align patch 21 4 left Iteration 1 Error: 1.741025 Iteration 2 Error: 0.153283 Iteration 3 Error: 0.016293 Align patch 22 3 left Iteration 1 Error: 1.155309 Iteration 2 Error: 0.113269 Iteration 3 Error: 0.019585 Align patch 23 2 left Iteration 1 Error: 1.128244 Iteration 2 Error: 0.102570 Iteration 3 Error: 0.018091 Align patch 24 1 left Iteration 1 Error: 1.309431 Iteration 2 Error: 0.234204 Iteration 3 Error: 0.040052 Align patch 25 0 left Iteration 1 Error: 0.753854 Iteration 2 Error: 0.109583 Iteration 3 Error: 0.018308 3D Fitting completed. Patch alignment time: 15.54(sec) Local motion has been corrected. Process thread exits. Computational time: 24.594740 sec Total time: 30.764017 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00018hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00018hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.797314s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00018hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.306407s ........................................ >>>>>>TIME<<<<<< FFT: 0.982253s Defocus_U Defocus_V Angle CCC 13765.63 13207.03 81.99 0.069537 Final Values Defocus_U Defocus_V Angle CCC 13770.32 13214.84 82.30 0.117837 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00019hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00019hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.352e-01 1.005e-01 CC threshold: 0.738 Mean Std: 43.24 7.58 Num Hot pixels: 183 Hot pixel threshold: 88.70 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.337955 Iteration 2 Error: 0.126980 Iteration 3 Error: 0.026349 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.31 0.11 ...... Frame ( 3) shift: -0.61 0.22 ...... Frame ( 4) shift: -0.92 0.32 ...... Frame ( 5) shift: -1.23 0.43 ...... Frame ( 6) shift: -1.40 0.46 ...... Frame ( 7) shift: -1.44 0.42 ...... Frame ( 8) shift: -1.48 0.38 ...... Frame ( 9) shift: -1.51 0.36 ...... Frame ( 10) shift: -1.52 0.34 ...... Frame ( 11) shift: -1.54 0.33 ...... Frame ( 12) shift: -1.55 0.32 ...... Frame ( 13) shift: -1.58 0.31 ...... Frame ( 14) shift: -1.60 0.31 ...... Frame ( 15) shift: -1.64 0.33 ...... Frame ( 16) shift: -1.68 0.37 ...... Frame ( 17) shift: -1.72 0.42 ...... Frame ( 18) shift: -1.74 0.48 ...... Frame ( 19) shift: -1.75 0.55 ...... Frame ( 20) shift: -1.76 0.63 ...... Frame ( 21) shift: -1.78 0.68 ...... Frame ( 22) shift: -1.82 0.72 ...... Frame ( 23) shift: -1.87 0.75 ...... Frame ( 24) shift: -1.89 0.78 ...... Frame ( 25) shift: -1.89 0.82 ...... Frame ( 26) shift: -1.88 0.85 ...... Frame ( 27) shift: -1.89 0.90 ...... Frame ( 28) shift: -1.91 0.98 ...... Frame ( 29) shift: -1.92 1.06 ...... Frame ( 30) shift: -1.94 1.14 ...... Frame ( 31) shift: -1.95 1.21 ...... Frame ( 32) shift: -1.96 1.29 ...... Frame ( 33) shift: -1.97 1.37 ...... Frame ( 34) shift: -1.99 1.45 ...... Frame ( 35) shift: -2.00 1.53 ...... Frame ( 36) shift: -2.03 1.58 ...... Frame ( 37) shift: -2.06 1.60 ...... Frame ( 38) shift: -2.09 1.62 ...... Frame ( 39) shift: -2.13 1.64 ...... Frame ( 40) shift: -2.16 1.66 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.178138 Iteration 2 Error: 0.231872 Iteration 3 Error: 0.063881 Iteration 4 Error: 0.022174 Align patch 2 23 left Iteration 1 Error: 1.027200 Iteration 2 Error: 0.166940 Iteration 3 Error: 0.032412 Align patch 3 22 left Iteration 1 Error: 0.591912 Iteration 2 Error: 0.090988 Iteration 3 Error: 0.023581 Align patch 4 21 left Iteration 1 Error: 0.896198 Iteration 2 Error: 0.077578 Iteration 3 Error: 0.018202 Align patch 5 20 left Iteration 1 Error: 1.018754 Iteration 2 Error: 0.115335 Iteration 3 Error: 0.021955 Align patch 6 19 left Iteration 1 Error: 0.779083 Iteration 2 Error: 0.163738 Iteration 3 Error: 0.051632 Iteration 4 Error: 0.024522 Align patch 7 18 left Iteration 1 Error: 0.658923 Iteration 2 Error: 0.076204 Iteration 3 Error: 0.023815 Align patch 8 17 left Iteration 1 Error: 0.439945 Iteration 2 Error: 0.047010 Align patch 9 16 left Iteration 1 Error: 0.541346 Iteration 2 Error: 0.064093 Iteration 3 Error: 0.017869 Align patch 10 15 left Iteration 1 Error: 0.436527 Iteration 2 Error: 0.056067 Iteration 3 Error: 0.010092 Align patch 11 14 left Iteration 1 Error: 0.770834 Iteration 2 Error: 0.163203 Iteration 3 Error: 0.041899 Align patch 12 13 left Iteration 1 Error: 0.721976 Iteration 2 Error: 0.123661 Iteration 3 Error: 0.038139 Align patch 13 12 left Iteration 1 Error: 0.614989 Iteration 2 Error: 0.076815 Iteration 3 Error: 0.011527 Align patch 14 11 left Iteration 1 Error: 0.645507 Iteration 2 Error: 0.087867 Iteration 3 Error: 0.021654 Align patch 15 10 left Iteration 1 Error: 0.415554 Iteration 2 Error: 0.057787 Iteration 3 Error: 0.015070 Align patch 16 9 left Iteration 1 Error: 0.902763 Iteration 2 Error: 0.150367 Iteration 3 Error: 0.036359 Align patch 17 8 left Iteration 1 Error: 0.815879 Iteration 2 Error: 0.126850 Iteration 3 Error: 0.027298 Align patch 18 7 left Iteration 1 Error: 0.977113 Iteration 2 Error: 0.088256 Iteration 3 Error: 0.019904 Align patch 19 6 left Iteration 1 Error: 0.746124 Iteration 2 Error: 0.084492 Iteration 3 Error: 0.014043 Align patch 20 5 left Iteration 1 Error: 0.604761 Iteration 2 Error: 0.085602 Iteration 3 Error: 0.013018 Align patch 21 4 left Iteration 1 Error: 1.006902 Iteration 2 Error: 0.155507 Iteration 3 Error: 0.044911 Align patch 22 3 left Iteration 1 Error: 1.094115 Iteration 2 Error: 0.187873 Iteration 3 Error: 0.053898 Iteration 4 Error: 0.026480 Align patch 23 2 left Iteration 1 Error: 0.802826 Iteration 2 Error: 0.071466 Iteration 3 Error: 0.016944 Align patch 24 1 left Iteration 1 Error: 0.493097 Iteration 2 Error: 0.042546 Align patch 25 0 left Iteration 1 Error: 0.455826 Iteration 2 Error: 0.067205 Iteration 3 Error: 0.008873 3D Fitting completed. Patch alignment time: 15.61(sec) Local motion has been corrected. Process thread exits. Computational time: 24.531115 sec Total time: 30.673265 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00019hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00019hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.752893s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00019hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.393068s ........................................ >>>>>>TIME<<<<<< FFT: 1.064423s Defocus_U Defocus_V Angle CCC 10464.83 11253.95 12.17 0.068782 Final Values Defocus_U Defocus_V Angle CCC 10471.08 11275.84 12.49 0.119792 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00019hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00019hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.003e-01 CC threshold: 0.737 Mean Std: 44.08 7.57 Num Hot pixels: 180 Hot pixel threshold: 89.50 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.123272 Iteration 2 Error: 0.113013 Iteration 3 Error: 0.021935 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.23 0.04 ...... Frame ( 3) shift: -0.46 0.08 ...... Frame ( 4) shift: -0.69 0.11 ...... Frame ( 5) shift: -0.91 0.15 ...... Frame ( 6) shift: -0.99 0.21 ...... Frame ( 7) shift: -0.91 0.29 ...... Frame ( 8) shift: -0.83 0.36 ...... Frame ( 9) shift: -0.79 0.46 ...... Frame ( 10) shift: -0.80 0.56 ...... Frame ( 11) shift: -0.81 0.67 ...... Frame ( 12) shift: -0.81 0.77 ...... Frame ( 13) shift: -0.82 0.86 ...... Frame ( 14) shift: -0.83 0.95 ...... Frame ( 15) shift: -0.83 1.05 ...... Frame ( 16) shift: -0.82 1.15 ...... Frame ( 17) shift: -0.81 1.25 ...... Frame ( 18) shift: -0.81 1.31 ...... Frame ( 19) shift: -0.82 1.34 ...... Frame ( 20) shift: -0.82 1.37 ...... Frame ( 21) shift: -0.82 1.45 ...... Frame ( 22) shift: -0.80 1.58 ...... Frame ( 23) shift: -0.77 1.71 ...... Frame ( 24) shift: -0.79 1.74 ...... Frame ( 25) shift: -0.84 1.67 ...... Frame ( 26) shift: -0.89 1.61 ...... Frame ( 27) shift: -0.94 1.58 ...... Frame ( 28) shift: -0.97 1.59 ...... Frame ( 29) shift: -1.01 1.59 ...... Frame ( 30) shift: -1.00 1.62 ...... Frame ( 31) shift: -0.95 1.65 ...... Frame ( 32) shift: -0.90 1.68 ...... Frame ( 33) shift: -0.89 1.70 ...... Frame ( 34) shift: -0.93 1.70 ...... Frame ( 35) shift: -0.96 1.70 ...... Frame ( 36) shift: -0.96 1.71 ...... Frame ( 37) shift: -0.93 1.71 ...... Frame ( 38) shift: -0.91 1.72 ...... Frame ( 39) shift: -0.88 1.73 ...... Frame ( 40) shift: -0.86 1.73 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.040407 Iteration 2 Error: 0.299949 Iteration 3 Error: 0.137920 Iteration 4 Error: 0.092943 Iteration 5 Error: 0.028649 Align patch 2 23 left Iteration 1 Error: 1.139195 Iteration 2 Error: 0.134813 Iteration 3 Error: 0.035595 Align patch 3 22 left Iteration 1 Error: 1.010412 Iteration 2 Error: 0.099013 Iteration 3 Error: 0.012758 Align patch 4 21 left Iteration 1 Error: 0.327652 Iteration 2 Error: 0.058213 Iteration 3 Error: 0.019739 Align patch 5 20 left Iteration 1 Error: 0.649326 Iteration 2 Error: 0.106533 Iteration 3 Error: 0.019974 Align patch 6 19 left Iteration 1 Error: 0.729453 Iteration 2 Error: 0.153243 Iteration 3 Error: 0.071432 Iteration 4 Error: 0.039976 Align patch 7 18 left Iteration 1 Error: 0.869058 Iteration 2 Error: 0.143565 Iteration 3 Error: 0.042473 Align patch 8 17 left Iteration 1 Error: 0.937168 Iteration 2 Error: 0.118046 Iteration 3 Error: 0.034061 Align patch 9 16 left Iteration 1 Error: 0.443535 Iteration 2 Error: 0.055796 Iteration 3 Error: 0.011433 Align patch 10 15 left Iteration 1 Error: 0.613202 Iteration 2 Error: 0.074358 Iteration 3 Error: 0.017776 Align patch 11 14 left Iteration 1 Error: 0.961982 Iteration 2 Error: 0.124811 Iteration 3 Error: 0.031947 Align patch 12 13 left Iteration 1 Error: 1.009635 Iteration 2 Error: 0.151733 Iteration 3 Error: 0.039029 Align patch 13 12 left Iteration 1 Error: 0.701234 Iteration 2 Error: 0.105207 Iteration 3 Error: 0.024655 Align patch 14 11 left Iteration 1 Error: 0.474451 Iteration 2 Error: 0.074161 Iteration 3 Error: 0.014047 Align patch 15 10 left Iteration 1 Error: 0.525093 Iteration 2 Error: 0.083075 Iteration 3 Error: 0.024487 Align patch 16 9 left Iteration 1 Error: 0.790013 Iteration 2 Error: 0.099442 Iteration 3 Error: 0.023083 Align patch 17 8 left Iteration 1 Error: 0.829624 Iteration 2 Error: 0.151900 Iteration 3 Error: 0.025416 Align patch 18 7 left Iteration 1 Error: 1.220569 Iteration 2 Error: 0.152480 Iteration 3 Error: 0.035196 Align patch 19 6 left Iteration 1 Error: 0.525523 Iteration 2 Error: 0.055862 Iteration 3 Error: 0.013104 Align patch 20 5 left Iteration 1 Error: 0.408404 Iteration 2 Error: 0.042075 Align patch 21 4 left Iteration 1 Error: 0.874643 Iteration 2 Error: 0.133332 Iteration 3 Error: 0.041791 Align patch 22 3 left Iteration 1 Error: 0.834550 Iteration 2 Error: 0.132828 Iteration 3 Error: 0.025494 Align patch 23 2 left Iteration 1 Error: 0.568268 Iteration 2 Error: 0.075699 Iteration 3 Error: 0.016836 Align patch 24 1 left Iteration 1 Error: 0.703909 Iteration 2 Error: 0.079985 Iteration 3 Error: 0.011362 Align patch 25 0 left Iteration 1 Error: 0.574216 Iteration 2 Error: 0.086367 Iteration 3 Error: 0.014514 3D Fitting completed. Patch alignment time: 15.75(sec) Local motion has been corrected. Process thread exits. Computational time: 25.215788 sec Total time: 30.852785 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00019hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00019hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.754274s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00019hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.182722s ........................................ >>>>>>TIME<<<<<< FFT: 1.033413s Defocus_U Defocus_V Angle CCC 10164.06 9695.31 89.79 0.058300 Final Values Defocus_U Defocus_V Angle CCC 10171.88 9700.00 89.47 0.111571 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00019hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00019hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.350e-01 1.004e-01 CC threshold: 0.737 Mean Std: 44.80 7.55 Num Hot pixels: 184 Hot pixel threshold: 90.09 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.337214 Iteration 2 Error: 0.078855 Iteration 3 Error: 0.009601 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.32 -0.08 ...... Frame ( 3) shift: -0.65 -0.17 ...... Frame ( 4) shift: -0.97 -0.25 ...... Frame ( 5) shift: -1.30 -0.34 ...... Frame ( 6) shift: -1.50 -0.36 ...... Frame ( 7) shift: -1.57 -0.32 ...... Frame ( 8) shift: -1.64 -0.27 ...... Frame ( 9) shift: -1.65 -0.25 ...... Frame ( 10) shift: -1.61 -0.24 ...... Frame ( 11) shift: -1.57 -0.23 ...... Frame ( 12) shift: -1.55 -0.24 ...... Frame ( 13) shift: -1.55 -0.26 ...... Frame ( 14) shift: -1.56 -0.28 ...... Frame ( 15) shift: -1.58 -0.26 ...... Frame ( 16) shift: -1.64 -0.21 ...... Frame ( 17) shift: -1.69 -0.17 ...... Frame ( 18) shift: -1.72 -0.16 ...... Frame ( 19) shift: -1.73 -0.21 ...... Frame ( 20) shift: -1.74 -0.25 ...... Frame ( 21) shift: -1.76 -0.27 ...... Frame ( 22) shift: -1.81 -0.27 ...... Frame ( 23) shift: -1.86 -0.26 ...... Frame ( 24) shift: -1.89 -0.26 ...... Frame ( 25) shift: -1.91 -0.25 ...... Frame ( 26) shift: -1.92 -0.25 ...... Frame ( 27) shift: -1.95 -0.23 ...... Frame ( 28) shift: -2.01 -0.20 ...... Frame ( 29) shift: -2.06 -0.18 ...... Frame ( 30) shift: -2.10 -0.16 ...... Frame ( 31) shift: -2.13 -0.16 ...... Frame ( 32) shift: -2.17 -0.15 ...... Frame ( 33) shift: -2.22 -0.17 ...... Frame ( 34) shift: -2.29 -0.21 ...... Frame ( 35) shift: -2.37 -0.26 ...... Frame ( 36) shift: -2.42 -0.23 ...... Frame ( 37) shift: -2.44 -0.13 ...... Frame ( 38) shift: -2.46 -0.04 ...... Frame ( 39) shift: -2.49 0.06 ...... Frame ( 40) shift: -2.51 0.16 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.503967 Iteration 2 Error: 0.245453 Iteration 3 Error: 0.051224 Iteration 4 Error: 0.027545 Align patch 2 23 left Iteration 1 Error: 2.050669 Iteration 2 Error: 0.221879 Iteration 3 Error: 0.053730 Iteration 4 Error: 0.012748 Align patch 3 22 left Iteration 1 Error: 1.358291 Iteration 2 Error: 0.308463 Iteration 3 Error: 0.078755 Iteration 4 Error: 0.029578 Align patch 4 21 left Iteration 1 Error: 0.940363 Iteration 2 Error: 0.109427 Iteration 3 Error: 0.021711 Align patch 5 20 left Iteration 1 Error: 0.924155 Iteration 2 Error: 0.084619 Iteration 3 Error: 0.017615 Align patch 6 19 left Iteration 1 Error: 0.949800 Iteration 2 Error: 0.090511 Iteration 3 Error: 0.030985 Align patch 7 18 left Iteration 1 Error: 1.103915 Iteration 2 Error: 0.157044 Iteration 3 Error: 0.019990 Align patch 8 17 left Iteration 1 Error: 0.498775 Iteration 2 Error: 0.079555 Iteration 3 Error: 0.012321 Align patch 9 16 left Iteration 1 Error: 0.575665 Iteration 2 Error: 0.055590 Iteration 3 Error: 0.014827 Align patch 10 15 left Iteration 1 Error: 0.681547 Iteration 2 Error: 0.070571 Iteration 3 Error: 0.013268 Align patch 11 14 left Iteration 1 Error: 0.813543 Iteration 2 Error: 0.098923 Iteration 3 Error: 0.029482 Align patch 12 13 left Iteration 1 Error: 0.747820 Iteration 2 Error: 0.105107 Iteration 3 Error: 0.021005 Align patch 13 12 left Iteration 1 Error: 0.800064 Iteration 2 Error: 0.132784 Iteration 3 Error: 0.035930 Align patch 14 11 left Iteration 1 Error: 0.537893 Iteration 2 Error: 0.069946 Iteration 3 Error: 0.013996 Align patch 15 10 left Iteration 1 Error: 0.328113 Iteration 2 Error: 0.032820 Align patch 16 9 left Iteration 1 Error: 0.781517 Iteration 2 Error: 0.141755 Iteration 3 Error: 0.044099 Align patch 17 8 left Iteration 1 Error: 0.947311 Iteration 2 Error: 0.191274 Iteration 3 Error: 0.029941 Align patch 18 7 left Iteration 1 Error: 0.775320 Iteration 2 Error: 0.133800 Iteration 3 Error: 0.021487 Align patch 19 6 left Iteration 1 Error: 0.618709 Iteration 2 Error: 0.068688 Iteration 3 Error: 0.009571 Align patch 20 5 left Iteration 1 Error: 0.438647 Iteration 2 Error: 0.045612 Align patch 21 4 left Iteration 1 Error: 1.600258 Iteration 2 Error: 0.177785 Iteration 3 Error: 0.034387 Align patch 22 3 left Iteration 1 Error: 1.276190 Iteration 2 Error: 0.202604 Iteration 3 Error: 0.028646 Align patch 23 2 left Iteration 1 Error: 1.186867 Iteration 2 Error: 0.110805 Iteration 3 Error: 0.013421 Align patch 24 1 left Iteration 1 Error: 0.770337 Iteration 2 Error: 0.055146 Iteration 3 Error: 0.008750 Align patch 25 0 left Iteration 1 Error: 0.383275 Iteration 2 Error: 0.039763 3D Fitting completed. Patch alignment time: 15.33(sec) Local motion has been corrected. Process thread exits. Computational time: 24.505922 sec Total time: 30.266821 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00019hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00019hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.597139s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00019hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.448722s ........................................ >>>>>>TIME<<<<<< FFT: 0.940642s Defocus_U Defocus_V Angle CCC 12630.87 13517.59 5.74 0.071037 Final Values Defocus_U Defocus_V Angle CCC 12655.87 13517.59 5.74 0.119707 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00019hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00019hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.004e-01 CC threshold: 0.737 Mean Std: 44.46 7.42 Num Hot pixels: 222 Hot pixel threshold: 89.00 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.565563 Iteration 2 Error: 0.155403 Iteration 3 Error: 0.027300 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.35 0.05 ...... Frame ( 3) shift: -0.70 0.11 ...... Frame ( 4) shift: -1.06 0.16 ...... Frame ( 5) shift: -1.41 0.22 ...... Frame ( 6) shift: -1.61 0.25 ...... Frame ( 7) shift: -1.66 0.27 ...... Frame ( 8) shift: -1.71 0.29 ...... Frame ( 9) shift: -1.72 0.31 ...... Frame ( 10) shift: -1.69 0.34 ...... Frame ( 11) shift: -1.66 0.37 ...... Frame ( 12) shift: -1.68 0.38 ...... Frame ( 13) shift: -1.76 0.39 ...... Frame ( 14) shift: -1.83 0.40 ...... Frame ( 15) shift: -1.87 0.43 ...... Frame ( 16) shift: -1.87 0.49 ...... Frame ( 17) shift: -1.88 0.54 ...... Frame ( 18) shift: -1.92 0.57 ...... Frame ( 19) shift: -1.98 0.58 ...... Frame ( 20) shift: -2.05 0.59 ...... Frame ( 21) shift: -2.13 0.64 ...... Frame ( 22) shift: -2.24 0.75 ...... Frame ( 23) shift: -2.34 0.85 ...... Frame ( 24) shift: -2.41 0.89 ...... Frame ( 25) shift: -2.44 0.86 ...... Frame ( 26) shift: -2.47 0.84 ...... Frame ( 27) shift: -2.50 0.86 ...... Frame ( 28) shift: -2.53 0.94 ...... Frame ( 29) shift: -2.57 1.01 ...... Frame ( 30) shift: -2.56 1.04 ...... Frame ( 31) shift: -2.52 1.04 ...... Frame ( 32) shift: -2.48 1.04 ...... Frame ( 33) shift: -2.46 1.07 ...... Frame ( 34) shift: -2.45 1.12 ...... Frame ( 35) shift: -2.44 1.18 ...... Frame ( 36) shift: -2.43 1.21 ...... Frame ( 37) shift: -2.44 1.23 ...... Frame ( 38) shift: -2.44 1.24 ...... Frame ( 39) shift: -2.45 1.26 ...... Frame ( 40) shift: -2.45 1.27 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.921511 Iteration 2 Error: 0.287136 Iteration 3 Error: 0.133152 Iteration 4 Error: 0.028870 Align patch 2 23 left Iteration 1 Error: 1.417171 Iteration 2 Error: 0.129210 Iteration 3 Error: 0.046249 Align patch 3 22 left Iteration 1 Error: 0.695517 Iteration 2 Error: 0.161873 Iteration 3 Error: 0.037626 Align patch 4 21 left Iteration 1 Error: 0.451474 Iteration 2 Error: 0.061894 Iteration 3 Error: 0.012979 Align patch 5 20 left Iteration 1 Error: 0.699509 Iteration 2 Error: 0.102183 Iteration 3 Error: 0.016175 Align patch 6 19 left Iteration 1 Error: 2.446410 Iteration 2 Error: 0.248997 Iteration 3 Error: 0.087758 Iteration 4 Error: 0.020983 Align patch 7 18 left Iteration 1 Error: 1.714415 Iteration 2 Error: 0.159111 Iteration 3 Error: 0.051615 Iteration 4 Error: 0.021551 Align patch 8 17 left Iteration 1 Error: 1.372167 Iteration 2 Error: 0.146511 Iteration 3 Error: 0.023595 Align patch 9 16 left Iteration 1 Error: 0.545073 Iteration 2 Error: 0.079901 Iteration 3 Error: 0.019616 Align patch 10 15 left Iteration 1 Error: 0.525067 Iteration 2 Error: 0.063717 Iteration 3 Error: 0.024111 Align patch 11 14 left Iteration 1 Error: 0.956842 Iteration 2 Error: 0.164953 Iteration 3 Error: 0.033078 Align patch 12 13 left Iteration 1 Error: 1.256926 Iteration 2 Error: 0.286380 Iteration 3 Error: 0.101452 Iteration 4 Error: 0.031807 Align patch 13 12 left Iteration 1 Error: 0.812975 Iteration 2 Error: 0.143316 Iteration 3 Error: 0.042037 Align patch 14 11 left Iteration 1 Error: 0.458362 Iteration 2 Error: 0.066711 Iteration 3 Error: 0.015477 Align patch 15 10 left Iteration 1 Error: 0.789222 Iteration 2 Error: 0.072735 Iteration 3 Error: 0.009660 Align patch 16 9 left Iteration 1 Error: 0.764199 Iteration 2 Error: 0.134771 Iteration 3 Error: 0.043321 Align patch 17 8 left Iteration 1 Error: 0.801470 Iteration 2 Error: 0.127094 Iteration 3 Error: 0.017713 Align patch 18 7 left Iteration 1 Error: 0.815634 Iteration 2 Error: 0.104356 Iteration 3 Error: 0.024441 Align patch 19 6 left Iteration 1 Error: 0.486464 Iteration 2 Error: 0.074102 Iteration 3 Error: 0.015535 Align patch 20 5 left Iteration 1 Error: 0.459530 Iteration 2 Error: 0.038612 Align patch 21 4 left Iteration 1 Error: 1.123804 Iteration 2 Error: 0.261029 Iteration 3 Error: 0.064878 Iteration 4 Error: 0.019466 Align patch 22 3 left Iteration 1 Error: 1.090663 Iteration 2 Error: 0.153756 Iteration 3 Error: 0.027234 Align patch 23 2 left Iteration 1 Error: 0.879138 Iteration 2 Error: 0.127274 Iteration 3 Error: 0.037181 Align patch 24 1 left Iteration 1 Error: 0.810137 Iteration 2 Error: 0.109608 Iteration 3 Error: 0.014549 Align patch 25 0 left Iteration 1 Error: 0.717261 Iteration 2 Error: 0.074365 Iteration 3 Error: 0.016914 3D Fitting completed. Patch alignment time: 15.63(sec) Local motion has been corrected. Process thread exits. Computational time: 24.533260 sec Total time: 30.187986 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00019hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00019hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.549391s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00019hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.092014s ........................................ >>>>>>TIME<<<<<< FFT: 1.023338s Defocus_U Defocus_V Angle CCC 13783.22 13189.44 82.66 0.071166 Final Values Defocus_U Defocus_V Angle CCC 13789.47 13189.44 82.98 0.120650 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00020hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00020hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.002e-01 CC threshold: 0.736 Mean Std: 41.40 7.02 Num Hot pixels: 210 Hot pixel threshold: 83.51 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.885540 Iteration 2 Error: 0.220965 Iteration 3 Error: 0.056630 Iteration 4 Error: 0.016585 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.12 -0.02 ...... Frame ( 3) shift: -0.24 -0.03 ...... Frame ( 4) shift: -0.35 -0.05 ...... Frame ( 5) shift: -0.47 -0.07 ...... Frame ( 6) shift: -0.53 -0.06 ...... Frame ( 7) shift: -0.52 -0.03 ...... Frame ( 8) shift: -0.51 0.00 ...... Frame ( 9) shift: -0.45 0.06 ...... Frame ( 10) shift: -0.35 0.16 ...... Frame ( 11) shift: -0.25 0.26 ...... Frame ( 12) shift: -0.19 0.33 ...... Frame ( 13) shift: -0.19 0.37 ...... Frame ( 14) shift: -0.18 0.41 ...... Frame ( 15) shift: -0.12 0.45 ...... Frame ( 16) shift: 0.00 0.50 ...... Frame ( 17) shift: 0.12 0.54 ...... Frame ( 18) shift: 0.21 0.58 ...... Frame ( 19) shift: 0.28 0.61 ...... Frame ( 20) shift: 0.34 0.64 ...... Frame ( 21) shift: 0.40 0.68 ...... Frame ( 22) shift: 0.45 0.72 ...... Frame ( 23) shift: 0.50 0.77 ...... Frame ( 24) shift: 0.55 0.82 ...... Frame ( 25) shift: 0.60 0.87 ...... Frame ( 26) shift: 0.65 0.93 ...... Frame ( 27) shift: 0.69 0.99 ...... Frame ( 28) shift: 0.73 1.07 ...... Frame ( 29) shift: 0.78 1.15 ...... Frame ( 30) shift: 0.82 1.21 ...... Frame ( 31) shift: 0.85 1.24 ...... Frame ( 32) shift: 0.89 1.28 ...... Frame ( 33) shift: 0.94 1.29 ...... Frame ( 34) shift: 1.00 1.28 ...... Frame ( 35) shift: 1.06 1.27 ...... Frame ( 36) shift: 1.10 1.27 ...... Frame ( 37) shift: 1.10 1.28 ...... Frame ( 38) shift: 1.11 1.29 ...... Frame ( 39) shift: 1.11 1.30 ...... Frame ( 40) shift: 1.11 1.32 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.966303 Iteration 2 Error: 0.276417 Iteration 3 Error: 0.080829 Iteration 4 Error: 0.028260 Align patch 2 23 left Iteration 1 Error: 1.314272 Iteration 2 Error: 0.291816 Iteration 3 Error: 0.103352 Iteration 4 Error: 0.048775 Align patch 3 22 left Iteration 1 Error: 0.539749 Iteration 2 Error: 0.109313 Iteration 3 Error: 0.025055 Align patch 4 21 left Iteration 1 Error: 0.718172 Iteration 2 Error: 0.153450 Iteration 3 Error: 0.031053 Align patch 5 20 left Iteration 1 Error: 0.870395 Iteration 2 Error: 0.182542 Iteration 3 Error: 0.029207 Align patch 6 19 left Iteration 1 Error: 1.518165 Iteration 2 Error: 0.411344 Iteration 3 Error: 0.148510 Iteration 4 Error: 0.073037 Iteration 5 Error: 0.031709 Align patch 7 18 left Iteration 1 Error: 0.978725 Iteration 2 Error: 0.156289 Iteration 3 Error: 0.069667 Iteration 4 Error: 0.026257 Align patch 8 17 left Iteration 1 Error: 0.567775 Iteration 2 Error: 0.065977 Iteration 3 Error: 0.019445 Align patch 9 16 left Iteration 1 Error: 0.603864 Iteration 2 Error: 0.120747 Iteration 3 Error: 0.023910 Align patch 10 15 left Iteration 1 Error: 0.937963 Iteration 2 Error: 0.149806 Iteration 3 Error: 0.027633 Align patch 11 14 left Iteration 1 Error: 1.679680 Iteration 2 Error: 0.338572 Iteration 3 Error: 0.125832 Iteration 4 Error: 0.043135 Align patch 12 13 left Iteration 1 Error: 0.633678 Iteration 2 Error: 0.122001 Iteration 3 Error: 0.040790 Align patch 13 12 left Iteration 1 Error: 0.764380 Iteration 2 Error: 0.059690 Iteration 3 Error: 0.021109 Align patch 14 11 left Iteration 1 Error: 0.654412 Iteration 2 Error: 0.114634 Iteration 3 Error: 0.025014 Align patch 15 10 left Iteration 1 Error: 0.683555 Iteration 2 Error: 0.121234 Iteration 3 Error: 0.017077 Align patch 16 9 left Iteration 1 Error: 1.623103 Iteration 2 Error: 0.314887 Iteration 3 Error: 0.094440 Iteration 4 Error: 0.030674 Align patch 17 8 left Iteration 1 Error: 0.805235 Iteration 2 Error: 0.109936 Iteration 3 Error: 0.032601 Align patch 18 7 left Iteration 1 Error: 0.526514 Iteration 2 Error: 0.064415 Iteration 3 Error: 0.014587 Align patch 19 6 left Iteration 1 Error: 0.576047 Iteration 2 Error: 0.116377 Iteration 3 Error: 0.024743 Align patch 20 5 left Iteration 1 Error: 0.660292 Iteration 2 Error: 0.105694 Iteration 3 Error: 0.023469 Align patch 21 4 left Iteration 1 Error: 0.755235 Iteration 2 Error: 0.209908 Iteration 3 Error: 0.073296 Iteration 4 Error: 0.024755 Align patch 22 3 left Iteration 1 Error: 0.634418 Iteration 2 Error: 0.121846 Iteration 3 Error: 0.025181 Align patch 23 2 left Iteration 1 Error: 0.785341 Iteration 2 Error: 0.123827 Iteration 3 Error: 0.035916 Align patch 24 1 left Iteration 1 Error: 0.590309 Iteration 2 Error: 0.155867 Iteration 3 Error: 0.041468 Align patch 25 0 left Iteration 1 Error: 0.870735 Iteration 2 Error: 0.176184 Iteration 3 Error: 0.025682 3D Fitting completed. Patch alignment time: 16.03(sec) Local motion has been corrected. Process thread exits. Computational time: 25.221697 sec Total time: 31.453098 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00020hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00020hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.739519s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00020hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.775982s ........................................ >>>>>>TIME<<<<<< FFT: 0.922290s Defocus_U Defocus_V Angle CCC 8560.55 9412.11 13.80 0.034852 Final Values Defocus_U Defocus_V Angle CCC 8569.92 9408.99 13.80 0.068649 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00020hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00020hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.351e-01 1.005e-01 CC threshold: 0.738 Mean Std: 41.98 7.33 Num Hot pixels: 178 Hot pixel threshold: 85.95 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.721629 Iteration 2 Error: 0.116841 Iteration 3 Error: 0.024259 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.14 -0.02 ...... Frame ( 3) shift: -0.27 -0.03 ...... Frame ( 4) shift: -0.41 -0.05 ...... Frame ( 5) shift: -0.54 -0.07 ...... Frame ( 6) shift: -0.62 -0.07 ...... Frame ( 7) shift: -0.64 -0.05 ...... Frame ( 8) shift: -0.66 -0.03 ...... Frame ( 9) shift: -0.62 0.04 ...... Frame ( 10) shift: -0.54 0.16 ...... Frame ( 11) shift: -0.46 0.29 ...... Frame ( 12) shift: -0.41 0.39 ...... Frame ( 13) shift: -0.38 0.48 ...... Frame ( 14) shift: -0.35 0.57 ...... Frame ( 15) shift: -0.32 0.64 ...... Frame ( 16) shift: -0.30 0.71 ...... Frame ( 17) shift: -0.27 0.77 ...... Frame ( 18) shift: -0.23 0.81 ...... Frame ( 19) shift: -0.15 0.84 ...... Frame ( 20) shift: -0.08 0.86 ...... Frame ( 21) shift: -0.04 0.86 ...... Frame ( 22) shift: -0.04 0.83 ...... Frame ( 23) shift: -0.04 0.80 ...... Frame ( 24) shift: -0.04 0.80 ...... Frame ( 25) shift: -0.06 0.81 ...... Frame ( 26) shift: -0.07 0.83 ...... Frame ( 27) shift: -0.05 0.86 ...... Frame ( 28) shift: 0.01 0.92 ...... Frame ( 29) shift: 0.07 0.97 ...... Frame ( 30) shift: 0.11 1.01 ...... Frame ( 31) shift: 0.15 1.03 ...... Frame ( 32) shift: 0.18 1.06 ...... Frame ( 33) shift: 0.17 1.06 ...... Frame ( 34) shift: 0.13 1.06 ...... Frame ( 35) shift: 0.08 1.05 ...... Frame ( 36) shift: 0.09 1.07 ...... Frame ( 37) shift: 0.15 1.12 ...... Frame ( 38) shift: 0.21 1.17 ...... Frame ( 39) shift: 0.27 1.21 ...... Frame ( 40) shift: 0.33 1.26 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.873340 Iteration 2 Error: 0.257073 Iteration 3 Error: 0.082391 Iteration 4 Error: 0.031500 Align patch 2 23 left Iteration 1 Error: 1.260888 Iteration 2 Error: 0.208579 Iteration 3 Error: 0.049931 Align patch 3 22 left Iteration 1 Error: 0.722076 Iteration 2 Error: 0.074950 Iteration 3 Error: 0.020635 Align patch 4 21 left Iteration 1 Error: 0.513470 Iteration 2 Error: 0.085950 Iteration 3 Error: 0.016244 Align patch 5 20 left Iteration 1 Error: 0.332876 Iteration 2 Error: 0.107092 Iteration 3 Error: 0.025724 Align patch 6 19 left Iteration 1 Error: 1.446484 Iteration 2 Error: 0.253847 Iteration 3 Error: 0.090582 Iteration 4 Error: 0.021093 Align patch 7 18 left Iteration 1 Error: 1.110310 Iteration 2 Error: 0.140926 Iteration 3 Error: 0.034374 Align patch 8 17 left Iteration 1 Error: 0.716879 Iteration 2 Error: 0.080109 Iteration 3 Error: 0.014664 Align patch 9 16 left Iteration 1 Error: 0.544164 Iteration 2 Error: 0.098020 Iteration 3 Error: 0.018200 Align patch 10 15 left Iteration 1 Error: 0.469025 Iteration 2 Error: 0.067515 Iteration 3 Error: 0.012173 Align patch 11 14 left Iteration 1 Error: 0.690413 Iteration 2 Error: 0.118279 Iteration 3 Error: 0.028474 Align patch 12 13 left Iteration 1 Error: 0.610901 Iteration 2 Error: 0.113376 Iteration 3 Error: 0.023506 Align patch 13 12 left Iteration 1 Error: 0.740211 Iteration 2 Error: 0.077871 Iteration 3 Error: 0.014694 Align patch 14 11 left Iteration 1 Error: 0.471770 Iteration 2 Error: 0.052468 Iteration 3 Error: 0.007199 Align patch 15 10 left Iteration 1 Error: 0.531435 Iteration 2 Error: 0.061141 Iteration 3 Error: 0.010474 Align patch 16 9 left Iteration 1 Error: 0.415453 Iteration 2 Error: 0.064128 Iteration 3 Error: 0.019510 Align patch 17 8 left Iteration 1 Error: 0.633955 Iteration 2 Error: 0.094300 Iteration 3 Error: 0.020724 Align patch 18 7 left Iteration 1 Error: 0.798783 Iteration 2 Error: 0.049364 Align patch 19 6 left Iteration 1 Error: 0.485378 Iteration 2 Error: 0.066594 Iteration 3 Error: 0.011494 Align patch 20 5 left Iteration 1 Error: 0.607226 Iteration 2 Error: 0.076706 Iteration 3 Error: 0.012714 Align patch 21 4 left Iteration 1 Error: 0.729890 Iteration 2 Error: 0.135313 Iteration 3 Error: 0.026705 Align patch 22 3 left Iteration 1 Error: 0.743293 Iteration 2 Error: 0.105884 Iteration 3 Error: 0.030192 Align patch 23 2 left Iteration 1 Error: 0.625798 Iteration 2 Error: 0.112139 Iteration 3 Error: 0.026489 Align patch 24 1 left Iteration 1 Error: 0.541469 Iteration 2 Error: 0.054447 Iteration 3 Error: 0.007802 Align patch 25 0 left Iteration 1 Error: 0.625839 Iteration 2 Error: 0.037095 3D Fitting completed. Patch alignment time: 15.05(sec) Local motion has been corrected. Process thread exits. Computational time: 24.044413 sec Total time: 30.107958 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00020hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00020hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.559008s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00020hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.573627s ........................................ >>>>>>TIME<<<<<< FFT: 0.915677s Defocus_U Defocus_V Angle CCC 12179.69 12679.69 0.10 0.061419 Final Values Defocus_U Defocus_V Angle CCC 12179.69 12692.19 1.35 0.103104 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00020hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00020hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.003e-01 CC threshold: 0.737 Mean Std: 41.74 7.00 Num Hot pixels: 206 Hot pixel threshold: 83.72 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.625151 Iteration 2 Error: 0.123584 Iteration 3 Error: 0.020401 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.17 0.00 ...... Frame ( 3) shift: -0.34 0.01 ...... Frame ( 4) shift: -0.51 0.01 ...... Frame ( 5) shift: -0.68 0.02 ...... Frame ( 6) shift: -0.76 0.02 ...... Frame ( 7) shift: -0.75 0.02 ...... Frame ( 8) shift: -0.73 0.03 ...... Frame ( 9) shift: -0.72 0.06 ...... Frame ( 10) shift: -0.72 0.13 ...... Frame ( 11) shift: -0.72 0.19 ...... Frame ( 12) shift: -0.70 0.25 ...... Frame ( 13) shift: -0.64 0.32 ...... Frame ( 14) shift: -0.58 0.38 ...... Frame ( 15) shift: -0.55 0.43 ...... Frame ( 16) shift: -0.55 0.48 ...... Frame ( 17) shift: -0.54 0.53 ...... Frame ( 18) shift: -0.51 0.59 ...... Frame ( 19) shift: -0.46 0.67 ...... Frame ( 20) shift: -0.41 0.76 ...... Frame ( 21) shift: -0.37 0.83 ...... Frame ( 22) shift: -0.34 0.91 ...... Frame ( 23) shift: -0.31 0.98 ...... Frame ( 24) shift: -0.27 1.02 ...... Frame ( 25) shift: -0.24 1.03 ...... Frame ( 26) shift: -0.21 1.05 ...... Frame ( 27) shift: -0.19 1.08 ...... Frame ( 28) shift: -0.18 1.14 ...... Frame ( 29) shift: -0.17 1.20 ...... Frame ( 30) shift: -0.16 1.21 ...... Frame ( 31) shift: -0.16 1.18 ...... Frame ( 32) shift: -0.15 1.16 ...... Frame ( 33) shift: -0.15 1.13 ...... Frame ( 34) shift: -0.15 1.09 ...... Frame ( 35) shift: -0.14 1.06 ...... Frame ( 36) shift: -0.12 1.06 ...... Frame ( 37) shift: -0.09 1.10 ...... Frame ( 38) shift: -0.05 1.13 ...... Frame ( 39) shift: -0.01 1.16 ...... Frame ( 40) shift: 0.02 1.19 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.041696 Iteration 2 Error: 0.310074 Iteration 3 Error: 0.124185 Iteration 4 Error: 0.046660 Align patch 2 23 left Iteration 1 Error: 1.573771 Iteration 2 Error: 0.309734 Iteration 3 Error: 0.090962 Iteration 4 Error: 0.040220 Align patch 3 22 left Iteration 1 Error: 0.570422 Iteration 2 Error: 0.100963 Iteration 3 Error: 0.025128 Align patch 4 21 left Iteration 1 Error: 0.857261 Iteration 2 Error: 0.125973 Iteration 3 Error: 0.030189 Align patch 5 20 left Iteration 1 Error: 0.795206 Iteration 2 Error: 0.099424 Iteration 3 Error: 0.017596 Align patch 6 19 left Iteration 1 Error: 1.338244 Iteration 2 Error: 0.129826 Iteration 3 Error: 0.043601 Align patch 7 18 left Iteration 1 Error: 0.819716 Iteration 2 Error: 0.107981 Iteration 3 Error: 0.030483 Align patch 8 17 left Iteration 1 Error: 0.781200 Iteration 2 Error: 0.118922 Iteration 3 Error: 0.042065 Align patch 9 16 left Iteration 1 Error: 0.764208 Iteration 2 Error: 0.085753 Iteration 3 Error: 0.023993 Align patch 10 15 left Iteration 1 Error: 0.573656 Iteration 2 Error: 0.110688 Iteration 3 Error: 0.015869 Align patch 11 14 left Iteration 1 Error: 1.620165 Iteration 2 Error: 0.170391 Iteration 3 Error: 0.053084 Iteration 4 Error: 0.022767 Align patch 12 13 left Iteration 1 Error: 0.676409 Iteration 2 Error: 0.168924 Iteration 3 Error: 0.053256 Iteration 4 Error: 0.029524 Align patch 13 12 left Iteration 1 Error: 0.485744 Iteration 2 Error: 0.108845 Iteration 3 Error: 0.035062 Align patch 14 11 left Iteration 1 Error: 0.905427 Iteration 2 Error: 0.081226 Iteration 3 Error: 0.012919 Align patch 15 10 left Iteration 1 Error: 0.634080 Iteration 2 Error: 0.146956 Iteration 3 Error: 0.031973 Align patch 16 9 left Iteration 1 Error: 0.836192 Iteration 2 Error: 0.234931 Iteration 3 Error: 0.056856 Iteration 4 Error: 0.022475 Align patch 17 8 left Iteration 1 Error: 0.696606 Iteration 2 Error: 0.082087 Iteration 3 Error: 0.024026 Align patch 18 7 left Iteration 1 Error: 0.865921 Iteration 2 Error: 0.078995 Iteration 3 Error: 0.016969 Align patch 19 6 left Iteration 1 Error: 0.494573 Iteration 2 Error: 0.064351 Iteration 3 Error: 0.017863 Align patch 20 5 left Iteration 1 Error: 0.492062 Iteration 2 Error: 0.077808 Iteration 3 Error: 0.015332 Align patch 21 4 left Iteration 1 Error: 0.566079 Iteration 2 Error: 0.183086 Iteration 3 Error: 0.055439 Iteration 4 Error: 0.020530 Align patch 22 3 left Iteration 1 Error: 0.563427 Iteration 2 Error: 0.058378 Iteration 3 Error: 0.013706 Align patch 23 2 left Iteration 1 Error: 0.924312 Iteration 2 Error: 0.116026 Iteration 3 Error: 0.041270 Align patch 24 1 left Iteration 1 Error: 0.858956 Iteration 2 Error: 0.077108 Iteration 3 Error: 0.012813 Align patch 25 0 left Iteration 1 Error: 0.716132 Iteration 2 Error: 0.128358 Iteration 3 Error: 0.032917 3D Fitting completed. Patch alignment time: 15.68(sec) Local motion has been corrected. Process thread exits. Computational time: 24.604563 sec Total time: 31.149307 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00020hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00020hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.762129s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00020hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.390800s ........................................ >>>>>>TIME<<<<<< FFT: 1.046827s Defocus_U Defocus_V Angle CCC 13265.63 12624.99 86.33 0.057047 Final Values Defocus_U Defocus_V Angle CCC 13260.95 12639.06 86.33 0.097057 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00021hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00021hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.002e-01 CC threshold: 0.736 Mean Std: 42.66 7.28 Num Hot pixels: 238 Hot pixel threshold: 86.31 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.225488 Iteration 2 Error: 0.204030 Iteration 3 Error: 0.060553 Iteration 4 Error: 0.014002 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.22 -0.04 ...... Frame ( 3) shift: -0.45 -0.09 ...... Frame ( 4) shift: -0.67 -0.13 ...... Frame ( 5) shift: -0.90 -0.18 ...... Frame ( 6) shift: -0.99 -0.15 ...... Frame ( 7) shift: -0.95 -0.05 ...... Frame ( 8) shift: -0.92 0.05 ...... Frame ( 9) shift: -0.87 0.14 ...... Frame ( 10) shift: -0.81 0.20 ...... Frame ( 11) shift: -0.75 0.27 ...... Frame ( 12) shift: -0.69 0.35 ...... Frame ( 13) shift: -0.64 0.43 ...... Frame ( 14) shift: -0.58 0.52 ...... Frame ( 15) shift: -0.51 0.64 ...... Frame ( 16) shift: -0.42 0.77 ...... Frame ( 17) shift: -0.33 0.91 ...... Frame ( 18) shift: -0.29 1.01 ...... Frame ( 19) shift: -0.31 1.06 ...... Frame ( 20) shift: -0.33 1.12 ...... Frame ( 21) shift: -0.29 1.20 ...... Frame ( 22) shift: -0.18 1.32 ...... Frame ( 23) shift: -0.07 1.44 ...... Frame ( 24) shift: -0.01 1.51 ...... Frame ( 25) shift: 0.01 1.55 ...... Frame ( 26) shift: 0.02 1.59 ...... Frame ( 27) shift: 0.07 1.65 ...... Frame ( 28) shift: 0.14 1.74 ...... Frame ( 29) shift: 0.21 1.83 ...... Frame ( 30) shift: 0.23 1.87 ...... Frame ( 31) shift: 0.20 1.86 ...... Frame ( 32) shift: 0.17 1.85 ...... Frame ( 33) shift: 0.16 1.87 ...... Frame ( 34) shift: 0.16 1.91 ...... Frame ( 35) shift: 0.16 1.95 ...... Frame ( 36) shift: 0.17 1.97 ...... Frame ( 37) shift: 0.18 1.97 ...... Frame ( 38) shift: 0.19 1.97 ...... Frame ( 39) shift: 0.20 1.98 ...... Frame ( 40) shift: 0.21 1.98 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.775064 Iteration 2 Error: 0.199869 Iteration 3 Error: 0.082328 Iteration 4 Error: 0.022804 Align patch 2 23 left Iteration 1 Error: 0.792284 Iteration 2 Error: 0.165544 Iteration 3 Error: 0.048957 Align patch 3 22 left Iteration 1 Error: 0.621227 Iteration 2 Error: 0.090745 Iteration 3 Error: 0.019077 Align patch 4 21 left Iteration 1 Error: 0.817346 Iteration 2 Error: 0.127746 Iteration 3 Error: 0.039678 Align patch 5 20 left Iteration 1 Error: 0.597047 Iteration 2 Error: 0.109963 Iteration 3 Error: 0.025832 Align patch 6 19 left Iteration 1 Error: 1.545532 Iteration 2 Error: 0.284987 Iteration 3 Error: 0.050160 Iteration 4 Error: 0.021487 Align patch 7 18 left Iteration 1 Error: 0.914449 Iteration 2 Error: 0.145928 Iteration 3 Error: 0.042483 Align patch 8 17 left Iteration 1 Error: 0.893349 Iteration 2 Error: 0.148908 Iteration 3 Error: 0.050503 Iteration 4 Error: 0.016177 Align patch 9 16 left Iteration 1 Error: 0.712053 Iteration 2 Error: 0.120536 Iteration 3 Error: 0.039874 Align patch 10 15 left Iteration 1 Error: 0.829943 Iteration 2 Error: 0.199013 Iteration 3 Error: 0.049132 Align patch 11 14 left Iteration 1 Error: 0.631679 Iteration 2 Error: 0.100416 Iteration 3 Error: 0.016510 Align patch 12 13 left Iteration 1 Error: 1.216539 Iteration 2 Error: 0.289664 Iteration 3 Error: 0.100696 Iteration 4 Error: 0.058170 Iteration 5 Error: 0.026835 Align patch 13 12 left Iteration 1 Error: 0.706647 Iteration 2 Error: 0.136570 Iteration 3 Error: 0.049611 Align patch 14 11 left Iteration 1 Error: 0.568406 Iteration 2 Error: 0.073550 Iteration 3 Error: 0.022264 Align patch 15 10 left Iteration 1 Error: 0.595161 Iteration 2 Error: 0.056677 Iteration 3 Error: 0.013299 Align patch 16 9 left Iteration 1 Error: 0.894229 Iteration 2 Error: 0.128562 Iteration 3 Error: 0.025278 Align patch 17 8 left Iteration 1 Error: 0.798244 Iteration 2 Error: 0.177541 Iteration 3 Error: 0.029689 Align patch 18 7 left Iteration 1 Error: 0.456612 Iteration 2 Error: 0.061850 Iteration 3 Error: 0.021085 Align patch 19 6 left Iteration 1 Error: 0.827868 Iteration 2 Error: 0.138572 Iteration 3 Error: 0.031803 Align patch 20 5 left Iteration 1 Error: 0.658444 Iteration 2 Error: 0.053920 Iteration 3 Error: 0.012448 Align patch 21 4 left Iteration 1 Error: 0.978159 Iteration 2 Error: 0.150942 Iteration 3 Error: 0.032816 Align patch 22 3 left Iteration 1 Error: 0.689098 Iteration 2 Error: 0.152539 Iteration 3 Error: 0.030917 Align patch 23 2 left Iteration 1 Error: 0.628390 Iteration 2 Error: 0.128507 Iteration 3 Error: 0.018348 Align patch 24 1 left Iteration 1 Error: 0.462958 Iteration 2 Error: 0.078886 Iteration 3 Error: 0.013656 Align patch 25 0 left Iteration 1 Error: 0.667108 Iteration 2 Error: 0.125724 Iteration 3 Error: 0.026236 3D Fitting completed. Patch alignment time: 15.51(sec) Local motion has been corrected. Process thread exits. Computational time: 25.003832 sec Total time: 32.045578 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00021hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00021hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.582723s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00021hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.400251s ........................................ >>>>>>TIME<<<<<< FFT: 1.059481s Defocus_U Defocus_V Angle CCC 8363.28 9250.00 13.60 0.044625 Final Values Defocus_U Defocus_V Angle CCC 8371.09 9260.95 13.92 0.089903 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00021hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00021hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.002e-01 CC threshold: 0.736 Mean Std: 40.07 6.87 Num Hot pixels: 215 Hot pixel threshold: 81.30 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.012779 Iteration 2 Error: 0.202886 Iteration 3 Error: 0.041758 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.08 -0.10 ...... Frame ( 3) shift: -0.16 -0.21 ...... Frame ( 4) shift: -0.24 -0.31 ...... Frame ( 5) shift: -0.32 -0.41 ...... Frame ( 6) shift: -0.39 -0.48 ...... Frame ( 7) shift: -0.46 -0.51 ...... Frame ( 8) shift: -0.52 -0.54 ...... Frame ( 9) shift: -0.53 -0.48 ...... Frame ( 10) shift: -0.48 -0.32 ...... Frame ( 11) shift: -0.43 -0.16 ...... Frame ( 12) shift: -0.37 -0.03 ...... Frame ( 13) shift: -0.31 0.07 ...... Frame ( 14) shift: -0.24 0.17 ...... Frame ( 15) shift: -0.18 0.28 ...... Frame ( 16) shift: -0.13 0.39 ...... Frame ( 17) shift: -0.08 0.50 ...... Frame ( 18) shift: -0.06 0.54 ...... Frame ( 19) shift: -0.07 0.52 ...... Frame ( 20) shift: -0.08 0.49 ...... Frame ( 21) shift: -0.05 0.48 ...... Frame ( 22) shift: 0.01 0.48 ...... Frame ( 23) shift: 0.07 0.48 ...... Frame ( 24) shift: 0.10 0.54 ...... Frame ( 25) shift: 0.09 0.65 ...... Frame ( 26) shift: 0.09 0.77 ...... Frame ( 27) shift: 0.11 0.85 ...... Frame ( 28) shift: 0.15 0.91 ...... Frame ( 29) shift: 0.20 0.97 ...... Frame ( 30) shift: 0.24 1.02 ...... Frame ( 31) shift: 0.27 1.07 ...... Frame ( 32) shift: 0.31 1.11 ...... Frame ( 33) shift: 0.36 1.16 ...... Frame ( 34) shift: 0.44 1.20 ...... Frame ( 35) shift: 0.52 1.25 ...... Frame ( 36) shift: 0.55 1.30 ...... Frame ( 37) shift: 0.52 1.36 ...... Frame ( 38) shift: 0.50 1.42 ...... Frame ( 39) shift: 0.48 1.48 ...... Frame ( 40) shift: 0.45 1.54 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.933041 Iteration 2 Error: 0.269520 Iteration 3 Error: 0.086631 Iteration 4 Error: 0.033971 Align patch 2 23 left Iteration 1 Error: 0.669053 Iteration 2 Error: 0.146109 Iteration 3 Error: 0.058863 Iteration 4 Error: 0.021530 Align patch 3 22 left Iteration 1 Error: 0.649775 Iteration 2 Error: 0.114915 Iteration 3 Error: 0.030103 Align patch 4 21 left Iteration 1 Error: 0.534304 Iteration 2 Error: 0.140711 Iteration 3 Error: 0.038014 Align patch 5 20 left Iteration 1 Error: 0.893392 Iteration 2 Error: 0.081133 Iteration 3 Error: 0.015742 Align patch 6 19 left Iteration 1 Error: 0.792608 Iteration 2 Error: 0.145290 Iteration 3 Error: 0.060662 Iteration 4 Error: 0.016907 Align patch 7 18 left Iteration 1 Error: 0.612653 Iteration 2 Error: 0.190038 Iteration 3 Error: 0.080530 Iteration 4 Error: 0.038829 Align patch 8 17 left Iteration 1 Error: 0.792382 Iteration 2 Error: 0.117398 Iteration 3 Error: 0.032625 Align patch 9 16 left Iteration 1 Error: 0.705328 Iteration 2 Error: 0.125081 Iteration 3 Error: 0.023751 Align patch 10 15 left Iteration 1 Error: 1.134261 Iteration 2 Error: 0.113669 Iteration 3 Error: 0.013943 Align patch 11 14 left Iteration 1 Error: 0.593259 Iteration 2 Error: 0.113305 Iteration 3 Error: 0.029029 Align patch 12 13 left Iteration 1 Error: 0.704525 Iteration 2 Error: 0.108514 Iteration 3 Error: 0.033209 Align patch 13 12 left Iteration 1 Error: 0.728163 Iteration 2 Error: 0.137595 Iteration 3 Error: 0.040600 Align patch 14 11 left Iteration 1 Error: 0.605990 Iteration 2 Error: 0.120118 Iteration 3 Error: 0.030945 Align patch 15 10 left Iteration 1 Error: 0.516883 Iteration 2 Error: 0.098779 Iteration 3 Error: 0.019401 Align patch 16 9 left Iteration 1 Error: 0.558632 Iteration 2 Error: 0.051903 Iteration 3 Error: 0.012535 Align patch 17 8 left Iteration 1 Error: 0.305199 Iteration 2 Error: 0.110218 Iteration 3 Error: 0.022371 Align patch 18 7 left Iteration 1 Error: 0.501447 Iteration 2 Error: 0.095626 Iteration 3 Error: 0.025025 Align patch 19 6 left Iteration 1 Error: 0.608295 Iteration 2 Error: 0.058007 Iteration 3 Error: 0.019691 Align patch 20 5 left Iteration 1 Error: 0.531839 Iteration 2 Error: 0.120855 Iteration 3 Error: 0.023545 Align patch 21 4 left Iteration 1 Error: 0.488328 Iteration 2 Error: 0.123674 Iteration 3 Error: 0.036104 Align patch 22 3 left Iteration 1 Error: 0.766509 Iteration 2 Error: 0.113675 Iteration 3 Error: 0.026524 Align patch 23 2 left Iteration 1 Error: 0.797300 Iteration 2 Error: 0.172975 Iteration 3 Error: 0.042661 Align patch 24 1 left Iteration 1 Error: 0.600427 Iteration 2 Error: 0.096217 Iteration 3 Error: 0.018283 Align patch 25 0 left Iteration 1 Error: 0.482702 Iteration 2 Error: 0.091030 Iteration 3 Error: 0.017916 3D Fitting completed. Patch alignment time: 15.47(sec) Local motion has been corrected. Process thread exits. Computational time: 24.694319 sec Total time: 30.924524 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00021hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00021hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.660050s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00021hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.369185s ........................................ >>>>>>TIME<<<<<< FFT: 0.940133s Defocus_U Defocus_V Angle CCC 9386.70 9785.18 4.60 0.038374 Final Values Defocus_U Defocus_V Angle CCC 9405.46 9785.18 3.66 0.071540 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00021hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00021hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.349e-01 1.002e-01 CC threshold: 0.736 Mean Std: 42.15 7.14 Num Hot pixels: 208 Hot pixel threshold: 85.00 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.894973 Iteration 2 Error: 0.099827 Iteration 3 Error: 0.021258 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.29 -0.03 ...... Frame ( 3) shift: -0.59 -0.06 ...... Frame ( 4) shift: -0.88 -0.10 ...... Frame ( 5) shift: -1.18 -0.13 ...... Frame ( 6) shift: -1.31 -0.11 ...... Frame ( 7) shift: -1.29 -0.04 ...... Frame ( 8) shift: -1.27 0.03 ...... Frame ( 9) shift: -1.25 0.11 ...... Frame ( 10) shift: -1.23 0.18 ...... Frame ( 11) shift: -1.22 0.26 ...... Frame ( 12) shift: -1.18 0.31 ...... Frame ( 13) shift: -1.12 0.35 ...... Frame ( 14) shift: -1.06 0.39 ...... Frame ( 15) shift: -1.05 0.43 ...... Frame ( 16) shift: -1.09 0.48 ...... Frame ( 17) shift: -1.14 0.53 ...... Frame ( 18) shift: -1.14 0.57 ...... Frame ( 19) shift: -1.10 0.60 ...... Frame ( 20) shift: -1.06 0.63 ...... Frame ( 21) shift: -1.05 0.65 ...... Frame ( 22) shift: -1.08 0.66 ...... Frame ( 23) shift: -1.10 0.67 ...... Frame ( 24) shift: -1.11 0.72 ...... Frame ( 25) shift: -1.10 0.80 ...... Frame ( 26) shift: -1.08 0.89 ...... Frame ( 27) shift: -1.07 0.95 ...... Frame ( 28) shift: -1.06 0.98 ...... Frame ( 29) shift: -1.04 1.01 ...... Frame ( 30) shift: -1.05 1.06 ...... Frame ( 31) shift: -1.08 1.12 ...... Frame ( 32) shift: -1.11 1.18 ...... Frame ( 33) shift: -1.10 1.22 ...... Frame ( 34) shift: -1.07 1.24 ...... Frame ( 35) shift: -1.03 1.26 ...... Frame ( 36) shift: -1.00 1.27 ...... Frame ( 37) shift: -0.97 1.27 ...... Frame ( 38) shift: -0.95 1.27 ...... Frame ( 39) shift: -0.93 1.27 ...... Frame ( 40) shift: -0.90 1.27 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.456266 Iteration 2 Error: 0.097149 Iteration 3 Error: 0.041187 Align patch 2 23 left Iteration 1 Error: 1.276111 Iteration 2 Error: 0.136766 Iteration 3 Error: 0.039734 Align patch 3 22 left Iteration 1 Error: 1.101919 Iteration 2 Error: 0.140300 Iteration 3 Error: 0.031811 Align patch 4 21 left Iteration 1 Error: 0.485392 Iteration 2 Error: 0.041787 Align patch 5 20 left Iteration 1 Error: 0.661262 Iteration 2 Error: 0.098782 Iteration 3 Error: 0.032576 Align patch 6 19 left Iteration 1 Error: 1.376820 Iteration 2 Error: 0.154350 Iteration 3 Error: 0.034834 Align patch 7 18 left Iteration 1 Error: 0.697253 Iteration 2 Error: 0.090741 Iteration 3 Error: 0.017939 Align patch 8 17 left Iteration 1 Error: 0.816317 Iteration 2 Error: 0.165826 Iteration 3 Error: 0.032825 Align patch 9 16 left Iteration 1 Error: 0.383360 Iteration 2 Error: 0.088117 Iteration 3 Error: 0.019267 Align patch 10 15 left Iteration 1 Error: 0.462873 Iteration 2 Error: 0.080938 Iteration 3 Error: 0.012116 Align patch 11 14 left Iteration 1 Error: 0.736865 Iteration 2 Error: 0.109062 Iteration 3 Error: 0.031913 Align patch 12 13 left Iteration 1 Error: 1.300089 Iteration 2 Error: 0.106605 Iteration 3 Error: 0.018383 Align patch 13 12 left Iteration 1 Error: 0.608454 Iteration 2 Error: 0.126944 Iteration 3 Error: 0.026000 Align patch 14 11 left Iteration 1 Error: 0.583007 Iteration 2 Error: 0.053835 Iteration 3 Error: 0.018581 Align patch 15 10 left Iteration 1 Error: 0.467752 Iteration 2 Error: 0.065770 Iteration 3 Error: 0.010260 Align patch 16 9 left Iteration 1 Error: 0.823681 Iteration 2 Error: 0.178090 Iteration 3 Error: 0.040701 Align patch 17 8 left Iteration 1 Error: 0.638803 Iteration 2 Error: 0.050562 Iteration 3 Error: 0.014573 Align patch 18 7 left Iteration 1 Error: 0.526188 Iteration 2 Error: 0.091371 Iteration 3 Error: 0.028488 Align patch 19 6 left Iteration 1 Error: 0.521459 Iteration 2 Error: 0.071772 Iteration 3 Error: 0.022962 Align patch 20 5 left Iteration 1 Error: 0.899459 Iteration 2 Error: 0.090702 Iteration 3 Error: 0.014643 Align patch 21 4 left Iteration 1 Error: 0.542768 Iteration 2 Error: 0.091907 Iteration 3 Error: 0.015712 Align patch 22 3 left Iteration 1 Error: 0.918677 Iteration 2 Error: 0.139147 Iteration 3 Error: 0.030858 Align patch 23 2 left Iteration 1 Error: 0.694628 Iteration 2 Error: 0.094153 Iteration 3 Error: 0.024852 Align patch 24 1 left Iteration 1 Error: 1.169574 Iteration 2 Error: 0.122659 Iteration 3 Error: 0.021666 Align patch 25 0 left Iteration 1 Error: 0.825394 Iteration 2 Error: 0.092673 Iteration 3 Error: 0.019035 3D Fitting completed. Patch alignment time: 14.08(sec) Local motion has been corrected. Process thread exits. Computational time: 22.998159 sec Total time: 28.787807 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00021hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00021hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.749831s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00021hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.346285s ........................................ >>>>>>TIME<<<<<< FFT: 0.792393s Defocus_U Defocus_V Angle CCC 11578.14 12378.92 8.19 0.052982 Final Values Defocus_U Defocus_V Angle CCC 11584.39 12378.93 7.56 0.092825 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00021hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00021hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.001e-01 CC threshold: 0.735 Mean Std: 39.54 6.81 Num Hot pixels: 204 Hot pixel threshold: 80.41 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.772929 Iteration 2 Error: 0.416377 Iteration 3 Error: 0.157860 Iteration 4 Error: 0.065065 Iteration 5 Error: 0.026420 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.17 0.09 ...... Frame ( 3) shift: -0.34 0.18 ...... Frame ( 4) shift: -0.52 0.28 ...... Frame ( 5) shift: -0.69 0.37 ...... Frame ( 6) shift: -0.78 0.48 ...... Frame ( 7) shift: -0.78 0.62 ...... Frame ( 8) shift: -0.79 0.76 ...... Frame ( 9) shift: -0.80 0.91 ...... Frame ( 10) shift: -0.81 1.06 ...... Frame ( 11) shift: -0.82 1.21 ...... Frame ( 12) shift: -0.82 1.37 ...... Frame ( 13) shift: -0.80 1.53 ...... Frame ( 14) shift: -0.77 1.70 ...... Frame ( 15) shift: -0.75 1.86 ...... Frame ( 16) shift: -0.72 2.03 ...... Frame ( 17) shift: -0.70 2.19 ...... Frame ( 18) shift: -0.64 2.36 ...... Frame ( 19) shift: -0.55 2.53 ...... Frame ( 20) shift: -0.47 2.70 ...... Frame ( 21) shift: -0.43 2.83 ...... Frame ( 22) shift: -0.43 2.91 ...... Frame ( 23) shift: -0.43 2.98 ...... Frame ( 24) shift: -0.43 3.10 ...... Frame ( 25) shift: -0.42 3.24 ...... Frame ( 26) shift: -0.42 3.39 ...... Frame ( 27) shift: -0.40 3.49 ...... Frame ( 28) shift: -0.36 3.56 ...... Frame ( 29) shift: -0.32 3.62 ...... Frame ( 30) shift: -0.28 3.70 ...... Frame ( 31) shift: -0.22 3.78 ...... Frame ( 32) shift: -0.16 3.87 ...... Frame ( 33) shift: -0.17 3.94 ...... Frame ( 34) shift: -0.26 3.98 ...... Frame ( 35) shift: -0.35 4.03 ...... Frame ( 36) shift: -0.39 4.12 ...... Frame ( 37) shift: -0.37 4.25 ...... Frame ( 38) shift: -0.35 4.38 ...... Frame ( 39) shift: -0.34 4.52 ...... Frame ( 40) shift: -0.32 4.65 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.323659 Iteration 2 Error: 0.843318 Iteration 3 Error: 0.425233 Iteration 4 Error: 0.213380 Iteration 5 Error: 0.124179 Align patch 1 24 left Iteration 1 Error: 3.157037 Iteration 2 Error: 0.593699 Iteration 3 Error: 0.159004 Iteration 4 Error: 0.052751 Iteration 5 Error: 0.021520 Align patch 2 23 left Iteration 1 Error: 3.085794 Iteration 2 Error: 1.639865 Iteration 3 Error: 0.760152 Iteration 4 Error: 0.372177 Iteration 5 Error: 0.260490 Align patch 2 23 left Iteration 1 Error: 3.093927 Iteration 2 Error: 0.723153 Iteration 3 Error: 0.273692 Iteration 4 Error: 0.118240 Iteration 5 Error: 0.048253 Align patch 3 22 left Iteration 1 Error: 3.103553 Iteration 2 Error: 0.888749 Iteration 3 Error: 0.353808 Iteration 4 Error: 0.210995 Iteration 5 Error: 0.116644 Align patch 3 22 left Iteration 1 Error: 2.633699 Iteration 2 Error: 0.592883 Iteration 3 Error: 0.228893 Iteration 4 Error: 0.092873 Iteration 5 Error: 0.057017 Align patch 4 21 left Iteration 1 Error: 1.236222 Iteration 2 Error: 0.267183 Iteration 3 Error: 0.160935 Iteration 4 Error: 0.060089 Iteration 5 Error: 0.034041 Align patch 5 20 left Iteration 1 Error: 1.242998 Iteration 2 Error: 0.291524 Iteration 3 Error: 0.070286 Iteration 4 Error: 0.024587 Align patch 6 19 left Iteration 1 Error: 3.958203 Iteration 2 Error: 1.532964 Iteration 3 Error: 0.621689 Iteration 4 Error: 0.299732 Iteration 5 Error: 0.145522 Align patch 6 19 left Iteration 1 Error: 3.228753 Iteration 2 Error: 0.778868 Iteration 3 Error: 0.130288 Iteration 4 Error: 0.052346 Iteration 5 Error: 0.015169 Align patch 7 18 left Iteration 1 Error: 3.350207 Iteration 2 Error: 1.366061 Iteration 3 Error: 0.461323 Iteration 4 Error: 0.347203 Iteration 5 Error: 0.167124 Align patch 7 18 left Iteration 1 Error: 3.232495 Iteration 2 Error: 0.702525 Iteration 3 Error: 0.218703 Iteration 4 Error: 0.072024 Iteration 5 Error: 0.037430 Align patch 8 17 left Iteration 1 Error: 1.604093 Iteration 2 Error: 0.735315 Iteration 3 Error: 0.418629 Iteration 4 Error: 0.459175 Iteration 5 Error: 0.399041 Align patch 8 17 left Iteration 1 Error: 2.222187 Iteration 2 Error: 0.620880 Iteration 3 Error: 0.190171 Iteration 4 Error: 0.073201 Iteration 5 Error: 0.036790 Align patch 9 16 left Iteration 1 Error: 0.877777 Iteration 2 Error: 0.179645 Iteration 3 Error: 0.067445 Iteration 4 Error: 0.020920 Align patch 10 15 left Iteration 1 Error: 0.478793 Iteration 2 Error: 0.109152 Iteration 3 Error: 0.032232 Align patch 11 14 left Iteration 1 Error: 2.534941 Iteration 2 Error: 0.571060 Iteration 3 Error: 0.280552 Iteration 4 Error: 0.093200 Iteration 5 Error: 0.048734 Align patch 12 13 left Iteration 1 Error: 3.122558 Iteration 2 Error: 0.718469 Iteration 3 Error: 0.336421 Iteration 4 Error: 0.162569 Iteration 5 Error: 0.071956 Align patch 12 13 left Iteration 1 Error: 2.358884 Iteration 2 Error: 0.393313 Iteration 3 Error: 0.099465 Iteration 4 Error: 0.031426 Align patch 13 12 left Iteration 1 Error: 1.240193 Iteration 2 Error: 0.231480 Iteration 3 Error: 0.136776 Iteration 4 Error: 0.060726 Iteration 5 Error: 0.037966 Align patch 14 11 left Iteration 1 Error: 0.755288 Iteration 2 Error: 0.101805 Iteration 3 Error: 0.055189 Iteration 4 Error: 0.015768 Align patch 15 10 left Iteration 1 Error: 1.324337 Iteration 2 Error: 0.299539 Iteration 3 Error: 0.069777 Iteration 4 Error: 0.029229 Align patch 16 9 left Iteration 1 Error: 0.926858 Iteration 2 Error: 0.261758 Iteration 3 Error: 0.127091 Iteration 4 Error: 0.055740 Iteration 5 Error: 0.033917 Align patch 17 8 left Iteration 1 Error: 0.955585 Iteration 2 Error: 0.174206 Iteration 3 Error: 0.050264 Iteration 4 Error: 0.013265 Align patch 18 7 left Iteration 1 Error: 0.756895 Iteration 2 Error: 0.149748 Iteration 3 Error: 0.077487 Iteration 4 Error: 0.029855 Align patch 19 6 left Iteration 1 Error: 1.133844 Iteration 2 Error: 0.250243 Iteration 3 Error: 0.148094 Iteration 4 Error: 0.075633 Iteration 5 Error: 0.040004 Align patch 20 5 left Iteration 1 Error: 1.476900 Iteration 2 Error: 0.193795 Iteration 3 Error: 0.046341 Align patch 21 4 left Iteration 1 Error: 1.108034 Iteration 2 Error: 0.146874 Iteration 3 Error: 0.032931 Align patch 22 3 left Iteration 1 Error: 0.948252 Iteration 2 Error: 0.214741 Iteration 3 Error: 0.075733 Iteration 4 Error: 0.032502 Align patch 23 2 left Iteration 1 Error: 1.243183 Iteration 2 Error: 0.268789 Iteration 3 Error: 0.051345 Iteration 4 Error: 0.015573 Align patch 24 1 left Iteration 1 Error: 1.771464 Iteration 2 Error: 0.339463 Iteration 3 Error: 0.083976 Iteration 4 Error: 0.035767 Align patch 25 0 left Iteration 1 Error: 1.879122 Iteration 2 Error: 0.285817 Iteration 3 Error: 0.045540 3D Fitting completed. Patch alignment time: 23.90(sec) Local motion has been corrected. Process thread exits. Computational time: 33.469849 sec Total time: 40.360977 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00021hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00021hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.785085s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00021hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.556576s ........................................ >>>>>>TIME<<<<<< FFT: 0.921157s Defocus_U Defocus_V Angle CCC 14044.93 13380.86 82.14 0.047925 Final Values Defocus_U Defocus_V Angle CCC 14052.74 13382.42 81.83 0.078068 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00022hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00022hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.351e-01 1.004e-01 CC threshold: 0.737 Mean Std: 42.44 7.30 Num Hot pixels: 221 Hot pixel threshold: 86.24 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.650475 Iteration 2 Error: 0.076027 Iteration 3 Error: 0.014187 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.20 -0.00 ...... Frame ( 3) shift: -0.39 -0.01 ...... Frame ( 4) shift: -0.59 -0.01 ...... Frame ( 5) shift: -0.79 -0.01 ...... Frame ( 6) shift: -0.84 0.02 ...... Frame ( 7) shift: -0.75 0.07 ...... Frame ( 8) shift: -0.66 0.13 ...... Frame ( 9) shift: -0.60 0.21 ...... Frame ( 10) shift: -0.57 0.30 ...... Frame ( 11) shift: -0.54 0.40 ...... Frame ( 12) shift: -0.53 0.49 ...... Frame ( 13) shift: -0.55 0.58 ...... Frame ( 14) shift: -0.58 0.66 ...... Frame ( 15) shift: -0.58 0.73 ...... Frame ( 16) shift: -0.56 0.79 ...... Frame ( 17) shift: -0.55 0.85 ...... Frame ( 18) shift: -0.55 0.86 ...... Frame ( 19) shift: -0.56 0.83 ...... Frame ( 20) shift: -0.58 0.81 ...... Frame ( 21) shift: -0.60 0.76 ...... Frame ( 22) shift: -0.63 0.71 ...... Frame ( 23) shift: -0.66 0.65 ...... Frame ( 24) shift: -0.68 0.62 ...... Frame ( 25) shift: -0.68 0.61 ...... Frame ( 26) shift: -0.68 0.61 ...... Frame ( 27) shift: -0.66 0.62 ...... Frame ( 28) shift: -0.61 0.65 ...... Frame ( 29) shift: -0.56 0.68 ...... Frame ( 30) shift: -0.52 0.72 ...... Frame ( 31) shift: -0.49 0.76 ...... Frame ( 32) shift: -0.45 0.80 ...... Frame ( 33) shift: -0.42 0.87 ...... Frame ( 34) shift: -0.40 0.99 ...... Frame ( 35) shift: -0.37 1.10 ...... Frame ( 36) shift: -0.36 1.16 ...... Frame ( 37) shift: -0.36 1.17 ...... Frame ( 38) shift: -0.37 1.19 ...... Frame ( 39) shift: -0.38 1.20 ...... Frame ( 40) shift: -0.38 1.21 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.337224 Iteration 2 Error: 0.143368 Iteration 3 Error: 0.037960 Align patch 2 23 left Iteration 1 Error: 1.434462 Iteration 2 Error: 0.263401 Iteration 3 Error: 0.075148 Iteration 4 Error: 0.025546 Align patch 3 22 left Iteration 1 Error: 0.710847 Iteration 2 Error: 0.127678 Iteration 3 Error: 0.030774 Align patch 4 21 left Iteration 1 Error: 1.115281 Iteration 2 Error: 0.180884 Iteration 3 Error: 0.039075 Align patch 5 20 left Iteration 1 Error: 1.065047 Iteration 2 Error: 0.191736 Iteration 3 Error: 0.035590 Align patch 6 19 left Iteration 1 Error: 1.651994 Iteration 2 Error: 0.189085 Iteration 3 Error: 0.031630 Align patch 7 18 left Iteration 1 Error: 1.363048 Iteration 2 Error: 0.221093 Iteration 3 Error: 0.058001 Iteration 4 Error: 0.016244 Align patch 8 17 left Iteration 1 Error: 1.540177 Iteration 2 Error: 0.238036 Iteration 3 Error: 0.071236 Iteration 4 Error: 0.016622 Align patch 9 16 left Iteration 1 Error: 0.939709 Iteration 2 Error: 0.217024 Iteration 3 Error: 0.071666 Iteration 4 Error: 0.024973 Align patch 10 15 left Iteration 1 Error: 1.026984 Iteration 2 Error: 0.187841 Iteration 3 Error: 0.036502 Align patch 11 14 left Iteration 1 Error: 0.690821 Iteration 2 Error: 0.083458 Iteration 3 Error: 0.020610 Align patch 12 13 left Iteration 1 Error: 0.584109 Iteration 2 Error: 0.087688 Iteration 3 Error: 0.015609 Align patch 13 12 left Iteration 1 Error: 0.904043 Iteration 2 Error: 0.200558 Iteration 3 Error: 0.061358 Iteration 4 Error: 0.016032 Align patch 14 11 left Iteration 1 Error: 0.762017 Iteration 2 Error: 0.140268 Iteration 3 Error: 0.042033 Align patch 15 10 left Iteration 1 Error: 0.883371 Iteration 2 Error: 0.184198 Iteration 3 Error: 0.031856 Align patch 16 9 left Iteration 1 Error: 0.735476 Iteration 2 Error: 0.084268 Iteration 3 Error: 0.017921 Align patch 17 8 left Iteration 1 Error: 0.658868 Iteration 2 Error: 0.083959 Iteration 3 Error: 0.016190 Align patch 18 7 left Iteration 1 Error: 0.729064 Iteration 2 Error: 0.075458 Iteration 3 Error: 0.017042 Align patch 19 6 left Iteration 1 Error: 0.665179 Iteration 2 Error: 0.092766 Iteration 3 Error: 0.016172 Align patch 20 5 left Iteration 1 Error: 1.022500 Iteration 2 Error: 0.106254 Iteration 3 Error: 0.018683 Align patch 21 4 left Iteration 1 Error: 1.407557 Iteration 2 Error: 0.098594 Iteration 3 Error: 0.015800 Align patch 22 3 left Iteration 1 Error: 0.843504 Iteration 2 Error: 0.095880 Iteration 3 Error: 0.019891 Align patch 23 2 left Iteration 1 Error: 1.149759 Iteration 2 Error: 0.136583 Iteration 3 Error: 0.033588 Align patch 24 1 left Iteration 1 Error: 0.590709 Iteration 2 Error: 0.059789 Iteration 3 Error: 0.016888 Align patch 25 0 left Iteration 1 Error: 0.888423 Iteration 2 Error: 0.109433 Iteration 3 Error: 0.020626 3D Fitting completed. Patch alignment time: 15.14(sec) Local motion has been corrected. Process thread exits. Computational time: 24.082718 sec Total time: 29.798409 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00022hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00022hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.577008s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00022hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.467762s ........................................ >>>>>>TIME<<<<<< FFT: 0.794831s Defocus_U Defocus_V Angle CCC 13580.08 14341.80 10.03 0.069942 Final Values Defocus_U Defocus_V Angle CCC 13578.56 14352.79 10.03 0.115308 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00022hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00022hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.353e-01 1.006e-01 CC threshold: 0.739 Mean Std: 42.89 7.40 Num Hot pixels: 198 Hot pixel threshold: 87.31 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.656589 Iteration 2 Error: 0.072716 Iteration 3 Error: 0.014403 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.26 0.03 ...... Frame ( 3) shift: -0.53 0.06 ...... Frame ( 4) shift: -0.79 0.09 ...... Frame ( 5) shift: -1.06 0.12 ...... Frame ( 6) shift: -1.17 0.14 ...... Frame ( 7) shift: -1.14 0.17 ...... Frame ( 8) shift: -1.11 0.20 ...... Frame ( 9) shift: -1.05 0.23 ...... Frame ( 10) shift: -0.96 0.28 ...... Frame ( 11) shift: -0.88 0.34 ...... Frame ( 12) shift: -0.81 0.39 ...... Frame ( 13) shift: -0.76 0.46 ...... Frame ( 14) shift: -0.72 0.52 ...... Frame ( 15) shift: -0.69 0.55 ...... Frame ( 16) shift: -0.70 0.55 ...... Frame ( 17) shift: -0.70 0.55 ...... Frame ( 18) shift: -0.73 0.55 ...... Frame ( 19) shift: -0.78 0.56 ...... Frame ( 20) shift: -0.83 0.56 ...... Frame ( 21) shift: -0.85 0.57 ...... Frame ( 22) shift: -0.83 0.59 ...... Frame ( 23) shift: -0.81 0.62 ...... Frame ( 24) shift: -0.79 0.64 ...... Frame ( 25) shift: -0.77 0.65 ...... Frame ( 26) shift: -0.75 0.67 ...... Frame ( 27) shift: -0.74 0.69 ...... Frame ( 28) shift: -0.73 0.72 ...... Frame ( 29) shift: -0.72 0.74 ...... Frame ( 30) shift: -0.72 0.77 ...... Frame ( 31) shift: -0.73 0.82 ...... Frame ( 32) shift: -0.75 0.86 ...... Frame ( 33) shift: -0.78 0.89 ...... Frame ( 34) shift: -0.83 0.93 ...... Frame ( 35) shift: -0.88 0.96 ...... Frame ( 36) shift: -0.90 0.99 ...... Frame ( 37) shift: -0.89 1.00 ...... Frame ( 38) shift: -0.88 1.01 ...... Frame ( 39) shift: -0.86 1.03 ...... Frame ( 40) shift: -0.85 1.04 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.728136 Iteration 2 Error: 0.192379 Iteration 3 Error: 0.044584 Align patch 2 23 left Iteration 1 Error: 1.355420 Iteration 2 Error: 0.149203 Iteration 3 Error: 0.048303 Align patch 3 22 left Iteration 1 Error: 0.690801 Iteration 2 Error: 0.098846 Iteration 3 Error: 0.026972 Align patch 4 21 left Iteration 1 Error: 0.503769 Iteration 2 Error: 0.084686 Iteration 3 Error: 0.017446 Align patch 5 20 left Iteration 1 Error: 0.459812 Iteration 2 Error: 0.037986 Align patch 6 19 left Iteration 1 Error: 1.833404 Iteration 2 Error: 0.219205 Iteration 3 Error: 0.073516 Iteration 4 Error: 0.016835 Align patch 7 18 left Iteration 1 Error: 1.199545 Iteration 2 Error: 0.125586 Iteration 3 Error: 0.019054 Align patch 8 17 left Iteration 1 Error: 0.613085 Iteration 2 Error: 0.097598 Iteration 3 Error: 0.025945 Align patch 9 16 left Iteration 1 Error: 0.434947 Iteration 2 Error: 0.073433 Iteration 3 Error: 0.014237 Align patch 10 15 left Iteration 1 Error: 0.490403 Iteration 2 Error: 0.057961 Iteration 3 Error: 0.015688 Align patch 11 14 left Iteration 1 Error: 0.710722 Iteration 2 Error: 0.082605 Iteration 3 Error: 0.018126 Align patch 12 13 left Iteration 1 Error: 0.464513 Iteration 2 Error: 0.052653 Iteration 3 Error: 0.016619 Align patch 13 12 left Iteration 1 Error: 0.459222 Iteration 2 Error: 0.059549 Iteration 3 Error: 0.014151 Align patch 14 11 left Iteration 1 Error: 0.503451 Iteration 2 Error: 0.044801 Align patch 15 10 left Iteration 1 Error: 0.691465 Iteration 2 Error: 0.081458 Iteration 3 Error: 0.020931 Align patch 16 9 left Iteration 1 Error: 0.710501 Iteration 2 Error: 0.089565 Iteration 3 Error: 0.014338 Align patch 17 8 left Iteration 1 Error: 1.002786 Iteration 2 Error: 0.147769 Iteration 3 Error: 0.022907 Align patch 18 7 left Iteration 1 Error: 0.762676 Iteration 2 Error: 0.130941 Iteration 3 Error: 0.041111 Align patch 19 6 left Iteration 1 Error: 0.517934 Iteration 2 Error: 0.038504 Align patch 20 5 left Iteration 1 Error: 0.604087 Iteration 2 Error: 0.079176 Iteration 3 Error: 0.011733 Align patch 21 4 left Iteration 1 Error: 1.286417 Iteration 2 Error: 0.192615 Iteration 3 Error: 0.038202 Align patch 22 3 left Iteration 1 Error: 0.988683 Iteration 2 Error: 0.095793 Iteration 3 Error: 0.025024 Align patch 23 2 left Iteration 1 Error: 1.596260 Iteration 2 Error: 0.180619 Iteration 3 Error: 0.030050 Align patch 24 1 left Iteration 1 Error: 0.598494 Iteration 2 Error: 0.077882 Iteration 3 Error: 0.013164 Align patch 25 0 left Iteration 1 Error: 0.688210 Iteration 2 Error: 0.098514 Iteration 3 Error: 0.023769 3D Fitting completed. Patch alignment time: 14.50(sec) Local motion has been corrected. Process thread exits. Computational time: 23.675833 sec Total time: 29.374619 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00022hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00022hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.793983s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00022hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.188898s ........................................ >>>>>>TIME<<<<<< FFT: 1.007435s Defocus_U Defocus_V Angle CCC 8710.94 9179.69 1.68 0.050373 Final Values Defocus_U Defocus_V Angle CCC 8709.37 9181.25 1.06 0.101691 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00022hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00022hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.002e-01 CC threshold: 0.736 Mean Std: 42.30 7.11 Num Hot pixels: 203 Hot pixel threshold: 84.97 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.694524 Iteration 2 Error: 0.090805 Iteration 3 Error: 0.018810 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.24 -0.12 ...... Frame ( 3) shift: -0.47 -0.24 ...... Frame ( 4) shift: -0.71 -0.36 ...... Frame ( 5) shift: -0.95 -0.47 ...... Frame ( 6) shift: -1.07 -0.49 ...... Frame ( 7) shift: -1.06 -0.42 ...... Frame ( 8) shift: -1.06 -0.34 ...... Frame ( 9) shift: -1.03 -0.26 ...... Frame ( 10) shift: -0.98 -0.19 ...... Frame ( 11) shift: -0.92 -0.11 ...... Frame ( 12) shift: -0.87 -0.04 ...... Frame ( 13) shift: -0.82 0.02 ...... Frame ( 14) shift: -0.77 0.09 ...... Frame ( 15) shift: -0.75 0.12 ...... Frame ( 16) shift: -0.75 0.13 ...... Frame ( 17) shift: -0.75 0.14 ...... Frame ( 18) shift: -0.74 0.15 ...... Frame ( 19) shift: -0.73 0.16 ...... Frame ( 20) shift: -0.71 0.17 ...... Frame ( 21) shift: -0.70 0.20 ...... Frame ( 22) shift: -0.71 0.25 ...... Frame ( 23) shift: -0.72 0.30 ...... Frame ( 24) shift: -0.68 0.34 ...... Frame ( 25) shift: -0.59 0.37 ...... Frame ( 26) shift: -0.51 0.40 ...... Frame ( 27) shift: -0.48 0.41 ...... Frame ( 28) shift: -0.50 0.41 ...... Frame ( 29) shift: -0.52 0.41 ...... Frame ( 30) shift: -0.51 0.40 ...... Frame ( 31) shift: -0.47 0.37 ...... Frame ( 32) shift: -0.43 0.35 ...... Frame ( 33) shift: -0.41 0.36 ...... Frame ( 34) shift: -0.43 0.42 ...... Frame ( 35) shift: -0.45 0.47 ...... Frame ( 36) shift: -0.49 0.51 ...... Frame ( 37) shift: -0.55 0.55 ...... Frame ( 38) shift: -0.61 0.58 ...... Frame ( 39) shift: -0.67 0.62 ...... Frame ( 40) shift: -0.73 0.65 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.905334 Iteration 2 Error: 0.427838 Iteration 3 Error: 0.134847 Iteration 4 Error: 0.065848 Iteration 5 Error: 0.029292 Align patch 2 23 left Iteration 1 Error: 1.332761 Iteration 2 Error: 0.211095 Iteration 3 Error: 0.039328 Align patch 3 22 left Iteration 1 Error: 1.089346 Iteration 2 Error: 0.106859 Iteration 3 Error: 0.036789 Align patch 4 21 left Iteration 1 Error: 0.528851 Iteration 2 Error: 0.113250 Iteration 3 Error: 0.018662 Align patch 5 20 left Iteration 1 Error: 0.630486 Iteration 2 Error: 0.115928 Iteration 3 Error: 0.023530 Align patch 6 19 left Iteration 1 Error: 1.308556 Iteration 2 Error: 0.188242 Iteration 3 Error: 0.037180 Align patch 7 18 left Iteration 1 Error: 1.713545 Iteration 2 Error: 0.284104 Iteration 3 Error: 0.064985 Iteration 4 Error: 0.023146 Align patch 8 17 left Iteration 1 Error: 0.556917 Iteration 2 Error: 0.129629 Iteration 3 Error: 0.036369 Align patch 9 16 left Iteration 1 Error: 0.529951 Iteration 2 Error: 0.068454 Iteration 3 Error: 0.018034 Align patch 10 15 left Iteration 1 Error: 0.484028 Iteration 2 Error: 0.076635 Iteration 3 Error: 0.012621 Align patch 11 14 left Iteration 1 Error: 0.766979 Iteration 2 Error: 0.116452 Iteration 3 Error: 0.037942 Align patch 12 13 left Iteration 1 Error: 0.675752 Iteration 2 Error: 0.252277 Iteration 3 Error: 0.072141 Iteration 4 Error: 0.022719 Align patch 13 12 left Iteration 1 Error: 0.606132 Iteration 2 Error: 0.124347 Iteration 3 Error: 0.027354 Align patch 14 11 left Iteration 1 Error: 0.725774 Iteration 2 Error: 0.114787 Iteration 3 Error: 0.031796 Align patch 15 10 left Iteration 1 Error: 0.542235 Iteration 2 Error: 0.064102 Iteration 3 Error: 0.018123 Align patch 16 9 left Iteration 1 Error: 0.609320 Iteration 2 Error: 0.137496 Iteration 3 Error: 0.040353 Align patch 17 8 left Iteration 1 Error: 0.723200 Iteration 2 Error: 0.117233 Iteration 3 Error: 0.022638 Align patch 18 7 left Iteration 1 Error: 0.491766 Iteration 2 Error: 0.122225 Iteration 3 Error: 0.032100 Align patch 19 6 left Iteration 1 Error: 0.586458 Iteration 2 Error: 0.067616 Iteration 3 Error: 0.012241 Align patch 20 5 left Iteration 1 Error: 0.452461 Iteration 2 Error: 0.071088 Iteration 3 Error: 0.013272 Align patch 21 4 left Iteration 1 Error: 0.746768 Iteration 2 Error: 0.067642 Iteration 3 Error: 0.024630 Align patch 22 3 left Iteration 1 Error: 1.154463 Iteration 2 Error: 0.130634 Iteration 3 Error: 0.024372 Align patch 23 2 left Iteration 1 Error: 0.785645 Iteration 2 Error: 0.106480 Iteration 3 Error: 0.020014 Align patch 24 1 left Iteration 1 Error: 0.717634 Iteration 2 Error: 0.081095 Iteration 3 Error: 0.018240 Align patch 25 0 left Iteration 1 Error: 0.589785 Iteration 2 Error: 0.101186 Iteration 3 Error: 0.025020 3D Fitting completed. Patch alignment time: 14.92(sec) Local motion has been corrected. Process thread exits. Computational time: 24.069099 sec Total time: 29.713779 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00022hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00022hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.546423s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00022hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.745609s ........................................ >>>>>>TIME<<<<<< FFT: 0.937958s Defocus_U Defocus_V Angle CCC 11390.63 12191.41 5.72 0.051250 Final Values Defocus_U Defocus_V Angle CCC 11403.13 12228.91 5.41 0.088354 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00011sq_v01_00022hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00022hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 42.56 7.20 Num Hot pixels: 205 Hot pixel threshold: 85.74 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.761620 Iteration 2 Error: 0.119959 Iteration 3 Error: 0.021896 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.34 -0.10 ...... Frame ( 3) shift: -0.67 -0.19 ...... Frame ( 4) shift: -1.01 -0.29 ...... Frame ( 5) shift: -1.35 -0.39 ...... Frame ( 6) shift: -1.50 -0.49 ...... Frame ( 7) shift: -1.48 -0.61 ...... Frame ( 8) shift: -1.45 -0.72 ...... Frame ( 9) shift: -1.40 -0.76 ...... Frame ( 10) shift: -1.33 -0.74 ...... Frame ( 11) shift: -1.25 -0.71 ...... Frame ( 12) shift: -1.19 -0.65 ...... Frame ( 13) shift: -1.15 -0.58 ...... Frame ( 14) shift: -1.11 -0.50 ...... Frame ( 15) shift: -1.11 -0.43 ...... Frame ( 16) shift: -1.15 -0.38 ...... Frame ( 17) shift: -1.19 -0.32 ...... Frame ( 18) shift: -1.16 -0.27 ...... Frame ( 19) shift: -1.07 -0.24 ...... Frame ( 20) shift: -0.97 -0.20 ...... Frame ( 21) shift: -0.88 -0.20 ...... Frame ( 22) shift: -0.80 -0.22 ...... Frame ( 23) shift: -0.72 -0.24 ...... Frame ( 24) shift: -0.64 -0.22 ...... Frame ( 25) shift: -0.57 -0.16 ...... Frame ( 26) shift: -0.51 -0.10 ...... Frame ( 27) shift: -0.44 -0.04 ...... Frame ( 28) shift: -0.37 0.03 ...... Frame ( 29) shift: -0.30 0.10 ...... Frame ( 30) shift: -0.26 0.10 ...... Frame ( 31) shift: -0.24 0.04 ...... Frame ( 32) shift: -0.23 -0.03 ...... Frame ( 33) shift: -0.22 -0.04 ...... Frame ( 34) shift: -0.24 0.02 ...... Frame ( 35) shift: -0.25 0.07 ...... Frame ( 36) shift: -0.27 0.08 ...... Frame ( 37) shift: -0.28 0.03 ...... Frame ( 38) shift: -0.29 -0.01 ...... Frame ( 39) shift: -0.31 -0.06 ...... Frame ( 40) shift: -0.32 -0.10 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.726294 Iteration 2 Error: 0.340129 Iteration 3 Error: 0.161842 Iteration 4 Error: 0.077237 Iteration 5 Error: 0.031047 Align patch 2 23 left Iteration 1 Error: 0.874887 Iteration 2 Error: 0.129237 Iteration 3 Error: 0.024673 Align patch 3 22 left Iteration 1 Error: 0.794682 Iteration 2 Error: 0.118827 Iteration 3 Error: 0.024590 Align patch 4 21 left Iteration 1 Error: 0.728610 Iteration 2 Error: 0.111977 Iteration 3 Error: 0.025966 Align patch 5 20 left Iteration 1 Error: 0.660201 Iteration 2 Error: 0.075165 Iteration 3 Error: 0.017665 Align patch 6 19 left Iteration 1 Error: 1.210307 Iteration 2 Error: 0.216374 Iteration 3 Error: 0.050604 Iteration 4 Error: 0.026696 Align patch 7 18 left Iteration 1 Error: 0.917304 Iteration 2 Error: 0.147248 Iteration 3 Error: 0.038506 Align patch 8 17 left Iteration 1 Error: 0.603186 Iteration 2 Error: 0.139628 Iteration 3 Error: 0.027867 Align patch 9 16 left Iteration 1 Error: 0.454720 Iteration 2 Error: 0.086438 Iteration 3 Error: 0.012668 Align patch 10 15 left Iteration 1 Error: 0.535278 Iteration 2 Error: 0.044635 Align patch 11 14 left Iteration 1 Error: 0.935646 Iteration 2 Error: 0.157983 Iteration 3 Error: 0.026366 Align patch 12 13 left Iteration 1 Error: 0.760858 Iteration 2 Error: 0.088272 Iteration 3 Error: 0.014535 Align patch 13 12 left Iteration 1 Error: 0.430771 Iteration 2 Error: 0.066510 Iteration 3 Error: 0.011827 Align patch 14 11 left Iteration 1 Error: 0.512169 Iteration 2 Error: 0.091934 Iteration 3 Error: 0.017257 Align patch 15 10 left Iteration 1 Error: 0.400266 Iteration 2 Error: 0.059804 Iteration 3 Error: 0.009795 Align patch 16 9 left Iteration 1 Error: 0.692798 Iteration 2 Error: 0.142336 Iteration 3 Error: 0.024966 Align patch 17 8 left Iteration 1 Error: 0.486388 Iteration 2 Error: 0.087460 Iteration 3 Error: 0.017832 Align patch 18 7 left Iteration 1 Error: 0.685950 Iteration 2 Error: 0.101469 Iteration 3 Error: 0.022457 Align patch 19 6 left Iteration 1 Error: 0.758756 Iteration 2 Error: 0.142737 Iteration 3 Error: 0.027500 Align patch 20 5 left Iteration 1 Error: 0.768011 Iteration 2 Error: 0.113098 Iteration 3 Error: 0.015584 Align patch 21 4 left Iteration 1 Error: 0.744631 Iteration 2 Error: 0.088918 Iteration 3 Error: 0.015147 Align patch 22 3 left Iteration 1 Error: 0.897461 Iteration 2 Error: 0.120607 Iteration 3 Error: 0.028376 Align patch 23 2 left Iteration 1 Error: 0.957869 Iteration 2 Error: 0.090813 Iteration 3 Error: 0.021472 Align patch 24 1 left Iteration 1 Error: 1.457194 Iteration 2 Error: 0.182968 Iteration 3 Error: 0.035102 Align patch 25 0 left Iteration 1 Error: 1.130752 Iteration 2 Error: 0.115214 Iteration 3 Error: 0.017038 3D Fitting completed. Patch alignment time: 14.57(sec) Local motion has been corrected. Process thread exits. Computational time: 23.898672 sec Total time: 30.750544 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00022hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00022hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.564840s Reading file: gc_18feb27f_CTD_g1_00017gr_00011sq_v01_00022hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.125616s ........................................ >>>>>>TIME<<<<<< FFT: 0.929315s Defocus_U Defocus_V Angle CCC 14701.21 14040.98 82.95 0.065636 Final Values Defocus_U Defocus_V Angle CCC 14712.15 14045.67 82.32 0.106825 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00013sq_v01_00002hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00002hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.325e-01 9.864e-02 CC threshold: 0.724 Mean Std: 17.34 10.07 Num Hot pixels: 34 Hot pixel threshold: 77.75 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.655109 Iteration 2 Error: 0.067207 Iteration 3 Error: 0.009938 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.02 -0.00 ...... Frame ( 3) shift: 0.04 -0.00 ...... Frame ( 4) shift: 0.06 -0.00 ...... Frame ( 5) shift: 0.08 -0.00 ...... Frame ( 6) shift: 0.10 0.01 ...... Frame ( 7) shift: 0.12 0.03 ...... Frame ( 8) shift: 0.13 0.05 ...... Frame ( 9) shift: 0.14 0.08 ...... Frame ( 10) shift: 0.15 0.10 ...... Frame ( 11) shift: 0.16 0.12 ...... Frame ( 12) shift: 0.16 0.15 ...... Frame ( 13) shift: 0.15 0.19 ...... Frame ( 14) shift: 0.15 0.22 ...... Frame ( 15) shift: 0.15 0.24 ...... Frame ( 16) shift: 0.16 0.24 ...... Frame ( 17) shift: 0.17 0.24 ...... Frame ( 18) shift: 0.17 0.25 ...... Frame ( 19) shift: 0.16 0.27 ...... Frame ( 20) shift: 0.15 0.30 ...... Frame ( 21) shift: 0.18 0.32 ...... Frame ( 22) shift: 0.26 0.35 ...... Frame ( 23) shift: 0.33 0.38 ...... Frame ( 24) shift: 0.38 0.44 ...... Frame ( 25) shift: 0.38 0.52 ...... Frame ( 26) shift: 0.39 0.61 ...... Frame ( 27) shift: 0.39 0.69 ...... Frame ( 28) shift: 0.39 0.76 ...... Frame ( 29) shift: 0.38 0.84 ...... Frame ( 30) shift: 0.38 0.91 ...... Frame ( 31) shift: 0.37 0.97 ...... Frame ( 32) shift: 0.36 1.03 ...... Frame ( 33) shift: 0.39 1.07 ...... Frame ( 34) shift: 0.46 1.10 ...... Frame ( 35) shift: 0.53 1.12 ...... Frame ( 36) shift: 0.57 1.13 ...... Frame ( 37) shift: 0.57 1.11 ...... Frame ( 38) shift: 0.58 1.10 ...... Frame ( 39) shift: 0.58 1.09 ...... Frame ( 40) shift: 0.59 1.07 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 4.872092 Iteration 2 Error: 0.929978 Iteration 3 Error: 0.327902 Iteration 4 Error: 0.252395 Iteration 5 Error: 0.175197 Align patch 1 24 left Iteration 1 Error: 5.666934 Iteration 2 Error: 0.550917 Iteration 3 Error: 0.093029 Iteration 4 Error: 0.031234 Align patch 2 23 left Iteration 1 Error: 4.596272 Iteration 2 Error: 0.919211 Iteration 3 Error: 0.336651 Iteration 4 Error: 0.171913 Iteration 5 Error: 0.058852 Align patch 2 23 left Iteration 1 Error: 4.964582 Iteration 2 Error: 0.638436 Iteration 3 Error: 0.073365 Iteration 4 Error: 0.024305 Align patch 3 22 left Iteration 1 Error: 2.687133 Iteration 2 Error: 0.617934 Iteration 3 Error: 0.391591 Iteration 4 Error: 0.237015 Iteration 5 Error: 0.131954 Align patch 3 22 left Iteration 1 Error: 3.699412 Iteration 2 Error: 0.594044 Iteration 3 Error: 0.147719 Iteration 4 Error: 0.045732 Align patch 4 21 left Iteration 1 Error: 0.626066 Iteration 2 Error: 0.103836 Iteration 3 Error: 0.014505 Align patch 5 20 left Iteration 1 Error: 2.297881 Iteration 2 Error: 0.088032 Iteration 3 Error: 0.018233 Align patch 6 19 left Iteration 1 Error: 4.652627 Iteration 2 Error: 0.900206 Iteration 3 Error: 0.332355 Iteration 4 Error: 0.202856 Iteration 5 Error: 0.093998 Align patch 6 19 left Iteration 1 Error: 5.302093 Iteration 2 Error: 0.443312 Iteration 3 Error: 0.066909 Iteration 4 Error: 0.026462 Align patch 7 18 left Iteration 1 Error: 3.975022 Iteration 2 Error: 0.417926 Iteration 3 Error: 0.086204 Iteration 4 Error: 0.017569 Align patch 8 17 left Iteration 1 Error: 2.610106 Iteration 2 Error: 0.833085 Iteration 3 Error: 0.344535 Iteration 4 Error: 0.185058 Iteration 5 Error: 0.094883 Align patch 8 17 left Iteration 1 Error: 3.429828 Iteration 2 Error: 0.490908 Iteration 3 Error: 0.138552 Iteration 4 Error: 0.024975 Align patch 9 16 left Iteration 1 Error: 1.035684 Iteration 2 Error: 0.151859 Iteration 3 Error: 0.026238 Align patch 10 15 left Iteration 1 Error: 1.380715 Iteration 2 Error: 0.053871 Iteration 3 Error: 0.008315 Align patch 11 14 left Iteration 1 Error: 3.259223 Iteration 2 Error: 2.509202 Iteration 3 Error: 0.441473 Iteration 4 Error: 0.159896 Iteration 5 Error: 0.076458 Align patch 11 14 left Iteration 1 Error: 4.774597 Iteration 2 Error: 0.383617 Iteration 3 Error: 0.105291 Iteration 4 Error: 0.037241 Align patch 12 13 left Iteration 1 Error: 2.549470 Iteration 2 Error: 0.452772 Iteration 3 Error: 0.314386 Iteration 4 Error: 0.200795 Iteration 5 Error: 0.114458 Align patch 12 13 left Iteration 1 Error: 4.025572 Iteration 2 Error: 0.307593 Iteration 3 Error: 0.081335 Iteration 4 Error: 0.030947 Align patch 13 12 left Iteration 1 Error: 2.000256 Iteration 2 Error: 0.665710 Iteration 3 Error: 0.546374 Iteration 4 Error: 0.393659 Iteration 5 Error: 0.273114 Align patch 13 12 left Iteration 1 Error: 0.989992 Iteration 2 Error: 0.113336 Iteration 3 Error: 0.028943 Align patch 14 11 left Iteration 1 Error: 1.764181 Iteration 2 Error: 0.111874 Iteration 3 Error: 0.027140 Align patch 15 10 left Iteration 1 Error: 1.429483 Iteration 2 Error: 0.053259 Iteration 3 Error: 0.005224 Align patch 16 9 left Iteration 1 Error: 4.812943 Iteration 2 Error: 0.554499 Iteration 3 Error: 0.216658 Iteration 4 Error: 0.160921 Iteration 5 Error: 0.109391 Align patch 16 9 left Iteration 1 Error: 3.813607 Iteration 2 Error: 0.383395 Iteration 3 Error: 0.118060 Iteration 4 Error: 0.039740 Align patch 17 8 left Iteration 1 Error: 2.114223 Iteration 2 Error: 0.406733 Iteration 3 Error: 0.181407 Iteration 4 Error: 0.055459 Iteration 5 Error: 0.020883 Align patch 18 7 left Iteration 1 Error: 1.475445 Iteration 2 Error: 0.108043 Iteration 3 Error: 0.018328 Align patch 19 6 left Iteration 1 Error: 1.853142 Iteration 2 Error: 0.235022 Iteration 3 Error: 0.049807 Align patch 20 5 left Iteration 1 Error: 2.509494 Iteration 2 Error: 0.256534 Iteration 3 Error: 0.053160 Iteration 4 Error: 0.013934 Align patch 21 4 left Iteration 1 Error: 3.924853 Iteration 2 Error: 0.530032 Iteration 3 Error: 0.264818 Iteration 4 Error: 0.144583 Iteration 5 Error: 0.074610 Align patch 21 4 left Iteration 1 Error: 4.081921 Iteration 2 Error: 0.356683 Iteration 3 Error: 0.137750 Iteration 4 Error: 0.039531 Align patch 22 3 left Iteration 1 Error: 2.188970 Iteration 2 Error: 0.418995 Iteration 3 Error: 0.150348 Iteration 4 Error: 0.058522 Iteration 5 Error: 0.026182 Align patch 23 2 left Iteration 1 Error: 1.282941 Iteration 2 Error: 0.093178 Iteration 3 Error: 0.015982 Align patch 24 1 left Iteration 1 Error: 2.253941 Iteration 2 Error: 0.173481 Iteration 3 Error: 0.017841 Align patch 25 0 left Iteration 1 Error: 2.538362 Iteration 2 Error: 0.181037 Iteration 3 Error: 0.021274 3D Fitting completed. Patch alignment time: 24.51(sec) Local motion has been corrected. Process thread exits. Computational time: 33.509552 sec Total time: 39.409714 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00002hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00002hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.567650s Reading file: gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00002hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.488752s ........................................ >>>>>>TIME<<<<<< FFT: 0.942286s Defocus_U Defocus_V Angle CCC 21613.28 21144.53 78.49 -0.047990 Final Values Defocus_U Defocus_V Angle CCC 21611.75 21133.65 81.33 -0.172539 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00013sq_v01_00003hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00003hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.997e-02 CC threshold: 0.734 Mean Std: 38.65 6.62 Num Hot pixels: 245 Hot pixel threshold: 78.36 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.323532 Iteration 2 Error: 0.381376 Iteration 3 Error: 0.108873 Iteration 4 Error: 0.046573 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.01 -0.04 ...... Frame ( 3) shift: 0.02 -0.09 ...... Frame ( 4) shift: 0.04 -0.13 ...... Frame ( 5) shift: 0.05 -0.18 ...... Frame ( 6) shift: 0.13 -0.19 ...... Frame ( 7) shift: 0.30 -0.18 ...... Frame ( 8) shift: 0.46 -0.17 ...... Frame ( 9) shift: 0.58 -0.13 ...... Frame ( 10) shift: 0.65 -0.05 ...... Frame ( 11) shift: 0.73 0.03 ...... Frame ( 12) shift: 0.83 0.06 ...... Frame ( 13) shift: 0.97 0.04 ...... Frame ( 14) shift: 1.11 0.02 ...... Frame ( 15) shift: 1.24 -0.01 ...... Frame ( 16) shift: 1.36 -0.05 ...... Frame ( 17) shift: 1.47 -0.10 ...... Frame ( 18) shift: 1.55 -0.12 ...... Frame ( 19) shift: 1.58 -0.12 ...... Frame ( 20) shift: 1.62 -0.12 ...... Frame ( 21) shift: 1.72 -0.14 ...... Frame ( 22) shift: 1.89 -0.18 ...... Frame ( 23) shift: 2.05 -0.23 ...... Frame ( 24) shift: 2.18 -0.23 ...... Frame ( 25) shift: 2.28 -0.18 ...... Frame ( 26) shift: 2.38 -0.13 ...... Frame ( 27) shift: 2.46 -0.12 ...... Frame ( 28) shift: 2.53 -0.13 ...... Frame ( 29) shift: 2.61 -0.14 ...... Frame ( 30) shift: 2.70 -0.17 ...... Frame ( 31) shift: 2.81 -0.22 ...... Frame ( 32) shift: 2.92 -0.27 ...... Frame ( 33) shift: 2.95 -0.30 ...... Frame ( 34) shift: 2.91 -0.30 ...... Frame ( 35) shift: 2.87 -0.30 ...... Frame ( 36) shift: 2.90 -0.27 ...... Frame ( 37) shift: 3.00 -0.20 ...... Frame ( 38) shift: 3.09 -0.13 ...... Frame ( 39) shift: 3.19 -0.06 ...... Frame ( 40) shift: 3.29 0.01 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.097288 Iteration 2 Error: 0.265279 Iteration 3 Error: 0.119127 Iteration 4 Error: 0.051854 Iteration 5 Error: 0.035178 Align patch 2 23 left Iteration 1 Error: 0.918755 Iteration 2 Error: 0.171174 Iteration 3 Error: 0.079610 Iteration 4 Error: 0.016838 Align patch 3 22 left Iteration 1 Error: 0.859988 Iteration 2 Error: 0.113191 Iteration 3 Error: 0.035832 Align patch 4 21 left Iteration 1 Error: 1.012162 Iteration 2 Error: 0.292794 Iteration 3 Error: 0.060589 Iteration 4 Error: 0.024871 Align patch 5 20 left Iteration 1 Error: 1.210596 Iteration 2 Error: 0.191672 Iteration 3 Error: 0.044840 Align patch 6 19 left Iteration 1 Error: 0.799637 Iteration 2 Error: 0.229239 Iteration 3 Error: 0.120892 Iteration 4 Error: 0.080966 Iteration 5 Error: 0.037819 Align patch 7 18 left Iteration 1 Error: 1.043476 Iteration 2 Error: 0.241536 Iteration 3 Error: 0.120480 Iteration 4 Error: 0.045395 Align patch 8 17 left Iteration 1 Error: 1.950757 Iteration 2 Error: 0.355514 Iteration 3 Error: 0.122992 Iteration 4 Error: 0.030771 Align patch 9 16 left Iteration 1 Error: 0.889319 Iteration 2 Error: 0.172253 Iteration 3 Error: 0.087186 Iteration 4 Error: 0.031935 Align patch 10 15 left Iteration 1 Error: 0.855886 Iteration 2 Error: 0.203395 Iteration 3 Error: 0.042589 Align patch 11 14 left Iteration 1 Error: 1.416978 Iteration 2 Error: 0.353253 Iteration 3 Error: 0.150063 Iteration 4 Error: 0.053946 Iteration 5 Error: 0.027804 Align patch 12 13 left Iteration 1 Error: 0.613456 Iteration 2 Error: 0.121456 Iteration 3 Error: 0.038840 Align patch 13 12 left Iteration 1 Error: 0.881726 Iteration 2 Error: 0.231585 Iteration 3 Error: 0.062235 Iteration 4 Error: 0.023967 Align patch 14 11 left Iteration 1 Error: 1.086831 Iteration 2 Error: 0.124353 Iteration 3 Error: 0.034114 Align patch 15 10 left Iteration 1 Error: 0.686605 Iteration 2 Error: 0.190722 Iteration 3 Error: 0.064667 Iteration 4 Error: 0.041699 Align patch 16 9 left Iteration 1 Error: 0.773636 Iteration 2 Error: 0.136846 Iteration 3 Error: 0.040605 Align patch 17 8 left Iteration 1 Error: 0.792491 Iteration 2 Error: 0.262035 Iteration 3 Error: 0.065477 Iteration 4 Error: 0.022796 Align patch 18 7 left Iteration 1 Error: 0.980642 Iteration 2 Error: 0.293859 Iteration 3 Error: 0.120044 Iteration 4 Error: 0.058401 Iteration 5 Error: 0.023812 Align patch 19 6 left Iteration 1 Error: 0.757851 Iteration 2 Error: 0.139531 Iteration 3 Error: 0.048832 Align patch 20 5 left Iteration 1 Error: 1.485781 Iteration 2 Error: 0.239845 Iteration 3 Error: 0.056564 Iteration 4 Error: 0.023636 Align patch 21 4 left Iteration 1 Error: 0.887716 Iteration 2 Error: 0.168074 Iteration 3 Error: 0.034369 Align patch 22 3 left Iteration 1 Error: 0.862486 Iteration 2 Error: 0.103451 Iteration 3 Error: 0.050160 Iteration 4 Error: 0.017454 Align patch 23 2 left Iteration 1 Error: 1.020607 Iteration 2 Error: 0.254551 Iteration 3 Error: 0.090965 Iteration 4 Error: 0.022234 Align patch 24 1 left Iteration 1 Error: 0.800193 Iteration 2 Error: 0.286465 Iteration 3 Error: 0.110722 Iteration 4 Error: 0.041027 Align patch 25 0 left Iteration 1 Error: 1.026738 Iteration 2 Error: 0.257211 Iteration 3 Error: 0.094109 Iteration 4 Error: 0.031122 3D Fitting completed. Patch alignment time: 16.17(sec) Local motion has been corrected. Process thread exits. Computational time: 25.716652 sec Total time: 32.485409 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00003hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00003hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.770769s Reading file: gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00003hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.000728s ........................................ >>>>>>TIME<<<<<< FFT: 0.933563s Defocus_U Defocus_V Angle CCC 12898.49 13765.72 14.43 0.032622 Final Values Defocus_U Defocus_V Angle CCC 12912.54 13770.43 15.37 0.052903 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00013sq_v01_00003hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00003hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.343e-01 9.996e-02 CC threshold: 0.734 Mean Std: 36.81 6.49 Num Hot pixels: 219 Hot pixel threshold: 75.73 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.003182 Iteration 2 Error: 0.158376 Iteration 3 Error: 0.043971 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.04 -0.14 ...... Frame ( 3) shift: 0.08 -0.29 ...... Frame ( 4) shift: 0.12 -0.43 ...... Frame ( 5) shift: 0.16 -0.58 ...... Frame ( 6) shift: 0.18 -0.70 ...... Frame ( 7) shift: 0.17 -0.79 ...... Frame ( 8) shift: 0.17 -0.89 ...... Frame ( 9) shift: 0.16 -0.94 ...... Frame ( 10) shift: 0.16 -0.95 ...... Frame ( 11) shift: 0.15 -0.96 ...... Frame ( 12) shift: 0.20 -0.97 ...... Frame ( 13) shift: 0.29 -0.99 ...... Frame ( 14) shift: 0.39 -1.02 ...... Frame ( 15) shift: 0.44 -1.05 ...... Frame ( 16) shift: 0.46 -1.08 ...... Frame ( 17) shift: 0.48 -1.12 ...... Frame ( 18) shift: 0.54 -1.17 ...... Frame ( 19) shift: 0.66 -1.25 ...... Frame ( 20) shift: 0.77 -1.33 ...... Frame ( 21) shift: 0.82 -1.38 ...... Frame ( 22) shift: 0.82 -1.41 ...... Frame ( 23) shift: 0.81 -1.43 ...... Frame ( 24) shift: 0.83 -1.47 ...... Frame ( 25) shift: 0.88 -1.52 ...... Frame ( 26) shift: 0.94 -1.56 ...... Frame ( 27) shift: 0.96 -1.56 ...... Frame ( 28) shift: 0.94 -1.50 ...... Frame ( 29) shift: 0.93 -1.43 ...... Frame ( 30) shift: 0.94 -1.43 ...... Frame ( 31) shift: 0.97 -1.48 ...... Frame ( 32) shift: 0.99 -1.53 ...... Frame ( 33) shift: 1.05 -1.58 ...... Frame ( 34) shift: 1.13 -1.60 ...... Frame ( 35) shift: 1.21 -1.63 ...... Frame ( 36) shift: 1.28 -1.61 ...... Frame ( 37) shift: 1.34 -1.56 ...... Frame ( 38) shift: 1.41 -1.50 ...... Frame ( 39) shift: 1.47 -1.44 ...... Frame ( 40) shift: 1.53 -1.38 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.024845 Iteration 2 Error: 0.167452 Iteration 3 Error: 0.031072 Align patch 2 23 left Iteration 1 Error: 0.870619 Iteration 2 Error: 0.343940 Iteration 3 Error: 0.068252 Iteration 4 Error: 0.044116 Align patch 3 22 left Iteration 1 Error: 0.905834 Iteration 2 Error: 0.157100 Iteration 3 Error: 0.039598 Align patch 4 21 left Iteration 1 Error: 1.390477 Iteration 2 Error: 0.157505 Iteration 3 Error: 0.033552 Align patch 5 20 left Iteration 1 Error: 1.155848 Iteration 2 Error: 0.177557 Iteration 3 Error: 0.050700 Iteration 4 Error: 0.014540 Align patch 6 19 left Iteration 1 Error: 0.849440 Iteration 2 Error: 0.200362 Iteration 3 Error: 0.065373 Iteration 4 Error: 0.023151 Align patch 7 18 left Iteration 1 Error: 1.081592 Iteration 2 Error: 0.245456 Iteration 3 Error: 0.089551 Iteration 4 Error: 0.030379 Align patch 8 17 left Iteration 1 Error: 1.097025 Iteration 2 Error: 0.218008 Iteration 3 Error: 0.042167 Align patch 9 16 left Iteration 1 Error: 1.229895 Iteration 2 Error: 0.179035 Iteration 3 Error: 0.056275 Iteration 4 Error: 0.019881 Align patch 10 15 left Iteration 1 Error: 1.047066 Iteration 2 Error: 0.247391 Iteration 3 Error: 0.048322 Align patch 11 14 left Iteration 1 Error: 0.947259 Iteration 2 Error: 0.126740 Iteration 3 Error: 0.074081 Iteration 4 Error: 0.025885 Align patch 12 13 left Iteration 1 Error: 0.851611 Iteration 2 Error: 0.210829 Iteration 3 Error: 0.069069 Iteration 4 Error: 0.029604 Align patch 13 12 left Iteration 1 Error: 0.636887 Iteration 2 Error: 0.134553 Iteration 3 Error: 0.038393 Align patch 14 11 left Iteration 1 Error: 0.885341 Iteration 2 Error: 0.204127 Iteration 3 Error: 0.081370 Iteration 4 Error: 0.026878 Align patch 15 10 left Iteration 1 Error: 0.627583 Iteration 2 Error: 0.110576 Iteration 3 Error: 0.029509 Align patch 16 9 left Iteration 1 Error: 0.944460 Iteration 2 Error: 0.169628 Iteration 3 Error: 0.065615 Iteration 4 Error: 0.030092 Align patch 17 8 left Iteration 1 Error: 0.545892 Iteration 2 Error: 0.091825 Iteration 3 Error: 0.036381 Align patch 18 7 left Iteration 1 Error: 1.193251 Iteration 2 Error: 0.228856 Iteration 3 Error: 0.043492 Align patch 19 6 left Iteration 1 Error: 0.811039 Iteration 2 Error: 0.174695 Iteration 3 Error: 0.041809 Align patch 20 5 left Iteration 1 Error: 0.888403 Iteration 2 Error: 0.228781 Iteration 3 Error: 0.088215 Iteration 4 Error: 0.025012 Align patch 21 4 left Iteration 1 Error: 1.149733 Iteration 2 Error: 0.164193 Iteration 3 Error: 0.059443 Iteration 4 Error: 0.025970 Align patch 22 3 left Iteration 1 Error: 0.877875 Iteration 2 Error: 0.198174 Iteration 3 Error: 0.068386 Iteration 4 Error: 0.018833 Align patch 23 2 left Iteration 1 Error: 1.435062 Iteration 2 Error: 0.300950 Iteration 3 Error: 0.094495 Iteration 4 Error: 0.029721 Align patch 24 1 left Iteration 1 Error: 1.043943 Iteration 2 Error: 0.233440 Iteration 3 Error: 0.076725 Iteration 4 Error: 0.026348 Align patch 25 0 left Iteration 1 Error: 0.852027 Iteration 2 Error: 0.143000 Iteration 3 Error: 0.065163 Iteration 4 Error: 0.020300 3D Fitting completed. Patch alignment time: 16.40(sec) Local motion has been corrected. Process thread exits. Computational time: 26.448795 sec Total time: 32.432602 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00003hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00003hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.778529s Reading file: gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00003hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.202834s ........................................ >>>>>>TIME<<<<<< FFT: 1.050661s Defocus_U Defocus_V Angle CCC 10931.67 11318.39 26.66 0.019168 Final Values Defocus_U Defocus_V Angle CCC 10933.24 11310.58 29.81 0.027432 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00013sq_v01_00003hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00003hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 40.72 6.89 Num Hot pixels: 235 Hot pixel threshold: 82.03 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.268426 Iteration 2 Error: 0.279645 Iteration 3 Error: 0.069514 Iteration 4 Error: 0.021966 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.06 -0.04 ...... Frame ( 3) shift: -0.11 -0.08 ...... Frame ( 4) shift: -0.17 -0.11 ...... Frame ( 5) shift: -0.22 -0.15 ...... Frame ( 6) shift: -0.18 -0.21 ...... Frame ( 7) shift: -0.05 -0.29 ...... Frame ( 8) shift: 0.09 -0.36 ...... Frame ( 9) shift: 0.23 -0.47 ...... Frame ( 10) shift: 0.37 -0.59 ...... Frame ( 11) shift: 0.52 -0.72 ...... Frame ( 12) shift: 0.60 -0.80 ...... Frame ( 13) shift: 0.63 -0.84 ...... Frame ( 14) shift: 0.66 -0.87 ...... Frame ( 15) shift: 0.68 -0.94 ...... Frame ( 16) shift: 0.70 -1.04 ...... Frame ( 17) shift: 0.72 -1.14 ...... Frame ( 18) shift: 0.76 -1.20 ...... Frame ( 19) shift: 0.84 -1.24 ...... Frame ( 20) shift: 0.91 -1.27 ...... Frame ( 21) shift: 0.97 -1.29 ...... Frame ( 22) shift: 1.02 -1.29 ...... Frame ( 23) shift: 1.07 -1.30 ...... Frame ( 24) shift: 1.12 -1.34 ...... Frame ( 25) shift: 1.16 -1.41 ...... Frame ( 26) shift: 1.20 -1.49 ...... Frame ( 27) shift: 1.28 -1.59 ...... Frame ( 28) shift: 1.39 -1.72 ...... Frame ( 29) shift: 1.49 -1.85 ...... Frame ( 30) shift: 1.56 -1.93 ...... Frame ( 31) shift: 1.59 -1.95 ...... Frame ( 32) shift: 1.62 -1.97 ...... Frame ( 33) shift: 1.63 -1.98 ...... Frame ( 34) shift: 1.63 -1.99 ...... Frame ( 35) shift: 1.62 -2.00 ...... Frame ( 36) shift: 1.66 -1.97 ...... Frame ( 37) shift: 1.74 -1.91 ...... Frame ( 38) shift: 1.82 -1.84 ...... Frame ( 39) shift: 1.90 -1.78 ...... Frame ( 40) shift: 1.99 -1.72 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.765013 Iteration 2 Error: 0.151167 Iteration 3 Error: 0.049917 Align patch 2 23 left Iteration 1 Error: 0.863908 Iteration 2 Error: 0.176014 Iteration 3 Error: 0.043183 Align patch 3 22 left Iteration 1 Error: 1.167106 Iteration 2 Error: 0.322995 Iteration 3 Error: 0.168882 Iteration 4 Error: 0.074716 Iteration 5 Error: 0.038724 Align patch 4 21 left Iteration 1 Error: 0.612843 Iteration 2 Error: 0.118285 Iteration 3 Error: 0.042367 Align patch 5 20 left Iteration 1 Error: 1.274899 Iteration 2 Error: 0.278241 Iteration 3 Error: 0.051464 Iteration 4 Error: 0.013577 Align patch 6 19 left Iteration 1 Error: 0.962637 Iteration 2 Error: 0.258458 Iteration 3 Error: 0.049773 Align patch 7 18 left Iteration 1 Error: 0.719450 Iteration 2 Error: 0.170792 Iteration 3 Error: 0.035642 Align patch 8 17 left Iteration 1 Error: 0.856274 Iteration 2 Error: 0.141739 Iteration 3 Error: 0.048877 Align patch 9 16 left Iteration 1 Error: 0.646258 Iteration 2 Error: 0.126847 Iteration 3 Error: 0.033368 Align patch 10 15 left Iteration 1 Error: 0.806229 Iteration 2 Error: 0.129356 Iteration 3 Error: 0.027144 Align patch 11 14 left Iteration 1 Error: 1.873206 Iteration 2 Error: 0.145740 Iteration 3 Error: 0.045463 Align patch 12 13 left Iteration 1 Error: 0.973293 Iteration 2 Error: 0.139983 Iteration 3 Error: 0.029092 Align patch 13 12 left Iteration 1 Error: 0.911231 Iteration 2 Error: 0.153232 Iteration 3 Error: 0.046360 Align patch 14 11 left Iteration 1 Error: 0.897420 Iteration 2 Error: 0.146185 Iteration 3 Error: 0.020672 Align patch 15 10 left Iteration 1 Error: 0.831580 Iteration 2 Error: 0.138646 Iteration 3 Error: 0.030087 Align patch 16 9 left Iteration 1 Error: 0.754299 Iteration 2 Error: 0.153103 Iteration 3 Error: 0.028133 Align patch 17 8 left Iteration 1 Error: 0.885820 Iteration 2 Error: 0.241799 Iteration 3 Error: 0.065374 Iteration 4 Error: 0.035778 Align patch 18 7 left Iteration 1 Error: 0.695337 Iteration 2 Error: 0.098695 Iteration 3 Error: 0.034673 Align patch 19 6 left Iteration 1 Error: 0.821074 Iteration 2 Error: 0.137814 Iteration 3 Error: 0.035687 Align patch 20 5 left Iteration 1 Error: 1.022588 Iteration 2 Error: 0.224623 Iteration 3 Error: 0.055471 Iteration 4 Error: 0.014840 Align patch 21 4 left Iteration 1 Error: 0.952097 Iteration 2 Error: 0.266393 Iteration 3 Error: 0.080768 Iteration 4 Error: 0.032924 Align patch 22 3 left Iteration 1 Error: 0.992854 Iteration 2 Error: 0.220236 Iteration 3 Error: 0.043928 Align patch 23 2 left Iteration 1 Error: 1.330641 Iteration 2 Error: 0.150043 Iteration 3 Error: 0.030434 Align patch 24 1 left Iteration 1 Error: 1.119410 Iteration 2 Error: 0.182329 Iteration 3 Error: 0.050441 Iteration 4 Error: 0.013298 Align patch 25 0 left Iteration 1 Error: 1.229434 Iteration 2 Error: 0.163002 Iteration 3 Error: 0.055962 Iteration 4 Error: 0.014869 3D Fitting completed. Patch alignment time: 16.03(sec) Local motion has been corrected. Process thread exits. Computational time: 25.363247 sec Total time: 30.968622 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00003hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00003hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.807027s Reading file: gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00003hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.524193s ........................................ >>>>>>TIME<<<<<< FFT: 1.023659s Defocus_U Defocus_V Angle CCC 12488.28 13343.75 4.70 0.048609 Final Values Defocus_U Defocus_V Angle CCC 12489.84 13348.44 4.70 0.082936 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00013sq_v01_00003hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00003hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.001e-01 CC threshold: 0.735 Mean Std: 40.95 7.01 Num Hot pixels: 224 Hot pixel threshold: 83.02 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.475369 Iteration 2 Error: 0.303930 Iteration 3 Error: 0.063635 Iteration 4 Error: 0.025278 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.02 -0.17 ...... Frame ( 3) shift: 0.03 -0.33 ...... Frame ( 4) shift: 0.05 -0.50 ...... Frame ( 5) shift: 0.06 -0.67 ...... Frame ( 6) shift: 0.11 -0.82 ...... Frame ( 7) shift: 0.17 -0.95 ...... Frame ( 8) shift: 0.24 -1.08 ...... Frame ( 9) shift: 0.28 -1.17 ...... Frame ( 10) shift: 0.30 -1.19 ...... Frame ( 11) shift: 0.32 -1.22 ...... Frame ( 12) shift: 0.36 -1.25 ...... Frame ( 13) shift: 0.41 -1.28 ...... Frame ( 14) shift: 0.46 -1.31 ...... Frame ( 15) shift: 0.52 -1.33 ...... Frame ( 16) shift: 0.59 -1.33 ...... Frame ( 17) shift: 0.67 -1.33 ...... Frame ( 18) shift: 0.74 -1.36 ...... Frame ( 19) shift: 0.81 -1.40 ...... Frame ( 20) shift: 0.89 -1.45 ...... Frame ( 21) shift: 0.98 -1.46 ...... Frame ( 22) shift: 1.09 -1.42 ...... Frame ( 23) shift: 1.21 -1.39 ...... Frame ( 24) shift: 1.32 -1.38 ...... Frame ( 25) shift: 1.42 -1.38 ...... Frame ( 26) shift: 1.53 -1.39 ...... Frame ( 27) shift: 1.58 -1.43 ...... Frame ( 28) shift: 1.57 -1.51 ...... Frame ( 29) shift: 1.57 -1.59 ...... Frame ( 30) shift: 1.66 -1.65 ...... Frame ( 31) shift: 1.83 -1.71 ...... Frame ( 32) shift: 2.01 -1.76 ...... Frame ( 33) shift: 2.13 -1.80 ...... Frame ( 34) shift: 2.19 -1.81 ...... Frame ( 35) shift: 2.25 -1.83 ...... Frame ( 36) shift: 2.33 -1.85 ...... Frame ( 37) shift: 2.43 -1.89 ...... Frame ( 38) shift: 2.53 -1.92 ...... Frame ( 39) shift: 2.64 -1.96 ...... Frame ( 40) shift: 2.74 -1.99 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.822917 Iteration 2 Error: 0.144460 Iteration 3 Error: 0.036796 Align patch 2 23 left Iteration 1 Error: 0.774710 Iteration 2 Error: 0.087251 Iteration 3 Error: 0.027105 Align patch 3 22 left Iteration 1 Error: 0.834235 Iteration 2 Error: 0.167984 Iteration 3 Error: 0.050022 Iteration 4 Error: 0.020180 Align patch 4 21 left Iteration 1 Error: 1.069178 Iteration 2 Error: 0.157737 Iteration 3 Error: 0.045390 Align patch 5 20 left Iteration 1 Error: 1.380715 Iteration 2 Error: 0.136545 Iteration 3 Error: 0.042775 Align patch 6 19 left Iteration 1 Error: 0.788635 Iteration 2 Error: 0.130710 Iteration 3 Error: 0.035578 Align patch 7 18 left Iteration 1 Error: 1.005679 Iteration 2 Error: 0.119245 Iteration 3 Error: 0.026694 Align patch 8 17 left Iteration 1 Error: 0.756562 Iteration 2 Error: 0.155209 Iteration 3 Error: 0.046877 Align patch 9 16 left Iteration 1 Error: 0.727240 Iteration 2 Error: 0.245569 Iteration 3 Error: 0.112052 Iteration 4 Error: 0.043485 Align patch 10 15 left Iteration 1 Error: 1.124548 Iteration 2 Error: 0.121671 Iteration 3 Error: 0.015175 Align patch 11 14 left Iteration 1 Error: 0.551063 Iteration 2 Error: 0.078055 Iteration 3 Error: 0.016728 Align patch 12 13 left Iteration 1 Error: 0.892376 Iteration 2 Error: 0.087736 Iteration 3 Error: 0.018713 Align patch 13 12 left Iteration 1 Error: 0.938625 Iteration 2 Error: 0.142568 Iteration 3 Error: 0.027692 Align patch 14 11 left Iteration 1 Error: 0.576159 Iteration 2 Error: 0.186060 Iteration 3 Error: 0.023360 Align patch 15 10 left Iteration 1 Error: 0.675337 Iteration 2 Error: 0.101110 Iteration 3 Error: 0.019255 Align patch 16 9 left Iteration 1 Error: 1.003977 Iteration 2 Error: 0.219177 Iteration 3 Error: 0.070998 Iteration 4 Error: 0.022416 Align patch 17 8 left Iteration 1 Error: 0.820783 Iteration 2 Error: 0.103310 Iteration 3 Error: 0.021153 Align patch 18 7 left Iteration 1 Error: 0.855198 Iteration 2 Error: 0.163878 Iteration 3 Error: 0.032772 Align patch 19 6 left Iteration 1 Error: 0.855699 Iteration 2 Error: 0.221880 Iteration 3 Error: 0.078803 Iteration 4 Error: 0.039151 Align patch 20 5 left Iteration 1 Error: 1.173166 Iteration 2 Error: 0.209280 Iteration 3 Error: 0.058283 Iteration 4 Error: 0.020099 Align patch 21 4 left Iteration 1 Error: 1.140288 Iteration 2 Error: 0.221354 Iteration 3 Error: 0.077458 Iteration 4 Error: 0.038975 Align patch 22 3 left Iteration 1 Error: 0.648418 Iteration 2 Error: 0.138744 Iteration 3 Error: 0.030982 Align patch 23 2 left Iteration 1 Error: 1.162457 Iteration 2 Error: 0.225190 Iteration 3 Error: 0.048456 Align patch 24 1 left Iteration 1 Error: 2.316355 Iteration 2 Error: 0.506561 Iteration 3 Error: 0.200568 Iteration 4 Error: 0.104814 Iteration 5 Error: 0.060253 Align patch 24 1 left Iteration 1 Error: 1.693283 Iteration 2 Error: 0.329423 Iteration 3 Error: 0.088498 Iteration 4 Error: 0.029216 Align patch 25 0 left Iteration 1 Error: 0.775244 Iteration 2 Error: 0.113206 Iteration 3 Error: 0.016988 3D Fitting completed. Patch alignment time: 17.15(sec) Local motion has been corrected. Process thread exits. Computational time: 26.588383 sec Total time: 32.158043 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00003hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00003hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.735915s Reading file: gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00003hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.521188s ........................................ >>>>>>TIME<<<<<< FFT: 1.021660s Defocus_U Defocus_V Angle CCC 13353.52 12779.30 80.49 0.049196 Final Values Defocus_U Defocus_V Angle CCC 13370.70 12774.61 82.68 0.082351 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00013sq_v01_00004hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00004hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.998e-02 CC threshold: 0.734 Mean Std: 34.34 6.23 Num Hot pixels: 210 Hot pixel threshold: 71.73 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.010178 Iteration 2 Error: 0.537550 Iteration 3 Error: 0.145192 Iteration 4 Error: 0.061182 Iteration 5 Error: 0.030784 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.33 0.13 ...... Frame ( 3) shift: 0.67 0.25 ...... Frame ( 4) shift: 1.00 0.38 ...... Frame ( 5) shift: 1.33 0.51 ...... Frame ( 6) shift: 1.54 0.52 ...... Frame ( 7) shift: 1.61 0.42 ...... Frame ( 8) shift: 1.69 0.32 ...... Frame ( 9) shift: 1.76 0.27 ...... Frame ( 10) shift: 1.83 0.28 ...... Frame ( 11) shift: 1.90 0.29 ...... Frame ( 12) shift: 2.02 0.36 ...... Frame ( 13) shift: 2.17 0.49 ...... Frame ( 14) shift: 2.33 0.62 ...... Frame ( 15) shift: 2.45 0.73 ...... Frame ( 16) shift: 2.54 0.83 ...... Frame ( 17) shift: 2.64 0.93 ...... Frame ( 18) shift: 2.71 0.99 ...... Frame ( 19) shift: 2.77 1.02 ...... Frame ( 20) shift: 2.83 1.04 ...... Frame ( 21) shift: 2.90 1.06 ...... Frame ( 22) shift: 2.98 1.10 ...... Frame ( 23) shift: 3.06 1.13 ...... Frame ( 24) shift: 3.18 1.20 ...... Frame ( 25) shift: 3.33 1.30 ...... Frame ( 26) shift: 3.48 1.39 ...... Frame ( 27) shift: 3.58 1.49 ...... Frame ( 28) shift: 3.63 1.58 ...... Frame ( 29) shift: 3.68 1.68 ...... Frame ( 30) shift: 3.79 1.72 ...... Frame ( 31) shift: 3.94 1.72 ...... Frame ( 32) shift: 4.09 1.71 ...... Frame ( 33) shift: 4.17 1.80 ...... Frame ( 34) shift: 4.19 1.98 ...... Frame ( 35) shift: 4.20 2.16 ...... Frame ( 36) shift: 4.24 2.27 ...... Frame ( 37) shift: 4.29 2.29 ...... Frame ( 38) shift: 4.35 2.31 ...... Frame ( 39) shift: 4.40 2.33 ...... Frame ( 40) shift: 4.46 2.35 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.982935 Iteration 2 Error: 0.363931 Iteration 3 Error: 0.138424 Iteration 4 Error: 0.080869 Iteration 5 Error: 0.057425 Align patch 1 24 left Iteration 1 Error: 1.075797 Iteration 2 Error: 0.270814 Iteration 3 Error: 0.075192 Iteration 4 Error: 0.032082 Align patch 2 23 left Iteration 1 Error: 0.679766 Iteration 2 Error: 0.181403 Iteration 3 Error: 0.064460 Iteration 4 Error: 0.029004 Align patch 3 22 left Iteration 1 Error: 1.137324 Iteration 2 Error: 0.161176 Iteration 3 Error: 0.068863 Iteration 4 Error: 0.041441 Align patch 4 21 left Iteration 1 Error: 1.065716 Iteration 2 Error: 0.192551 Iteration 3 Error: 0.051875 Iteration 4 Error: 0.016985 Align patch 5 20 left Iteration 1 Error: 1.682570 Iteration 2 Error: 0.212713 Iteration 3 Error: 0.048570 Align patch 6 19 left Iteration 1 Error: 0.798766 Iteration 2 Error: 0.459371 Iteration 3 Error: 0.119686 Iteration 4 Error: 0.075760 Iteration 5 Error: 0.037602 Align patch 7 18 left Iteration 1 Error: 0.888167 Iteration 2 Error: 0.250788 Iteration 3 Error: 0.119954 Iteration 4 Error: 0.053822 Iteration 5 Error: 0.038090 Align patch 8 17 left Iteration 1 Error: 0.551122 Iteration 2 Error: 0.091587 Iteration 3 Error: 0.024731 Align patch 9 16 left Iteration 1 Error: 1.038971 Iteration 2 Error: 0.396351 Iteration 3 Error: 0.108835 Iteration 4 Error: 0.030109 Align patch 10 15 left Iteration 1 Error: 1.050644 Iteration 2 Error: 0.177197 Iteration 3 Error: 0.047533 Align patch 11 14 left Iteration 1 Error: 1.131788 Iteration 2 Error: 0.392009 Iteration 3 Error: 0.132883 Iteration 4 Error: 0.046784 Align patch 12 13 left Iteration 1 Error: 1.101067 Iteration 2 Error: 0.218880 Iteration 3 Error: 0.078290 Iteration 4 Error: 0.028671 Align patch 13 12 left Iteration 1 Error: 0.906192 Iteration 2 Error: 0.246935 Iteration 3 Error: 0.065047 Iteration 4 Error: 0.027113 Align patch 14 11 left Iteration 1 Error: 0.971032 Iteration 2 Error: 0.191003 Iteration 3 Error: 0.060934 Iteration 4 Error: 0.022532 Align patch 15 10 left Iteration 1 Error: 0.920410 Iteration 2 Error: 0.303653 Iteration 3 Error: 0.108122 Iteration 4 Error: 0.048197 Align patch 16 9 left Iteration 1 Error: 2.274069 Iteration 2 Error: 0.462508 Iteration 3 Error: 0.115804 Iteration 4 Error: 0.049058 Align patch 17 8 left Iteration 1 Error: 1.106414 Iteration 2 Error: 0.206769 Iteration 3 Error: 0.057199 Iteration 4 Error: 0.026896 Align patch 18 7 left Iteration 1 Error: 1.531639 Iteration 2 Error: 0.255205 Iteration 3 Error: 0.110429 Iteration 4 Error: 0.041948 Align patch 19 6 left Iteration 1 Error: 1.152949 Iteration 2 Error: 0.330645 Iteration 3 Error: 0.127207 Iteration 4 Error: 0.047906 Align patch 20 5 left Iteration 1 Error: 0.835350 Iteration 2 Error: 0.306706 Iteration 3 Error: 0.117494 Iteration 4 Error: 0.049280 Align patch 21 4 left Iteration 1 Error: 1.252309 Iteration 2 Error: 0.238825 Iteration 3 Error: 0.062265 Iteration 4 Error: 0.018697 Align patch 22 3 left Iteration 1 Error: 1.684978 Iteration 2 Error: 0.224489 Iteration 3 Error: 0.061015 Iteration 4 Error: 0.021277 Align patch 23 2 left Iteration 1 Error: 0.973347 Iteration 2 Error: 0.143829 Iteration 3 Error: 0.052605 Iteration 4 Error: 0.013809 Align patch 24 1 left Iteration 1 Error: 1.267578 Iteration 2 Error: 0.175463 Iteration 3 Error: 0.055345 Iteration 4 Error: 0.023676 Align patch 25 0 left Iteration 1 Error: 1.199971 Iteration 2 Error: 0.180398 Iteration 3 Error: 0.067136 Iteration 4 Error: 0.015901 3D Fitting completed. Patch alignment time: 18.40(sec) Local motion has been corrected. Process thread exits. Computational time: 28.150711 sec Total time: 34.951519 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00004hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00004hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.568705s Reading file: gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00004hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.141689s ........................................ >>>>>>TIME<<<<<< FFT: 0.954989s Defocus_U Defocus_V Angle CCC 8683.59 9386.75 29.15 0.010607 Final Values Defocus_U Defocus_V Angle CCC 8821.69 9571.98 19.08 0.021087 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00013sq_v01_00004hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00004hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.001e-01 CC threshold: 0.735 Mean Std: 38.63 6.66 Num Hot pixels: 231 Hot pixel threshold: 78.56 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.420918 Iteration 2 Error: 0.229045 Iteration 3 Error: 0.058072 Iteration 4 Error: 0.022720 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: 0.12 0.08 ...... Frame ( 3) shift: 0.25 0.17 ...... Frame ( 4) shift: 0.37 0.25 ...... Frame ( 5) shift: 0.50 0.34 ...... Frame ( 6) shift: 0.60 0.39 ...... Frame ( 7) shift: 0.68 0.42 ...... Frame ( 8) shift: 0.77 0.45 ...... Frame ( 9) shift: 0.83 0.45 ...... Frame ( 10) shift: 0.87 0.43 ...... Frame ( 11) shift: 0.91 0.42 ...... Frame ( 12) shift: 0.96 0.43 ...... Frame ( 13) shift: 1.03 0.47 ...... Frame ( 14) shift: 1.10 0.52 ...... Frame ( 15) shift: 1.16 0.54 ...... Frame ( 16) shift: 1.22 0.53 ...... Frame ( 17) shift: 1.29 0.52 ...... Frame ( 18) shift: 1.38 0.52 ...... Frame ( 19) shift: 1.51 0.54 ...... Frame ( 20) shift: 1.64 0.56 ...... Frame ( 21) shift: 1.71 0.53 ...... Frame ( 22) shift: 1.73 0.43 ...... Frame ( 23) shift: 1.75 0.34 ...... Frame ( 24) shift: 1.81 0.32 ...... Frame ( 25) shift: 1.91 0.39 ...... Frame ( 26) shift: 2.01 0.46 ...... Frame ( 27) shift: 2.08 0.50 ...... Frame ( 28) shift: 2.13 0.52 ...... Frame ( 29) shift: 2.18 0.53 ...... Frame ( 30) shift: 2.22 0.55 ...... Frame ( 31) shift: 2.25 0.58 ...... Frame ( 32) shift: 2.29 0.60 ...... Frame ( 33) shift: 2.35 0.66 ...... Frame ( 34) shift: 2.44 0.74 ...... Frame ( 35) shift: 2.54 0.82 ...... Frame ( 36) shift: 2.66 0.84 ...... Frame ( 37) shift: 2.81 0.81 ...... Frame ( 38) shift: 2.96 0.77 ...... Frame ( 39) shift: 3.12 0.74 ...... Frame ( 40) shift: 3.27 0.71 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.921556 Iteration 2 Error: 0.145207 Iteration 3 Error: 0.033171 Align patch 2 23 left Iteration 1 Error: 0.754212 Iteration 2 Error: 0.129967 Iteration 3 Error: 0.041276 Align patch 3 22 left Iteration 1 Error: 0.675402 Iteration 2 Error: 0.182088 Iteration 3 Error: 0.067246 Iteration 4 Error: 0.016863 Align patch 4 21 left Iteration 1 Error: 1.053282 Iteration 2 Error: 0.147879 Iteration 3 Error: 0.035302 Align patch 5 20 left Iteration 1 Error: 1.072251 Iteration 2 Error: 0.466278 Iteration 3 Error: 0.225177 Iteration 4 Error: 0.094265 Iteration 5 Error: 0.049151 Align patch 6 19 left Iteration 1 Error: 0.845169 Iteration 2 Error: 0.165726 Iteration 3 Error: 0.048346 Align patch 7 18 left Iteration 1 Error: 0.908619 Iteration 2 Error: 0.135042 Iteration 3 Error: 0.044457 Align patch 8 17 left Iteration 1 Error: 0.530033 Iteration 2 Error: 0.112616 Iteration 3 Error: 0.031531 Align patch 9 16 left Iteration 1 Error: 0.798755 Iteration 2 Error: 0.147747 Iteration 3 Error: 0.030000 Align patch 10 15 left Iteration 1 Error: 1.361187 Iteration 2 Error: 0.149643 Iteration 3 Error: 0.043726 Align patch 11 14 left Iteration 1 Error: 0.831357 Iteration 2 Error: 0.183825 Iteration 3 Error: 0.042795 Align patch 12 13 left Iteration 1 Error: 0.570907 Iteration 2 Error: 0.133115 Iteration 3 Error: 0.028872 Align patch 13 12 left Iteration 1 Error: 0.765251 Iteration 2 Error: 0.205020 Iteration 3 Error: 0.048704 Align patch 14 11 left Iteration 1 Error: 0.830739 Iteration 2 Error: 0.137217 Iteration 3 Error: 0.050979 Iteration 4 Error: 0.032940 Align patch 15 10 left Iteration 1 Error: 1.178178 Iteration 2 Error: 0.322056 Iteration 3 Error: 0.104945 Iteration 4 Error: 0.077995 Iteration 5 Error: 0.039040 Align patch 16 9 left Iteration 1 Error: 0.681427 Iteration 2 Error: 0.135974 Iteration 3 Error: 0.044027 Align patch 17 8 left Iteration 1 Error: 0.589822 Iteration 2 Error: 0.129218 Iteration 3 Error: 0.046220 Align patch 18 7 left Iteration 1 Error: 1.620029 Iteration 2 Error: 0.205642 Iteration 3 Error: 0.062126 Iteration 4 Error: 0.014326 Align patch 19 6 left Iteration 1 Error: 0.873818 Iteration 2 Error: 0.132511 Iteration 3 Error: 0.028597 Align patch 20 5 left Iteration 1 Error: 0.763090 Iteration 2 Error: 0.167256 Iteration 3 Error: 0.067601 Iteration 4 Error: 0.029258 Align patch 21 4 left Iteration 1 Error: 1.133597 Iteration 2 Error: 0.102445 Iteration 3 Error: 0.016326 Align patch 22 3 left Iteration 1 Error: 1.492216 Iteration 2 Error: 0.315387 Iteration 3 Error: 0.134540 Iteration 4 Error: 0.031814 Align patch 23 2 left Iteration 1 Error: 0.769568 Iteration 2 Error: 0.142810 Iteration 3 Error: 0.023360 Align patch 24 1 left Iteration 1 Error: 0.939310 Iteration 2 Error: 0.287518 Iteration 3 Error: 0.083045 Iteration 4 Error: 0.040338 Align patch 25 0 left Iteration 1 Error: 0.591918 Iteration 2 Error: 0.094968 Iteration 3 Error: 0.029803 3D Fitting completed. Patch alignment time: 15.42(sec) Local motion has been corrected. Process thread exits. Computational time: 24.889532 sec Total time: 32.610851 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00004hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00004hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.555306s Reading file: gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00004hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 1.795278s ........................................ >>>>>>TIME<<<<<< FFT: 0.926161s Defocus_U Defocus_V Angle CCC 10960.90 11300.87 7.26 0.029453 Final Values Defocus_U Defocus_V Angle CCC 10948.41 11388.40 0.80 0.046104 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00013sq_v01_00004hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00004hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.345e-01 1.000e-01 CC threshold: 0.735 Mean Std: 38.59 6.69 Num Hot pixels: 205 Hot pixel threshold: 78.73 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.348714 Iteration 2 Error: 0.251366 Iteration 3 Error: 0.061656 Iteration 4 Error: 0.017157 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.24 -0.01 ...... Frame ( 3) shift: -0.47 -0.02 ...... Frame ( 4) shift: -0.71 -0.03 ...... Frame ( 5) shift: -0.95 -0.04 ...... Frame ( 6) shift: -1.08 -0.04 ...... Frame ( 7) shift: -1.10 -0.03 ...... Frame ( 8) shift: -1.12 -0.03 ...... Frame ( 9) shift: -1.11 0.01 ...... Frame ( 10) shift: -1.05 0.07 ...... Frame ( 11) shift: -0.99 0.13 ...... Frame ( 12) shift: -0.88 0.18 ...... Frame ( 13) shift: -0.72 0.21 ...... Frame ( 14) shift: -0.56 0.24 ...... Frame ( 15) shift: -0.47 0.30 ...... Frame ( 16) shift: -0.45 0.37 ...... Frame ( 17) shift: -0.42 0.44 ...... Frame ( 18) shift: -0.37 0.47 ...... Frame ( 19) shift: -0.29 0.46 ...... Frame ( 20) shift: -0.21 0.44 ...... Frame ( 21) shift: -0.12 0.47 ...... Frame ( 22) shift: -0.03 0.52 ...... Frame ( 23) shift: 0.07 0.57 ...... Frame ( 24) shift: 0.15 0.63 ...... Frame ( 25) shift: 0.22 0.70 ...... Frame ( 26) shift: 0.29 0.77 ...... Frame ( 27) shift: 0.37 0.79 ...... Frame ( 28) shift: 0.44 0.77 ...... Frame ( 29) shift: 0.51 0.74 ...... Frame ( 30) shift: 0.59 0.78 ...... Frame ( 31) shift: 0.67 0.86 ...... Frame ( 32) shift: 0.74 0.95 ...... Frame ( 33) shift: 0.84 1.00 ...... Frame ( 34) shift: 0.95 1.02 ...... Frame ( 35) shift: 1.07 1.04 ...... Frame ( 36) shift: 1.14 1.09 ...... Frame ( 37) shift: 1.16 1.18 ...... Frame ( 38) shift: 1.19 1.27 ...... Frame ( 39) shift: 1.21 1.36 ...... Frame ( 40) shift: 1.24 1.45 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.621775 Iteration 2 Error: 0.083512 Iteration 3 Error: 0.016615 Align patch 2 23 left Iteration 1 Error: 0.644488 Iteration 2 Error: 0.149946 Iteration 3 Error: 0.047911 Align patch 3 22 left Iteration 1 Error: 0.748064 Iteration 2 Error: 0.112552 Iteration 3 Error: 0.018683 Align patch 4 21 left Iteration 1 Error: 0.696910 Iteration 2 Error: 0.200716 Iteration 3 Error: 0.057449 Iteration 4 Error: 0.018417 Align patch 5 20 left Iteration 1 Error: 0.636598 Iteration 2 Error: 0.127719 Iteration 3 Error: 0.044066 Align patch 6 19 left Iteration 1 Error: 0.683212 Iteration 2 Error: 0.223438 Iteration 3 Error: 0.057152 Iteration 4 Error: 0.027125 Align patch 7 18 left Iteration 1 Error: 0.791343 Iteration 2 Error: 0.136449 Iteration 3 Error: 0.055769 Iteration 4 Error: 0.025754 Align patch 8 17 left Iteration 1 Error: 0.962158 Iteration 2 Error: 0.138896 Iteration 3 Error: 0.023147 Align patch 9 16 left Iteration 1 Error: 0.685153 Iteration 2 Error: 0.134022 Iteration 3 Error: 0.049452 Align patch 10 15 left Iteration 1 Error: 0.715618 Iteration 2 Error: 0.109328 Iteration 3 Error: 0.026187 Align patch 11 14 left Iteration 1 Error: 0.647565 Iteration 2 Error: 0.140328 Iteration 3 Error: 0.028120 Align patch 12 13 left Iteration 1 Error: 0.680988 Iteration 2 Error: 0.103575 Iteration 3 Error: 0.031233 Align patch 13 12 left Iteration 1 Error: 0.442681 Iteration 2 Error: 0.062851 Iteration 3 Error: 0.019721 Align patch 14 11 left Iteration 1 Error: 0.637502 Iteration 2 Error: 0.078846 Iteration 3 Error: 0.018109 Align patch 15 10 left Iteration 1 Error: 0.693277 Iteration 2 Error: 0.126610 Iteration 3 Error: 0.040684 Align patch 16 9 left Iteration 1 Error: 0.770464 Iteration 2 Error: 0.141608 Iteration 3 Error: 0.046098 Align patch 17 8 left Iteration 1 Error: 0.791176 Iteration 2 Error: 0.124112 Iteration 3 Error: 0.032969 Align patch 18 7 left Iteration 1 Error: 0.714620 Iteration 2 Error: 0.156828 Iteration 3 Error: 0.034895 Align patch 19 6 left Iteration 1 Error: 0.751031 Iteration 2 Error: 0.296022 Iteration 3 Error: 0.098467 Iteration 4 Error: 0.038690 Align patch 20 5 left Iteration 1 Error: 0.703030 Iteration 2 Error: 0.173279 Iteration 3 Error: 0.039271 Align patch 21 4 left Iteration 1 Error: 0.675134 Iteration 2 Error: 0.163702 Iteration 3 Error: 0.048550 Align patch 22 3 left Iteration 1 Error: 0.592884 Iteration 2 Error: 0.103382 Iteration 3 Error: 0.024173 Align patch 23 2 left Iteration 1 Error: 0.774488 Iteration 2 Error: 0.175213 Iteration 3 Error: 0.035293 Align patch 24 1 left Iteration 1 Error: 0.608410 Iteration 2 Error: 0.112029 Iteration 3 Error: 0.034033 Align patch 25 0 left Iteration 1 Error: 0.834128 Iteration 2 Error: 0.171957 Iteration 3 Error: 0.043278 3D Fitting completed. Patch alignment time: 15.83(sec) Local motion has been corrected. Process thread exits. Computational time: 25.602840 sec Total time: 32.653706 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00004hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00004hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.755942s Reading file: gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00004hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.510151s ........................................ >>>>>>TIME<<<<<< FFT: 1.053923s Defocus_U Defocus_V Angle CCC 13923.82 14732.43 9.18 0.045434 Final Values Defocus_U Defocus_V Angle CCC 13939.46 14760.58 11.44 0.065147 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00013sq_v01_00004hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00004hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 40.27 6.89 Num Hot pixels: 209 Hot pixel threshold: 81.59 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 0.767404 Iteration 2 Error: 0.132214 Iteration 3 Error: 0.031736 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.07 0.07 ...... Frame ( 3) shift: -0.14 0.14 ...... Frame ( 4) shift: -0.20 0.22 ...... Frame ( 5) shift: -0.27 0.29 ...... Frame ( 6) shift: -0.29 0.33 ...... Frame ( 7) shift: -0.27 0.34 ...... Frame ( 8) shift: -0.24 0.35 ...... Frame ( 9) shift: -0.23 0.36 ...... Frame ( 10) shift: -0.23 0.36 ...... Frame ( 11) shift: -0.22 0.37 ...... Frame ( 12) shift: -0.20 0.37 ...... Frame ( 13) shift: -0.17 0.37 ...... Frame ( 14) shift: -0.14 0.37 ...... Frame ( 15) shift: -0.08 0.33 ...... Frame ( 16) shift: 0.01 0.23 ...... Frame ( 17) shift: 0.09 0.14 ...... Frame ( 18) shift: 0.13 0.10 ...... Frame ( 19) shift: 0.14 0.12 ...... Frame ( 20) shift: 0.14 0.14 ...... Frame ( 21) shift: 0.18 0.14 ...... Frame ( 22) shift: 0.27 0.12 ...... Frame ( 23) shift: 0.36 0.09 ...... Frame ( 24) shift: 0.43 0.05 ...... Frame ( 25) shift: 0.49 -0.02 ...... Frame ( 26) shift: 0.55 -0.08 ...... Frame ( 27) shift: 0.61 -0.13 ...... Frame ( 28) shift: 0.65 -0.17 ...... Frame ( 29) shift: 0.69 -0.21 ...... Frame ( 30) shift: 0.70 -0.20 ...... Frame ( 31) shift: 0.69 -0.16 ...... Frame ( 32) shift: 0.67 -0.12 ...... Frame ( 33) shift: 0.72 -0.10 ...... Frame ( 34) shift: 0.83 -0.10 ...... Frame ( 35) shift: 0.94 -0.11 ...... Frame ( 36) shift: 1.02 -0.08 ...... Frame ( 37) shift: 1.06 -0.01 ...... Frame ( 38) shift: 1.10 0.06 ...... Frame ( 39) shift: 1.14 0.13 ...... Frame ( 40) shift: 1.18 0.20 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.733681 Iteration 2 Error: 0.208899 Iteration 3 Error: 0.043364 Align patch 2 23 left Iteration 1 Error: 0.451887 Iteration 2 Error: 0.079009 Iteration 3 Error: 0.019891 Align patch 3 22 left Iteration 1 Error: 0.525837 Iteration 2 Error: 0.070212 Iteration 3 Error: 0.025520 Align patch 4 21 left Iteration 1 Error: 0.765664 Iteration 2 Error: 0.173147 Iteration 3 Error: 0.047870 Align patch 5 20 left Iteration 1 Error: 0.992172 Iteration 2 Error: 0.223079 Iteration 3 Error: 0.045860 Align patch 6 19 left Iteration 1 Error: 1.143445 Iteration 2 Error: 0.118396 Iteration 3 Error: 0.018836 Align patch 7 18 left Iteration 1 Error: 0.577184 Iteration 2 Error: 0.089340 Iteration 3 Error: 0.015487 Align patch 8 17 left Iteration 1 Error: 0.703668 Iteration 2 Error: 0.121736 Iteration 3 Error: 0.015208 Align patch 9 16 left Iteration 1 Error: 0.679735 Iteration 2 Error: 0.104667 Iteration 3 Error: 0.020962 Align patch 10 15 left Iteration 1 Error: 1.534492 Iteration 2 Error: 0.165090 Iteration 3 Error: 0.042872 Align patch 11 14 left Iteration 1 Error: 1.347705 Iteration 2 Error: 0.133062 Iteration 3 Error: 0.036619 Align patch 12 13 left Iteration 1 Error: 0.829763 Iteration 2 Error: 0.107415 Iteration 3 Error: 0.020788 Align patch 13 12 left Iteration 1 Error: 0.595641 Iteration 2 Error: 0.080682 Iteration 3 Error: 0.023865 Align patch 14 11 left Iteration 1 Error: 0.508737 Iteration 2 Error: 0.085462 Iteration 3 Error: 0.015537 Align patch 15 10 left Iteration 1 Error: 1.066106 Iteration 2 Error: 0.112242 Iteration 3 Error: 0.042112 Align patch 16 9 left Iteration 1 Error: 1.127307 Iteration 2 Error: 0.135620 Iteration 3 Error: 0.041558 Align patch 17 8 left Iteration 1 Error: 0.857676 Iteration 2 Error: 0.238724 Iteration 3 Error: 0.076458 Iteration 4 Error: 0.030202 Align patch 18 7 left Iteration 1 Error: 0.572261 Iteration 2 Error: 0.084439 Iteration 3 Error: 0.012587 Align patch 19 6 left Iteration 1 Error: 0.674910 Iteration 2 Error: 0.069037 Iteration 3 Error: 0.020948 Align patch 20 5 left Iteration 1 Error: 0.721604 Iteration 2 Error: 0.174633 Iteration 3 Error: 0.061633 Iteration 4 Error: 0.027054 Align patch 21 4 left Iteration 1 Error: 0.739319 Iteration 2 Error: 0.177446 Iteration 3 Error: 0.046256 Align patch 22 3 left Iteration 1 Error: 1.039491 Iteration 2 Error: 0.171366 Iteration 3 Error: 0.039520 Align patch 23 2 left Iteration 1 Error: 0.633815 Iteration 2 Error: 0.086616 Iteration 3 Error: 0.020438 Align patch 24 1 left Iteration 1 Error: 0.629830 Iteration 2 Error: 0.137948 Iteration 3 Error: 0.051538 Iteration 4 Error: 0.019604 Align patch 25 0 left Iteration 1 Error: 0.818157 Iteration 2 Error: 0.198120 Iteration 3 Error: 0.038622 3D Fitting completed. Patch alignment time: 15.64(sec) Local motion has been corrected. Process thread exits. Computational time: 24.206842 sec Total time: 30.502544 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00004hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00004hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.569533s Reading file: gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00004hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.458679s ........................................ >>>>>>TIME<<<<<< FFT: 1.039380s Defocus_U Defocus_V Angle CCC 12781.25 12132.81 84.50 0.041471 Final Values Defocus_U Defocus_V Angle CCC 12784.41 12164.10 84.50 0.070138 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00013sq_v01_00005hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00005hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.993e-02 CC threshold: 0.734 Mean Std: 36.19 6.45 Num Hot pixels: 237 Hot pixel threshold: 74.92 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.571593 Iteration 2 Error: 0.404759 Iteration 3 Error: 0.135787 Iteration 4 Error: 0.052193 Iteration 5 Error: 0.026130 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.00 0.01 ...... Frame ( 3) shift: -0.01 0.03 ...... Frame ( 4) shift: -0.01 0.04 ...... Frame ( 5) shift: -0.01 0.06 ...... Frame ( 6) shift: 0.06 0.04 ...... Frame ( 7) shift: 0.20 -0.01 ...... Frame ( 8) shift: 0.35 -0.06 ...... Frame ( 9) shift: 0.48 -0.09 ...... Frame ( 10) shift: 0.60 -0.11 ...... Frame ( 11) shift: 0.71 -0.13 ...... Frame ( 12) shift: 0.82 -0.12 ...... Frame ( 13) shift: 0.93 -0.08 ...... Frame ( 14) shift: 1.04 -0.05 ...... Frame ( 15) shift: 1.12 -0.00 ...... Frame ( 16) shift: 1.17 0.05 ...... Frame ( 17) shift: 1.23 0.11 ...... Frame ( 18) shift: 1.30 0.14 ...... Frame ( 19) shift: 1.38 0.14 ...... Frame ( 20) shift: 1.47 0.14 ...... Frame ( 21) shift: 1.59 0.18 ...... Frame ( 22) shift: 1.75 0.25 ...... Frame ( 23) shift: 1.90 0.33 ...... Frame ( 24) shift: 2.05 0.36 ...... Frame ( 25) shift: 2.19 0.35 ...... Frame ( 26) shift: 2.33 0.35 ...... Frame ( 27) shift: 2.43 0.38 ...... Frame ( 28) shift: 2.50 0.44 ...... Frame ( 29) shift: 2.56 0.50 ...... Frame ( 30) shift: 2.62 0.55 ...... Frame ( 31) shift: 2.67 0.57 ...... Frame ( 32) shift: 2.73 0.60 ...... Frame ( 33) shift: 2.82 0.59 ...... Frame ( 34) shift: 2.95 0.55 ...... Frame ( 35) shift: 3.08 0.51 ...... Frame ( 36) shift: 3.20 0.54 ...... Frame ( 37) shift: 3.31 0.66 ...... Frame ( 38) shift: 3.41 0.78 ...... Frame ( 39) shift: 3.51 0.89 ...... Frame ( 40) shift: 3.62 1.01 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.241248 Iteration 2 Error: 0.216408 Iteration 3 Error: 0.044317 Align patch 2 23 left Iteration 1 Error: 1.025142 Iteration 2 Error: 0.186612 Iteration 3 Error: 0.049648 Align patch 3 22 left Iteration 1 Error: 0.590406 Iteration 2 Error: 0.140271 Iteration 3 Error: 0.062009 Iteration 4 Error: 0.021648 Align patch 4 21 left Iteration 1 Error: 1.306355 Iteration 2 Error: 0.159473 Iteration 3 Error: 0.039802 Align patch 5 20 left Iteration 1 Error: 1.039573 Iteration 2 Error: 0.319172 Iteration 3 Error: 0.142077 Iteration 4 Error: 0.072712 Iteration 5 Error: 0.036918 Align patch 6 19 left Iteration 1 Error: 0.897595 Iteration 2 Error: 0.272201 Iteration 3 Error: 0.145283 Iteration 4 Error: 0.046412 Align patch 7 18 left Iteration 1 Error: 0.703726 Iteration 2 Error: 0.184549 Iteration 3 Error: 0.077561 Iteration 4 Error: 0.025889 Align patch 8 17 left Iteration 1 Error: 0.821501 Iteration 2 Error: 0.257316 Iteration 3 Error: 0.085335 Iteration 4 Error: 0.031062 Align patch 9 16 left Iteration 1 Error: 0.673066 Iteration 2 Error: 0.143799 Iteration 3 Error: 0.047488 Align patch 10 15 left Iteration 1 Error: 1.064069 Iteration 2 Error: 0.378268 Iteration 3 Error: 0.197080 Iteration 4 Error: 0.108329 Iteration 5 Error: 0.055647 Align patch 10 15 left Iteration 1 Error: 0.735106 Iteration 2 Error: 0.081636 Iteration 3 Error: 0.027358 Align patch 11 14 left Iteration 1 Error: 1.359739 Iteration 2 Error: 0.250938 Iteration 3 Error: 0.084748 Iteration 4 Error: 0.052595 Iteration 5 Error: 0.017712 Align patch 12 13 left Iteration 1 Error: 0.965674 Iteration 2 Error: 0.180091 Iteration 3 Error: 0.048229 Align patch 13 12 left Iteration 1 Error: 0.450969 Iteration 2 Error: 0.096988 Iteration 3 Error: 0.036287 Align patch 14 11 left Iteration 1 Error: 1.256912 Iteration 2 Error: 0.252776 Iteration 3 Error: 0.083370 Iteration 4 Error: 0.016396 Align patch 15 10 left Iteration 1 Error: 0.907403 Iteration 2 Error: 0.160442 Iteration 3 Error: 0.047747 Align patch 16 9 left Iteration 1 Error: 0.861038 Iteration 2 Error: 0.205876 Iteration 3 Error: 0.114966 Iteration 4 Error: 0.038648 Align patch 17 8 left Iteration 1 Error: 1.188581 Iteration 2 Error: 0.179470 Iteration 3 Error: 0.050081 Iteration 4 Error: 0.016929 Align patch 18 7 left Iteration 1 Error: 0.739884 Iteration 2 Error: 0.104377 Iteration 3 Error: 0.038009 Align patch 19 6 left Iteration 1 Error: 0.730049 Iteration 2 Error: 0.133198 Iteration 3 Error: 0.032896 Align patch 20 5 left Iteration 1 Error: 0.762284 Iteration 2 Error: 0.234081 Iteration 3 Error: 0.057160 Iteration 4 Error: 0.019057 Align patch 21 4 left Iteration 1 Error: 0.856728 Iteration 2 Error: 0.212529 Iteration 3 Error: 0.126345 Iteration 4 Error: 0.033107 Align patch 22 3 left Iteration 1 Error: 1.076878 Iteration 2 Error: 0.240426 Iteration 3 Error: 0.067047 Iteration 4 Error: 0.028587 Align patch 23 2 left Iteration 1 Error: 1.150513 Iteration 2 Error: 0.435348 Iteration 3 Error: 0.165808 Iteration 4 Error: 0.090885 Iteration 5 Error: 0.061851 Align patch 23 2 left Iteration 1 Error: 1.128581 Iteration 2 Error: 0.181070 Iteration 3 Error: 0.080329 Iteration 4 Error: 0.021145 Align patch 24 1 left Iteration 1 Error: 1.775820 Iteration 2 Error: 0.450788 Iteration 3 Error: 0.285334 Iteration 4 Error: 0.113070 Iteration 5 Error: 0.053794 Align patch 24 1 left Iteration 1 Error: 1.485093 Iteration 2 Error: 0.214544 Iteration 3 Error: 0.064663 Iteration 4 Error: 0.022681 Align patch 25 0 left Iteration 1 Error: 0.988183 Iteration 2 Error: 0.164371 Iteration 3 Error: 0.038518 3D Fitting completed. Patch alignment time: 19.80(sec) Local motion has been corrected. Process thread exits. Computational time: 29.072790 sec Total time: 34.912289 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00005hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00005hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.871468s Reading file: gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00005hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.104552s ........................................ >>>>>>TIME<<<<<< FFT: 0.779292s Defocus_U Defocus_V Angle CCC 8718.79 9207.13 15.17 0.012390 Final Values Defocus_U Defocus_V Angle CCC 8782.81 9111.90 3.02 0.022534 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00013sq_v01_00005hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00005hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.344e-01 9.993e-02 CC threshold: 0.734 Mean Std: 36.91 7.74 Num Hot pixels: 148 Hot pixel threshold: 83.33 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 53.005386 Iteration 2 Error: 50.855404 Iteration 3 Error: 53.504620 Iteration 4 Error: 53.283985 Iteration 5 Error: 50.355240 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -13.47 10.53 ...... Frame ( 3) shift: -26.94 21.06 ...... Frame ( 4) shift: -40.41 31.60 ...... Frame ( 5) shift: -53.88 42.13 ...... Frame ( 6) shift: -72.55 44.12 ...... Frame ( 7) shift: -96.42 37.57 ...... Frame ( 8) shift: -120.29 31.02 ...... Frame ( 9) shift: -141.21 33.63 ...... Frame ( 10) shift: -159.19 45.39 ...... Frame ( 11) shift: -177.16 57.14 ...... Frame ( 12) shift: -188.61 82.11 ...... Frame ( 13) shift: -193.52 120.27 ...... Frame ( 14) shift: -198.43 158.43 ...... Frame ( 15) shift: -201.33 177.54 ...... Frame ( 16) shift: -202.22 177.59 ...... Frame ( 17) shift: -203.11 177.65 ...... Frame ( 18) shift: -204.02 177.74 ...... Frame ( 19) shift: -204.96 177.86 ...... Frame ( 20) shift: -205.90 177.99 ...... Frame ( 21) shift: -206.77 178.11 ...... Frame ( 22) shift: -207.58 178.22 ...... Frame ( 23) shift: -208.39 178.33 ...... Frame ( 24) shift: -209.16 178.40 ...... Frame ( 25) shift: -209.88 178.42 ...... Frame ( 26) shift: -210.61 178.44 ...... Frame ( 27) shift: -211.36 178.57 ...... Frame ( 28) shift: -212.12 178.82 ...... Frame ( 29) shift: -212.88 179.08 ...... Frame ( 30) shift: -213.76 179.27 ...... Frame ( 31) shift: -214.76 179.40 ...... Frame ( 32) shift: -215.76 179.53 ...... Frame ( 33) shift: -216.66 179.64 ...... Frame ( 34) shift: -217.48 179.74 ...... Frame ( 35) shift: -218.30 179.83 ...... Frame ( 36) shift: -219.21 179.90 ...... Frame ( 37) shift: -220.21 179.94 ...... Frame ( 38) shift: -221.21 179.98 ...... Frame ( 39) shift: -222.21 180.02 ...... Frame ( 40) shift: -223.22 180.06 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 36.007038 Iteration 2 Error: 22.201157 Iteration 3 Error: 32.810310 Iteration 4 Error: 37.938583 Iteration 5 Error: 47.213253 Align patch 1 24 left Iteration 1 Error: 16.185379 Iteration 2 Error: 26.883793 Iteration 3 Error: 19.591457 Iteration 4 Error: 11.740174 Iteration 5 Error: 7.910569 Align patch 2 23 left Iteration 1 Error: 3.515488 Iteration 2 Error: 2.414801 Iteration 3 Error: 0.772324 Iteration 4 Error: 0.431491 Iteration 5 Error: 0.339567 Align patch 2 23 left Iteration 1 Error: 8.488420 Iteration 2 Error: 2.340158 Iteration 3 Error: 2.755950 Iteration 4 Error: 1.386234 Iteration 5 Error: 0.752552 Align patch 3 22 left Iteration 1 Error: 36.431084 Iteration 2 Error: 30.258970 Iteration 3 Error: 34.663170 Iteration 4 Error: 35.990185 Iteration 5 Error: 33.569931 Align patch 3 22 left Iteration 1 Error: 4.747885 Iteration 2 Error: 1.127604 Iteration 3 Error: 0.464084 Iteration 4 Error: 0.229695 Iteration 5 Error: 0.130784 Align patch 4 21 left Iteration 1 Error: 36.066692 Iteration 2 Error: 38.523293 Iteration 3 Error: 39.002193 Iteration 4 Error: 35.965416 Iteration 5 Error: 35.938641 Align patch 4 21 left Iteration 1 Error: 57.821121 Iteration 2 Error: 57.500679 Iteration 3 Error: 43.662483 Iteration 4 Error: 33.146118 Iteration 5 Error: 57.501263 Align patch 5 20 left Iteration 1 Error: 50.823299 Iteration 2 Error: 50.823299 Iteration 3 Error: 36.883232 Iteration 4 Error: 37.362522 Iteration 5 Error: 35.985657 Align patch 5 20 left Iteration 1 Error: 58.364559 Iteration 2 Error: 57.523262 Iteration 3 Error: 57.719696 Iteration 4 Error: 57.511257 Iteration 5 Error: 57.532887 Align patch 6 19 left Iteration 1 Error: 49.104301 Iteration 2 Error: 46.625942 Iteration 3 Error: 36.875710 Iteration 4 Error: 37.613750 Iteration 5 Error: 39.595009 Align patch 6 19 left Iteration 1 Error: 41.871357 Iteration 2 Error: 24.313026 Iteration 3 Error: 27.298386 Iteration 4 Error: 55.650078 Iteration 5 Error: 37.005619 Align patch 7 18 left Iteration 1 Error: 36.112225 Iteration 2 Error: 18.272573 Iteration 3 Error: 6.411251 Iteration 4 Error: 39.089195 Iteration 5 Error: 0.876272 Align patch 7 18 left Iteration 1 Error: 26.313232 Iteration 2 Error: 5.135682 Iteration 3 Error: 2.793864 Iteration 4 Error: 1.720391 Iteration 5 Error: 0.873096 Align patch 8 17 left Iteration 1 Error: 36.253738 Iteration 2 Error: 35.939919 Iteration 3 Error: 37.639965 Iteration 4 Error: 36.104076 Iteration 5 Error: 36.332912 Align patch 8 17 left Iteration 1 Error: 7.055658 Iteration 2 Error: 1.702868 Iteration 3 Error: 0.728035 Iteration 4 Error: 0.720401 Iteration 5 Error: 0.308048 Align patch 9 16 left Iteration 1 Error: 3.151511 Iteration 2 Error: 0.947696 Iteration 3 Error: 17.969332 Iteration 4 Error: 1.779910 Iteration 5 Error: 0.803406 Align patch 9 16 left Iteration 1 Error: 33.139252 Iteration 2 Error: 1.440305 Iteration 3 Error: 0.363338 Iteration 4 Error: 0.138544 Iteration 5 Error: 0.217867 Align patch 10 15 left Iteration 1 Error: 37.559799 Iteration 2 Error: 38.344990 Iteration 3 Error: 36.630959 Iteration 4 Error: 37.329716 Iteration 5 Error: 42.655266 Align patch 10 15 left Iteration 1 Error: 58.587372 Iteration 2 Error: 57.531937 Iteration 3 Error: 57.540413 Iteration 4 Error: 57.503067 Iteration 5 Error: 54.146126 Align patch 11 14 left Iteration 1 Error: 37.281452 Iteration 2 Error: 36.126606 Iteration 3 Error: 31.794699 Iteration 4 Error: 28.966316 Iteration 5 Error: 27.661642 Align patch 11 14 left Iteration 1 Error: 72.433235 Iteration 2 Error: 57.797623 Iteration 3 Error: 43.424435 Iteration 4 Error: 62.005951 Iteration 5 Error: 59.448051 Align patch 12 13 left Iteration 1 Error: 40.161793 Iteration 2 Error: 40.638897 Iteration 3 Error: 2.008140 Iteration 4 Error: 0.331906 Iteration 5 Error: 0.268936 Align patch 12 13 left Iteration 1 Error: 43.473373 Iteration 2 Error: 48.302094 Iteration 3 Error: 2.310244 Iteration 4 Error: 58.254234 Iteration 5 Error: 61.269096 Align patch 13 12 left Iteration 1 Error: 35.663525 Iteration 2 Error: 36.873180 Iteration 3 Error: 25.344868 Iteration 4 Error: 32.095325 Iteration 5 Error: 2.064234 Align patch 13 12 left Iteration 1 Error: 9.740702 Iteration 2 Error: 9.209582 Iteration 3 Error: 3.459922 Iteration 4 Error: 1.710562 Iteration 5 Error: 0.865134 Align patch 14 11 left Iteration 1 Error: 36.028206 Iteration 2 Error: 32.187237 Iteration 3 Error: 35.822620 Iteration 4 Error: 34.892971 Iteration 5 Error: 35.637203 Align patch 14 11 left Iteration 1 Error: 8.965155 Iteration 2 Error: 1.748386 Iteration 3 Error: 4.843210 Iteration 4 Error: 10.209277 Iteration 5 Error: 3.104110 Align patch 15 10 left Iteration 1 Error: 30.890671 Iteration 2 Error: 31.832336 Iteration 3 Error: 32.127319 Iteration 4 Error: 39.182205 Iteration 5 Error: 25.854832 Align patch 15 10 left Iteration 1 Error: 58.222107 Iteration 2 Error: 13.434214 Iteration 3 Error: 1.917843 Iteration 4 Error: 0.670353 Iteration 5 Error: 0.490054 Align patch 16 9 left Iteration 1 Error: 41.046356 Iteration 2 Error: 36.217583 Iteration 3 Error: 31.568808 Iteration 4 Error: 40.310078 Iteration 5 Error: 29.067453 Align patch 16 9 left Iteration 1 Error: 58.128902 Iteration 2 Error: 54.176609 Iteration 3 Error: 30.772715 Iteration 4 Error: 25.832767 Iteration 5 Error: 54.445641 Align patch 17 8 left Iteration 1 Error: 50.823299 Iteration 2 Error: 40.057957 Iteration 3 Error: 26.324362 Iteration 4 Error: 25.876822 Iteration 5 Error: 25.882977 Align patch 17 8 left Iteration 1 Error: 4.228050 Iteration 2 Error: 1.531415 Iteration 3 Error: 0.464680 Iteration 4 Error: 0.233586 Iteration 5 Error: 0.106111 Align patch 18 7 left Iteration 1 Error: 15.130760 Iteration 2 Error: 3.531414 Iteration 3 Error: 5.768445 Iteration 4 Error: 2.514677 Iteration 5 Error: 1.519536 Align patch 18 7 left Iteration 1 Error: 14.336984 Iteration 2 Error: 2.081171 Iteration 3 Error: 0.975922 Iteration 4 Error: 0.418960 Iteration 5 Error: 0.172147 Align patch 19 6 left Iteration 1 Error: 36.779301 Iteration 2 Error: 38.372974 Iteration 3 Error: 37.059143 Iteration 4 Error: 50.823299 Iteration 5 Error: 37.427277 Align patch 19 6 left Iteration 1 Error: 4.612504 Iteration 2 Error: 0.615315 Iteration 3 Error: 0.153958 Iteration 4 Error: 0.055098 Iteration 5 Error: 0.031706 Align patch 20 5 left Iteration 1 Error: 37.382767 Iteration 2 Error: 37.449425 Iteration 3 Error: 35.942177 Iteration 4 Error: 35.937618 Iteration 5 Error: 34.996292 Align patch 20 5 left Iteration 1 Error: 11.243240 Iteration 2 Error: 2.185153 Iteration 3 Error: 0.908584 Iteration 4 Error: 0.272923 Iteration 5 Error: 0.124708 Align patch 21 4 left Iteration 1 Error: 38.098591 Iteration 2 Error: 39.903202 Iteration 3 Error: 22.144272 Iteration 4 Error: 24.065269 Iteration 5 Error: 35.968060 Align patch 21 4 left Iteration 1 Error: 43.570232 Iteration 2 Error: 25.322920 Iteration 3 Error: 20.346746 Iteration 4 Error: 23.074169 Iteration 5 Error: 20.121876 Align patch 22 3 left Iteration 1 Error: 18.851622 Iteration 2 Error: 35.983864 Iteration 3 Error: 35.946854 Iteration 4 Error: 35.966400 Iteration 5 Error: 20.589336 Align patch 22 3 left Iteration 1 Error: 9.834432 Iteration 2 Error: 2.131254 Iteration 3 Error: 1.078695 Iteration 4 Error: 0.630922 Iteration 5 Error: 0.431232 Align patch 23 2 left Iteration 1 Error: 21.222488 Iteration 2 Error: 18.119879 Iteration 3 Error: 12.503282 Iteration 4 Error: 8.884645 Iteration 5 Error: 2.108015 Align patch 23 2 left Iteration 1 Error: 4.628870 Iteration 2 Error: 1.038165 Iteration 3 Error: 0.570168 Iteration 4 Error: 0.267761 Iteration 5 Error: 0.088601 Align patch 24 1 left Iteration 1 Error: 36.002468 Iteration 2 Error: 35.960857 Iteration 3 Error: 36.003593 Iteration 4 Error: 37.571796 Iteration 5 Error: 27.805998 Align patch 24 1 left Iteration 1 Error: 7.215591 Iteration 2 Error: 0.653788 Iteration 3 Error: 0.273131 Iteration 4 Error: 0.040907 Align patch 25 0 left Iteration 1 Error: 51.689068 Iteration 2 Error: 46.765388 Iteration 3 Error: 36.431675 Iteration 4 Error: 38.208580 Iteration 5 Error: 32.625546 Align patch 25 0 left Iteration 1 Error: 28.020535 Iteration 2 Error: 26.299690 Iteration 3 Error: 25.927736 Iteration 4 Error: 41.325249 Iteration 5 Error: 57.655251 3D Fitting completed. Patch alignment time: 40.96(sec) Local motion has been corrected. Process thread exits. Computational time: 49.971024 sec Total time: 56.468758 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00005hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00005hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.680771s Reading file: gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00005hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.372082s ........................................ >>>>>>TIME<<<<<< FFT: 0.929431s Defocus_U Defocus_V Angle CCC 11732.40 12455.11 11.06 0.131638 Final Values Defocus_U Defocus_V Angle CCC 11723.02 12458.24 11.38 0.270972 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00013sq_v01_00006hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00006hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.001e-01 CC threshold: 0.735 Mean Std: 41.02 7.01 Num Hot pixels: 236 Hot pixel threshold: 83.07 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.555450 Iteration 2 Error: 0.319941 Iteration 3 Error: 0.088399 Iteration 4 Error: 0.026635 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.05 -0.15 ...... Frame ( 3) shift: -0.10 -0.30 ...... Frame ( 4) shift: -0.15 -0.46 ...... Frame ( 5) shift: -0.20 -0.61 ...... Frame ( 6) shift: -0.18 -0.67 ...... Frame ( 7) shift: -0.08 -0.65 ...... Frame ( 8) shift: 0.01 -0.63 ...... Frame ( 9) shift: 0.10 -0.57 ...... Frame ( 10) shift: 0.19 -0.46 ...... Frame ( 11) shift: 0.27 -0.36 ...... Frame ( 12) shift: 0.35 -0.26 ...... Frame ( 13) shift: 0.42 -0.16 ...... Frame ( 14) shift: 0.48 -0.06 ...... Frame ( 15) shift: 0.55 -0.01 ...... Frame ( 16) shift: 0.60 -0.01 ...... Frame ( 17) shift: 0.66 -0.02 ...... Frame ( 18) shift: 0.73 -0.01 ...... Frame ( 19) shift: 0.80 -0.01 ...... Frame ( 20) shift: 0.87 0.00 ...... Frame ( 21) shift: 0.95 0.03 ...... Frame ( 22) shift: 1.03 0.07 ...... Frame ( 23) shift: 1.12 0.11 ...... Frame ( 24) shift: 1.23 0.15 ...... Frame ( 25) shift: 1.36 0.20 ...... Frame ( 26) shift: 1.50 0.24 ...... Frame ( 27) shift: 1.63 0.30 ...... Frame ( 28) shift: 1.77 0.37 ...... Frame ( 29) shift: 1.91 0.44 ...... Frame ( 30) shift: 2.01 0.49 ...... Frame ( 31) shift: 2.08 0.53 ...... Frame ( 32) shift: 2.14 0.57 ...... Frame ( 33) shift: 2.24 0.62 ...... Frame ( 34) shift: 2.39 0.70 ...... Frame ( 35) shift: 2.53 0.78 ...... Frame ( 36) shift: 2.63 0.80 ...... Frame ( 37) shift: 2.68 0.77 ...... Frame ( 38) shift: 2.73 0.74 ...... Frame ( 39) shift: 2.78 0.71 ...... Frame ( 40) shift: 2.83 0.68 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.648336 Iteration 2 Error: 0.154187 Iteration 3 Error: 0.022762 Align patch 2 23 left Iteration 1 Error: 1.115601 Iteration 2 Error: 0.266448 Iteration 3 Error: 0.080328 Iteration 4 Error: 0.047796 Align patch 3 22 left Iteration 1 Error: 0.834058 Iteration 2 Error: 0.092582 Iteration 3 Error: 0.023432 Align patch 4 21 left Iteration 1 Error: 0.661335 Iteration 2 Error: 0.157147 Iteration 3 Error: 0.042540 Align patch 5 20 left Iteration 1 Error: 0.643745 Iteration 2 Error: 0.069683 Iteration 3 Error: 0.013340 Align patch 6 19 left Iteration 1 Error: 0.721277 Iteration 2 Error: 0.274998 Iteration 3 Error: 0.130937 Iteration 4 Error: 0.048811 Align patch 7 18 left Iteration 1 Error: 0.794101 Iteration 2 Error: 0.109758 Iteration 3 Error: 0.049036 Align patch 8 17 left Iteration 1 Error: 0.929381 Iteration 2 Error: 0.183065 Iteration 3 Error: 0.047425 Align patch 9 16 left Iteration 1 Error: 1.065740 Iteration 2 Error: 0.122744 Iteration 3 Error: 0.032904 Align patch 10 15 left Iteration 1 Error: 1.277325 Iteration 2 Error: 0.203886 Iteration 3 Error: 0.062849 Iteration 4 Error: 0.025498 Align patch 11 14 left Iteration 1 Error: 1.502448 Iteration 2 Error: 0.196158 Iteration 3 Error: 0.078765 Iteration 4 Error: 0.025266 Align patch 12 13 left Iteration 1 Error: 1.315237 Iteration 2 Error: 0.116287 Iteration 3 Error: 0.027151 Align patch 13 12 left Iteration 1 Error: 0.554866 Iteration 2 Error: 0.148792 Iteration 3 Error: 0.042058 Align patch 14 11 left Iteration 1 Error: 0.524055 Iteration 2 Error: 0.117595 Iteration 3 Error: 0.025762 Align patch 15 10 left Iteration 1 Error: 0.875793 Iteration 2 Error: 0.114498 Iteration 3 Error: 0.027547 Align patch 16 9 left Iteration 1 Error: 1.320574 Iteration 2 Error: 0.166479 Iteration 3 Error: 0.034331 Align patch 17 8 left Iteration 1 Error: 1.022040 Iteration 2 Error: 0.123410 Iteration 3 Error: 0.022813 Align patch 18 7 left Iteration 1 Error: 0.556189 Iteration 2 Error: 0.149036 Iteration 3 Error: 0.084879 Iteration 4 Error: 0.031613 Align patch 19 6 left Iteration 1 Error: 0.648201 Iteration 2 Error: 0.230625 Iteration 3 Error: 0.070587 Iteration 4 Error: 0.033953 Align patch 20 5 left Iteration 1 Error: 0.685734 Iteration 2 Error: 0.127728 Iteration 3 Error: 0.033054 Align patch 21 4 left Iteration 1 Error: 1.465267 Iteration 2 Error: 0.168535 Iteration 3 Error: 0.037356 Align patch 22 3 left Iteration 1 Error: 0.747342 Iteration 2 Error: 0.150709 Iteration 3 Error: 0.024935 Align patch 23 2 left Iteration 1 Error: 0.628794 Iteration 2 Error: 0.118164 Iteration 3 Error: 0.039602 Align patch 24 1 left Iteration 1 Error: 0.819089 Iteration 2 Error: 0.164880 Iteration 3 Error: 0.042544 Align patch 25 0 left Iteration 1 Error: 1.197364 Iteration 2 Error: 0.207583 Iteration 3 Error: 0.048601 3D Fitting completed. Patch alignment time: 15.22(sec) Local motion has been corrected. Process thread exits. Computational time: 23.842825 sec Total time: 29.449833 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00006hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00006hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.556921s Reading file: gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00006hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.340404s ........................................ >>>>>>TIME<<<<<< FFT: 0.928086s Defocus_U Defocus_V Angle CCC 11970.70 12806.64 13.30 0.050745 Final Values Defocus_U Defocus_V Angle CCC 11986.32 12812.90 12.67 0.085104 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00013sq_v01_00006hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00006hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.347e-01 1.002e-01 CC threshold: 0.736 Mean Std: 39.61 6.88 Num Hot pixels: 224 Hot pixel threshold: 80.88 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.503364 Iteration 2 Error: 0.295560 Iteration 3 Error: 0.080047 Iteration 4 Error: 0.031600 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.17 -0.19 ...... Frame ( 3) shift: -0.33 -0.37 ...... Frame ( 4) shift: -0.50 -0.56 ...... Frame ( 5) shift: -0.67 -0.74 ...... Frame ( 6) shift: -0.73 -0.86 ...... Frame ( 7) shift: -0.68 -0.91 ...... Frame ( 8) shift: -0.63 -0.96 ...... Frame ( 9) shift: -0.59 -0.96 ...... Frame ( 10) shift: -0.55 -0.92 ...... Frame ( 11) shift: -0.51 -0.88 ...... Frame ( 12) shift: -0.40 -0.84 ...... Frame ( 13) shift: -0.22 -0.81 ...... Frame ( 14) shift: -0.04 -0.78 ...... Frame ( 15) shift: 0.05 -0.74 ...... Frame ( 16) shift: 0.05 -0.70 ...... Frame ( 17) shift: 0.05 -0.66 ...... Frame ( 18) shift: 0.10 -0.60 ...... Frame ( 19) shift: 0.20 -0.52 ...... Frame ( 20) shift: 0.30 -0.45 ...... Frame ( 21) shift: 0.38 -0.36 ...... Frame ( 22) shift: 0.44 -0.25 ...... Frame ( 23) shift: 0.50 -0.14 ...... Frame ( 24) shift: 0.57 -0.06 ...... Frame ( 25) shift: 0.67 -0.01 ...... Frame ( 26) shift: 0.76 0.05 ...... Frame ( 27) shift: 0.88 0.09 ...... Frame ( 28) shift: 1.01 0.13 ...... Frame ( 29) shift: 1.13 0.17 ...... Frame ( 30) shift: 1.25 0.20 ...... Frame ( 31) shift: 1.36 0.21 ...... Frame ( 32) shift: 1.46 0.23 ...... Frame ( 33) shift: 1.56 0.28 ...... Frame ( 34) shift: 1.64 0.35 ...... Frame ( 35) shift: 1.72 0.42 ...... Frame ( 36) shift: 1.79 0.48 ...... Frame ( 37) shift: 1.84 0.53 ...... Frame ( 38) shift: 1.89 0.57 ...... Frame ( 39) shift: 1.95 0.62 ...... Frame ( 40) shift: 2.00 0.67 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.845923 Iteration 2 Error: 0.204867 Iteration 3 Error: 0.053951 Iteration 4 Error: 0.014405 Align patch 2 23 left Iteration 1 Error: 0.986767 Iteration 2 Error: 0.195870 Iteration 3 Error: 0.058188 Iteration 4 Error: 0.025453 Align patch 3 22 left Iteration 1 Error: 0.736605 Iteration 2 Error: 0.227890 Iteration 3 Error: 0.062450 Iteration 4 Error: 0.027719 Align patch 4 21 left Iteration 1 Error: 0.632648 Iteration 2 Error: 0.149867 Iteration 3 Error: 0.029905 Align patch 5 20 left Iteration 1 Error: 0.762300 Iteration 2 Error: 0.098691 Iteration 3 Error: 0.027790 Align patch 6 19 left Iteration 1 Error: 0.704949 Iteration 2 Error: 0.109768 Iteration 3 Error: 0.027428 Align patch 7 18 left Iteration 1 Error: 0.679420 Iteration 2 Error: 0.105248 Iteration 3 Error: 0.038806 Align patch 8 17 left Iteration 1 Error: 0.722997 Iteration 2 Error: 0.104464 Iteration 3 Error: 0.021758 Align patch 9 16 left Iteration 1 Error: 0.514232 Iteration 2 Error: 0.082063 Iteration 3 Error: 0.027391 Align patch 10 15 left Iteration 1 Error: 0.624960 Iteration 2 Error: 0.100439 Iteration 3 Error: 0.021810 Align patch 11 14 left Iteration 1 Error: 0.580289 Iteration 2 Error: 0.252534 Iteration 3 Error: 0.075893 Iteration 4 Error: 0.035276 Align patch 12 13 left Iteration 1 Error: 0.526425 Iteration 2 Error: 0.161025 Iteration 3 Error: 0.072985 Iteration 4 Error: 0.028947 Align patch 13 12 left Iteration 1 Error: 0.611782 Iteration 2 Error: 0.061488 Iteration 3 Error: 0.015407 Align patch 14 11 left Iteration 1 Error: 0.756051 Iteration 2 Error: 0.162879 Iteration 3 Error: 0.037039 Align patch 15 10 left Iteration 1 Error: 0.632431 Iteration 2 Error: 0.099813 Iteration 3 Error: 0.038965 Align patch 16 9 left Iteration 1 Error: 0.631016 Iteration 2 Error: 0.113808 Iteration 3 Error: 0.062295 Iteration 4 Error: 0.019708 Align patch 17 8 left Iteration 1 Error: 0.733358 Iteration 2 Error: 0.218186 Iteration 3 Error: 0.075413 Iteration 4 Error: 0.031660 Align patch 18 7 left Iteration 1 Error: 0.664203 Iteration 2 Error: 0.088734 Iteration 3 Error: 0.013209 Align patch 19 6 left Iteration 1 Error: 0.428354 Iteration 2 Error: 0.064832 Iteration 3 Error: 0.013934 Align patch 20 5 left Iteration 1 Error: 0.520473 Iteration 2 Error: 0.083613 Iteration 3 Error: 0.015658 Align patch 21 4 left Iteration 1 Error: 0.532221 Iteration 2 Error: 0.066580 Iteration 3 Error: 0.011973 Align patch 22 3 left Iteration 1 Error: 0.802293 Iteration 2 Error: 0.091797 Iteration 3 Error: 0.029166 Align patch 23 2 left Iteration 1 Error: 0.489567 Iteration 2 Error: 0.056108 Iteration 3 Error: 0.020150 Align patch 24 1 left Iteration 1 Error: 0.647043 Iteration 2 Error: 0.054912 Iteration 3 Error: 0.009797 Align patch 25 0 left Iteration 1 Error: 0.748619 Iteration 2 Error: 0.122818 Iteration 3 Error: 0.021501 3D Fitting completed. Patch alignment time: 15.40(sec) Local motion has been corrected. Process thread exits. Computational time: 24.631842 sec Total time: 30.445095 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00006hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00006hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.790117s Reading file: gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00006hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.493185s ........................................ >>>>>>TIME<<<<<< FFT: 0.938722s Defocus_U Defocus_V Angle CCC 12624.98 13152.37 3.01 0.050565 Final Values Defocus_U Defocus_V Angle CCC 12629.67 13163.31 3.32 0.081000 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00013sq_v01_00006hln_00004enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00006hln_00004enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.002e-01 CC threshold: 0.736 Mean Std: 42.60 7.22 Num Hot pixels: 245 Hot pixel threshold: 85.94 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.131778 Iteration 2 Error: 0.193455 Iteration 3 Error: 0.044725 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.27 -0.04 ...... Frame ( 3) shift: -0.54 -0.07 ...... Frame ( 4) shift: -0.82 -0.11 ...... Frame ( 5) shift: -1.09 -0.14 ...... Frame ( 6) shift: -1.19 -0.17 ...... Frame ( 7) shift: -1.13 -0.18 ...... Frame ( 8) shift: -1.06 -0.20 ...... Frame ( 9) shift: -1.01 -0.20 ...... Frame ( 10) shift: -0.96 -0.19 ...... Frame ( 11) shift: -0.92 -0.18 ...... Frame ( 12) shift: -0.87 -0.12 ...... Frame ( 13) shift: -0.81 -0.00 ...... Frame ( 14) shift: -0.75 0.11 ...... Frame ( 15) shift: -0.67 0.19 ...... Frame ( 16) shift: -0.58 0.23 ...... Frame ( 17) shift: -0.49 0.27 ...... Frame ( 18) shift: -0.38 0.33 ...... Frame ( 19) shift: -0.25 0.41 ...... Frame ( 20) shift: -0.12 0.49 ...... Frame ( 21) shift: -0.03 0.53 ...... Frame ( 22) shift: 0.01 0.51 ...... Frame ( 23) shift: 0.05 0.50 ...... Frame ( 24) shift: 0.10 0.48 ...... Frame ( 25) shift: 0.15 0.46 ...... Frame ( 26) shift: 0.20 0.43 ...... Frame ( 27) shift: 0.28 0.44 ...... Frame ( 28) shift: 0.38 0.47 ...... Frame ( 29) shift: 0.47 0.51 ...... Frame ( 30) shift: 0.55 0.53 ...... Frame ( 31) shift: 0.62 0.53 ...... Frame ( 32) shift: 0.68 0.54 ...... Frame ( 33) shift: 0.71 0.58 ...... Frame ( 34) shift: 0.68 0.66 ...... Frame ( 35) shift: 0.66 0.73 ...... Frame ( 36) shift: 0.70 0.79 ...... Frame ( 37) shift: 0.81 0.82 ...... Frame ( 38) shift: 0.91 0.85 ...... Frame ( 39) shift: 1.01 0.88 ...... Frame ( 40) shift: 1.11 0.91 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.215271 Iteration 2 Error: 0.142986 Iteration 3 Error: 0.023381 Align patch 2 23 left Iteration 1 Error: 0.799876 Iteration 2 Error: 0.156811 Iteration 3 Error: 0.036494 Align patch 3 22 left Iteration 1 Error: 0.653941 Iteration 2 Error: 0.141376 Iteration 3 Error: 0.026698 Align patch 4 21 left Iteration 1 Error: 0.528405 Iteration 2 Error: 0.106246 Iteration 3 Error: 0.021772 Align patch 5 20 left Iteration 1 Error: 0.877767 Iteration 2 Error: 0.119212 Iteration 3 Error: 0.020420 Align patch 6 19 left Iteration 1 Error: 0.831085 Iteration 2 Error: 0.111769 Iteration 3 Error: 0.025857 Align patch 7 18 left Iteration 1 Error: 1.336585 Iteration 2 Error: 0.214835 Iteration 3 Error: 0.059362 Iteration 4 Error: 0.024806 Align patch 8 17 left Iteration 1 Error: 0.641092 Iteration 2 Error: 0.129589 Iteration 3 Error: 0.043754 Align patch 9 16 left Iteration 1 Error: 0.547370 Iteration 2 Error: 0.103487 Iteration 3 Error: 0.021356 Align patch 10 15 left Iteration 1 Error: 0.609790 Iteration 2 Error: 0.069107 Iteration 3 Error: 0.016761 Align patch 11 14 left Iteration 1 Error: 0.692125 Iteration 2 Error: 0.184886 Iteration 3 Error: 0.049717 Align patch 12 13 left Iteration 1 Error: 0.744071 Iteration 2 Error: 0.199962 Iteration 3 Error: 0.088511 Iteration 4 Error: 0.033370 Align patch 13 12 left Iteration 1 Error: 0.737908 Iteration 2 Error: 0.110969 Iteration 3 Error: 0.029063 Align patch 14 11 left Iteration 1 Error: 0.724165 Iteration 2 Error: 0.108602 Iteration 3 Error: 0.025941 Align patch 15 10 left Iteration 1 Error: 0.489379 Iteration 2 Error: 0.056465 Iteration 3 Error: 0.012295 Align patch 16 9 left Iteration 1 Error: 0.686027 Iteration 2 Error: 0.221541 Iteration 3 Error: 0.040973 Align patch 17 8 left Iteration 1 Error: 0.898522 Iteration 2 Error: 0.124780 Iteration 3 Error: 0.047626 Align patch 18 7 left Iteration 1 Error: 0.888689 Iteration 2 Error: 0.146249 Iteration 3 Error: 0.031298 Align patch 19 6 left Iteration 1 Error: 0.726319 Iteration 2 Error: 0.071728 Iteration 3 Error: 0.014788 Align patch 20 5 left Iteration 1 Error: 0.717864 Iteration 2 Error: 0.114384 Iteration 3 Error: 0.022626 Align patch 21 4 left Iteration 1 Error: 0.770934 Iteration 2 Error: 0.198944 Iteration 3 Error: 0.076566 Iteration 4 Error: 0.016177 Align patch 22 3 left Iteration 1 Error: 0.646161 Iteration 2 Error: 0.107140 Iteration 3 Error: 0.036647 Align patch 23 2 left Iteration 1 Error: 0.721007 Iteration 2 Error: 0.076847 Iteration 3 Error: 0.025720 Align patch 24 1 left Iteration 1 Error: 0.731704 Iteration 2 Error: 0.085718 Iteration 3 Error: 0.017750 Align patch 25 0 left Iteration 1 Error: 0.625798 Iteration 2 Error: 0.164408 Iteration 3 Error: 0.037254 3D Fitting completed. Patch alignment time: 15.98(sec) Local motion has been corrected. Process thread exits. Computational time: 24.975933 sec Total time: 31.631269 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00006hln_00004enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00006hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.732468s Reading file: gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00006hln_00004enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.300449s ........................................ >>>>>>TIME<<<<<< FFT: 1.021038s Defocus_U Defocus_V Angle CCC 13083.99 13947.27 6.79 0.062334 Final Values Defocus_U Defocus_V Angle CCC 13085.55 13958.21 6.48 0.105849 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00013sq_v01_00006hln_00005enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00006hln_00005enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 42.93 7.14 Num Hot pixels: 254 Hot pixel threshold: 85.79 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.247219 Iteration 2 Error: 0.266832 Iteration 3 Error: 0.061057 Iteration 4 Error: 0.019520 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.14 -0.04 ...... Frame ( 3) shift: -0.27 -0.09 ...... Frame ( 4) shift: -0.41 -0.13 ...... Frame ( 5) shift: -0.54 -0.17 ...... Frame ( 6) shift: -0.56 -0.16 ...... Frame ( 7) shift: -0.47 -0.09 ...... Frame ( 8) shift: -0.37 -0.02 ...... Frame ( 9) shift: -0.29 0.07 ...... Frame ( 10) shift: -0.22 0.19 ...... Frame ( 11) shift: -0.15 0.31 ...... Frame ( 12) shift: -0.09 0.41 ...... Frame ( 13) shift: -0.04 0.48 ...... Frame ( 14) shift: 0.00 0.55 ...... Frame ( 15) shift: 0.04 0.63 ...... Frame ( 16) shift: 0.06 0.70 ...... Frame ( 17) shift: 0.08 0.77 ...... Frame ( 18) shift: 0.13 0.83 ...... Frame ( 19) shift: 0.20 0.90 ...... Frame ( 20) shift: 0.28 0.96 ...... Frame ( 21) shift: 0.35 1.01 ...... Frame ( 22) shift: 0.42 1.05 ...... Frame ( 23) shift: 0.49 1.10 ...... Frame ( 24) shift: 0.56 1.14 ...... Frame ( 25) shift: 0.62 1.18 ...... Frame ( 26) shift: 0.69 1.23 ...... Frame ( 27) shift: 0.78 1.27 ...... Frame ( 28) shift: 0.89 1.30 ...... Frame ( 29) shift: 1.01 1.34 ...... Frame ( 30) shift: 1.07 1.38 ...... Frame ( 31) shift: 1.08 1.42 ...... Frame ( 32) shift: 1.09 1.47 ...... Frame ( 33) shift: 1.16 1.49 ...... Frame ( 34) shift: 1.30 1.51 ...... Frame ( 35) shift: 1.44 1.52 ...... Frame ( 36) shift: 1.51 1.55 ...... Frame ( 37) shift: 1.53 1.59 ...... Frame ( 38) shift: 1.55 1.64 ...... Frame ( 39) shift: 1.56 1.69 ...... Frame ( 40) shift: 1.58 1.73 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 1.072995 Iteration 2 Error: 0.153274 Iteration 3 Error: 0.032229 Align patch 2 23 left Iteration 1 Error: 1.373636 Iteration 2 Error: 0.321390 Iteration 3 Error: 0.090235 Iteration 4 Error: 0.048176 Align patch 3 22 left Iteration 1 Error: 0.877438 Iteration 2 Error: 0.198960 Iteration 3 Error: 0.060851 Iteration 4 Error: 0.026953 Align patch 4 21 left Iteration 1 Error: 0.644944 Iteration 2 Error: 0.110030 Iteration 3 Error: 0.038567 Align patch 5 20 left Iteration 1 Error: 0.567488 Iteration 2 Error: 0.095980 Iteration 3 Error: 0.030953 Align patch 6 19 left Iteration 1 Error: 0.923040 Iteration 2 Error: 0.222774 Iteration 3 Error: 0.061149 Iteration 4 Error: 0.026447 Align patch 7 18 left Iteration 1 Error: 0.953820 Iteration 2 Error: 0.157071 Iteration 3 Error: 0.034446 Align patch 8 17 left Iteration 1 Error: 0.768047 Iteration 2 Error: 0.112784 Iteration 3 Error: 0.027843 Align patch 9 16 left Iteration 1 Error: 0.723406 Iteration 2 Error: 0.111248 Iteration 3 Error: 0.030103 Align patch 10 15 left Iteration 1 Error: 0.665911 Iteration 2 Error: 0.161300 Iteration 3 Error: 0.032200 Align patch 11 14 left Iteration 1 Error: 1.035549 Iteration 2 Error: 0.173217 Iteration 3 Error: 0.075137 Iteration 4 Error: 0.026720 Align patch 12 13 left Iteration 1 Error: 0.517301 Iteration 2 Error: 0.109634 Iteration 3 Error: 0.022335 Align patch 13 12 left Iteration 1 Error: 0.848004 Iteration 2 Error: 0.087287 Iteration 3 Error: 0.026422 Align patch 14 11 left Iteration 1 Error: 0.815322 Iteration 2 Error: 0.122305 Iteration 3 Error: 0.051480 Iteration 4 Error: 0.014312 Align patch 15 10 left Iteration 1 Error: 0.668646 Iteration 2 Error: 0.129325 Iteration 3 Error: 0.039376 Align patch 16 9 left Iteration 1 Error: 0.643915 Iteration 2 Error: 0.126755 Iteration 3 Error: 0.058094 Iteration 4 Error: 0.030887 Align patch 17 8 left Iteration 1 Error: 0.687767 Iteration 2 Error: 0.132825 Iteration 3 Error: 0.041021 Align patch 18 7 left Iteration 1 Error: 0.849359 Iteration 2 Error: 0.092390 Iteration 3 Error: 0.017922 Align patch 19 6 left Iteration 1 Error: 0.842170 Iteration 2 Error: 0.173590 Iteration 3 Error: 0.039446 Align patch 20 5 left Iteration 1 Error: 1.164187 Iteration 2 Error: 0.258337 Iteration 3 Error: 0.059358 Iteration 4 Error: 0.018366 Align patch 21 4 left Iteration 1 Error: 0.559132 Iteration 2 Error: 0.161968 Iteration 3 Error: 0.091185 Iteration 4 Error: 0.050019 Iteration 5 Error: 0.022652 Align patch 22 3 left Iteration 1 Error: 0.657700 Iteration 2 Error: 0.215028 Iteration 3 Error: 0.087006 Iteration 4 Error: 0.035348 Align patch 23 2 left Iteration 1 Error: 1.315674 Iteration 2 Error: 0.124121 Iteration 3 Error: 0.027963 Align patch 24 1 left Iteration 1 Error: 0.883923 Iteration 2 Error: 0.173441 Iteration 3 Error: 0.045869 Align patch 25 0 left Iteration 1 Error: 1.015904 Iteration 2 Error: 0.244815 Iteration 3 Error: 0.063654 Iteration 4 Error: 0.020079 3D Fitting completed. Patch alignment time: 16.46(sec) Local motion has been corrected. Process thread exits. Computational time: 25.856016 sec Total time: 31.905197 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00006hln_00005enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00006hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.677667s Reading file: gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00006hln_00005enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.332603s ........................................ >>>>>>TIME<<<<<< FFT: 0.939651s Defocus_U Defocus_V Angle CCC 15126.87 14427.87 84.59 0.058147 Final Values Defocus_U Defocus_V Angle CCC 15115.91 14451.33 84.59 0.096342 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00013sq_v01_00007hln_00002enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00007hln_00002enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.348e-01 1.002e-01 CC threshold: 0.736 Mean Std: 43.00 7.22 Num Hot pixels: 223 Hot pixel threshold: 86.34 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 1.155781 Iteration 2 Error: 0.209782 Iteration 3 Error: 0.050078 Iteration 4 Error: 0.013781 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.14 0.08 ...... Frame ( 3) shift: -0.28 0.17 ...... Frame ( 4) shift: -0.42 0.25 ...... Frame ( 5) shift: -0.56 0.34 ...... Frame ( 6) shift: -0.61 0.37 ...... Frame ( 7) shift: -0.57 0.36 ...... Frame ( 8) shift: -0.53 0.35 ...... Frame ( 9) shift: -0.47 0.34 ...... Frame ( 10) shift: -0.41 0.33 ...... Frame ( 11) shift: -0.34 0.32 ...... Frame ( 12) shift: -0.28 0.32 ...... Frame ( 13) shift: -0.22 0.32 ...... Frame ( 14) shift: -0.15 0.32 ...... Frame ( 15) shift: -0.09 0.34 ...... Frame ( 16) shift: -0.03 0.39 ...... Frame ( 17) shift: 0.04 0.44 ...... Frame ( 18) shift: 0.10 0.50 ...... Frame ( 19) shift: 0.17 0.56 ...... Frame ( 20) shift: 0.23 0.62 ...... Frame ( 21) shift: 0.25 0.67 ...... Frame ( 22) shift: 0.22 0.69 ...... Frame ( 23) shift: 0.19 0.71 ...... Frame ( 24) shift: 0.23 0.75 ...... Frame ( 25) shift: 0.35 0.83 ...... Frame ( 26) shift: 0.46 0.90 ...... Frame ( 27) shift: 0.55 0.97 ...... Frame ( 28) shift: 0.62 1.04 ...... Frame ( 29) shift: 0.68 1.11 ...... Frame ( 30) shift: 0.74 1.19 ...... Frame ( 31) shift: 0.80 1.25 ...... Frame ( 32) shift: 0.87 1.32 ...... Frame ( 33) shift: 0.94 1.39 ...... Frame ( 34) shift: 1.02 1.46 ...... Frame ( 35) shift: 1.10 1.52 ...... Frame ( 36) shift: 1.17 1.55 ...... Frame ( 37) shift: 1.21 1.55 ...... Frame ( 38) shift: 1.26 1.54 ...... Frame ( 39) shift: 1.30 1.54 ...... Frame ( 40) shift: 1.34 1.53 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 0.891739 Iteration 2 Error: 0.271784 Iteration 3 Error: 0.087250 Iteration 4 Error: 0.028428 Align patch 2 23 left Iteration 1 Error: 0.673255 Iteration 2 Error: 0.098143 Iteration 3 Error: 0.016106 Align patch 3 22 left Iteration 1 Error: 0.986115 Iteration 2 Error: 0.192038 Iteration 3 Error: 0.044110 Align patch 4 21 left Iteration 1 Error: 0.822248 Iteration 2 Error: 0.148785 Iteration 3 Error: 0.040198 Align patch 5 20 left Iteration 1 Error: 0.674633 Iteration 2 Error: 0.068822 Iteration 3 Error: 0.012996 Align patch 6 19 left Iteration 1 Error: 0.606032 Iteration 2 Error: 0.128714 Iteration 3 Error: 0.032965 Align patch 7 18 left Iteration 1 Error: 0.616693 Iteration 2 Error: 0.081459 Iteration 3 Error: 0.019203 Align patch 8 17 left Iteration 1 Error: 0.500149 Iteration 2 Error: 0.084458 Iteration 3 Error: 0.022885 Align patch 9 16 left Iteration 1 Error: 0.816466 Iteration 2 Error: 0.105984 Iteration 3 Error: 0.027356 Align patch 10 15 left Iteration 1 Error: 0.631793 Iteration 2 Error: 0.101929 Iteration 3 Error: 0.016964 Align patch 11 14 left Iteration 1 Error: 1.057127 Iteration 2 Error: 0.220420 Iteration 3 Error: 0.054002 Iteration 4 Error: 0.011379 Align patch 12 13 left Iteration 1 Error: 0.789411 Iteration 2 Error: 0.113892 Iteration 3 Error: 0.033835 Align patch 13 12 left Iteration 1 Error: 0.647191 Iteration 2 Error: 0.042000 Align patch 14 11 left Iteration 1 Error: 0.646848 Iteration 2 Error: 0.085878 Iteration 3 Error: 0.021624 Align patch 15 10 left Iteration 1 Error: 0.745316 Iteration 2 Error: 0.117051 Iteration 3 Error: 0.032238 Align patch 16 9 left Iteration 1 Error: 1.401666 Iteration 2 Error: 0.207979 Iteration 3 Error: 0.040959 Align patch 17 8 left Iteration 1 Error: 1.094009 Iteration 2 Error: 0.098049 Iteration 3 Error: 0.030930 Align patch 18 7 left Iteration 1 Error: 0.788204 Iteration 2 Error: 0.109305 Iteration 3 Error: 0.010735 Align patch 19 6 left Iteration 1 Error: 0.361895 Iteration 2 Error: 0.063090 Iteration 3 Error: 0.020711 Align patch 20 5 left Iteration 1 Error: 0.510427 Iteration 2 Error: 0.063609 Iteration 3 Error: 0.015538 Align patch 21 4 left Iteration 1 Error: 2.113859 Iteration 2 Error: 0.219337 Iteration 3 Error: 0.063207 Iteration 4 Error: 0.014495 Align patch 22 3 left Iteration 1 Error: 1.381829 Iteration 2 Error: 0.160133 Iteration 3 Error: 0.058970 Iteration 4 Error: 0.012152 Align patch 23 2 left Iteration 1 Error: 0.989901 Iteration 2 Error: 0.120423 Iteration 3 Error: 0.031338 Align patch 24 1 left Iteration 1 Error: 0.574474 Iteration 2 Error: 0.053220 Iteration 3 Error: 0.012253 Align patch 25 0 left Iteration 1 Error: 0.686286 Iteration 2 Error: 0.134308 Iteration 3 Error: 0.025574 3D Fitting completed. Patch alignment time: 16.09(sec) Local motion has been corrected. Process thread exits. Computational time: 24.752024 sec Total time: 31.247919 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00007hln_00002enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00007hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.690309s Reading file: gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00007hln_00002enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.484233s ........................................ >>>>>>TIME<<<<<< FFT: 0.930984s Defocus_U Defocus_V Angle CCC 11259.70 11744.22 3.37 0.054353 Final Values Defocus_U Defocus_V Angle CCC 11289.40 11752.04 3.06 0.095560 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. . -InMrc 18feb27f_CTD_g1_00017gr_00013sq_v01_00007hln_00003enn.frames.mrc -InTiff -InSuffix -OutMrc gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00007hln_00003enn.frames_mc2.mrc -ArcDir -FullSum -Gain gain_ref.mrc -Dark -DefectFile -DefectMap -TmpFile -LogFile -Serial 0 -Patch 5 5 20 -Iter 5 -Tol 0.05 -Bft 100.00 -PhaseOnly 0 -StackZ 40 -FtBin 1.00 -InitDose 0.00 -FmDose 1.08 -PixSize 1.06 -kV 300 -Throw 0 -Trunc 0 -Group 3 -FmRef -1 -OutStack 1 -RotGain 0 -FlipGain 0 -Align 1 -Tilt 0.00 0.00 -Mag 1.00 1.00 61.30 -InFmMotion 1 -Crop 0 0 -Gpu 0 GPU 0 memory: 12189 MB Try to Load gain reference from MRC file. Gain has beed loaded from MRC file. ...... gain_ref.mrc Stack size: 3710 3838 40 Stack mode: 6 Stack 0001 has been loaded, 0 stacks left. Warning: Dark reference size does not match frame size. ...... Frame size: 3710 3838 ...... Dark size: 0 0 Detect bad and hot pixels. CC Mean Std: 1.346e-01 1.001e-01 CC threshold: 0.735 Mean Std: 43.93 7.25 Num Hot pixels: 221 Hot pixel threshold: 87.42 Mag stretch: 1.004 -61.300 Patch based alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 2.003685 Iteration 2 Error: 0.550057 Iteration 3 Error: 0.204090 Iteration 4 Error: 0.092791 Iteration 5 Error: 0.042619 Full-frame alignment shift ...... Frame ( 1) shift: 0.00 0.00 ...... Frame ( 2) shift: -0.17 0.01 ...... Frame ( 3) shift: -0.34 0.03 ...... Frame ( 4) shift: -0.51 0.04 ...... Frame ( 5) shift: -0.69 0.06 ...... Frame ( 6) shift: -0.72 0.13 ...... Frame ( 7) shift: -0.62 0.26 ...... Frame ( 8) shift: -0.52 0.39 ...... Frame ( 9) shift: -0.41 0.52 ...... Frame ( 10) shift: -0.29 0.65 ...... Frame ( 11) shift: -0.17 0.78 ...... Frame ( 12) shift: -0.03 0.87 ...... Frame ( 13) shift: 0.11 0.94 ...... Frame ( 14) shift: 0.26 1.01 ...... Frame ( 15) shift: 0.42 1.08 ...... Frame ( 16) shift: 0.59 1.14 ...... Frame ( 17) shift: 0.75 1.19 ...... Frame ( 18) shift: 0.88 1.29 ...... Frame ( 19) shift: 0.96 1.42 ...... Frame ( 20) shift: 1.05 1.55 ...... Frame ( 21) shift: 1.22 1.74 ...... Frame ( 22) shift: 1.48 1.97 ...... Frame ( 23) shift: 1.74 2.21 ...... Frame ( 24) shift: 1.92 2.38 ...... Frame ( 25) shift: 2.01 2.49 ...... Frame ( 26) shift: 2.11 2.60 ...... Frame ( 27) shift: 2.18 2.71 ...... Frame ( 28) shift: 2.24 2.81 ...... Frame ( 29) shift: 2.29 2.91 ...... Frame ( 30) shift: 2.34 3.01 ...... Frame ( 31) shift: 2.37 3.09 ...... Frame ( 32) shift: 2.41 3.18 ...... Frame ( 33) shift: 2.44 3.27 ...... Frame ( 34) shift: 2.46 3.37 ...... Frame ( 35) shift: 2.48 3.48 ...... Frame ( 36) shift: 2.50 3.56 ...... Frame ( 37) shift: 2.51 3.63 ...... Frame ( 38) shift: 2.52 3.70 ...... Frame ( 39) shift: 2.54 3.77 ...... Frame ( 40) shift: 2.55 3.84 Global motion been corrected. Global motion corrected sum saved. Start to align patches. Align patch 1 24 left Iteration 1 Error: 2.639193 Iteration 2 Error: 0.371201 Iteration 3 Error: 0.127580 Iteration 4 Error: 0.057121 Iteration 5 Error: 0.039062 Align patch 2 23 left Iteration 1 Error: 1.561917 Iteration 2 Error: 0.231000 Iteration 3 Error: 0.112995 Iteration 4 Error: 0.050146 Iteration 5 Error: 0.018029 Align patch 3 22 left Iteration 1 Error: 1.744381 Iteration 2 Error: 0.352847 Iteration 3 Error: 0.109143 Iteration 4 Error: 0.030852 Align patch 4 21 left Iteration 1 Error: 0.780465 Iteration 2 Error: 0.255504 Iteration 3 Error: 0.102886 Iteration 4 Error: 0.053721 Iteration 5 Error: 0.019779 Align patch 5 20 left Iteration 1 Error: 0.463576 Iteration 2 Error: 0.061557 Iteration 3 Error: 0.021036 Align patch 6 19 left Iteration 1 Error: 1.217483 Iteration 2 Error: 0.176939 Iteration 3 Error: 0.070596 Iteration 4 Error: 0.033017 Align patch 7 18 left Iteration 1 Error: 1.700269 Iteration 2 Error: 0.267055 Iteration 3 Error: 0.081337 Iteration 4 Error: 0.026371 Align patch 8 17 left Iteration 1 Error: 1.317931 Iteration 2 Error: 0.359751 Iteration 3 Error: 0.102915 Iteration 4 Error: 0.042627 Align patch 9 16 left Iteration 1 Error: 1.287445 Iteration 2 Error: 0.389636 Iteration 3 Error: 0.150823 Iteration 4 Error: 0.069390 Iteration 5 Error: 0.035892 Align patch 10 15 left Iteration 1 Error: 0.647261 Iteration 2 Error: 0.121099 Iteration 3 Error: 0.032432 Align patch 11 14 left Iteration 1 Error: 0.887559 Iteration 2 Error: 0.181200 Iteration 3 Error: 0.053616 Iteration 4 Error: 0.020764 Align patch 12 13 left Iteration 1 Error: 1.187956 Iteration 2 Error: 0.219847 Iteration 3 Error: 0.078624 Iteration 4 Error: 0.023703 Align patch 13 12 left Iteration 1 Error: 1.191483 Iteration 2 Error: 0.243813 Iteration 3 Error: 0.092340 Iteration 4 Error: 0.032595 Align patch 14 11 left Iteration 1 Error: 0.368782 Iteration 2 Error: 0.126258 Iteration 3 Error: 0.047579 Align patch 15 10 left Iteration 1 Error: 0.778662 Iteration 2 Error: 0.125447 Iteration 3 Error: 0.045744 Align patch 16 9 left Iteration 1 Error: 1.047533 Iteration 2 Error: 0.221832 Iteration 3 Error: 0.075859 Iteration 4 Error: 0.027284 Align patch 17 8 left Iteration 1 Error: 0.776339 Iteration 2 Error: 0.184151 Iteration 3 Error: 0.047462 Align patch 18 7 left Iteration 1 Error: 1.224531 Iteration 2 Error: 0.186169 Iteration 3 Error: 0.051420 Iteration 4 Error: 0.028576 Align patch 19 6 left Iteration 1 Error: 0.600949 Iteration 2 Error: 0.102825 Iteration 3 Error: 0.045523 Align patch 20 5 left Iteration 1 Error: 0.582273 Iteration 2 Error: 0.130600 Iteration 3 Error: 0.042217 Align patch 21 4 left Iteration 1 Error: 1.554869 Iteration 2 Error: 0.240585 Iteration 3 Error: 0.058184 Iteration 4 Error: 0.021568 Align patch 22 3 left Iteration 1 Error: 0.872691 Iteration 2 Error: 0.145587 Iteration 3 Error: 0.036456 Align patch 23 2 left Iteration 1 Error: 1.352573 Iteration 2 Error: 0.190120 Iteration 3 Error: 0.062819 Iteration 4 Error: 0.014695 Align patch 24 1 left Iteration 1 Error: 0.675683 Iteration 2 Error: 0.106774 Iteration 3 Error: 0.025669 Align patch 25 0 left Iteration 1 Error: 1.143190 Iteration 2 Error: 0.190457 Iteration 3 Error: 0.060338 Iteration 4 Error: 0.022912 3D Fitting completed. Patch alignment time: 16.38(sec) Local motion has been corrected. Process thread exits. Computational time: 25.631290 sec Total time: 32.094288 sec *************************************************************************************************** Version: /programs/x86_64-linux/gctf/1.18/bin/Gctf-v1.18_sm_30_cu8.0_x86_64 v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination. *************************************************************************************************** Opening gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00007hln_00003enn.frames_mc2_Stk.mrc for initial test and preperation ....... *************************************************************************************************** User input parameters: --apix 1.060 --kv 300.00 --cs 2.70 --ac 0.07 --do_EPA 1 --do_Hres_ref 1 --dstep 5.00 --resL 15.00 --do_mdef_refine 1 --mdef_aveN 3 --boxsize 1024 All parameters to be used: General options: --apix 1.060 --dstep 5.000 --kv 300.00 --cs 2.70 --ac 0.07 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 150.00 --defL 5000.00 --defH 90000.00 --defS 500.00 --astm 1000.00 --resL 15.00 --resH 4.00 --boxsize 1024 --overlap 0.50 --convsize 85 --refine_2d_T 1 --smooth_resL 20.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 1 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 1 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 1 --mdef_ave_type 0 --mdef_aveN 3 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options: --do_phase_flip 0 Validation options: --do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.22 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0 All 1 files to be searched and refined: gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00007hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< PREPARATION: 1.809398s Reading file: gc_18feb27f_CTD_g1_00017gr_00013sq_v01_00007hln_00003enn.frames_mc2_Stk.mrc >>>>>>TIME<<<<<< READING: 2.358542s ........................................ >>>>>>TIME<<<<<< FFT: 1.057654s Defocus_U Defocus_V Angle CCC 10996.09 11800.78 6.47 0.055869 Final Values Defocus_U Defocus_V Angle CCC 11014.85 11822.67 7.10 0.101650 Final Values (Hres refine) Processing done successfully. ------------------------------------------------------------------------------------------------------------------------------- Writing TIFF images. . Writing TIFF images. .